Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_file Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Role FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values X1000gp3_AA X1000gp3_AC X1000gp3_AF X1000gp3_AFR_AF X1000gp3_AMR_AF X1000gp3_AN X1000gp3_CIEND X1000gp3_CIPOS X1000gp3_CS X1000gp3_DP X1000gp3_EAS_AF X1000gp3_END X1000gp3_EUR_AF X1000gp3_IMPRECISE X1000gp3_MC X1000gp3_MEINFO X1000gp3_MEND X1000gp3_MLEN X1000gp3_MSTART X1000gp3_NS X1000gp3_SAS_AF X1000gp3_SVLEN X1000gp3_SVTYPE X1000gp3_TSD ACHILLES_Lineage_Results_Top_Genes BCNoise CGC_Cancer.Germline.Mut CGC_Cancer.Molecular.Genetics CGC_Cancer.Somatic.Mut CGC_Cancer.Syndrome CGC_Chr CGC_Chr.Band CGC_GeneID CGC_Name CGC_Other.Germline.Mut CGC_Tissue.Type COSMIC_n_overlapping_mutations COSMIC_overlapping_mutation_descriptions COSMIC_overlapping_primary_sites ClinVar_ASSEMBLY ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_rs DP2 DP50 ESP_AA ESP_AAC ESP_AA_AC ESP_AA_AGE ESP_AA_GTC ESP_AvgAAsampleReadDepth ESP_AvgEAsampleReadDepth ESP_AvgSampleReadDepth ESP_CA ESP_CDP ESP_CG ESP_CP ESP_Chromosome ESP_DBSNP ESP_DP ESP_EA_AC ESP_EA_AGE ESP_EA_GTC ESP_EXOME_CHIP ESP_FG ESP_GL ESP_GM ESP_GS ESP_GTC ESP_GTS ESP_GWAS_PUBMED ESP_MAF ESP_PH ESP_PP ESP_Position ESP_TAC ESP_TotalAAsamplesCovered ESP_TotalEAsamplesCovered ESP_TotalSamplesCovered Ensembl_so_accession Ensembl_so_term FDP50 Familial_Cancer_Genes_Reference Familial_Cancer_Genes_Synonym HGNC_Accession.Numbers HGNC_CCDS.IDs HGNC_Chromosome HGNC_Date.Modified HGNC_Date.Name.Changed HGNC_Date.Symbol.Changed HGNC_Ensembl.Gene.ID HGNC_Ensembl.ID.supplied.by.Ensembl. HGNC_Entrez.Gene.ID.supplied.by.NCBI. HGNC_Enzyme.IDs HGNC_Gene.family.description HGNC_HGNC.ID HGNC_Locus.Group HGNC_Locus.Type HGNC_Name.Synonyms HGNC_OMIM.ID.supplied.by.NCBI. HGNC_Previous.Names HGNC_Previous.Symbols HGNC_Primary.IDs HGNC_Pubmed.IDs HGNC_Record.Type HGNC_RefSeq.IDs HGNC_RefSeq.supplied.by.NCBI. HGNC_Secondary.IDs HGNC_Status HGNC_Synonyms HGNC_UCSC.ID.supplied.by.UCSC. HGNC_UniProt.ID.supplied.by.UniProt. HGNC_VEGA.IDs HGVS_coding_DNA_change HGVS_genomic_change HGVS_protein_change IC IHP NT ORegAnno_bin OVERLAP QSI QSI_NT QSI_ref RC Repeat SGT SUBDP50 SVTYPE TAR TIR TOR TQSI TQSI_NT UniProt_alt_uniprot_accessions alt_allele_seen build ccds_id dbNSFP_1000Gp1_AC dbNSFP_1000Gp1_AF dbNSFP_1000Gp1_AFR_AC dbNSFP_1000Gp1_AFR_AF dbNSFP_1000Gp1_AMR_AC dbNSFP_1000Gp1_AMR_AF dbNSFP_1000Gp1_ASN_AC dbNSFP_1000Gp1_ASN_AF dbNSFP_1000Gp1_EUR_AC dbNSFP_1000Gp1_EUR_AF dbNSFP_Ancestral_allele dbNSFP_CADD_phred dbNSFP_CADD_raw dbNSFP_CADD_raw_rankscore dbNSFP_ESP6500_AA_AF dbNSFP_ESP6500_EA_AF dbNSFP_Ensembl_geneid dbNSFP_Ensembl_transcriptid dbNSFP_FATHMM_pred dbNSFP_FATHMM_rankscore dbNSFP_FATHMM_score dbNSFP_GERP.._NR dbNSFP_GERP.._RS dbNSFP_GERP.._RS_rankscore dbNSFP_Interpro_domain dbNSFP_LRT_Omega dbNSFP_LRT_converted_rankscore dbNSFP_LRT_pred dbNSFP_LRT_score dbNSFP_LR_pred dbNSFP_LR_rankscore dbNSFP_LR_score dbNSFP_MutationAssessor_pred dbNSFP_MutationAssessor_rankscore dbNSFP_MutationAssessor_score dbNSFP_MutationTaster_converted_rankscore dbNSFP_MutationTaster_pred dbNSFP_MutationTaster_score dbNSFP_Polyphen2_HDIV_pred dbNSFP_Polyphen2_HDIV_rankscore dbNSFP_Polyphen2_HDIV_score dbNSFP_Polyphen2_HVAR_pred dbNSFP_Polyphen2_HVAR_rankscore dbNSFP_Polyphen2_HVAR_score dbNSFP_RadialSVM_pred dbNSFP_RadialSVM_rankscore dbNSFP_RadialSVM_score dbNSFP_Reliability_index dbNSFP_SIFT_converted_rankscore dbNSFP_SIFT_pred dbNSFP_SIFT_score dbNSFP_SLR_test_statistic dbNSFP_SiPhy_29way_logOdds dbNSFP_SiPhy_29way_logOdds_rankscore dbNSFP_SiPhy_29way_pi dbNSFP_UniSNP_ids dbNSFP_Uniprot_aapos dbNSFP_Uniprot_acc dbNSFP_Uniprot_id dbNSFP_aaalt dbNSFP_aapos dbNSFP_aapos_FATHMM dbNSFP_aapos_SIFT dbNSFP_aaref dbNSFP_cds_strand dbNSFP_codonpos dbNSFP_fold.degenerate dbNSFP_genename dbNSFP_hg18_pos.1.coor. dbNSFP_phastCons100way_vertebrate dbNSFP_phastCons100way_vertebrate_rankscore dbNSFP_phastCons46way_placental dbNSFP_phastCons46way_placental_rankscore dbNSFP_phastCons46way_primate dbNSFP_phastCons46way_primate_rankscore dbNSFP_phyloP100way_vertebrate dbNSFP_phyloP100way_vertebrate_rankscore dbNSFP_phyloP46way_placental dbNSFP_phyloP46way_placental_rankscore dbNSFP_phyloP46way_primate dbNSFP_phyloP46way_primate_rankscore dbNSFP_refcodon gencode_transcript_name gencode_transcript_status gencode_transcript_tags gencode_transcript_type gene_id gene_type havana_transcript iHpol id qual read_depth secondary_variant_classification somatic strand tandem_repeat_unit transcript_id MT-ND4 4538 __UNKNOWN__ __UNKNOWN__ M 11033 11033 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrM:11033delA ENST00000361381.2 + 1 274 c.274delA c.(274-276)aaafs p.K93fs P03905 NU4M_HUMAN mitochondrially encoded NADH dehydrogenase 4 93 NA NA NA cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281) integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747) NADH dehydrogenase (ubiquinone) activity (GO:0008137) breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1) 13 CACTATCACGAAAAAAACTCT 0.423 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 385 376.79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.23 mitochondria 2014-02-03 2005-02-15 2005-02-16 ENSG00000198886 ENSG00000198886 4538 1.6.5.3 "Mitochondrial respiratory chain complex / Complex I" 7459 protein-coding gene gene with protein product "complex I ND4 subunit", "NADH-ubiquinone oxidoreductase chain 4" 516003 "NADH dehydrogenase 4", "Leber optic neuropathy" MTND4, LHON NA 8103501 Standard YP_003024035 NA Approved ND4, NAD4 P03905 ENST00000361381.2:c.274delA chrM.hg19:g.11033delA ENSP00000354961:p.Lys93fs 6 7 ref NA False 62 62 PASS 7 PASS ref->het 0 NA 188,194 142,143 54,50 1 1 Q6RL39|Q6RQN9|Q8HNR8 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MT-ND4-201 KNOWN basic|appris_principal protein_coding NA protein_coding PASS NA None 385 True + A ENST00000361381.2 DRAM2 128338 __UNKNOWN__ __UNKNOWN__ 1 111663087 111663111 __UNKNOWN__ Intron DEL TTGTCATTCAATTCCTTTCCAAGTG TTGTCATTCAATTCCTTTCCAAGTG - rs200094440 LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:111663087_111663111delTTGTCATTCAATTCCTTTCCAAGTG ENST00000286692.4 - 6 1135 DRAM2_ENST00000484310.1_Intron|DRAM2_ENST00000539140.1_Intron Q6UX65 DRAM2_HUMAN DNA-damage regulated autophagy modulator 2 NA NA NA NA apoptotic process (GO:0006915)|regulation of autophagy (GO:0010506) cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|microtubule cytoskeleton (GO:0015630) endometrium(1)|large_intestine(5)|lung(3) 9 TACTTAAATCTTGTCATTCAATTCCTTTCCAAGTGTAGCCACATT 0.329 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 157 157.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.71 AY336747 CCDS30801.1 1p13.3 2010-07-08 2009-06-12 2009-06-12 ENSG00000156171 ENSG00000156171 128338 28769 protein-coding gene gene with protein product 613360 "transmembrane protein 77" TMEM77 NA 12975309 Standard NM_178454 NM_178454 NA Approved MGC54289, PRO180, WWFQ154, RP5-1180E21.1 uc001ead.4 Q6UX65 OTTHUMG00000011911 ENST00000286692.4:c.517+26CACTTGGAAAGGAATTGAATGACAA>- chr1.hg19:g.111663087_111663111delTTGTCATTCAATTCCTTTCCAAGTG 0 3 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 160,164 33,37 23,17 1 1 B3SUG9|Q4VWF6|Q86VD3|Q8NBQ4 True hg19 CCDS30801.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DRAM2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000032930.3 PASS NA None 157 True - TTGTCATTCAATTCCTTTCCAAGTG ENST00000286692.4 ZNF687 57592 __UNKNOWN__ __UNKNOWN__ 1 151259498 151259502 __UNKNOWN__ Frame_Shift_Del DEL AGGCC AGGCC - LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:151259498_151259502delAGGCC ENST00000368879.2 + 2 829_833 c.731_735delAGGCC c.(730-735)aaggccfs p.KA244fs NM_020832.1 NP_065883.1 Q8N1G0 ZN687_HUMAN zinc finger protein 687 244 Pro-rich. NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleolus (GO:0005730)|nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2) 32 Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181) TCCAGCCCTAAGGCCACGGACATCC 0.639 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 359 370.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.5 CCDS992.1 1q21.2 2008-05-02 ENSG00000143373 ENSG00000143373 57592 29277 protein-coding gene gene with protein product 610568 NA 10718198 Standard NM_020832 NM_020832 NA Approved KIAA1441 uc001exq.3 Q8N1G0 OTTHUMG00000012347 ENST00000368879.2:c.731_735delAGGCC chr1.hg19:g.151259498_151259502delAGGCC ENSP00000357874:p.Lys244fs 0 3 ref NA False 66 66 PASS 1 PASS ref->het 0 NA 311,317 19,20 49,42 1 1 D3DV17|Q68DQ8|Q9H937|Q9P2A7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF687-201 KNOWN basic protein_coding NA protein_coding PASS NA None 359 True + AGGCC ENST00000368879.2 ZNF638 27332 __UNKNOWN__ __UNKNOWN__ 2 71650324 71650325 __UNKNOWN__ Frame_Shift_Ins INS - - CAGT LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:71650324_71650325insCAGT ENST00000409544.1 + 22 4310_4311 c.3680_3681insCAGT c.(3679-3684)gacagtfs p.-1228fs ZNF638_ENST00000264447.4_Frame_Shift_Ins_p.-1228fs|ZNF638_ENST00000355812.3_Intron|ZNF638_ENST00000409407.1_Frame_Shift_Ins_p.-168fs NM_001252612.1 NP_001239541.1 Q14966 ZN638_HUMAN zinc finger protein 638 NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270) breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1) 63 TTACCATCTGACAGTGTGTTTG 0.391 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 438 444.57 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.81 D83032 CCDS1917.1 2p13.1 2013-02-12 2004-07-29 2004-07-30 ENSG00000075292 ENSG00000075292 27332 "RNA binding motif (RRM) containing" 17894 protein-coding gene gene with protein product 614349 "zinc finger, matrin-like" ZFML NA 8647861 Standard NM_014497 NM_014497 NA Approved NP220, MGC26130, Zfp638 uc002shy.3 Q14966 OTTHUMG00000129735 ENST00000409544.1:c.3681_3684dupCAGT chr2.hg19:g.71650325_71650328dupCAGT ENSP00000386433:p.Ser1228fs 2 2 ref NA False 72 72 PASS 1 PASS ref->het 0 NA 315,315 62,65 60,58 1 1 B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37 True hg19 CCDS1917.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF638-002 NOVEL alternative_5_UTR|basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000327431.1 PASS NA None 438 True + CAGT ENST00000409544.1 NRP2 8828 __UNKNOWN__ __UNKNOWN__ 2 206605373 206605391 __UNKNOWN__ Splice_Site DEL GCTGCCGGGTCACAGGTGA GCTGCCGGGTCACAGGTGA - rs139711818 byFrequency LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:206605373_206605391delGCTGCCGGGTCACAGGTGA ENST00000357785.5 + 8 1308_1322 c.1277_1291delGCTGCCGGGTCACAGGTGA c.(1276-1293)ggctgccgggtcacaggt>ggt p.GCRVTG426fs NRP2_ENST00000357118.4_Splice_Site_p.GCRVTG426fs|NRP2_ENST00000272849.3_Splice_Site_p.GCRVTG426fs|NRP2_ENST00000412873.2_Splice_Site_p.GCRVTG426fs|NRP2_ENST00000540841.1_Splice_Site_p.GCRVTG426fs|NRP2_ENST00000417189.1_Splice_Site_p.GCRVTG426fs|NRP2_ENST00000355117.4_Splice_Site_p.GCRVTG426fs|NRP2_ENST00000540178.1_Splice_Site_p.GCRVTG426fs|NRP2_ENST00000360409.3_Splice_Site_p.GCRVTG426fs Q99435 NELL2_HUMAN neuropilin 2 0 EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}. NA NA NA extracellular region (GO:0005576) calcium ion binding (GO:0005509) NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2) 52 GAGCTCTTCGGCTGCCGGGTCACAGGTGAGGTGGGGGCT 0.584 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 117 120.89 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0 AF016098 CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1 2q33.3 2008-05-23 ENSG00000118257 ENSG00000118257 8828 8005 protein-coding gene gene with protein product 602070 NA 9529250, 9331348 Standard NM_003872 NA Approved VEGF165R2 uc002vaw.3 O60462 OTTHUMG00000132893 ENST00000357785.5:c.1291+1GCTGCCGGGTCACAGGTGA>- chr2.hg19:g.206605373_206605391delGCTGCCGGGTCACAGGTGA 0 7 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 69,73 25,25 26,23 2 2 B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2 True hg19 CCDS46496.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NRP2-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000336467.1 PASS NA None 117 Frame_Shift_Del True + GCTGCCGGGTCACAGGTGA ENST00000357785.5 DCLK3 85443 __UNKNOWN__ __UNKNOWN__ 3 36756357 36756358 __UNKNOWN__ 3'UTR INS - - C rs201380997|rs550710808|rs150467309|rs377748120|rs61596675|rs386660198|rs140432947 byFrequency LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:36756357_36756358insC ENST00000416516.2 - 0 2898_2899 NM_033403.1 NP_208382.1 Q9C098 DCLK3_HUMAN doublecortin-like kinase 3 NA NA NA NA cytoplasm (GO:0005737)|nucleus (GO:0005634) ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674) breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2) 48 TATAATTCATTTTTGAATTTTT 0.361 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 144 155.08 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 30.74 AB051552 CCDS43064.1 3p22.3 2007-04-02 2007-04-02 2007-04-02 ENSG00000163673 ENSG00000163673 85443 19005 protein-coding gene gene with protein product 613167 "doublecortin and CaM kinase-like 3" DCAMKL3 NA 11214970, 16869982 Standard XM_047355 NM_033403 NA Approved KIAA1765, DCDC3C uc003cgi.2 Q9C098 OTTHUMG00000155805 ENST00000416516.2:c.*462->G chr3.hg19:g.36756357_36756358insC 1 5 ref NA False 47 47 PASS 0 PASS ref->het 0 NA 24,24 73,73 5,5 1 1 True hg19 CCDS43064.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DCLK3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000341727.1 PASS NA None 144 True - C ENST00000416516.2 DCLK3 85443 __UNKNOWN__ __UNKNOWN__ 3 36756362 36756370 __UNKNOWN__ 3'UTR DEL AATTTTTGT AATTTTTGT - rs201380997|rs550710808|rs559012851|rs144499868|rs377748120|rs367615127|rs201440330|rs2361305|rs2885238|rs200520415|rs386660198|rs2885237|rs200612380|rs140432947 byFrequency LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:36756362_36756370delAATTTTTGT ENST00000416516.2 - 0 2886_2894 NM_033403.1 NP_208382.1 Q9C098 DCLK3_HUMAN doublecortin-like kinase 3 NA NA NA NA cytoplasm (GO:0005737)|nucleus (GO:0005634) ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674) breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2) 48 TTCATTTTTGAATTTTTGTGCTGTCATCA 0.354 NA NA NA NA NA NA NA 1395 0.278554 0.2163 0.3372 5008 , , NA 17521 0.2897 NA 0.2783 False NA ,,, NA NA NA 2504 0.3098 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 99 154.33 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 30.74 AB051552 CCDS43064.1 3p22.3 2007-04-02 2007-04-02 2007-04-02 ENSG00000163673 ENSG00000163673 85443 19005 protein-coding gene gene with protein product 613167 "doublecortin and CaM kinase-like 3" DCAMKL3 NA 11214970, 16869982 Standard XM_047355 NM_033403 NA Approved KIAA1765, DCDC3C uc003cgi.2 Q9C098 OTTHUMG00000155805 ENST00000416516.2:c.*457ACAAAAATT>- chr3.hg19:g.36756362_36756370delAATTTTTGT 0 6 ref NA False 67 66 PASS 1 PASS ref->het 0 NA 26,26 73,73 4,4 1 1 True hg19 CCDS43064.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DCLK3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000341727.1 PASS NA None 99 True - AATTTTTGT ENST00000416516.2 CCDC109B 55013 __UNKNOWN__ __UNKNOWN__ 4 110608550 110608574 __UNKNOWN__ Intron DEL TAATAGTTTAAACATTTTATTGCTG TAATAGTTTAAACATTTTATTGCTG - rs192437998 byFrequency LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:110608550_110608574delTAATAGTTTAAACATTTTATTGCTG ENST00000394650.4 + 8 1066 NM_017918.4 NP_060388.2 Q9NWR8 MCUB_HUMAN coiled-coil domain containing 109B NA NA NA NA mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851) calcium channel complex (GO:0034704)|integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of membrane (GO:0031224)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246) calcium channel inhibitor activity (GO:0019855) breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(1) 9 OV - Ovarian serous cystadenocarcinoma(123;6.65e-06) CATTTGCCACTAATAGTTTAAACATTTTATTGCTGTAAGGAGACG 0.391 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 128 138.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.33 BC002633 CCDS3683.2 4q25 2011-05-24 ENSG00000005059 ENSG00000005059 55013 26076 protein-coding gene gene with protein product NA NA 12477932 Standard NM_017918 NM_017918 NA Approved FLJ20647 uc011cfs.2 Q9NWR8 OTTHUMG00000161103 ENST00000394650.4:c.934-97TAATAGTTTAAACATTTTATTGCTG>- chr4.hg19:g.110608550_110608574delTAATAGTTTAAACATTTTATTGCTG 0 3 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 101,104 43,43 32,30 2 2 A8K4Y3|Q6IAC1 True hg19 CCDS3683.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCDC109B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254865.1 PASS NA None 128 True + TAATAGTTTAAACATTTTATTGCTG ENST00000394650.4 PBX2 5089 __UNKNOWN__ __UNKNOWN__ 6 32153247 32153265 __UNKNOWN__ 3'UTR DEL CCCCTTTCTCTTACCAGAA CCCCTTTCTCTTACCAGAA - LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:32153247_32153265delCCCCTTTCTCTTACCAGAA ENST00000375050.4 - 0 2457_2475 XXbac-BPG300A18.13_ENST00000559458.1_RNA NM_002586.4 NP_002577.2 P40425 PBX2_HUMAN pre-B-cell leukemia homeobox 2 NA NA NA NA embryonic limb morphogenesis (GO:0030326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634)|transcription factor complex (GO:0005667) chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134) endometrium(1)|kidney(1)|lung(9)|ovary(1)|prostate(2) 14 TCTGTTTGTCCCCCTTTCTCTTACCAGAACCCCTTTGGC 0.416 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 191 208.82 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.46 CCDS4748.1 6p21.32 2011-06-20 2007-01-30 ENSG00000204304 ENSG00000204304 5089 "Homeoboxes / TALE class" 8633 protein-coding gene gene with protein product 176311 "pre-B-cell leukemia transcription factor 2" NA 7835890 Standard NM_002586 NA Approved G17, HOX12, PBX2MHC uc003oav.1 P40425 OTTHUMG00000031116 ENST00000375050.4:c.*912TTCTGGTAAGAGAAAGGGG>- chr6.hg19:g.32153247_32153265delCCCCTTTCTCTTACCAGAA 0 5 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 175,198 14,17 31,32 1 1 A2BFJ2 True hg19 CCDS4748.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PBX2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076194.4 PASS NA None 191 True - CCCCTTTCTCTTACCAGAA ENST00000375050.4 LRWD1 222229 __UNKNOWN__ __UNKNOWN__ 7 102107782 102107782 __UNKNOWN__ Intron DEL C C - rs200451942 LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:102107782delC ENST00000292616.5 + 4 584 NM_152892.1 NP_690852.1 Q9UFC0 LRWD1_HUMAN leucine-rich repeats and WD repeat domain containing 1 NA NA NA NA chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933) chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064) central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2) 20 CCCTCTTGCACCAGGTCACAG 0.627 NA NA NA NA NA NA OREG0018231 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 110 112.86 NA NA NA NA NA 42 33 36 NA NA NA NA 7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 102107782 NA 2203 4300 6503 SO:0001627 intron_variant 0.63 AL133057 CCDS34715.1 7q22.1 2013-01-10 ENSG00000161036 ENSG00000161036 222229 "WD repeat domain containing" 21769 protein-coding gene gene with protein product "origin recognition complex associated", "centromere protein 33" 615167 NA 20932478, 20850016, 20180869 Standard NM_152892 NM_152892 NA Approved DKFZp434K1815, ORCA, CENP-33 uc003uzn.3 Q9UFC0 OTTHUMG00000157718 ENST00000292616.5:c.433-4C>- chr7.hg19:g.102107782delC 1 3 ref 1364 False 33 33 PASS 2 PASS ref->het 0 NA 76,77 24,25 9,7 1 1 A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2 True hg19 CCDS34715.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LRWD1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000349493.1 PASS NA None 110 True + C ENST00000292616.5 DNLZ 728489 __UNKNOWN__ __UNKNOWN__ 9 139257226 139257229 __UNKNOWN__ Intron DEL AAAT AAAT - rs377215399|rs138545865 byFrequency LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:139257226_139257229delAAAT ENST00000371738.3 - 2 443 DNLZ_ENST00000371739.3_Intron NM_001080849.1 NP_001074318.1 Q5SXM8 DNLZ_HUMAN DNL-type zinc finger NA NA NA NA mitochondrion (GO:0005739) zinc ion binding (GO:0008270) central_nervous_system(1)|prostate(1) 2 Myeloproliferative disorder(178;0.0821) OV - Ovarian serous cystadenocarcinoma(145;2.42e-06)|Epithelial(140;3.3e-06) AAAATTTAACAAATAAAAACGCAC 0.485 NA NA NA NA NA NA NA 746 0.148962 0.0628 0.1153 5008 , , NA 22545 0.2827 NA 0.1312 False NA ,,, NA NA NA 2504 0.1697 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 57 57.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AL592301 CCDS35179.1 9q34.3 2013-01-10 2007-12-18 2007-12-18 ENSG00000213221 ENSG00000213221 728489 "Zinc fingers" 33879 protein-coding gene gene with protein product "translocase of inner mitochondrial membrane 15 homolog (yeast)", "HSP70 escort protein" NA "chromosome 9 open reading frame 151" C9orf151 NA 21530495, 22162012 Standard NM_001080849 NM_001080849 NA Approved RP11-413M3.2, ZIM17, bA413M3.2, TIMM15, HEP uc004chf.2 Q5SXM8 OTTHUMG00000020931 ENST00000371738.3:c.368+211ATTT>- chr9.hg19:g.139257226_139257229delAAAT 0 8 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 8,8 37,38 12,11 1 1 B2RUX5|B9EJE1 True hg19 CCDS35179.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DNLZ-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000055075.2 PASS NA None 57 True - AAAT ENST00000371738.3 VTI1A 143187 __UNKNOWN__ __UNKNOWN__ 10 114575612 114575627 __UNKNOWN__ 3'UTR DEL CAGCCCTGTTCCTACA CAGCCCTGTTCCTACA - rs35483743 LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:114575612_114575627delCAGCCCTGTTCCTACA ENST00000393077.2 + 0 1240_1255 NM_145206.2 NP_660207.2 Q96AJ9 VTI1A_HUMAN vesicle transport through interaction with t-SNAREs 1A NA NA NA NA intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147) clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|neuron projection terminus (GO:0044306)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)|synaptic vesicle (GO:0008021) SNAP receptor activity (GO:0005484) VTI1A/TCF7L2(8) breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1) 6 Colorectal(252;0.0314)|Breast(234;0.183) Epithelial(162;0.0126)|all cancers(201;0.0487) TCCAGCAAGCCAGCCCTGTTCCTACACAGGCCTCAT 0.472 NA NA T TCF7L2 colorectal NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Dom yes NA 10 10q25.2 143187 vesicle transport through interaction with t-SNAREs homolog 1A NA E 0 NA NA NA NA NA 215 211.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.38 BC017052 CCDS7575.2 10q25.2 2012-12-10 2012-12-10 ENSG00000151532 ENSG00000151532 143187 17792 protein-coding gene gene with protein product 614316 "vesicle transport through interaction with t-SNAREs homolog 1A (yeast)" NA 9446565 Standard NM_145206 NA Approved MVti1, Vti1a, Vti1-rp2 uc001kzz.3 Q96AJ9 OTTHUMG00000019063 ENST00000393077.2:c.*485CAGCCCTGTTCCTACA>- chr10.hg19:g.114575612_114575627delCAGCCCTGTTCCTACA 0 2 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 161,164 41,42 41,39 1 1 A2A307|B4E137|Q5W0D7 True hg19 CCDS7575.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA VTI1A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000050397.2 PASS NA None 215 True + CAGCCCTGTTCCTACA ENST00000393077.2 CTR9 9646 __UNKNOWN__ __UNKNOWN__ 11 10772870 10772891 __UNKNOWN__ 5'UTR DEL AGCCGTCACTCACCTCTGGATT AGCCGTCACTCACCTCTGGATT - LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:10772870_10772891delAGCCGTCACTCACCTCTGGATT ENST00000361367.2 + 0 337_358 NM_014633.3 NP_055448.1 Q6PD62 CTR9_HUMAN CTR9, Paf1/RNA polymerase II complex component NA NA NA NA cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055) Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327) breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1) 40 all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111) CCAGAGCCGGAGCCGTCACTCACCTCTGGATTAGCCTGAAGC 0.667 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 124 126.33 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.58 D63875 CCDS7805.1 11p15.3 2013-07-03 2013-07-03 2006-05-22 ENSG00000198730 ENSG00000198730 9646 "Tetratricopeptide (TTC) repeat domain containing" 16850 protein-coding gene gene with protein product 609366 "SH2 domain binding protein 1 (tetratricopeptide repeat containing)", "Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)" SH2BP1 NA 8590280, 8636124 Standard NM_014633 NM_014633 NA Approved KIAA0155, TSBP, p150TSP uc001mja.3 Q6PD62 OTTHUMG00000165789 ENST00000361367.2:c.-69AGCCGTCACTCACCTCTGGATT>- chr11.hg19:g.10772870_10772891delAGCCGTCACTCACCTCTGGATT 0 3 ref NA False 73 73 PASS 1 PASS ref->het 0 NA 122,128 9,10 21,14 1 1 D3DQV8|Q15015 True hg19 CCDS7805.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CTR9-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000386215.1 PASS NA None 124 True + AGCCGTCACTCACCTCTGGATT ENST00000361367.2 RDX 5962 __UNKNOWN__ __UNKNOWN__ 11 110102617 110102618 __UNKNOWN__ Frame_Shift_Ins INS - - A rs370958814 LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:110102617_110102618insA ENST00000528498.1 - 14 2037_2038 c.1728_1729insT c.(1726-1731)cgtatcfs p.I577fs RDX_ENST00000343115.4_Frame_Shift_Ins_p.I577fs|RDX_ENST00000405097.1_Frame_Shift_Ins_p.I577fs|RDX_ENST00000544551.1_Frame_Shift_Ins_p.I441fs|RDX_ENST00000530301.1_Frame_Shift_Ins_p.I173fs|RDX_ENST00000528900.1_Frame_Shift_Ins_p.I230fs NM_001260493.1 NP_001247422.1 P35241 RADI_HUMAN radixin 577 NA NA NA actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628) apical part of cell (GO:0045177)|cell tip (GO:0051286)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315) poly(A) RNA binding (GO:0044822) endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1) 18 all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544) Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248) AACTCATCGATACGCTGCTTTG 0.406 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(55;25 1062 11040 28755 44273) PASS NA NA NA NA NA 0 NA NA NA NA NA 404 394.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.43 BC020751 CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1 11q23 2008-03-17 ENSG00000137710 5962 9944 protein-coding gene gene with protein product 179410 "deafness, autosomal recessive 24" DFNB24 NA 8486357, 17226784 Standard NM_002906 NM_001260492 NA Approved uc031qdy.1 P35241 ENST00000528498.1:c.1729dupT chr11.hg19:g.110102618_110102618dupA ENSP00000432112:p.Ile577fs 2 2 ref NA False 70 70 PASS 1 PASS ref->het 0 NA 300,302 58,59 40,38 1 1 A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61 True hg19 CCDS58174.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RDX-006 PUTATIVE basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000390531.1 PASS NA None 404 True - A ENST00000528498.1 BCAT1 586 __UNKNOWN__ __UNKNOWN__ 12 24967167 24967168 __UNKNOWN__ 3'UTR INS - - A LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:24967167_24967168insA ENST00000261192.7 - 0 5461_5462 NM_001178091.1|NM_005504.6 NP_001171562.1|NP_005495.2 P54687 BCAT1_HUMAN branched chain amino-acid transaminase 1, cytosolic NA NA NA NA branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cell proliferation (GO:0008283)|cellular nitrogen compound metabolic process (GO:0034641)|G1/S transition of mitotic cell cycle (GO:0000082)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829)|mitochondrion (GO:0005739) branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655) breast(1)|large_intestine(1)|lung(3)|prostate(2) 7 Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196) Gabapentin(DB00996)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161) AATTTTAGAGTCAAGACATGAA 0.332 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 203 198.09 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.18 CCDS44845.1, CCDS53760.1, CCDS53761.1, CCDS53762.1, CCDS53763.1 12p12.1 2012-10-02 2010-05-07 ENSG00000060982 ENSG00000060982 586 2.6.1.42 976 protein-coding gene gene with protein product 113520 "branched chain aminotransferase 1, cytosolic" BCT1 NA 9165094 Standard NM_005504 NM_005504 NA Approved uc010six.2 P54687 OTTHUMG00000169053 ENST00000261192.7:c.*3775->T chr12.hg19:g.24967167_24967168insA 1 2 ref NA False 101 99 PASS 0 PASS ref->het 0 NA 113,114 55,55 33,33 1 1 B3KY27|B7Z2M5|B7Z5L0|F5H5E4|Q68DQ7|Q96MY9 True hg19 CCDS44845.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BCAT1-001 KNOWN upstream_uORF|basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000402080.1 PASS NA None 203 True - A ENST00000261192.7 GALNT6 11226 __UNKNOWN__ __UNKNOWN__ 12 51773184 51773184 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:51773184delG ENST00000543196.2 - 2 587 c.382delC c.(382-384)ctgfs p.L128fs GALNT6_ENST00000356317.3_Frame_Shift_Del_p.L128fs Q8NCL4 GALT6_HUMAN polypeptide N-acetylgalactosaminyltransferase 6 128 NA NA NA cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493) Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471) carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653) endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1) 27 TGGGTCTCCAGGGGGGTCCAC 0.582 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 183 189.6 NA NA NA NA NA 75 82 80 NA NA NA NA 12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 51773184 NA 2203 4300 6503 SO:0001589 frameshift_variant 0.11 Y08565 CCDS8813.1 12q13 2014-03-13 2014-03-13 ENSG00000139629 ENSG00000139629 11226 "Glycosyltransferase family 2 domain containing" 4128 protein-coding gene gene with protein product "polypeptide GalNAc transferase 6" 605148 "UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)" NA 10464263 Standard NM_007210 NM_007210 NA Approved GalNAc-T6 uc001ryl.1 Q8NCL4 ENST00000543196.2:c.382delC chr12.hg19:g.51773184delG ENSP00000444171:p.Leu128fs 5 6 ref NA False 52 52 PASS 6 PASS ref->het 0 NA 99,101 62,62 21,20 1 1 Q8IYH4|Q9H6G2|Q9UIV5 True hg19 CCDS8813.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GALNT6-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000469735.1 PASS NA None 183 True - G ENST00000543196.2 DNAH3 55567 __UNKNOWN__ __UNKNOWN__ 16 21122982 21123004 __UNKNOWN__ Frame_Shift_Del DEL TTGAATCAGATGGTCTTTAAGAT TTGAATCAGATGGTCTTTAAGAT - rs377067819 LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:21122982_21123004delTTGAATCAGATGGTCTTTAAGAT ENST00000261383.3 - 14 2041_2063 c.2042_2064delATCTTAAAGACCATCTGATTCAA c.(2041-2064)aatcttaaagaccatctgattcaafs p.NLKDHLIQ681fs DNAH3_ENST00000415178.1_Frame_Shift_Del_p.NLKDHLIQ681fs NM_017539.1 NP_060009.1 Q8TD57 DYH3_HUMAN dynein, axonemal, heavy chain 3 681 Stem. {ECO:0000250}. NA NA NA cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018) axonemal dynein complex (GO:0005858)|microtubule (GO:0005874) ATP binding (GO:0005524)|microtubule motor activity (GO:0003777) NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6) 202 GBM - Glioblastoma multiforme(48;0.207) CCACTTGGAATTGAATCAGATGGTCTTTAAGATTTTGAGCTCG 0.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 349 337.94 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.44 U83574 CCDS10594.1 16p12.2 2008-08-01 2006-09-04 ENSG00000158486 ENSG00000158486 55567 "Axonemal dyneins" 2949 protein-coding gene gene with protein product 603334 "dynein, axonemal, heavy polypeptide 3" NA 9256245, 9373155 Standard NM_017539 NM_017539 NA Approved Dnahc3b, DLP3, Hsadhc3, DKFZp434N074 uc010vbe.2 Q8TD57 OTTHUMG00000090677 ENST00000261383.3:c.2042_2064delATCTTAAAGACCATCTGATTCAA chr16.hg19:g.21122982_21123004delTTGAATCAGATGGTCTTTAAGAT ENSP00000261383:p.Asn681fs 0 4 ref NA False 69 69 PASS 1 PASS ref->het 0 NA 289,292 91,91 43,41 1 1 O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35 True hg19 CCDS10594.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DNAH3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000207361.1 PASS NA None 349 True - TTGAATCAGATGGTCTTTAAGAT ENST00000261383.3 SCNN1G 6340 __UNKNOWN__ __UNKNOWN__ 16 23197740 23197762 __UNKNOWN__ Frame_Shift_Del DEL CGTCTGCGCCGCCTCCTCTGGAT CGTCTGCGCCGCCTCCTCTGGAT - rs536006286|rs144697586 LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:23197740_23197762delCGTCTGCGCCGCCTCCTCTGGAT ENST00000300061.2 + 2 291_313 c.148_170delCGTCTGCGCCGCCTCCTCTGGAT c.(148-171)cgtctgcgccgcctcctctggatcfs p.RLRRLLWI50fs NM_001039.3 NP_001030.2 P51170 SCNNG_HUMAN sodium channel, non-voltage-gated 1, gamma subunit 50 NA NA NA excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085) external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706) ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699) p.R50C(1)|p.R53C(1) NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2) 34 GBM - Glioblastoma multiforme(48;0.0366) Amiloride(DB00594)|Triamterene(DB00384) GTCCCGCGGCCGTCTGCGCCGCCTCCTCTGGATCGGGTTCACA 0.619 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 2 Substitution - Missense(2) large_intestine(2) NA NA NA NA NA 760 736.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 2.6 U48937 CCDS10608.1 16p12 2012-02-28 2012-02-28 ENSG00000166828 ENSG00000166828 6340 "Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels" 10602 protein-coding gene gene with protein product 600761 "sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma" NA 7490094 Standard NM_001039 NM_001039 NA Approved ENaCgamma, SCNEG uc002dlm.1 P51170 OTTHUMG00000131609 ENST00000300061.2:c.148_170delCGTCTGCGCCGCCTCCTCTGGAT chr16.hg19:g.23197740_23197762delCGTCTGCGCCGCCTCCTCTGGAT ENSP00000300061:p.Arg50fs 0 3 ref NA False 130 130 PASS 1 PASS ref->het 0 NA 617,635 92,94 177,159 1 1 P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2 True hg19 CCDS10608.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SCNN1G-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254496.1 PASS NA None 760 True + CGTCTGCGCCGCCTCCTCTGGAT ENST00000300061.2 MYLPF 29895 __UNKNOWN__ __UNKNOWN__ 16 30388954 30388963 __UNKNOWN__ Intron DEL CCTTGTGTCA CCTTGTGTCA - LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:30388954_30388963delCCTTGTGTCA ENST00000322861.7 + 6 437 NM_013292.3 NP_037424.2 myosin light chain, phosphorylatable, fast skeletal muscle NA NA NA NA large_intestine(2)|lung(4) 6 Colorectal(24;0.193) TCGCAACTCCCCTTGTGTCACCTCTCTCCA 0.638 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 201 192.61 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.1 AF363061 CCDS10677.1 16p11.2 2013-01-10 ENSG00000180209 ENSG00000180209 29895 "Myosins / Light chain", "EF-hand domain containing" 29824 protein-coding gene gene with protein product "myosin, light chain 11, regulatory", "myosin regulatory light chain 2" NA NA 6179945 Standard NM_013292 NM_013292 NA Approved MRLC2, HUMMLC2B, MYL11 uc002dxv.1 Q96A32 OTTHUMG00000132399 ENST00000322861.7:c.357-12CCTTGTGTCA>- chr16.hg19:g.30388954_30388963delCCTTGTGTCA 0 5 ref NA False 52 52 PASS 1 PASS ref->het 0 NA 196,198 8,8 15,13 1 1 True hg19 CCDS10677.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MYLPF-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255530.3 PASS NA None 201 True + CCTTGTGTCA ENST00000322861.7 YBX2 51087 __UNKNOWN__ __UNKNOWN__ 17 7193626 7193628 __UNKNOWN__ In_Frame_Del DEL AGA AGA - LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:7193626_7193628delAGA ENST00000007699.5 - 5 749_751 c.686_688delTCT c.(685-690)ttctac>tac p.F229del NM_015982.3 NP_057066.2 Q9Y2T7 YBOX2_HUMAN Y box binding protein 2 229 Pro-rich.|Required for mRNA-binding. NA NA NA mRNA stabilization (GO:0048255)|negative regulation of binding (GO:0051100)|negative regulation of translation (GO:0017148)|oocyte development (GO:0048599)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|translational attenuation (GO:0009386) cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844) chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lipid binding (GO:0008289)|mRNA 3'-UTR binding (GO:0003730)|ribonucleoprotein complex binding (GO:0043021)|translation regulator activity (GO:0045182) cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|skin(3) 12 CGCCGTCGGTAGAAGAAGGGTGG 0.65 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 191 173.92 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 1.93 AF096834 CCDS11098.1 17p13.1 2013-12-20 ENSG00000006047 ENSG00000006047 51087 17948 protein-coding gene gene with protein product 611447 NA 10100484, 9780336 Standard NM_015982 NM_015982 NA Approved MSY2, CSDA3 uc002gfq.2 Q9Y2T7 OTTHUMG00000177992 ENST00000007699.5:c.686_688delTCT chr17.hg19:g.7193629_7193631delAGA ENSP00000007699:p.Phe229del 1 4 ref NA False 182 133 PASS 2 PASS ref->het 0 NA 101,104 57,58 35,32 1 1 D3DTP1|Q8N4P0 True hg19 CCDS11098.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA YBX2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000440172.2 PASS NA None 191 True - AGA ENST00000007699.5 ZC3H4 23211 __UNKNOWN__ __UNKNOWN__ 19 47570642 47570667 __UNKNOWN__ Frame_Shift_Del DEL GTGGCTGAACTGCTGCAGCTGTGACC GTGGCTGAACTGCTGCAGCTGTGACC - rs372774850|rs200657942|rs539808218|rs200770094 LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:47570642_47570667delGTGGCTGAACTGCTGCAGCTGTGACC ENST00000253048.5 - 15 2895_2920 c.2858_2883delGGTCACAGCTGCAGCAGTTCAGCCAC c.(2857-2883)cggtcacagctgcagcagttcagccacfs p.RSQLQQFSH953fs ZC3H4_ENST00000594019.1_Intron NM_015168.1 NP_055983.1 Q9UPT8 ZC3H4_HUMAN zinc finger CCCH-type containing 4 953 NA NA NA metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822) NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1) 41 all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889) OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372) CCTTCTTGATGTGGCTGAACTGCTGCAGCTGTGACCGTGGGTCCCG 0.673 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 348 339.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.01 AB028987 CCDS42582.1 19q13.33 2012-07-05 2007-10-18 2007-10-18 ENSG00000130749 23211 "Zinc fingers, CCCH-type domain containing" 17808 protein-coding gene gene with protein product NA "chromosome 19 open reading frame 7" C19orf7 NA Standard NM_015168 NA Approved KIAA1064 uc002pga.4 Q9UPT8 ENST00000253048.5:c.2858_2883delGGTCACAGCTGCAGCAGTTCAGCCAC chr19.hg19:g.47570642_47570667delGTGGCTGAACTGCTGCAGCTGTGACC ENSP00000253048:p.Arg953fs 0 4 ref NA False 79 79 PASS 1 PASS ref->het 0 NA 283,289 34,35 87,81 1 1 Q9Y420 True hg19 CCDS42582.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZC3H4-001 KNOWN non_canonical_U12|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000466667.1 PASS NA None 348 True - GTGGCTGAACTGCTGCAGCTGTGACC ENST00000253048.5 LAMA5 3911 __UNKNOWN__ __UNKNOWN__ 20 60894796 60894797 __UNKNOWN__ Frame_Shift_Ins INS - - GTGTGGC rs369123104 LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:60894796_60894797insGTGTGGC ENST00000252999.3 - 51 6880_6881 c.6814_6815insGCCACAC c.(6814-6816)ctgfs p.L2272fs NM_005560.3 NP_005551.3 O15230 LAMA5_HUMAN laminin, alpha 5 2272 Domain II and I. NA NA NA angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446) basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634) integrin binding (GO:0005178)|structural molecule activity (GO:0005198) breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2) 81 Breast(26;1.57e-08) BRCA - Breast invasive adenocarcinoma(19;4.36e-06) CGCATGGCCCAGTGTGGCCTCG 0.703 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 189 175.21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.46 AF443072 CCDS33502.1 20q13.2-q13.3 2013-03-01 ENSG00000130702 ENSG00000130702 3911 "Laminins" 6485 protein-coding gene gene with protein product 601033 NA 9271224 Standard NM_005560 NM_005560 NA Approved uc002ycq.3 O15230 OTTHUMG00000032908 ENST00000252999.3:c.6808_6814dupGCCACAC chr20.hg19:g.60894797_60894803dupGTGTGGC ENSP00000252999:p.Leu2272fs 2 3 ref NA False 56 56 PASS 1 PASS ref->het 0 NA 128,130 20,21 39,36 1 1 Q8TDF8|Q8WZA7|Q9H1P1 True hg19 CCDS33502.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LAMA5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000080014.2 PASS NA None 189 True - GTGTGGC ENST00000252999.3 TPTE 7179 __UNKNOWN__ __UNKNOWN__ 21 10914415 10914420 __UNKNOWN__ In_Frame_Del DEL ATTTGG ATTTGG - LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:10914415_10914420delATTTGG ENST00000361285.4 - 21 1628_1633 c.1299_1304delCCAAAT c.(1297-1305)atccaaata>ata p.433_435IQI>I TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_In_Frame_Del_p.395_397IQI>I|TPTE_ENST00000298232.7_In_Frame_Del_p.415_417IQI>I NM_199261.2 NP_954870 P56180 TPTE_HUMAN transmembrane phosphatase with tensin homology 433 C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}. NA NA NA peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165) integral component of membrane (GO:0016021) ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138) NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1) 130 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) CTCCATTTCTATTTGGATTTTTAGAT 0.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 424 377.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.56 AF007118 CCDS74771.1, CCDS74772.1, CCDS74773.1 21p11 2011-06-09 ENSG00000166157 ENSG00000274391 7179 "Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs" 12023 protein-coding gene gene with protein product "PTEN-related tyrosine phosphatase", "cancer/testis antigen 44" 604336 NA 10830953, 14659893 Standard NM_001290224 NA Approved PTEN2, CT44 uc002yip.1 P56180 OTTHUMG00000074127 ENST00000361285.4:c.1299_1304delCCAAAT chr21.hg19:g.10914415_10914420delATTTGG ENSP00000355208:p.Ile433_Gln434del 0 5 ref NA False 40 40 PASS 1 PASS ref->het 0 NA 366,370 27,28 36,34 1 1 B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8 True hg19 CCDS13560.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TPTE-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000157413.1 PASS NA None 424 True - ATTTGG ENST00000361285.4 EP300 2033 __UNKNOWN__ __UNKNOWN__ 22 41545736 41545739 __UNKNOWN__ Intron DEL CTGT CTGT - LTS-001_T LTS-001_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:41545736_41545739delCTGT ENST00000263253.7 + 14 3598 NM_001429.3 NP_001420.2 Q09472 EP300_HUMAN E1A binding protein p300 NA NA NA NA apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032) cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667) acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270) NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16) 171 TTCTGAATTGCTGTCTTGTTATGT 0.368 NA NA "T, N, F, Mis, O" "MLL, RUNXBP2" "colorectal, breast, pancreatic, AML, ALL, DLBCL" NA NA NA Rubinstein-Taybi syndrome NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Rec yes NA 22 22q13 2033 300 kd E1A-Binding protein gene NA "L, E" 0 NA NA NA NA NA 219 241.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.48 Familial Cancer Database Broad Thumb-Hallux syndrome U01877 CCDS14010.1 22q13.2 2011-07-01 ENSG00000100393 ENSG00000100393 2033 "Chromatin-modifying enzymes / K-acetyltransferases" 3373 protein-coding gene gene with protein product "histone acetyltransferase p300" 602700 NA 7523245 Standard NM_001429 NM_001429 NA Approved p300, KAT3B uc003azl.4 Q09472 OTTHUMG00000150937 ENST00000263253.7:c.2380-26CTGT>- chr22.hg19:g.41545736_41545739delCTGT 0 3 ref NA False 51 51 PASS 1 PASS ref->het 0 NA 167,167 45,46 27,26 1 1 B1AKC2 True hg19 CCDS14010.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EP300-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000320600.1 PASS NA None 219 True + CTGT ENST00000263253.7 MT-ND1 4535 __UNKNOWN__ __UNKNOWN__ M 3584 3584 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-002_T LTS-002_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrM:3584delA ENST00000361390.2 + 1 278 c.278delA c.(277-279)aacfs p.N93fs P03886 NU1M_HUMAN mitochondrially encoded NADH dehydrogenase 1 93 NA NA NA NA cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281) integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747) NADH dehydrogenase (ubiquinone) activity (GO:0008137) NA NA breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1) 34 NA NA Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236) CCCCATACCCAACCCCCTGGT 0.532 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 520 523.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 2.34 NA NA mitochondria 2011-07-04 2005-02-15 2005-02-16 ENSG00000198888 ENSG00000198888 4535 1.6.5.3 "Mitochondrial respiratory chain complex / Complex I" 7455 protein-coding gene gene with protein product "complex I ND1 subunit", "NADH-ubiquinone oxidoreductase chain 1" 516000 "NADH dehydrogenase 1" MTND1 NA Standard YP_003024026 NA Approved ND1, NAD1 P03886 ENST00000361390.2:c.278delA chrM.hg19:g.3584delA ENSP00000354687:p.Asn93fs 1 5 ref NA False 76 76 PASS 2 PASS ref->het 0 NA 374,378 82,82 63,60 1 1 C0JKH6|Q37523 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MT-ND1-201 KNOWN basic|appris_principal protein_coding NA protein_coding PASS NA None 520 NA True + A ENST00000361390.2 TTN 7273 __UNKNOWN__ __UNKNOWN__ 2 179490158 179490158 __UNKNOWN__ Intron DEL C C - LTS-002_T LTS-002_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:179490158delC ENST00000589042.1 - 241 44649 TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000591111.1_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron NM_001267550.1 NP_001254479.1 Q8WZ42 TITIN_HUMAN titin NA NA NA NA NA adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941) condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018) actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433) NA NA NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26) 1448 NA OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) NA CATGAAACAGCAATCTAGTAT 0.318 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 228 255.08 NA NA NA NA NA 106 102 103 NA NA NA NA 2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 179490158 NA 1806 4058 5864 SO:0001627 intron_variant 0.02 NA NA X90568 CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1 2q31 2014-09-17 2004-02-13 ENSG00000155657 ENSG00000155657 7273 "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing" 12403 protein-coding gene gene with protein product 188840 "cardiomyopathy, dilated 1G (autosomal dominant)" CMD1G NA 2129545, 10051295 Standard NM_133378 NM_003319 NA Approved CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5 uc031rqd.1 Q8WZ42 OTTHUMG00000154448 ENST00000589042.1:c.44425-35G>- chr2.hg19:g.179490158delC 0 2 ref NA False 64 64 PASS 1 PASS ref->het 0 NA 129,129 81,82 18,17 1 1 A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9 True hg19 CCDS59435.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TTN-018 PUTATIVE basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000450680.2 PASS NA None 228 NA True - C ENST00000589042.1 RPL15 6138 __UNKNOWN__ __UNKNOWN__ 3 23961955 23961955 __UNKNOWN__ 3'UTR DEL G G - LTS-002_T LTS-002_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:23961955delG ENST00000307839.5 + 0 2217 RPL15_ENST00000413699.1_3'UTR|RPL15_ENST00000456530.2_Intron|NKIRAS1_ENST00000421515.2_Intron NM_001253379.1|NM_001253380.1|NM_002948.3 NP_001240308.1|NP_001240309.1|NP_002939.2 P61313 RL15_HUMAN ribosomal protein L15 NA NA NA NA NA cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083) cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribosome (GO:0005840) poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735) NA NA endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1) 7 NA NA CCACAAAGTTGGACCATCACT 0.433 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 336 314.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.69 NA NA AB007173 CCDS2640.1, CCDS58818.1 3p24.1 2011-04-06 ENSG00000174748 ENSG00000174748 6138 "L ribosomal proteins" 10306 protein-coding gene gene with protein product 604174 NA 9582194 Standard NM_002948 NM_002948 NA Approved RPL10, RPLY10, RPYL10, EC45, L15 uc003ccp.3 P61313 OTTHUMG00000130485 ENST00000307839.5:c.*963G>- chr3.hg19:g.23961955delG 1 2 ref NA False 52 52 PASS 2 PASS ref->het 0 NA 249,251 67,67 20,18 1 1 P39030|P41051|Q5U0C0|Q642I1|Q6IPX6|Q8WYP2|Q96C44|Q9H2E5 True hg19 CCDS2640.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPL15-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252885.3 PASS NA None 336 NA True + G ENST00000307839.5 TAPBP 6892 __UNKNOWN__ __UNKNOWN__ 6 33281108 33281115 __UNKNOWN__ Intron DEL GGGCCCGC GGGCCCGC - LTS-002_T LTS-002_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:33281108_33281115delGGGCCCGC ENST00000489157.1 - 2 421 TAPBP_ENST00000426633.2_Frame_Shift_Del_p.RAL117fs|TAPBP_ENST00000434618.2_Frame_Shift_Del_p.RAL117fs|TAPBP_ENST00000475304.1_Frame_Shift_Del_p.RAL117fs|TAPBP_ENST00000456592.2_Frame_Shift_Del_p.RAL117fs O15533 TPSN_HUMAN TAP binding protein (tapasin) NA NA NA NA NA amide transport (GO:0042886)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|peptide antigen stabilization (GO:0050823)|peptide transport (GO:0015833)|protein complex assembly (GO:0006461)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of membrane (GO:0016021)|MHC class I peptide loading complex (GO:0042824) MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)|peptide antigen-transporting ATPase activity (GO:0015433)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)|unfolded protein binding (GO:0051082) NA NA endometrium(2)|large_intestine(5)|lung(8)|ovary(3) 18 NA NA GCCCCATCCAGGGCCCGCGGGCAGTTCT 0.683 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 146 157.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.73 NA NA Y13582 CCDS34426.1, CCDS34427.1, CCDS34428.1, CCDS34427.2, CCDS34428.2 6p21.3 2014-09-17 ENSG00000231925 ENSG00000231925 6892 "Immunoglobulin superfamily / C1-set domain containing" 11566 protein-coding gene gene with protein product 601962 NA 9238042 Standard NM_003190 NA Approved TAPA uc003odz.3 O15533 OTTHUMG00000031090 ENST00000489157.1:c.208+355GCGGGCCC>- chr6.hg19:g.33281108_33281115delGGGCCCGC 0 4 ref NA False 58 58 PASS 1 PASS ref->het 0 NA 116,121 10,10 24,20 1 1 A2AB91|A2ABC0|B0V003|B0V0A6|B2ZUA4|E9PGM2|O15210|O15272|Q5STJ8|Q5STK6|Q5STQ5|Q5STQ6|Q66K65|Q96KK7|Q9HAN8|Q9UEE0|Q9UEE4|Q9UIZ6|Q9Y6K2 True hg19 CCDS34427.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TAPBP-006 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000276425.2 PASS NA None 146 NA True - GGGCCCGC ENST00000489157.1 PCMTD1 115294 __UNKNOWN__ __UNKNOWN__ 8 52731064 52731070 __UNKNOWN__ 3'UTR DEL ACTAGGT ACTAGGT - LTS-002_T LTS-002_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:52731064_52731070delACTAGGT ENST00000360540.5 - 0 3321_3327 PCMTD1_ENST00000544451.1_3'UTR NM_052937.2 NP_443169.2 Q96MG8 PCMD1_HUMAN protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1 NA NA NA NA NA cytoplasm (GO:0005737) protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719) NA NA NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1) 37 NA Lung NSC(129;0.0795)|all_lung(136;0.144) NA ATTCAAGGTAACTAGGTACTTCAAAAG 0.329 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 361 365.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 14.9 NA NA CCDS6148.1, CCDS69480.1 8q11.23 2010-08-05 ENSG00000168300 ENSG00000168300 115294 30483 protein-coding gene gene with protein product NA NA Standard NM_052937 XM_005251146 NA Approved FLJ10883 uc003xqx.4 Q96MG8 OTTHUMG00000164246 ENST00000360540.5:c.*1847ACCTAGT>- chr8.hg19:g.52731064_52731070delACTAGGT 0 2 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 313,314 15,42 59,49 1 1 Q96FK9 True hg19 CCDS6148.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PCMTD1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000377909.2 PASS NA None 361 NA True - ACTAGGT ENST00000360540.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ 13 19775272 19775272 __UNKNOWN__ IGR DEL C C - LTS-002_T LTS-002_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:19775272delC NA RP11-408E5.4 (13776 upstream) : RP11-408E5.5 (61664 downstream) NA NA NA NA NA NA NA NA NA NA TACCCTCCCACCCCCACATAT 0.338 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 566 523.75 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.09 NA NA NA NA NA NA NA chr13.hg19:g.19775272delC 4 8 ref NA False 59 59 PASS 5 PASS ref->het 0 NA 379,399 138,141 47,45 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 566 NA True C GPM6B 2824 __UNKNOWN__ __UNKNOWN__ X 13790997 13791001 __UNKNOWN__ Stop_Codon_Del DEL CATTT CATTT - rs147732407 byFrequency LTS-002_T LTS-002_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:13790997_13791001delCATTT ENST00000316715.4 - 0 1423_1427 GPM6B_ENST00000493677.1_Stop_Codon_Del|GPM6B_ENST00000454189.2_3'UTR NM_001001995.1 NP_001001995.1 Q13491 GPM6B_HUMAN glycoprotein M6B NA NA NA NA NA cell differentiation (GO:0030154)|extracellular matrix assembly (GO:0085029)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of serotonin uptake (GO:0051612)|nervous system development (GO:0007399)|ossification (GO:0001503)|positive regulation of bone mineralization (GO:0030501)|protein transport (GO:0015031)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of focal adhesion assembly (GO:0051893) integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886) NA NA central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|ovary(1)|pancreas(1) 6 NA NA CTCTGGCAAACATTTATGTGTAAGA 0.429 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 554 555.92 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001567 stop_retained_variant 1.55 NA NA CCDS14158.1, CCDS35206.1, CCDS35207.1, CCDS48084.1 Xp22.2 2010-08-03 ENSG00000046653 ENSG00000046653 2824 4461 protein-coding gene gene with protein product 300051 NA 8661015 Standard NM_001001995 NM_001001995 NA Approved M6B, MGC17150, MGC54284 uc004cvw.3 Q13491 OTTHUMG00000021162 ENST00000316715.4:c.986_*3delAAATG chrX.hg19:g.13790997_13791001delCATTT ENSP00000316861:p.*329Pheext*48 0 4 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 453,458 75,75 47,43 1 1 O76077|Q86X43|Q8N956 True hg19 CCDS35206.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GPM6B-003 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000055823.2 PASS NA None 554 NA True - CATTT ENST00000316715.4 ANKIB1 54467 __UNKNOWN__ __UNKNOWN__ 7 92016036 92016036 __UNKNOWN__ Intron DEL T T - LTS-003_T LTS-003_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:92016036delT ENST00000265742.3 + 12 2128 NM_019004.1 NP_061877.1 Q9P2G1 AKIB1_HUMAN ankyrin repeat and IBR domain containing 1 NA NA NA NA NA zinc ion binding (GO:0008270) NA NA cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1) 41 all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692) STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) NA TCTTTTTCTATTTTCATCTTA 0.308 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 217 227.79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.3 NA NA AB037807 CCDS47639.1 7q21.3 2013-01-10 ENSG00000001629 ENSG00000001629 54467 NA "Ankyrin repeat domain containing" 22215 protein-coding gene gene with protein product NA NA Standard NM_019004 NA Approved DKFZP434A0225, KIAA1386 uc003ulw.2 Q9P2G1 OTTHUMG00000155859 ENST00000265742.3:c.1752+79T>- chr7.hg19:g.92016036delT 3 5 ref NA False 37 37 PASS 4 PASS ref->het 0 NA 130,131 55,55 30,29 1 1 Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49 True hg19 CCDS47639.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ANKIB1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000342018.1 PASS NA None 217 NA True + T ENST00000265742.3 ZBTB6 10773 __UNKNOWN__ __UNKNOWN__ 9 125670522 125670523 __UNKNOWN__ 3'UTR DEL AT AT - LTS-003_T LTS-003_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:125670522_125670523delAT ENST00000373659.3 - 0 3917_3918 NM_006626.5 NP_006617.1 Q15916 ZBTB6_HUMAN zinc finger and BTB domain containing 6 NA NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) NA NA breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(1)|skin(1) 11 NA TATCAGAAACATAAACTAAATG 0.262 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 316 312.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA X82018 CCDS6846.1 9q33.1-q33.3 2013-01-08 2006-04-10 2006-04-10 ENSG00000186130 ENSG00000186130 10773 NA "-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing" 16764 protein-coding gene gene with protein product 605976 "zinc finger protein 482" ZNF482 NA 7958847 Standard NM_006626 NM_006626 NA Approved ZID uc004bnh.4 Q15916 OTTHUMG00000020628 ENST00000373659.3:c.*2555AT>- chr9.hg19:g.125670522_125670523delAT 0 4 ref NA False 49 49 PASS 1 PASS ref->het 0 NA 224,224 67,67 24,24 1 1 A8K8N6 True hg19 CCDS6846.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZBTB6-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000053962.1 PASS NA None 316 NA True - AT ENST00000373659.3 OLFM1 10439 __UNKNOWN__ __UNKNOWN__ 9 137982234 137982235 __UNKNOWN__ Intron INS - - TT rs10672761|rs397744056|rs199972738 byFrequency LTS-003_T LTS-003_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:137982234_137982235insTT ENST00000371796.3 + 2 333 OLFM1_ENST00000277415.11_Intron|OLFM1_ENST00000371793.3_Intron|OLFM1_ENST00000392991.4_Intron|OLFM1_ENST00000252854.4_Intron NM_001282612.1 NP_001269541.1 Q99784 NOE1_HUMAN olfactomedin 1 NA NA NA NA NA negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259) alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202) beta-amyloid binding (GO:0001540) NA NA endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2) 21 Myeloproliferative disorder(178;0.0333) Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07) NA gtgtgtgtttgtgtgtgtgtgt 0.525 NA NA NA NA NA NA NA NA NA 2178 0.434904 0.4728 0.2867 5008 , , NA 19279 0.5288 NA 0.3698 False NA ,,, NA NA NA 2504 0.4591 NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 91 113.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.41 NA NA AF035301 CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1 9q34.3 2014-01-20 ENSG00000130558 ENSG00000130558 10439 NA 17187 protein-coding gene gene with protein product "pancortin" 605366 NA 9039501 Standard NM_014279 NM_006334 NA Approved NOE1, OlfA, AMY, NOELIN uc004cfl.4 Q99784 OTTHUMG00000020897 ENST00000371796.3:c.219+44->TT chr9.hg19:g.137982234_137982235insTT 3 4 ref NA False 54 53 PASS 1 PASS ref->het 0 NA 26,27 52,53 23,21 1 1 Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OLFM1-003 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000054973.1 PASS NA None 91 NA True + T ENST00000371796.3 CDK12 51755 __UNKNOWN__ __UNKNOWN__ 17 37646871 37646871 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-003_T LTS-003_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:37646871delT ENST00000447079.4 + 3 2026 c.1993delT c.(1993-1995)ttafs p.L666fs CDK12_ENST00000430627.2_Frame_Shift_Del_p.L666fs NM_015083.1|NM_016507.2 NP_055898.1|NP_057591.2 Q9NYV4 CDK12_HUMAN cyclin-dependent kinase 12 666 NA NA NA NA mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380) cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634) ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353) NA NA NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3) 70 NA GACACGTCACTTACTCACAGA 0.448 NA NA "Mis, N, F" NA serous ovarian NA NA NA NA TCGA Ovarian(9;0.13) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Rec yes NA 17 17q12 51755 cyclin-dependent kinase 12 NA E 0 NA NA NA NA NA NA NA 150 157.23 NA NA NA NA NA 81 72 75 NA NA NA NA 17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 37646871 NA 2203 4300 6503 SO:0001589 frameshift_variant 0.22 NA NA AF227198 CCDS11337.1, CCDS45666.1 17q12 2011-10-25 2009-12-16 2009-12-16 ENSG00000167258 ENSG00000167258 51755 NA "Cyclin-dependent kinases" 24224 protein-coding gene gene with protein product "CDC2 related protein kinase 7" 615514 "Cdc2-related kinase, arginine/serine-rich" CRKRS NA 10048485, 11683387, 19884882 Standard NM_016507 XM_005257456 NA Approved CRK7, CRKR, KIAA0904 uc010cvv.3 Q9NYV4 OTTHUMG00000133214 ENST00000447079.4:c.1993delT chr17.hg19:g.37646871delT ENSP00000398880:p.Leu666fs 1 2 ref NA False 107 78 PASS 2 PASS ref->het 0 NA 32,32 97,97 20,20 1 1 A7E2B2|B4DYX4|B9EIQ6|O94978 True hg19 CCDS11337.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDK12-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000256941.4 PASS NA None 150 NA True + T ENST00000447079.4 TMEM104 54868 __UNKNOWN__ __UNKNOWN__ 17 72832982 72832983 __UNKNOWN__ Intron INS - - C rs397798879|rs11389066|rs200196382 byFrequency LTS-003_T LTS-003_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:72832982_72832983insC ENST00000417024.2 + 10 915 TMEM104_ENST00000335464.5_3'UTR|TMEM104_ENST00000582773.1_Intron|TMEM104_ENST00000582330.1_3'UTR Q8NE00 TM104_HUMAN transmembrane protein 104 NA NA NA NA NA integral component of membrane (GO:0016021) NA NA NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1) 19 all_lung(278;0.23) NA TGTTCTCCCCACCCACCTTCCA 0.634 NA NA NA NA NA NA NA NA NA CCCC|CCC|CCCC|deletion 1529 0.305312 0.3192 0.2003 5008 , , NA 17025 0.3978 NA 0.2952 False NA ,,, NA NA NA 2504 0.2761 NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 48 56.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.61 NA NA AK074029 CCDS32723.1 17q25.1 2005-12-19 ENSG00000109066 54868 NA 25984 protein-coding gene gene with protein product NA NA Standard NM_017728 NM_017728 NA Approved FLJ20255, FLJ00021 uc002jls.4 Q8NE00 ENST00000417024.2:c.770-2043->C chr17.hg19:g.72832985_72832985dupC 4 7 ref NA False 31 31 PASS 3 PASS ref->het 0 NA 7,7 36,38 6,4 1 1 Q8TEU1|Q9NT56|Q9NXH1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM104-002 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000444438.1 PASS NA None 48 NA True + C ENST00000417024.2 CA14 23632 __UNKNOWN__ __UNKNOWN__ 1 150237170 150237183 __UNKNOWN__ 3'UTR DEL TGTCCTCCTTCCCC TGTCCTCCTTCCCC - LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:150237170_150237183delTGTCCTCCTTCCCC ENST00000369111.4 + 0 2095_2108 NM_012113.1 NP_036245.1 Q9ULX7 CAH14_HUMAN carbonic anhydrase XIV NA NA NA bicarbonate transport (GO:0015701)|small molecule metabolic process (GO:0044281) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) carbonate dehydratase activity (GO:0004089)|metal ion binding (GO:0046872) central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(2) 18 Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171) LUSC - Lung squamous cell carcinoma(543;0.171) Acetazolamide(DB00819)|Zonisamide(DB00909) AGTAAGCAGATGTCCTCCTTCCCCTGGACATCTC 0.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 447 442.58 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.56 AB025904 CCDS947.1 1q21 2008-02-05 ENSG00000118298 ENSG00000118298 23632 "Carbonic anhydrases" 1372 protein-coding gene gene with protein product 604832 NA 10512682 Standard NM_012113 XM_005245059 NA Approved uc001etx.3 Q9ULX7 OTTHUMG00000012549 ENST00000369111.4:c.*124TGTCCTCCTTCCCC>- chr1.hg19:g.150237170_150237183delTGTCCTCCTTCCCC 0 4 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 411,417 12,12 55,51 1 1 Q5TB24|Q8NCF4 True hg19 CCDS947.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CA14-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000035064.2 PASS NA None 447 True + TGTCCTCCTTCCCC ENST00000369111.4 ANKRD36 375248 __UNKNOWN__ __UNKNOWN__ 2 97833401 97833402 __UNKNOWN__ Intron INS - - ATTAATCA rs377717858|rs5832832 LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:97833401_97833402insATTAATCA ENST00000461153.2 + 22 1804 ANKRD36_ENST00000420699.2_Intron A6QL64 AN36A_HUMAN ankyrin repeat domain 36 NA NA NA endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1) 23 ATACATGACATATTAATCATTA 0.351 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 339 404.02 NA NA 478,1540 NA 4,470,535 NA NA NA NA NA 0 0 NA dbSNP_114 24 886,3278 NA 13,860,1209 no intron ANKRD36 NM_001164315.1 NA 17,1330,1744 A1A1,A1R,RR NA 21.2776,23.6868,22.0641 NA NA NA 1364,4818 NA NA NA SO:0001627 intron_variant 0.53 BC046186 CCDS54379.1 2q11.2 2013-09-24 ENSG00000135976 ENSG00000135976 375248 "Ankyrin repeat domain containing" 24079 protein-coding gene gene with protein product NA NA 12975309 Standard NM_001164315 NA Approved UNQ2430 uc010yva.2 A6QL64 OTTHUMG00000155256 ENST00000461153.2:c.1561-30->ATTAATCA chr2.hg19:g.97833402_97833409dupATTAATCA 2 3 ref NA False 36 36 PASS 1 PASS ref->het 0 NA 275,277 28,31 39,44 1 1 B4E3I8|Q6UX02|Q86X62|Q9HCD1 True hg19 CCDS54379.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ANKRD36-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000339154.5 PASS NA None 339 True + ATTAATCA ENST00000461153.2 ATP5G3 518 __UNKNOWN__ __UNKNOWN__ 2 176046272 176046305 __UNKNOWN__ 5'UTR DEL GCACGCCGTCAGCTTGGGCCCCGTGCCCAGTGAG GCACGCCGTCAGCTTGGGCCCCGTGCCCAGTGAG - rs563726092|rs531380843 LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:176046272_176046305delGCACGCCGTCAGCTTGGGCCCCGTGCCCAGTGAG ENST00000392541.3 - 0 86_119 ATP5G3_ENST00000284727.4_Intron|ATP5G3_ENST00000409194.1_Intron P48201 AT5G3_HUMAN ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C3 (subunit 9) NA NA NA ATP hydrolysis coupled proton transport (GO:0015991)|ATP synthesis coupled proton transport (GO:0015986) integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263) hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215) large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1) 5 OV - Ovarian serous cystadenocarcinoma(117;0.147) AGGCTCCCGTGCACGCCGTCAGCTTGGGCCCCGTGCCCAGTGAGGCGCCGGCAC 0.701 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(30;387 605 18606 28805 47989) PASS NA NA NA 0 NA 299 274.62 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.04 BC106881 CCDS2263.1 2q31.1 2012-10-12 2010-06-11 ENSG00000154518 ENSG00000154518 518 "Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type" 843 protein-coding gene gene with protein product 602736 "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9) isoform 3", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)" NA 7698763 Standard NM_001689 NM_001002258 NA Approved uc002ujz.4 P48201 OTTHUMG00000132425 ENST00000392541.3:c.-184CTCACTGGGCACGGGGCCCAAGCTGACGGCGTGC>- chr2.hg19:g.176046272_176046305delGCACGCCGTCAGCTTGGGCCCCGTGCCCAGTGAG 0 3 ref NA False 62 62 PASS 1 PASS ref->het 0 NA 264,274 21,22 60,53 1 1 B2R4Z0|D3DPF0|Q4ZFX7 True hg19 CCDS2263.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ATP5G3-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000334494.1 PASS NA None 299 True - GCACGCCGTCAGCTTGGGCCCCGTGCCCAGTGAG ENST00000392541.3 MYRIP 25924 __UNKNOWN__ __UNKNOWN__ 3 40211449 40211461 __UNKNOWN__ Frame_Shift_Del DEL AAAACAGAAGAGC AAAACAGAAGAGC - LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:40211449_40211461delAAAACAGAAGAGC ENST00000302541.6 + 8 1080_1092 c.738_750delAAAACAGAAGAGC c.(736-750)cgaaaacagaagagcfs p.RKQKS246fs MYRIP_ENST00000396217.3_Frame_Shift_Del_p.RKQKS157fs|MYRIP_ENST00000539167.1_Frame_Shift_Del_p.RKQKS59fs|MYRIP_ENST00000425621.1_Frame_Shift_Del_p.RKQKS246fs|MYRIP_ENST00000444716.1_Frame_Shift_Del_p.RKQKS246fs|MYRIP_ENST00000459828.1_3'UTR NM_001284423.1|NM_001284426.1|NM_015460.2 NP_001271352.1|NP_001271355.1|NP_056275.2 Q8NFW9 MYRIP_HUMAN myosin VIIA and Rab interacting protein 246 Myosin-binding.|Negative regulation of PKA-binding. {ECO:0000250}. NA NA intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024) actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202) zinc ion binding (GO:0008270) breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 34 KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206) AGATTATACGAAAACAGAAGAGCAAAAGTGAGC 0.507 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 420 394.11 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.57 AF396687 CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1 3p21.33 2010-08-20 ENSG00000170011 ENSG00000170011 25924 "A-kinase anchor proteins" 19156 protein-coding gene gene with protein product "synaptotagmin-like protein homologue lacking C2 domains-c", "rab effector MYRIP", "Slp homologue lacking C2 domains" 611790 NA 11964381, 12221080 Standard NM_015460 NM_001284425 NA Approved DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C uc003cka.3 Q8NFW9 OTTHUMG00000131392 ENST00000302541.6:c.738_750delAAAACAGAAGAGC chr3.hg19:g.40211449_40211461delAAAACAGAAGAGC ENSP00000301972:p.Arg246fs 0 5 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 357,358 34,34 58,58 1 1 B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4 True hg19 CCDS2689.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MYRIP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254181.2 PASS NA None 420 True + AAAACAGAAGAGC ENST00000302541.6 MECOM 2122 __UNKNOWN__ __UNKNOWN__ 3 169200974 169200979 __UNKNOWN__ Intron DEL TTTTAT TTTTAT - rs372281390 LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:169200974_169200979delTTTTAT ENST00000494292.1 - 2 135 MECOM_ENST00000485957.1_Intron NM_004991.3 NP_004982.2 Q13465 MDS1_HUMAN MDS1 and EVI1 complex locus NA NA NA regulation of transcription, DNA-templated (GO:0006355) sequence-specific DNA binding transcription factor activity (GO:0003700) NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4) 85 AAAACCATTGttttatttttattttt 0.306 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 210 202.83 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 10.35 S82592, AF164154 CCDS3205.1, CCDS54669.1, CCDS54670.1 3q26.2 2013-01-08 2009-08-07 2009-08-07 ENSG00000085276 ENSG00000085276 2122 "Zinc fingers, C2H2-type" 3498 protein-coding gene gene with protein product 165215 "myelodysplasia syndrome 1", "ecotropic viral integration site 1" MDS1, EVI1 NA 2115646, 8171026, 8643684 Standard NM_005241, NM_004991 NM_001105077 NA Approved MDS1-EVI1, PRDM3 uc011bpj.1 Q03112 OTTHUMG00000158596 ENST00000494292.1:c.38-101662ATAAAA>- chr3.hg19:g.169200980_169200985delTTTTAT 2 10 ref NA False 39 39 PASS 3 PASS ref->het 0 NA 148,164 5,5 98,83 1 1 Q13466|Q6FH90 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MECOM-004 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000351517.3 PASS NA None 210 True - TTTTAT ENST00000494292.1 IK 3550 __UNKNOWN__ __UNKNOWN__ 5 140028042 140028043 __UNKNOWN__ Intron INS - - T rs369546377|rs557124153 byFrequency LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:140028042_140028043insT ENST00000417647.2 + 2 155 IK_ENST00000523672.1_Intron NM_006083.3 NP_006074.2 Q13123 RED_HUMAN IK cytokine, down-regulator of HLA II NA NA NA cell-cell signaling (GO:0007267)|immune response (GO:0006955) extracellular space (GO:0005615)|nucleus (GO:0005634) identical protein binding (GO:0042802) large_intestine(1) 1 all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128) KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) atTAACGTCAATTTTTTTTGTC 0.426 NA NA NA NA NA NA TTTTTTTT|TTTTTTTT|TTTTTTTTT|insertion 11 0.00219649 0.0023 0 5008 , , NA 19325 0.004 NA 0.004 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 NA 140 139.91 NA NA 2,3598 NA 0,2,1798 NA NA NA NA NA -4.5 0 NA 140 6,7860 NA 0,6,3927 no intron IK NM_006083.3 NA 0,8,5725 A1A1,A1R,RR NA 0.0763,0.0556,0.0698 NA NA NA 8,11458 NA NA NA SO:0001627 intron_variant 0 BC051295 CCDS47280.1 5q31.3 2008-08-07 ENSG00000113141 ENSG00000113141 3550 5958 protein-coding gene gene with protein product 600549 NA 7970704 Standard NM_006083 NM_006083 NA Approved uc003lgq.3 Q13123 OTTHUMG00000163374 ENST00000417647.2:c.17-13->T chr5.hg19:g.140028050_140028050dupT 9 9 ref NA False 55 55 PASS 8 PASS ref->het 0 NA 82,82 38,38 18,18 1 1 Q6IPD8 True hg19 CCDS47280.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IK-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000372897.1 PASS NA None 140 True + T ENST00000417647.2 PANK3 79646 __UNKNOWN__ __UNKNOWN__ 5 167987882 167987907 __UNKNOWN__ Intron DEL TATCATGAAGAACAGGTCTCAATGCC TATCATGAAGAACAGGTCTCAATGCC - LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:167987882_167987907delTATCATGAAGAACAGGTCTCAATGCC ENST00000239231.6 - 5 1253 PANK3_ENST00000520504.1_Intron|MIR103A1_ENST00000362165.1_RNA NM_024594.3 NP_078870.1 Q9H999 PANK3_HUMAN pantothenate kinase 3 NA NA NA coenzyme A biosynthetic process (GO:0015937) cytoplasm (GO:0005737) ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594) NS(1)|cervix(2)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1) 16 Renal(175;0.000159)|Lung NSC(126;0.0441)|all_lung(126;0.0909) Medulloblastoma(196;0.0208)|all_neural(177;0.0416) Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.0989)|OV - Ovarian serous cystadenocarcinoma(192;0.147)|Epithelial(171;0.188) ACCACTCAAATATCATGAAGAACAGGTCTCAATGCCTTCATAGCCC 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 154 139.13 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AK022961 CCDS4368.1 5q35.1 2008-02-05 ENSG00000120137 ENSG00000120137 79646 19365 protein-coding gene gene with protein product 606161 NA 11479594 Standard NM_024594 NM_024594 NA Approved FLJ12899 uc003lzz.2 Q9H999 OTTHUMG00000130410 ENST00000239231.6:c.936+490GGCATTGAGACCTGTTCTTCATGATA>- chr5.hg19:g.167987882_167987907delTATCATGAAGAACAGGTCTCAATGCC 0 4 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 170,170 9,9 18,18 1 1 D3DQL1|Q53FJ9|Q7RTX4 True hg19 CCDS4368.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PANK3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252793.2 PASS NA None 154 True - TATCATGAAGAACAGGTCTCAATGCC ENST00000239231.6 AF121898.3 0 __UNKNOWN__ __UNKNOWN__ 8 88735657 88735658 __UNKNOWN__ RNA INS - - AG rs80328007|rs34297365|rs10674559 byFrequency LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:88735657_88735658insAG ENST00000517711.1 - 0 69 AF121898.3_ENST00000440763.2_RNA|AF121898.3_ENST00000518494.1_RNA NA NA NA NA GGAGGGCAATCGGGAATTTCAC 0.545 NA NA NA NA NA NA 3717 0.742212 0.8699 0.5807 5008 , , NA 18605 0.5853 NA 0.7823 False NA ,,, NA NA NA 2504 0.8047 NA NA NA PASS NA NA NA 0 NA 91 91.21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.93 NA NA NA NA NA ENST00000517711.1: chr8.hg19:g.88735657_88735658insAG 1 3 ref NA False 36 36 PASS 0 PASS ref->het 0 NA 12,12 69,72 8,6 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AF121898.3-002 KNOWN basic antisense NA antisense OTTHUMT00000375298.1 PASS NA None 91 True - AG ENST00000517711.1 PUS7L 83448 __UNKNOWN__ __UNKNOWN__ 12 44148868 44148885 __UNKNOWN__ In_Frame_Del DEL GTATTTCACTAATCTTGA GTATTTCACTAATCTTGA - LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:44148868_44148885delGTATTTCACTAATCTTGA ENST00000416848.2 - 2 652_669 c.164_181delTCAAGATTAGTGAAATAC c.(163-183)ttcaagattagtgaaatacaa>taa p.55_61FKISEIQ>* PUS7L_ENST00000431332.3_Intron|PUS7L_ENST00000551923.1_In_Frame_Del_p.55_61FKISEIQ>*|PUS7L_ENST00000553166.1_In_Frame_Del_p.55_61FKISEIQ>*|PUS7L_ENST00000344862.5_In_Frame_Del_p.55_61FKISEIQ>* NM_001098615.1|NM_001271826.1 NP_001092085.1|NP_001258755.1 Q9H0K6 PUS7L_HUMAN pseudouridylate synthase 7 homolog (S. cerevisiae)-like 55 NA NA pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033) pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723) NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 32 all_cancers(12;0.00027) Lung NSC(34;0.114)|all_lung(34;0.24) GBM - Glioblastoma multiforme(48;0.0402) GGCTCAAGTTGTATTTCACTAATCTTGAAAATAGGCTC 0.326 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 368 359.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.56 BX647494 CCDS8743.1, CCDS61104.1 12q12 2006-02-07 ENSG00000129317 83448 25276 protein-coding gene gene with protein product NA NA 11230166 Standard NM_031292 NM_001098615 NA Approved DKFZP434G1415 uc001rnr.5 Q9H0K6 OTTHUMG00000169423 ENST00000416848.2:c.164_181delTCAAGATTAGTGAAATAC chr12.hg19:g.44148868_44148885delGTATTTCACTAATCTTGA ENSP00000415899:p.Phe55_Gln61delins* 0 5 ref NA False 102 101 PASS 1 PASS ref->het 0 NA 297,299 65,67 31,30 1 1 B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2 True hg19 CCDS8743.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PUS7L-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000403931.1 PASS NA None 368 True - GTATTTCACTAATCTTGA ENST00000416848.2 PTGES3 10728 __UNKNOWN__ __UNKNOWN__ 12 57081783 57081793 __UNKNOWN__ Splice_Site DEL TTGTGAACGGG TTGTGAACGGG - rs374470578 LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:57081783_57081793delTTGTGAACGGG ENST00000262033.6 - 1 291_301 c.-9_1delCCCGTTCACAA c.(-11-3)gccccgttcacaatg>gctg PTGES3_ENST00000448157.2_Splice_Site|PTGES3_ENST00000414274.3_Splice_Site|PTGES3_ENST00000436399.2_Splice_Site|PTGES3_ENST00000456859.2_Splice_Site NM_006601.5 NP_006592.3 Q15185 TEBP_HUMAN prostaglandin E synthase 3 (cytosolic) NA NA NA arachidonic acid metabolic process (GO:0019369)|cell proliferation (GO:0008283)|chaperone cofactor-dependent protein refolding (GO:0070389)|cyclooxygenase pathway (GO:0019371)|glucocorticoid receptor signaling pathway (GO:0042921)|glycogen biosynthetic process (GO:0005978)|lung saccule development (GO:0060430)|prostaglandin biosynthetic process (GO:0001516)|RNA-dependent DNA replication (GO:0006278)|signal transduction (GO:0007165)|skin development (GO:0043588)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723) chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697) prostaglandin-E synthase activity (GO:0050220)|telomerase activity (GO:0003720)|unfolded protein binding (GO:0051082) large_intestine(1)|lung(1) 2 CGCACTCACATTGTGAACGGGGCAGGGGGAC 0.692 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 116 127.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 1.82 BC003005 CCDS31836.1, CCDS61158.1, CCDS61159.1, CCDS61160.1, CCDS73485.1 12q13.13 2012-03-14 ENSG00000110958 ENSG00000110958 10728 16049 protein-coding gene gene with protein product 607061 NA 8114727, 12077419 Standard NM_006601 XR_245889 NA Approved p23, TEBP, cPGES uc001slu.4 Q15185 OTTHUMG00000170217 ENST00000262033.6:c.2+1CCCGTTCACAA>- chr12.hg19:g.57081783_57081793delTTGTGAACGGG 0 4 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 102,109 5,5 23,16 1 1 A8K7D0|B4DHP2|B4DP11|B4DP21|Q8WU70 True hg19 CCDS31836.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PTGES3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000408054.1 PASS NA None 116 Frame_Shift_Del True - TTGTGAACGGG ENST00000262033.6 RP11-281J9.2 0 __UNKNOWN__ __UNKNOWN__ 16 78083418 78083420 __UNKNOWN__ RNA DEL GCA GCA - rs12924914|rs57738729|rs78500520|rs75368265 byFrequency LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:78083418_78083420delGCA ENST00000563114.1 - 0 41 NA NA NA NA TGCTGCTGCTGCAGGAGGCTCCA 0.517 NA NA NA NA NA NA 2289 0.457069 0.236 0.5216 5008 , , NA 21657 0.506 NA 0.5596 False NA ,,, NA NA NA 2504 0.5542 NA NA NA PASS NA NA NA 0 NA 25 21.95 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA ENST00000563114.1: chr16.hg19:g.78083418_78083420delGCA 0 4 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 3,3 21,21 1,1 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-281J9.2-001 KNOWN basic antisense NA antisense OTTHUMT00000434014.1 PASS NA None 25 True - GCA ENST00000563114.1 TP53 7157 __UNKNOWN__ __UNKNOWN__ 17 7578181 7578181 __UNKNOWN__ Frame_Shift_Del DEL G G - rs138983188 LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:7578181delG ENST00000269305.4 - 6 857 c.668delC c.(667-669)cctfs p.P223fs TP53_ENST00000445888.2_Frame_Shift_Del_p.P223fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.P223fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.P223fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.P223fs|TP53_ENST00000574684.1_Intron|TP53_ENST00000420246.2_Frame_Shift_Del_p.P223fs NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 223 Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A. NA P -> A (in a sporadic cancer; somatic mutation).|P -> H (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> R (in a sporadic cancer; somatic mutation).|P -> S (in a sporadic cancer; somatic mutation).|P -> T (in a sporadic cancer; somatic mutation). NA apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032) chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657) ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270) p.?(11)|p.0?(8)|p.P223L(4)|p.P223H(2)|p.Y220_P223delYEPP(1)|p.P223R(1)|p.V218_E224delVPYEPPE(1) NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) Acetylsalicylic acid(DB00945) CCAGACCTCAGGCGGCTCATA 0.542 NA 111 "Mis, N, F" NA "breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types" "breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types" NA Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(47;798 1329 9957 10801) PASS yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 NA "L, E, M, O" 28 Unknown(11)|Whole gene deletion(8)|Substitution - Missense(7)|Deletion - In frame(2) biliary_tract(5)|endometrium(5)|bone(4)|upper_aerodigestive_tract(3)|central_nervous_system(2)|oesophagus(2)|thyroid(1)|stomach(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|meninges(1)|prostate(1) NA 127 125.93 NA NA NA 87 81 83 NA NA NA NA 17 NA NA NA NA NA NA 7578181 2203 4300 6503 SO:0001589 frameshift_variant 0.01 Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; AF307851 CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1 17p13.1 2014-09-17 2008-01-16 ENSG00000141510 ENSG00000141510 7157 11998 protein-coding gene gene with protein product "Li-Fraumeni syndrome" 191170 NA 6396087, 3456488, 2047879 Standard NM_000546 NM_001126115 NA Approved p53, LFS1 uc002gij.3 P04637 OTTHUMG00000162125 ENST00000269305.4:c.668delC chr17.hg19:g.7578181delG ENSP00000269305:p.Pro223fs 1 4 ref NA False 77 77 PASS 2 PASS ref->het 0 NA 75,77 36,38 16,15 1 1 Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61 True hg19 CCDS11118.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TP53-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000367397.1 PASS NA None 127 True - G ENST00000269305.4 NF1 4763 __UNKNOWN__ __UNKNOWN__ 17 29670014 29670042 __UNKNOWN__ Splice_Site DEL TTATCTTTAATAGAGTCCAGAGGAAGTAT TTATCTTTAATAGAGTCCAGAGGAAGTAT - rs199474784 LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:29670014_29670042delTTATCTTTAATAGAGTCCAGAGGAAGTAT ENST00000358273.4 + 48 7445_7461 c.7062_7078delTTATCTTTAATAGAGTCCAGAGGAAGTAT c.(7060-7080)aattatctttaatagagtcca>aaca p.YL**SP2355fs NF1_ENST00000356175.3_Splice_Site_p.YL**SP2334fs|NF1_ENST00000444181.2_Splice_Site_p.YL**SP148fs|NF1_ENST00000417592.2_Splice_Site_p.YL**SP68fs NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 2355 NA NA actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060) axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634) phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099) p.0?(8)|p.?(5)|p.E2357*(2) NF1/ACCN1(2) autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9) 599 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) CATCTCATGATTATCTTTAATAGAGTCCAGAGGAAGTATTTATGGCAAT 0.362 NA NA "D, Mis, N, F, S, O" NA "neurofibroma, glioma" "neurofibroma, glioma" NA Neurofibromatosis, type 1 TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS yes Rec yes Neurofibromatosis type 1 17 17q12 4763 neurofibromatosis type 1 gene NA O 15 Whole gene deletion(8)|Unknown(5)|Substitution - Nonsense(2) soft_tissue(7)|lung(5)|autonomic_ganglia(2)|central_nervous_system(1) GRCh37 CM013781|CS072265|CS076640 NF1 M|S NA 274 252.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 1.25 Familial Cancer Database NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome CCDS11264.1, CCDS42292.1, CCDS45645.1 17q11.2 2014-09-17 2008-07-31 ENSG00000196712 ENSG00000196712 4763 7765 protein-coding gene gene with protein product "neurofibromatosis", "von Recklinghausen disease", "Watson disease" 613113 NA 1715669 Standard NM_000267 NM_000267 NA Approved uc002hgg.3 P21359 OTTHUMG00000132871 ENST00000358273.4:c.7063-1TTATCTTTAATAGAGTCCAGAGGAAGTAT>- chr17.hg19:g.29670014_29670042delTTATCTTTAATAGAGTCCAGAGGAAGTAT 0 4 ref NA False 97 97 PASS 1 PASS ref->het 0 NA 212,214 55,55 66,65 2 2 O00662|Q14284|Q14930|Q14931|Q9UMK3 True hg19 CCDS42292.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NF1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000256351.2 PASS NA None 274 Frame_Shift_Del True + TTATCTTTAATAGAGTCCAGAGGAAGTAT ENST00000358273.4 NARF 26502 __UNKNOWN__ __UNKNOWN__ 17 80417742 80417742 __UNKNOWN__ Intron DEL A A - rs57897512 byFrequency LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:80417742delA ENST00000457415.3 + 2 128 NARF_ENST00000345415.7_Intron|NARF_ENST00000309794.11_Intron|NARF_ENST00000581743.1_Intron|NARF_ENST00000390006.4_Intron|NARF_ENST00000412079.2_Intron Q9UHQ1 NARF_HUMAN nuclear prelamin A recognition factor NA NA NA lamin filament (GO:0005638)|nuclear lamina (GO:0005652)|nuclear lumen (GO:0031981)|nucleus (GO:0005634) lamin binding (GO:0005521) endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 24 Breast(20;0.00106)|all_neural(118;0.0804) OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369) gactccgtctaaaaaaataaa 0.468 NA NA NA NA NA NA ?|AAAAAAA|AAAAAA|unsure 2951 0.589257 0.5802 0.6268 5008 , , NA 23177 0.9117 NA 0.3757 False NA ,,, NA NA NA 2504 0.4622 NA NA NA PASS NA NA NA 0 NA 44 66.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.14 BC000438 CCDS32777.1, CCDS42403.1, CCDS42404.1 17q25.3 2011-12-19 ENSG00000141562 ENSG00000141562 26502 29916 protein-coding gene gene with protein product "iron-only hydrogenase-like protein 2" 605349 NA 10514485, 15667261 Standard NM_031968 NM_031968 NA Approved FLJ10067, DKFZp434G0420, IOP2 uc002kfg.4 Q9UHQ1 ENST00000457415.3:c.28-126A>- chr17.hg19:g.80417742delA 6 10 ref NA False 35 35 PASS 7 PASS ref->het 0 NA 3,3 26,26 14,15 1 1 A6NCJ3|B3KPX2|K4DI98|Q96AY9|Q9BWC6 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NARF-018 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000443578.1 PASS NA None 44 True + A ENST00000457415.3 PIGA 5277 __UNKNOWN__ __UNKNOWN__ X 15337947 15337948 __UNKNOWN__ 3'UTR INS - - A LTS-004_T LTS-004_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:15337947_15337948insA ENST00000333590.4 - 0 3219_3220 PIGA_ENST00000428964.1_3'UTR|PIGA_ENST00000542278.1_3'UTR NM_002641.3 NP_002632.1 P37287 PIGA_HUMAN phosphatidylinositol glycan anchor biosynthesis, class A NA NA NA C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|positive regulation of metabolic process (GO:0009893)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254) endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)|membrane (GO:0016020) phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)|UDP-glycosyltransferase activity (GO:0008194) endometrium(2)|kidney(2)|large_intestine(2)|ovary(1)|prostate(2)|urinary_tract(1) 10 Hepatocellular(33;0.183) GACAGTTTAAGAATTAAATGAC 0.257 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 255 272.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.24 BC038236 CCDS14165.1, CCDS48086.1, CCDS48086.2 Xp22.1 2014-09-17 2008-07-31 ENSG00000165195 ENSG00000165195 5277 2.4.1.198 "Glycosyltransferase group 1 domain containing", "Phosphatidylinositol glycan anchor biosynthesis" 8957 protein-coding gene gene with protein product "paroxysmal nocturnal hemoglobinuria", "phosphatidylinositol N-acetylglucosaminyltransferase" 311770 "phosphatidylinositol glycan, class A (paroxysmal nocturnal hemoglobinuria)" NA 8500164 Standard NM_002641 NM_002641 NA Approved GPI3 uc004cwr.3 P37287 OTTHUMG00000021174 ENST00000333590.4:c.*1681->T chrX.hg19:g.15337949_15337949dupA 3 4 ref NA False 75 75 PASS 2 PASS ref->het 0 NA 174,174 52,52 24,25 1 1 B4E0V2|Q16025|Q16250 True hg19 CCDS14165.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PIGA-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000055854.1 PASS NA None 255 True - A ENST00000333590.4 SESTD1 91404 __UNKNOWN__ __UNKNOWN__ 2 179973244 179973245 __UNKNOWN__ 3'UTR DEL GG GG - LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:179973244_179973245delGG ENST00000428443.3 - 0 3788_3789 NM_178123.4 NP_835224.3 Q86VW0 SESD1_HUMAN SEC14 and spectrin domains 1 NA NA NA NA NA phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314) NA breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3) 30 OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147) tgaggatgtaggggcactggat 0.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 200 217.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.39 NA NA AK096232 CCDS33338.1 2q31.3 2014-01-28 ENSG00000187231 ENSG00000187231 91404 NA 18379 protein-coding gene gene with protein product NA NA 12837271 Standard NM_178123 NM_178123 NA Approved DKFZp434O0515, Solo uc002uni.4 Q86VW0 OTTHUMG00000154554 ENST00000428443.3:c.*1382CC>- chr2.hg19:g.179973246_179973247delGG 2 4 ref NA False 104 86 PASS 4 PASS ref->het 0 NA 71,72 106,108 26,25 1 1 Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2 True hg19 CCDS33338.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SESTD1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000335916.2 PASS NA None 200 True - G ENST00000428443.3 SH3RF1 57630 __UNKNOWN__ __UNKNOWN__ 4 170087938 170087939 __UNKNOWN__ Intron INS - - G rs35417195|rs147968175 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:170087938_170087939insG ENST00000284637.9 - 3 735 SH3RF1_ENST00000508685.1_Intron NM_020870.3 NP_065921.2 Q7Z6J0 SH3R1_HUMAN SH3 domain containing ring finger 1 NA NA NA NA NA negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|protein ubiquitination (GO:0016567)|regulation of JNK cascade (GO:0046328) cell projection (GO:0042995)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794) ligase activity (GO:0016874)|zinc ion binding (GO:0008270) NA NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4) 31 Prostate(90;0.00267)|Renal(120;0.0183) GBM - Glioblastoma multiforme(119;0.0287) GCTCGTTACTTTGACTGGACCT 0.475 NA NA NA NA NA NA NA NA NA NA NA NA G|-|G|deletion 2010 0.401358 0.5492 0.2997 5008 , , NA 17129 0.2778 NA 0.3489 False NA ,,, NA NA NA 2504 0.455 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 36 31.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA BC033203 CCDS34099.1 4q32.3 2013-01-09 2006-02-13 2006-02-13 ENSG00000154447 ENSG00000154447 57630 NA "RING-type (C3HC4) zinc fingers" 17650 protein-coding gene gene with protein product "plenty of SH3 domains" NA "SH3 multiple domains 2" SH3MD2 NA 9482736 Standard NM_020870 NM_020870 NA Approved POSH, RNF142, KIAA1494 uc003isa.1 Q7Z6J0 OTTHUMG00000161010 ENST00000284637.9:c.394-10108->C chr4.hg19:g.170087938_170087939insG 1 3 ref NA False 33 33 PASS 0 PASS ref->het 0 NA 5,5 29,29 2,2 1 1 Q05BT2|Q8IW46|Q9HAM2|Q9P234 True hg19 CCDS34099.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SH3RF1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000363382.3 PASS NA None 36 True - G ENST00000284637.9 RASGRF2 5924 __UNKNOWN__ __UNKNOWN__ 5 80504493 80504493 __UNKNOWN__ Intron DEL C C - rs139747197 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:80504493delC ENST00000265080.4 + 22 3223 CKMT2-AS1_ENST00000503483.2_RNA NM_006909.2 NP_008840.1 O14827 RGRF2_HUMAN Ras protein-specific guanine nucleotide-releasing factor 2 NA NA NA NA NA apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268) cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886) Rho guanyl-nucleotide exchange factor activity (GO:0005089) NA biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 75 Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357) OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29) gcctcagcctcccgagtagct 0.537 NA NA NA NA NA NA NA NA NA NA NA NA CCC|CCC|CC|deletion 1215 0.242612 0.236 0.4063 5008 , , NA 16317 0.0437 NA 0.3012 False NA ,,, NA NA NA 2504 0.2802 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 27 24.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.59 NA NA AF023130 CCDS4052.1 5q13 2013-01-10 ENSG00000113319 ENSG00000113319 5924 NA "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing" 9876 protein-coding gene gene with protein product 606614 NA Standard NM_006909 NM_006909 NA Approved GRF2, Ras-GRF2 uc003kha.2 O14827 OTTHUMG00000119015 ENST00000265080.4:c.3156+236C>- chr5.hg19:g.80504493delC 2 5 ref NA False 34 34 PASS 3 PASS ref->hom 0 NA 0,0 20,20 6,6 1 1 B9EG89|Q9UK56 True hg19 CCDS4052.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RASGRF2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000239215.2 PASS NA None 27 True + C ENST00000265080.4 SLC16A10 117247 __UNKNOWN__ __UNKNOWN__ 6 111498825 111498825 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:111498825delT ENST00000368851.5 + 3 1074 c.899delT c.(898-900)atafs p.I300fs SLC16A10_ENST00000465319.1_3'UTR|SLC16A10_ENST00000368850.3_5'UTR NM_018593.4 NP_061063.2 Q8TF71 MOT10_HUMAN solute carrier family 16 (aromatic amino acid transporter), member 10 300 NA NA NA NA amino acid transport (GO:0006865)|aromatic amino acid transport (GO:0015801)|ion transport (GO:0006811)|transmembrane transport (GO:0055085) basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) NA endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2) 12 all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466) OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132) Droxidopa(DB06262)|Glycine(DB00145)|L-Alanine(DB00160)|L-Arginine(DB00125)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Cystine(DB00138)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Histidine(DB00117)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Lysine(DB00123)|L-Methionine(DB00134)|L-Phenylalanine(DB00120)|L-Proline(DB00172)|L-Serine(DB00133)|L-Threonine(DB00156)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|L-Valine(DB00161)|Liothyronine(DB00279)|Liotrix(DB01583)|Pyruvic acid(DB00119) GCAGTTGGAATACCACTTGCA 0.373 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 347 337.37 NA NA 91 88 89 NA NA NA 6 NA NA NA 111498825 2203 4300 6503 SO:0001589 frameshift_variant 0.01 NA NA AF116652 CCDS5089.1 6q21-q22 2014-01-28 2013-07-18 ENSG00000112394 ENSG00000112394 117247 NA "Solute carriers" 17027 protein-coding gene gene with protein product 607550 "solute carrier family 16 (monocarboxylic acid transporters), member 10" NA 11278508, 11827462 Standard NM_018593 NA Approved TAT1, MCT10 uc003pus.3 Q8TF71 OTTHUMG00000015371 ENST00000368851.5:c.899delT chr6.hg19:g.111498825delT ENSP00000357844:p.Ile300fs 0 3 ref NA False 85 38 PASS 1 PASS ref->het 0 NA 104,105 217,219 11,11 1 1 B3KWY0|Q6ZMG0|Q8WVI5 True hg19 CCDS5089.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC16A10-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041822.2 PASS NA None 347 True + T ENST00000368851.5 TMEM176A 55365 __UNKNOWN__ __UNKNOWN__ 7 150499164 150499165 __UNKNOWN__ Intron INS - - TTCTC rs368112702|rs373639194|rs137988135|rs28364765|rs148829186 LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:150499164_150499165insTTCTC ENST00000484928.1 + 3 755 TMEM176A_ENST00000004103.3_Intron|TMEM176A_ENST00000461345.1_Intron Q96HP8 T176A_HUMAN transmembrane protein 176A NA NA NA NA NA negative regulation of dendritic cell differentiation (GO:2001199) integral component of membrane (GO:0016021) NA breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1) 12 OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) ttcttctccttttctcttctct 0.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 90 109.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF258340 CCDS5909.1 7q36.1 2006-09-04 ENSG00000002933 ENSG00000002933 55365 NA 24930 protein-coding gene gene with protein product 610334 NA 12097419, 8889548 Standard NM_018487 NM_018487 NA Approved HCA112 uc003whx.1 Q96HP8 OTTHUMG00000158114 ENST00000484928.1:c.175-138->TTCTC chr7.hg19:g.150499170_150499174dupTTCTC 6 5 ref NA False 51 49 PASS 5 PASS ref->het 0 NA 13,13 56,58 26,26 2 2 D3DX00|Q9NYC7 True hg19 CCDS5909.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM176A-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000350222.1 PASS NA None 90 True + TTCTC ENST00000484928.1 MYBL1 4603 __UNKNOWN__ __UNKNOWN__ 8 67514762 67514763 __UNKNOWN__ Intron INS - - A rs550620295 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:67514762_67514763insA ENST00000522677.3 - 2 431 MYBL1_ENST00000524176.2_Intron|MYBL1_ENST00000517885.1_Intron NM_001080416.2|NM_001144755.1 NP_001073885.1|NP_001138227.1 P10243 MYBA_HUMAN v-myb avian myeloblastosis viral oncogene homolog-like 1 NA NA NA NA NA positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893) nucleus (GO:0005634) chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077) NA breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1) 25 Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938) ATCCTCACTACAAAAAAAACAC 0.337 NA NA NA NA NA NA NA NA NA NA NA NA AAAAAAAA|AAAAAAAA|AAAAAAAAA|insertion 3 0.000599042 0 0 5008 , , NA 11040 0.002 NA 0.001 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 316 332.53 NA , 1,3543 NA 0,1,1771 NA NA NA NA , -1.8 0.3 NA 111 3,7837 NA 0,3,3917 no intron,intron MYBL1 NM_001144755.1,NM_001080416.2 , 0,4,5688 A1A1,A1R,RR NA 0.0383,0.0282,0.0351 , , NA 4,11380 NA NA NA SO:0001627 intron_variant 1.22 NA NA X13294 CCDS47867.1, CCDS55241.1 8q22 2013-07-09 2013-07-09 ENSG00000185697 ENSG00000185697 4603 NA 7547 protein-coding gene gene with protein product 159405 NA Standard XM_034274 XM_005251251 NA Approved AMYB, A-myb uc003xwj.3 P10243 OTTHUMG00000164559 ENST00000522677.3:c.21-4->T chr8.hg19:g.67514770_67514770dupA 9 9 ref NA False 74 74 PASS 8 PASS ref->het 0 NA 163,167 107,112 43,38 1 1 E7EW29|Q495F9 True hg19 CCDS47867.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MYBL1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000379221.3 PASS NA None 316 True - A ENST00000522677.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 9 69067893 69067897 __UNKNOWN__ IGR DEL AAAAG AAAAG - rs371397689|rs368445978|rs143981985 LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:69067893_69067897delAAAAG NA MIR1299 (65572 upstream) : PGM5P2 (12342 downstream) NA NA NA NA NA NA NA taagaagagaaaaagagaagatgaa 0.273 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 117 141.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 9.51 NA NA NA NA NA NA NA NA chr9.hg19:g.69067893_69067897delAAAAG 0 6 ref NA False 36 36 PASS 1 PASS ref->het 0 NA 81,96 18,55 26,25 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 117 True AAAAG TTC40 0 __UNKNOWN__ __UNKNOWN__ 10 134713266 134713266 __UNKNOWN__ Intron DEL G G - rs534992748|rs138315034 LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:134713266delG ENST00000368586.5 - 23 3025 TTC40_ENST00000368582.2_Intron NM_001200049.2 NP_001186978.2 NA NA NA NA NA NA breast(1)|endometrium(5)|lung(19)|urinary_tract(3) 28 CTACACAGGTGGTATTCTAAG 0.612 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 61 61.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.69 NA NA NA NA NA NA NA NA ENST00000368586.5:c.2925-96C>- chr10.hg19:g.134713266delG 1 4 ref NA False 53 53 PASS 2 PASS ref->het 0 NA 9,9 45,46 6,5 1 1 True hg19 CCDS58101.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TTC40-001 PUTATIVE basic|appris_candidate_longest|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000051095.3 PASS NA None 61 True - G ENST00000368586.5 CDCA5 113130 __UNKNOWN__ __UNKNOWN__ 11 64851525 64851525 __UNKNOWN__ 5'UTR DEL A A - LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:64851525delA ENST00000275517.3 - 0 98 NM_080668.3 NP_542399.1 Q96FF9 CDCA5_HUMAN cell division cycle associated 5 NA NA NA NA NA double-strand break repair (GO:0006302)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|regulation of cohesin localization to chromatin (GO:0071922) chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886) chromatin binding (GO:0003682) NA large_intestine(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 7 CACTCGCTGCAAAAAACGTTC 0.657 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 483 530.36 NA NA 2 3 3 NA NA NA 11 NA NA NA 64851525 628 1441 2069 SO:0001623 5_prime_UTR_variant 1.5 NA NA BG354578 CCDS8091.1 11q13.1 2011-01-31 ENSG00000146670 ENSG00000146670 113130 NA 14626 protein-coding gene gene with protein product "sororin" 609374 NA 12188893, 15837422 Standard NM_080668 NM_080668 NA Approved uc001ocp.2 Q96FF9 OTTHUMG00000150420 ENST00000275517.3:c.-75T>- chr11.hg19:g.64851525delA 5 6 ref NA False 190 125 PASS 6 PASS ref->het 0 NA 272,278 145,149 67,59 1 1 A8K625 True hg19 CCDS8091.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDCA5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000385186.1 PASS NA None 483 True - A ENST00000275517.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 12 1675127 1675128 __UNKNOWN__ IGR INS - - GAG rs61171230|rs397947534 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:1675127_1675128insGAG NA LINC00942 (58643 upstream) : FBXL14 (30 downstream) NA NA NA NA NA NA NA AGAGAGAGAGAGAGAACAAGAA 0.391 NA NA NA NA NA NA NA NA NA NA NA NA 874 0.174521 0.2284 0.1888 5008 , , NA 21039 0.0764 NA 0.2197 False NA ,,, NA NA NA 2504 0.1462 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 68 74.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA NA chr12.hg19:g.1675128_1675130dupGAG 2 2 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 3,3 53,54 13,12 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 68 True GAG PARP11 57097 __UNKNOWN__ __UNKNOWN__ 12 3954213 3954215 __UNKNOWN__ Intron DEL CAC CAC - rs140053851|rs60668774 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:3954213_3954215delCAC ENST00000228820.4 - 2 163 PARP11_ENST00000427057.2_Intron|PARP11_ENST00000447133.3_Intron|PARP11_ENST00000397096.2_Intron NM_020367.4 NP_065100.2 Q9NR21 PAR11_HUMAN poly (ADP-ribose) polymerase family, member 11 NA NA NA NA NA NAD+ ADP-ribosyltransferase activity (GO:0003950) NA central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1) 17 all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264) TATGAAACTTCACCATATTATGA 0.345 NA NA NA NA NA NA NA NA NA NA NA NA 1334 0.266374 0.1604 0.1614 5008 , , NA 19480 0.5188 NA 0.1223 False NA ,,, NA NA NA 2504 0.3722 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 154 182.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.43 NA NA AF263540 CCDS8523.2, CCDS66281.1 12p13.3 2014-01-28 2004-08-25 2004-08-26 ENSG00000111224 ENSG00000111224 57097 NA "Poly (ADP-ribose) polymerases" 1186 protein-coding gene gene with protein product NA "chromosome 12 open reading frame 6" C12orf6 NA 15273990 Standard NM_001286522 NA Approved uc001qml.2 Q9NR21 OTTHUMG00000156442 ENST00000228820.4:c.19-15029GTG>- chr12.hg19:g.3954213_3954215delCAC 0 3 ref NA False 48 47 PASS 1 PASS ref->het 0 NA 11,11 123,130 19,18 1 1 B4DRQ0|Q68DS1|Q8N5Y9 True hg19 CCDS8523.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PARP11-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000344213.1 PASS NA None 154 True - CAC ENST00000228820.4 M6PR 4074 __UNKNOWN__ __UNKNOWN__ 12 9093106 9093107 __UNKNOWN__ 3'UTR INS - - A rs201697448 LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:9093106_9093107insA ENST00000000412.3 - 0 2609_2610 PHC1_ENST00000536844.1_Intron|PHC1_ENST00000433083.2_3'UTR NM_002355.3 NP_002346.1 P20645 MPRD_HUMAN mannose-6-phosphate receptor (cation dependent) NA NA NA NA NA endosome to lysosome transport (GO:0008333)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165) endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020) mannose binding (GO:0005537)|mannose transmembrane transporter activity (GO:0015578)|transmembrane signaling receptor activity (GO:0004888) NA cervix(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(1) 11 Hepatocellular(102;0.137) BRCA - Breast invasive adenocarcinoma(232;0.0146) Alglucosidase alfa(DB01272) TGTTTAGAAAGAAAAAAATCAC 0.347 NA NA NA NA NA NA NA NA NA NA NA NA AAAAAAA|AAAAAAA|AAAAAAAA|insertion 1870 0.373403 0.2103 0.3905 5008 , , NA 17574 0.4107 NA 0.4344 False NA ,,, NA NA NA 2504 0.4806 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 109 148.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.46 NA NA CCDS8598.1, CCDS73440.1 12p13.31 2013-09-20 ENSG00000003056 ENSG00000003056 4074 NA 6752 protein-coding gene gene with protein product 154540 NA Standard NM_002355 NA Approved uc001qvf.3 P20645 OTTHUMG00000168276 ENST00000000412.3:c.*1308->T chr12.hg19:g.9093113_9093113dupA 8 10 ref NA False 48 47 PASS 7 PASS ref->het 0 NA 8,9 88,91 12,11 1 1 A8K528|D3DUV5 True hg19 CCDS8598.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA M6PR-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000399130.1 PASS NA None 109 True - A ENST00000000412.3 TIMELESS 8914 __UNKNOWN__ __UNKNOWN__ 12 56824949 56824949 __UNKNOWN__ Intron DEL C C - rs79733408 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:56824949delC ENST00000553532.1 - 9 972 TIMELESS_ENST00000229201.4_Intron|TIMELESS_ENST00000554616.1_Intron timeless circadian clock NA NA NA NA NA NA NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1) 49 accagcctggccaacatggtg 0.557 NA NA NA NA NA NA NA NA NA NA NA NA CC|CC|C|deletion 1940 0.38738 0.0961 0.5159 5008 , , NA 14741 0.6567 NA 0.3966 False NA ,,, NA NA NA 2504 0.4029 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 28 31.23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.43 NA NA AF098162 CCDS8918.1 12q13.3 2012-12-14 2012-12-14 ENSG00000111602 ENSG00000111602 8914 NA 11813 protein-coding gene gene with protein product "Tof1 homolog (S. cerevisiae)", "timeless circadian clock 1" 603887 "timeless (Drosophila) homolog", "timeless homolog (Drosophila)" NA 9856465 Standard NM_003920 NM_003920 NA Approved hTIM, TIM, TIM1 uc001slf.2 Q9UNS1 OTTHUMG00000170600 ENST00000553532.1:c.822-197G>- chr12.hg19:g.56824949delC 1 2 ref NA False 30 30 PASS 2 PASS ref->het 0 NA 2,3 20,20 5,6 1 1 True hg19 CCDS8918.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TIMELESS-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000409771.1 PASS NA None 28 True - C ENST00000553532.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 12 75069641 75069642 __UNKNOWN__ IGR DEL AG AG - rs141269073|rs374875776 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:75069641_75069642delAG NA ATXN7L3B (134418 upstream) : RP11-81K13.1 (345106 downstream) NA NA NA NA NA NA NA aggcaaagaaagagaaatactg 0.347 NA NA NA NA NA NA NA NA NA NA NA NA 171 0.0341454 0.1225 0.0115 5008 , , NA 20183 0 NA 0.001 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 38 41.84 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.23 NA NA NA NA NA NA NA NA chr12.hg19:g.75069643_75069644delAG 1 6 ref NA False 34 34 PASS 2 PASS ref->hom 0 NA 0,0 33,34 6,5 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 38 True AG MLXIP 22877 __UNKNOWN__ __UNKNOWN__ 12 122617316 122617316 __UNKNOWN__ Intron DEL G G - rs142744873|rs11315875 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:122617316delG ENST00000319080.7 + 8 1224 MLXIP_ENST00000538698.1_5'UTR MLX interacting protein NA NA NA NA NA NA NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3) 20 all_neural(191;0.0837)|Medulloblastoma(191;0.163) Lung NSC(355;0.0659) OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233) Acaggtgcttggggctacaga 0.413 NA NA NA NA NA NA NA NA NA NA NA NA GGG|GGGG|GGG|insertion 2462 0.491613 0.3699 0.5605 5008 , , NA 20429 0.4831 NA 0.5636 False NA ,,, NA NA NA 2504 0.5419 NA NA NA Esophageal Squamous(105;787 1493 16200 18566 52466) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 75 74.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.02 NA NA AB020674 CCDS73540.1 12q21.31 2013-05-21 ENSG00000175727 22877 NA "Basic helix-loop-helix proteins" 17055 protein-coding gene gene with protein product 608090 NA 10048485, 11073985 Standard NM_014938 XM_006719290 NA Approved MONDOA, KIAA0867, MIR, bHLHe36 uc001ubq.3 Q9HAP2 ENST00000319080.7:c.1092+386G>- chr12.hg19:g.122617316delG 3 4 ref NA False 34 34 PASS 4 PASS ref->het 0 NA 8,8 63,64 4,3 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MLXIP-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000401718.2 PASS NA None 75 True + G ENST00000319080.7 ENOX1 55068 __UNKNOWN__ __UNKNOWN__ 13 43839534 43839539 __UNKNOWN__ Splice_Site DEL ATTTGA ATTTGA - rs137965041 LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:43839534_43839539delATTTGA ENST00000261488.6 - 14 2183_2188 c.1606_1611delTCAAAT c.(1606-1611)tcaaatdel p.SN536del ENOX1_ENST00000412891.1_Splice_Site_p.SN536del NM_001242863.1|NM_017993.3 NP_001229792.1|NP_060463.2 Q8TC92 ENOX1_HUMAN ecto-NOX disulfide-thiol exchanger 1 536 NA NA NA NA rhythmic process (GO:0048511) extracellular region (GO:0005576)|plasma membrane (GO:0005886) nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|oxidoreductase activity (GO:0016491) p.N537I(2) NA breast(1)|endometrium(3)|large_intestine(7)|lung(18)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(1) 34 Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406) GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172) TGGTACCTACATTTGAATCCTCATGG 0.383 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 2 Substitution - Missense(2) lung(2) NA NA NA NA NA 416 392.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 1.34 NA NA EF432052 CCDS9389.1 13q14.11 2013-02-12 ENSG00000120658 ENSG00000120658 55068 NA "RNA binding motif (RRM) containing" 25474 protein-coding gene gene with protein product 610914 NA 11360993 Standard NM_017993 NM_001127615 NA Approved FLJ10094, PIG38, CNOX, cCNOX uc001uza.4 Q8TC92 OTTHUMG00000016818 ENST00000261488.6:c.1611+1TCAAAT>- chr13.hg19:g.43839534_43839539delATTTGA 0 3 ref NA False 137 97 PASS 1 PASS ref->het 0 NA 217,219 164,165 42,40 1 1 A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0 True hg19 CCDS9389.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENOX1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044717.2 PASS NA None 416 In_Frame_Del True - ATTTGA ENST00000261488.6 AP4S1 11154 __UNKNOWN__ __UNKNOWN__ 14 31542302 31542315 __UNKNOWN__ Intron DEL TAAGTGATGCCAAA TAAGTGATGCCAAA - LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:31542302_31542315delTAAGTGATGCCAAA ENST00000542754.2 + 4 687 AP4S1_ENST00000554609.1_Intron|AP4S1_ENST00000216366.4_Intron|AP4S1_ENST00000313566.6_Intron|AP4S1_ENST00000334725.4_Intron|AP4S1_ENST00000554345.1_Intron NM_001128126.2|NM_001254728.1 NP_001121598.1|NP_001241657.1 Q9Y587 AP4S1_HUMAN adaptor-related protein complex 4, sigma 1 subunit NA NA NA NA NA coated pit (GO:0005905)|Golgi apparatus (GO:0005794) protein transporter activity (GO:0008565)|transporter activity (GO:0005215) NA lung(1) 1 Hepatocellular(127;0.0877)|Breast(36;0.176) LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.221) GBM - Glioblastoma multiforme(265;0.00553) AGTTAAAACTTAAGTGATGCCAAATTTTCTTTAT 0.308 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(128;620 2365 4508 44145) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 594 581.36 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 5.42 NA NA AB030654 CCDS9642.1, CCDS45093.1, CCDS58309.1, CCDS58310.1 14q12 2012-06-29 ENSG00000100478 ENSG00000100478 11154 NA 575 protein-coding gene gene with protein product 607243 NA 10436028, 21620353 Standard NM_007077 NA Approved CLA20, AP47B, SPG52 uc001wqw.4 Q9Y587 OTTHUMG00000140202 ENST00000542754.2:c.294+123TAAGTGATGCCAAA>- chr14.hg19:g.31542302_31542315delTAAGTGATGCCAAA 0 7 ref NA False 56 56 PASS 1 PASS ref->het 0 NA 551,561 42,43 76,78 1 1 G3V2N8|Q6IAQ4|Q86U36|Q9BVE7 True hg19 CCDS45093.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AP4S1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000409723.1 PASS NA None 594 True + TAAGTGATGCCAAA ENST00000542754.2 DUOX1 53905 __UNKNOWN__ __UNKNOWN__ 15 45445719 45445746 __UNKNOWN__ Intron DEL TGTGTGTGTGTGTGTGTGTGTGTGTGTA TGTGTGTGTGTGTGTGTGTGTGTGTGTA - rs1706805 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:45445719_45445746delTGTGTGTGTGTGTGTGTGTGTGTGTGTA ENST00000321429.4 + 27 3931 DUOX1_ENST00000561166.1_Intron|CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000559221.1_Intron|DUOX1_ENST00000389037.3_Intron NM_017434.3 NP_059130.2 Q9NRD9 DUOX1_HUMAN dual oxidase 1 NA NA NA NA NA cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590) apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021) calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601) NA breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1) 57 all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027) all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717) tgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtATAATGGGGAG 0.518 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 84 80.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.66 NA NA AF213465 CCDS32221.1 15q21 2013-01-10 ENSG00000137857 53905 NA "EF-hand domain containing" 3062 protein-coding gene gene with protein product "NADPH thyroid oxidase 1", "flavoprotein NADPH oxidase", "nicotinamide adenine dinucleotide phosphate oxidase" 606758 NA 10806195 Standard NM_017434 XM_005254463 NA Approved NOXEF1, THOX1, LNOX1 uc001zut.1 Q9NRD9 ENST00000321429.4:c.3524+42TGTGTGTGTGTGTGTGTGTGTGTGTGTA>- chr15.hg19:g.45445719_45445746delTGTGTGTGTGTGTGTGTGTGTGTGTGTA 0 3 ref NA False 89 54 PASS 1 PASS ref->het 0 NA 5,9 31,33 48,44 1 1 A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1 True hg19 CCDS32221.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DUOX1-006 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000416251.1 PASS NA None 84 True + TGTGTGTGTGTGTGTGTGTGTGTGTGTA ENST00000321429.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 15 90839475 90839478 __UNKNOWN__ IGR DEL TTAC TTAC - rs374266665|rs71151584|rs143399230|rs377555586 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:90839475_90839478delTTAC NA AC091167.1 (1120 upstream) : GABARAPL3 (51340 downstream) NA NA NA NA NA NA NA GCGCGGTCTATTACTTTGTAATAT 0.422 NA NA NA NA NA NA NA NA NA NA NA NA 767 0.153155 0.3472 0.1311 5008 , , NA 21232 0 NA 0.1571 False NA ,,, NA NA NA 2504 0.0603 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 49 48.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA NA chr15.hg19:g.90839475_90839478delTTAC 0 4 ref NA False 71 66 PASS 1 PASS ref->het 0 NA 4,4 39,39 6,6 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 49 True TTAC NEDD4L 23327 __UNKNOWN__ __UNKNOWN__ 18 55997930 55997933 __UNKNOWN__ Intron DEL TTCT TTCT - rs201883056|rs144384654|rs200156489 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:55997930_55997933delTTCT ENST00000256830.9 + 11 813 NEDD4L_ENST00000456986.1_Intron|NEDD4L_ENST00000456173.2_Intron|NEDD4L_ENST00000382850.4_Intron|NEDD4L_ENST00000586263.1_Intron|NEDD4L_ENST00000356462.6_Intron|NEDD4L_ENST00000256832.7_Intron|NEDD4L_ENST00000431212.2_Intron|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000357895.5_Intron|NEDD4L_ENST00000400345.3_Intron|NEDD4L_ENST00000435432.2_Intron Q96PU5 NED4L_HUMAN neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase NA NA NA NA NA cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104) cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842) NA breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4) 37 GGATCCCTACTTCTTTCTAGTGTT 0.485 NA NA NA NA NA NA NA NA NA NA NA NA 1683 0.336062 0.4349 0.3703 5008 , , NA 19668 0.2897 NA 0.3042 False NA ,,, NA NA NA 2504 0.2587 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 45 51.43 NA ,,,,,,,, 1468,2106 NA 325,818,644 NA NA NA NA ,,,,,,,, -5.3 0 NA dbSNP_110 14 2362,5494 NA 369,1624,1935 no intron,intron,intron,intron,intron,intron,intron,intron,intron NEDD4L NM_015277.5,NM_001144971.1,NM_001144970.2,NM_001144969.1,NM_001144968.1,NM_001144967.2,NM_001144966.2,NM_001144965.1,NM_001144964.1 ,,,,,,,, 694,2442,2579 A1A1,A1R,RR NA 30.0662,41.0744,33.5083 ,,,,,,,, ,,,,,,,, NA 3830,7600 NA NA NA SO:0001627 intron_variant 0.45 NA NA AF210730 CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1 18q21.31 2014-08-12 2012-02-23 ENSG00000049759 23327 NA 7728 protein-coding gene gene with protein product 606384 "neural precursor cell expressed, developmentally down-regulated 4-like" NA 10594025, 11244092, 18322022 Standard NM_001144965 NA Approved KIAA0439, RSP5, NEDD4-2 uc002lgy.3 Q96PU5 OTTHUMG00000179875 ENST00000256830.9:c.814-37TTCT>- chr18.hg19:g.55997934_55997937delTTCT 1 5 ref NA False 36 36 PASS 2 PASS ref->het 0 NA 6,6 34,36 6,5 1 1 O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NEDD4L-037 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000449050.2 PASS NA None 45 True + TTCT ENST00000256830.9 STX16-NPEPL1 100534593 __UNKNOWN__ __UNKNOWN__ 20 57246478 57246479 __UNKNOWN__ Intron INS - - T rs11481330 byFrequency LTS-005_T LTS-005_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:57246478_57246479insT ENST00000530122.1 + 7 1365 STX16_ENST00000355957.5_Intron|STX16_ENST00000361770.5_Intron|STX16_ENST00000358029.4_Intron|STX16_ENST00000496003.1_Intron|STX16_ENST00000359617.4_Intron|STX16_ENST00000371141.4_Intron|STX16_ENST00000361830.3_Intron|STX16_ENST00000371132.4_Intron STX16-NPEPL1 readthrough (NMD candidate) NA NA NA NA NA NA NA TGCACCTGTCCTTTAtgtgtgt 0.347 NA NA NA NA NA NA NA NA NA NA NA NA TTT|TTT|TTTT|insertion 893 0.178315 0.1838 0.1628 5008 , , NA 15175 0.1171 NA 0.2217 False NA ,,, NA NA NA 2504 0.2004 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 118 125.91 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 4.22 NA NA 20q13.32 2013-05-09 2013-05-09 ENSG00000254995 ENSG00000254995 100534593 NA 41993 other readthrough NA NA Standard NR_037945.1 NR_037945 NA Approved OTTHUMG00000167390 ENST00000530122.1:c.792+125->T chr20.hg19:g.57246481_57246481dupT 4 4 ref NA False 32 32 PASS 3 PASS ref->het 0 NA 62,68 26,27 30,25 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA STX16-NPEPL1-001 KNOWN basic|appris_principal|readthrough_transcript nonsense_mediated_decay NA protein_coding OTTHUMT00000394467.1 PASS NA None 118 True + T ENST00000530122.1 DNASE2B 58511 __UNKNOWN__ __UNKNOWN__ 1 84874104 84874111 __UNKNOWN__ Intron DEL TAATATAT TAATATAT - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:84874104_84874111delTAATATAT ENST00000370665.3 + 3 336 DNASE2B_ENST00000370662.3_5'UTR NM_021233.2 NP_067056.2 Q8WZ79 DNS2B_HUMAN deoxyribonuclease II beta NA NA NA NA apoptotic DNA fragmentation (GO:0006309) extracellular region (GO:0005576)|intracellular (GO:0005622)|lysosome (GO:0005764) deoxyribonuclease II activity (GO:0004531) NA endometrium(1)|lung(4)|skin(1) 6 all cancers(265;0.00303)|Epithelial(280;0.0112)|OV - Ovarian serous cystadenocarcinoma(397;0.0808) ATTATAACCCTAATATATTCCTGCAGAG 0.389 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(54;788 1175 11852 16034 30034) PASS NA NA NA NA NA 0 NA NA NA NA NA 516 508.08 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF274571 CCDS694.1, CCDS44167.1 1p22.3 2008-02-05 ENSG00000137976 ENSG00000137976 58511 28875 protein-coding gene gene with protein product 608057 NA 12594037, 11376952 Standard NM_021233 NM_021233 NA Approved DLAD uc001djt.1 Q8WZ79 OTTHUMG00000009860 ENST00000370665.3:c.304-9TAATATAT>- chr1.hg19:g.84874104_84874111delTAATATAT 0 3 ref NA False 91 91 PASS 1 PASS ref->het 0 NA 397,400 103,103 62,59 1 1 Q5VXD0|Q5VXD1|Q8WZ80|Q9NQW3 True hg19 CCDS44167.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DNASE2B-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000027248.1 PASS NA None 516 True + TAATATAT ENST00000370665.3 HSD3B1 3283 __UNKNOWN__ __UNKNOWN__ 1 120050139 120050139 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:120050139delT ENST00000369413.3 + 2 185 c.40delT c.(40-42)tttfs p.F14fs HSD3B1_ENST00000235547.6_Frame_Shift_Del_p.F16fs|HSD3B1_ENST00000528909.1_Frame_Shift_Del_p.F14fs P14060 3BHS1_HUMAN hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 14 NA NA NA androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202) endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868) 3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769) NA central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1) 32 all_neural(166;0.219) all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624) Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554) Trilostane(DB01108) AGCAGGAGGGTTTCTGGGACA 0.542 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 187 195.22 NA NA NA NA NA 105 96 99 NA NA NA NA 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 120050139 NA 2203 4300 6503 SO:0001589 frameshift_variant 0.94 NA NA S45679 CCDS903.1 1p12 2014-06-03 ENSG00000203857 ENSG00000203857 3283 1.1.1.145, 5.3.3.1 "Short chain dehydrogenase/reductase superfamily / Extended SDR fold" 5217 protein-coding gene gene with protein product "short chain dehydrogenase/reductase family 11E, member 1" 109715 HSDB3, HSD3B NA 2779585, 19027726 Standard NM_000862 NM_000862 NA Approved SDR11E1 uc001ehv.1 P14060 OTTHUMG00000012525 ENST00000369413.3:c.40delT chr1.hg19:g.120050139delT ENSP00000358421:p.Phe14fs 2 5 ref NA False 30 30 PASS 3 PASS ref->het 0 NA 114,116 51,52 24,21 1 1 A8K691|Q14545|Q8IV65 True hg19 CCDS903.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HSD3B1-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000034993.3 PASS NA None 187 True + T ENST00000369413.3 ASAP2 8853 __UNKNOWN__ __UNKNOWN__ 2 9525421 9525422 __UNKNOWN__ Frame_Shift_Del DEL AT AT - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:9525421_9525422delAT ENST00000281419.3 + 21 2404_2405 c.2064_2065delAT c.(2062-2067)gaatatfs p.Y689fs ASAP2_ENST00000315273.4_Frame_Shift_Del_p.Y689fs NM_003887.2 NP_003878.1 O43150 ASAP2_HUMAN ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 689 NA NA NA positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312) Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886) ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270) NA breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1) 36 TTCACGTTGAATATGAATGGCG 0.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 363 341.63 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.59 NA NA AB007860 CCDS1661.1, CCDS46224.1 2p24 2013-01-10 2008-09-22 2008-09-22 ENSG00000151693 ENSG00000151693 8853 "ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing" 2721 protein-coding gene gene with protein product "centaurin, beta 3" 603817 "development and differentiation enhancing factor 2" DDEF2 NA 10022920, 9455477 Standard NM_003887 NM_003887 NA Approved KIAA0400, PAP, SHAG1, CENTB3 uc002qzh.2 O43150 OTTHUMG00000117485 ENST00000281419.3:c.2064_2065delAT chr2.hg19:g.9525423_9525424delAT ENSP00000281419:p.Tyr689fs 1 3 ref NA False 130 64 PASS 2 PASS ref->het 0 NA 196,199 140,142 28,24 1 1 D6W4Y8 True hg19 CCDS1661.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ASAP2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000237522.1 PASS NA None 363 True + AT ENST00000281419.3 ACTR2 10097 __UNKNOWN__ __UNKNOWN__ 2 65454975 65454976 __UNKNOWN__ 5'UTR INS - - A LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:65454975_65454976insA ENST00000260641.5 + 0 89_90 ACTR2_ENST00000377982.4_5'UTR|ACTR2_ENST00000476840.1_3'UTR|ACTR2_ENST00000542850.1_5'UTR NM_005722.3 NP_005713.1 P61160 ARP2_HUMAN ARP2 actin-related protein 2 homolog (yeast) NA NA NA NA Arp2/3 complex-mediated actin nucleation (GO:0034314)|asymmetric cell division (GO:0008356)|cellular component movement (GO:0006928)|cilium assembly (GO:0042384)|cytoplasmic transport (GO:0016482)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|meiotic chromosome movement towards spindle pole (GO:0016344)|meiotic cytokinesis (GO:0033206)|spindle localization (GO:0051653) actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020) ATP binding (GO:0005524)|structural constituent of cytoskeleton (GO:0005200) NA NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|prostate(1) 12 GCAAGAGGAAGAAGAGAAAACG 0.663 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 156 161.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.73 NA NA AF006082 CCDS1881.1, CCDS46307.1 2p14 2008-05-20 2001-11-28 ENSG00000138071 ENSG00000138071 10097 169 protein-coding gene gene with protein product 604221 "ARP2 (actin-related protein 2, yeast) homolog" NA 9230079 Standard NM_001005386 NM_001005386 NA Approved ARP2 uc002sdp.3 P61160 OTTHUMG00000129540 ENST00000260641.5:c.-68->A chr2.hg19:g.65454977_65454977dupA 3 4 ref NA False 151 146 PASS 2 PASS ref->het 0 NA 96,101 37,40 23,17 1 1 B2RCP5|D6W5F4|E9PF41|O15142|Q96C82 True hg19 CCDS1881.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACTR2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251730.1 PASS NA None 156 True + A ENST00000260641.5 ADRA2B 151 __UNKNOWN__ __UNKNOWN__ 2 96780529 96780530 __UNKNOWN__ 3'UTR INS - - GCA LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:96780529_96780530insGCA ENST00000409345.3 - 0 1454_1455 NM_000682.5 NP_000673 P18089 ADA2B_HUMAN adrenoceptor alpha 2B NA NA NA NA activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|MAPK cascade (GO:0000165)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of vascular smooth muscle contraction (GO:0003056) integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379) NA endometrium(2)|large_intestine(2)|lung(9)|ovary(3) 16 Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Etomidate(DB00292)|Fenoldopam(DB00800)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246) ACCCCACAGGGGCAGCGCAGGC 0.663 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 176 187.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.75 NA NA M34041 CCDS56129.1 2q11.1 2014-05-06 2012-05-09 ENSG00000222040 ENSG00000274286 151 "GPCR / Class A : Adrenoceptors : alpha" 282 protein-coding gene gene with protein product 104260 "adrenergic, alpha-2B-, receptor" ADRA2L1, ADRA2RL1 NA 2164221 Standard NM_000682 NA Approved ADRARL1 uc021vlh.1 P18089 OTTHUMG00000188276 ENST00000409345.3:c.*16->TGC chr2.hg19:g.96780530_96780532dupGCA 2 4 ref NA False 96 96 PASS 1 PASS ref->het 0 NA 112,119 40,41 24,18 1 1 Q4TUH9|Q53RF2|Q9BZK0 True hg19 CCDS56129.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ADRA2B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000334990.1 PASS NA None 176 True - GCA ENST00000409345.3 NLGN1 22871 __UNKNOWN__ __UNKNOWN__ 3 173518146 173518146 __UNKNOWN__ Intron DEL T T - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:173518146delT ENST00000457714.1 + 4 922 NLGN1_ENST00000545397.1_Intron|NLGN1_ENST00000401917.3_Intron|NLGN1_ENST00000361589.4_Intron NM_014932.2 NP_055747.1 Q8N2Q7 NLGN1_HUMAN neuroligin 1 NA NA NA NA alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553) cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202) cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872) NA breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1) 83 Ovarian(172;0.0025) LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13) GATGAAGGTATTTTTTTTCAC 0.348 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 469 437.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.1 NA NA AB028993 CCDS3222.1 3q26.32 2008-07-18 ENSG00000169760 ENSG00000169760 22871 14291 protein-coding gene gene with protein product 600568 NA 10767552, 10819331 Standard NM_014932 NM_014932 NA Approved KIAA1070 uc003fio.1 Q8N2Q7 OTTHUMG00000157005 ENST00000457714.1:c.494-7324T>- chr3.hg19:g.173518146delT 7 9 ref NA False 107 107 PASS 8 PASS ref->het 0 NA 345,347 79,79 47,46 1 1 Q9UPT2 True hg19 CCDS3222.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NLGN1-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000347054.3 PASS NA None 469 True + T ENST00000457714.1 NAT8L 339983 __UNKNOWN__ __UNKNOWN__ 4 2069618 2069619 __UNKNOWN__ 3'UTR DEL CA CA - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:2069618_2069619delCA ENST00000331662.3 + 0 4373_4374 NAT8L_ENST00000423729.2_3'UTR Q8N9F0 NAT8L_HUMAN N-acetyltransferase 8-like (GCN5-related, putative) NA NA NA NA metabolic process (GO:0008152)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586) cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966) aspartate N-acetyltransferase activity (GO:0017188) NA haematopoietic_and_lymphoid_tissue(1)|lung(1) 2 OV - Ovarian serous cystadenocarcinoma(23;0.0315) GGCTGATGGCCACAGAGCTGAC 0.599 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 707 685.72 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.45 NA NA AK094797 CCDS3359.1, CCDS3359.2 4p16.3 2011-11-16 2008-09-24 ENSG00000185818 ENSG00000185818 339983 26742 protein-coding gene gene with protein product 610647 "N-acetyltransferase 8-like" NA 11397015 Standard NM_178557 NM_178557 NA Approved FLJ37478, Hcml3 uc003geq.2 Q8N9F0 OTTHUMG00000121151 ENST00000331662.3:c.*3765CA>- chr4.hg19:g.2069620_2069621delCA 1 3 ref NA False 125 87 PASS 2 PASS ref->het 0 NA 476,480 177,179 58,53 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NAT8L-001 KNOWN basic protein_coding NA protein_coding OTTHUMT00000241636.3 PASS NA None 707 True + CA ENST00000331662.3 HGFAC 3083 __UNKNOWN__ __UNKNOWN__ 4 3444595 3444610 __UNKNOWN__ Frame_Shift_Del DEL CCCCGCCCAGGGCAGT CCCCGCCCAGGGCAGT - rs140087184 byFrequency LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:3444595_3444610delCCCCGCCCAGGGCAGT ENST00000382774.3 + 2 369_384 c.254_269delCCCCGCCCAGGGCAGT c.(253-270)cccccgcccagggcagttfs p.PPPRAV85fs HGFAC_ENST00000511533.1_Frame_Shift_Del_p.PPPRAV85fs NM_001528.2 NP_001519.1 Q04756 HGFA_HUMAN HGF activator 85 NA NA NA proteolysis (GO:0006508) extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791) serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236) NA central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2) 22 UCEC - Uterine corpus endometrioid carcinoma (64;0.163) GGGCTCCCGCCCCCGCCCAGGGCAGTTCCCTCGAGC 0.671 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 275 292.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.31 NA NA D14012 CCDS3369.1, CCDS75098.1 4p16 2008-02-07 ENSG00000109758 ENSG00000109758 3083 3.4.21.- 4894 protein-coding gene gene with protein product 604552 NA 7683665, 8226803 Standard XM_005247966 NA Approved HGFAP, HGFA uc003ghc.3 Q04756 OTTHUMG00000090281 ENST00000382774.3:c.254_269delCCCCGCCCAGGGCAGT chr4.hg19:g.3444595_3444610delCCCCGCCCAGGGCAGT ENSP00000372224:p.Pro85fs 0 8 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 231,240 41,41 31,22 2 2 Q14726|Q2M1W7|Q53X47 True hg19 CCDS3369.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HGFAC-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000206607.3 PASS NA None 275 True + CCCCGCCCAGGGCAGT ENST00000382774.3 FAM13A 10144 __UNKNOWN__ __UNKNOWN__ 4 89708826 89708849 __UNKNOWN__ Intron DEL ACACAGCGACTAATTTGGGTGTAT ACACAGCGACTAATTTGGGTGTAT - rs34283157 LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:89708826_89708849delACACAGCGACTAATTTGGGTGTAT ENST00000264344.5 - 10 1479 FAM13A_ENST00000502459.1_Intron|FAM13A_ENST00000511976.1_Intron|FAM13A_ENST00000395002.2_Intron|FAM13A_ENST00000513837.1_Intron|FAM13A_ENST00000503556.1_Intron|FAM13A_ENST00000508369.1_Intron NM_014883.3 NP_055698.2 O94988 FA13A_HUMAN family with sequence similarity 13, member A NA NA NA NA regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264) cytosol (GO:0005829) GTPase activator activity (GO:0005096) NA NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2) 55 TATGACTATAACACAGCGACTAATTTGGGTGTATATTTCTTTTA 0.388 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 134 130.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.46 NA NA AB020721 CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1 4q22.1 2011-09-07 2009-01-20 2009-01-20 ENSG00000138640 ENSG00000138640 10144 "Rho GTPase activating proteins" 19367 protein-coding gene gene with protein product 613299 "family with sequence similarity 13, member A1" FAM13A1 NA Standard NM_014883 NA Approved KIAA0914, ARHGAP48 uc003hse.2 O94988 OTTHUMG00000161006 ENST00000264344.5:c.1271+54ATACACCCAAATTAGTCGCTGTGT>- chr4.hg19:g.89708826_89708849delACACAGCGACTAATTTGGGTGTAT 0 4 ref NA False 55 55 PASS 1 PASS ref->het 0 NA 104,105 35,36 27,26 1 1 B4DLC1|Q24JP0|Q5PR21|Q8NBA3 True hg19 CCDS34029.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM13A-022 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000363371.1 PASS NA None 134 True - ACACAGCGACTAATTTGGGTGTAT ENST00000264344.5 SYNGAP1 8831 __UNKNOWN__ __UNKNOWN__ 6 33393655 33393664 __UNKNOWN__ Frame_Shift_Del DEL GGAGGGGCGG GGAGGGGCGG - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:33393655_33393664delGGAGGGGCGG ENST00000418600.2 + 3 371_380 c.270_279delGGAGGGGCGG c.(268-279)gtggaggggcggfs p.VEGR90fs SYNGAP1_ENST00000293748.5_Frame_Shift_Del_p.VEGR90fs|SYNGAP1_ENST00000496374.1_3'UTR NM_006772.2 NP_006763.2 Q96PV0 SYGP1_HUMAN synaptic Ras GTPase activating protein 1 90 NA NA NA dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542) cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235) Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099) NA breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1) 43 CCGTGCCGGTGGAGGGGCGGCCCCACGGCG 0.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 239 233.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.27 NA NA AB067525 CCDS34434.2 6p21.3 2010-06-25 2010-06-25 ENSG00000197283 ENSG00000197283 8831 11497 protein-coding gene gene with protein product 603384 "synaptic Ras GTPase activating protein 1 homolog (rat)" NA 9581761, 18323856 Standard XM_166407 NM_006772 NA Approved SYNGAP, RASA5, KIAA1938 uc011dri.2 Q96PV0 OTTHUMG00000031096 ENST00000418600.2:c.270_279delGGAGGGGCGG chr6.hg19:g.33393655_33393664delGGAGGGGCGG ENSP00000403636:p.Val90fs 0 6 ref NA False 67 67 PASS 1 PASS ref->het 0 NA 201,206 5,5 34,29 2 2 A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2 True hg19 CCDS34434.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SYNGAP1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076151.4 PASS NA None 239 True + GGAGGGGCGG ENST00000418600.2 AK9 221264 __UNKNOWN__ __UNKNOWN__ 6 109820279 109820300 __UNKNOWN__ Frame_Shift_Del DEL AGTGCCCCCTGAACTCTGCTGC AGTGCCCCCTGAACTCTGCTGC - rs36022523 LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:109820279_109820300delAGTGCCCCCTGAACTCTGCTGC ENST00000424296.2 - 36 5069_5090 c.4993_5014delGCAGCAGAGTTCAGGGGGCACT c.(4993-5016)gcagcagagttcagggggcactacfs p.AAEFRGHY1665fs RP5-919F19.5_ENST00000423747.2_RNA NM_001145128.2 NP_001138600.2 Q5TCS8 KAD9_HUMAN adenylate kinase 9 1665 NA NA NA ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569) cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634) ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145) NA NA ATTTTATAGTAGTGCCCCCTGAACTCTGCTGCAAATTCCAAG 0.401 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 156 143.6 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 NA NA AK131244, BC146443, BC087860 CCDS5077.1, CCDS55048.1 6q21 2013-04-29 2013-04-29 2013-04-29 221264 2.7.4.3 33814 protein-coding gene gene with protein product 615358 "chromosome 6 open reading frame 224", "adenylate kinase domain containing 2", "chromosome 6 open reading frame 199", "adenylate kinase domain containing 1" C6orf224, AKD2, C6orf199, AKD1 NA 23416111 Standard NM_001145128 NM_145025 NA Approved FLJ42177, FLJ25791, dJ70A9.1, MGC26954 Q5TCS8 ENST00000424296.2:c.4993_5014delGCAGCAGAGTTCAGGGGGCACT chr6.hg19:g.109820279_109820300delAGTGCCCCCTGAACTCTGCTGC ENSP00000410186:p.Ala1665fs 0 3 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 140,140 21,21 18,18 1 1 A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4 True hg19 CCDS55048.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AK9-202 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding PASS NA None 156 True - AGTGCCCCCTGAACTCTGCTGC ENST00000424296.2 HECW1 23072 __UNKNOWN__ __UNKNOWN__ 7 43546875 43546875 __UNKNOWN__ Intron DEL G G - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:43546875delG ENST00000453890.1 + 20 3974 HECW1_ENST00000395891.2_Intron Q76N89 HECW1_HUMAN HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 NA NA NA NA protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787) cytoplasm (GO:0005737) ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842) NA NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3) 125 TCCAGTGCTTGGCACTGAATT 0.453 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 157 143.89 NA NA NA NA NA 90 94 93 NA NA NA NA 7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 43546875 NA 1845 4086 5931 SO:0001627 intron_variant 0 NA NA AB048365 CCDS5469.2, CCDS69286.1 7p13 2004-12-13 ENSG00000002746 ENSG00000002746 23072 22195 protein-coding gene gene with protein product 610384 NA 12690205, 14684739 Standard NM_015052 XM_005249665 NA Approved KIAA0322, NEDL1 uc003tid.1 Q76N89 OTTHUMG00000128917 ENST00000453890.1:c.3650+19G>- chr7.hg19:g.43546875delG 1 2 ref NA False 41 41 PASS 2 PASS ref->het 0 NA 93,93 45,45 16,16 1 1 A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HECW1-002 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000338775.1 PASS NA None 157 True + G ENST00000453890.1 MGAM 8972 __UNKNOWN__ __UNKNOWN__ 7 141722111 141722148 __UNKNOWN__ Frame_Shift_Del DEL TTGCAGCTCTCCACTCGACTGCCTAGCACTAACGTGTA TTGCAGCTCTCCACTCGACTGCCTAGCACTAACGTGTA - rs372476144|rs201266519|rs376595784 LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:141722111_141722148delTTGCAGCTCTCCACTCGACTGCCTAGCACTAACGTGTA ENST00000475668.2 + 7 808_845 c.754_791delTTGCAGCTCTCCACTCGACTGCCTAGCACTAACGTGTA c.(754-792)ttgcagctctccactcgactgcctagcactaacgtgtatfs p.LQLSTRLPSTNVY252fs MGAM_ENST00000549489.2_Frame_Shift_Del_p.LQLSTRLPSTNVY252fs O43451 MGA_HUMAN maltase-glucoamylase (alpha-glucosidase) 252 Maltase. NA NA NA carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983) extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450) p.V263M(2) NA cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2) 13 Melanoma(164;0.0272) Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878) TGACCAGTTCTTGCAGCTCTCCACTCGACTGCCTAGCACTAACGTGTATGGCCTGGGA 0.508 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 2 Substitution - Missense(2) ovary(2) NA NA NA NA NA 105 99.76 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.01 NA NA AF016833 CCDS47727.1 7q34 2012-10-03 ENSG00000257335 ENSG00000257335 8972 7043 protein-coding gene gene with protein product 154360 NA 9446624 Standard NM_004668 NA Approved MGA uc003vwy.3 O43451 OTTHUMG00000158395 ENST00000475668.2:c.754_791delTTGCAGCTCTCCACTCGACTGCCTAGCACTAACGTGTA chr7.hg19:g.141722111_141722148delTTGCAGCTCTCCACTCGACTGCCTAGCACTAACGTGTA ENSP00000417515:p.Leu252fs 0 4 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 94,94 21,21 37,37 1 1 Q0VAX6|Q75ME7|Q86UM5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MGAM-007 PUTATIVE basic|appris_principal protein_coding NA protein_coding OTTHUMT00000351290.4 PASS NA None 105 True + TTGCAGCTCTCCACTCGACTGCCTAGCACTAACGTGTA ENST00000475668.2 SLCO5A1 81796 __UNKNOWN__ __UNKNOWN__ 8 70602288 70602288 __UNKNOWN__ Intron DEL G G - rs368075578 byFrequency LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:70602288delG ENST00000524945.1 - 6 2339 SLCO5A1_ENST00000260126.4_Intron|SLCO5A1_ENST00000530307.1_Intron NM_001146008.1 NP_001139480.1 Q9H2Y9 SO5A1_HUMAN solute carrier organic anion transporter family, member 5A1 NA NA NA NA integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) transporter activity (GO:0005215) NA NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1) 53 Breast(64;0.0654) Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594) ttgcgggtacgggggggcgcc 0.537 NA NA NA NA NA NA NA NA NA NA NA 1263 0.252196 0.0401 0.2363 5008 , , NA 14633 0.3839 NA 0.3032 False NA ,,, NA NA NA 2504 0.362 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 34 58.62 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF205075 CCDS6205.1, CCDS55242.1, CCDS55243.1 8q13.1 2013-05-22 2003-11-25 2003-11-26 ENSG00000137571 ENSG00000137571 81796 "Solute carriers" 19046 protein-coding gene gene with protein product 613543 "solute carrier family 21 (organic anion transporter), member 15" SLC21A15 NA 12507753 Standard NM_030958 NM_030958 NA Approved OATPRP4, OATP-J, OATP5A1 uc003xyl.3 Q9H2Y9 OTTHUMG00000165121 ENST00000524945.1:c.1623-7710C>- chr8.hg19:g.70602288delG 6 8 ref NA False 66 66 PASS 7 PASS ref->hom 0 NA 0,0 4,4 34,41 1 1 A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0 True hg19 CCDS55243.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLCO5A1-004 PUTATIVE basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000381991.1 PASS NA None 34 True - G ENST00000524945.1 ZCCHC7 84186 __UNKNOWN__ __UNKNOWN__ 9 37357828 37357828 __UNKNOWN__ 3'UTR DEL G G - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:37357828delG ENST00000336755.5 + 0 2301 ZCCHC7_ENST00000461038.1_3'UTR NM_032226.2 NP_115602.2 Q8N3Z6 ZCHC7_HUMAN zinc finger, CCHC domain containing 7 NA NA NA NA cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634) poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270) NA central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1) 30 GBM - Glioblastoma multiforme(29;0.0137) TGAAGAGGCAGGGAATTGAGC 0.353 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 141 150.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.45 NA NA AK026264 CCDS6608.2 9p13.1 2008-05-02 ENSG00000147905 ENSG00000147905 84186 "Zinc fingers, CCHC domain containing" 26209 protein-coding gene gene with protein product NA NA Standard NM_032226 NM_032226 NA Approved FLJ22611, AIR1 uc003zzq.3 Q8N3Z6 OTTHUMG00000019915 ENST00000336755.5:c.*563G>- chr9.hg19:g.37357828delG 2 3 ref NA False 32 32 PASS 3 PASS ref->het 0 NA 97,98 35,36 12,10 1 1 B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0 True hg19 CCDS6608.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZCCHC7-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000052453.2 PASS NA None 141 True + G ENST00000336755.5 OSTF1 26578 __UNKNOWN__ __UNKNOWN__ 9 77762076 77762079 __UNKNOWN__ 3'UTR DEL CAGC CAGC - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:77762076_77762079delCAGC ENST00000346234.6 + 0 1214_1217 NM_012383.4 NP_036515.4 Q92882 OSTF1_HUMAN osteoclast stimulating factor 1 NA NA NA NA ossification (GO:0001503)|signal transduction (GO:0007165) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622) NA endometrium(1)|skin(1) 2 AGAAAATTGTCAGCTATTCTGACA 0.289 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 221 207.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.25 NA NA U63717 CCDS6651.1 9q13-q21.2 2013-01-10 ENSG00000134996 ENSG00000134996 26578 "Ankyrin repeat domain containing" 8510 protein-coding gene gene with protein product 610180 NA 10092216 Standard NM_012383 NM_012383 NA Approved SH3P2, OSF, bA235O14.1 uc004ajv.4 Q92882 OTTHUMG00000020033 ENST00000346234.6:c.*422CAGC>- chr9.hg19:g.77762076_77762079delCAGC 0 3 ref NA False 49 49 PASS 1 PASS ref->het 0 NA 148,149 40,40 29,28 1 1 Q5W126|Q96IJ4 True hg19 CCDS6651.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OSTF1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000052704.1 PASS NA None 221 True + CAGC ENST00000346234.6 SARDH 1757 __UNKNOWN__ __UNKNOWN__ 9 136568016 136568045 __UNKNOWN__ Splice_Site DEL ACGGTGGACCCCAGCTACGCACCGTGTCGT ACGGTGGACCCCAGCTACGCACCGTGTCGT - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:136568016_136568045delACGGTGGACCCCAGCTACGCACCGTGTCGT ENST00000371872.4 - 13 1918_1926 c.1661_1669delACGACACGGTGCGTAGCTGGGGTCCACCGT c.(1660-1671)cacgacacggtg>ctg p.554_557HDTV>L SARDH_ENST00000422262.2_Splice_Site_p.386_389HDTV>L|SARDH_ENST00000439388.1_Splice_Site_p.554_557HDTV>L|SARDH_ENST00000371868.1_5'UTR NM_007101.3 NP_009032.2 Q9UL12 SARDH_HUMAN sarcosine dehydrogenase 554 NA NA NA glycine catabolic process (GO:0006546) mitochondrion (GO:0005739) aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480) NA central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3) 44 OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05) ACGGACCCCCACGGTGGACCCCAGCTACGCACCGTGTCGTGGTGGGGCGG 0.683 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 130 115.88 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 1.08 NA NA CCDS6978.1 9q33-q34 2008-02-05 ENSG00000123453 ENSG00000123453 1757 1.5.99.2 10536 protein-coding gene gene with protein product 604455 DMGDHL1 NA 10444331 Standard NM_007101 NA Approved SDH uc004cep.4 Q9UL12 OTTHUMG00000020879 ENST00000371872.4:c.1668+1ACGACACGGTGCGTAGCTGGGGTCCACCGT>- chr9.hg19:g.136568016_136568045delACGGTGGACCCCAGCTACGCACCGTGTCGT 0 6 ref NA False 56 56 PASS 1 PASS ref->het 0 NA 98,104 19,21 25,17 1 1 B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3 True hg19 CCDS6978.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SARDH-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000054931.1 PASS NA None 130 In_Frame_Del True - ACGGTGGACCCCAGCTACGCACCGTGTCGT ENST00000371872.4 GOLGA7B 401647 __UNKNOWN__ __UNKNOWN__ 10 99609997 99609997 __UNKNOWN__ 5'UTR DEL G G - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:99609997delG ENST00000370602.1 + 0 2 NM_001010917.2 NP_001010917.1 Q2TAP0 GOG7B_HUMAN golgin A7 family, member B NA NA NA NA Golgi apparatus (GO:0005794)|membrane (GO:0016020) NA endometrium(1)|large_intestine(3)|prostate(1) 5 ACCTGCTCCCGGGGTCAGCAC 0.816 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 38 40.27 NA NA NA NA NA 1 3 2 NA NA NA NA 10 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 99609997 NA 329 973 1302 SO:0001623 5_prime_UTR_variant 0 NA NA BC008047 CCDS31265.1 10q24.2 2011-10-25 2010-02-12 2008-10-03 ENSG00000155265 ENSG00000155265 401647 31668 protein-coding gene gene with protein product 614189 "chromosome 10 open reading frame 133", "chromosome 10 open reading frame 132", "golgi autoantigen, golgin subfamily a, 7B" C10orf133, C10orf132 NA Standard NM_001010917 NM_001010917 NA Approved bA459F3.4, bA451M19.3 uc001kos.3 Q2TAP0 OTTHUMG00000018869 ENST00000370602.1:c.-64G>- chr10.hg19:g.99609997delG 3 4 ref NA False 30 30 PASS 4 PASS ref->het 0 NA 22,23 10,11 6,4 1 1 Q5T4F5 True hg19 CCDS31265.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GOLGA7B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000049752.1 PASS NA None 38 True + G ENST00000370602.1 ARID2 196528 __UNKNOWN__ __UNKNOWN__ 12 46287391 46287391 __UNKNOWN__ Intron DEL T T - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:46287391delT ENST00000334344.6 + 20 5443 ARID2_ENST00000457135.1_Intron|ARID2_ENST00000444670.1_Intron|ARID2_ENST00000479608.1_Intron|ARID2_ENST00000422737.1_Intron NM_152641.2 NP_689854.2 Q68CP9 ARID2_HUMAN AT rich interactive domain 2 (ARID, RFX-like) NA NA NA NA chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) NA NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2) 116 Lung SC(27;0.192)|Renal(347;0.236) Lung NSC(34;0.106)|all_lung(34;0.22) OV - Ovarian serous cystadenocarcinoma(5;0.00691) GBM - Glioblastoma multiforme(48;0.0153) ATCTTTATTCTTTTTTTTCCT 0.323 NA NA "N, S, F" NA hepatocellular carcinoma NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Rec yes NA 12 12q12 196528 AT rich interactive domain 2 NA E 0 NA NA NA NA NA 151 166.19 NA NA NA NA NA 67 73 71 NA NA NA NA 12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 46287391 NA 2203 4300 6503 SO:0001627 intron_variant 0 NA NA CCDS31783.1 12q13.11 2013-02-07 ENSG00000189079 ENSG00000189079 196528 "-" 18037 protein-coding gene gene with protein product 609539 NA Standard XM_350875 NM_152641 NA Approved KIAA1557, DKFZp686G052, FLJ30619, BAF200 uc001ros.1 Q68CP9 OTTHUMG00000150487 ENST00000334344.6:c.5272-22T>- chr12.hg19:g.46287391delT 7 10 ref NA False 40 40 PASS 8 PASS ref->het 0 NA 84,84 46,46 20,20 1 1 Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5 True hg19 CCDS31783.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARID2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000318380.2 PASS NA None 151 True + T ENST00000334344.6 VDR 7421 __UNKNOWN__ __UNKNOWN__ 12 48235448 48235449 __UNKNOWN__ 3'UTR DEL TT TT - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:48235448_48235449delTT ENST00000395324.2 - 0 4632_4633 VDR_ENST00000229022.3_3'UTR P11473 VDR_HUMAN vitamin D (1,25- dihydroxyvitamin D3) receptor NA NA NA NA bile acid signaling pathway (GO:0038183)|calcium ion transport (GO:0006816)|cell morphogenesis (GO:0000902)|cellular calcium ion homeostasis (GO:0006874)|decidualization (GO:0046697)|gene expression (GO:0010467)|intestinal absorption (GO:0050892)|lactation (GO:0007595)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|regulation of calcidiol 1-monooxygenase activity (GO:0060558)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin D receptor signaling pathway (GO:0070561) nucleoplasm (GO:0005654)|nucleus (GO:0005634) calcitriol binding (GO:1902098)|calcitriol receptor activity (GO:0008434)|DNA binding (GO:0003677)|lithocholic acid binding (GO:1902121)|lithocholic acid receptor activity (GO:0038186)|retinoid X receptor binding (GO:0046965)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270) NA central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(3)|skin(2) 22 Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214) GBM - Glioblastoma multiforme(48;0.17) Alfacalcidol(DB01436)|Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910) TCTGGCAAACTTTTTTTCTCTT 0.381 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 259 266.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.64 NA NA J03258 CCDS8757.1, CCDS55820.1 12q12-q14 2014-06-13 ENSG00000111424 7421 "Nuclear hormone receptors" 12679 protein-coding gene gene with protein product "protein phosphatase 1, regulatory subunit 163" 601769 NA 1662663 Standard NM_001017536 NA Approved NR1I1, PPP1R163 uc001rql.3 P11473 ENST00000395324.2:c.*3081AA>- chr12.hg19:g.48235452_48235453delTT 5 8 ref NA False 44 44 PASS 7 PASS ref->het 0 NA 194,197 49,49 20,17 1 1 B2R5Q1|G3V1V9|Q5PSV3 True hg19 CCDS8757.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA VDR-001 KNOWN alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000406433.1 PASS NA None 259 True - T ENST00000395324.2 CAB39L 81617 __UNKNOWN__ __UNKNOWN__ 13 49906212 49906237 __UNKNOWN__ Splice_Site DEL CAGCTCCCCTAGCAGCTAGAGGAAAA CAGCTCCCCTAGCAGCTAGAGGAAAA - rs201100340|rs539332301 LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:49906212_49906237delCAGCTCCCCTAGCAGCTAGAGGAAAA ENST00000355854.4 - 8 1188_1202 c.691_705delTTTTCCTCTAGCTGCTAGGGGAGCTG c.(691-705)ttttcctctagctgcdel p.FSSSC231fs CAB39L_ENST00000410043.1_Splice_Site_p.FSSSC231fs|CAB39L_ENST00000409130.1_Splice_Site_p.FSSSC87fs|CAB39L_ENST00000409308.1_Splice_Site_p.FSSSC231fs|CAB39L_ENST00000347776.5_Splice_Site_p.FSSSC231fs NM_030925.2 NP_112187.2 Q9H9S4 CB39L_HUMAN calcium binding protein 39-like 231 NA NA NA cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062) NA breast(1)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|stomach(1) 12 Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19) KIRC - Kidney renal clear cell carcinoma(9;0.206) GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226) GGTCCAGGATCAGCTCCCCTAGCAGCTAGAGGAAAACACAAAACCA 0.425 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 250 229.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0 NA NA AK022639 CCDS9416.2 13q14.11 2008-02-05 ENSG00000102547 ENSG00000102547 81617 20290 protein-coding gene gene with protein product 612175 NA Standard NM_030925 NM_030925 NA Approved bA103J18.3, FLJ12577, MO2L uc001vcw.3 Q9H9S4 OTTHUMG00000016914 ENST00000355854.4:c.691-1TTTTCCTCTAGCTGCTAGGGGAGCTG>- chr13.hg19:g.49906212_49906237delCAGCTCCCCTAGCAGCTAGAGGAAAA 0 5 ref NA False 62 62 PASS 1 PASS ref->het 0 NA 195,198 34,34 48,46 1 1 Q5TAW6|Q6WG71|Q96FG1|Q9BZ33 True hg19 CCDS9416.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CAB39L-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044908.3 PASS NA None 250 Frame_Shift_Del True - CAGCTCCCCTAGCAGCTAGAGGAAAA ENST00000355854.4 SLC15A1 6564 __UNKNOWN__ __UNKNOWN__ 13 99363920 99363924 __UNKNOWN__ Intron DEL GTTTT GTTTT - rs199609535|rs4001067|rs397842390|rs6145194|rs528538925 LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:99363920_99363924delGTTTT ENST00000376503.5 - 11 956 NM_005073.3 NP_005064.1 P46059 S15A1_HUMAN solute carrier family 15 (oligopeptide transporter), member 1 NA NA NA NA digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810) integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886) peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427) NA breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 30 all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610) ATTGCttttggttttgttttgtttt 0.312 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 64 67.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA U13173 CCDS9489.1 13q32.3 2013-05-22 ENSG00000088386 ENSG00000088386 6564 "Solute carriers" 10920 protein-coding gene gene with protein product "peptide transporter HPEPT1", "bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)", "solute carrier family 15 oligopeptide transporter member 1" 600544 NA 7896779 Standard NM_005073 NM_005073 NA Approved PEPT1, HPECT1, HPEPT1 uc001vno.3 P46059 OTTHUMG00000017255 ENST00000376503.5:c.900+183AAAAC>- chr13.hg19:g.99363930_99363934delGTTTT 4 8 ref NA False 40 39 PASS 5 PASS ref->het 0 NA 6,6 46,48 15,15 1 1 Q5VW82 True hg19 CCDS9489.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC15A1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000045560.3 PASS NA None 64 True - GTTTT ENST00000376503.5 NFATC4 4776 __UNKNOWN__ __UNKNOWN__ 14 24836176 24836176 __UNKNOWN__ 5'UTR DEL G G - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:24836176delG ENST00000413692.2 + 0 60 NFATC4_ENST00000440487.2_Intron|NFATC4_ENST00000554591.1_5'UTR NM_001136022.1|NM_001198967.1 NP_001129494.1|NP_001185896.1 Q14934 NFAC4_HUMAN nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4 NA NA NA NA cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366) cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667) RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713) NA breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2) 34 GBM - Glioblastoma multiforme(265;0.018) GGGCGGCGTTGGGGGTGCGGC 0.587 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 194 195.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 2.16 NA NA BC053855 CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1 14q11.2 2009-11-24 ENSG00000100968 ENSG00000100968 4776 "Nuclear factor of activated T-cells" 7778 protein-coding gene gene with protein product 602699 NA 7749981 Standard NM_004554 NM_004554 NA Approved NFAT3 uc010tok.2 Q14934 OTTHUMG00000029351 ENST00000413692.2:c.-85G>- chr14.hg19:g.24836176delG 4 6 ref NA False 162 92 PASS 5 PASS ref->het 0 NA 52,53 106,110 36,31 1 1 B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68 True hg19 CCDS45089.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NFATC4-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000414125.2 PASS NA None 194 True + G ENST00000413692.2 ST3GAL2 6483 __UNKNOWN__ __UNKNOWN__ 16 70428979 70428979 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:70428979delG ENST00000393640.4 - 2 2546 c.439delC c.(439-441)cacfs p.H147fs RP11-529K1.4_ENST00000566960.1_RNA|ST3GAL2_ENST00000342907.2_Frame_Shift_Del_p.H147fs Q16842 SIA4B_HUMAN ST3 beta-galactoside alpha-2,3-sialyltransferase 2 147 NA NA NA amino sugar metabolic process (GO:0006040)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281) extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173) beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836) NA breast(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1) 11 Ovarian(137;0.0694) CGGCACTGGTGGGGGTCCCGG 0.627 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 282 274.23 NA NA NA NA NA 95 103 100 NA NA NA NA 16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 70428979 NA 2198 4300 6498 SO:0001589 frameshift_variant 1.14 NA NA U63090 CCDS10890.1 16q22.3 2013-03-01 2003-01-14 2005-02-07 ENSG00000157350 ENSG00000157350 6483 2.4.99.4 "Sialyltransferases" 10863 protein-coding gene gene with protein product 607188 "sialyltransferase 4B (beta-galactosidase alpha-2,3-sialytransferase)" SIAT4B NA 9266697, 8920913 Standard NM_006927 NM_006927 NA Approved ST3GALII, ST3GalA.2 uc002eyx.2 Q16842 OTTHUMG00000137580 ENST00000393640.4:c.439delC chr16.hg19:g.70428979delG ENSP00000377257:p.His147fs 4 7 ref NA False 216 53 PASS 5 PASS ref->het 0 NA 99,104 157,157 28,23 2 1 O00654 True hg19 CCDS10890.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ST3GAL2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000268968.1 PASS NA None 282 True - G ENST00000393640.4 SIN3B 23309 __UNKNOWN__ __UNKNOWN__ 19 16989164 16989200 __UNKNOWN__ Splice_Site DEL ACATGTACCGTCGCGGGACCCTCTGCCGGGCCAAGCA ACATGTACCGTCGCGGGACCCTCTGCCGGGCCAAGCA - rs375962555|rs558015742 LTS-006_T LTS-006_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:16989164_16989200delACATGTACCGTCGCGGGACCCTCTGCCGGGCCAAGCA ENST00000248054.5 + 18 3146_3182 c.3125_3161delACATGTACCGTCGCGGGACCCTCTGCCGGGCCAAGCA c.(3124-3162)tacatgtaccgtcgcgggaccctctgccgggccaagcag>tg p.YMYRRGTLCRAKQ1042fs SIN3B_ENST00000594235.1_3'UTR|SIN3B_ENST00000379803.1_Splice_Site_p.YMYRRGTLCRAKQ1074fs|SIN3B_ENST00000595541.1_Splice_Site_p.YMYRRGTLCRAKQ632fs SIN3 transcription regulator family member B NA NA NA NA NA endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1) 26 TCCGAGGACTACATGTACCGTCGCGGGACCCTCTGCCGGGCCAAGCAGGTGCCAGGG 0.675 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 304 287.89 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0.8 NA NA AB014600 CCDS32946.1, CCDS74308.1 19p13.12 2013-08-21 2013-08-21 23309 19354 protein-coding gene gene with protein product 607777 "SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)" NA 9734811 Standard NM_015260 XM_005259832 NA Approved KIAA0700 uc002ney.2 O75182 ENST00000248054.5:c.3162+1ACATGTACCGTCGCGGGACCCTCTGCCGGGCCAAGCA>- chr19.hg19:g.16989164_16989200delACATGTACCGTCGCGGGACCCTCTGCCGGGCCAAGCA 0 3 ref NA False 67 67 PASS 1 PASS ref->het 0 NA 285,292 25,25 30,23 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SIN3B-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000462846.1 PASS NA None 304 Frame_Shift_Del True + ACATGTACCGTCGCGGGACCCTCTGCCGGGCCAAGCA ENST00000248054.5 CCNL2 81669 __UNKNOWN__ __UNKNOWN__ 1 1334053 1334057 __UNKNOWN__ Splice_Site DEL TAGAG TAGAG - rs368050244|rs3831366 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:1334053_1334057delTAGAG ENST00000400809.3 - 2 294 c.e2-2 CCNL2_ENST00000408918.4_Splice_Site NM_030937.4 NP_112199.2 Q96S94 CCNL2_HUMAN cyclin L2 NA NA NA NA NA regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) p.?(1) NA central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(2) 13 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146) CATGGCCACCTAGAGTAGAAGAAAG 0.507 NA NA NA NA NA NA NA NA NA 371 0.0740815 0.1021 0.0331 5008 , , NA 15997 0.0843 NA 0.0487 False NA ,,, NA NA NA 2504 0.0808 NA NA NA PASS NA NA NA NA NA 1 Unknown(1) large_intestine(1) NA NA NA NA NA 159 160.39 NA , 315,3951 NA 16,283,1834 NA NA NA NA , 4.8 1 NA dbSNP_107 96 304,7940 NA 10,284,3828 no splice-3,splice-3 CCNL2 NM_030937.4,NM_001039577.3 , 26,567,5662 A1A1,A1R,RR NA 3.6875,7.384,4.948 , , NA 619,11891 NA NA NA SO:0001630 splice_region_variant 0.1 AF251294 CCDS30557.1, CCDS30558.1 1p36.33 2014-07-03 ENSG00000221978 ENSG00000221978 81669 20570 protein-coding gene gene with protein product "cyclin S" 613482 "cyclin M" CCNM NA 14725631 Standard NM_030937 NM_030937 NA Approved ania-6b, PCEE, SB138, HLA-ISO, CCNS uc001afi.2 Q96S94 OTTHUMG00000002917 ENST00000400809.3:c.289-2CTCTA>- chr1.hg19:g.1334053_1334057delTAGAG 0 4 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 135,136 10,10 15,14 1 1 A8K8A3|B1B152|Q5T2N5|Q5T2N6|Q6IQ12|Q7Z4Z8|Q8N3C9|Q8N3D5|Q8NHE3|Q8TEL0|Q96B00 True hg19 CCDS30557.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCNL2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000008146.2 PASS NA None 159 Intron True - TAGAG ENST00000400809.3 MMEL1 79258 __UNKNOWN__ __UNKNOWN__ 1 2535093 2535094 __UNKNOWN__ Intron DEL CT CT - rs35090174 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:2535093_2535094delCT ENST00000378412.3 - 11 1203 MMEL1_ENST00000288709.6_Intron|MMEL1_ENST00000502556.1_Intron Q495T6 MMEL1_HUMAN membrane metallo-endopeptidase-like 1 NA NA NA NA NA endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021) metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270) NA cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1) 27 all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634) all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123) Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131) AGATGGGTGACTCTGTTCCAGG 0.589 NA NA NA NA NA NA NA NA NA 2395 0.478235 0.5454 0.4452 5008 , , NA 19292 0.5288 NA 0.3121 False NA ,,, NA NA NA 2504 0.5297 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 89 93.27 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF336981 CCDS30569.1, CCDS30569.2 1p36 2008-02-05 ENSG00000142606 ENSG00000142606 79258 14668 protein-coding gene gene with protein product NA "membrane metallo-endopeptidase-like 2" MMEL2 NA Standard NM_033467 NM_033467 NA Approved SEP, NL1, NL2, NEPII uc001ajy.2 Q495T6 OTTHUMG00000000846 ENST00000378412.3:c.1041+228AG>- chr1.hg19:g.2535095_2535096delCT 1 2 ref NA False 56 45 PASS 2 PASS ref->hom 0 NA 0,0 78,79 12,11 1 1 B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9 True hg19 CCDS30569.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MMEL1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000002395.2 PASS NA None 89 True - CT ENST00000378412.3 COL24A1 255631 __UNKNOWN__ __UNKNOWN__ 1 86210241 86210242 __UNKNOWN__ Intron INS - - T rs397755328|rs11387251 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:86210241_86210242insT ENST00000370571.2 - 57 5039 COL24A1_ENST00000436319.1_Intron NM_152890.5 NP_690850.2 Q17RW2 COOA1_HUMAN collagen, type XXIV, alpha 1 NA NA NA NA NA extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244) collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578) extracellular matrix structural constituent (GO:0005201) NA NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 101 all cancers(265;0.0627)|Epithelial(280;0.0689) TTCTGCCAGGGTTTTATCAAAC 0.342 NA NA NA NA NA NA NA NA NA TTTT|TTTT|TTTTT|insertion 4232 0.845048 0.68 0.817 5008 , , NA 16615 0.9296 NA 0.9672 False NA ,,, NA NA NA 2504 0.8753 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 111 105.94 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.32 AF410793 CCDS41353.1 1p22.3-p22.2 2013-01-16 ENSG00000171502 ENSG00000171502 255631 "Collagens" 20821 protein-coding gene gene with protein product 610025 NA Standard NM_152890 NM_152890 NA Approved uc001dlj.3 Q17RW2 OTTHUMG00000010629 ENST00000370571.2:c.4672+106->A chr1.hg19:g.86210245_86210245dupT 5 5 ref NA False 53 45 PASS 4 PASS ref->hom 0 NA 0,0 97,98 19,18 1 1 C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5 True hg19 CCDS41353.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COL24A1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000029335.4 PASS NA None 111 True - T ENST00000370571.2 MIA3 375056 __UNKNOWN__ __UNKNOWN__ 1 222817758 222817759 __UNKNOWN__ Intron INS - - ACAGGGGGC rs530219574 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:222817758_222817759insACAGGGGGC ENST00000344922.5 + 7 3502 MIA3_ENST00000470521.1_Intron|MIA3_ENST00000340535.7_5'UTR|MIA3_ENST00000344441.6_Intron|MIA3_ENST00000344507.1_Intron NM_198551.2 NP_940953.2 Q5JRA6 MIA3_HUMAN melanoma inhibitory activity family, member 3 NA NA NA NA NA chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060) endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020) NA breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1) 80 GBM - Glioblastoma multiforme(131;0.0199) AGCTCTGAAAAACAGGGGGCCC 0.574 NA NA NA NA NA NA NA NA NA 44 0.00878594 0 0 5008 , , NA 17306 0.0208 NA 0 False NA ,,, NA NA NA 2504 0.0235 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 456 468.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.11 CCDS41470.1, CCDS73035.1 1p36.33 2012-12-13 2006-07-25 ENSG00000154305 ENSG00000154305 375056 24008 protein-coding gene gene with protein product "C219 reactive peptide", "transport and golgi organization" 613455 NA 15183315 Standard NM_198551 XM_005273121 NA Approved UNQ6077, FLJ39207, KIAA0268, TANGO uc001hnl.3 Q5JRA6 OTTHUMG00000037543 ENST00000344922.5:c.3478-1137->ACAGGGGGC chr1.hg19:g.222817759_222817767dupACAGGGGGC 2 6 ref NA False 110 110 PASS 1 PASS ref->het 0 NA 374,378 10,10 69,65 1 1 A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580 True hg19 CCDS41470.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MIA3-001 NOVEL basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000091489.4 PASS NA None 456 True + ACAGGGGGC ENST00000344922.5 IRF2BP2 359948 __UNKNOWN__ __UNKNOWN__ 1 234740917 234740918 __UNKNOWN__ 3'UTR INS - - AGTTATAAT rs58042860|rs201078650|rs3045215 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:234740917_234740918insAGTTATAAT ENST00000366610.3 - 0 3711_3712 IRF2BP2_ENST00000366609.3_3'UTR NM_001077397.1 NP_001070865.1 Q7Z5L9 I2BP2_HUMAN interferon regulatory factor 2 binding protein 2 NA NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleus (GO:0005634) metal ion binding (GO:0046872) NA central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1) 11 Ovarian(103;0.0303) all_cancers(173;0.0236)|Prostate(94;0.0115) OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05) GGTCAAATTCCAAAGTGCCTAG 0.356 NA NA NA NA NA NA NA NA NA 3012 0.601438 0.8676 0.5519 5008 , , NA 20888 0.2639 NA 0.7724 False NA ,,, NA NA NA 2504 0.4489 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 241 239.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.02 AY278023 CCDS1602.1, CCDS41475.1 1q42.3 2008-02-05 ENSG00000168264 ENSG00000168264 359948 21729 protein-coding gene gene with protein product 615332 NA 12799427 Standard NM_182972 NM_182972 NA Approved IRF-2BP2 uc001hwg.3 Q7Z5L9 OTTHUMG00000037981 ENST00000366610.3:c.*1966->ATTATAACT chr1.hg19:g.234740917_234740918insAGTTATAAT 1 3 ref NA False 90 90 PASS 0 PASS ref->het 0 NA 204,204 5,5 28,28 1 1 B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8 True hg19 CCDS41475.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IRF2BP2-001 NOVEL basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000092704.1 PASS NA None 241 True - AGTTATAAT ENST00000366610.3 SERTAD2 9792 __UNKNOWN__ __UNKNOWN__ 2 64860030 64860035 __UNKNOWN__ 3'UTR DEL TTCAAA TTCAAA - rs201991281|rs56349338|rs140625215 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:64860030_64860035delTTCAAA ENST00000313349.3 - 0 4268_4273 NM_014755.2 NP_055570.1 Q14140 SRTD2_HUMAN SERTA domain containing 2 NA NA NA NA NA negative regulation of cell growth (GO:0030308)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleus (GO:0005634) transcription coactivator activity (GO:0003713) NA breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|skin(1) 12 AAAAACTCACTTCAAATTCAAAGCTC 0.398 NA NA NA NA NA NA NA NA NA 1125 0.224641 0.0605 0.3112 5008 , , NA 19366 0.3423 NA 0.3151 False NA ,,, NA NA NA 2504 0.1708 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 214 211.83 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.15 D50917 CCDS33210.1 2p15 2007-05-01 ENSG00000179833 ENSG00000179833 9792 30784 protein-coding gene gene with protein product "transcriptional regulator interacting with the PHS-bromodomain 2" NA NA 8590280, 11331592 Standard NM_014755 NM_014755 NA Approved TRIP-Br2, KIAA0127, Sei-2 uc002sde.2 Q14140 OTTHUMG00000152678 ENST00000313349.3:c.*3031TTTGAA>- chr2.hg19:g.64860036_64860041delTTCAAA 1 3 ref NA False 48 48 PASS 2 PASS ref->het 0 NA 183,185 12,12 30,29 1 1 Q53TS2 True hg19 CCDS33210.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SERTAD2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000327322.2 PASS NA None 214 True - TTCAAA ENST00000313349.3 STARD7 56910 __UNKNOWN__ __UNKNOWN__ 2 96851115 96851120 __UNKNOWN__ 3'UTR DEL AAAACA AAAACA - rs11164062|rs200172621|rs553895920|rs369808661 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:96851115_96851120delAAAACA ENST00000337288.5 - 0 2844_2849 NM_020151.3 NP_064536.2 Q9NQZ5 STAR7_HUMAN StAR-related lipid transfer (START) domain containing 7 NA NA NA NA NA mitochondrion (GO:0005739) lipid binding (GO:0008289) NA endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|stomach(2) 14 AGCAAGCAGGaaaacaaaaacaaaaa 0.369 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 225 223.72 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.68 AF270647 CCDS2017.2 2p11.1 2011-09-12 2007-08-16 ENSG00000084090 ENSG00000084090 56910 "StAR-related lipid transfer (START) domain containing" 18063 protein-coding gene gene with protein product NA "START domain containing 7" NA Standard NM_020151 NA Approved GTT1 uc002svm.4 Q9NQZ5 OTTHUMG00000130457 ENST00000337288.5:c.*1353TGTTTT>- chr2.hg19:g.96851121_96851126delAAAACA 3 10 ref NA False 31 31 PASS 4 PASS ref->het 0 NA 147,153 4,5 83,77 1 1 D3DXG9|Q53T44|Q6GU43|Q969M6 True hg19 CCDS2017.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA STARD7-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252848.2 PASS NA None 225 True - AAAACA ENST00000337288.5 CPO 130749 __UNKNOWN__ __UNKNOWN__ 2 207821136 207821137 __UNKNOWN__ Intron INS - - CAG rs386654491|rs201819640|rs56678664|rs141567906 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:207821136_207821137insCAG ENST00000272852.3 + 3 313 NM_173077.2 NP_775100.1 Q8IVL8 CBPO_HUMAN carboxypeptidase O NA NA NA NA NA extracellular region (GO:0005576) metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270) NA endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1) 14 LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142) atcatcatcatcatcagcagca 0.475 NA NA NA NA NA NA NA NA NA 900 0.179712 0.1536 0.1095 5008 , , NA 18965 0.2431 NA 0.1988 False NA ,,, NA NA NA 2504 0.18 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 26 23.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS2372.1 2q34 2012-02-10 ENSG00000144410 ENSG00000144410 130749 21011 protein-coding gene gene with protein product "metallocarboxypeptidase O", "metallocarboxypeptidase C" 609563 NA 11836249 Standard NM_173077 NM_173077 NA Approved uc002vby.2 Q8IVL8 OTTHUMG00000088987 ENST00000272852.3:c.267+848->CAG chr2.hg19:g.207821136_207821137insCAG 1 1 ref NA False 46 45 PASS 0 PASS ref->hom 0 NA 0,0 24,25 2,2 1 1 Q2M277|Q7RTW7 True hg19 CCDS2372.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CPO-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000202040.2 PASS NA None 26 True + CAG ENST00000272852.3 STT3B 201595 __UNKNOWN__ __UNKNOWN__ 3 31574393 31574394 __UNKNOWN__ 5'UTR INS - - TCCTCC rs529181821|rs375544928 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:31574393_31574394insTCCTCC ENST00000295770.2 + 0 112_113 STT3B_ENST00000453168.1_3'UTR NM_178862.1 NP_849193.1 Q8TCJ2 STT3B_HUMAN STT3B, subunit of the oligosaccharyltransferase complex (catalytic) NA NA NA NA NA co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986) integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250) dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579) NA autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1) 19 ctcctttttcttcctcctcctc 0.738 NA NA NA NA NA NA NA NA NA 441 0.0880591 0.0015 0.0274 5008 , , NA 11704 0.3095 NA 0.0586 False NA ,,, NA NA NA 2504 0.0501 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 258 257.92 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.84 AK027789 CCDS2650.1 3p24.1 2013-03-06 2013-03-06 ENSG00000163527 ENSG00000163527 201595 2.4.99.18 30611 protein-coding gene gene with protein product "source of immunodominant MHC associated peptides", "dolichyl-diphosphooligosaccharide protein glycotransferase" 608605 "STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)" NA 12887896, 12439619 Standard NM_178862 XM_006713017 NA Approved SIMP, FLJ90106, STT3-B uc011axe.2 Q8TCJ2 OTTHUMG00000130673 ENST00000295770.2:c.-97->TCCTCC chr3.hg19:g.31574394_31574399dupTCCTCC 9 7 ref NA False 68 68 PASS 7 PASS ref->het 0 NA 162,167 8,8 90,86 1 1 Q96JZ4|Q96KY7 True hg19 CCDS2650.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA STT3B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253166.2 PASS NA None 258 True + TCC ENST00000295770.2 PDCD6IP 10015 __UNKNOWN__ __UNKNOWN__ 3 33910703 33910704 __UNKNOWN__ 3'UTR INS - - ATAAT rs377454303|rs10637025 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:33910703_33910704insATAAT ENST00000307296.3 + 0 5670_5671 PDCD6IP_ENST00000457054.2_3'UTR Q8WUM4 PDC6I_HUMAN programmed cell death 6 interacting protein NA NA NA NA NA apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982) calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803) NA central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1) 23 tCAGAAACAGGATAATTTGTTA 0.302 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 243 243.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 BC020066 CCDS2660.1, CCDS54561.1 3p22.3 2012-08-30 2001-11-29 ENSG00000170248 ENSG00000170248 10015 8766 protein-coding gene gene with protein product "ALG-2 interacting protein X" 608074 "programmed cell death 6-interacting protein" NA 9880530 Standard NM_001162429 NA Approved Alix, AIP1, Hp95 uc003cfy.4 Q8WUM4 OTTHUMG00000130751 ENST00000307296.3:c.*2687->ATAAT chr3.hg19:g.33910704_33910708dupATAAT 2 3 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 209,209 12,13 18,18 1 1 C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5 True hg19 CCDS2660.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PDCD6IP-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000253251.2 PASS NA None 243 True + ATAAT ENST00000307296.3 ITGA9 3680 __UNKNOWN__ __UNKNOWN__ 3 37670986 37670990 __UNKNOWN__ Intron DEL ATAAA ATAAA - rs147632699|rs199594011 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:37670986_37670990delATAAA ENST00000264741.5 + 16 2095 ITGA9_ENST00000422441.1_3'UTR NM_002207.2 NP_002198.2 Q13797 ITA9_HUMAN integrin, alpha 9 NA NA NA NA NA axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060) basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886) metal ion binding (GO:0046872) NA breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1) 44 KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197) ctgcaaaatgaTAAAATAAACAGTC 0.483 NA NA NA NA NA NA NA NA NA 900 0.179712 0.1316 0.1599 5008 , , NA 21684 0.2202 NA 0.2217 False NA ,,, NA NA NA 2504 0.1738 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 219 202.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.01 L24158 CCDS2669.1 3p21.3 2010-03-23 ENSG00000144668 ENSG00000144668 3680 "Integrins" 6145 protein-coding gene gene with protein product "integrin, alpha 4-like" 603963 NA 8245132, 8290272 Standard NM_002207 NM_002207 NA Approved RLC, ITGA4L, ALPHA-RLC uc003chd.3 Q13797 OTTHUMG00000130815 ENST00000264741.5:c.1839+159ATAAA>- chr3.hg19:g.37670991_37670995delATAAA 1 7 ref NA False 38 38 PASS 2 PASS ref->het 0 NA 195,195 8,8 15,15 1 1 Q14638 True hg19 CCDS2669.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ITGA9-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253361.1 PASS NA None 219 True + ATAAA ENST00000264741.5 XXcos-LUCA11.5 0 __UNKNOWN__ __UNKNOWN__ 3 50400900 50400901 __UNKNOWN__ Intron INS - - GTGTGTGCACAGAGC rs143159818 LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:50400900_50400901insGTGTGTGCACAGAGC ENST00000606589.1 + 3 245 CACNA2D2_ENST00000435965.1_3'UTR|CACNA2D2_ENST00000360963.3_3'UTR|CACNA2D2_ENST00000424201.2_3'UTR|CACNA2D2_ENST00000266039.3_3'UTR|CACNA2D2_ENST00000429770.1_3'UTR|CACNA2D2_ENST00000395083.1_3'UTR|CACNA2D2_ENST00000423994.2_3'UTR NA NA NA NA NA NA NA TCCCCACCtgtgtgtgtgtgtg 0.589 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 133 185.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.9 NA NA NA NA NA ENST00000606589.1:c.128-2827->GTGTGTGCACAGAGC chr3.hg19:g.50400900_50400901insGTGTGTGCACAGAGC 1 2 ref NA False 39 39 PASS 0 PASS ref->het 0 NA 135,142 5,5 48,41 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA XXcos-LUCA11.5-001 PUTATIVE basic|appris_principal|readthrough_transcript protein_coding NA protein_coding OTTHUMT00000470670.1 PASS NA None 133 True + GTGTGTGCACAGAGC ENST00000606589.1 TMEM45A 55076 __UNKNOWN__ __UNKNOWN__ 3 100295909 100295910 __UNKNOWN__ 3'UTR INS - - TTGTCT rs199733796|rs5851214 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:100295909_100295910insTTGTCT ENST00000403410.1 + 0 1543_1544 TMEM45A_ENST00000323523.4_3'UTR Q9NWC5 TM45A_HUMAN transmembrane protein 45A NA NA NA NA NA integral component of membrane (GO:0016021) NA breast(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2) 11 TCTTTTTTACATTGTTCTTGGT 0.347 NA NA NA NA NA NA NA NA NA 1253 0.2502 0.3843 0.2493 5008 , , NA 18917 0.3185 NA 0.1213 False NA ,,, NA NA NA 2504 0.1319 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 453 461.52 NA 1436,2816 NA 258,920,948 NA NA NA NA 2.1 0 NA dbSNP_114 38 989,7257 NA 60,869,3194 no utr-3 TMEM45A NM_018004.1 318,1789,4142 A1A1,A1R,RR NA 11.9937,33.7723,19.4031 NA 2425,10073 NA NA NA SO:0001624 3_prime_UTR_variant 0.55 AK000996 CCDS2937.1 3q12.2 2005-02-04 ENSG00000181458 ENSG00000181458 55076 25480 protein-coding gene gene with protein product NA NA 12477932 Standard NM_018004 XM_005247568 NA Approved FLJ10134, DERP7 uc003dtz.1 Q9NWC5 OTTHUMG00000150327 ENST00000403410.1:c.*48->TTGTCT chr3.hg19:g.100295909_100295910insTTGTCT 1 4 ref NA False 49 49 PASS 0 PASS ref->het 0 NA 384,385 11,11 54,56 1 1 Q53YW5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM45A-002 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000317572.2 PASS NA None 453 True + TTGTCT ENST00000403410.1 PPA2 27068 __UNKNOWN__ __UNKNOWN__ 4 106290829 106290830 __UNKNOWN__ 3'UTR INS - - CTTGGGGAAAAAGAGT rs16345|rs11267164 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:106290829_106290830insCTTGGGGAAAAAGAGT ENST00000341695.5 - 0 1087_1088 PPA2_ENST00000357415.4_3'UTR|PPA2_ENST00000432483.2_3'UTR|PPA2_ENST00000354147.3_3'UTR|PPA2_ENST00000348706.5_3'UTR|PPA2_ENST00000380004.2_3'UTR NM_176869.2 NP_789845.1 Q9H2U2 IPYR2_HUMAN pyrophosphatase (inorganic) 2 NA NA NA NA NA diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418) extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759) inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|protein serine/threonine phosphatase activity (GO:0004722) NA breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1) 11 Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;2.03e-07) TGTCTCTAGCACTTGGAGTCCT 0.371 NA NA NA NA NA NA NA NA NA 1740 0.347444 0.4523 0.3271 5008 , , NA 17623 0.4395 NA 0.2803 False NA ,,, NA NA NA 2504 0.1943 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 1091 1025.88 NA ,,, 1767,4,2493 NA 379,4,1005,0,0,744 NA NA NA NA ,,, 2.7 0 NA dbSNP_130 77 2042,4,6206 NA 271,2,1498,1,0,2354 no utr-3,utr-3,utr-3,utr-3 PPA2 NM_176869.2,NM_176867.3,NM_176866.2,NM_006903.4 ,,, 650,6,2503,1,0,3098 A1A1,A1A2,A1R,A2A2,A2R,RR NA 24.794,41.5338,30.497 ,,, ,,, NA 3809,8,8699 NA NA NA SO:0001624 3_prime_UTR_variant 1.19 CCDS3667.1, CCDS3668.2, CCDS3669.2, CCDS34043.1 4q25 2005-10-07 ENSG00000138777 ENSG00000138777 27068 28883 protein-coding gene gene with protein product 609988 NA 11042152 Standard NM_176869 NM_176869 NA Approved FLJ20459 uc003hxl.3 Q9H2U2 OTTHUMG00000128781 ENST00000341695.5:c.*53->ACTCTTTTTCCCCAAG chr4.hg19:g.106290829_106290830insCTTGGGGAAAAAGAGT 1 2 ref NA False 62 62 PASS 0 PASS ref->het 0 NA 949,951 23,23 106,106 1 1 B4DLP7|F8WDN9|I6L9B6|Q4W5E9|Q6PG51|Q8TBW0|Q96E55|Q9H0T0|Q9NX37|Q9P033|Q9ULX0 True hg19 CCDS3667.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPA2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250704.4 PASS NA None 1091 True - CTTGGGGAAAAAGAGT ENST00000341695.5 PALLD 23022 __UNKNOWN__ __UNKNOWN__ 4 169612557 169612565 __UNKNOWN__ Intron DEL TGTGGCTCC TGTGGCTCC - LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:169612557_169612565delTGTGGCTCC ENST00000505667.1 + 8 1674 PALLD_ENST00000335742.7_Intron|PALLD_ENST00000512127.1_Intron|PALLD_ENST00000261509.6_Intron|PALLD_ENST00000333488.4_Intron Q8WX93 PALLD_HUMAN palladin, cytoskeletal associated protein NA NA NA NA NA cytoskeleton organization (GO:0007010) actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634) muscle alpha-actinin binding (GO:0051371) NA breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4) 48 Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144) GBM - Glioblastoma multiforme(119;0.204) ACAATGTTTTTGTGGCTCCCTGGAAATGT 0.368 NA NA NA NA NA NA Pancreatic Cancer, Familial Clustering of NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(109;1482 1532 18347 40239 51172) PASS NA NA NA NA NA 0 NA NA NA NA NA 174 161.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.91 Familial Cancer Database incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1 AB023209 CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1 4q32.3 2013-01-11 ENSG00000129116 ENSG00000129116 23022 "Immunoglobulin superfamily / I-set domain containing" 17068 protein-coding gene gene with protein product 608092 NA 10231032, 10931874 Standard NM_016081 NM_001166108 NA Approved KIAA0992, SIH002, CGI-151 uc011cjx.2 Q8WX93 OTTHUMG00000161097 ENST00000505667.1:c.1501+114TGTGGCTCC>- chr4.hg19:g.169612557_169612565delTGTGGCTCC 0 6 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 159,160 4,4 16,16 1 1 B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9 True hg19 CCDS54818.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PALLD-002 NOVEL basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000363762.1 PASS NA None 174 True + TGTGGCTCC ENST00000505667.1 SORBS2 8470 __UNKNOWN__ __UNKNOWN__ 4 186510778 186510779 __UNKNOWN__ Intron INS - - AACTC rs1160906|rs368056851|rs145379817 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:186510778_186510779insAACTC ENST00000437304.2 - 22 2997 SORBS2_ENST00000431808.1_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000284776.7_Intron|RP11-301L8.2_ENST00000411847.1_RNA|SORBS2_ENST00000418609.1_Intron|SORBS2_ENST00000355634.5_Intron NM_001145673.1 NP_001139145.1 O94875 SRBS2_HUMAN sorbin and SH3 domain containing 2 NA NA NA NA NA actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477) actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018) cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307) NA endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1) 53 all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244) OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205) GGGAGTGAGCAAACTCAAGCAA 0.446 NA NA NA NA NA NA NA NA NA 1100 0.219649 0.2912 0.1254 5008 , , NA 20291 0.3065 NA 0.1233 False NA ,,, NA NA NA 2504 0.1994 NA NA NA Esophageal Squamous(153;41 2433 9491 36028) PASS NA NA NA NA NA 0 NA NA NA NA NA 169 180.94 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.21 CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1 4q35.1 2008-02-05 ENSG00000154556 ENSG00000154556 8470 24098 protein-coding gene gene with protein product "Arg/Abl interacting protein" NA NA 9211900, 9872452 Standard NM_003603 NM_021069 NA Approved ARGBP2, KIAA0777 uc003iym.3 O94875 OTTHUMG00000157215 ENST00000437304.2:c.2413+53->GAGTT chr4.hg19:g.186510779_186510783dupAACTC 2 3 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 136,138 6,6 26,25 1 1 A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0 True hg19 CCDS47175.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SORBS2-009 PUTATIVE basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000347952.2 PASS NA None 169 True - AACTC ENST00000437304.2 BTF3 689 __UNKNOWN__ __UNKNOWN__ 5 72795161 72795165 __UNKNOWN__ Intron DEL ATCTC ATCTC - rs3057009 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:72795161_72795165delATCTC ENST00000335895.8 + 2 220 BTF3_ENST00000380591.3_Intron|BTF3_ENST00000514505.2_Intron NM_001207.4 NP_001198.2 O00478 BT3A3_HUMAN basic transcription factor 3 NA NA NA NA NA T cell mediated immunity (GO:0002456) cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886) NA endometrium(1)|large_intestine(2)|lung(2) 5 Lung NSC(167;0.00405)|Ovarian(174;0.0175) OV - Ovarian serous cystadenocarcinoma(47;2.73e-54) GAGCTAGCAAATCTCGAGGAGCGGG 0.405 NA NA NA NA NA NA NA NA NA 1514 0.302316 0.5151 0.121 5008 , , NA 17566 0.5427 NA 0.0706 False NA ,,, NA NA NA 2504 0.1339 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 110 108.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.43 M90352 CCDS4019.1, CCDS34185.1 5q13.3 2010-06-17 ENSG00000145741 ENSG00000145741 689 1125 protein-coding gene gene with protein product 602542 "nascent-polypeptide-associated complex beta polypeptide" NACB NA 2320128, 1386332, 15716105 Standard NM_001207 NM_001207 NA Approved BTF3a, BTF3b uc003kcr.1 P20290 OTTHUMG00000102031 ENST00000335895.8:c.69+134ATCTC>- chr5.hg19:g.72795161_72795165delATCTC 0 3 ref NA False 36 36 PASS 1 PASS ref->het 0 NA 101,101 4,4 8,8 1 1 B4DWI7|E9PCP5 True hg19 CCDS4019.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BTF3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000219815.2 PASS NA None 110 True + ATCTC ENST00000335895.8 C6orf62 81688 __UNKNOWN__ __UNKNOWN__ 6 24720523 24720528 __UNKNOWN__ 5'UTR DEL GGCGGG GGCGGG - rs202020137|rs201841846 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:24720523_24720528delGGCGGG ENST00000378119.4 - 0 536_541 C6orf62_ENST00000540769.1_5'UTR NM_030939.4 NP_112201.1 Q9GZU0 CF062_HUMAN chromosome 6 open reading frame 62 NA NA NA NA NA intracellular (GO:0005622) NA endometrium(2)|kidney(3)|large_intestine(2)|lung(3) 10 aggcggcggcggcgggggcgCTGCTG 0.728 NA NA NA NA NA NA NA NA NA 457 0.091254 0.003 0.1916 5008 , , NA 7143 0.2827 NA 0.007 False NA ,,, NA NA NA 2504 0.0286 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 362 389.83 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 8.23 AL136632 CCDS4559.1 6p22.1 2011-12-13 ENSG00000112308 ENSG00000112308 81688 20998 protein-coding gene gene with protein product "HBV X-transactivated protein 12" NA NA 11230166 Standard NM_030939 NM_030939 NA Approved FLJ12619, DKFZP564G182, XTP12 uc003nel.3 Q9GZU0 OTTHUMG00000014361 ENST00000378119.4:c.-1632CCCGCC>- chr6.hg19:g.24720523_24720528delGGCGGG 0 7 ref NA False 174 174 PASS 1 PASS ref->het 0 NA 301,334 11,12 117,83 1 1 Q3LIB6|Q5JVZ2|Q5JVZ3|Q6IA63|Q9H1Z2 True hg19 CCDS4559.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C6orf62-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000040017.1 PASS NA None 362 True - GGCGGG ENST00000378119.4 ZSCAN12 9753 __UNKNOWN__ __UNKNOWN__ 6 28349845 28349864 __UNKNOWN__ 3'UTR DEL CAAGCTATAAGTGATCCTCC CAAGCTATAAGTGATCCTCC - rs70983940|rs373360241|rs3832424|rs369210512 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:28349845_28349864delCAAGCTATAAGTGATCCTCC ENST00000361028.1 - 0 2362_2381 ZSCAN12_ENST00000396827.3_Intron O43309 ZSC12_HUMAN zinc finger and SCAN domain containing 12 NA NA NA NA NA transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA breast(2)|endometrium(3)|urinary_tract(1) 6 TTTTGCTAGTCAAGCTATAAGTGATCCTCCCAAGCTTTCC 0.427 NA NA NA NA NA NA NA NA NA 1418 0.283147 0.4811 0.2478 5008 , , NA 22029 0.1607 NA 0.2406 False NA ,,, NA NA NA 2504 0.2106 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 272 266.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.3 AB007886 6p21 2013-01-08 2007-02-20 2007-02-20 ENSG00000158691 ENSG00000158691 9753 "-", "Zinc fingers, C2H2-type" 13172 protein-coding gene gene with protein product 603978 "zinc finger protein 305", "zinc finger protein 96" ZNF305, ZNF96 NA 9244436 Standard NM_014724 NM_001163391 NA Approved KIAA0426, ZNF29K1, ZFP96, dJ29K1.2 uc011dlh.2 O43309 OTTHUMG00000014522 ENST00000361028.1:c.*421GGAGGATCACTTATAGCTTG>- chr6.hg19:g.28349845_28349864delCAAGCTATAAGTGATCCTCC 0 5 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 297,301 6,6 35,34 1 1 O43724 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZSCAN12-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000040190.1 PASS NA None 272 True - CAAGCTATAAGTGATCCTCC ENST00000361028.1 ZNF451 26036 __UNKNOWN__ __UNKNOWN__ 6 57034835 57034839 __UNKNOWN__ 3'UTR DEL TGTGG TGTGG - rs76264878|rs71813980 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:57034835_57034839delTGTGG ENST00000370706.4 + 0 4998_5002 RP11-203B9.4_ENST00000592785.1_RNA|RP11-203B9.4_ENST00000589263.1_RNA|RP11-203B9.4_ENST00000586432.1_RNA|ZNF451_ENST00000357489.3_3'UTR|RP11-203B9.4_ENST00000586053.1_RNA|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000589312.1_RNA|RP11-203B9.4_ENST00000586466.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000589394.1_RNA|RP11-203B9.4_ENST00000588819.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000590164.1_RNA|RP11-203B9.4_ENST00000589549.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA NM_001031623.2 NP_001026794.1 Q9Y4E5 ZN451_HUMAN zinc finger protein 451 NA NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) NA central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 32 Lung NSC(77;0.145) LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13) AAGAAGCTTTTGTGGTGTGTGTGGT 0.41 NA NA NA NA NA NA NA NA NA 593 0.118411 0.208 0.0951 5008 , , NA 18612 0.0893 NA 0.0954 False NA ,,, NA NA NA 2504 0.0675 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 298 296.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AB011148 CCDS4960.1, CCDS43477.1, CCDS59026.1 6p12.1 2012-08-08 ENSG00000112200 ENSG00000112200 26036 "Zinc fingers, C2H2-type" 21091 protein-coding gene gene with protein product 615708 NA 9628581 Standard NM_015555 NM_001031623 NA Approved KIAA0576, COASTER, dJ417I1.1, KIAA1702 uc003pdm.2 Q9Y4E5 OTTHUMG00000014916 ENST00000370706.4:c.*1572TGTGG>- chr6.hg19:g.57034835_57034839delTGTGG 0 5 ref NA False 51 51 PASS 1 PASS ref->het 0 NA 273,276 8,8 31,30 1 1 Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1 True hg19 CCDS43477.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF451-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041035.2 PASS NA None 298 True + TGTGG ENST00000370706.4 FGFR1OP 11116 __UNKNOWN__ __UNKNOWN__ 6 167454237 167454238 __UNKNOWN__ 3'UTR INS - - ATTCAGTACCA rs11275310|rs68120222|rs374407953 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:167454237_167454238insATTCAGTACCA ENST00000366847.4 + 0 2202_2203 RP11-517H2.6_ENST00000609590.1_RNA NM_007045.2 NP_008976.1 O95684 FR1OP_HUMAN FGFR1 oncogene partner NA NA NA NA NA G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein tyrosine kinase activity (GO:0061099)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284) centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471) protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|protein tyrosine kinase inhibitor activity (GO:0030292) NA large_intestine(2)|ovary(1)|stomach(1) 4 Breast(66;1.48e-05)|Ovarian(120;0.0607) OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231) CCTTGAAACTTAAATGCATCTG 0.317 NA NA TRUE FGFR1 "MPD, NHL" NA NA NA NA NA NA 1960 0.391374 0.3601 0.3631 5008 , , NA 17680 0.4534 NA 0.4473 False NA ,,, NA NA NA 2504 0.3323 NA NA NA PASS NA Dom yes NA 6 6q27 11116 FGFR1 oncogene partner (FOP) NA L 0 NA NA NA NA NA 286 291.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 Y18046 CCDS5296.1, CCDS5297.1, CCDS75550.1 6q27 2008-02-05 ENSG00000213066 ENSG00000213066 11116 17012 protein-coding gene gene with protein product 605392 NA 9949182, 10373756 Standard NM_007045 NM_007045 NA Approved FOP uc003qvj.3 O95684 OTTHUMG00000016011 ENST00000366847.4:c.*772->ATTCAGTACCA chr6.hg19:g.167454237_167454238insATTCAGTACCA 1 3 ref NA False 38 38 PASS 0 PASS ref->het 0 NA 252,252 6,6 23,23 1 1 A8K1D1|B2R705|Q49AI0|Q5R3F6|Q96EW1 True hg19 CCDS5296.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FGFR1OP-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000043099.2 PASS NA None 286 True + ATTCAGTACCA ENST00000366847.4 POU6F2 11281 __UNKNOWN__ __UNKNOWN__ 7 39379699 39379700 __UNKNOWN__ Intron DEL CA CA - rs397802042|rs5883685 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:39379699_39379700delCA ENST00000518318.2 + 5 927 POU6F2_ENST00000517348.1_Intron|POU6F2_ENST00000403058.1_Intron|POU6F2_ENST00000559001.1_Intron P78424 PO6F2_HUMAN POU class 6 homeobox 2 NA NA NA NA NA central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601) nucleus (GO:0005634) DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2) 42 GCAGAGGGACCACACAAAACTT 0.505 NA NA NA NA NA NA NA NA NA 2826 0.564297 0.5575 0.549 5008 , , NA 16773 0.7431 NA 0.5586 False NA ,,, NA NA NA 2504 0.4059 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 68 76.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.13 U91934 CCDS34620.2, CCDS55103.1 7p14.1 2011-06-20 2007-07-13 ENSG00000106536 ENSG00000106536 11281 "Homeoboxes / POU class" 21694 protein-coding gene gene with protein product "Retina-derived POU-domain factor-1" 609062 "POU domain, class 6, transcription factor 2" NA 8601806 Standard NM_007252 NM_007252 NA Approved RPF-1 uc003thb.2 P78424 OTTHUMG00000150803 ENST00000518318.2:c.885+85CA>- chr7.hg19:g.39379703_39379704delCA 2 3 ref NA False 34 33 PASS 3 PASS ref->hom 0 NA 0,0 61,63 6,5 1 1 A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7 True hg19 CCDS55103.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA POU6F2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000320145.5 PASS NA None 68 True + CA ENST00000518318.2 PHKG1 5260 __UNKNOWN__ __UNKNOWN__ 7 56149475 56149476 __UNKNOWN__ Intron INS - - GCAGGT rs199775883|rs200265462|rs369497317 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:56149475_56149476insGCAGGT ENST00000297373.2 - 9 987 PHKG1_ENST00000537360.1_Intron|PHKG1_ENST00000452681.2_Intron NM_001258460.1|NM_006213.4 NP_001245389.1|NP_006204.1 Q16816 PHKG1_HUMAN phosphorylase kinase, gamma 1 (muscle) NA NA NA NA NA carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964) ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|tau-protein kinase activity (GO:0050321) NA endometrium(1)|large_intestine(1)|lung(5) 7 Breast(14;0.214) Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099) GGGGAACCGAGAATGTCAAGGC 0.649 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Melanoma(184;580 2064 5329 24177 35303) PASS NA NA NA NA NA 0 NA NA NA NA NA 347 326.07 NA 42,4222 NA 1,40,2091 NA NA NA NA -4.9 0 NA dbSNP_134 26 315,7939 NA 5,305,3817 no intron PHKG1 NM_006213.3 6,345,5908 A1A1,A1R,RR NA 3.8163,0.985,2.8519 NA 357,12161 NA NA NA SO:0001627 intron_variant 2.5 X80590 CCDS5525.1, CCDS59057.1 7p11.2 2009-07-10 ENSG00000164776 ENSG00000164776 5260 2.7.11.19 8930 protein-coding gene gene with protein product 172470 PHKG NA 8530014 Standard NM_006213 NM_001258459 NA Approved uc011kdb.2 Q16816 OTTHUMG00000023869 ENST00000297373.2:c.793-27->ACCTGC chr7.hg19:g.56149475_56149476insGCAGGT 1 3 ref NA False 37 37 PASS 0 PASS ref->het 0 NA 292,303 6,7 47,35 1 1 B7Z1D0|F5H2S1|Q75LP5 True hg19 CCDS5525.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PHKG1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251587.1 PASS NA None 347 True - GCAGGT ENST00000297373.2 REPIN1 29803 __UNKNOWN__ __UNKNOWN__ 7 150069396 150069407 __UNKNOWN__ In_Frame_Del DEL CCGCCAGGGGCC CCGCCAGGGGCC - rs3832490 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:150069396_150069407delCCGCCAGGGGCC ENST00000489432.2 + 3 1420_1431 c.1237_1248delCCGCCAGGGGCC c.(1237-1248)ccgccaggggccdel p.PPGA413del REPIN1_ENST00000479668.1_3'UTR|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000425389.2_In_Frame_Del_p.PPGA356del|REPIN1_ENST00000540729.1_In_Frame_Del_p.PPGA356del|REPIN1_ENST00000444957.1_In_Frame_Del_p.PPGA356del|REPIN1_ENST00000397281.2_In_Frame_Del_p.PPGA356del NM_001099695.1 NP_001093165.1 Q9BWE0 REPI1_HUMAN replication initiator 1 356 NA NA NA NA DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273) cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822) p.P356_A359delPPGA(1) NA cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1) 14 Ovarian(565;0.183)|Melanoma(164;0.226) OV - Ovarian serous cystadenocarcinoma(82;0.011) CCAGGAGCCGCCGCCAGGGGCCCCGCCAGAGC 0.783 NA NA NA NA NA NA NA NA NA 714 0.142572 0.3207 0.0533 5008 , , NA 8637 0.0724 NA 0.0348 False NA ,,, NA NA NA 2504 0.1483 NA NA NA PASS NA NA NA NA NA 1 Deletion - In frame(1) prostate(1) NA NA NA NA NA 187 202.09 NA ,,, 481,1369 NA 176,129,620 NA NA NA NA ,,, -7.4 0 NA dbSNP_107 1 202,4558 NA 64,74,2242 no coding,coding,coding,coding REPIN1 NM_014374.3,NM_013400.3,NM_001099696.2,NM_001099695.1 ,,, 240,203,2862 A1A1,A1R,RR NA 4.2437,26.0,10.3328 ,,, ,,, NA 683,5927 NA NA NA SO:0001651 inframe_deletion 1.02 AF201303 CCDS43677.1, CCDS47745.1 7q36.1 2013-01-08 2003-08-07 2003-08-08 29803 "Zinc fingers, C2H2-type" 17922 protein-coding gene gene with protein product "replication initiation region protein (60kD)", "zinc finger protein AP4", "zinc finger protein 464 (RIP60)" NA "zinc finger protein 464 (RIP60)" ZNF464 NA 10606657 Standard NM_014374 NM_013400 NA Approved RIP60, AP4, H_DJ0584D14.12, Zfp464 uc010lpr.1 Q9BWE0 ENST00000489432.2:c.1237_1248delCCGCCAGGGGCC chr7.hg19:g.150069396_150069407delCCGCCAGGGGCC ENSP00000417291:p.Pro413_Ala416del 0 6 ref NA False 83 83 PASS 1 PASS ref->het 0 NA 162,176 12,12 42,29 1 1 C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5 True hg19 CCDS47745.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA REPIN1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000350705.2 PASS NA None 187 True + CCGCCAGGGGCC ENST00000489432.2 RBM33 155435 __UNKNOWN__ __UNKNOWN__ 7 155573480 155573481 __UNKNOWN__ 3'UTR INS - - ATCACCTCTCA rs372558938|rs368356897 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:155573480_155573481insATCACCTCTCA ENST00000401878.3 + 0 9456_9457 RBM33_ENST00000341148.3_3'UTR NM_053043.2 NP_444271.2 Q96EV2 RBM33_HUMAN RNA binding motif protein 33 NA NA NA NA NA nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822) NA breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1) 27 all_neural(206;0.101) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.011) UCEC - Uterine corpus endometrioid carcinoma (81;0.2) TTTACCACTCCATCACCTCTCA 0.49 NA NA NA NA NA NA NA NA NA 78 0.0155751 0.031 0.0115 5008 , , NA 22106 0.0228 NA 0.002 False NA ,,, NA NA NA 2504 0.0041 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 365 400.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.03 AL832196 CCDS5941.2 7q36.3 2013-02-12 ENSG00000184863 ENSG00000184863 155435 "RNA binding motif (RRM) containing" 27223 protein-coding gene gene with protein product NA "proline rich 8" PRR8 NA Standard NM_001008408 NM_053043 NA Approved DKFZp686F102, MGC20460, DKFZp434D1319 uc010lqk.1 Q96EV2 OTTHUMG00000150260 ENST00000401878.3:c.*5746->ATCACCTCTCA chr7.hg19:g.155573481_155573491dupATCACCTCTCA 2 3 ref NA False 39 39 PASS 1 PASS ref->het 0 NA 288,295 14,14 63,58 1 1 A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0 True hg19 CCDS5941.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RBM33-007 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000317225.3 PASS NA None 365 True + ATCACCTCTCA ENST00000401878.3 SLC7A13 157724 __UNKNOWN__ __UNKNOWN__ 8 87226635 87226642 __UNKNOWN__ Stop_Codon_Del DEL CCGACATC CCGACATC - rs202114931|rs56993779|rs200509135 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:87226635_87226642delCCGACATC ENST00000297524.3 - 0 1516_1523 SLC7A13_ENST00000419776.2_3'UTR NM_138817.2 NP_620172.2 Q8TCU3 S7A13_HUMAN solute carrier family 7 (anionic amino acid transporter), member 13 NA NA NA NA NA integral component of membrane (GO:0016021) amino acid transmembrane transporter activity (GO:0015171) NA breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3) 45 GTTTGCACTTCCGACATCTATTCCTCAG 0.312 NA NA NA NA NA NA NA NA NA 968 0.193291 0.0401 0.1931 5008 , , NA 18381 0.3323 NA 0.1372 False NA ,,, NA NA NA 2504 0.3149 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 920 868.18 NA 231,4025 NA 8,215,1905 NA NA NA NA 3 0 NA dbSNP_129 39 992,7256 NA 76,840,3208 no frameshift SLC7A13 NM_138817.2 84,1055,5113 A1A1,A1R,RR NA 12.0272,5.4276,9.7809 NA 1223,11281 NA NA NA SO:0001567 stop_retained_variant 1.15 AJ417661 CCDS34917.1 8q21.3 2013-07-15 2011-07-12 ENSG00000164893 ENSG00000164893 157724 "Solute carriers" 23092 protein-coding gene gene with protein product NA NA 11907033, 11943479 Standard NM_138817 XM_005250804 NA Approved AGT-1, XAT2 uc003ydq.1 Q8TCU3 OTTHUMG00000163663 ENST00000297524.3:c.1413_*7delGATGTCGG chr8.hg19:g.87226635_87226642delCCGACATC 0 3 ref NA False 59 59 PASS 1 PASS ref->het 0 NA 864,872 36,38 82,77 1 1 Q05C37|Q08AH9|Q96N84 True hg19 CCDS34917.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC7A13-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000374704.1 PASS NA None 920 True - CCGACATC ENST00000297524.3 KIAA1161 57462 __UNKNOWN__ __UNKNOWN__ 9 34369683 34369687 __UNKNOWN__ 3'UTR DEL TGAGA TGAGA - rs374451075|rs66653119 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:34369683_34369687delTGAGA ENST00000297625.7 - 0 3378_3382 NM_020702.3 NP_065753.2 Q6NSJ0 K1161_HUMAN KIAA1161 NA NA NA NA NA carbohydrate metabolic process (GO:0005975)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of protein kinase B signaling (GO:0051897)|skeletal muscle fiber development (GO:0048741) integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965) hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553) NA breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1) 12 LUSC - Lung squamous cell carcinoma(29;0.0107) GBM - Glioblastoma multiforme(74;0.126) AGAAAATGGCTGAGATGAAAGACCT 0.527 NA NA NA NA NA NA NA NA NA 1813 0.362021 0.3283 0.3199 5008 , , NA 19424 0.6617 NA 0.1879 False NA ,,, NA NA NA 2504 0.3078 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 253 253.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.29 AB032987 9p11.2 2009-11-06 ENSG00000164976 ENSG00000164976 57462 19918 protein-coding gene gene with protein product NA NA 10574461 Standard XM_351807 XM_006716808 NA Approved NET37 uc003zue.4 Q6NSJ0 OTTHUMG00000019816 ENST00000297625.7:c.*1114TCTCA>- chr9.hg19:g.34369683_34369687delTGAGA 0 2 ref NA False 36 36 PASS 1 PASS ref->het 0 NA 217,223 12,12 44,38 1 1 Q5T587|Q5T588|Q9ULQ9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KIAA1161-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000052158.1 PASS NA None 253 True - TGAGA ENST00000297625.7 NTNG2 84628 __UNKNOWN__ __UNKNOWN__ 9 135118448 135118448 __UNKNOWN__ 3'UTR DEL A A - rs3831218|rs142738640 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:135118448delA ENST00000393229.3 + 0 3319 NM_032536.2 NP_115925.2 Q96CW9 NTNG2_HUMAN netrin G2 NA NA NA NA NA axonogenesis (GO:0007409) anchored component of plasma membrane (GO:0046658)|axon (GO:0030424) NA central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2) 29 OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173) GCCTCCCCACACTGAAAGGCT 0.582 NA NA NA NA NA NA NA NA NA A|A|-|deletion 1377 0.27496 0.2262 0.3718 5008 , , NA 14767 0.3274 NA 0.169 False NA ,,, NA NA NA 2504 0.3272 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 202 209.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.21 AB058760 CCDS6946.1 9q34 2013-03-01 2003-12-02 2003-12-03 ENSG00000196358 ENSG00000196358 84628 "Netrins" 14288 protein-coding gene gene with protein product "Netrin-G2" NA "netrin G1" NTNG1 NA Standard NM_032536 NM_032536 NA Approved KIAA1857, Lmnt2 uc004cbh.2 Q96CW9 OTTHUMG00000020835 ENST00000393229.3:c.*950A>- chr9.hg19:g.135118448delA 0 5 ref NA False 39 39 PASS 1 PASS ref->het 0 NA 164,169 20,20 26,23 1 1 Q5JUJ2|Q6UXY0|Q96JH0 True hg19 CCDS6946.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NTNG2-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000054779.1 PASS NA None 202 True + A ENST00000393229.3 EDF1 8721 __UNKNOWN__ __UNKNOWN__ 9 139760577 139760602 __UNKNOWN__ Intron DEL GCCCCGGCCCAGCGTCCGCCCCGCCC GCCCCGGCCCAGCGTCCGCCCCGCCC - rs531974108|rs371196027|rs566481246|rs374525120 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:139760577_139760602delGCCCCGGCCCAGCGTCCGCCCCGCCC ENST00000224073.1 - 1 106 EDF1_ENST00000371649.1_Intron|EDF1_ENST00000371648.4_Intron NM_003792.2 NP_003783.1 O60869 EDF1_HUMAN endothelial differentiation-related factor 1 NA NA NA NA NA endothelial cell differentiation (GO:0045446)|multicellular organismal development (GO:0007275)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634) poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713) NA lung(1) 1 all_cancers(76;0.0841)|all_epithelial(76;0.217) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171) acggtccgtggccccggcccagcgtccgccccgcccggcccggccG 0.757 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 170 198.36 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.28 AJ005259 CCDS7011.1, CCDS7012.1, CCDS65193.1 9q34.3 2009-11-06 ENSG00000107223 ENSG00000107223 8721 3164 protein-coding gene gene with protein product "multiprotein bridging factor-1" 605107 NA 9813014, 15112053 Standard NM_003792 NA Approved EDF-1 uc004cjt.1 O60869 OTTHUMG00000020948 ENST00000224073.1:c.78+30GGGCGGGGCGGACGCTGGGCCGGGGC>- chr9.hg19:g.139760577_139760602delGCCCCGGCCCAGCGTCCGCCCCGCCC 0 7 ref NA False 48 48 PASS 1 PASS ref->het 0 NA 229,243 6,7 47,32 1 1 Q5T5T2|Q9UIM1 True hg19 CCDS7011.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EDF1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000055143.1 PASS NA None 170 True - GCCCCGGCCCAGCGTCCGCCCCGCCC ENST00000224073.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 10 133770659 133770660 __UNKNOWN__ IGR INS - - GGGAGTC rs201620472 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:133770659_133770660insGGGAGTC NA PPP2R2D (640 upstream) : BNIP3 (10917 downstream) NA NA NA NA NA NA NA CGAGGGGAGTGGGGAGTCGGGC 0.569 NA NA NA NA NA NA NA NA NA 14 0.00279553 0 0.0014 5008 , , NA 16139 0.0129 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 313 324.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.01 NA NA NA NA NA chr10.hg19:g.133770660_133770666dupGGGAGTC 2 5 ref NA False 49 49 PASS 1 PASS ref->het 0 NA 245,252 15,15 56,51 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 313 True GGGAGTC FNBP4 23360 __UNKNOWN__ __UNKNOWN__ 11 47788664 47788669 __UNKNOWN__ In_Frame_Del DEL GGTGGT GGTGGT - rs59413596|rs67450550|rs397711020 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:47788664_47788669delGGTGGT ENST00000263773.5 - 1 184_189 c.172_177delACCACC c.(172-177)accaccdel p.TT58del FNBP4_ENST00000534003.1_5'UTR NM_015308.2 NP_056123.2 Q8N3X1 FNBP4_HUMAN formin binding protein 4 58 NA NA NA NA nucleus (GO:0005634) p.T58_T59delTT(3) NA NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2) 44 CAGTCACCGCGGTGGTGGTGGTCGTC 0.748 NA NA NA NA NA NA NA NA NA 1722 0.34385 0.084 0.317 5008 , , NA 12964 0.4345 NA 0.4304 False NA ,,, NA NA NA 2504 0.5317 NA NA NA PASS NA NA NA NA NA 3 Deletion - In frame(3) prostate(1)|breast(1)|central_nervous_system(1) NA NA NA NA NA 129 130.94 NA 233,2043 NA 62,109,967 NA NA NA NA -2.3 0 NA dbSNP_130 3 1924,3380 NA 655,614,1383 no coding FNBP4 NM_015308.2 717,723,2350 A1A1,A1R,RR NA 36.2745,10.2373,28.4565 NA 2157,5423 NA NA NA SO:0001651 inframe_deletion 2.59 BC037404 CCDS41644.1 11q12.1 2008-02-05 ENSG00000109920 ENSG00000109920 23360 19752 protein-coding gene gene with protein product 615265 NA 10231032 Standard NM_015308 NA Approved KIAA1014 uc009ylv.3 Q8N3X1 OTTHUMG00000166533 ENST00000263773.5:c.172_177delACCACC chr11.hg19:g.47788670_47788675delGGTGGT ENSP00000263773:p.Thr58_Thr59del 2 4 ref NA False 74 74 PASS 4 PASS ref->het 0 NA 96,111 6,6 38,23 1 1 Q9H985|Q9NT81|Q9Y2L7 True hg19 CCDS41644.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FNBP4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000390237.3 PASS NA None 129 True - GGT ENST00000263773.5 TMEM25 84866 __UNKNOWN__ __UNKNOWN__ 11 118406329 118406336 __UNKNOWN__ 3'UTR DEL AGTGTGGA AGTGTGGA - rs201161451|rs141837942|rs45576832|rs201441880|rs200347751 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:118406329_118406336delAGTGTGGA ENST00000313236.5 + 0 2188_2195 TMEM25_ENST00000533102.1_Frame_Shift_Del_p.VWK378fs|TMEM25_ENST00000359862.4_3'UTR|TMEM25_ENST00000442938.2_Intron|TMEM25_ENST00000411589.2_3'UTR|TMEM25_ENST00000354064.7_3'UTR|TMEM25_ENST00000524725.1_3'UTR|TMEM25_ENST00000354284.4_Intron NM_032780.3 NP_116169.2 Q86YD3 TMM25_HUMAN transmembrane protein 25 NA NA NA NA NA extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) NA endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|stomach(1) 13 all_hematologic(175;0.0349) Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735) BRCA - Breast invasive adenocarcinoma(274;3.04e-05) ATAATTCAACAGTGTGGAAGCTTTAGGG 0.481 NA NA NA NA NA NA NA NA NA 1272 0.253994 0.1445 0.0677 5008 , , NA 20008 0.5466 NA 0.1352 False NA ,,, NA NA NA 2504 0.3548 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 635 616.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.52 AK075437 CCDS8398.1, CCDS44745.1, CCDS44746.1, CCDS44747.1, CCDS44748.1 11q23.3 2013-01-11 ENSG00000149582 ENSG00000149582 84866 "Immunoglobulin superfamily / C2-set domain containing" 25890 protein-coding gene gene with protein product 613934 NA 15254712, 12975309 Standard NM_032780 NM_001144034 NA Approved FLJ14399 uc010rye.2 Q86YD3 OTTHUMG00000166339 ENST00000313236.5:c.*1041AGTGTGGA>- chr11.hg19:g.118406329_118406336delAGTGTGGA 0 3 ref NA False 50 50 PASS 1 PASS ref->het 0 NA 612,620 14,14 51,46 1 1 A8K8J4|B0YJA6|B0YJA7|B0YJA9|G5E9U4|Q6UW89|Q86UA7|Q8NBL5|Q96KA6|Q96MW9 True hg19 CCDS8398.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM25-009 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000389266.1 PASS NA None 635 True + AGTGTGGA ENST00000313236.5 KLRC1 3821 __UNKNOWN__ __UNKNOWN__ 12 10598702 10598706 __UNKNOWN__ 3'UTR DEL AAATC AAATC - rs143299847|rs566812255 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:10598702_10598706delAAATC ENST00000359151.3 - 0 1327_1331 KLRC1_ENST00000544822.1_3'UTR|KLRC1_ENST00000347831.5_3'UTR|KLRC1_ENST00000536188.1_Intron|KLRC1_ENST00000408006.3_3'UTR NM_002259.4 NP_002250 P26715 NKG2A_HUMAN killer cell lectin-like receptor subfamily C, member 1 NA NA NA NA NA cell surface receptor signaling pathway (GO:0007166)|regulation of immune response (GO:0050776) integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888) NA NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|skin(1) 16 aaatgattaaaaatcaatgatgttt 0.332 NA NA NA NA NA NA NA NA NA 1320 0.263578 0.5257 0.1599 5008 , , NA 16688 0.2212 NA 0.1779 False NA ,,, NA NA NA 2504 0.1145 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 1013 998.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 10.22 U54782 CCDS8625.1, CCDS8626.1 12p13 2010-06-30 ENSG00000134545 ENSG00000134545 3821 "Killer cell lectin-like receptors", "CD molecules" 6374 protein-coding gene gene with protein product "NKG2-1/B activating NK receptor" 161555 NKG2 NA 9598306 Standard NM_002259 NM_002259 NA Approved NKG2-A, NKG2-B, CD159a uc001qyl.3 P26715 ENST00000359151.3:c.*448GATTT>- chr12.hg19:g.10598702_10598706delAAATC 0 5 ref NA False 53 53 PASS 1 PASS ref->het 0 NA 909,939 23,23 130,124 1 1 True hg19 CCDS8625.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KLRC1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000400115.1 PASS NA None 1013 True - AAATC ENST00000359151.3 SPTBN5 51332 __UNKNOWN__ __UNKNOWN__ 15 42185297 42185298 __UNKNOWN__ Intron INS - - CCCAT rs375528479|rs2271285|rs55835308|rs374427556 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:42185297_42185298insCCCAT ENST00000320955.6 - 3 444 RP11-23P13.6_ENST00000309874.2_RNA|RP11-23P13.6_ENST00000564432.2_RNA NM_016642.2 NP_057726.4 Q9NRC6 SPTN5_HUMAN spectrin, beta, non-erythrocytic 5 NA NA NA NA NA actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260) cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091) actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507) NA NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 62 all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173) all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908) GGTCAGCCCAGCCTCACCTGTC 0.629 NA NA NA NA NA NA NA NA NA 397 0.0792732 0.0666 0.0663 5008 , , NA 18360 0.2044 NA 0.0199 False NA ,,, NA NA NA 2504 0.0378 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 221 211.31 NA 216,3682 NA 16,184,1749 NA NA NA NA -1.9 0 NA dbSNP_129 17 167,7805 NA 4,159,3823 no intron SPTBN5 NM_016642.2 20,343,5572 A1A1,A1R,RR NA 2.0948,5.5413,3.2266 NA 383,11487 NA NA NA SO:0001627 intron_variant 1.75 AF233523 CCDS61599.1 15q21 2010-08-17 ENSG00000137877 ENSG00000137877 51332 15680 protein-coding gene gene with protein product "beta V spectrin" 605916 NA 10764729 Standard NM_016642 NM_016642 NA Approved HUSPECV, BSPECV, HUBSPECV uc001zos.4 Q9NRC6 ENST00000320955.6:c.217-38->ATGGG chr15.hg19:g.42185297_42185298insCCCAT 1 3 ref NA False 41 41 PASS 0 PASS ref->het 0 NA 187,191 5,5 29,25 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SPTBN5-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000420237.1 PASS NA None 221 True - CCCAT ENST00000320955.6 GSE1 23199 __UNKNOWN__ __UNKNOWN__ 16 85706417 85706423 __UNKNOWN__ 3'UTR DEL TTATTTC TTATTTC - rs3060245|rs375467114 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:85706417_85706423delTTATTTC ENST00000253458.7 + 0 4102_4108 GSE1_ENST00000405402.2_3'UTR|GSE1_ENST00000393243.1_3'UTR NM_014615.2 NP_055430.1 Q14687 GSE1_HUMAN Gse1 coiled-coil protein NA NA NA NA NA NA NA CTCTCCCACATTATTTCTTAATCTGAA 0.415 NA NA NA NA NA NA NA NA NA 786 0.156949 0.0378 0.2017 5008 , , NA 18032 0.2004 NA 0.2783 False NA ,,, NA NA NA 2504 0.1166 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 212 209.04 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.67 D80004 CCDS10952.1, CCDS45539.1, CCDS62007.1 16q24.1 2012-12-07 2012-12-07 2012-10-02 ENSG00000131149 ENSG00000131149 23199 28979 protein-coding gene gene with protein product "genetic suppressor element 1" NA "KIAA0182", "Gse1 coiled-coil protein homolog (mouse)" KIAA0182 NA 8724849, 8786132 Standard NM_014615 NM_014615 NA Approved uc002fix.4 Q14687 OTTHUMG00000137650 ENST00000253458.7:c.*278TTATTTC>- chr16.hg19:g.85706417_85706423delTTATTTC 0 5 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 193,194 6,6 22,21 1 1 D3DUM4|Q8IY61|Q96GA4|Q9BW09 True hg19 CCDS10952.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GSE1-002 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000325527.1 PASS NA None 212 True + TTATTTC ENST00000253458.7 ALDH3A2 224 __UNKNOWN__ __UNKNOWN__ 17 19561012 19561019 __UNKNOWN__ Intron DEL ACTGAATT ACTGAATT - rs534772670|rs372698552|rs3034928|rs3841513 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:19561012_19561019delACTGAATT ENST00000339618.4 + 5 901 ALDH3A2_ENST00000395575.2_Intron|ALDH3A2_ENST00000581518.1_Intron|ALDH3A2_ENST00000579855.1_Intron|ALDH3A2_ENST00000176643.6_Intron NM_001031806.1 NP_001026976.1 P51648 AL3A2_HUMAN aldehyde dehydrogenase 3 family, member A2 NA NA NA NA NA cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714) endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777) aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814) NA endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1) 13 all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245) TGAATATTTGACTGAATTACTGAATTAT 0.322 NA NA NA NA NA NA NA NA NA 3027 0.604433 0.3336 0.6398 5008 , , NA 18872 0.9018 NA 0.5388 False NA ,,, NA NA NA 2504 0.7065 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 290 313.33 NA , 1623,2635 NA 325,973,831 NA NA NA NA , -4.3 0 NA dbSNP_107 46 4232,3976 NA 1112,2008,984 no intron,intron ALDH3A2 NM_001031806.1,NM_000382.2 , 1437,2981,1815 A1A1,A1R,RR NA 48.4405,38.1165,46.9678 , , NA 5855,6611 NA NA NA SO:0001627 intron_variant 0.82 L47162 CCDS11210.1, CCDS32589.1 17p11.2 2010-05-07 ENSG00000072210 ENSG00000072210 224 1.2.1.3 "Aldehyde dehydrogenases" 403 protein-coding gene gene with protein product "fatty aldehyde dehydrogenase" 609523 SLS, ALDH10 NA 7894487 Standard NM_000382 NA Approved FALDH uc002gwa.1 P51648 OTTHUMG00000059471 ENST00000339618.4:c.681-39ACTGAATT>- chr17.hg19:g.19561020_19561027delACTGAATT 1 3 ref NA False 31 31 PASS 2 PASS ref->het 0 NA 285,285 7,7 51,52 1 1 Q6I9T3|Q93011|Q96J37 True hg19 CCDS32589.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ALDH3A2-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000132269.1 PASS NA None 290 True + ACTGAATT ENST00000339618.4 INTS2 57508 __UNKNOWN__ __UNKNOWN__ 17 60005240 60005254 __UNKNOWN__ 5'UTR DEL GAACCGGGACTGTAG GAACCGGGACTGTAG - rs200008356|rs375818761 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:60005240_60005254delGAACCGGGACTGTAG ENST00000251334.6 - 0 98_112 INTS2_ENST00000444766.3_Intron Q9H0H0 INT2_HUMAN integrator complex subunit 2 NA NA NA NA NA snRNA processing (GO:0016180) integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020) NA NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2) 38 CACAAAGGCAGAACCGGGACTGTAGGAACGGAAAA 0.581 NA NA NA NA NA NA NA NA NA 20 0.00399361 0 0 5008 , , NA 20705 0.0198 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 413 385.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.44 AB033113 CCDS45750.1 17q23.2 2006-04-26 2006-03-15 2006-03-15 ENSG00000108506 57508 29241 protein-coding gene gene with protein product 611346 "KIAA1287" KIAA1287 NA 16239144 Standard NM_020748 NR_026641 NA Approved INT2 uc002izn.3 Q9H0H0 ENST00000251334.6:c.-258CTACAGTCCCGGTTC>- chr17.hg19:g.60005240_60005254delGAACCGGGACTGTAG 0 3 ref NA False 166 166 PASS 1 PASS ref->het 0 NA 409,417 15,15 57,49 1 1 Q9ULD3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA INTS2-002 NOVEL basic|appris_principal|exp_conf protein_coding NA protein_coding OTTHUMT00000445369.1 PASS NA None 413 True - GAACCGGGACTGTAG ENST00000251334.6 CCT8 10694 __UNKNOWN__ __UNKNOWN__ 21 30439440 30439441 __UNKNOWN__ Intron INS - - TGGTA rs200022038 LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:30439440_30439441insTGGTA ENST00000286788.4 - 5 588 CCT8_ENST00000470450.1_Intron|CCT8_ENST00000540844.1_Intron|CCT8_ENST00000542732.1_Intron NM_006585.2 NP_006576.2 P50990 TCPQ_HUMAN chaperonin containing TCP1, subunit 8 (theta) NA NA NA NA NA 'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457) aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199) ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623) NA breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3) 14 TAAAGTAGCTTATTTTGGTAAC 0.307 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 290 276.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.81 Z37163 CCDS33528.1, CCDS68180.1 21q21.3 2011-09-02 ENSG00000156261 ENSG00000156261 10694 "Heat Shock Proteins / Chaperonins" 1623 protein-coding gene gene with protein product NA "chromosome 21 open reading frame 112" C21orf112 NA 7890169 Standard NM_006585 NA Approved Cctq, PRED71 uc002ynb.3 P50990 OTTHUMG00000044595 ENST00000286788.4:c.382-48->TACCA chr21.hg19:g.30439440_30439441insTGGTA 1 6 ref NA False 31 31 PASS 0 PASS ref->het 0 NA 251,252 11,11 23,23 1 1 A6NN54|B4DEM7|B4DQH4|Q4VBP8 True hg19 CCDS33528.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCT8-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000171822.1 PASS NA None 290 True - TGGTA ENST00000286788.4 RPL3 6122 __UNKNOWN__ __UNKNOWN__ 22 39713697 39713698 __UNKNOWN__ Intron INS - - GGAAAAT rs563150068 byFrequency LTS-007_T LTS-007_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:39713697_39713698insGGAAAAT ENST00000216146.4 - 3 370 RPL3_ENST00000465618.1_Intron|RPL3_ENST00000401609.1_Intron NM_000967.3|NM_001033853.1 NP_000958.1|NP_001029025.1 P39023 RL3_HUMAN ribosomal protein L3 NA NA NA NA NA cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083) cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)|nucleus (GO:0005634) poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735) NA breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 12 Melanoma(58;0.04) Homoharringtonine(DB04865) AATGTTTTCTAGGAAAATGCAA 0.51 NA NA NA NA NA NA NA NA NA 10 0.00199681 0 0 5008 , , NA 19645 0.0099 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 116 128.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.51 AB007166 CCDS13988.1 22q13 2011-04-06 ENSG00000100316 ENSG00000100316 6122 "L ribosomal proteins" 10332 protein-coding gene gene with protein product 604163 NA 2891103, 9582194 Standard NM_000967 NM_000967 NA Approved L3 uc003axi.3 P39023 OTTHUMG00000151079 ENST00000216146.4:c.197-63->ATTTTCC chr22.hg19:g.39713698_39713704dupGGAAAAT 2 2 ref NA False 40 40 PASS 1 PASS ref->het 0 NA 94,96 3,3 15,14 1 1 B2RDV9|Q15548|Q5I0G0 True hg19 CCDS13988.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPL3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000321196.1 PASS NA None 116 True - GGAAAAT ENST00000216146.4 MACF1 23499 __UNKNOWN__ __UNKNOWN__ 1 39568403 39568403 __UNKNOWN__ Intron DEL C C - LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:39568403delC ENST00000372915.3 + 1 307 MACF1_ENST00000484793.1_Frame_Shift_Del_p.F83fs|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000602421.1_Frame_Shift_Del_p.F83fs|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron Q9UPN3 MACF1_HUMAN microtubule-actin crosslinking factor 1 NA NA NA NA ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587) actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822) NA breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10) 203 Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204) CCTTCTGCTTCCCCCATTGCA 0.453 NA NA NA NA NA NA NA NA NA NA OREG0013391 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 419 425.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.35 NA NA AB007934 CCDS435.1 1p32-p31 2013-01-10 ENSG00000127603 ENSG00000127603 23499 "EF-hand domain containing" 13664 protein-coding gene gene with protein product "actin cross-linking factor", "620 kDa actin binding protein", "macrophin 1", "trabeculin-alpha", "actin cross-linking family protein 7" 608271 NA 7635207, 10529403 Standard NM_033044 NM_012090 NA Approved KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776 uc031pmc.1 Q9UPN3 OTTHUMG00000007754 ENST00000372915.3:c.220+18293C>- chr1.hg19:g.39568403delC 4 5 ref 886 False 99 92 PASS 5 PASS ref->het 0 NA 269,273 102,102 46,44 1 1 B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MACF1-028 NOVEL not_organism_supported|basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000392096.1 PASS NA None 419 NA True + C ENST00000372915.3 MEIS1 4211 __UNKNOWN__ __UNKNOWN__ 2 66775052 66775053 __UNKNOWN__ Intron INS - - T rs367812339 LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:66775052_66775053insT ENST00000272369.9 + 9 1345 MEIS1_ENST00000560281.2_Intron|MEIS1_ENST00000488550.1_Intron|MEIS1_ENST00000409517.1_Intron|MEIS1_ENST00000444274.2_Intron|MEIS1_ENST00000407092.2_Intron|MEIS1_ENST00000495021.2_Intron|MEIS1_ENST00000398506.2_Intron NM_002398.2 NP_002389.1 O00470 MEIS1_HUMAN Meis homeobox 1 NA NA NA NA angiogenesis (GO:0001525)|definitive hemopoiesis (GO:0060216)|lens morphogenesis in camera-type eye (GO:0002089)|megakaryocyte development (GO:0035855)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron differentiation (GO:0045665) nucleus (GO:0005634)|transcription factor complex (GO:0005667) chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705) NA breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|prostate(2)|skin(1)|urinary_tract(1) 24 TGATGCACACGTATCTTTTTTA 0.386 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 560 558.15 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.12 NA NA CCDS46309.1 2p14 2011-06-20 2007-02-15 ENSG00000143995 ENSG00000143995 4211 "Homeoboxes / TALE class" 7000 protein-coding gene gene with protein product 601739 "Meis1 (mouse) homolog", "Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)" NA 7565694 Standard NM_002398 NM_002398 NA Approved uc002sdu.3 O00470 OTTHUMG00000150714 ENST00000272369.9:c.889-22->T chr2.hg19:g.66775053_66775053dupT 2 2 ref NA False 284 170 PASS 1 PASS ref->het 0 NA 350,354 158,160 58,55 1 1 A8MV50 True hg19 CCDS46309.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MEIS1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000319725.4 PASS NA None 560 NA True + T ENST00000272369.9 Unknown 0 __UNKNOWN__ __UNKNOWN__ 2 133027837 133027840 __UNKNOWN__ IGR DEL AGGA AGGA - rs186350601|rs62166758 LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:133027837_133027840delAGGA NA ANKRD30BL (12295 upstream) : AC097532.2 (15527 downstream) NA NA NA NA NA NA agacagacagaggaagacagagac 0.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 54 37.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 8.71 NA NA NA NA NA NA NA chr2.hg19:g.133027837_133027840delAGGA 0 3 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 17,144 21,28 16,2 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 54 NA True AGGA MTERFD2 0 __UNKNOWN__ __UNKNOWN__ 2 242036552 242036556 __UNKNOWN__ Intron DEL ACTAC ACTAC - rs538426936 LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:242036552_242036556delACTAC ENST00000495694.1 - 2 556 MTERFD2_ENST00000406593.1_Intron|MTERFD2_ENST00000391980.2_Intron|MTERFD2_ENST00000464344.2_Intron Q7Z6M4 MTEF4_HUMAN NA NA NA NA rRNA processing (GO:0006364) cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739) rRNA binding (GO:0019843) NA endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3) 20 all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238) Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886) ACTTGCTGTTACTACACTAATCACG 0.415 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 734 729.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.7 NA NA NA NA NA NA NA ENST00000495694.1:c.520+2254GTAGT>- chr2.hg19:g.242036552_242036556delACTAC 0 3 ref NA False 75 75 PASS 1 PASS ref->het 0 NA 692,701 20,20 66,61 1 1 A8K6K0|Q9P0E0 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MTERFD2-016 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000323887.1 PASS NA None 734 NA True - ACTAC ENST00000495694.1 THBS2 7058 __UNKNOWN__ __UNKNOWN__ 6 169622547 169622547 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:169622547delC ENST00000366787.3 - 20 3267 c.3018delG c.(3016-3018)gggfs p.G1006fs THBS2_ENST00000488355.1_5'UTR|XXyac-YX65C7_A.2_ENST00000444188.1_RNA NM_003247.2 NP_003238.2 P35442 TSP2_HUMAN thrombospondin 2 1006 TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}. NA NA NA cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965) basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091) calcium ion binding (GO:0005509)|heparin binding (GO:0008201) NA NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1) 111 Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247) OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379) AGTCCACAGACCCAAACTCGT 0.512 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(91;219 1934 18562 44706) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 319 308.88 NA NA NA 91 89 90 NA NA NA NA 6 NA NA NA NA NA NA 169622547 2203 4300 6503 SO:0001589 frameshift_variant 1.15 NA NA CCDS34574.1 6q27 2008-07-28 ENSG00000186340 ENSG00000186340 7058 11786 protein-coding gene gene with protein product 188061 NA 18455130 Standard NM_003247 NM_003247 NA Approved TSP2 uc003qwt.3 P35442 OTTHUMG00000045408 ENST00000366787.3:c.3018delG chr6.hg19:g.169622547delC ENSP00000355751:p.Gly1006fs 2 3 ref NA False 178 133 PASS 3 PASS ref->het 0 NA 200,205 90,91 27,24 1 1 A6H8N1|A7E232|Q5RI52 True hg19 CCDS34574.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA THBS2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000105439.1 PASS NA None 319 NA True - C ENST00000366787.3 PDE1C 5137 __UNKNOWN__ __UNKNOWN__ 7 31904631 31904632 __UNKNOWN__ Frame_Shift_Ins INS - - T LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:31904631_31904632insT ENST00000396193.1 - 8 1447_1448 c.854_855insA c.(853-855)aatfs p.N285fs PDE1C_ENST00000396191.1_Frame_Shift_Ins_p.N225fs|PDE1C_ENST00000396182.2_Frame_Shift_Ins_p.N225fs|PDE1C_ENST00000321453.7_Frame_Shift_Ins_p.N225fs|PDE1C_ENST00000396184.3_Frame_Shift_Ins_p.N225fs NM_001191058.1 NP_001177987.1 Q14123 PDE1C_HUMAN phosphodiesterase 1C, calmodulin-dependent 70kDa 225 Catalytic. {ECO:0000250}. NA NA NA activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165) cytosol (GO:0005829) calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872) NA NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 81 GBM - Glioblastoma multiforme(11;0.216) Caffeine(DB00201) TATGGTAAGGATTTTTGTGCTT 0.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 281 275.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 NA NA U40371 CCDS5437.1, CCDS55099.1, CCDS55100.1 7p15.1-p14.3 2008-05-15 2002-08-29 ENSG00000154678 ENSG00000154678 5137 3.1.4.17 "Phosphodiesterases" 8776 protein-coding gene gene with protein product 602987 "phosphodiesterase 1C, calmodulin-dependent (70kD)" NA 8557689 Standard XM_005249769 NA Approved Hcam3 uc003tco.2 Q14123 OTTHUMG00000023836 ENST00000396193.1:c.855dupA chr7.hg19:g.31904636_31904636dupT ENSP00000379496:p.Asn285fs 6 6 ref NA False 51 51 PASS 5 PASS ref->het 0 NA 215,217 45,45 23,23 1 1 B3KPC6|E9PE92|Q14124|Q8NB10 True hg19 CCDS55100.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PDE1C-001 NOVEL basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000215075.1 PASS NA None 281 NA True - T ENST00000396193.1 CTSB 1508 __UNKNOWN__ __UNKNOWN__ 8 11705380 11705381 __UNKNOWN__ Intron INS - - AGCCCCAGCTGGGCGAGGC rs145929462|rs149445749|rs5030657 byFrequency LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:11705380_11705381insAGCCCCAGCTGGGCGAGGC ENST00000353047.6 - 7 786 CTSB_ENST00000434271.1_Intron|CTSB_ENST00000345125.3_Intron|CTSB_ENST00000530640.2_Intron|CTSB_ENST00000415599.2_Intron|CTSB_ENST00000453527.2_Intron|CTSB_ENST00000533455.1_Intron|CTSB_ENST00000534510.1_Intron|CTSB_ENST00000531089.1_Intron NM_001908.3 NP_001899.1 P07858 CATB_HUMAN cathepsin B NA NA NA NA cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224) endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471) collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394) NA breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1) 16 all_epithelial(15;0.205) STAD - Stomach adenocarcinoma(15;0.00546) COAD - Colon adenocarcinoma(149;0.184) CCCCACGGAGAAGACCTGGGGC 0.653 NA NA NA NA NA NA NA NA NA NA 1642 0.327875 0.3011 0.3343 5008 , , NA 18604 0.2708 NA 0.3847 False NA ,,, NA NA NA 2504 0.3599 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 54 58.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.5 NA NA M14221 CCDS5986.1 8p23.1 2012-10-02 ENSG00000164733 ENSG00000164733 1508 3.4.22.1 "Cathepsins" 2527 protein-coding gene gene with protein product 116810 NA 8112600, 3463996 Standard NM_147780 XM_006716244 NA Approved uc003wuq.3 P07858 OTTHUMG00000090799 ENST00000353047.6:c.533-49->GCCTCGCCCAGCTGGGGCT chr8.hg19:g.11705380_11705381insAGCCCCAGCTGGGCGAGGC 1 3 ref NA False 49 49 PASS 0 PASS ref->het 0 NA 13,14 16,16 26,25 1 1 B3KQR5|B3KRR5|Q503A6|Q96D87 True hg19 CCDS5986.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CTSB-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000207586.3 PASS NA None 54 NA True - AGCCCCAGCTGGGCGAGGC ENST00000353047.6 ZFP36L1 677 __UNKNOWN__ __UNKNOWN__ 14 69254857 69254861 __UNKNOWN__ 3'UTR DEL TAAAA TAAAA - LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:69254857_69254861delTAAAA ENST00000555997.1 - 0 2609_2613 ZFP36L1_ENST00000439696.2_3'UTR Q07352 TISB_HUMAN ZFP36 ring finger protein-like 1 NA NA NA NA gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570) cytosol (GO:0005829)|nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1) 21 all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401) ttcatttttttaaaataaaataaCC 0.234 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 56 71.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA X79066 CCDS9791.1 14q22-q24 2012-11-27 2012-11-27 2001-11-23 ENSG00000185650 677 "RING-type (C3HC4) zinc fingers" 1107 protein-coding gene gene with protein product 601064 "zinc finger protein, C3H type, 36-like 1", "zinc finger protein 36, C3H type-like 1" BRF1 NA 8024689 Standard NM_004926 NA Approved RNF162B, Berg36, ERF1, TIS11B, cMG1 uc021rve.1 Q07352 ENST00000555997.1:c.*2348TTTTA>- chr14.hg19:g.69254862_69254866delTAAAA 1 8 ref NA False 46 46 PASS 2 PASS ref->het 0 NA 30,31 14,14 19,19 2 2 Q13851 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZFP36L1-003 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000413226.1 PASS NA None 56 NA True - TAAAA ENST00000555997.1 TMOD3 29766 __UNKNOWN__ __UNKNOWN__ 15 52203196 52203197 __UNKNOWN__ 3'UTR INS - - C rs563314264|rs11446468|rs75379544 byFrequency LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:52203196_52203197insC ENST00000308580.7 + 0 3529_3530 NM_014547.4 NP_055362.1 Q9NYL9 TMOD3_HUMAN tropomodulin 3 (ubiquitous) NA NA NA NA striated muscle thin filament (GO:0005865) tropomyosin binding (GO:0005523) NA breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|stomach(1) 14 all cancers(107;0.00194) tctttttttTTCCCCGCATATG 0.475 NA NA NA NA NA NA NA NA NA NA CCCC|CCCC|CCCCC|insertion 1627 0.32488 0.2829 0.3746 5008 , , NA 17659 0.2768 NA 0.4155 False NA ,,, NA NA NA 2504 0.3027 NA NA NA Colon(122;1837 2251 18387 22826) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 61 61.95 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.13 NA NA AF177171 CCDS10145.1 15q21.1-q21.2 2008-05-14 ENSG00000138594 ENSG00000138594 29766 11873 protein-coding gene gene with protein product 605112 NA 10662549 Standard NM_014547 NA Approved UTMOD uc002abn.3 Q9NYL9 OTTHUMG00000131803 ENST00000308580.7:c.*2190->C chr15.hg19:g.52203200_52203200dupC 5 10 ref NA False 30 30 PASS 4 PASS ref->het 0 NA 8,10 38,40 14,13 2 2 B2R6G7|Q9NT43|Q9NZR0 True hg19 CCDS10145.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMOD3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254740.3 PASS NA None 61 NA True + C ENST00000308580.7 C17orf100 388327 __UNKNOWN__ __UNKNOWN__ 17 6556194 6556195 __UNKNOWN__ 3'UTR INS - - AGAAG rs150414123|rs59663818|rs144808411 byFrequency LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:6556194_6556195insAGAAG ENST00000391428.2 + 0 1224_1225 NM_001105520.1 NP_001098990.1 A8MU93 CQ100_HUMAN chromosome 17 open reading frame 100 NA NA NA NA NA NA AAAATAATCTTAGAAAGTGAGA 0.421 NA NA NA NA NA NA NA NA NA NA 1745 0.348442 0.5492 0.2435 5008 , , NA 18807 0.4256 NA 0.169 False NA ,,, NA NA NA 2504 0.2566 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 126 123.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.4 NA NA BC028174, BC038956, BC052606 CCDS73952.1 17p13.2 2014-04-10 ENSG00000212734 ENSG00000256806 388327 34494 protein-coding gene gene with protein product NA NA Standard NM_001105520 NM_001105520 NA Approved LOC388327 uc010clp.1 A8MU93 OTTHUMG00000188340 ENST00000391428.2:c.*467->AGAAG chr17.hg19:g.6556194_6556195insAGAAG 1 4 ref NA False 30 30 PASS 0 PASS ref->het 0 NA 101,104 5,5 15,13 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C17orf100-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000255575.2 PASS NA None 126 NA True + AGAAG ENST00000391428.2 C17orf66 0 __UNKNOWN__ __UNKNOWN__ 17 34185536 34185536 __UNKNOWN__ Intron DEL G G - rs398078973|rs35283303 byFrequency LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:34185536delG ENST00000311880.2 - 10 1088 C17orf66_ENST00000592980.1_Intron NM_152781.2 NP_689994.2 A2RTY3 HEAT9_HUMAN NA NA NA NA hematopoietic progenitor cell differentiation (GO:0002244) p.?(1) NA breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4) 38 Ovarian(249;0.17) UCEC - Uterine corpus endometrioid carcinoma (308;0.0184) GTGCCTATGAGGGGGCAGGGT 0.572 NA NA NA NA NA NA NA NA NA NA GGGG|GGGGG|GGGG|insertion 1523 0.304113 0.4463 0.2219 5008 , , NA 20786 0.3224 NA 0.1581 False NA ,,, NA NA NA 2504 0.3016 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 1 Unknown(1) stomach(1) NA NA NA NA NA 70 78.64 NA NA 1824,2440 NA 403,1018,711 39 36 37 NA NA 0.6 0 17 dbSNP_126 49 1465,6789 NA 122,1221,2784 no intron C17orf66 NM_152781.2 NA 525,2239,3495 A1A1,A1R,RR NA 17.749,42.7767,26.2742 NA NA 34185536 3289,9229 2197 4296 6493 SO:0001627 intron_variant 0.04 NA NA NA NA NA NA NA ENST00000311880.2:c.940-7C>- chr17.hg19:g.34185536delG 4 6 ref NA False 40 40 PASS 5 PASS ref->het 0 NA 13,13 51,51 6,7 1 1 B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46 True hg19 CCDS11299.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C17orf66-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256487.1 PASS NA None 70 NA True - G ENST00000311880.2 PRND 23627 __UNKNOWN__ __UNKNOWN__ 20 4706655 4706662 __UNKNOWN__ 3'UTR DEL TGCCATCA TGCCATCA - rs372297738|rs72019362|rs201063374|rs200406302 LTS-008_T LTS-008_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:4706655_4706662delTGCCATCA ENST00000305817.2 + 0 1529_1536 NM_012409.2 NP_036541.2 Q9UKY0 PRND_HUMAN prion protein 2 (dublet) NA NA NA NA protein homooligomerization (GO:0051260) anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886) NA breast(3)|endometrium(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1) 13 tacaggtgtgtgccatcatgcctgacta 0.529 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 24 22.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA AF106918 CCDS13081.1 20p13 2013-09-19 ENSG00000171864 ENSG00000171864 23627 15748 protein-coding gene gene with protein product "prion-like protein doppel" 604263 NA 10525406, 10577243 Standard NM_012409 NM_012409 NA Approved DPL, dJ1068H6.4, DOPPEL, PrPLP uc002wkz.3 Q9UKY0 OTTHUMG00000031789 ENST00000305817.2:c.*934TGCCATCA>- chr20.hg19:g.4706655_4706662delTGCCATCA 0 2 ref NA False 34 34 PASS 1 PASS ref->hom 0 NA 0,0 19,20 5,4 1 1 A7U7M5|Q9H311|Q9H312|Q9NTM4 True hg19 CCDS13081.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PRND-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000077827.2 PASS NA None 24 NA True + TGCCATCA ENST00000305817.2 GLYR1 84656 __UNKNOWN__ __UNKNOWN__ 16 4854294 4854302 __UNKNOWN__ 3'UTR DEL AGTGGCTCT AGTGGCTCT - rs200482180 byFrequency LTS-009_T LTS-009_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:4854294_4854302delAGTGGCTCT ENST00000321919.9 - 0 2673_2681 GLYR1_ENST00000436648.5_3'UTR|GLYR1_ENST00000381983.3_3'UTR NM_032569.3 NP_115958 Q49A26 GLYR1_HUMAN glyoxylate reductase 1 homolog (Arabidopsis) NA NA NA NA pentose-phosphate shunt (GO:0006098) cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634) DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616) NA NA endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|skin(1)|urinary_tract(1) 19 NA CCGAGGTAAGAGTGGCTCTTCAGAGCCAG 0.622 NA NA NA NA NA NA NA NA NA NA NA NA NA 81 0.0161741 0 0.0173 5008 , , NA 15974 0 NA 0.0249 False NA ,,, NA NA NA 2504 0.045 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 235 222.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.04 NA NA AF244907 CCDS10524.1 16p13.3 2010-02-17 ENSG00000140632 ENSG00000140632 84656 NA 24434 protein-coding gene gene with protein product "nuclear protein 60kDa" 610660 NA 16352664 Standard NM_032569 NM_032569 NA Approved BM045, HIBDL, NP60, N-PAC uc002cxx.4 Q49A26 OTTHUMG00000129530 ENST00000321919.9:c.*943AGAGCCACT>- chr16.hg19:g.4854294_4854302delAGTGGCTCT 0 3 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 226,234 5,5 24,22 1 1 B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2 True hg19 CCDS10524.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GLYR1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000251717.2 PASS NA None 235 True - AGTGGCTCT ENST00000321919.9 RP11-64J4.2 0 __UNKNOWN__ __UNKNOWN__ 17 3213869 3213870 __UNKNOWN__ RNA DEL AT AT - LTS-009_T LTS-009_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:3213869_3213870delAT ENST00000573491.1 - 0 359 NA NA NA NA NA NA NA NA GAGCCATTTCATATCCAACGAC 0.55 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 156 148.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2.11 NA NA NA NA NA NA NA NA ENST00000573491.1: chr17.hg19:g.3213871_3213872delAT 1 3 ref NA False 36 36 PASS 2 PASS ref->het 0 NA 65,67 73,75 15,12 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-64J4.2-001 KNOWN basic sense_overlapping NA sense_overlapping OTTHUMT00000438371.1 PASS NA None 156 True - AT ENST00000573491.1 NFATC1 4772 __UNKNOWN__ __UNKNOWN__ 18 77160367 77160368 __UNKNOWN__ Intron INS - - GCCCCG rs201551280 LTS-009_T LTS-009_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:77160367_77160368insGCCCCG ENST00000587635.1 + 1 221 NFATC1_ENST00000329101.4_5'UTR|NFATC1_ENST00000427363.2_Intron|NFATC1_ENST00000545796.1_5'UTR|NFATC1_ENST00000253506.5_Intron|NFATC1_ENST00000318065.5_5'UTR|NFATC1_ENST00000397790.2_Intron|NFATC1_ENST00000542384.1_Intron|NFATC1_ENST00000591814.1_Intron|NFATC1_ENST00000592223.1_5'UTR O95644 NFAC1_HUMAN nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1 NA NA NA NA calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366) cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667) FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212) NA NA NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1) 40 Esophageal squamous(42;0.0157)|Melanoma(33;0.144) NA OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257) Pseudoephedrine(DB00852) ccccggctcccgccccggcccc 0.767 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(151;1210 2593 28719 45011) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 165 173.64 NA ,,,, 833,1213 NA 334,165,524 NA NA NA NA ,,,, NA 0 NA 3 2026,2300 NA 811,404,948 no intron,utr-5,intron,utr-5,intron NFATC1 NM_172390.1,NM_172389.1,NM_172388.1,NM_172387.1,NM_006162.3 ,,,, 1145,569,1472 A1A1,A1R,RR NA 46.8331,40.7136,44.8682 ,,,, ,,,, NA 2859,3513 NA NA NA SO:0001627 intron_variant 5.4 NA NA U08015 CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1 18q23 2009-11-24 ENSG00000131196 ENSG00000131196 4772 NA "Nuclear factor of activated T-cells" 7775 protein-coding gene gene with protein product 600489 NA 8202141 Standard NM_172390 NM_001278669 NA Approved NF-ATC, NFATc, NFAT2 uc002lnf.3 O95644 OTTHUMG00000132897 ENST00000587635.1:c.127+4016->GCCCCG chr18.hg19:g.77160368_77160373dupGCCCCG 3 7 ref NA False 69 69 PASS 2 PASS ref->het 0 NA 114,127 4,4 63,51 2 2 B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NFATC1-005 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000450505.1 PASS NA None 165 True + GCCCCG ENST00000587635.1 COL6A2 1292 __UNKNOWN__ __UNKNOWN__ 21 47546390 47546391 __UNKNOWN__ Intron INS - - GGCCC rs371824276|rs370256484|rs200215200|rs138363207 byFrequency LTS-009_T LTS-009_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:47546390_47546391insGGCCC ENST00000300527.4 + 27 2526 COL6A2_ENST00000409416.1_Intron|COL6A2_ENST00000357838.4_Intron|COL6A2_ENST00000397763.1_Intron|COL6A2_ENST00000310645.5_Intron NM_001849.3 NP_001840.3 P12110 CO6A2_HUMAN collagen, type VI, alpha 2 NA NA NA NA axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749) collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982) NA NA NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1) 43 Breast(49;0.245) NA Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649) GACCCTGGCCTGGCCCGGCCTC 0.649 NA NA NA NA NA NA NA NA NA NA NA NA NA 196 0.0391374 0.0658 0.0014 5008 , , NA 5011 0.006 NA 0 False NA ,,, NA NA NA 2504 0.1043 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 308 289.49 NA ,, 0,91,243,3930 NA 0,0,0,0,0,9,82,10,214,1817 NA NA NA NA ,, -2.5 0 NA dbSNP_134 72 6,717,6,7523 NA 0,1,0,5,25,0,666,0,6,3423 no intron,intron,intron COL6A2 NM_058175.2,NM_058174.2,NM_001849.3 ,, 0,1,0,5,25,9,748,10,220,5240 A1A1,A1A2,A1A3,A1R,A2A2,A2A3,A2R,A3A3,A3R,RR NA 8.8342,7.833,8.4931 ,, ,, NA 6,808,249,11453 NA NA NA SO:0001627 intron_variant 0.68 NA NA M20777 CCDS13728.1, CCDS13729.1, CCDS13730.1 21q22.3 2014-09-17 ENSG00000142173 ENSG00000142173 1292 NA "Collagens" 2212 protein-coding gene gene with protein product 120240 NA Standard NM_001849 NA Approved uc002zia.1 P12110 OTTHUMG00000090489 ENST00000300527.4:c.2423-26->GGCCC chr21.hg19:g.47546391_47546395dupGGCCC 2 2 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 261,270 7,7 41,33 1 1 Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8 True hg19 CCDS13728.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COL6A2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000206971.1 PASS NA None 308 True + GGCCC ENST00000300527.4 TNRC6B 23112 __UNKNOWN__ __UNKNOWN__ 22 40719444 40719452 __UNKNOWN__ 3'UTR DEL GGAATATGA GGAATATGA - LTS-009_T LTS-009_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:40719444_40719452delGGAATATGA ENST00000301923.9 + 0 3591_3599 TNRC6B_ENST00000335727.9_3'UTR|TNRC6B_ENST00000454349.2_3'UTR NM_001024843.1 NP_001020014.1 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B NA NA NA NA epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417) cytosol (GO:0005829) nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822) NA NA breast(1) 1 NA TTTTTCGTTTGGAATATGAATCCAAAAAG 0.34 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 179 180.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.02 NA NA AB029016 CCDS46712.1, CCDS46713.1, CCDS54533.1 22q13 2006-08-22 ENSG00000100354 ENSG00000100354 23112 NA "Trinucleotide (CAG) repeat containing" 29190 protein-coding gene gene with protein product 610740 NA Standard NM_015088 NA Approved KIAA1093 uc011aor.2 Q9UPQ9 OTTHUMG00000151114 ENST00000301923.9:c.*207GGAATATGA>- chr22.hg19:g.40719444_40719452delGGAATATGA 0 3 ref NA False 50 50 PASS 1 PASS ref->het 0 NA 151,154 29,29 20,20 1 1 B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2 True hg19 CCDS46712.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNRC6B-201 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000321393.1 PASS NA None 179 True + GGAATATGA ENST00000301923.9 PLXNB2 23654 __UNKNOWN__ __UNKNOWN__ 22 50719614 50719656 __UNKNOWN__ Splice_Site DEL TCCTCCTGCAAGGCACAGCGGGCCTCCTAGGTTCTGCCGGGGC TCCTCCTGCAAGGCACAGCGGGCCTCCTAGGTTCTGCCGGGGC - rs185630451|rs200856270|rs192431671|rs560405939 byFrequency LTS-009_T LTS-009_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:50719614_50719656delTCCTCCTGCAAGGCACAGCGGGCCTCCTAGGTTCTGCCGGGGC ENST00000449103.1 - 23 3803_3807 c.3663_3667delGCCCCGGCAGAACCTAGGAGGCCCGCTGTGCCTTGCAGGAGGA c.(3661-3669)tggccccgg>tggg p.PR1222fs PLXNB2_ENST00000359337.4_Splice_Site_p.PR1222fs O15031 PLXB2_HUMAN plexin B2 1222 NA NA NA brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526) cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622) GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154) NA NA breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2) 66 all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) NA BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) TGCTGGCTCTTCCTCCTGCAAGGCACAGCGGGCCTCCTAGGTTCTGCCGGGGCTGGCCGCTCA 0.667 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 147 137.91 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 1.06 NA NA CCDS43035.1 22q13.33 2008-06-12 ENSG00000196576 ENSG00000196576 23654 NA "Plexins" 9104 protein-coding gene gene with protein product 604293 NA 10520995, 12183458 Standard NM_012401 NM_012401 NA Approved MM1, KIAA0315, PLEXB2 uc003bkv.4 O15031 OTTHUMG00000150219 ENST00000449103.1:c.3663-1GCCCCGGCAGAACCTAGGAGGCCCGCTGTGCCTTGCAGGAGGA>- chr22.hg19:g.50719614_50719656delTCCTCCTGCAAGGCACAGCGGGCCTCCTAGGTTCTGCCGGGGC 0 4 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 72,79 10,10 75,70 1 1 A6QRH0|Q7KZU3|Q9BSU7 True hg19 CCDS43035.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PLXNB2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000316874.3 PASS NA None 147 Frame_Shift_Del True - TCCTCCTGCAAGGCACAGCGGGCCTCCTAGGTTCTGCCGGGGC ENST00000449103.1 SRPK3 26576 __UNKNOWN__ __UNKNOWN__ X 153046686 153046699 __UNKNOWN__ Frame_Shift_Del DEL CGGGCCCGAGTCCT CGGGCCCGAGTCCT - rs113575208|rs61756676 LTS-009_T LTS-009_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:153046686_153046699delCGGGCCCGAGTCCT ENST00000489426.1 + 8 2642_2655 c.276_289delCGGGCCCGAGTCCT c.(274-291)tgcgggcccgagtcctcgfs p.GPESS93fs SRPK3_ENST00000370104.1_Frame_Shift_Del_p.GPESS26fs|SRPK3_ENST00000393786.3_Frame_Shift_Del_p.GPESS26fs|SRPK3_ENST00000370100.1_Intron|SRPK3_ENST00000370108.3_Frame_Shift_Del_p.GPESS26fs|SRPK3_ENST00000370101.3_Frame_Shift_Del_p.GPESS26fs Q9UPE1 SRPK3_HUMAN SRSF protein kinase 3 0 Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}. NA NA NA cell differentiation (GO:0030154)|muscle tissue development (GO:0060537)|skeletal muscle tissue development (GO:0007519) ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674) NA NA breast(1)|central_nervous_system(1)|endometrium(2)|lung(4)|ovary(2)|pancreas(2)|urinary_tract(1) 13 all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05) NA AGGCCTCCTGCGGGCCCGAGTCCTCGGGCTCCGA 0.678 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(167;766 3400 32156) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 156 144.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.37 NA NA AF027406 CCDS35441.1, CCDS55537.1, CCDS55538.1 Xq28 2010-06-23 2010-06-23 2006-08-17 ENSG00000184343 ENSG00000184343 26576 NA 11402 protein-coding gene gene with protein product NA "serine/threonine kinase 23", "SFRS protein kinase 3" STK23 NA 16140986 Standard NM_014370 NM_014370 NA Approved MSSK1 uc004fil.3 Q9UPE1 OTTHUMG00000024207 ENST00000489426.1:c.276_289delCGGGCCCGAGTCCT chrX.hg19:g.153046686_153046699delCGGGCCCGAGTCCT ENSP00000420058:p.Gly93fs 0 4 ref NA False 91 91 PASS 1 PASS ref->het 0 NA 105,106 41,43 27,24 1 1 Q13583|Q4F970|Q562F5|Q9UM62 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SRPK3-007 PUTATIVE basic|appris_candidate_longest|exp_conf protein_coding NA protein_coding OTTHUMT00000354502.1 PASS NA None 156 True + CGGGCCCGAGTCCT ENST00000489426.1 AK2 204 __UNKNOWN__ __UNKNOWN__ 1 33475576 33475577 __UNKNOWN__ 3'UTR DEL AG AG - rs72465520 LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:33475576_33475577delAG ENST00000373449.2 - 0 1593_1594 RP1-117O3.2_ENST00000427524.1_RNA NM_001199199.1|NM_013411.4 NP_001186128.1|NP_037543.1 adenylate kinase 2 NA NA NA NA NA kidney(1)|large_intestine(2)|lung(4)|skin(1) 8 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837) GCATTTGGTCAGTTAAGAAAGG 0.356 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 55 65.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 U84371 CCDS373.1, CCDS374.1 1p35.1 2014-09-17 ENSG00000004455 ENSG00000004455 204 2.7.4.3 "Adenylate kinases" 362 protein-coding gene gene with protein product 103020 NA 8843353, 6961883 Standard NM_001625 NM_013411 NA Approved uc001bwp.2 P54819 OTTHUMG00000004131 ENST00000373449.2:c.*854CT>- chr1.hg19:g.33475576_33475577delAG 0 2 ref NA False 40 40 PASS 1 PASS ref->het 0 NA 42,44 9,10 4,4 1 1 True hg19 CCDS373.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AK2-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000011884.1 PASS NA None 55 True - AG ENST00000373449.2 TNN 63923 __UNKNOWN__ __UNKNOWN__ 1 175092993 175092996 __UNKNOWN__ Intron DEL GAGT GAGT - rs55884210|rs63552764|rs398103378|rs398053548|rs10568684 byFrequency LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:175092993_175092996delGAGT ENST00000239462.4 + 12 3027 NM_022093.1 NP_071376.1 Q9UQP3 TENN_HUMAN tenascin N NA NA NA NA axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160) cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578) NA NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3) 156 Breast(1374;0.000962) KIRC - Kidney renal clear cell carcinoma(1967;0.00198) AGTATAGAGGGAGTGAGTGCTGGT 0.495 NA NA NA NA NA NA NA 4020 0.802716 0.8427 0.8473 5008 , , NA 21450 0.744 NA 0.833 False NA ,,, NA NA NA 2504 0.7464 NA NA NA PASS NA NA NA 0 NA 30 36.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AK127044 CCDS30943.1 1q23-q24 2013-02-11 ENSG00000120332 ENSG00000120332 63923 "Fibrinogen C domain containing", "Fibronectin type III domain containing" 22942 protein-coding gene gene with protein product NA NA Standard XM_040527 NM_022093 NA Approved uc001gkl.1 Q9UQP3 OTTHUMG00000034882 ENST00000239462.4:c.2914+194GAGT>- chr1.hg19:g.175092997_175093000delGAGT 1 4 ref NA False 30 30 PASS 2 PASS ref->het 0 NA 2,2 25,27 4,4 1 1 B9EGP3|Q5R360 True hg19 CCDS30943.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNN-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000084422.1 PASS NA None 30 True + GAGT ENST00000239462.4 ASPM 259266 __UNKNOWN__ __UNKNOWN__ 1 197097892 197097895 __UNKNOWN__ Intron DEL AAAT AAAT - rs200153543|rs202177335|rs150344996 byFrequency LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:197097892_197097895delAAAT ENST00000367409.4 - 10 3017 ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron NM_018136.4 NP_060606.3 Q8IZT6 ASPM_HUMAN asp (abnormal spindle) homolog, microcephaly associated (Drosophila) NA NA NA NA developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283) cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922) NA breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3) 165 tataaaaataaaataatataaaaa 0.201 NA NA NA NA NA NA NA 1073 0.214257 0.0431 0.2262 5008 , , NA 14423 0.1637 NA 0.4115 False NA ,,, NA NA NA 2504 0.2863 NA NA NA PASS NA NA NA 0 NA 20 31.31 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.01 AY367065 CCDS1389.1, CCDS55672.1 1q31 2008-02-05 2006-09-12 ENSG00000066279 ENSG00000066279 259266 19048 protein-coding gene gene with protein product 605481 "microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)" MCPH5 NA 11078481 Standard NM_018136 NM_018136 NA Approved Calmbp1, ASP, FLJ10517, FLJ10549 uc001gtu.3 Q8IZT6 OTTHUMG00000036277 ENST00000367409.4:c.2761-97ATTT>- chr1.hg19:g.197097892_197097895delAAAT 0 9 ref NA False 35 35 PASS 1 PASS ref->hom 0 NA 0,0 13,13 4,4 1 1 Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6 True hg19 CCDS1389.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ASPM-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000088256.1 PASS NA None 20 True - AAAT ENST00000367409.4 METAP1 23173 __UNKNOWN__ __UNKNOWN__ 4 99964663 99964664 __UNKNOWN__ Intron INS - - T LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:99964663_99964664insT ENST00000296411.6 + 7 789 METAP1_ENST00000544031.1_Intron NM_015143.2 NP_055958.2 P53582 MAP11_HUMAN methionyl aminopeptidase 1 NA NA NA NA N-terminal protein amino acid modification (GO:0031365)|peptidyl-methionine modification (GO:0018206)|phototransduction, visible light (GO:0007603)|platelet aggregation (GO:0070527)|protein initiator methionine removal (GO:0070084)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of translation (GO:0006417)|rhodopsin mediated signaling pathway (GO:0016056) cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic ribosome (GO:0022626) aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metalloaminopeptidase activity (GO:0070006)|metalloexopeptidase activity (GO:0008235) NA endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1) 17 OV - Ovarian serous cystadenocarcinoma(123;3.12e-07) TTAAAATTCAGTATCACTAACT 0.376 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 61 72.61 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 D42084 CCDS47110.1 4q23 2010-08-20 ENSG00000164024 ENSG00000164024 23173 3.4.11.18 15789 protein-coding gene gene with protein product "Peptidase M" 610151 NA 7788527, 12144506 Standard NM_015143 NM_015143 NA Approved KIAA0094, MetAP1A, MAP1A uc003huf.4 P53582 OTTHUMG00000161231 ENST00000296411.6:c.655+125->T chr4.hg19:g.99964664_99964664dupT 2 2 ref NA False 108 93 PASS 1 PASS ref->het 0 NA 25,25 28,28 6,6 1 1 B4E2E6 True hg19 CCDS47110.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA METAP1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000364237.1 PASS NA None 61 True + T ENST00000296411.6 RPL37 6167 __UNKNOWN__ __UNKNOWN__ 5 40828553 40828556 __UNKNOWN__ 3'UTR DEL ATGA ATGA - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:40828553_40828556delATGA ENST00000274242.5 - 0 4493_4496 NM_000997.4 NP_000988.1 P61927 RL37_HUMAN ribosomal protein L37 NA NA NA NA cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083) cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625) metal ion binding (GO:0046872)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735) NA lung(3)|ovary(1) 4 Breast(839;0.238) tacttgcttcatgaatgaaGGGCA 0.373 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Colon(188;1411 2035 4978 19588 31462) PASS NA NA NA 0 NA 514 502.84 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.72 L11567 CCDS3934.1 5p13.1 2013-09-23 ENSG00000145592 ENSG00000145592 6167 "L ribosomal proteins" 10347 protein-coding gene gene with protein product "60S ribosomal protein L37a" 604181 NA 7545944, 9582194 Standard NM_000997 NM_000997 NA Approved L37 uc003jme.1 P61927 OTTHUMG00000094774 ENST00000274242.5:c.*4053TCAT>- chr5.hg19:g.40828557_40828560delATGA 1 2 ref NA False 116 116 PASS 2 PASS ref->het 0 NA 400,406 74,75 51,50 1 1 B2R4H2|P02403|Q6IBB4|Q99883 True hg19 CCDS3934.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPL37-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000211583.2 PASS NA None 514 True - ATGA ENST00000274242.5 RPL37 6167 __UNKNOWN__ __UNKNOWN__ 5 40829042 40829060 __UNKNOWN__ 3'UTR DEL CTTTGAGACTCTAAATTAT CTTTGAGACTCTAAATTAT - rs568326591 LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:40829042_40829060delCTTTGAGACTCTAAATTAT ENST00000274242.5 - 0 3989_4007 NM_000997.4 NP_000988.1 P61927 RL37_HUMAN ribosomal protein L37 NA NA NA NA cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083) cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625) metal ion binding (GO:0046872)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735) NA lung(3)|ovary(1) 4 Breast(839;0.238) CCAAATCTTACTTTGAGACTCTAAATTATCTTTTTGTTT 0.393 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Colon(188;1411 2035 4978 19588 31462) PASS NA NA NA 0 NA 286 300.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.09 L11567 CCDS3934.1 5p13.1 2013-09-23 ENSG00000145592 ENSG00000145592 6167 "L ribosomal proteins" 10347 protein-coding gene gene with protein product "60S ribosomal protein L37a" 604181 NA 7545944, 9582194 Standard NM_000997 NM_000997 NA Approved L37 uc003jme.1 P61927 OTTHUMG00000094774 ENST00000274242.5:c.*3564ATAATTTAGAGTCTCAAAG>- chr5.hg19:g.40829042_40829060delCTTTGAGACTCTAAATTAT 0 6 ref NA False 37 37 PASS 1 PASS ref->het 0 NA 277,278 36,37 43,45 1 1 B2R4H2|P02403|Q6IBB4|Q99883 True hg19 CCDS3934.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPL37-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000211583.2 PASS NA None 286 True - CTTTGAGACTCTAAATTAT ENST00000274242.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ 5 95170821 95170827 __UNKNOWN__ IGR DEL CCCAGGA CCCAGGA - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:95170821_95170827delCCCAGGA NA GLRX (12112 upstream) : AC008592.4 (819 downstream) NA NA NA NA NA NA AGCGCGGCGGCCCAGGACCCCGGCCCA 0.652 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 12 16.93 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.43 NA NA NA NA NA chr5.hg19:g.95170821_95170827delCCCAGGA 0 4 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 6,6 6,6 1,1 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 12 True CCCAGGA SLC44A4 80736 __UNKNOWN__ __UNKNOWN__ 6 31833072 31833073 __UNKNOWN__ Intron INS - - G rs199617182|rs546801718|rs188972261 byFrequency LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:31833072_31833073insG ENST00000229729.6 - 17 1781 SLC44A4_ENST00000544672.1_Intron|SLC44A4_ENST00000375562.4_Intron NM_025257.2 NP_079533.2 Q53GD3 CTL4_HUMAN solute carrier family 44, member 4 NA NA NA NA acetylcholine biosynthetic process (GO:0008292)|acetylcholine secretion (GO:0061526)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of cell growth (GO:0030307)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085) extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) NA NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(1)|urinary_tract(2) 35 Choline(DB00122) AGCCACAAAGCGGGGGGGGAGC 0.55 NA NA NA NA NA NA NA ?|GGGGGGGG|GGGGGGGGG|unsure 37 0.00738818 0.0219 0.0029 5008 , , NA 18180 0.003 NA 0.002 False NA ,,, NA NA NA 2504 0.001 NA NA NA PASS NA NA NA 0 NA 303 325.84 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.37 AF134726 CCDS4724.2, CCDS54989.1, CCDS54990.1 6p21.3 2014-02-17 2005-09-06 2005-09-06 ENSG00000204385 ENSG00000204385 80736 "Solute carriers" 13941 protein-coding gene gene with protein product 606107 "chromosome 6 open reading frame 29" C6orf29 NA 10677542, 15715662, 24379411 Standard NM_025257 NA Approved NG22, CTL4, FLJ14491, TPPT uc010jti.3 Q53GD3 OTTHUMG00000031133 ENST00000229729.6:c.1760+18->C chr6.hg19:g.31833080_31833080dupG 9 9 ref NA False 115 112 PASS 8 PASS ref->het 0 NA 190,195 56,60 61,53 2 2 A2BED3|B0UXX8|B0UZY8|B4DU94|B4DWM2|E9PEK7|Q5JP84|Q5JQ93|Q658S8|Q6UX89|Q8TEW4|Q96C58|Q96K59|Q9Y332 True hg19 CCDS4724.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC44A4-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076234.3 PASS NA None 303 True - G ENST00000229729.6 ANKS1A 23294 __UNKNOWN__ __UNKNOWN__ 6 34857318 34857319 __UNKNOWN__ In_Frame_Ins INS - - GCG LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:34857318_34857319insGCG ENST00000360359.3 + 1 277_278 c.139_140insGCG c.(139-141)agc>aGCGgc p.53_54insG ANKS1A_ENST00000535627.1_In_Frame_Ins_p.53_54insG NM_015245.2 NP_056060.2 Q92625 ANS1A_HUMAN ankyrin repeat and sterile alpha motif domain containing 1A 53 Gly-rich. NA NA NA ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929) cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634) NA cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 31 cggcggcggcagcggcggcggc 0.772 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 87 81.04 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001652 inframe_insertion 1.24 D86982 CCDS4798.1 6p21.31 2013-01-10 2006-02-17 2006-02-17 ENSG00000064999 ENSG00000064999 23294 "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing" 20961 protein-coding gene gene with protein product 608994 "ankyrin repeat and SAM domain containing 1", "ankyrin repeat and sterile alpha motif domain containing 1" ANKS1 NA 9039502 Standard XM_166478 NM_015245 NA Approved KIAA0229 uc003ojx.4 Q92625 OTTHUMG00000014559 ENST00000360359.3:c.155_157dupGCG chr6.hg19:g.34857325_34857327dupGCG ENSP00000353518:p.Gly54_Gly55dup 7 3 ref NA False 171 125 PASS 6 PASS ref->het 0 NA 22,26 23,27 42,35 1 1 A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7 True hg19 CCDS4798.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ANKS1A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000040262.1 PASS NA None 87 True + GCG ENST00000360359.3 SYNJ2 8871 __UNKNOWN__ __UNKNOWN__ 6 158438132 158438133 __UNKNOWN__ Intron INS - - T LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:158438132_158438133insT ENST00000355585.4 + 2 202 SYNJ2_ENST00000367122.2_Intron|SYNJ2_ENST00000367121.3_Intron NM_001178088.1|NM_003898.3 NP_001171559.1|NP_003889.1 O15056 SYNJ2_HUMAN synaptojanin 2 NA NA NA NA phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829)|membrane (GO:0016020) nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723) NA biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 46 OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05) TTTGTGTTTTCTTTTTGGAGTG 0.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 115 124.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.26 AB002346 CCDS5254.1 6q25.3 2008-05-15 ENSG00000078269 ENSG00000078269 8871 11504 protein-coding gene gene with protein product 609410 NA Standard NM_003898 NA Approved INPP5H uc003qqx.2 O15056 OTTHUMG00000015904 ENST00000355585.4:c.128-103->T chr6.hg19:g.158438137_158438137dupT 6 9 ref NA False 71 71 PASS 5 PASS ref->het 0 NA 76,77 28,29 12,10 1 1 Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226 True hg19 CCDS5254.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SYNJ2-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000042858.2 PASS NA None 115 True + T ENST00000355585.4 RP1-170O19.22 0 __UNKNOWN__ __UNKNOWN__ 7 27192088 27192089 __UNKNOWN__ RNA INS - - GGCCT rs117819065|rs71823962|rs145281130|rs3216926 byFrequency LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:27192088_27192089insGGCCT ENST00000467897.2 - 0 91_92 HOXA-AS3_ENST00000524304.1_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000518947.2_RNA|HOXA-AS3_ENST00000521231.1_RNA|RP1-170O19.23_ENST00000498652.1_RNA|HOXA-AS3_ENST00000521197.1_RNA NA NA NA NA NA NA GGGAGCCGCCAGGCCTGGCCTG 0.693 NA NA NA NA NA NA NA 940 0.1877 0.0416 0.2334 5008 , , NA 12775 0.1379 NA 0.2843 False NA ,,, NA NA NA 2504 0.3047 NA NA NA PASS NA NA NA 0 NA 135 146.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.01 NA NA NA NA NA ENST00000467897.2: chr7.hg19:g.27192094_27192098dupGGCCT 3 2 ref NA False 44 44 PASS 2 PASS ref->het 0 NA 92,94 3,3 39,39 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP1-170O19.22-001 KNOWN basic|readthrough_transcript|exp_conf processed_transcript NA processed_transcript OTTHUMT00000473057.1 PASS NA None 135 True - GGCCT ENST00000467897.2 KCTD7 154881 __UNKNOWN__ __UNKNOWN__ 7 66106563 66106589 __UNKNOWN__ 3'UTR DEL ATCCCTGTTTCTCTGACTCCCTTTGTG ATCCCTGTTTCTCTGACTCCCTTTGTG - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:66106563_66106589delATCCCTGTTTCTCTGACTCCCTTTGTG ENST00000275532.3 + 0 3398_3424 NM_001167961.2|NM_153033.4 NP_001161433.1|NP_694578.1 Q96MP8 KCTD7_HUMAN potassium channel tetramerization domain containing 7 NA NA NA NA cell death (GO:0008219)|protein homooligomerization (GO:0051260) cytoplasm (GO:0005737)|plasma membrane (GO:0005886) NA central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1) 16 CGCTGGAGAAATCCCTGTTTCTCTGACTCCCTTTGTGATCCTCACAG 0.493 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 127 130.89 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.53 AK056631 CCDS5534.1, CCDS55117.1 7q11.21 2014-09-17 2013-06-20 ENSG00000243335 ENSG00000243335 154881 21957 protein-coding gene gene with protein product 611725 "potassium channel tetramerisation domain containing 7" NA 12477932 Standard NM_153033 NM_001167961 NA Approved FLJ32069, EPM3, CLN14 uc003tve.3 Q96MP8 OTTHUMG00000129543 ENST00000275532.3:c.*2370ATCCCTGTTTCTCTGACTCCCTTTGTG>- chr7.hg19:g.66106563_66106589delATCCCTGTTTCTCTGACTCCCTTTGTG 0 4 ref NA False 52 52 PASS 1 PASS ref->het 0 NA 132,136 14,14 16,16 1 1 A4D2M4|Q8IVR0 True hg19 CCDS5534.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KCTD7-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000251733.2 PASS NA None 127 True + ATCCCTGTTTCTCTGACTCCCTTTGTG ENST00000275532.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 8 55651606 55651606 __UNKNOWN__ IGR DEL T T - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:55651606delT NA RP1 (108212 upstream) : XKR4 (363342 downstream) NA NA NA NA NA NA ATGTCACTTATTTTTTTCTTC 0.373 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 308 301.73 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.69 NA NA NA NA NA chr8.hg19:g.55651606delT 6 9 ref NA False 145 128 PASS 7 PASS ref->het 0 NA 196,196 76,76 35,35 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 308 True T IFNA1 3439 __UNKNOWN__ __UNKNOWN__ 9 21441053 21441053 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:21441053delG ENST00000276927.1 + 1 614 c.547delG c.(547-549)gaafs p.E183fs NM_024013.2 NP_076918.1 P01562 IFNA1_HUMAN interferon, alpha 1 183 NA NA NA adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337) extracellular region (GO:0005576)|extracellular space (GO:0005615) cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132) NA kidney(1)|large_intestine(1)|lung(3)|ovary(2) 7 Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173) AAACTTGCAAGAAAGATTAAG 0.398 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 893 875.13 NA NA NA NA NA 110 126 121 NA NA NA NA 9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 21441053 NA 2203 4300 6503 SO:0001589 frameshift_variant 1.85 CCDS6508.1 9p22 2010-12-10 ENSG00000197919 ENSG00000197919 3439 "Interferons" 5417 protein-coding gene gene with protein product "IFN-alpha 1b", "interferon alpha 1b" 147660 NA 1385305 Standard NM_024013 NM_024013 NA Approved IFNA@, IFL, IFN, IFN-ALPHA, IFNA13, IFN-alphaD uc003zpd.2 P01562 OTTHUMG00000019673 ENST00000276927.1:c.547delG chr9.hg19:g.21441053delG ENSP00000276927:p.Glu183fs 0 5 ref NA False 219 173 PASS 1 PASS ref->het 0 NA 638,649 170,171 91,88 1 1 D4Q9M8|Q14605|Q2M1L8|Q52LB8|Q5VYQ2|Q7M4Q1|Q8WZ68|Q9UMJ3 True hg19 CCDS6508.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IFNA1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000051902.1 PASS NA None 893 True + G ENST00000276927.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 11 106889260 106889260 __UNKNOWN__ IGR DEL G G - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:106889260delG NA GUCY1A2 (10 upstream) : RP11-819C21.1 (293597 downstream) NA NA NA NA NA NA ctctccacttgctgccctgcc 0.662 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 14 16.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.29 NA NA NA NA NA chr11.hg19:g.106889260delG 0 2 ref NA False 37 37 PASS 1 PASS ref->het 0 NA 7,8 3,3 1,0 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 14 True G IFT46 56912 __UNKNOWN__ __UNKNOWN__ 11 118418134 118418135 __UNKNOWN__ Intron INS - - C rs552648792|rs533952686 byFrequency LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:118418134_118418135insC ENST00000264021.3 - 10 1091 IFT46_ENST00000530872.1_Intron|IFT46_ENST00000264020.2_Intron NM_001168618.1 NP_001162089.1 Q9NQC8 IFT46_HUMAN intraflagellar transport 46 NA NA NA NA cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)|protein stabilization (GO:0050821)|smoothened signaling pathway (GO:0007224) centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512) protein C-terminus binding (GO:0008022) NA central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4) 9 TTTTGATACTTTAAAAAAAttc 0.47 NA NA NA NA NA NA NA -|-|C|insertion 10 0.00199681 0 0.0043 5008 , , NA 17933 0 NA 0.006 False NA ,,, NA NA NA 2504 0.001 NA NA NA PASS NA NA NA 0 NA 23 22.44 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AL136934 CCDS8399.1, CCDS53718.1 11q23.3 2014-07-18 2014-07-03 2010-04-22 ENSG00000118096 ENSG00000118096 56912 "Intraflagellar transport homologs" 26146 protein-coding gene gene with protein product "cilia and flagella associated protein 32" NA "chromosome 11 open reading frame 60", "intraflagellar transport 46 homolog (Chlamydomonas)" C11orf60 NA 10873569, 19253336 Standard NM_020153 NM_020153 NA Approved C11orf2, FLJ21827, CFAP32 uc001pto.2 Q9NQC8 OTTHUMG00000166408 ENST00000264021.3:c.673-1566->G chr11.hg19:g.118418134_118418135insC 1 7 ref NA False 32 32 PASS 0 PASS ref->het 0 NA 1,1 16,17 6,6 1 1 A8K0F6|Q9H6V5 True hg19 CCDS53718.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IFT46-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000389627.1 PASS NA None 23 True - C ENST00000264021.3 C12orf73 728568 __UNKNOWN__ __UNKNOWN__ 12 104345286 104345286 __UNKNOWN__ 3'UTR DEL G G - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:104345286delG ENST00000378090.4 - 0 436 C12orf73_ENST00000543740.2_5'UTR|C12orf73_ENST00000547945.1_3'UTR|C12orf73_ENST00000553183.1_3'UTR|C12orf73_ENST00000547975.1_3'UTR|C12orf73_ENST00000549478.1_3'UTR NM_001135570.1 NP_001129042.1 Q69YU5 CL073_HUMAN chromosome 12 open reading frame 73 NA NA NA NA extracellular region (GO:0005576) NA prostate(1) 1 ATTATTCACAGAATTCTTGGC 0.353 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 228 242.63 NA NA NA NA NA 157 123 133 NA NA NA NA 12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 104345286 NA 692 1591 2283 SO:0001624 3_prime_UTR_variant 0.36 AK024037 CCDS44964.1 12q23.3 2008-10-01 ENSG00000204954 ENSG00000204954 728568 34450 protein-coding gene gene with protein product NA NA Standard NM_001135570 NM_001135570 NA Approved FLJ13975, DKFZp547P055 uc009zuj.2 Q69YU5 ENST00000378090.4:c.*15C>- chr12.hg19:g.104345286delG 0 3 ref NA False 230 166 PASS 1 PASS ref->het 0 NA 140,140 61,62 31,30 1 1 True hg19 CCDS44964.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C12orf73-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000407361.1 PASS NA None 228 True - G ENST00000378090.4 RB1 5925 __UNKNOWN__ __UNKNOWN__ 13 48953740 48953741 __UNKNOWN__ Frame_Shift_Del DEL TT TT - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:48953740_48953741delTT ENST00000267163.4 + 14 1481_1482 c.1343_1344delTT c.(1342-1344)cttfs p.L448fs NM_000321.2 NP_000312.2 P06400 RB_HUMAN retinoblastoma 1 448 Domain A.|Pocket; binds T and E1A. NA NA NA androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032) chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514) androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625) p.0?(15)|p.?(8)|p.L448L(1) NA NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31) 496 all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301) GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013) """Insulin(DB00071)|Insulin Regular(DB00030)" CGATACAAACTTGGAGTTCGCT 0.347 NA 6 "D, Mis, N, F, S" NA "retinoblastoma, sarcoma, breast, small cell lung" "retinoblastoma, sarcoma, breast, small cell lung" NA NA Hereditary Retinoblastoma TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS yes Rec yes Familial retinoblastoma 13 13q14 5925 retinoblastoma gene NA "L, E, M, O" 24 Whole gene deletion(15)|Unknown(8)|Substitution - coding silent(1) bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|large_intestine(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1) NA 30 28.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.04 Familial Cancer Database M15400 CCDS31973.1 13q14.2 2014-09-17 2008-07-31 ENSG00000139687 ENSG00000139687 5925 "Endogenous ligands" 9884 protein-coding gene gene with protein product "prepro-retinoblastoma-associated protein", "protein phosphatase 1, regulatory subunit 130" 614041 "osteosarcoma" OSRC NA 1857421, 15057823 Standard NM_000321 NA Approved RB, PPP1R130 uc001vcb.3 P06400 OTTHUMG00000016900 ENST00000267163.4:c.1343_1344delTT chr13.hg19:g.48953740_48953741delTT ENSP00000267163:p.Leu448fs 0 3 ref NA False 225 107 PASS 2 PASS ref->het 0 NA 3,3 26,26 0,0 1 1 A8K5E3|P78499|Q5VW46|Q8IZL4 True hg19 CCDS31973.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RB1-002 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000044884.1 PASS NA None 30 True + T ENST00000267163.4 MMP25 64386 __UNKNOWN__ __UNKNOWN__ 16 3105891 3105907 __UNKNOWN__ Intron DEL TTCAGCCGGGGCTGGCG TTCAGCCGGGGCTGGCG - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:3105891_3105907delTTCAGCCGGGGCTGGCG ENST00000336577.4 + 5 898 RP11-473M20.7_ENST00000572574.1_RNA|RP11-473M20.7_ENST00000570949.1_RNA|RP11-473M20.7_ENST00000576250.1_RNA|MMP25_ENST00000570755.1_3'UTR|RP11-473M20.7_ENST00000572930.1_RNA|RP11-473M20.7_ENST00000573130.1_RNA|RP11-473M20.7_ENST00000573878.1_RNA NM_022468.4 NP_071913.1 Q9H239 MMP28_HUMAN matrix metallopeptidase 25 NA NA NA NA negative regulation of macrophage chemotaxis (GO:0010760) cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578) calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270) NA endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1) 14 Marimastat(DB00786) GGAGCTGGGCTTCAGCCGGGGCTGGCGTGTGAATCCT 0.654 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSCLC(147;665 1067 3888 6863 19894 30469 40247 45633 51336) PASS NA NA NA 0 NA 30 27.84 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF145442 CCDS10492.1 16p13.3 2008-02-05 2005-08-08 ENSG00000008516 64386 14246 protein-coding gene gene with protein product 608482 "matrix metalloproteinase 25", "matrix metallopeptidase-like 1" MMPL1, MMP20 NA 10628838, 10706098 Standard NM_022468 NM_022468 NA Approved MT6-MMP uc002cth.3 Q9NPA2 ENST00000336577.4:c.662-1127TTCAGCCGGGGCTGGCG>- chr16.hg19:g.3105891_3105907delTTCAGCCGGGGCTGGCG 0 3 ref NA False 67 67 PASS 1 PASS ref->het 0 NA 19,19 11,11 1,1 1 1 Q96F04|Q96TE2 True hg19 CCDS10492.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MMP25-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000437116.1 PASS NA None 30 True + TTCAGCCGGGGCTGGCG ENST00000336577.4 DNAH3 55567 __UNKNOWN__ __UNKNOWN__ 16 20980984 20980988 __UNKNOWN__ Intron DEL TTTCT TTTCT - rs139683653|rs202243931|rs371946801|rs200261173 LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:20980984_20980988delTTTCT ENST00000261383.3 - 52 8458 DNAH3_ENST00000415178.1_Intron NM_017539.1 NP_060009.1 Q8TD57 DYH3_HUMAN dynein, axonemal, heavy chain 3 NA NA NA NA cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018) axonemal dynein complex (GO:0005858)|microtubule (GO:0005874) ATP binding (GO:0005524)|microtubule motor activity (GO:0003777) NA NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6) 202 GBM - Glioblastoma multiforme(48;0.207) GCCTGGTTCCTTTCTTAATTCCTCC 0.576 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 25 29.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 U83574 CCDS10594.1 16p12.2 2008-08-01 2006-09-04 ENSG00000158486 ENSG00000158486 55567 "Axonemal dyneins" 2949 protein-coding gene gene with protein product 603334 "dynein, axonemal, heavy polypeptide 3" NA 9256245, 9373155 Standard NM_017539 NM_017539 NA Approved Dnahc3b, DLP3, Hsadhc3, DKFZp434N074 uc010vbe.2 Q8TD57 OTTHUMG00000090677 ENST00000261383.3:c.8458+125AGAAA>- chr16.hg19:g.20980984_20980988delTTTCT 0 5 ref NA False 65 62 PASS 1 PASS ref->hom 0 NA 0,0 22,22 3,3 1 1 O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35 True hg19 CCDS10594.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DNAH3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000207361.1 PASS NA None 25 True - TTTCT ENST00000261383.3 COX10 1352 __UNKNOWN__ __UNKNOWN__ 17 14078315 14078315 __UNKNOWN__ Intron DEL A A - rs78443723 byFrequency LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:14078315delA ENST00000261643.3 + 5 772 COX10_ENST00000537334.1_Intron|COX10_ENST00000536205.1_Intron NM_001303.3 NP_001294.2 Q12887 COX10_HUMAN cytochrome c oxidase assembly homolog 10 (yeast) NA NA NA NA aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281) integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739) farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495) NA cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1) 14 all_lung(20;0.06)|Lung SC(565;0.168) UCEC - Uterine corpus endometrioid carcinoma (92;0.106) gacaaaagacagcatgtcgta 0.438 NA NA NA NA NA NA NA A|A|-|deletion 2715 0.542133 0.416 0.5447 5008 , , NA 11739 0.6339 NA 0.5716 False NA ,,, NA NA NA 2504 0.5859 NA NA NA PASS NA NA NA 0 NA 14 18.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 U09466 CCDS11166.1 17p12 2013-05-24 2012-10-15 ENSG00000006695 ENSG00000006695 1352 "Mitochondrial respiratory chain complex assembly factors" 2260 protein-coding gene gene with protein product "heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase" 602125 "COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)" NA 9177788, 12928484 Standard NM_001303 NM_001303 NA Approved uc002gof.4 Q12887 OTTHUMG00000058814 ENST00000261643.3:c.695+15051A>- chr17.hg19:g.14078315delA 0 2 ref NA False 86 82 PASS 1 PASS ref->het 0 NA 2,2 11,12 0,0 1 1 B2R6U5|B4DJ50|O15334|Q969F7 True hg19 CCDS11166.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COX10-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000130003.1 PASS NA None 14 True + A ENST00000261643.3 COX11 1353 __UNKNOWN__ __UNKNOWN__ 17 53041893 53041899 __UNKNOWN__ Intron DEL TTTAACT TTTAACT - rs201764136|rs3217151|rs141544971 byFrequency LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:53041893_53041899delTTTAACT ENST00000299335.3 - 2 661 COX11_ENST00000571584.1_Intron NM_004375.3 NP_004366.1 Q9Y6N1 COX11_HUMAN cytochrome c oxidase assembly homolog 11 (yeast) NA NA NA NA hydrogen ion transmembrane transport (GO:1902600)|negative regulation of glucokinase activity (GO:0033132)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585) integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739) copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055) NA endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|prostate(1) 9 GAATTTATACTTTAACTTTTAAGTTAC 0.266 NA NA NA NA NA NA NA 759 0.151558 0.0605 0.1585 5008 , , NA 19503 0.129 NA 0.2714 False NA ,,, NA NA NA 2504 0.1697 NA NA NA PASS NA NA NA 0 NA 30 29.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF044321 CCDS11583.1, CCDS58579.1 17q22 2012-10-15 2012-10-15 ENSG00000166260 1353 "Mitochondrial respiratory chain complex assembly factors" 2261 protein-coding gene gene with protein product "cytochrome c oxidase subunit 11", "cytochrome c oxidase assembly protein COX11" 603648 "COX11 (yeast) homolog, cytochrome c oxidase assembly protein", "COX11 cytochrome c oxidase assembly homolog (yeast)" NA 9878253 Standard NM_004375 NM_004375 NA Approved COX11P uc010wng.1 Q9Y6N1 ENST00000299335.3:c.522+158AGTTAAA>- chr17.hg19:g.53041893_53041899delTTTAACT 0 4 ref NA False 39 39 PASS 1 PASS ref->hom 0 NA 0,0 24,25 4,3 1 1 D3DTY5|I3L220|Q6FHB7|Q9BRX0|Q9UME8 True hg19 CCDS11583.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COX11-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000439182.1 PASS NA None 30 True - TTTAACT ENST00000299335.3 CCDC57 284001 __UNKNOWN__ __UNKNOWN__ 17 80085225 80085261 __UNKNOWN__ Intron DEL GCTCCATTCTAAGTCAGCCTGCGCCCGGGTGTACAGT GCTCCATTCTAAGTCAGCCTGCGCCCGGGTGTACAGT - rs74381415|rs386799937|rs79780738|rs71370218|rs571879109|rs559026375 byFrequency LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:80085225_80085261delGCTCCATTCTAAGTCAGCCTGCGCCCGGGTGTACAGT ENST00000389641.4 - 17 2603 CCDC57_ENST00000392346.2_Intron|CCDC57_ENST00000392347.1_Intron Q2TAC2 CCD57_HUMAN coiled-coil domain containing 57 NA NA NA NA NA endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1) 16 Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227) BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253) TCTCACCTGGGCTCCATTCTAAGTCAGCCTGCGCCCGGGTGTACAGTGCTCCATTCT 0.62 NA NA NA NA NA NA NA 2139 0.427117 0.5862 0.3746 5008 , , NA 15950 0.1359 NA 0.5169 False NA ,,, NA NA NA 2504 0.4571 NA NA NA PASS NA NA NA 0 NA 23 15.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.7 BC040264 17q25.3 2006-03-08 ENSG00000176155 ENSG00000176155 284001 27564 protein-coding gene gene with protein product NA NA 12477932 Standard NM_198082 XM_006722279 NA Approved FLJ00130, FLJ23754 uc002kdx.1 Q2TAC2 OTTHUMG00000140396 ENST00000389641.4:c.2566+306ACTGTACACCCGGGCGCAGGCTGACTTAGAATGGAGC>- chr17.hg19:g.80085225_80085261delGCTCCATTCTAAGTCAGCCTGCGCCCGGGTGTACAGT 0 3 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 1,1 8,12 15,12 1 1 A6NP51|A8MQC7|Q8IWG2|Q8TER3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCDC57-001 KNOWN basic|appris_candidate_longest protein_coding NA protein_coding OTTHUMT00000277182.3 PASS NA None 23 True - GCTCCATTCTAAGTCAGCCTGCGCCCGGGTGTACAGT ENST00000389641.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 18 832514 832514 __UNKNOWN__ IGR DEL C C - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:832514delC NA RP11-672L10.6 (18757 upstream) : RP11-672L10.3 (61921 downstream) NA NA NA NA NA NA TAAATCTGGACCCCCCCCAAA 0.468 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 87 94.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr18.hg19:g.832514delC 7 8 ref NA False 64 64 PASS 8 PASS ref->het 0 NA 48,49 26,26 12,12 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 87 True C STK11 6794 __UNKNOWN__ __UNKNOWN__ 19 1207201 1207204 __UNKNOWN__ Splice_Site DEL AAGT AAGT - rs587782096|rs112235354 LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:1207201_1207204delAAGT ENST00000326873.7 + 1 1462_1463 c.289_290delAAGT c.(289-291)aag>g p.K97fs STK11_ENST00000585748.1_Intron NM_000455.4 NP_000446.1 Q15831 STK11_HUMAN serine/threonine kinase 11 97 Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}. NA NA NA activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944) cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398) ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674) p.0?(20)|p.?(4) NA biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 328 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18) CAACGTGAAGAAGTAAGTATGGCT 0.593 NA 14 "D, Mis, N, F, S" NA "NSCLC, pancreatic" "jejunal harmartoma, ovarian, testicular, pancreatic" NA NA Peutz-Jeghers syndrome TSP Lung(3;<1E-08) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS yes Rec yes Peutz-Jeghers syndrome 19 19p13.3 6794 serine/threonine kinase 11 gene (LKB1) NA "E, M, O" 24 Whole gene deletion(20)|Unknown(3)|Deletion - Frameshift(1) cervix(15)|lung(4)|skin(1)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1) GRCh37 CI044195|CS012223|CS055617|CS067505 STK11 I|S NA 133 132.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0.15 Familial Cancer Database PJS, Hamartous Intestinal Polyposis U63333 CCDS45896.1 19p13.3 2014-09-17 2005-12-13 ENSG00000118046 6794 11389 protein-coding gene gene with protein product "polarization-related protein LKB1" 602216 "serine/threonine kinase 11 (Peutz-Jeghers syndrome)" NA 9425897 Standard NM_000455 XM_005259617 NA Approved PJS, LKB1 uc002lrl.1 Q15831 ENST00000326873.7:c.290+1AAGT>- chr19.hg19:g.1207205_1207208delAAGT 1 4 ref NA False 224 173 PASS 2 PASS ref->het 0 NA 71,72 38,42 23,19 1 1 B2RBX7|E7EW76 True hg19 CCDS45896.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA STK11-001 KNOWN non_canonical_U12|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000449839.3 PASS NA None 133 Frame_Shift_Del True + AAGT ENST00000326873.7 LRFN3 79414 __UNKNOWN__ __UNKNOWN__ 19 36430433 36430434 __UNKNOWN__ Frame_Shift_Del DEL AC AC - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:36430433_36430434delAC ENST00000588831.1 + 3 1160_1161 c.106_107delAC c.(106-108)acafs p.T36fs LRFN3_ENST00000246529.3_Frame_Shift_Del_p.T36fs Q9BTN0 LRFN3_HUMAN leucine rich repeat and fibronectin type III domain containing 3 36 LRRNT. NA NA NA cell adhesion (GO:0007155) cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211) NA cervix(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1) 12 all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.06) CCGCTGCCAGACACAGTCGCTG 0.713 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 169 167.82 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 3.83 BC003578 CCDS12483.1 19q13.13 2013-02-11 ENSG00000126243 79414 "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing" 28370 protein-coding gene gene with protein product "fibronectin type III, immunoglobulin and leucine rich repeat domains 1" 612809 NA 12975309, 16495444, 16828986 Standard NM_024509 NM_024509 NA Approved MGC2656, SALM4, FIGLER1 uc002oco.3 Q9BTN0 ENST00000588831.1:c.106_107delAC chr19.hg19:g.36430435_36430436delAC ENSP00000466989:p.Thr36fs 1 2 ref NA False 277 194 PASS 2 PASS ref->het 0 NA 97,110 54,55 19,7 2 1 Q6UY10 True hg19 CCDS12483.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LRFN3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000457403.2 PASS NA None 169 True + AC ENST00000588831.1 EFNB1 1947 __UNKNOWN__ __UNKNOWN__ X 68049455 68049455 __UNKNOWN__ 5'UTR DEL G G - LTS-010_T LTS-010_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:68049455delG ENST00000204961.4 + 0 616 NM_004429.4 NP_004420.1 P98172 EFNB1_HUMAN ephrin-B1 NA NA NA NA axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|embryonic pattern specification (GO:0009880)|ephrin receptor signaling pathway (GO:0048013)|neural crest cell migration (GO:0001755)|positive regulation of T cell proliferation (GO:0042102) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202) ephrin receptor binding (GO:0046875) NA breast(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(9)|ovary(1) 22 CCGGCCGGGCGGAGAAGAGCG 0.751 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 118 114.15 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.19 U09303 CCDS14391.1 Xq12 2011-03-09 ENSG00000090776 ENSG00000090776 1947 "Ephrins" 3226 protein-coding gene gene with protein product 300035 "craniofrontonasal syndrome (craniofrontonasal dysplasia)" EPLG2, CFNS NA 7774950, 16526919 Standard NM_004429 NM_004429 NA Approved LERK2, Elk-L uc004dxd.4 P98172 OTTHUMG00000021751 ENST00000204961.4:c.-165G>- chrX.hg19:g.68049455delG 1 5 ref NA False 287 207 PASS 2 PASS ref->het 0 NA 62,62 43,45 14,14 1 1 D3DVU0 True hg19 CCDS14391.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EFNB1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000057029.1 PASS NA None 118 True + G ENST00000204961.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ M 303 303 __UNKNOWN__ IGR DEL C C - LTS-011_T LTS-011_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrM:303delC NA None (None upstream) : MT-TF (273 downstream) NA NA NA NA NA NA NA TTCCACCAAACCCCCCCCTCC 0.418 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 466 438.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 13.54 NA NA NA NA NA NA NA NA chrM.hg19:g.303delC 7 14 ref NA False 448 62 PASS 8 PASS ref->het 0 NA 33,49 294,329 161,119 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 466 NA True C MLLT4 4301 __UNKNOWN__ __UNKNOWN__ 6 168366691 168366692 __UNKNOWN__ In_Frame_Ins INS - - GAG LTS-011_T LTS-011_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:168366691_168366692insGAG ENST00000447894.2 + 31 5202_5203 c.5202_5203insGAG c.(5203-5205)gag>GAGgag p.1735_1735E>EE MLLT4_ENST00000366806.2_In_Frame_Ins_p.1735_1735E>EE|MLLT4_ENST00000392112.1_Intron|MLLT4_ENST00000351017.4_In_Frame_Ins_p.1742_1742E>EE|MLLT4_ENST00000400822.3_In_Frame_Ins_p.1745_1745E>EE P55196 AFAD_HUMAN myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 1735 NA NA NA adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165) apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886) protein C-terminus binding (GO:0008022) NA NA breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 65 Breast(66;1.07e-05)|Ovarian(120;0.024) Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117) TTGCATACAATgaggaggagga 0.579 NA NA TRUE MLL AL NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Dom yes NA 6 6q27 4301 "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)" NA L 0 NA NA NA NA NA NA NA 265 270.63 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001652 inframe_insertion 2.02 NA NA AB011399 CCDS47517.1, CCDS75553.1 6q27 2008-02-05 2001-11-28 ENSG00000130396 ENSG00000130396 4301 NA 7137 protein-coding gene gene with protein product 159559 "myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4" NA 8242616 Standard NM_005936 NM_001040000 NA Approved AF-6, AF6 uc021zij.1 P55196 OTTHUMG00000016031 ENST00000447894.2:c.5218_5220dupGAG chr6.hg19:g.168366698_168366700dupGAG ENSP00000404595:p.Glu1740dup 7 3 ref NA False 90 90 PASS 6 PASS ref->het 0 NA 127,131 45,45 94,93 2 2 O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MLLT4-013 PUTATIVE basic|appris_candidate_longest protein_coding NA protein_coding OTTHUMT00000372077.1 PASS NA None 265 NA True + GAG ENST00000447894.2 MMP20 9313 __UNKNOWN__ __UNKNOWN__ 11 102468779 102468780 __UNKNOWN__ Intron INS - - G rs35415619|rs201415214|rs5794183|rs386756931 byFrequency LTS-011_T LTS-011_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:102468779_102468780insG ENST00000260228.2 - 7 966 MMP20_ENST00000544938.1_Intron NM_004771.3 NP_004762.2 Q9NPA2 MMP25_HUMAN matrix metallopeptidase 20 NA NA NA NA hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508) anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578) calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270) NA NA endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 27 all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139) Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033) Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13) BRCA - Breast invasive adenocarcinoma(274;0.0161) Marimastat(DB00786) attacaggcgtagacaccatgc 0.441 NA NA NA NA NA NA NA NA G|-|G|deletion 2599 0.51897 0.3835 0.5072 5008 , , NA 17580 0.5248 NA 0.5586 False NA ,,, NA NA NA 2504 0.6636 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 16 17.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA Y12779 CCDS8318.1 11q22.3 2008-05-22 2008-05-22 ENSG00000137674 9313 NA 7167 protein-coding gene gene with protein product "enamelysin" 604629 "matrix metalloproteinase 20 (enamelysin)" NA 9398237 Standard NM_004771 NA Approved uc001phc.3 O60882 ENST00000260228.2:c.954-3291->C chr11.hg19:g.102468779_102468780insG 1 2 ref NA False 30 30 PASS 0 PASS ref->hom 0 NA 0,0 15,17 1,0 1 1 D3DUA8|Q9H3Q0 True hg19 CCDS8318.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MMP20-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000398012.1 PASS NA None 16 NA True - G ENST00000260228.2 CUL5 8065 __UNKNOWN__ __UNKNOWN__ 11 107879712 107879713 __UNKNOWN__ 5'UTR DEL GG GG - LTS-011_T LTS-011_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:107879712_107879713delGG ENST00000393094.2 + 0 254_255 NM_003478.3 NP_003469.2 Q93034 CUL5_HUMAN cullin 5 NA NA NA NA calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032) Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886) calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625) NA NA endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1) 23 all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217) AGGTGGCCGCGGCGGGTGCAAC 0.649 NA NA NA NA NA NA NA NA OREG0021319 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 592 574.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.92 NA NA X81882 CCDS31668.1 11q22.3 2011-05-24 ENSG00000166266 ENSG00000166266 8065 NA 2556 protein-coding gene gene with protein product 601741 NA 8681378, 9037604 Standard XM_005271682 NA Approved VACM-1 uc001pjv.3 Q93034 OTTHUMG00000166369 ENST00000393094.2:c.-362GG>- chr11.hg19:g.107879712_107879713delGG 0 5 ref 1408 False 265 265 PASS 2 PASS ref->het 0 NA 439,458 93,94 71,51 2 2 A8K960|O14766|Q9BZC6 True hg19 CCDS31668.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CUL5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000389429.1 PASS NA None 592 NA True + G ENST00000393094.2 KLRC1 3821 __UNKNOWN__ __UNKNOWN__ 12 10598702 10598706 __UNKNOWN__ 3'UTR DEL AAATC AAATC - rs143299847|rs566812255 byFrequency LTS-011_T LTS-011_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:10598702_10598706delAAATC ENST00000359151.3 - 0 1327_1331 KLRC1_ENST00000408006.3_3'UTR|KLRC1_ENST00000544822.1_3'UTR|KLRC1_ENST00000536188.1_Intron|KLRC1_ENST00000347831.5_3'UTR NM_002259.4 NP_002250 P26715 NKG2A_HUMAN killer cell lectin-like receptor subfamily C, member 1 NA NA NA NA cell surface receptor signaling pathway (GO:0007166)|regulation of immune response (GO:0050776) integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888) NA NA NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|skin(1) 16 aaatgattaaaaatcaatgatgttt 0.332 NA NA NA NA NA NA NA NA 1320 0.263578 0.5257 0.1599 5008 , , NA 16688 0.2212 NA 0.1779 False NA ,,, NA NA NA 2504 0.1145 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 188 192.21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.72 NA NA U54782 CCDS8625.1, CCDS8626.1 12p13 2010-06-30 ENSG00000134545 ENSG00000134545 3821 NA "Killer cell lectin-like receptors", "CD molecules" 6374 protein-coding gene gene with protein product "NKG2-1/B activating NK receptor" 161555 NKG2 NA 9598306 Standard NM_002259 NM_002259 NA Approved NKG2-A, NKG2-B, CD159a uc001qyl.3 P26715 ENST00000359151.3:c.*448GATTT>- chr12.hg19:g.10598702_10598706delAAATC 0 5 ref NA False 44 44 PASS 1 PASS ref->het 0 NA 168,172 8,8 23,22 1 1 True hg19 CCDS8625.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KLRC1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000400115.1 PASS NA None 188 NA True - AAATC ENST00000359151.3 TTLL5 23093 __UNKNOWN__ __UNKNOWN__ 14 76211398 76211399 __UNKNOWN__ Intron INS - - A LTS-011_T LTS-011_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:76211398_76211399insA ENST00000557636.1 + 17 1538 TTLL5_ENST00000555422.1_Intron|TTLL5_ENST00000298832.9_Intron Q6EMB2 TTLL5_HUMAN tubulin tyrosine ligase-like family, member 5 NA NA NA NA fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351) centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634) ligase activity (GO:0016874) NA NA NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2) 50 BRCA - Breast invasive adenocarcinoma(234;0.029) AATGAAAACTTAAAAAATTTTT 0.371 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 144 145.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.63 NA NA AF107885 CCDS32124.1 14q24.3 2014-09-09 2005-07-29 2005-07-29 ENSG00000119685 ENSG00000119685 23093 NA "Tubulin tyrosine ligase-like family" 19963 protein-coding gene gene with protein product 612268 "KIAA0998" KIAA0998 NA 15890843 Standard NM_015072 NM_015072 NA Approved uc001xrx.3 Q6EMB2 OTTHUMG00000171611 ENST00000557636.1:c.1324-39->A chr14.hg19:g.76211404_76211404dupA 7 6 ref NA False 34 34 PASS 6 PASS ref->het 0 NA 99,101 25,25 20,20 1 1 B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TTLL5-016 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000414451.1 PASS NA None 144 NA True + A ENST00000557636.1 TMED8 283578 __UNKNOWN__ __UNKNOWN__ 14 77806329 77806330 __UNKNOWN__ 3'UTR INS - - TGAAGGAG rs201779396|rs11282388|rs113130190 byFrequency LTS-011_T LTS-011_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:77806329_77806330insTGAAGGAG ENST00000216468.7 - 0 2817_2818 NM_213601.1 NP_998766.1 Q6PL24 TMED8_HUMAN transmembrane emp24 protein transport domain containing 8 NA NA NA NA transport (GO:0006810) integral component of membrane (GO:0016021) NA NA breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4) 15 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.0281) GAATCTAACAATGAGTCAAAGG 0.455 NA NA NA NA NA NA NA NA 4300 0.858626 0.9183 0.7464 5008 , , NA 22129 0.9563 NA 0.825 False NA ,,, NA NA NA 2504 0.7914 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 94 97.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA AK095650 CCDS32125.1 14q24.3 2005-08-26 2005-08-26 2005-01-07 ENSG00000100580 283578 NA 18633 protein-coding gene gene with protein product NA "family with sequence similarity 15, member B", "transmembrane emp24 domain containing 8" FAM15B NA Standard NM_213601 NM_213601 NA Approved uc001xto.1 Q6PL24 ENST00000216468.7:c.*1785->CTCCTTCA chr14.hg19:g.77806329_77806330insTGAAGGAG 1 4 ref NA False 40 40 PASS 0 PASS ref->het 0 NA 23,24 52,52 21,21 2 2 B3KTI6|Q3MJB0|Q9P1V9 True hg19 CCDS32125.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMED8-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000414100.1 PASS NA None 94 NA True - TGAAGGAG ENST00000216468.7 KANSL1 284058 __UNKNOWN__ __UNKNOWN__ 17 44220864 44220867 __UNKNOWN__ Intron DEL AAAT AAAT - rs529272927 byFrequency LTS-011_T LTS-011_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:44220864_44220867delAAAT ENST00000575318.1 - 1 1323 KANSL1_ENST00000262419.6_Intron|KANSL1_ENST00000572904.1_Intron|KANSL1_ENST00000432791.1_Intron|KANSL1_ENST00000393476.3_Intron|KANSL1_ENST00000574590.1_Intron Q7Z3B3 KANL1_HUMAN KAT8 regulatory NSL complex subunit 1 NA NA NA NA chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982) histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) NA NA NA tcgtctcaaaaaataaataaataa 0.5 NA NA NA NA NA NA NA NA 435 0.086861 0.0159 0.1585 5008 , , NA 17537 0.001 NA 0.2406 False NA ,,, NA NA NA 2504 0.0624 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 22 22.05 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA BX538006 CCDS11503.1, CCDS11503.2, CCDS74084.1 17q21.31 2012-02-20 2012-02-20 2012-02-20 ENSG00000120071 ENSG00000120071 284058 NA 24565 protein-coding gene gene with protein product "centromere protein 36" 612452 "KIAA1267" KIAA1267 NA 10574462 Standard NM_015443 NM_015443 NA Approved DKFZP727C091, MSL1v1, CENP-36, NSL1 uc002ikd.3 Q7Z3B3 ENST00000575318.1:c.1289+27353ATTT>- chr17.hg19:g.44220872_44220875delAAAT 4 9 ref NA False 35 35 PASS 5 PASS ref->hom 0 NA 0,0 15,15 7,7 1 1 A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KANSL1-006 NOVEL not_organism_supported|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000440272.1 PASS NA None 22 NA True - AAAT ENST00000575318.1 KDM4B 23030 __UNKNOWN__ __UNKNOWN__ 19 5137327 5137337 __UNKNOWN__ Frame_Shift_Del DEL GCGCGGCCCAC GCGCGGCCCAC - rs139188885|rs34637944 byFrequency LTS-011_T LTS-011_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:5137327_5137337delGCGCGGCCCAC ENST00000159111.4 + 16 2581_2591 c.2363_2373delGCGCGGCCCAC c.(2362-2373)tgcgcggcccacfs p.CAAH788fs KDM4B_ENST00000536461.1_Frame_Shift_Del_p.CAAH822fs NM_015015.2 NP_055830 O94953 KDM4B_HUMAN lysine (K)-specific demethylase 4B 788 NA NA NA chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634) dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270) NA NA breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1) 32 TGTTCCCGGTGCGCGGCCCACGCCTGGACTG 0.682 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 267 241.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 2.32 NA NA AB020683 CCDS12138.1 19p13.3 2013-01-23 2009-04-06 2009-04-06 ENSG00000127663 23030 NA "Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing" 29136 protein-coding gene gene with protein product "tudor domain containing 14B" 609765 "jumonji domain containing 2B" JMJD2B NA 10048485, 15138608 Standard NM_015015 NM_015015 NA Approved KIAA0876, TDRD14B uc002mbq.4 O94953 ENST00000159111.4:c.2363_2373delGCGCGGCCCAC chr19.hg19:g.5137327_5137337delGCGCGGCCCAC ENSP00000159111:p.Cys788fs 0 4 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 200,206 34,36 22,17 1 1 B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40 True hg19 CCDS12138.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KDM4B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000450558.1 PASS NA None 267 NA True + GCGCGGCCCAC ENST00000159111.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 22 29890307 29890308 __UNKNOWN__ IGR INS - - AAAC rs361665|rs368203212|rs35022252|rs10628724 byFrequency LTS-011_T LTS-011_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:29890307_29890308insAAAC NA NEFH (2928 upstream) : THOC5 (11559 downstream) NA NA NA NA NA NA NA taccaaaaattaaacaaactac 0.505 NA NA NA NA NA NA NA NA 4248 0.848243 0.8661 0.7637 5008 , , NA 19123 0.9276 NA 0.7634 False NA ,,, NA NA NA 2504 0.8896 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 38 36.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.17 NA NA NA NA NA NA NA NA chr22.hg19:g.29890312_29890315dupAAAC 3 6 ref NA False 49 47 PASS 2 PASS ref->hom 0 NA 0,0 27,29 10,10 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 38 NA True AAAC UBQLN2 29978 __UNKNOWN__ __UNKNOWN__ X 56590535 56590535 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-011_T LTS-011_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:56590535delG ENST00000338222.5 + 1 510 c.229delG c.(229-231)gccfs p.A77fs NM_013444.3 NP_038472.2 Q9UHD9 UBQL2_HUMAN ubiquilin 2 77 Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}. NA NA NA cell death (GO:0008219) cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886) NA NA breast(2)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1) 21 GCTGATTTTTGCCGGAAAAAT 0.483 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(104;218 1492 6022 10838 28884) PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 225 222.94 NA NA NA NA NA 26 26 26 NA NA NA NA X NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 56590535 NA 2203 4299 6502 SO:0001589 frameshift_variant 0.14 NA NA AF189009 CCDS14374.1 Xp11.21 2014-09-17 ENSG00000188021 ENSG00000188021 29978 NA "Ubiquilin family" 12509 protein-coding gene gene with protein product "NEDD4 binding protein 4" 300264 NA 10675567 Standard NM_013444 NM_013444 NA Approved Chap1, Dsk2, RIHFB2157, LIC-2, CHAP1/DSK2, PLIC-2, N4BP4, PLIC2 uc004dus.3 Q9UHD9 OTTHUMG00000021669 ENST00000338222.5:c.229delG chrX.hg19:g.56590535delG ENSP00000345195:p.Ala77fs 0 5 ref NA False 111 109 PASS 1 PASS ref->het 0 NA 149,149 58,58 20,20 1 1 O94798|Q5D027|Q9H3W6|Q9HAZ4 True hg19 CCDS14374.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UBQLN2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000056891.1 PASS NA None 225 NA True + G ENST00000338222.5 ZNF512 84450 __UNKNOWN__ __UNKNOWN__ 2 27844929 27844947 __UNKNOWN__ 3'UTR DEL ATGCTGTTTATACTGGGAA ATGCTGTTTATACTGGGAA - LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:27844929_27844947delATGCTGTTTATACTGGGAA ENST00000355467.4 + 0 2388_2406 ZNF512_ENST00000379717.1_3'UTR|ZNF512_ENST00000556601.1_Intron|RP11-158I13.2_ENST00000505973.1_RNA NM_001271287.1|NM_001271288.1|NM_001271289.1|NM_001271318.1|NM_032434.3 NP_001258216.1|NP_001258217.1|NP_001258218.1|NP_001258247.1|NP_115810.2 Q96ME7 ZN512_HUMAN zinc finger protein 512 NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) NA breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 24 Acute lymphoblastic leukemia(172;0.155) GAACTACCCTATGCTGTTTATACTGGGAAATGCTTTGTA 0.374 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 92 91.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AL833748 CCDS1758.1, CCDS59428.1, CCDS59429.1 2p23 2008-02-05 ENSG00000243943 ENSG00000243943 84450 "Zinc fingers, C2H2-type" 29380 protein-coding gene gene with protein product NA NA 11347906 Standard NM_032434 NM_032434 NA Approved KIAA1805 uc002rla.4 Q96ME7 OTTHUMG00000097786 ENST00000355467.4:c.*619ATGCTGTTTATACTGGGAA>- chr2.hg19:g.27844929_27844947delATGCTGTTTATACTGGGAA 0 3 ref NA False 58 58 PASS 1 PASS ref->het 0 NA 64,67 20,21 17,19 1 1 B4DSM5|Q53RZ7|Q86XK6|Q96JM0 True hg19 CCDS1758.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF512-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000215029.2 PASS NA None 92 NA True + ATGCTGTTTATACTGGGAA ENST00000355467.4 RTN4 57142 __UNKNOWN__ __UNKNOWN__ 2 55200711 55200720 __UNKNOWN__ Frame_Shift_Del DEL TCTTTAACAT TCTTTAACAT - LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:55200711_55200720delTCTTTAACAT ENST00000394609.2 - 6 864_873 c.536_545delATGTTAAAGA c.(535-546)aatgttaaagatfs p.NVKD179fs RTN4_ENST00000402434.2_Frame_Shift_Del_p.NVKD325fs|RTN4_ENST00000486085.1_5'UTR|RTN4_ENST00000357376.3_Frame_Shift_Del_p.NVKD966fs|RTN4_ENST00000357732.4_Frame_Shift_Del_p.NVKD372fs|RTN4_ENST00000394611.2_Frame_Shift_Del_p.NVKD966fs|RTN4_ENST00000404909.1_Frame_Shift_Del_p.NVKD966fs|RTN4_ENST00000337526.6_Frame_Shift_Del_p.NVKD1172fs|RTN4_ENST00000405240.1_Frame_Shift_Del_p.NVKD966fs|RTN4_ENST00000354474.6_Frame_Shift_Del_p.NVKD940fs|RTN4_ENST00000317610.7_Frame_Shift_Del_p.NVKD353fs NM_007008.2 NP_008939.1 Q9NQC3 RTN4_HUMAN reticulon 4 1172 NA NA NA angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334) cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886) poly(A) RNA binding (GO:0044822) NA NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1) 36 AGCCATAGCATCTTTAACATTCTTATTTGC 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 184 174.79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 AF087901 CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1 2p14-p13 2008-05-23 ENSG00000115310 ENSG00000115310 57142 14085 protein-coding gene gene with protein product 604475 NA 10667797, 10773680 Standard NM_020532 NA Approved NSP-CL, KIAA0886, NOGO, ASY uc002rye.3 Q9NQC3 OTTHUMG00000129337 ENST00000394609.2:c.536_545delATGTTAAAGA chr2.hg19:g.55200711_55200720delTCTTTAACAT ENSP00000378107:p.Asn179fs 0 4 ref NA False 69 69 PASS 1 PASS ref->het 0 NA 162,166 16,16 14,16 1 1 O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6 True hg19 CCDS42685.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RTN4-008 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000326317.1 PASS NA None 184 NA True - TCTTTAACAT ENST00000394609.2 NEUROD1 4760 __UNKNOWN__ __UNKNOWN__ 2 182542422 182542455 __UNKNOWN__ 3'UTR DEL CAGCAGTAGTACCCAAAGGGCTGCCTTTTGTAAA CAGCAGTAGTACCCAAAGGGCTGCCTTTTGTAAA - rs41270211 byFrequency LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:182542422_182542455delCAGCAGTAGTACCCAAAGGGCTGCCTTTTGTAAA ENST00000295108.3 - 0 1590_1623 NEUROD1_ENST00000496876.1_Intron|CERKL_ENST00000479558.1_Intron NM_002500.4 NP_002491.2 Q13562 NDF1_HUMAN neuronal differentiation 1 NA NA NA NA amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019) cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134) NA endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 25 OV - Ovarian serous cystadenocarcinoma(117;0.088) TTGCACTTTGCAGCAGTAGTACCCAAAGGGCTGCCTTTTGTAAACACGACAGTC 0.436 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 42 42.88 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 U50823 CCDS2283.1 2q32 2013-05-21 2012-02-22 ENSG00000162992 ENSG00000162992 4760 "Basic helix-loop-helix proteins" 7762 protein-coding gene gene with protein product "beta-cell E-box transactivator 2", "neurogenic helix-loop-helix protein NEUROD" 601724 "neurogenic differentiation 1" NEUROD NA 7754368, 8786144 Standard NM_002500 NM_002500 NA Approved BETA2, BHF-1, NeuroD, bHLHa3, MODY6 uc002uof.4 Q13562 OTTHUMG00000132583 ENST00000295108.3:c.*95TTTACAAAAGGCAGCCCTTTGGGTACTACTGCTG>- chr2.hg19:g.182542422_182542455delCAGCAGTAGTACCCAAAGGGCTGCCTTTTGTAAA 0 4 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 29,30 8,8 16,15 1 1 B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8 True hg19 CCDS2283.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NEUROD1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255792.2 PASS NA None 42 NA True - CAGCAGTAGTACCCAAAGGGCTGCCTTTTGTAAA ENST00000295108.3 LEPREL1 55214 __UNKNOWN__ __UNKNOWN__ 3 189700811 189700811 __UNKNOWN__ Intron DEL G G - LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:189700811delG ENST00000319332.5 - 8 1522 LEPREL1_ENST00000427335.2_Intron NM_018192.3 NP_060662.2 Q8IVL5 P3H2_HUMAN leprecan-like 1 NA NA NA NA collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|peptidyl-proline hydroxylation (GO:0019511) basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794) iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797) NA NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(5) 41 all_cancers(143;4.01e-10)|Ovarian(172;0.0925) Lung(62;4.35e-05) GBM - Glioblastoma multiforme(93;0.02) L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126) CTCCTTTATAGGGTAAAAGTG 0.428 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 116 114.12 NA NA NA NA NA 129 124 126 NA NA NA NA 3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 189700811 NA 2203 4300 6503 SO:0001627 intron_variant 0.41 CCDS3294.1, CCDS46981.1 3q29 2014-01-28 ENSG00000090530 ENSG00000090530 55214 1.14.11.7 19317 protein-coding gene gene with protein product "prolyl 3-hydroxylase 2" 610341 NA 15063763, 21885030 Standard NM_018192 NM_018192 NA Approved FLJ10718, MLAT4, P3H2 uc011bsk.2 Q8IVL5 OTTHUMG00000156312 ENST00000319332.5:c.1324+23C>- chr3.hg19:g.189700811delG 2 3 ref NA False 196 125 PASS 3 PASS ref->het 0 NA 57,57 48,49 14,14 1 1 B3KPK0|B3KWI9|D3DNV8|Q9NVI2 True hg19 CCDS3294.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LEPREL1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000343855.1 PASS NA None 116 NA True - G ENST00000319332.5 RUFY3 22902 __UNKNOWN__ __UNKNOWN__ 4 71657400 71657413 __UNKNOWN__ Intron DEL CTGTATCTGCAAGC CTGTATCTGCAAGC - LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:71657400_71657413delCTGTATCTGCAAGC ENST00000381006.3 + 13 1916 RUFY3_ENST00000502653.1_Intron|RUFY3_ENST00000226328.4_3'UTR NM_001037442.2 NP_001032519.1 Q7L099 RUFY3_HUMAN RUN and FYVE domain containing 3 NA NA NA NA negative regulation of axonogenesis (GO:0050771) filopodium (GO:0030175)|growth cone (GO:0030426) NA endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1) 16 all_hematologic(202;0.248) Lung(101;0.235) TTGTTCATGTCTGTATCTGCAAGCCTGTTCTGCC 0.407 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 76 67.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF112221 CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1 4q13.3 2009-05-29 ENSG00000018189 ENSG00000018189 22902 "Zinc fingers, FYVE domain containing" 30285 protein-coding gene gene with protein product "single axon-related 1" 611194 NA 17439943 Standard NM_014961 NM_001130709 NA Approved RIPx, KIAA0871, Singar1 uc003hfr.3 Q7L099 OTTHUMG00000129910 ENST00000381006.3:c.1338-2089CTGTATCTGCAAGC>- chr4.hg19:g.71657400_71657413delCTGTATCTGCAAGC 0 2 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 56,58 15,16 11,10 1 1 B3KM25|B4DYW7|D9N163|O94948|Q9UI00 True hg19 CCDS34001.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RUFY3-002 NOVEL basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000252162.1 PASS NA None 76 NA True + CTGTATCTGCAAGC ENST00000381006.3 DDX60L 91351 __UNKNOWN__ __UNKNOWN__ 4 169278670 169278692 __UNKNOWN__ 3'UTR DEL AGAACAAGCTCTCTTGTCTCTCT AGAACAAGCTCTCTTGTCTCTCT - LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:169278670_169278692delAGAACAAGCTCTCTTGTCTCTCT ENST00000511577.1 - 0 5974_5996 DDX60L_ENST00000260184.7_3'UTR Q5H9U9 DDX6L_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like NA NA NA NA ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723) NA breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1) 43 Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132) GBM - Glioblastoma multiforme(119;0.175) cagagattggagaacaagctctcttgtctctctgttaaaggca 0.422 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 52 47.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AK092461 CCDS47161.1 4q32.3 2008-01-08 ENSG00000181381 91351 26429 protein-coding gene gene with protein product NA NA Standard NM_001012967 XM_005263341 NA Approved FLJ31033 uc003irq.4 Q5H9U9 ENST00000511577.1:c.*628AGAGAGACAAGAGAGCTTGTTCT>- chr4.hg19:g.169278670_169278692delAGAACAAGCTCTCTTGTCTCTCT 0 3 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 21,22 15,15 5,5 1 1 Q96ND6 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DDX60L-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000364839.1 PASS NA None 52 NA True - AGAACAAGCTCTCTTGTCTCTCT ENST00000511577.1 RASA1 5921 __UNKNOWN__ __UNKNOWN__ 5 86685305 86685334 __UNKNOWN__ In_Frame_Del DEL TGAACTTCGAACGCTCAGTAATGAGCGTGG TGAACTTCGAACGCTCAGTAATGAGCGTGG - LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:86685305_86685334delTGAACTTCGAACGCTCAGTAATGAGCGTGG ENST00000274376.6 + 24 3585_3614 c.3021_3050delTGAACTTCGAACGCTCAGTAATGAGCGTGG c.(3019-3051)gatgaacttcgaacgctcagtaatgagcgtggt>gat p.ELRTLSNERG1008del RASA1_ENST00000456692.2_In_Frame_Del_p.ELRTLSNERG831del|RASA1_ENST00000512763.1_In_Frame_Del_p.ELRTLSNERG841del|RASA1_ENST00000506290.1_In_Frame_Del_p.ELRTLSNERG842del NM_002890.2 NP_002881.1 P20936 RASA1_HUMAN RAS p21 protein activator (GTPase activating protein) 1 1008 NA NA NA blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570) cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726) glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102) p.R1016C(1)|p.R1016H(1) NA NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1) 48 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) CTCATTCAGATGAACTTCGAACGCTCAGTAATGAGCGTGGTGCACAGCAG 0.417 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 2 Substitution - Missense(2) upper_aerodigestive_tract(1)|prostate(1) GRCh37 CM083071 RASA1 M NA 119 115.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0 CCDS34200.1, CCDS47243.1 5q13 2013-02-14 ENSG00000145715 ENSG00000145715 5921 "Pleckstrin homology (PH) domain containing", "SH2 domain containing" 9871 protein-coding gene gene with protein product "capillary malformation-arteriovenous malformation" 139150 RASA NA 15917201 Standard NM_002890 NM_022650 NA Approved GAP, CM-AVM, p120GAP, p120RASGAP uc003kiw.3 P20936 OTTHUMG00000162605 ENST00000274376.6:c.3021_3050delTGAACTTCGAACGCTCAGTAATGAGCGTGG chr5.hg19:g.86685305_86685334delTGAACTTCGAACGCTCAGTAATGAGCGTGG ENSP00000274376:p.Glu1008_Gly1017del 0 3 ref NA False 40 40 PASS 1 PASS ref->het 0 NA 112,113 6,7 9,8 1 1 B2R6W3|Q9UDI1 True hg19 CCDS34200.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RASA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000369729.1 PASS NA None 119 NA True + TGAACTTCGAACGCTCAGTAATGAGCGTGG ENST00000274376.6 APC 324 __UNKNOWN__ __UNKNOWN__ 5 112116513 112116533 __UNKNOWN__ In_Frame_Del DEL AAGGCAATTGGAATATGAAGC AAGGCAATTGGAATATGAAGC - rs377493489|rs185154886 byFrequency LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:112116513_112116533delAAGGCAATTGGAATATGAAGC ENST00000457016.1 + 6 938_958 c.558_578delAAGGCAATTGGAATATGAAGC c.(556-579)agaaggcaattggaatatgaagca>aga p.RQLEYEA187del APC_ENST00000257430.4_In_Frame_Del_p.RQLEYEA187del|APC_ENST00000508376.2_In_Frame_Del_p.RQLEYEA187del P25054 APC_HUMAN adenomatous polyposis coli 187 Leu-rich. NA NA NA anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830) axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923) beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887) p.E190*(1)|p.Y191fs*2(1)|p.E192*(1)|p.Q188fs*2(1) NA NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20) 3261 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) ATATGACCAGAAGGCAATTGGAATATGAAGCAAGGCAAATC 0.339 NA 12 "D, Mis, N, F, S" NA "colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS" "colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS" NA NA Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis TSP Lung(16;0.13) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115) PASS yes Rec yes Adenomatous polyposis coli; Turcot syndrome 5 5q21 324 adenomatous polyposis of the colon gene NA "E, M, O" 4 Substitution - Nonsense(2)|Deletion - Frameshift(1)|Insertion - Frameshift(1) large_intestine(4) GRCh37 CM023005|CM990148 APC M NA 97 97.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0 Familial Cancer Database Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s, M74088 CCDS4107.1 5q21-q22 2014-09-17 2008-01-08 ENSG00000134982 ENSG00000134982 324 "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Armadillo repeat containing" 583 protein-coding gene gene with protein product "protein phosphatase 1, regulatory subunit 46" 611731 "adenomatosis polyposis coli" NA 1651563 Standard NM_000038 NM_001127511 NA Approved DP2, DP3, DP2.5, PPP1R46 uc003kpy.4 P25054 OTTHUMG00000128806 ENST00000457016.1:c.558_578delAAGGCAATTGGAATATGAAGC chr5.hg19:g.112116513_112116533delAAGGCAATTGGAATATGAAGC ENSP00000413133:p.Arg187_Ala193del 0 3 ref NA False 59 59 PASS 1 PASS ref->het 0 NA 121,130 4,4 8,6 2 2 D3DT03|Q15162|Q15163|Q93042 True hg19 CCDS4107.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA APC-201 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250738.2 PASS NA None 97 NA True + AAGGCAATTGGAATATGAAGC ENST00000457016.1 H2AFV 94239 __UNKNOWN__ __UNKNOWN__ 7 44887414 44887435 __UNKNOWN__ Intron DEL GACATGGCGCCCCCCGGCGGGC GACATGGCGCCCCCCGGCGGGC - rs147948728 LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:44887414_44887435delGACATGGCGCCCCCCGGCGGGC ENST00000308153.4 - 1 95 H2AFV_ENST00000222690.6_Intron|H2AFV_ENST00000446531.1_Intron|H2AFV_ENST00000350771.3_Intron|H2AFV_ENST00000381124.5_Intron|H2AFV_ENST00000437072.1_Intron|H2AFV_ENST00000349299.3_Intron|H2AFV_ENST00000521529.1_Intron NM_012412.4 NP_036544.1 Q71UI9 H2AV_HUMAN H2A histone family, member V NA NA NA NA extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634) DNA binding (GO:0003677) NA endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1) 9 CCGCAGCTGGGACATggcgccccccggcgggcggcgAGGGGC 0.73 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 432 447.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 3.45 AF081192 CCDS5495.1, CCDS5496.1, CCDS5497.1, CCDS5498.1, CCDS47581.1 7p13 2011-01-27 2004-03-26 ENSG00000105968 ENSG00000105968 94239 "Histones / Replication-independent" 20664 protein-coding gene gene with protein product NA H2AV NA Standard NM_012412 NM_012412 NA Approved MGC10170, MGC10831, MGC1947 uc003tma.2 Q71UI9 OTTHUMG00000129217 ENST00000308153.4:c.3+132GCCCGCCGGGGGGCGCCATGTC>- chr7.hg19:g.44887414_44887435delGACATGGCGCCCCCCGGCGGGC 0 5 ref NA False 202 202 PASS 1 PASS ref->het 0 NA 535,585 19,19 99,53 1 1 A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98 True hg19 CCDS5496.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA H2AFV-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000251305.1 PASS NA None 432 NA True - GACATGGCGCCCCCCGGCGGGC ENST00000308153.4 NDUFA5 4698 __UNKNOWN__ __UNKNOWN__ 7 123197726 123197753 __UNKNOWN__ Intron DEL CCGAGCCCGCGACAGTAGGGGTCAACAC CCGAGCCCGCGACAGTAGGGGTCAACAC - rs573568001 LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:123197726_123197753delCCGAGCCCGCGACAGTAGGGGTCAACAC ENST00000355749.2 - 1 481 NDUFA5_ENST00000471770.1_5'UTR|NDUFA5_ENST00000467117.1_Intron NM_001282419.1|NM_005000.2 NP_001269348.1|NP_004991.1 Q16718 NDUA5_HUMAN NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5 NA NA NA NA cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281) mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747) NADH dehydrogenase (ubiquinone) activity (GO:0008137) NA large_intestine(1)|urinary_tract(1) 2 AAAAGCACCGCCGAGCCCGCGACAGTAGGGGTCAACACCCGCGGGAAG 0.57 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 419 401.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.48 CCDS5788.1, CCDS64760.1, CCDS75655.1, CCDS75656.1 7q31.33 2013-06-19 2013-06-19 ENSG00000128609 ENSG00000128609 4698 "Mitochondrial respiratory chain complex / Complex I" 7688 protein-coding gene gene with protein product "complex I 13kDa subunit B", "ubiquinone reductase", "type I dehydrogenase", "NADH-ubiquinone oxidoreductase 13 kDa-B subunit" 601677 "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5 (13kD, B13)", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13kDa" NA 9763677, 9021153 Standard NM_005000 XM_005250371 NA Approved B13, NUFM, CI-13KD-B, UQOR13, CI-13kB uc003vks.3 Q16718 OTTHUMG00000157348 ENST00000355749.2:c.21+75GTGTTGACCCCTACTGTCGCGGGCTCGG>- chr7.hg19:g.123197726_123197753delCCGAGCCCGCGACAGTAGGGGTCAACAC 0 4 ref NA False 282 282 PASS 1 PASS ref->het 0 NA 423,430 19,20 55,51 1 1 B2RD98|Q5H9R2|Q6IRX7 True hg19 CCDS5788.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NDUFA5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000348533.1 PASS NA None 419 NA True - CCGAGCCCGCGACAGTAGGGGTCAACAC ENST00000355749.2 CTR9 9646 __UNKNOWN__ __UNKNOWN__ 11 10785268 10785274 __UNKNOWN__ Frame_Shift_Del DEL GGTTTGG GGTTTGG - LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:10785268_10785274delGGTTTGG ENST00000361367.2 + 9 1462_1468 c.1036_1042delGGTTTGG c.(1036-1044)ggtttgggafs p.GLG346fs NM_014633.3 NP_055448.1 Q6PD62 CTR9_HUMAN CTR9, Paf1/RNA polymerase II complex component 346 NA NA NA cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055) Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327) NA breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1) 40 all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111) CCCATTTTTTGGTTTGGGACAAATGTA 0.329 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 118 109.58 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 D63875 CCDS7805.1 11p15.3 2013-07-03 2013-07-03 2006-05-22 ENSG00000198730 ENSG00000198730 9646 "Tetratricopeptide (TTC) repeat domain containing" 16850 protein-coding gene gene with protein product 609366 "SH2 domain binding protein 1 (tetratricopeptide repeat containing)", "Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)" SH2BP1 NA 8590280, 8636124 Standard NM_014633 NM_014633 NA Approved KIAA0155, TSBP, p150TSP uc001mja.3 Q6PD62 OTTHUMG00000165789 ENST00000361367.2:c.1036_1042delGGTTTGG chr11.hg19:g.10785268_10785274delGGTTTGG ENSP00000355013:p.Gly346fs 0 6 ref NA False 52 52 PASS 1 PASS ref->het 0 NA 110,113 4,4 8,7 1 1 D3DQV8|Q15015 True hg19 CCDS7805.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CTR9-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000386215.1 PASS NA None 118 NA True + GGTTTGG ENST00000361367.2 HEPACAM 220296 __UNKNOWN__ __UNKNOWN__ 11 124792614 124792629 __UNKNOWN__ Intron DEL TGGGTGATTGGGTGGC TGGGTGATTGGGTGGC - rs11826299|rs568857575 byFrequency LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:124792614_124792629delTGGGTGATTGGGTGGC ENST00000298251.4 - 5 1283 NM_152722.4 NP_689935.2 hepatic and glial cell adhesion molecule NA NA NA NA NA breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 22 all_hematologic(175;0.215) Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308) GTTGATGGGATGGGTGATTGGGTGGCTGGGAGCTCA 0.509 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 121 121.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.38 AK098396 CCDS8456.1 11q24.2 2013-01-29 2011-02-11 ENSG00000165478 ENSG00000165478 220296 "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing" 26361 protein-coding gene gene with protein product "glial cell adhesion molecule" 611642 "hepatocyte cell adhesion molecule" NA 15885354, 15917256 Standard NM_152722 NM_152722 NA Approved FLJ25530, hepaCAM, GLIALCAM uc001qbk.3 Q14CZ8 OTTHUMG00000165938 ENST00000298251.4:c.877+11GCCACCCAATCACCCA>- chr11.hg19:g.124792614_124792629delTGGGTGATTGGGTGGC 0 3 ref NA False 67 67 PASS 1 PASS ref->het 0 NA 81,83 40,43 19,18 1 1 True hg19 CCDS8456.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HEPACAM-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000387125.1 PASS NA None 121 NA True - TGGGTGATTGGGTGGC ENST00000298251.4 FEM1B 10116 __UNKNOWN__ __UNKNOWN__ 15 68587915 68587917 __UNKNOWN__ 3'UTR DEL CTA CTA - LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:68587915_68587917delCTA ENST00000306917.4 + 0 6834_6836 NM_015322.4 NP_056137.1 Q9UK73 FEM1B_HUMAN fem-1 homolog b (C. elegans) NA NA NA NA apoptotic process (GO:0006915)|branching involved in prostate gland morphogenesis (GO:0060442)|epithelial cell maturation involved in prostate gland development (GO:0060743)|regulation of DNA damage checkpoint (GO:2000001)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of ubiquitin-protein transferase activity (GO:0051438) cytoplasm (GO:0005737)|nucleus (GO:0005634) death receptor binding (GO:0005123)|ubiquitin-protein transferase activity (GO:0004842) NA endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1) 9 CTGTTGTATTCTAGTAATTCACT 0.399 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 82 93.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.21 CCDS10228.1 15q22 2013-02-19 2001-11-28 ENSG00000169018 ENSG00000169018 10116 "Ankyrin repeat domain containing" 3649 protein-coding gene gene with protein product 613539 "FEM-1 (C. elegans) homolog b" NA 10623617 Standard NM_015322 NA Approved uc002arg.3 Q9UK73 OTTHUMG00000133285 ENST00000306917.4:c.*4337CTA>- chr15.hg19:g.68587915_68587917delCTA 0 3 ref NA False 154 96 PASS 1 PASS ref->het 0 NA 31,31 47,49 4,4 1 1 O43146 True hg19 CCDS10228.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FEM1B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257065.1 PASS NA None 82 NA True + CTA ENST00000306917.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 17 49209288 49209289 __UNKNOWN__ IGR INS - - C rs397774350|rs11376684 byFrequency LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:49209288_49209289insC NA SPAG9 (11062 upstream) : NME1 (21607 downstream) NA NA NA NA NA NA acgcctgtaatccagcactttg 0.47 NA NA NA NA NA NA NA CCC|CC|CCC|deletion 2481 0.495407 0.6142 0.5 5008 , , NA 16538 0.4345 NA 0.5288 False NA ,,, NA NA NA 2504 0.3599 NA NA NA PASS NA NA NA 0 NA 26 22.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr17.hg19:g.49209290_49209290dupC 3 2 ref NA False 30 30 PASS 2 PASS ref->hom 0 NA 0,0 25,28 1,2 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 26 NA True C TEN1 100134934 __UNKNOWN__ __UNKNOWN__ 17 73982218 73982233 __UNKNOWN__ Intron DEL ATCCGGTTTATCAGGA ATCCGGTTTATCAGGA - LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:73982218_73982233delATCCGGTTTATCAGGA ENST00000588202.1 + 2 271 TEN1-CDK3_ENST00000567351.1_RNA|TEN1_ENST00000416485.1_Intron|TEN1_ENST00000397640.1_Intron Q86WV5 TEN1L_HUMAN TEN1 CST complex subunit NA NA NA NA nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188) single-stranded DNA binding (GO:0003697) NA breast(1) 1 TTTGTAGTCTATCCGGTTTATCAGGAATCTTCAAAA 0.407 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 227 220.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS45780.1, CCDS45780.2 17q25.1 2013-05-23 2013-05-23 2011-06-14 ENSG00000257949 ENSG00000257949 100134934 37242 protein-coding gene gene with protein product 613130 "chromosome 17 open reading frame 106", "TEN1 telomerase capping complex subunit homolog (S. cerevisiae)" C17orf106 NA 19854130 Standard NM_001113324 NM_001113324 NA Approved FLJ39785 Q86WV5 OTTHUMG00000132686 ENST00000588202.1:c.-6-35ATCCGGTTTATCAGGA>- chr17.hg19:g.73982218_73982233delATCCGGTTTATCAGGA 0 2 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 262,270 8,8 24,23 1 1 I3L0C7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TEN1-005 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000449358.1 PASS NA None 227 NA True + ATCCGGTTTATCAGGA ENST00000588202.1 DHX35 60625 __UNKNOWN__ __UNKNOWN__ 20 37590990 37591014 __UNKNOWN__ Start_Codon_Del DEL CTCGTGACCTTTTACCCCAACATGG CTCGTGACCTTTTACCCCAACATGG - rs373968541 LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:37590990_37591014delCTCGTGACCTTTTACCCCAACATGG ENST00000252011.3 + 0 13_37 DHX35_ENST00000373323.4_Start_Codon_Del|DHX35_ENST00000373325.2_Start_Codon_Del NM_021931.3 NP_068750.2 Q9H5Z1 DHX35_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 35 NA NA NA NA mRNA splicing, via spliceosome (GO:0000398) catalytic step 2 spliceosome (GO:0071013) ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676) NA breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2) 40 Myeloproliferative disorder(115;0.00878) TGGAGCTAGCCTCGTGACCTTTTACCCCAACATGGCTGCGCCCGT 0.716 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 919 837.36 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001582 initiator_codon_variant 2.93 AK026412 CCDS13310.1, CCDS54463.1 20q11.22-q12 2003-06-13 2003-06-13 2003-06-13 ENSG00000101452 ENSG00000101452 60625 "DEAH-boxes" 15861 protein-coding gene gene with protein product NA "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35" C20orf15, DDX35 NA Standard NM_021931 NM_001190809 NA Approved FLJ22759, KAIA0875 uc002xjh.3 Q9H5Z1 OTTHUMG00000032463 ENST00000252011.3: chr20.hg19:g.37590990_37591014delCTCGTGACCTTTTACCCCAACATGG 0 3 ref NA False 204 204 PASS 1 PASS ref->het 0 NA 954,969 34,34 90,75 1 1 A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6 True hg19 CCDS13310.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DHX35-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000079212.2 PASS NA None 919 NA True + CTCGTGACCTTTTACCCCAACATGG ENST00000252011.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ Y 13842751 13842752 __UNKNOWN__ IGR INS - - CATCC LTS-012_T LTS-012_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrY:13842751_13842752insCATCC NA SLC9B1P1 (318034 upstream) : AC011293.1 (104690 downstream) NA NA NA NA NA NA tggaatggaatggaatggaatg 0.416 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA 533 431.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 55.86 NA NA NA NA NA chrY.hg19:g.13842751_13842752insCATCC 1 2 ref NA False 36 36 PASS 0 PASS ref->het 0 NA 136,394 8,20 371,385 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 533 NA True CATCC Unknown 0 __UNKNOWN__ __UNKNOWN__ M 303 304 __UNKNOWN__ IGR DEL CC CC - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrM:303_304delCC NA None (None upstream) : MT-TF (272 downstream) NA NA NA NA NA TTCCACCAAACCCCCCCCTCCC 0.416 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 352 372.31 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 6.36 NA NA NA NA NA chrM.hg19:g.309_310delCC 6 14 ref NA False 535 122 PASS 8 PASS ref->het 0 NA 49,56 200,215 112,92 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 352 True C TAS1R3 83756 __UNKNOWN__ __UNKNOWN__ 1 1268759 1268784 __UNKNOWN__ Splice_Site DEL GGTGAGCCGCCTTCCCGGCAGGCGGG GGTGAGCCGCCTTCCCGGCAGGCGGG - rs199520997|rs201750146|rs368910171|rs200623974|rs372269701|rs375055053 LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:1268759_1268784delGGTGAGCCGCCTTCCCGGCAGGCGGG ENST00000339381.5 + 5 1632 c.1600delGGTGAGCCGCCTTCCCGGCAGGCGGG c.(1600-1602)ggt>gt p.G534fs NM_152228.1 NP_689414 Q7RTX0 TS1R3_HUMAN taste receptor, type 1, member 3 534 NA NA NA detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527) kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1) 12 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217) Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146) GCAAAACCCAGGTGAGCCGCCTTCCCGGCAGGCGGGGGTGGGAACG 0.668 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 385 370.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 2.89 AC026283 CCDS30556.1 1p36 2012-08-22 ENSG00000169962 ENSG00000169962 83756 "Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors" 15661 protein-coding gene gene with protein product 605865 NA 11319557 Standard XM_006710939 NA Approved T1R3 uc010nyk.2 Q7RTX0 OTTHUMG00000003071 ENST00000339381.5:c.1600+1GGTGAGCCGCCTTCCCGGCAGGCGGG>- chr1.hg19:g.1268759_1268784delGGTGAGCCGCCTTCCCGGCAGGCGGG 0 8 ref NA False 75 75 PASS 1 PASS ref->het 0 NA 316,342 55,58 105,76 2 2 Q5TA49|Q8NGW9 True hg19 CCDS30556.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TAS1R3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000008493.1 PASS NA None 385 Frame_Shift_Del True + GGTGAGCCGCCTTCCCGGCAGGCGGG ENST00000339381.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ 1 146512626 146512626 __UNKNOWN__ IGR DEL G G - rs373970632|rs11345331|rs75947882 byFrequency LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:146512626delG NA RP4-704D21.2 (37449 upstream) : RNVU1-8 (38668 downstream) NA NA NA NA NA GGAATGAGAAGGGGCTAGGGA 0.373 NA NA NA NA NA NA |||unknown(NO_COVERAGE) 1752 0.34984 0.4932 0.2378 5008 , , NA 20738 0.5129 NA 0.171 False NA ,,, NA NA NA 2504 0.2515 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 85 80.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.36 NA NA NA NA NA chr1.hg19:g.146512626delG 3 4 ref NA False 51 45 PASS 4 PASS ref->hom 0 NA 0,0 69,75 16,13 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 85 True G TTC24 164118 __UNKNOWN__ __UNKNOWN__ 1 156554983 156555000 __UNKNOWN__ In_Frame_Del DEL GGCAAACGTTCCGGTGAG GGCAAACGTTCCGGTGAG - rs376431462 LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:156554983_156555000delGGCAAACGTTCCGGTGAG ENST00000368237.3 + 7 1416_1433 c.1416_1433delGGCAAACGTTCCGGTGAG c.(1414-1434)tcggcaaacgttccggtgagg>tcg p.ANVPVR473del TTC24_ENST00000368236.3_In_Frame_Del_p.ANVPVR473del|TTC24_ENST00000478081.1_3'UTR A2A3L6 TTC24_HUMAN tetratricopeptide repeat domain 24 473 NA NA NA p.A473P(1) breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1) 20 all_hematologic(923;0.088)|Hepatocellular(266;0.158) AGGAGAGGTCGGCAAACGTTCCGGTGAGGGCTGGGCCG 0.578 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 1 Substitution - Missense(1) lung(1) NA NA NA NA NA 487 469.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 2.54 CCDS53379.1 1q22 2013-01-10 ENSG00000187862 ENSG00000187862 164118 "Tetratricopeptide (TTC) repeat domain containing" 32348 protein-coding gene gene with protein product NA NA Standard XM_089384 NM_001105669 NA Approved uc021pbf.1 A2A3L6 OTTHUMG00000033202 ENST00000368237.3:c.1416_1433delGGCAAACGTTCCGGTGAG chr1.hg19:g.156554983_156555000delGGCAAACGTTCCGGTGAG ENSP00000357220:p.Ala473_Arg478del 0 4 ref NA False 74 74 PASS 1 PASS ref->het 0 NA 488,506 13,13 66,50 1 1 Q5T3H7 True hg19 CCDS53379.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TTC24-006 NOVEL basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000158547.1 PASS NA None 487 True + GGCAAACGTTCCGGTGAG ENST00000368237.3 NCSTN 23385 __UNKNOWN__ __UNKNOWN__ 1 160322755 160322756 __UNKNOWN__ Frame_Shift_Ins INS - - T LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:160322755_160322756insT ENST00000294785.5 + 9 1200_1201 c.1075_1076insT c.(1075-1077)gttfs p.V359fs NCSTN_ENST00000459963.1_3'UTR|NCSTN_ENST00000535857.1_Frame_Shift_Ins_p.V221fs|NCSTN_ENST00000368065.4_Frame_Shift_Ins_p.V101fs|NCSTN_ENST00000392212.4_Frame_Shift_Ins_p.V339fs|NCSTN_ENST00000368063.1_Frame_Shift_Ins_p.V339fs NM_015331.2 NP_056146.1 Q92542 NICA_HUMAN nicastrin 359 NA NA NA amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)|proteolysis (GO:0006508)|T cell proliferation (GO:0042098) endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886) endopeptidase activity (GO:0004175) breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(2) 34 all_cancers(52;8.15e-18)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.111) GTTAGAGAATGTTGACTCATTT 0.48 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 251 239.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 2.48 AF240468 CCDS1203.1 1q22-q23 2014-09-17 ENSG00000162736 ENSG00000162736 23385 17091 protein-coding gene gene with protein product 605254 NA 9039502, 10993067 Standard NM_015331 XM_005245053 NA Approved KIAA0253, APH2 uc001fvx.3 Q92542 OTTHUMG00000033110 ENST00000294785.5:c.1077dupT chr1.hg19:g.160322757_160322757dupT ENSP00000294785:p.Val359fs 3 3 ref NA False 44 44 PASS 2 PASS ref->het 0 NA 166,172 58,60 29,24 1 1 Q5T207|Q5T208|Q86VV5 True hg19 CCDS1203.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NCSTN-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000080622.1 PASS NA None 251 True + T ENST00000294785.5 SOAT1 6646 __UNKNOWN__ __UNKNOWN__ 1 179314237 179314248 __UNKNOWN__ Intron DEL TCATGCATAAAT TCATGCATAAAT - rs56287445 byFrequency LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:179314237_179314248delTCATGCATAAAT ENST00000367619.3 + 11 1260 SOAT1_ENST00000540564.1_Intron|SOAT1_ENST00000535686.1_Intron|SOAT1_ENST00000539888.1_Intron NM_003101.5 NP_003092.4 P35610 SOAT1_HUMAN sterol O-acyltransferase 1 NA NA NA NA cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol storage (GO:0010878)|macrophage derived foam cell differentiation (GO:0010742)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|very-low-density lipoprotein particle assembly (GO:0034379) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020) cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|sterol O-acyltransferase activity (GO:0004772) central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1) 20 Ezetimibe(DB00973)|Hesperetin(DB01094) GTTAATTTGGTCATGCATAAATTCACGAGGTA 0.406 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 268 258.88 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.44 L21934 CCDS1330.1, CCDS58047.1, CCDS58048.1 1q25 2008-08-26 2008-08-26 ENSG00000057252 ENSG00000057252 6646 2.3.1.26 11177 protein-coding gene gene with protein product "acyl-Coenzyme A: cholesterol acyltransferase" 102642 "sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1" SOAT, STAT NA 8407899 Standard NM_003101 NM_003101 NA Approved ACAT uc001gml.3 P35610 OTTHUMG00000035253 ENST00000367619.3:c.1117+26TCATGCATAAAT>- chr1.hg19:g.179314237_179314248delTCATGCATAAAT 0 3 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 145,147 87,88 36,33 1 1 A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4 True hg19 CCDS1330.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SOAT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000085286.2 PASS NA None 268 True + TCATGCATAAAT ENST00000367619.3 RGS8 85397 __UNKNOWN__ __UNKNOWN__ 1 182635105 182635133 __UNKNOWN__ Splice_Site DEL CTTATGAGAGAGAAGCACATCAAAGGAAT CTTATGAGAGAGAAGCACATCAAAGGAAT - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:182635105_182635133delCTTATGAGAGAGAAGCACATCAAAGGAAT ENST00000483095.2 - 5 421_449 c.164_192delATTCCTTTGATGTGCTTCTCTCTCATAAG c.(163-192)gattcctttgatgtgcttctctctcataag>g p.DSFDVLLSHK55fs RGS8_ENST00000258302.4_Splice_Site_p.DSFDVLLSHK73fs|RGS8_ENST00000367557.4_Splice_Site_p.DSFDVLLSHK55fs|RGS8_ENST00000367556.1_Splice_Site_p.DSFDVLLSHK55fs|RGS8_ENST00000491420.2_5'UTR P57771 RGS8_HUMAN regulator of G-protein signaling 8 55 NA NA NA positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032) cytoplasm (GO:0005737)|plasma membrane (GO:0005886) GTPase activator activity (GO:0005096) haematopoietic_and_lymphoid_tissue(1)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1) 5 TCTACTTACACTTATGAGAGAGAAGCACATCAAAGGAATCTGCCCACCT 0.419 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Ovarian(189;1262 3804 41973) PASS NA NA NA 0 NA NA NA NA NA 708 647.79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0.75 AF297015 CCDS1349.1, CCDS41443.1 1q25 2008-07-18 2007-08-14 ENSG00000135824 ENSG00000135824 85397 "Regulators of G-protein signaling" 16810 protein-coding gene gene with protein product 607189 "regulator of G-protein signalling 8" NA 11318611 Standard NM_033345 NM_001102450 NA Approved MGC119067, MGC119068, MGC119069 uc001gpm.1 P57771 OTTHUMG00000035219 ENST00000483095.2:c.193+1ATTCCTTTGATGTGCTTCTCTCTCATAAG>- chr1.hg19:g.182635105_182635133delCTTATGAGAGAGAAGCACATCAAAGGAAT 0 2 ref NA False 68 68 PASS 1 PASS ref->het 0 NA 782,793 22,22 92,81 1 1 B4DGL9|Q3SYD2 True hg19 CCDS41443.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RGS8-005 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000358979.1 PASS NA None 708 Frame_Shift_Del True - CTTATGAGAGAGAAGCACATCAAAGGAAT ENST00000483095.2 ANKRD36C 400986 __UNKNOWN__ __UNKNOWN__ 2 96601300 96601301 __UNKNOWN__ Intron INS - - TAATTGAG LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:96601300_96601301insTAATTGAG ENST00000456556.1 - 24 1747 Q5JPF3 AN36C_HUMAN ankyrin repeat domain 36C NA NA NA NA ion channel inhibitor activity (GO:0008200) breast(1)|endometrium(8)|kidney(5)|lung(4) 18 AACATAATGATTAATATATCAT 0.356 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 463 459.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.27 AL832836 2q11.1 2013-01-10 ENSG00000174501 ENSG00000174501 400986 "Ankyrin repeat domain containing" 32946 protein-coding gene gene with protein product "protein immuno-reactive with anti-PTH polyclonal antibodies" NA NA Standard NM_001010914 XR_251121 NA Approved DKFZp667P0924 uc002suz.1 Q5JPF3 OTTHUMG00000155211 ENST00000456556.1:c.1663-26->CTCAATTA chr2.hg19:g.96601300_96601301insTAATTGAG 1 2 ref NA False 38 38 PASS 0 PASS ref->het 0 NA 381,423 11,11 73,80 1 1 C9JZ08|Q15694|Q53S06|Q658V2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ANKRD36C-001 KNOWN not_best_in_genome_evidence|basic|appris_principal protein_coding NA protein_coding OTTHUMT00000338799.2 PASS NA None 463 True - TAATTGAG ENST00000456556.1 LIPT1 51601 __UNKNOWN__ __UNKNOWN__ 2 99771990 99772005 __UNKNOWN__ 5'UTR DEL GTCCCAAGAACATGGA GTCCCAAGAACATGGA - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:99771990_99772005delGTCCCAAGAACATGGA ENST00000340066.1 + 0 143_158 LIPT1_ENST00000393477.3_Intron|LIPT1_ENST00000393473.2_Intron|LIPT1_ENST00000393474.3_Intron|MRPL30_ENST00000410042.1_Intron|LIPT1_ENST00000393471.2_Intron Q9Y234 LIPT_HUMAN lipoyltransferase 1 NA NA NA NA cellular protein modification process (GO:0006464)|lipid metabolic process (GO:0006629)|protein lipoylation (GO:0009249) mitochondrion (GO:0005739) transferase activity, transferring acyl groups (GO:0016746) large_intestine(6)|lung(1) 7 Lipoic Acid(DB00166) GTAGCGAAGTGTCCCAAGAACATGGAAGGTAAGGAA 0.426 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(84;665 1268 21657 25485 30647) PASS NA NA NA 0 NA NA NA NA NA 212 212.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.26 AB017566 CCDS2039.1 2q11.2 2010-11-25 ENSG00000144182 ENSG00000144182 51601 2.3.1.181 29569 protein-coding gene gene with protein product 610284 NA 10103005 Standard NM_015929 NM_145197 NA Approved MGC12290, MGC13378 uc002szq.4 Q9Y234 OTTHUMG00000130640 ENST00000340066.1:c.-4GTCCCAAGAACATGGA>- chr2.hg19:g.99771990_99772005delGTCCCAAGAACATGGA 0 2 ref NA False 122 111 PASS 1 PASS ref->het 0 NA 127,131 54,54 13,13 2 1 Q4ZFZ1 True hg19 CCDS2039.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LIPT1-201 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253128.1 PASS NA None 212 True + GTCCCAAGAACATGGA ENST00000340066.1 MLTK 0 __UNKNOWN__ __UNKNOWN__ 2 174123409 174123414 __UNKNOWN__ Intron DEL TTTTGT TTTTGT - rs150855284|rs200739044|rs200393933 byFrequency LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:174123409_174123414delTTTTGT ENST00000375213.3 + 17 1437 MLK7-AS1_ENST00000423106.2_RNA|MLTK_ENST00000409176.2_Intron|MLK7-AS1_ENST00000422703.1_RNA NM_016653.2 NP_057737.2 Q9NYL2 MLTK_HUMAN NA NA NA NA activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950) cytoplasm (GO:0005737)|nucleus (GO:0005634) ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674) NA AATTCTGTAATTTTGTTTTTAATTCC 0.282 NA NA NA NA NA NA 668 0.133387 0.031 0.1009 5008 , , NA 18219 0.4812 NA 0.0328 False NA ,,, NA NA NA 2504 0.0399 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 45 46.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA NA NA NA ENST00000375213.3:c.1360-13TTTTGT>- chr2.hg19:g.174123409_174123414delTTTTGT 0 9 ref NA False 36 35 PASS 1 PASS ref->het 0 NA 3,3 40,41 2,2 1 1 B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9 True hg19 CCDS42777.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MLTK-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255401.1 PASS NA None 45 True + TTTTGT ENST00000375213.3 MPP4 58538 __UNKNOWN__ __UNKNOWN__ 2 202519583 202519606 __UNKNOWN__ In_Frame_Del DEL CTGGGATTAAATTCAATAAGTTGT CTGGGATTAAATTCAATAAGTTGT - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:202519583_202519606delCTGGGATTAAATTCAATAAGTTGT ENST00000409143.1 - 13 1397_1420 c.1161_1184delACAACTTATTGAATTTAATCCCAG c.(1159-1185)agacaacttattgaatttaatcccagc>agc p.RQLIEFNP387del MPP4_ENST00000409474.3_In_Frame_Del_p.RQLIEFNP445del|MPP4_ENST00000447335.2_In_Frame_Del_p.RQLIEFNP438del|MPP4_ENST00000396886.3_In_Frame_Del_p.RQLIEFNP370del|MPP4_ENST00000315506.7_In_Frame_Del_p.RQLIEFNP401del|MPP4_ENST00000359962.5_In_Frame_Del_p.RQLIEFNP445del|MPP4_ENST00000428900.2_In_Frame_Del_p.RQLIEFNP421del Q96JB8 MPP4_HUMAN membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4) 445 NA NA NA protein localization to synapse (GO:0035418) cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|presynaptic membrane (GO:0042734) kidney(1)|lung(11) 12 TTGAAAATGGCTGGGATTAAATTCAATAAGTTGTCTTCTGAGCT 0.344 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 362 334.85 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.06 AF316032 CCDS46491.1 2q33.2 2008-05-15 ENSG00000082126 ENSG00000082126 58538 13680 protein-coding gene gene with protein product 606575 DLG6 NA 11414766 Standard NM_033066 NA Approved uc002uyk.4 Q96JB8 OTTHUMG00000154525 ENST00000409143.1:c.1161_1184delACAACTTATTGAATTTAATCCCAG chr2.hg19:g.202519583_202519606delCTGGGATTAAATTCAATAAGTTGT ENSP00000387293:p.Arg387_Pro394del 0 3 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 404,405 10,10 34,34 1 1 C9IZK4|Q53TT3|Q6ZNH6|Q96Q43|Q96Q44 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MPP4-007 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000335779.1 PASS NA None 362 True - CTGGGATTAAATTCAATAAGTTGT ENST00000409143.1 OXTR 5021 __UNKNOWN__ __UNKNOWN__ 3 8809912 8809912 __UNKNOWN__ 5'UTR DEL T T - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:8809912delT ENST00000316793.3 - 0 586 CAV3_ENST00000472766.1_Intron NM_000916.3 NP_000907.2 P30559 OXYR_HUMAN oxytocin receptor NA NA NA NA cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537) apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886) oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000) NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1) 13 OV - Ovarian serous cystadenocarcinoma(96;0.15) Carbetocin(DB01282)|Oxytocin(DB00107) CTTCGAGCCCTTTACGGCTTG 0.751 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 143 144.86 NA NA NA NA NA 1 1 1 NA NA NA NA 3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8809912 NA 402 631 1033 SO:0001623 5_prime_UTR_variant 5.63 CCDS2570.1 3p25 2012-08-08 ENSG00000180914 ENSG00000180914 5021 "GPCR / Class A : Vasopressin and oxytocin receptors" 8529 protein-coding gene gene with protein product 167055 NA 1313946 Standard NM_000916 NA Approved uc003brc.3 P30559 OTTHUMG00000090537 ENST00000316793.3:c.-39A>- chr3.hg19:g.8809912delT 2 3 ref NA False 47 47 PASS 3 PASS ref->het 0 NA 65,84 31,41 48,19 1 1 Q15071 True hg19 CCDS2570.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OXTR-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000207061.2 PASS NA None 143 True - T ENST00000316793.3 OGG1 4968 __UNKNOWN__ __UNKNOWN__ 3 9799021 9799025 __UNKNOWN__ 3'UTR DEL GCGCT GCGCT - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:9799021_9799025delGCGCT ENST00000344629.7 + 0 1568_1572 OGG1_ENST00000302008.8_Intron|OGG1_ENST00000302036.7_Intron|OGG1_ENST00000349503.5_Intron|OGG1_ENST00000302003.7_3'UTR|OGG1_ENST00000449570.2_Intron|CAMK1_ENST00000256460.3_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000339511.5_3'UTR O15527 OGG1_HUMAN 8-oxoguanine DNA glycosylase NA NA NA NA acute inflammatory response (GO:0002526)|base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cellular response to cadmium ion (GO:0071276)|depurination (GO:0045007)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314) mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity (GO:0034039)|damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|oxidized purine nucleobase lesion DNA N-glycosylase activity (GO:0008534) kidney(2)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1) 8 Medulloblastoma(99;0.227) GAGGGAGACAGCGCTAAGGATGGTT 0.483 NA NA NA NA Base excision repair (BER), DNA glycosylases NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 551 521.23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.98 U96710 CCDS2576.1, CCDS2577.1, CCDS2578.1, CCDS2579.1, CCDS2580.1, CCDS2581.1, CCDS43046.1, CCDS46742.1 3p26 2010-11-23 ENSG00000114026 ENSG00000114026 4968 3.2.2.-, 4.2.99.18 8125 protein-coding gene gene with protein product "8-hydroxyguanine DNA glycosylase", "OGG1 type 1e", "OGG1 type 1d", "OGG1 type 1g", "OGG1 type 1h" 601982 NA 9207108, 10449904 Standard NM_016821 NM_002542 NA Approved HMMH, HOGG1, OGH1, MUTM uc003bsj.3 O15527 OTTHUMG00000097091 ENST00000344629.7:c.*191GCGCT>- chr3.hg19:g.9799021_9799025delGCGCT 0 2 ref NA False 72 72 PASS 1 PASS ref->het 0 NA 481,490 14,14 60,56 1 1 A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4 True hg19 CCDS2581.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OGG1-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000214223.2 PASS NA None 551 True + GCGCT ENST00000344629.7 DAZL 1618 __UNKNOWN__ __UNKNOWN__ 3 16628477 16628477 __UNKNOWN__ 3'UTR DEL C C - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:16628477delC ENST00000399444.2 - 0 2871 DAZL_ENST00000250863.8_3'UTR NM_001351.3 NP_001342.2 Q92904 DAZL_HUMAN deleted in azoospermia-like NA NA NA NA female meiosis II (GO:0007147)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|oocyte maturation (GO:0001556)|positive regulation of meiosis (GO:0045836)|positive regulation of translational initiation (GO:0045948)|spermatogenesis (GO:0007283) cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844) mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|translation activator activity (GO:0008494) RAF1/DAZL(2) endometrium(1)|large_intestine(3)|lung(4)|prostate(3) 11 TATTCCCTTACTTTTCCTTAA 0.284 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 171 191.33 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.29 BC027595 CCDS43059.1, CCDS54556.1 3p24 2013-02-12 ENSG00000092345 ENSG00000092345 1618 "RNA binding motif (RRM) containing" 2685 protein-coding gene gene with protein product 601486 DAZLA NA 8896558 Standard NM_001351 NM_001351 NA Approved DAZH, SPGYLA, MGC26406, DAZL1 uc003cbb.3 Q92904 OTTHUMG00000157050 ENST00000399444.2:c.*1690G>- chr3.hg19:g.16628477delC 0 4 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 125,127 31,32 15,13 1 1 O15396|Q5HYB4|Q92909 True hg19 CCDS43059.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DAZL-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000347261.2 PASS NA None 171 True - C ENST00000399444.2 ANXA5 308 __UNKNOWN__ __UNKNOWN__ 4 122605833 122605854 __UNKNOWN__ Splice_Site DEL CTGCCAAACAGAGTCTTAAAAG CTGCCAAACAGAGTCTTAAAAG - rs370104706|rs376942269 LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:122605833_122605854delCTGCCAAACAGAGTCTTAAAAG ENST00000296511.5 - 4 452_473 c.167_188delCTTTTAAGACTCTGTTTGGCAG c.(166-189)gcttttaagactctgtttggcagg>gg p.AFKTLFGR56fs ANXA5_ENST00000515017.1_Intron|ANXA5_ENST00000501272.2_Intron|ANXA5_ENST00000509016.1_5'UTR NM_001154.3 NP_001145.1 P08758 ANXA5_HUMAN annexin A5 56 NA NA NA blood coagulation (GO:0007596)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of coagulation (GO:0050819)|response to organic substance (GO:0010033)|signal transduction (GO:0007165) cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020) calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipase inhibitor activity (GO:0004859)|phospholipid binding (GO:0005543) NS(1)|breast(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1) 15 TGGTCTTACCCTGCCAAACAGAGTCTTAAAAGCTGCAGAGAT 0.401 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(191;1279 2147 16046 17806 52646)|GBM(88;628 1285 16585 32846 50188) PASS NA NA NA 0 NA NA NA NA NA 241 226.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0.3 U05770 CCDS3720.1 4q27 2008-02-05 ENSG00000164111 ENSG00000164111 308 "Annexins" 543 protein-coding gene gene with protein product 131230 ENX2, ANX5 NA 2960376 Standard NM_001154 NM_001154 NA Approved uc003idv.4 P08758 OTTHUMG00000133034 ENST00000296511.5:c.189+1CTTTTAAGACTCTGTTTGGCAG>- chr4.hg19:g.122605833_122605854delCTGCCAAACAGAGTCTTAAAAG 0 4 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 272,275 7,7 21,19 1 1 D3DNW7|Q6FHB3|Q6FI16|Q8WV69|Q9UDH9 True hg19 CCDS3720.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ANXA5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256636.2 PASS NA None 241 Frame_Shift_Del True - CTGCCAAACAGAGTCTTAAAAG ENST00000296511.5 ARSB 411 __UNKNOWN__ __UNKNOWN__ 5 78074102 78074112 __UNKNOWN__ 3'UTR DEL GTTGGGTAAAG GTTGGGTAAAG - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:78074102_78074112delGTTGGGTAAAG ENST00000264914.4 - 0 4246_4256 NM_000046.3 NP_000037.2 P15848 ARSB_HUMAN arylsulfatase B NA NA NA NA autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|lysosomal transport (GO:0007041)|lysosome organization (GO:0007040)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665) endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|rough endoplasmic reticulum (GO:0005791) arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943) breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 18 all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192) OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34) CAACCCAGGAGTTGGGTAAAGGTTGGTAAGA 0.422 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Melanoma(169;563 1968 25780 26156 52266) PASS NA NA NA 0 NA NA NA NA NA 150 154.04 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.06 M32373 CCDS4043.1, CCDS43334.1 5q14.1 2013-02-14 ENSG00000113273 ENSG00000113273 411 3.1.6.1 "Arylsulfatase family" 714 protein-coding gene gene with protein product 611542 NA 2303452 Standard NM_000046 NM_000046 NA Approved uc003kfq.3 P15848 OTTHUMG00000108129 ENST00000264914.4:c.*2118CTTTACCCAAC>- chr5.hg19:g.78074102_78074112delGTTGGGTAAAG 0 3 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 108,109 26,26 23,22 1 1 B2RC20|Q8N322|Q9UDI9 True hg19 CCDS4043.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARSB-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000226932.2 PASS NA None 150 True - GTTGGGTAAAG ENST00000264914.4 LYRM4 57128 __UNKNOWN__ __UNKNOWN__ 6 5138810 5138810 __UNKNOWN__ Intron DEL T T - rs11301112|rs200564319 byFrequency LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:5138810delT ENST00000480566.1 - 3 248 LYRM4_ENST00000468929.1_Intron|LYRM4_ENST00000330636.4_Intron|LYRM4_ENST00000464010.1_Intron Q9HD34 LYRM4_HUMAN LYR motif containing 4 NA NA NA NA small molecule metabolic process (GO:0044281) mitochondrial matrix (GO:0005759)|nucleus (GO:0005634) endometrium(1) 1 Ovarian(93;0.11) all_hematologic(90;0.0901) ATAATGACTGTTTTTTTTATG 0.274 NA NA NA NA NA NA TTTTTTTT|TTTTTTTT|TTTTTTT|deletion 4245 0.847644 0.8343 0.7507 5008 , , NA 15245 0.9226 NA 0.825 False NA ,,, NA NA NA 2504 0.8804 NA NA NA NSCLC(130;1006 2426 17608 36797) PASS NA NA NA 0 NA NA NA NA NA 197 210.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.35 AF258559 CCDS4493.1, CCDS54961.1 6p25.1 2008-02-05 2006-09-19 2006-09-19 ENSG00000214113 ENSG00000214113 57128 "LYR motif containing" 21365 protein-coding gene gene with protein product 613311 "chromosome 6 open reading frame 149" C6orf149 NA Standard NM_020408 XM_005249239 NA Approved CGI-203, ISD11 uc021ykw.1 Q9HD34 OTTHUMG00000014173 ENST00000480566.1:c.210+131A>- chr6.hg19:g.5138810delT 7 9 ref NA False 66 59 PASS 8 PASS ref->het 0 NA 11,13 165,168 21,19 1 1 A8K543|Q5XKP1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LYRM4-005 PUTATIVE basic|appris_principal protein_coding NA protein_coding OTTHUMT00000353483.1 PASS NA None 197 True - T ENST00000480566.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 42695934 42695934 __UNKNOWN__ IGR DEL A A - rs113558090 byFrequency LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:42695934delA NA PRPH2 (5622 upstream) : TBCC (16284 downstream) NA NA NA NA NA ATTTGGGGGGAAAAAAAAGAA 0.512 NA NA NA NA NA NA AAAAAAAA|AAAAAAAA|AAAAAAA|deletion 851 0.169928 0.2821 0.2003 5008 , , NA 12584 0.1081 NA 0.0895 False NA ,,, NA NA NA 2504 0.1431 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 77 76.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.63 NA NA NA NA NA chr6.hg19:g.42695934delA 7 11 ref NA False 56 30 PASS 8 PASS ref->het 0 NA 5,5 59,62 12,10 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 77 True A HDAC9 9734 __UNKNOWN__ __UNKNOWN__ 7 18707102 18707102 __UNKNOWN__ Intron DEL A A - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:18707102delA ENST00000441542.2 + 11 1731 HDAC9_ENST00000406072.1_3'UTR|HDAC9_ENST00000432645.2_Intron|HDAC9_ENST00000405010.3_3'UTR|HDAC9_ENST00000401921.1_Intron|HDAC9_ENST00000406451.4_Intron NM_178425.2 NP_848512.1 Q9UKV0 HDAC9_HUMAN histone deacetylase 9 NA NA NA NA B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667) histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134) breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 82 all_lung(11;0.187) Valproic Acid(DB00313) TAGGTTTAACAAAAAAATTTA 0.303 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 113 128.13 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF124924 CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1 7p21.1 2008-05-15 ENSG00000048052 ENSG00000048052 9734 14065 protein-coding gene gene with protein product 606543 NA 10523670, 10487760 Standard NM_178425 NA Approved KIAA0744, HDAC, MITR, HD7, HDAC7B uc003sui.3 Q9UKV0 OTTHUMG00000152487 ENST00000441542.2:c.1731+1003A>- chr7.hg19:g.18707102delA 6 9 ref NA False 70 70 PASS 7 PASS ref->het 0 NA 55,56 45,45 13,13 1 1 A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3 True hg19 CCDS47553.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HDAC9-021 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000376088.1 PASS NA None 113 True + A ENST00000441542.2 PABPC1 26986 __UNKNOWN__ __UNKNOWN__ 8 101724623 101724624 __UNKNOWN__ Frame_Shift_Ins INS - - A LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:101724623_101724624insA ENST00000318607.5 - 7 2066_2067 c.938_939insT c.(937-939)gagfs p.E313fs PABPC1_ENST00000522387.1_Frame_Shift_Ins_p.E281fs|PABPC1_ENST00000519004.1_Frame_Shift_Ins_p.E268fs|PABPC1_ENST00000519596.1_5'UTR NM_002568.3 NP_002559.2 P11940 PABP1_HUMAN poly(A) binding protein, cytoplasmic 1 313 RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}. NA NA NA cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413) catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529) nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494) breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1) 40 all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125) Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206) ATGGAGAAAACTCTTTCCGGAG 0.297 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 238 217.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.03 Y00345 CCDS6289.1 8q22.2-q23 2013-02-12 2004-04-20 ENSG00000070756 ENSG00000070756 26986 "RNA binding motif (RRM) containing" 8554 protein-coding gene gene with protein product 604679 "poly(A)-binding protein, cytoplasmic 2" PAB1, PABPC2 NA 2885805 Standard NM_002568 XM_005250861 NA Approved PABP1, PABPL1 uc003yjs.1 P11940 OTTHUMG00000164779 ENST00000318607.5:c.938_939insT chr8.hg19:g.101724623_101724624insA ENSP00000313007:p.Glu313fs 1 4 ref NA False 37 37 PASS 0 PASS ref->het 0 NA 186,187 34,56 17,18 1 1 Q15097|Q93004 True hg19 CCDS6289.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PABPC1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000380217.1 PASS NA None 238 True - A ENST00000318607.5 PABPC1 26986 __UNKNOWN__ __UNKNOWN__ 8 101724626 101724627 __UNKNOWN__ Frame_Shift_Del DEL TT TT - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:101724626_101724627delTT ENST00000318607.5 - 7 2063_2064 c.935_936delAA c.(934-936)aaafs p.K312fs PABPC1_ENST00000522387.1_Frame_Shift_Del_p.K280fs|PABPC1_ENST00000519004.1_Frame_Shift_Del_p.K267fs|PABPC1_ENST00000519596.1_5'UTR NM_002568.3 NP_002559.2 P11940 PABP1_HUMAN poly(A) binding protein, cytoplasmic 1 312 RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}. NA NA NA cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413) catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529) nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494) breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1) 40 all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125) Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206) GAGAAAACTCTTTCCGGAGACG 0.307 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 242 221.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.01 Y00345 CCDS6289.1 8q22.2-q23 2013-02-12 2004-04-20 ENSG00000070756 ENSG00000070756 26986 "RNA binding motif (RRM) containing" 8554 protein-coding gene gene with protein product 604679 "poly(A)-binding protein, cytoplasmic 2" PAB1, PABPC2 NA 2885805 Standard NM_002568 XM_005250861 NA Approved PABP1, PABPL1 uc003yjs.1 P11940 OTTHUMG00000164779 ENST00000318607.5:c.935_936delAA chr8.hg19:g.101724626_101724627delTT ENSP00000313007:p.Lys312fs 1 4 ref NA False 39 39 PASS 3 PASS ref->het 0 NA 187,188 34,56 25,26 1 1 Q15097|Q93004 True hg19 CCDS6289.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PABPC1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000380217.1 PASS NA None 242 True - T ENST00000318607.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ 8 124454537 124454538 __UNKNOWN__ IGR INS - - C rs78782462 byFrequency LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:124454537_124454538insC NA WDYHV1 (57 upstream) : FBXO32 (55590 downstream) NA NA NA NA NA AGATGAGCTTTCTACTTATTAA 0.416 NA NA NA NA NA NA C|C|CC|insertion 583 0.116414 0.0885 0.1023 5008 , , NA 17214 0.0645 NA 0.2396 False NA ,,, NA NA NA 2504 0.091 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 38 44.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr8.hg19:g.124454538_124454538dupC 2 4 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 3,3 33,33 2,2 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 38 True C Unknown 0 __UNKNOWN__ __UNKNOWN__ 10 30978288 30978289 __UNKNOWN__ IGR INS - - AGTTT rs71023602|rs71281533|rs66467809 byFrequency LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:30978288_30978289insAGTTT NA RP11-14C22.3 (31824 upstream) : SVILP1 (4301 downstream) NA NA NA NA NA CCACGCCAAGCCTGATCAGAAG 0.535 NA NA NA NA NA NA 130 0.0259585 0.0204 0.0476 5008 , , NA 26169 0.0159 NA 0.0348 False NA ,,, NA NA NA 2504 0.0194 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 191 183.58 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.88 NA NA NA NA NA chr10.hg19:g.30978288_30978289insAGTTT 1 2 ref NA False 81 78 PASS 0 PASS ref->het 0 NA 107,161 67,74 6,3 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 191 True AGTTT PPP2R1B 5519 __UNKNOWN__ __UNKNOWN__ 11 111630591 111630601 __UNKNOWN__ Frame_Shift_Del DEL CAAAACTTTTG CAAAACTTTTG - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:111630591_111630601delCAAAACTTTTG ENST00000341980.6 - 5 620_630 c.614_624delCAAAAGTTTTG c.(613-624)gcaaaagttttgfs p.AKVL205fs PPP2R1B_ENST00000427203.2_Frame_Shift_Del_p.AKVL44fs|PPP2R1B_ENST00000527614.1_Frame_Shift_Del_p.AKVL205fs|PPP2R1B_ENST00000393055.2_Intron|PPP2R1B_ENST00000426998.2_Frame_Shift_Del_p.AKVL141fs|PPP2R1B_ENST00000311129.5_Frame_Shift_Del_p.AKVL205fs P30154 2AAB_HUMAN protein phosphatase 2, regulatory subunit A, beta 205 NA NA NA apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241) extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121) endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2) 22 all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425) BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761) TGTCTAATTCCAAAACTTTTGCAAATTCACC 0.393 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 259 259.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 2 AF087438 CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1 11q23.1 2010-06-18 2010-04-14 ENSG00000137713 ENSG00000137713 5519 3.1.3.16 "Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits" 9303 protein-coding gene gene with protein product "PP2A-A-beta", "protein phosphatase 2A, regulatory subunit A, beta isoform" 603113 "protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform" NA 2159327, 9795170 Standard NM_002716 NM_181699 NA Approved PR65B, PP2A-Abeta uc001plw.1 P30154 OTTHUMG00000166741 ENST00000341980.6:c.614_624delCAAAAGTTTTG chr11.hg19:g.111630591_111630601delCAAAACTTTTG ENSP00000343317:p.Ala205fs 0 4 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 255,262 14,14 34,28 1 1 A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8 True hg19 CCDS53708.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPP2R1B-005 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000391300.1 PASS NA None 259 True - CAAAACTTTTG ENST00000341980.6 ERC1 23085 __UNKNOWN__ __UNKNOWN__ 12 1299178 1299179 __UNKNOWN__ 3'UTR INS - - AGAAGAATGTTTTT LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:1299178_1299179insAGAAGAATGTTTTT ENST00000536573.2 + 0 1242_1243 ERC1_ENST00000546231.2_Frame_Shift_Ins_p.-771fs|ERC1_ENST00000589028.1_Frame_Shift_Ins_p.-771fs|ERC1_ENST00000543086.3_Frame_Shift_Ins_p.-743fs|ERC1_ENST00000397203.2_Frame_Shift_Ins_p.-771fs|ERC1_ENST00000355446.5_Frame_Shift_Ins_p.-771fs|ERC1_ENST00000360905.4_Frame_Shift_Ins_p.-771fs Q8IUD2 RB6I2_HUMAN ELKS/RAB6-interacting/CAST family member 1 NA NA NA NA I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147) cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734) leucine zipper domain binding (GO:0043522) NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 38 all_epithelial(11;0.0698)|Ovarian(42;0.107) OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567) GGTGGAAAATGAGAAGAATGAC 0.401 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 473 459.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.35 AB015617 CCDS8508.1, CCDS53732.1 12p13.3 2008-02-05 2006-08-14 2006-08-14 ENSG00000082805 ENSG00000082805 23085 17072 protein-coding gene gene with protein product 607127 "RAB6 interacting protein 2" RAB6IP2 NA 10697956, 11929610 Standard NM_015064 NM_178040 NA Approved ELKS, KIAA1081, CAST2, MGC12974 uc001qjb.2 Q8IUD2 OTTHUMG00000130138 ENST00000536573.2:c.*1240->AGAAGAATGTTTTT chr12.hg19:g.1299178_1299179insAGAAGAATGTTTTT 1 3 ref NA False 52 52 PASS 0 PASS ref->het 0 NA 344,345 28,28 99,98 1 1 A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ERC1-003 KNOWN basic|exp_conf processed_transcript NA protein_coding OTTHUMT00000397934.4 PASS NA None 473 True + AGAAGAATGTTTTT ENST00000536573.2 NUP107 57122 __UNKNOWN__ __UNKNOWN__ 12 69120342 69120347 __UNKNOWN__ In_Frame_Del DEL TTCGCT TTCGCT - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:69120342_69120347delTTCGCT ENST00000539906.1 + 19 1797_1802 c.1553_1558delTTCGCT c.(1552-1560)cttcgcttt>ctt p.RF519del NUP107_ENST00000378905.2_In_Frame_Del_p.RF397del|NUP107_ENST00000229179.4_In_Frame_Del_p.RF548del P57740 NU107_HUMAN nucleoporin 107kDa 548 NA NA NA carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032) centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634) nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056) NUP107/LGR5(2) breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2) 39 Breast(13;6.25e-06) Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694) GGACACCTGCTTCGCTTTATGACTCA 0.369 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 491 460.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 1.51 AK055629 CCDS8985.1 12q14 2004-03-19 ENSG00000111581 ENSG00000111581 57122 29914 protein-coding gene gene with protein product 607617 NA 12552102, 12705868 Standard NM_020401 XM_005269037 NA Approved NUP84 uc001suf.3 P57740 OTTHUMG00000169265 ENST00000539906.1:c.1553_1558delTTCGCT chr12.hg19:g.69120342_69120347delTTCGCT ENSP00000441448:p.Arg519_Phe520del 0 4 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 406,409 30,31 72,70 1 1 B4DZ67|Q6PJE1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NUP107-003 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000403200.1 PASS NA None 491 True + TTCGCT ENST00000539906.1 BRCA2 675 __UNKNOWN__ __UNKNOWN__ 13 32914091 32914094 __UNKNOWN__ Frame_Shift_Del DEL ACAG ACAG - rs397507356|rs80358781 LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:32914091_32914094delACAG ENST00000380152.3 + 11 5832_5835 c.5599_5602delACAG c.(5599-5604)acagacfs p.TD1867fs BRCA2_ENST00000544455.1_Frame_Shift_Del_p.TD1867fs P51587 BRCA2_HUMAN breast cancer 2, early onset 1867 NA NA NA brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283) BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141) gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697) NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3) 183 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) AGACATATTTACAGACAGTTTCAG 0.333 NA NA "D, Mis, N, F, S" NA "breast, ovarian, pancreatic" "breast, ovarian, pancreatic, leukemia (FANCB, FANCD1)" NA Homologous recombination Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia TCGA Ovarian(8;0.087) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332) PASS yes Rec yes Hereditary breast/ovarian cancer 13 13q12 675 familial breast/ovarian cancer gene 2 NA "L, E" 0 NA NA NA NA NA 154 159.41 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 Familial Cancer Database incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups) U43746 CCDS9344.1 13q12-q13 2014-09-17 2003-10-14 ENSG00000139618 ENSG00000139618 675 "Fanconi anemia, complementation groups" 1101 protein-coding gene gene with protein product "BRCA1/BRCA2-containing complex, subunit 2" 600185 "Fanconi anemia, complementation group D1" FANCD1, FACD, FANCD NA 8091231, 7581463, 15057823 Standard NM_000059 NM_000059 NA Approved FAD, FAD1, BRCC2 uc001uub.1 P51587 OTTHUMG00000017411 ENST00000380152.3:c.5599_5602delACAG chr13.hg19:g.32914095_32914098delACAG ENSP00000369497:p.Thr1867fs 1 4 ref NA False 69 69 PASS 2 PASS ref->het 0 NA 58,60 83,83 14,14 2 2 O00183|O15008|Q13879|Q5TBJ7 True hg19 CCDS9344.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BRCA2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000046000.2 PASS NA None 154 True + ACAG ENST00000380152.3 COMMD6 170622 __UNKNOWN__ __UNKNOWN__ 13 76111854 76111859 __UNKNOWN__ Intron DEL TGCTCC TGCTCC - rs375005753 LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:76111854_76111859delTGCTCC ENST00000377615.3 - 2 207 COMMD6_ENST00000460675.1_Intron|COMMD6_ENST00000355801.4_Intron|COMMD6_ENST00000406936.3_Intron Q7Z4G1 COMD6_HUMAN COMM domain containing 6 NA NA NA NA negative regulation of NF-kappaB transcription factor activity (GO:0032088) cytoplasm (GO:0005737)|nucleus (GO:0005634) NF-kappaB binding (GO:0051059) breast(1)|lung(1)|urinary_tract(1) 3 Breast(118;0.0979)|Prostate(6;0.122) GBM - Glioblastoma multiforme(99;0.0104) ACATCTTTCTTGCTCCAGAGCCTCGC 0.612 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 197 190.36 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.96 AY542161 CCDS9451.1, CCDS9452.1 13q22 2004-02-18 ENSG00000188243 ENSG00000188243 170622 24015 protein-coding gene gene with protein product 612377 NA 15799966 Standard XM_085023 NM_203497 NA Approved Acrg uc001vjn.1 Q7Z4G1 OTTHUMG00000017089 ENST00000377615.3:c.42+40GGAGCA>- chr13.hg19:g.76111854_76111859delTGCTCC 0 5 ref NA False 47 47 PASS 1 PASS ref->het 0 NA 183,188 5,5 19,15 1 1 A6NF28|B7ZLN0|Q5TBK4 True hg19 CCDS9451.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COMMD6-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000045288.4 PASS NA None 197 True - TGCTCC ENST00000377615.3 GLOD4 51031 __UNKNOWN__ __UNKNOWN__ 17 673587 673605 __UNKNOWN__ Intron DEL AGGGAAGGACAAAGTTCTT AGGGAAGGACAAAGTTCTT - rs557258383 LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:673587_673605delAGGGAAGGACAAAGTTCTT ENST00000301329.6 - 6 716 GLOD4_ENST00000536578.1_Intron|GLOD4_ENST00000301328.5_Intron NM_016080.3 NP_057164.3 Q9HC38 GLOD4_HUMAN glyoxalase domain containing 4 NA NA NA NA extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739) endometrium(1)|large_intestine(1)|prostate(1) 3 UCEC - Uterine corpus endometrioid carcinoma (25;0.022) GACCTCAAGAAGGGAAGGACAAAGTTCTTAGCTGGGTTG 0.429 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 135 127.48 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.68 AF177342 CCDS32520.1 17p13.3 2008-02-05 2007-03-14 2007-03-14 ENSG00000167699 51031 14111 protein-coding gene gene with protein product NA "chromosome 17 open reading frame 25" C17orf25 NA 11642406, 12528892 Standard NM_016080 NM_016080 NA Approved CGI-150, HC71 uc002fru.3 Q9HC38 ENST00000301329.6:c.630+55AAGAACTTTGTCCTTCCCT>- chr17.hg19:g.673587_673605delAGGGAAGGACAAAGTTCTT 0 4 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 124,126 22,22 19,18 1 1 D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1 True hg19 CCDS32520.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GLOD4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000437188.3 PASS NA None 135 True - AGGGAAGGACAAAGTTCTT ENST00000301329.6 TXNDC2 84203 __UNKNOWN__ __UNKNOWN__ 18 9886771 9886788 __UNKNOWN__ In_Frame_Del DEL CCCAAGCAGGATGACAGC CCCAAGCAGGATGACAGC - rs527970943 LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:9886771_9886788delCCCAAGCAGGATGACAGC ENST00000306084.6 + 2 494_511 c.295_312delCCCAAGCAGGATGACAGC c.(295-312)cccaagcaggatgacagcdel p.PKQDDS99del TXNDC2_ENST00000357775.5_In_Frame_Del_p.PKQDDS32del|TXNDC2_ENST00000426718.3_3'UTR|TXNDC2_ENST00000536353.2_In_Frame_Del_p.PKQDDS32del NM_001098529.1 NP_001091999.1 Q86VQ3 TXND2_HUMAN thioredoxin domain containing 2 (spermatozoa) 99 NA NA NA cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283) cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520) nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791) NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1) 31 CACCAGCCATCCCAAGCAGGATGACAGCCCCAAGTCCT 0.573 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 1043 1047.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 2.64 AF080095 CCDS11846.1, CCDS42414.1 18p11.31-p11.2 2009-03-11 2009-03-11 2007-08-16 ENSG00000168454 ENSG00000168454 84203 16470 protein-coding gene gene with protein product "sperm-specific thioredoxin 1" NA NA 11230166, 11399755 Standard NM_001098529 NA Approved SPTRX1 uc002koi.4 Q86VQ3 OTTHUMG00000131602 ENST00000306084.6:c.295_312delCCCAAGCAGGATGACAGC chr18.hg19:g.9886771_9886788delCCCAAGCAGGATGACAGC ENSP00000304908:p.Pro99_Ser104del 0 4 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 926,947 64,66 182,168 1 1 A5YM73|Q8N7U4|Q96RX3|Q9H0L8 True hg19 CCDS42414.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TXNDC2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000254487.1 PASS NA None 1043 True + CCCAAGCAGGATGACAGC ENST00000306084.6 TMEM259 91304 __UNKNOWN__ __UNKNOWN__ 19 1011838 1011857 __UNKNOWN__ Intron DEL GGCCTGCTTGGCTCCCGCCC GGCCTGCTTGGCTCCCGCCC - rs538906148|rs371837146|rs113138803|rs10420656|rs374586188 byFrequency LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:1011838_1011857delGGCCTGCTTGGCTCCCGCCC ENST00000356663.3 - 6 1064 TMEM259_ENST00000333175.5_Intron NM_001033026.1 NP_001028198.1 Q4ZIN3 MBRL_HUMAN transmembrane protein 259 NA NA NA NA cytoplasm (GO:0005737)|integral component of membrane (GO:0016021) NA GGGCTGCGAGGGCCTGCTTGGCTCCCGCCCGGCCAGCCCC 0.664 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 304 304.33 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 13 BC008957 CCDS12052.1, CCDS32862.1 19p13.3 2013-02-06 2013-02-06 2013-02-06 ENSG00000182087 ENSG00000182087 91304 17039 protein-coding gene gene with protein product "membralin", "aspecific BCL2 ARE-binding protein 1" 611011 "chromosome 19 open reading frame 6" C19orf6 NA 12638133, 16084606 Standard NM_033420 XM_005259675 NA Approved MGC4022, ASBABP1, MBRL uc002lqr.1 Q4ZIN3 ENST00000356663.3:c.942+33GGGCGGGAGCCAAGCAGGCC>- chr19.hg19:g.1011838_1011857delGGCCTGCTTGGCTCCCGCCC 0 6 ref NA False 49 49 PASS 1 PASS ref->het 0 NA 266,310 6,6 115,71 2 2 O60392|Q8NF79|Q96H30 True hg19 CCDS32862.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM259-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000458236.1 PASS NA None 304 True - GGCCTGCTTGGCTCCCGCCC ENST00000356663.3 TNNT1 7138 __UNKNOWN__ __UNKNOWN__ 19 55649437 55649439 __UNKNOWN__ In_Frame_Del DEL CTC CTC - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:55649437_55649439delCTC ENST00000588981.1 - 10 595_597 c.391_393delGAG c.(391-393)gagdel p.E131del TNNT1_ENST00000587465.2_In_Frame_Del_p.E61del|TNNT1_ENST00000585321.2_In_Frame_Del_p.E61del|TNNT1_ENST00000536926.1_In_Frame_Del_p.E120del|TNNT1_ENST00000356783.5_In_Frame_Del_p.E120del|TNNT1_ENST00000588426.1_In_Frame_Del_p.E28del|TNNT1_ENST00000587758.1_In_Frame_Del_p.E120del|TNNT1_ENST00000592920.1_5'UTR|TNNT1_ENST00000291901.8_In_Frame_Del_p.E131del NM_003283.4 NP_003274.3 P13805 TNNT1_HUMAN troponin T type 1 (skeletal, slow) 131 NA NA NA muscle filament sliding (GO:0030049)|negative regulation of muscle contraction (GO:0045932)|skeletal muscle contraction (GO:0003009)|slow-twitch skeletal muscle fiber contraction (GO:0031444) cytosol (GO:0005829)|troponin complex (GO:0005861) tropomyosin binding (GO:0005523) endometrium(2)|kidney(3)|lung(4)|ovary(1) 10 BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.047) TCCTCATCTTCTCCTCCTGTGGG 0.576 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 412 396.82 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.1 CCDS12917.1, CCDS46185.1, CCDS59421.1 19q13.4 2014-09-17 2005-09-12 ENSG00000105048 7138 11948 protein-coding gene gene with protein product "slow skeletal muscle troponin T", "troponin T1, skeletal, slow", "nemaline myopathy type 5" 191041 "troponin T1, skeletal, slow" NA 1505979 Standard NM_003283 XM_006723343 NA Approved ANM, STNT, TNT, TNTS, FLJ98147, MGC104241, NEM5 uc002qjb.4 P13805 ENST00000588981.1:c.391_393delGAG chr19.hg19:g.55649440_55649442delCTC ENSP00000467176:p.Glu131del 1 4 ref NA False 53 53 PASS 2 PASS ref->het 0 NA 292,295 73,73 39,36 1 1 O95472|Q16061|Q5U0E1 True hg19 CCDS12917.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNNT1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000451825.2 PASS NA None 412 True - CTC ENST00000588981.1 SLC7A3 84889 __UNKNOWN__ __UNKNOWN__ X 70148783 70148793 __UNKNOWN__ Frame_Shift_Del DEL GTCTTAGAGAT GTCTTAGAGAT - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:70148783_70148793delGTCTTAGAGAT ENST00000374299.3 - 3 574_584 c.430_440delATCTCTAAGAC c.(430-441)atctctaagactfs p.ISKT144fs SLC7A3_ENST00000298085.4_Frame_Shift_Del_p.ISKT144fs Q8WY07 CTR3_HUMAN solute carrier family 7 (cationic amino acid transporter, y+ system), member 3 144 NA NA NA amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189) breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1) 31 Renal(35;0.156) L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129) CCCCTGCAGAGTCTTAGAGATGTGGTTCCCA 0.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 257 250.72 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.21 AF320612 CCDS14404.1 Xq12 2013-05-22 ENSG00000165349 ENSG00000165349 84889 "Solute carriers" 11061 protein-coding gene gene with protein product 300443 NA 11591158 Standard NM_032803 NM_001048164 NA Approved CAT-3, ATRC3, FLJ14541 uc004dyn.3 Q8WY07 OTTHUMG00000021780 ENST00000374299.3:c.430_440delATCTCTAAGAC chrX.hg19:g.70148783_70148793delGTCTTAGAGAT ENSP00000363417:p.Ile144fs 0 3 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 197,203 58,59 27,22 2 2 D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7 True hg19 CCDS14404.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC7A3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000057080.1 PASS NA None 257 True - GTCTTAGAGAT ENST00000374299.3 FUNDC2 65991 __UNKNOWN__ __UNKNOWN__ X 154288466 154288474 __UNKNOWN__ 3'UTR DEL ATCTATTTG ATCTATTTG - LTS-013_T LTS-013_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:154288466_154288474delATCTATTTG ENST00000369498.3 + 0 6343_6351 NM_023934.3 NP_076423.2 Q9BWH2 FUND2_HUMAN FUN14 domain containing 2 NA NA NA NA mitochondrion (GO:0005739)|nucleus (GO:0005634) breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1) 13 all_cancers(53;3.51e-17)|all_epithelial(53;5.13e-11)|all_lung(58;3.84e-07)|Lung NSC(58;1.2e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) CAGAAAAACAATCTATTTGATCATGTAGT 0.273 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 135 130.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.25 AF267862 CCDS14763.1 Xq28 2010-03-12 ENSG00000165775 ENSG00000165775 65991 24925 protein-coding gene gene with protein product NA NA 12477932 Standard NM_023934 NM_023934 NA Approved HCBP6, DC44 uc004fmw.3 Q9BWH2 OTTHUMG00000013504 ENST00000369498.3:c.*5527ATCTATTTG>- chrX.hg19:g.154288466_154288474delATCTATTTG 0 7 ref NA False 59 59 PASS 1 PASS ref->het 0 NA 86,86 36,36 20,20 1 1 B2R7W5|D3DWY5|Q8NHX8|Q9H2I6 True hg19 CCDS14763.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FUNDC2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000037641.3 PASS NA None 135 True + ATCTATTTG ENST00000369498.3 RESP18 389075 __UNKNOWN__ __UNKNOWN__ 2 220194247 220194248 __UNKNOWN__ Intron INS - - ATT rs3832109|rs35419388|rs397959261 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:220194247_220194248insATT ENST00000333527.5 - 4 465 RESP18_ENST00000392083.1_Intron NM_001007089.3 NP_001007090.3 Q5W5W9 RES18_HUMAN regulated endocrine-specific protein 18 NA NA NA NA in utero embryonic development (GO:0001701) extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|rough endoplasmic reticulum lumen (GO:0048237)|secretory granule (GO:0030141) NA NA endometrium(1)|prostate(1) 2 aggacctctgaattctcacagt 0.49 NA NA NA NA NA NA NA NA NA NA 2360 0.471246 0.9402 0.33 5008 , , NA 22640 0.1825 NA 0.2763 False NA ,,, NA NA NA 2504 0.4356 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 71 87.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.32 NA NA AF437883 CCDS33382.2 2q35 2012-12-07 2012-12-07 ENSG00000182698 ENSG00000182698 389075 33762 protein-coding gene gene with protein product 612721 "regulated endocrine-specific protein 18 homolog (rat)" NA 17951542, 7988462 Standard NM_001007089 NM_001007089 NA Approved uc002vlc.4 Q5W5W9 OTTHUMG00000150223 ENST00000333527.5:c.465+110->AAT chr2.hg19:g.220194248_220194250dupATT 2 2 ref NA False 48 47 PASS 1 PASS ref->het 0 NA 3,3 56,57 12,11 1 1 A8MQ49|Q38I23|Q5W5X0 True hg19 CCDS33382.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RESP18-001 PUTATIVE basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000316885.1 PASS NA None 71 NA True - ATT ENST00000333527.5 CMTM6 54918 __UNKNOWN__ __UNKNOWN__ 3 32529449 32529450 __UNKNOWN__ Frame_Shift_Ins INS - - T LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:32529449_32529450insT ENST00000205636.3 - 3 1056_1057 c.394_395insA c.(394-396)tcafs p.S132fs NM_017801.2 NP_060271.1 Q9NX76 CKLF6_HUMAN CKLF-like MARVEL transmembrane domain containing 6 132 MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}. NA NA NA chemotaxis (GO:0006935) extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020) NA NA breast(1)|endometrium(1) 2 AATCTCAGCTGAAGTCCTGTCA 0.332 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 75 77.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.49 NA NA AK000403 CCDS2653.1 3p22.2 2006-08-25 2005-11-08 2005-11-08 ENSG00000091317 ENSG00000091317 54918 19177 protein-coding gene gene with protein product 607889 "chemokine-like factor super family 6", "chemokine-like factor superfamily 6" CKLFSF6 NA Standard NM_017801 NA Approved FLJ20396 uc003cfa.1 Q9NX76 OTTHUMG00000130747 ENST00000205636.3:c.394_395insA chr3.hg19:g.32529449_32529450insT ENSP00000205636:p.Ser132fs 1 2 ref NA False 69 69 PASS 0 PASS ref->het 0 NA 44,44 27,28 5,4 1 1 Q6IAC4 True hg19 CCDS2653.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CMTM6-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253247.1 PASS NA None 75 NA True - T ENST00000205636.3 SNX4 8723 __UNKNOWN__ __UNKNOWN__ 3 125179732 125179733 __UNKNOWN__ Intron INS - - ATAA rs375681454|rs67670439|rs112803860 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:125179732_125179733insATAA ENST00000251775.4 - 10 879 SNX4_ENST00000536067.1_Intron NM_003794.2 NP_003785.1 O95219 SNX4_HUMAN sorting nexin 4 NA NA NA NA endocytic recycling (GO:0032456)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031) cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|early endosome membrane (GO:0031901)|membrane (GO:0016020)|protein complex (GO:0043234) epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459) NA NA breast(2)|central_nervous_system(1)|lung(6)|ovary(1)|skin(1) 11 ACACACATTGCATAGAGTTACT 0.366 NA NA NA NA NA NA NA NA NA NA 2615 0.522165 0.6573 0.5605 5008 , , NA 20530 0.4226 NA 0.4304 False NA ,,, NA NA NA 2504 0.5092 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 36 35.26 NA NA 2638,1610 NA 826,986,312 NA NA NA NA NA -0.8 0 NA dbSNP_130 35 3510,4732 NA 735,2040,1346 no intron SNX4 NM_003794.2 NA 1561,3026,1658 A1A1,A1R,RR NA 42.5868,37.9002,49.2234 NA NA NA 6148,6342 NA NA NA SO:0001627 intron_variant 0.08 NA NA AF065485 CCDS3032.1 3q21.2 2014-02-12 ENSG00000114520 ENSG00000114520 8723 "Sorting nexins" 11175 protein-coding gene gene with protein product 605931 NA 9819414 Standard NM_003794 NM_003794 NA Approved ATG24B uc003eib.4 O95219 OTTHUMG00000159575 ENST00000251775.4:c.855-28->TTAT chr3.hg19:g.125179732_125179733insATAA 1 2 ref NA False 35 35 PASS 0 PASS ref->het 0 NA 1,1 27,27 8,8 1 1 B3KMH0|B4DQV4|D3DNA3 True hg19 CCDS3032.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SNX4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000356299.1 PASS NA None 36 NA True - ATAA ENST00000251775.4 MGLL 11343 __UNKNOWN__ __UNKNOWN__ 3 127455086 127455087 __UNKNOWN__ 5'UTR INS - - A rs5852521|rs75701761|rs397803417 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:127455086_127455087insA ENST00000398101.3 - 0 113_114 MGLL_ENST00000398104.1_Intron|MGLL_ENST00000265052.5_Intron|MGLL_ENST00000453507.2_Intron|MGLL_ENST00000434178.2_Intron Q99685 MGLL_HUMAN monoglyceride lipase NA NA NA NA acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433) endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202) acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803) NA NA cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2) 6 CAAATTGCTTTAAAAAAATGGA 0.332 NA NA NA NA NA NA NA NA NA NA AAAAAAA|AAAAAAA|AAAAAAAA|insertion 1841 0.367612 0.3411 0.4524 5008 , , NA 21891 0.2341 NA 0.5179 False NA ,,, NA NA NA 2504 0.3262 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 57 52.71 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.3 NA NA BC000551 CCDS43148.1, CCDS46902.1, CCDS58852.1 3p13-q13.33 2014-03-14 ENSG00000074416 ENSG00000074416 11343 3.1.1.23 17038 protein-coding gene gene with protein product 609699 NA 9495531 Standard NM_007283 NM_007283 NA Approved HU-K5, MGL uc003ejx.4 Q99685 OTTHUMG00000159641 ENST00000398101.3:c.-386->T chr3.hg19:g.127455093_127455093dupA 8 7 ref NA False 36 32 PASS 7 PASS ref->het 0 NA 3,3 40,40 14,14 1 1 B3KRC2|B7Z9D1|Q6IBG9|Q96AA5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MGLL-004 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000356720.1 PASS NA None 57 NA True - A ENST00000398101.3 MUC4 4585 __UNKNOWN__ __UNKNOWN__ 3 195490839 195490845 __UNKNOWN__ Intron DEL TCCAGAT TCCAGAT - rs34858176|rs386670089|rs6781330|rs560466806|rs140802196 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:195490839_195490845delTCCAGAT ENST00000346145.4 - 10 1376 MUC4_ENST00000349607.4_Intron|MUC4_ENST00000463781.3_Intron|MUC4_ENST00000475231.1_Intron NM_004532.5 NP_004523.3 Q99102 MUC4_HUMAN mucin 4, cell surface associated NA NA NA NA cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687) extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982) ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197) NA NA NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 51 all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) GBM - Glioblastoma multiforme(46;2.37e-05) CTACTCCTTATCCAGATGCCACCTCCC 0.628 NA NA NA NA NA NA NA NA NA NA 541 0.108027 0.0287 0.098 5008 , , NA 16137 0.2113 NA 0.1054 False NA ,,, NA NA NA 2504 0.1186 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 46 55.13 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.06 NA NA AJ276359 CCDS3310.1, CCDS3311.1, CCDS54700.1 3q29 2007-01-19 2006-03-14 ENSG00000145113 ENSG00000145113 4585 "Mucins" 7514 protein-coding gene gene with protein product 158372 "mucin 4, tracheobronchial" NA 1673336 Standard NM_018406 NM_004532 NA Approved uc021xjp.1 Q99102 OTTHUMG00000151827 ENST00000346145.4:c.1336+70ATCTGGA>- chr3.hg19:g.195490839_195490845delTCCAGAT 0 3 ref NA False 67 54 PASS 1 PASS ref->hom 0 NA 0,0 40,40 4,4 1 1 O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81 True hg19 CCDS3310.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MUC4-015 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000341862.1 PASS NA None 46 NA True - TCCAGAT ENST00000346145.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 3 196340859 196340860 __UNKNOWN__ IGR INS - - A rs138499207 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:196340859_196340860insA NA FBXO45 (24929 upstream) : LINC01063 (17508 downstream) NA NA NA NA NA NA NA ctcgtctcctcaaaaaatacaa 0.574 NA NA NA NA NA NA NA NA NA NA AAAAAA|AAAAAA|AAAAAAA|insertion 1887 0.376797 0.1982 0.4251 5008 , , NA 16081 0.5942 NA 0.4414 False NA ,,, NA NA NA 2504 0.2935 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 21 21.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA chr3.hg19:g.196340865_196340865dupA 7 7 ref NA False 42 42 PASS 6 PASS ref->hom 0 NA 0,0 18,19 4,4 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 21 NA True A ZDHHC11B 653082 __UNKNOWN__ __UNKNOWN__ 5 712045 712046 __UNKNOWN__ 3'UTR INS - - TCT LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:712045_712046insTCT ENST00000508859.2 - 0 1507_1508 ZDHHC11_ENST00000424784.2_Intron|ZDHHC11B_ENST00000522356.1_5'UTR P0C7U3 ZH11B_HUMAN zinc finger, DHHC-type containing 11B NA NA NA NA integral component of membrane (GO:0016021) protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270) NA NA lung(3)|stomach(1) 4 GGCCCATCAGCTCTTAAGCAGC 0.569 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 21 33.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.37 NA NA 5p15.33 2007-01-29 ENSG00000206077 653082 "Zinc fingers, DHHC-type" 32962 protein-coding gene gene with protein product NA NA Standard XM_926053 XM_003118532 NA Approved P0C7U3 ENST00000508859.2:c.*360->AGA chr5.hg19:g.712046_712048dupTCT 2 3 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 8,8 7,11 6,3 1 1 A6NHR3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZDHHC11B-001 PUTATIVE basic|appris_candidate_longest protein_coding NA protein_coding OTTHUMT00000367532.2 PASS NA None 21 NA True - TCT ENST00000508859.2 DIMT1 27292 __UNKNOWN__ __UNKNOWN__ 5 61689741 61689741 __UNKNOWN__ Intron DEL T T - rs397822232|rs202070474|rs3215345 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:61689741delT ENST00000199320.4 - 8 824 KIF2A_ENST00000509663.2_Intron|DIMT1_ENST00000506390.1_Intron NM_014473.2 NP_055288.1 Q9UNQ2 DIM1_HUMAN DIM1 dimethyladenosine transferase 1 homolog (S. cerevisiae) NA NA NA NA cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634) 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity (GO:0052909)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179) NA NA NA CCGCCTGGACTTTTTTTTCCT 0.373 NA NA NA NA NA NA NA NA NA NA TTTTTTTT|TTTTTTTT|TTTTTTT|deletion 1020 0.203674 0.1929 0.1556 5008 , , NA 17260 0.2173 NA 0.2634 False NA ,,, NA NA NA 2504 0.1769 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 44 42.45 NA NA NA 52 48 49 NA NA NA NA 5 NA NA NA NA NA NA 61689741 2200 4289 6489 SO:0001627 intron_variant 0.04 NA NA AF102147 CCDS3981.1 5q12.1 2011-08-11 2011-08-11 2011-08-11 ENSG00000086189 ENSG00000086189 27292 30217 protein-coding gene gene with protein product 612499 "DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)" DIMT1L NA 11124703 Standard NM_014473 NM_014473 NA Approved HSA9761 uc003jta.3 Q9UNQ2 OTTHUMG00000131223 ENST00000199320.4:c.663+40A>- chr5.hg19:g.61689741delT 7 8 ref NA False 34 31 PASS 8 PASS ref->het 0 NA 1,1 37,38 6,5 1 1 O76025|Q9BU77|Q9UES1 True hg19 CCDS3981.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DIMT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253967.1 PASS NA None 44 NA True - T ENST00000199320.4 KLHL3 26249 __UNKNOWN__ __UNKNOWN__ 5 136997777 136997777 __UNKNOWN__ Intron DEL C C - rs70979550 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:136997777delC ENST00000309755.4 - 7 1080 KLHL3_ENST00000506873.1_Intron|KLHL3_ENST00000541417.1_Intron|KLHL3_ENST00000394937.3_Intron|KLHL3_ENST00000508657.1_Intron|KLHL3_ENST00000506491.1_Intron NM_017415.2 NP_059111.2 Q9UH77 KLHL3_HUMAN kelch-like family member 3 NA NA NA NA distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294) Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829) structural molecule activity (GO:0005198) NA NA breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1) 21 all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233) GBM - Glioblastoma multiforme(465;0.0223) TTTCAAACAACCCTCAATCTG 0.308 NA NA NA NA NA NA NA NA NA NA CCC|CCC|CC|deletion 1574 0.314297 0.2216 0.268 5008 , , NA 13553 0.5565 NA 0.2843 False NA ,,, NA NA NA 2504 0.2536 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 40 47.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.85 NA NA AB032955 CCDS4192.1, CCDS58969.1, CCDS58970.1 5q31 2013-01-30 2013-01-30 ENSG00000146021 ENSG00000146021 26249 "Kelch-like", "BTB/POZ domain containing" 6354 protein-coding gene gene with protein product 605775 "kelch (Drosophila)-like 3", "kelch-like 3 (Drosophila)" NA 10843806 Standard NM_017415 NA Approved KIAA1129 uc010jek.3 Q9UH77 OTTHUMG00000129155 ENST00000309755.4:c.637-57G>- chr5.hg19:g.136997777delC 2 5 ref NA False 46 46 PASS 3 PASS ref->het 0 NA 2,2 23,27 15,11 1 1 B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6 True hg19 CCDS4192.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KLHL3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251220.2 PASS NA None 40 NA True - C ENST00000309755.4 FAF2 23197 __UNKNOWN__ __UNKNOWN__ 5 175933692 175933699 __UNKNOWN__ Intron DEL GTGTGTGC GTGTGTGC - rs10563462|rs542311242|rs539856906|rs79663231|rs201822943|rs113700453|rs397713712|rs56224183|rs113529427 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:175933692_175933699delGTGTGTGC ENST00000261942.6 + 11 1208 NM_014613.2 NP_055428.1 Q96CS3 FAF2_HUMAN Fas associated factor family member 2 NA NA NA NA lipid particle organization (GO:0034389)|negative regulation of catalytic activity (GO:0043086)|response to unfolded protein (GO:0006986) Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811) lipase binding (GO:0035473)|lipase inhibitor activity (GO:0055102)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625) NA NA breast(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1) 10 CTTCAGAGTtgtgtgtgcgtgtgtgcgt 0.413 NA NA NA NA NA NA NA NA NA NA 3089 0.616813 0.5968 0.6657 5008 , , NA 20340 0.5516 NA 0.6769 False NA ,,, NA NA NA 2504 0.6145 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 28 30.09 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA BC015791 CCDS34296.1 5q35.2 2011-06-28 2008-07-25 2008-07-25 ENSG00000113194 ENSG00000113194 23197 "UBX domain containing" 24666 protein-coding gene gene with protein product "expressed in T cells and eosinophils in atopic dermatitis", "UBX domain protein 3B" NA "UBX domain containing 8" UBXD8 NA 10048485, 12372427 Standard NM_014613 NM_014613 NA Approved ETEA, KIAA0887, UBXN3B uc003mej.4 Q96CS3 OTTHUMG00000163228 ENST00000261942.6:c.1156-70GTGTGTGC>- chr5.hg19:g.175933700_175933707delGTGTGTGC 1 3 ref NA False 36 36 PASS 2 PASS ref->het 0 NA 2,2 25,25 1,1 1 1 O94963|Q8IUF2|Q9BRP2|Q9BVM7 True hg19 CCDS34296.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAF2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000372194.1 PASS NA None 28 NA True + GTGTGTGC ENST00000261942.6 DCDC2 51473 __UNKNOWN__ __UNKNOWN__ 6 24302037 24302037 __UNKNOWN__ Frame_Shift_Del DEL G G - rs368811969 LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:24302037delG ENST00000378454.3 - 4 764 c.463delC c.(463-465)cgcfs p.R155fs NM_001195610.1|NM_016356.3 NP_001182539.1|NP_057440.2 Q9UHG0 DCDC2_HUMAN doublecortin domain containing 2 155 Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}. NA NA NA cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542) NA NA breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1) 32 Ovarian(999;0.101) ATAAGGAGGCGAGAAGCTGGG 0.443 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 387 398.19 NA NA NA 125 122 123 NA NA NA NA 6 NA NA NA NA NA NA 24302037 2203 4300 6503 SO:0001589 frameshift_variant 1.65 NA NA AB032980 CCDS4550.1 6p22.1 2008-02-05 ENSG00000146038 ENSG00000146038 51473 18141 protein-coding gene gene with protein product 605755 NA 10601354, 10574461 Standard NM_016356 NM_001195610 NA Approved RU2, KIAA1154, DCDC2A uc003ndx.3 Q9UHG0 OTTHUMG00000016275 ENST00000378454.3:c.463delC chr6.hg19:g.24302037delG ENSP00000367715:p.Arg155fs 0 3 ref NA False 105 100 PASS 1 PASS ref->het 0 NA 242,246 99,100 48,44 2 2 Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6 True hg19 CCDS4550.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DCDC2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000043604.1 PASS NA None 387 NA True - G ENST00000378454.3 RPS6KA2 6196 __UNKNOWN__ __UNKNOWN__ 6 167115913 167115923 __UNKNOWN__ Intron DEL GCTTGTCTAGC GCTTGTCTAGC - rs59168062|rs79724755|rs398066495|rs62438699 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:167115913_167115923delGCTTGTCTAGC ENST00000510118.1 - 3 515 RPS6KA2_ENST00000503859.1_Intron Q15349 KS6A2_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 2 NA NA NA NA axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666) cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819) ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711) NA NA central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1) 45 Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105) OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05) Tttgtctagtgcttgtctagcgcttgtctag 0.46 NA NA NA NA NA NA NA NA NA NA 4705 0.939497 0.9546 0.9265 5008 , , NA 20687 0.9633 NA 0.8787 False NA ,,, NA NA NA 2504 0.9663 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 156 139.48 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA L07598 CCDS5294.1, CCDS34570.1 6q27 2011-04-05 2002-08-29 ENSG00000071242 ENSG00000071242 6196 10431 protein-coding gene gene with protein product 601685 "ribosomal protein S6 kinase, 90kD, polypeptide 2" NA 8141249 Standard NM_021135 NM_001006932 NA Approved RSK, RSK3, HU-2 uc003qvc.1 Q15349 OTTHUMG00000016007 ENST00000510118.1:c.174+68427GCTAGACAAGC>- chr6.hg19:g.167115913_167115923delGCTTGTCTAGC 1 2 ref NA False 37 37 PASS 2 PASS ref->het 0 NA 34,35 70,71 50,50 1 1 B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPS6KA2-005 KNOWN basic protein_coding NA protein_coding OTTHUMT00000362836.2 PASS NA None 156 NA True - GCTTGTCTAGC ENST00000510118.1 C7orf10 0 __UNKNOWN__ __UNKNOWN__ 7 40356330 40356330 __UNKNOWN__ Intron DEL T T - LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:40356330delT ENST00000335693.4 + 9 764 C7orf10_ENST00000401647.2_Intron|C7orf10_ENST00000309930.5_Intron NM_001193313.1 NP_001180242.1 Q9HAC7 SUCHY_HUMAN NA NA NA NA metabolic process (GO:0008152) mitochondrion (GO:0005739) succinate-hydroxymethylglutarate CoA-transferase activity (GO:0047369) NA NA endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2) 18 AGCTGTTCTATTTTATTTATT 0.328 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 167 193.98 NA NA NA 37 36 37 NA NA NA NA 7 NA NA NA NA NA NA 40356330 1812 4058 5870 SO:0001627 intron_variant 0.5 NA NA NA NA NA NA NA ENST00000335693.4:c.742-29T>- chr7.hg19:g.40356330delT 3 7 ref NA False 30 30 PASS 4 PASS ref->het 0 NA 107,108 47,47 12,11 1 1 A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1 True hg19 CCDS55105.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C7orf10-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000338388.1 PASS NA None 167 NA True + T ENST00000335693.4 NAA35 60560 __UNKNOWN__ __UNKNOWN__ 9 88631382 88631383 __UNKNOWN__ Intron INS - - GTT rs368374310|rs200088322|rs111986647|rs567745006|rs10651022 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:88631382_88631383insGTT ENST00000361671.5 + 18 1701 NM_024635.3 NP_078911.3 Q5VZE5 NAA35_HUMAN N(alpha)-acetyltransferase 35, NatC auxiliary subunit NA NA NA NA negative regulation of apoptotic process (GO:0043066)|smooth muscle cell proliferation (GO:0048659) cytoplasm (GO:0005737)|NatC complex (GO:0031417) NA NA central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(9)|ovary(2)|skin(2)|urinary_tract(1) 25 AAATATCTATCGTTAATATATG 0.282 NA NA NA NA NA NA NA NA NA NA 1853 0.370008 0.652 0.3112 5008 , , NA 17465 0.3641 NA 0.2137 False NA ,,, NA NA NA 2504 0.1973 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 40 54.36 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AK025266 CCDS6673.1 9q22.1 2010-01-14 2010-01-14 2010-01-14 ENSG00000135040 ENSG00000135040 60560 "N(alpha)-acetyltransferase subunits" 24340 protein-coding gene gene with protein product NA "MAK10 homolog, amino-acid N-acetyltransferase subunit (S. cerevisiae)" MAK10 NA 14702039, 19660095 Standard NM_024635 NM_024635 NA Approved FLJ21613, FLJ22643, bA379P1.1 uc004aoi.4 Q5VZE5 OTTHUMG00000020131 ENST00000361671.5:c.1569-71->GTT chr9.hg19:g.88631383_88631385dupGTT 2 2 ref NA False 52 50 PASS 1 PASS ref->hom 0 NA 0,0 35,36 7,6 1 1 Q5VZE6|Q9H631|Q9H703 True hg19 CCDS6673.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NAA35-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000052906.1 PASS NA None 40 NA True + GTT ENST00000361671.5 PRPF4 9128 __UNKNOWN__ __UNKNOWN__ 9 116045312 116045312 __UNKNOWN__ Intron DEL A A - rs77287785 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:116045312delA ENST00000374198.4 + 5 585 PRPF4_ENST00000374199.4_Intron|PRPF4_ENST00000488937.1_3'UTR NM_001244926.1|NM_004697.4 NP_001231855.1|NP_004688.2 O43172 PRP4_HUMAN pre-mRNA processing factor 4 NA NA NA NA gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375) Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001) NA NA NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2) 23 TTACCGAATGAATTCACCTTC 0.368 NA NA NA NA NA NA NA NA NA NA AA|AA|A|deletion 643 0.128395 0.0076 0.0476 5008 , , NA 21133 0.3155 NA 0.0805 False NA ,,, NA NA NA 2504 0.2055 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 39 41.23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF001687 CCDS6791.1, CCDS59142.1 9q31-q33 2013-10-03 2013-10-03 ENSG00000136875 ENSG00000136875 9128 "WD repeat domain containing" 17349 protein-coding gene gene with protein product "PRP4/STK/WD splicing factor", "U4/U6 small nuclear ribonucleoprotein Prp4" 607795 "PRP4 pre-mRNA processing factor 4 homolog (yeast)" NA 9257651, 9404889 Standard NM_004697 NM_004697 NA Approved Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60 uc004bgx.3 O43172 OTTHUMG00000020517 ENST00000374198.4:c.484-100A>- chr9.hg19:g.116045312delA 1 2 ref NA False 54 50 PASS 2 PASS ref->hom 0 NA 0,0 35,37 4,3 1 1 O43445|O43864|Q5T1M8|Q96DG2|Q96IK4 True hg19 CCDS6791.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PRPF4-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000053708.2 PASS NA None 39 NA True + A ENST00000374198.4 PDE3B 5140 __UNKNOWN__ __UNKNOWN__ 11 14690423 14690424 __UNKNOWN__ Intron INS - - C rs11408185 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:14690423_14690424insC ENST00000455098.2 + 1 1223 PDE3B_ENST00000282096.4_Intron|PDE3B_ENST00000534317.1_Intron Q13370 PDE3B_HUMAN phosphodiesterase 3B, cGMP-inhibited NA NA NA NA angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796) cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020) 3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422) NA NA NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 39 Caffeine(DB00201) TGTTTTGGAAGCTGTTTGTCTC 0.46 NA NA NA NA NA NA NA NA NA NA CC|C|CC|deletion 3358 0.670527 0.7057 0.7003 5008 , , NA 19460 0.6786 NA 0.6173 False NA ,,, NA NA NA 2504 0.6483 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 26 24.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA U38178 CCDS7817.1 11p15.2 2008-03-18 ENSG00000152270 ENSG00000152270 5140 3.1.4.17 "Phosphodiesterases" 8779 protein-coding gene gene with protein product 602047 NA 8884271, 16395595 Standard NM_000922 NM_000922 NA Approved HcGIP1 uc001mln.3 Q13370 OTTHUMG00000165898 ENST00000455098.2:c.978+23824->C chr11.hg19:g.14690424_14690424dupC 2 2 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 1,1 24,24 1,1 1 1 B7ZM37|O00639|Q14408|Q6SEI4 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PDE3B-002 KNOWN alternative_5_UTR|basic|appris_principal protein_coding NA protein_coding OTTHUMT00000386975.1 PASS NA None 26 NA True + C ENST00000455098.2 M6PR 4074 __UNKNOWN__ __UNKNOWN__ 12 9099044 9099047 __UNKNOWN__ Intron DEL GAGA GAGA - rs191914110 LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:9099044_9099047delGAGA ENST00000000412.3 - 2 468 NM_002355.3 NP_002346.1 P20645 MPRD_HUMAN mannose-6-phosphate receptor (cation dependent) NA NA NA NA endosome to lysosome transport (GO:0008333)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165) endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020) mannose binding (GO:0005537)|mannose transmembrane transporter activity (GO:0015578)|transmembrane signaling receptor activity (GO:0004888) NA NA cervix(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(1) 11 Hepatocellular(102;0.137) BRCA - Breast invasive adenocarcinoma(232;0.0146) Alglucosidase alfa(DB01272) GTAGGATCAGGAGAGAGAGGAAAG 0.441 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 138 139.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.31 NA NA CCDS8598.1, CCDS73440.1 12p13.31 2013-09-20 ENSG00000003056 ENSG00000003056 4074 6752 protein-coding gene gene with protein product 154540 NA Standard NM_002355 NA Approved uc001qvf.3 P20645 OTTHUMG00000168276 ENST00000000412.3:c.1-43TCTC>- chr12.hg19:g.9099048_9099051delGAGA 2 3 ref NA False 43 43 PASS 4 PASS ref->het 0 NA 76,79 39,39 23,21 1 1 A8K528|D3DUV5 True hg19 CCDS8598.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA M6PR-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000399130.1 PASS NA None 138 NA True - GA ENST00000000412.3 ARID2 196528 __UNKNOWN__ __UNKNOWN__ 12 46246615 46246615 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:46246615delT ENST00000334344.6 + 15 4881 c.4709delT c.(4708-4710)atafs p.I1570fs ARID2_ENST00000422737.1_Frame_Shift_Del_p.I1421fs|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Frame_Shift_Del_p.I1180fs|ARID2_ENST00000457135.1_Frame_Shift_Del_p.I178fs NM_152641.2 NP_689854.2 Q68CP9 ARID2_HUMAN AT rich interactive domain 2 (ARID, RFX-like) 1570 NA NA NA chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) NA NA NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2) 116 Lung SC(27;0.192)|Renal(347;0.236) Lung NSC(34;0.106)|all_lung(34;0.22) OV - Ovarian serous cystadenocarcinoma(5;0.00691) GBM - Glioblastoma multiforme(48;0.0153) AAAGTAGCAATAGAAAGTGCT 0.443 NA NA "N, S, F" NA hepatocellular carcinoma NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Rec yes NA 12 12q12 196528 AT rich interactive domain 2 NA E 0 NA NA NA NA NA NA NA 138 139.72 NA NA NA 60 48 52 NA NA NA NA 12 NA NA NA NA NA NA 46246615 2203 4300 6503 SO:0001589 frameshift_variant 0.19 NA NA CCDS31783.1 12q13.11 2013-02-07 ENSG00000189079 ENSG00000189079 196528 "-" 18037 protein-coding gene gene with protein product 609539 NA Standard XM_350875 NM_152641 NA Approved KIAA1557, DKFZp686G052, FLJ30619, BAF200 uc001ros.1 Q68CP9 OTTHUMG00000150487 ENST00000334344.6:c.4709delT chr12.hg19:g.46246615delT ENSP00000335044:p.Ile1570fs 0 4 ref NA False 87 85 PASS 1 PASS ref->het 0 NA 70,72 51,52 16,15 1 1 Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5 True hg19 CCDS31783.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARID2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000318380.2 PASS NA None 138 NA True + T ENST00000334344.6 ZNF605 100289635 __UNKNOWN__ __UNKNOWN__ 12 133499749 133499752 __UNKNOWN__ 3'UTR DEL TAAA TAAA - LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:133499749_133499752delTAAA ENST00000392321.3 - 0 4451_4454 ZNF605_ENST00000360187.4_3'UTR NM_001164715.1 NP_001158187.1 Q86T29 ZN605_HUMAN zinc finger protein 605 NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA NA breast(1)|kidney(16)|large_intestine(5)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 28 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_cancers(7;0.00227)|all_epithelial(31;0.142) OV - Ovarian serous cystadenocarcinoma(86;9.24e-09)|Epithelial(86;2.11e-07)|all cancers(50;5.27e-06) actttacttctaaataaactccaa 0.319 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 95 99.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.01 NA NA AL832623 CCDS31938.1, CCDS53850.1 12q24.33 2013-01-08 2009-09-11 2009-09-11 ENSG00000196458 100289635 "Zinc fingers, C2H2-type", "-" 28068 protein-coding gene gene with protein product NA NA Standard NM_183238 NM_183238 NA Approved uc001uli.3 Q86T29 ENST00000392321.3:c.*2210TTTA>- chr12.hg19:g.133499753_133499756delTAAA 1 6 ref NA False 41 41 PASS 2 PASS ref->het 0 NA 51,53 27,27 16,16 2 2 B3KVG4|D3DXJ0|Q86T91 True hg19 CCDS53850.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF605-002 NOVEL basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000397136.1 PASS NA None 95 NA True - TAAA ENST00000392321.3 MTMR6 9107 __UNKNOWN__ __UNKNOWN__ 13 25820441 25820442 __UNKNOWN__ 3'UTR INS - - T LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:25820441_25820442insT ENST00000381801.5 - 0 5555_5556 MTMR6_ENST00000540661.1_Intron NM_004685.3 NP_004676.3 Q9Y217 MTMR6_HUMAN myotubularin related protein 6 NA NA NA NA peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281) cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634) calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725) NA NA breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3) 36 Lung SC(185;0.0225)|Breast(139;0.0351) all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164) GGTATATATACTTTTTTTTGAG 0.262 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 76 74.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.39 NA NA AF072928 CCDS9313.1 13q12 2011-06-09 ENSG00000139505 ENSG00000139505 9107 "Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins" 7453 protein-coding gene gene with protein product 603561 NA 9736772 Standard NM_004685 NM_004685 NA Approved uc001uqf.4 Q9Y217 OTTHUMG00000016606 ENST00000381801.5:c.*2929->A chr13.hg19:g.25820449_25820449dupT 9 8 ref NA False 38 38 PASS 8 PASS ref->het 0 NA 31,31 30,31 14,14 1 1 B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80 True hg19 CCDS9313.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MTMR6-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044225.1 PASS NA None 76 NA True - T ENST00000381801.5 ACTN4 81 __UNKNOWN__ __UNKNOWN__ 19 39218726 39218729 __UNKNOWN__ Intron DEL TCTC TCTC - LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:39218726_39218729delTCTC ENST00000252699.2 + 19 2494 ACTN4_ENST00000390009.3_Intron|ACTN4_ENST00000424234.2_Intron|ACTN4_ENST00000497637.1_Intron NM_004924.4 NP_004915.2 O43707 ACTN4_HUMAN actinin, alpha 4 NA NA NA NA actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830) cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018) actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803) NA NA NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3) 30 all_cancers(60;1.57e-05)|Ovarian(47;0.103) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) tctctctccttctctctttctcCC 0.608 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Colon(168;199 1940 10254 46213 46384) PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 228 225.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.74 NA NA D89980 CCDS12518.1 19q13 2013-01-10 ENSG00000130402 ENSG00000130402 81 "EF-hand domain containing" 166 protein-coding gene gene with protein product 604638 "focal segmental glomerulosclerosis 1" FSGS1 NA 9461087, 10700177 Standard NM_004924 NA Approved uc002oja.2 O43707 OTTHUMG00000137382 ENST00000252699.2:c.2418+60TCTC>- chr19.hg19:g.39218726_39218729delTCTC 1 4 ref NA False 75 75 PASS 3 PASS ref->het 0 NA 141,148 55,57 35,27 1 1 A4K467|D6PXK4|O76048 True hg19 CCDS12518.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACTN4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000268091.1 PASS NA None 228 NA True + TC ENST00000252699.2 TTI1 9675 __UNKNOWN__ __UNKNOWN__ 20 36628853 36628854 __UNKNOWN__ Intron INS - - CGGCCAGCGCAGGCTTCCCTCCCGCGTGGG rs71189908|rs72460889|rs61739167|rs150432768 byFrequency LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:36628853_36628854insCGGCCAGCGCAGGCTTCCCTCCCGCGTGGG ENST00000373448.2 - 6 2891 TTI1_ENST00000449821.1_Intron|TTI1_ENST00000373447.3_Intron NM_014657.1 NP_055472.1 O43156 TTI1_HUMAN TELO2 interacting protein 1 NA NA NA NA regulation of TOR signaling (GO:0032006) cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932) NA NA breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3) 47 GGTCAGTACGACGGCCAGCGCA 0.554 NA NA NA NA NA NA NA NA NA NA 2035 0.40635 0.3926 0.3775 5008 , , NA 25978 0.4028 NA 0.4334 False NA ,,, NA NA NA 2504 0.4213 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 276 202.93 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.46 NA NA BC013121 CCDS13300.1 20q11.23 2011-11-10 2011-11-10 2010-06-22 ENSG00000101407 ENSG00000101407 9675 29029 protein-coding gene gene with protein product "smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)" 614425 "KIAA0406", "Tel2 interacting protein 1 homolog (S. pombe)" KIAA0406 NA 9455477, 20427287, 20371770 Standard NM_014657 NM_014657 NA Approved smg-10 uc002xhl.3 O43156 OTTHUMG00000032433 ENST00000373448.2:c.2653-1123->CCCACGCGGGAGGGAAGCCTGCGCTGGCCG chr20.hg19:g.36628853_36628854insCGGCCAGCGCAGGCTTCCCTCCCGCGTGGG 2 2 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 4,5 8,8 260,259 2 2 D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0 True hg19 CCDS13300.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TTI1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000079138.2 PASS NA None 276 NA True - CGGCCAGCGCAGGCTTCCCTCCCGCGTGGG ENST00000373448.2 MYO18B 84700 __UNKNOWN__ __UNKNOWN__ 22 26219623 26219623 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-014_T LTS-014_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:26219623delC ENST00000407587.2 + 13 2842 c.2673delC c.(2671-2673)ctcfs p.L891fs MYO18B_ENST00000536101.1_Frame_Shift_Del_p.L891fs|MYO18B_ENST00000335473.7_Frame_Shift_Del_p.L891fs Q8IUG5 MY18B_HUMAN myosin XVIIIB 891 Myosin motor. NA NA NA cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461) ATP binding (GO:0005524)|motor activity (GO:0003774) NA NA NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2) 146 GATGGGGCCTCGAGGATGAGG 0.592 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 222 215.84 NA NA NA 172 167 169 NA NA NA NA 22 NA NA NA NA NA NA 26219623 2057 4189 6246 SO:0001589 frameshift_variant 0.27 NA NA AJ310931 CCDS54507.1 22q12.1 2011-09-27 ENSG00000133454 ENSG00000133454 84700 "Myosins / Myosin superfamily : Class XVIII" 18150 protein-coding gene gene with protein product 607295 NA 12209013, 12547197 Standard NM_032608 NM_032608 NA Approved BK125H2.1 uc003abz.1 Q8IUG5 OTTHUMG00000151129 ENST00000407587.2:c.2673delC chr22.hg19:g.26219623delC ENSP00000386096:p.Leu891fs 0 3 ref NA False 331 98 PASS 1 PASS ref->het 0 NA 39,39 155,157 22,20 1 1 B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MYO18B-006 NOVEL non_canonical_conserved|basic|appris_candidate_longest|exp_conf protein_coding NA protein_coding OTTHUMT00000400691.1 PASS NA None 222 NA True + C ENST00000407587.2 Unknown 0 __UNKNOWN__ __UNKNOWN__ M 310 311 __UNKNOWN__ IGR DEL CT CT - LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrM:310_311delCT NA None (None upstream) : MT-TF (265 downstream) NA NA NA NA NA NA NA NA NA AAACCCCCCCCTCCCCCCGCTT 0.411 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 64 139.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 4.91 NA NA NA NA NA chrM.hg19:g.310_311delCT 0 14 ref NA False 337 123 PASS 1 PASS ref->het 0 NA 17,20 35,43 103,97 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 64 True CT NOTCH2 4853 __UNKNOWN__ __UNKNOWN__ 1 120456556 120456557 __UNKNOWN__ 3'UTR DEL AT AT - LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:120456556_120456557delAT ENST00000256646.2 - 0 9007_9008 NM_024408.3 NP_077719.2 Q04721 NOTC2_HUMAN notch 2 NA NA NA NA NA apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367) cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235) calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872) NA NA breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1) 158 all_neural(166;0.153) all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809) Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133) NA GCACTTGAACATATAAAGTCCA 0.421 NA NA "N, F, Mis" NA "marginal zone lymphoma, DLBCL" NA NA NA Alagille Syndrome NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Dom yes NA 1 1p13-p11 4853 Notch homolog 2 NA L 0 NA NA NA NA NA NA NA 113 122.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.5 Familial Cancer Database ALGS1, ALGS2.Alagille-Watson syndrome AF315356 CCDS908.1 1p13-p11 2013-01-10 2010-06-24 ENSG00000134250 ENSG00000134250 4853 "Ankyrin repeat domain containing" 7882 protein-coding gene gene with protein product 600275 "Notch (Drosophila) homolog 2", "Notch homolog 2 (Drosophila)" NA 7698746 Standard NM_024408 NM_001200001 NA Approved uc001eik.3 Q04721 OTTHUMG00000012177 ENST00000256646.2:c.*1373AT>- chr1.hg19:g.120456558_120456559delAT 1 4 ref NA False 68 68 PASS 2 PASS ref->het 0 NA 43,44 60,62 14,12 1 1 Q5T3X7|Q99734|Q9H240 True hg19 CCDS908.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NOTCH2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000033679.1 PASS NA None 113 True - AT ENST00000256646.2 INTS7 25896 __UNKNOWN__ __UNKNOWN__ 1 212154526 212154542 __UNKNOWN__ Splice_Site DEL AAAAGATCTAGAAGAAA AAAAGATCTAGAAGAAA - LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:212154526_212154542delAAAAGATCTAGAAGAAA ENST00000366994.3 - 10 1237_1243 c.1133_1139delTTTCTTCTAGATCTTTT c.(1132-1140)gtttcttct>gt p.VSS378fs INTS7_ENST00000366993.3_Splice_Site_p.VSS378fs|INTS7_ENST00000366992.3_Splice_Site_p.VSS378fs|INTS7_ENST00000440600.2_Splice_Site_p.VSS329fs|INTS7_ENST00000469606.1_5'UTR NM_001199811.1|NM_001199812.1|NM_015434.3 NP_001186740.1|NP_001186741.1|NP_056249.1 Q9NVH2 INT7_HUMAN integrator complex subunit 7 378 NA NA NA NA cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180) chromosome (GO:0005694)|integrator complex (GO:0032039) NA NA NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 20 OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852) NA TTCCAGTGCCAAAAGATCTAGAAGAAAAACAGTAAAC 0.382 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 201 172.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0 AK022509 CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1 1q32.3 2008-02-05 2006-03-15 2006-03-15 ENSG00000143493 ENSG00000143493 25896 24484 protein-coding gene gene with protein product 611350 "chromosome 1 open reading frame 73" C1orf73 NA 16239144 Standard NM_015434 NM_015434 NA Approved DKFZP434B168, INT7 uc001hiw.2 Q9NVH2 OTTHUMG00000037119 ENST00000366994.3:c.1133-1TTTCTTCTAGATCTTTT>- chr1.hg19:g.212154526_212154542delAAAAGATCTAGAAGAAA 0 7 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 160,160 17,17 31,32 1 1 B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3 True hg19 CCDS1501.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA INTS7-001 NOVEL basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000090142.1 PASS NA None 201 Frame_Shift_Del True - AAAAGATCTAGAAGAAA ENST00000366994.3 COL4A3 1285 __UNKNOWN__ __UNKNOWN__ 2 228125901 228125901 __UNKNOWN__ Intron DEL A A - LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:228125901delA ENST00000396578.3 + 20 1312 AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA NM_000091.4 NP_000082.2 Q01955 CO4A3_HUMAN collagen, type IV, alpha 3 (Goodpasture antigen) NA NA NA NA NA activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605) basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576) extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198) NA NA NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1) 55 all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247) Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187) NA GTCCTCTATTAAGTTTACATT 0.418 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 126 123.77 NA NA NA NA NA 47 43 44 NA NA NA NA 2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 228125901 NA 692 1591 2283 SO:0001627 intron_variant 0 CCDS42829.1 2q36-q37 2014-09-17 ENSG00000169031 ENSG00000169031 1285 "Collagens" 2204 protein-coding gene gene with protein product "tumstatin" 120070 NA 1737849 Standard NM_000091 NM_000091 NA Approved uc002vom.2 Q01955 OTTHUMG00000149891 ENST00000396578.3:c.1150+68A>- chr2.hg19:g.228125901delA 1 3 ref NA False 57 57 PASS 2 PASS ref->het 0 NA 55,56 52,53 16,16 1 1 Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1 True hg19 CCDS42829.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COL4A3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000331409.2 PASS NA None 126 True + A ENST00000396578.3 PXK 54899 __UNKNOWN__ __UNKNOWN__ 3 58406296 58406300 __UNKNOWN__ Intron DEL GTAAA GTAAA - LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:58406296_58406300delGTAAA ENST00000356151.2 + 18 1637 PXK_ENST00000302779.5_Intron|PXK_ENST00000463280.1_Splice_Site|PXK_ENST00000383716.3_Intron|PXK_ENST00000479241.1_Intron|PXK_ENST00000536660.1_Intron|PXK_ENST00000484288.1_3'UTR|PXK_ENST00000383715.4_3'UTR NM_017771.3 NP_060241.2 PX domain containing serine/threonine kinase NA NA NA NA NA NA NA cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22) NA TGAATTTTCGGTAAAGTAAACTATG 0.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 1015 988.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.07 AY274811 CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1 3p21.2 2008-02-05 ENSG00000168297 ENSG00000168297 54899 23326 protein-coding gene gene with protein product 611450 NA Standard NM_017771 XM_005265255 NA Approved FLJ20335 uc003djz.1 Q7Z7A4 OTTHUMG00000159149 ENST00000356151.2:c.1529-4179GTAAA>- chr3.hg19:g.58406301_58406305delGTAAA 1 3 ref NA False 93 93 PASS 2 PASS ref->het 0 NA 926,936 22,22 114,108 1 1 True hg19 CCDS2889.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PXK-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000353499.1 PASS NA None 1015 True + GTAAA ENST00000356151.2 HNF4G 3174 __UNKNOWN__ __UNKNOWN__ 8 76452275 76452275 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:76452275delT ENST00000396423.2 + 1 172 c.48delT c.(46-48)actfs p.T16fs HNF4G_ENST00000354370.1_Intron NM_004133.4 NP_004124.4 Q14541 HNF4G_HUMAN hepatocyte nuclear factor 4, gamma 0 NA NA NA NA endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367) nucleoplasm (GO:0005654) ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270) NA NA breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2) 37 Breast(64;0.0448) BRCA - Breast invasive adenocarcinoma(89;0.161) NA CTTACACAACTTTGGAGTTTG 0.348 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 433 428.53 NA NA NA NA NA 143 141 142 NA NA NA NA 8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 76452275 NA 1859 4095 5954 SO:0001589 frameshift_variant 1.52 CCDS6220.2 8q21-q22 2013-01-16 ENSG00000164749 ENSG00000164749 3174 "Nuclear hormone receptors" 5026 protein-coding gene gene with protein product 605966 NA 8622695, 12220494 Standard NM_004133 NM_004133 NA Approved NR2A2 uc003yar.3 Q14541 OTTHUMG00000149920 ENST00000396423.2:c.48delT chr8.hg19:g.76452275delT ENSP00000379701:p.Thr16fs 2 3 ref NA False 190 103 PASS 3 PASS ref->het 0 NA 195,197 187,189 48,45 1 1 Q7Z2V9|Q9UH81|Q9UIS6 True hg19 CCDS6220.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HNF4G-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000313913.1 PASS NA None 433 True + T ENST00000396423.2 RSF1 51773 __UNKNOWN__ __UNKNOWN__ 11 77448665 77448692 __UNKNOWN__ Intron DEL GGGTGTGTGTGTGTGTGTGTGTGTGTGT GGGTGTGTGTGTGTGTGTGTGTGTGTGT - rs572660632|rs57437159|rs57778792|rs375411839|rs6592744|rs200861541|rs138480472 byFrequency LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:77448665_77448692delGGGTGTGTGTGTGTGTGTGTGTGTGTGT ENST00000308488.6 - 4 881 RSF1_ENST00000360355.2_Intron Q96T23 RSF1_HUMAN remodeling and spacing factor 1 NA NA NA NA NA CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434) nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213) histone binding (GO:0042393)|zinc ion binding (GO:0008270) NA NA breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 43 all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152) Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31) NA GTGTTTTGGGGGgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgt 0.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 65 59.98 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF380176, AF227948 CCDS8253.1 11q14.1 2013-01-28 2006-05-25 2006-05-25 ENSG00000048649 ENSG00000048649 51773 "Zinc fingers, PHD-type" 18118 protein-coding gene gene with protein product 608522 "hepatitis B virus x associated protein" HBXAP NA 11788598, 12972596 Standard NM_016578 NM_016578 NA Approved XAP8, RSF-1, p325 uc001oyn.3 Q96T23 OTTHUMG00000150433 ENST00000308488.6:c.578+3083ACACACACACACACACACACACACACCC>- chr11.hg19:g.77448665_77448692delGGGTGTGTGTGTGTGTGTGTGTGTGTGT 0 7 ref NA False 50 44 PASS 1 PASS ref->hom 0 NA 0,0 55,55 9,10 2 1 Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0 True hg19 CCDS8253.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RSF1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000318075.2 PASS NA None 65 True - GGGTGTGTGTGTGTGTGTGTGTGTGTGT ENST00000308488.6 Unknown 0 __UNKNOWN__ __UNKNOWN__ 11 77719464 77719465 __UNKNOWN__ IGR INS - - A rs34517579|rs148136171|rs201075945 byFrequency LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:77719464_77719465insA NA INTS4 (13740 upstream) : RP11-7I15.3 (7295 downstream) NA NA NA NA NA NA NA NA NA agccAGGTCTTTTTAAAATATC 0.431 NA NA NA NA NA NA NA NA NA -|-|A|insertion 2541 0.507388 0.7315 0.4049 5008 , , NA 17521 0.6181 NA 0.3579 False NA ,,, NA NA NA 2504 0.317 NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 90 89.58 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.34 NA NA NA NA NA chr11.hg19:g.77719464_77719465insA 1 6 ref NA False 49 48 PASS 0 PASS ref->het 0 NA 5,5 77,80 9,6 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 90 True A Unknown 0 __UNKNOWN__ __UNKNOWN__ 16 33539585 33539586 __UNKNOWN__ IGR DEL AC AC - LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:33539585_33539586delAC NA BMS1P8 (40493 upstream) : IGHV3OR16-12 (65644 downstream) NA NA NA NA NA NA NA NA NA AGAGTACTCTACCTCAGATTCC 0.366 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 508 506.09 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 2.09 NA NA NA NA NA chr16.hg19:g.33539585_33539586delAC 0 3 ref NA False 89 33 PASS 1 PASS ref->het 0 NA 317,346 146,184 32,28 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 508 True AC ST3GAL2 6483 __UNKNOWN__ __UNKNOWN__ 16 70414622 70414623 __UNKNOWN__ 3'UTR DEL AA AA - rs549106665 byFrequency LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:70414622_70414623delAA ENST00000393640.4 - 0 4129_4130 RP11-529K1.4_ENST00000566960.1_RNA|ST3GAL2_ENST00000342907.2_3'UTR Q16842 SIA4B_HUMAN ST3 beta-galactoside alpha-2,3-sialyltransferase 2 NA NA NA NA NA amino sugar metabolic process (GO:0006040)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281) extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173) beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836) NA NA breast(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1) 11 Ovarian(137;0.0694) NA AGCCCCAGGCAAAGTTACCCCC 0.634 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 259 250.01 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.28 U63090 CCDS10890.1 16q22.3 2013-03-01 2003-01-14 2005-02-07 ENSG00000157350 ENSG00000157350 6483 2.4.99.4 "Sialyltransferases" 10863 protein-coding gene gene with protein product 607188 "sialyltransferase 4B (beta-galactosidase alpha-2,3-sialytransferase)" SIAT4B NA 9266697, 8920913 Standard NM_006927 NM_006927 NA Approved ST3GALII, ST3GalA.2 uc002eyx.2 Q16842 OTTHUMG00000137580 ENST00000393640.4:c.*970TT>- chr16.hg19:g.70414622_70414623delAA 1 3 ref NA False 107 107 PASS 3 PASS ref->het 0 NA 171,174 57,59 33,28 1 1 O00654 True hg19 CCDS10890.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ST3GAL2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000268968.1 PASS NA None 259 True - A ENST00000393640.4 KRT222 125113 __UNKNOWN__ __UNKNOWN__ 17 38811995 38811996 __UNKNOWN__ Intron INS - - TT LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:38811995_38811996insTT ENST00000476049.1 - 6 1010 Q8N1A0 KT222_HUMAN keratin 222 NA NA NA NA NA intermediate filament (GO:0005882) structural molecule activity (GO:0005198) NA NA breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(2)|skin(1) 15 NA AACCTTTTAGATATATGTAGAT 0.302 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 65 79.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AK092967 CCDS11371.1 17q21.2 2013-06-25 2009-08-25 2009-08-25 ENSG00000213424 ENSG00000213424 125113 "-" 28695 protein-coding gene gene with protein product NA "keratin 222 pseudogene" KRT222P NA 16831889 Standard NM_152349 NM_152349 NA Approved KA21, MGC45562 uc002hvc.2 Q8N1A0 OTTHUMG00000133374 ENST00000476049.1:c.885+577->AA chr17.hg19:g.38811995_38811996insTT 3 2 ref NA False 201 90 PASS 1 PASS ref->het 0 NA 5,5 51,52 10,9 1 1 Q7Z368 True hg19 CCDS11371.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KRT222-001 KNOWN basic|appris_principal|readthrough_transcript|CCDS nonsense_mediated_decay NA protein_coding OTTHUMT00000447539.1 PASS NA None 65 True - T ENST00000476049.1 HOXB2 3212 __UNKNOWN__ __UNKNOWN__ 17 46623000 46623001 __UNKNOWN__ 5'UTR DEL AC AC - LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:46623000_46623001delAC ENST00000330070.4 - 0 440_441 HOXB-AS1_ENST00000508688.1_RNA|HOXB-AS1_ENST00000504972.3_RNA|HOXB-AS1_ENST00000435312.1_RNA NM_002145.3 NP_002136.1 P14652 HXB2_HUMAN homeobox B2 NA NA NA NA NA anterior/posterior pattern specification (GO:0009952)|blood circulation (GO:0008015)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|neural nucleus development (GO:0048857)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA NA NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1) 11 NA TCCAAAAACAACAGTTAAATCT 0.436 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 241 230.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.87 CCDS11527.1 17q21.32 2012-02-22 2005-12-22 ENSG00000173917 ENSG00000173917 3212 "Homeoboxes / ANTP class : HOXL subclass" 5113 protein-coding gene gene with protein product 142967 "homeo box B2" HOX2, HOX2H NA 1973146, 1358459 Standard XM_005257276 NA Approved uc002inm.3 P14652 OTTHUMG00000159930 ENST00000330070.4:c.-728GT>- chr17.hg19:g.46623000_46623001delAC 0 7 ref NA False 88 88 PASS 1 PASS ref->het 0 NA 154,159 56,57 29,24 2 2 P10913|P17485 True hg19 CCDS11527.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HOXB2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000358384.2 PASS NA None 241 True - AC ENST00000330070.4 COLEC12 81035 __UNKNOWN__ __UNKNOWN__ 18 371506 371511 __UNKNOWN__ Intron DEL GGTGCA GGTGCA - rs147138965 byFrequency LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:371506_371511delGGTGCA ENST00000400256.3 - 3 266 NM_130386.2 NP_569057 Q5KU26 COL12_HUMAN collectin sub-family member 12 NA NA NA NA NA carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898) collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329) NA NA cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2) 46 all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426) NA AGGGCCCTGGGGTGCAGGGAGGACCC 0.505 NA NA NA NA NA NA NA NA NA 756 0.150958 0.0325 0.1412 5008 , , NA 19533 0.1756 NA 0.2127 False NA ,,, NA NA NA 2504 0.229 NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 33 29.61 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AB038518 CCDS32782.1 18p11.32 2013-09-19 ENSG00000158270 ENSG00000158270 81035 "Collectins" 16016 protein-coding gene gene with protein product 607621 NA 11162630 Standard NM_130386 NA Approved SRCL, CL-P1, SCARA4 uc002kkm.3 Q5KU26 OTTHUMG00000178145 ENST00000400256.3:c.59-13984TGCACC>- chr18.hg19:g.371506_371511delGGTGCA 0 5 ref NA False 42 41 PASS 1 PASS ref->hom 0 NA 0,0 29,29 3,3 1 1 Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7 True hg19 CCDS32782.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COLEC12-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000440746.1 PASS NA None 33 True - GGTGCA ENST00000400256.3 ENOSF1 55556 __UNKNOWN__ __UNKNOWN__ 18 679449 679450 __UNKNOWN__ Intron INS - - CC rs386386820|rs397696631|rs34733085 byFrequency LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:679449_679450insCC ENST00000251101.7 - 12 965 ENOSF1_ENST00000383578.3_Intron|ENOSF1_ENST00000319815.6_Intron|ENOSF1_ENST00000583973.1_Intron|ENOSF1_ENST00000340116.7_Intron|ENOSF1_ENST00000580982.1_Intron NM_017512.5 NP_059982.2 Q7L5Y1 ENOF1_HUMAN enolase superfamily member 1 NA NA NA NA NA cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275) mitochondrion (GO:0005739) isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287) NA NA endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1) 10 NA cctcagatgatcctcccgcctc 0.505 NA NA NA NA NA NA NA NA NA 1994 0.398163 0.4871 0.2925 5008 , , NA 19586 0.4315 NA 0.3022 False NA ,,, NA NA NA 2504 0.4172 NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 90 104.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.86 X67098 CCDS11822.1, CCDS11823.1, CCDS45821.1 18p11.32 2005-01-26 ENSG00000132199 ENSG00000132199 55556 30365 protein-coding gene gene with protein product 607427 NA 14508106 Standard NM_017512 NM_001126123 NA Approved HSRTSBETA, rTS, TYMSAS uc002kku.4 Q7L5Y1 OTTHUMG00000131470 ENST00000251101.7:c.877-712->GG chr18.hg19:g.679450_679451dupCC 4 5 ref NA False 55 46 PASS 2 PASS ref->hom 0 NA 0,0 84,86 8,6 1 1 A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6 True hg19 CCDS11822.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENOSF1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254312.2 PASS NA None 90 True - C ENST00000251101.7 ROCK1 6093 __UNKNOWN__ __UNKNOWN__ 18 18530901 18530902 __UNKNOWN__ 3'UTR DEL AC AC - LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:18530901_18530902delAC ENST00000399799.2 - 0 5448_5449 NM_005406.2 NP_005397.1 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein kinase 1 NA NA NA NA NA actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939) cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726) ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674) NA NA NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2) 16 Melanoma(1;0.165) NA TAAAAAAAAAACAAAACTTCAG 0.351 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 361 423.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 5.38 CCDS11870.2 18q11.2 2013-01-10 ENSG00000067900 ENSG00000067900 6093 2.7.11.1 "Pleckstrin homology (PH) domain containing" 10251 protein-coding gene gene with protein product 601702 NA 8617235 Standard NM_005406 NM_005406 NA Approved p160ROCK uc002kte.3 Q13464 OTTHUMG00000131723 ENST00000399799.2:c.*444GT>- chr18.hg19:g.18530901_18530902delAC 0 14 ref NA False 55 55 PASS 1 PASS ref->het 0 NA 257,272 50,64 66,53 1 1 B0YJ91|Q2KHM4|Q59GZ4 True hg19 CCDS11870.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ROCK1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254641.2 PASS NA None 361 True - AC ENST00000399799.2 Unknown 0 __UNKNOWN__ __UNKNOWN__ Y 59022474 59022475 __UNKNOWN__ IGR INS - - A LTS-015_T LTS-015_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrY:59022474_59022475insA NA None (None upstream) : SPRY3 (78004 downstream) NA NA NA NA NA NA NA NA NA gaccctgtctcaaaaaaaagaa 0.366 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 85 76.26 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chrY.hg19:g.59022482_59022482dupA 9 13 ref NA False 32 32 PASS 8 PASS ref->het 0 NA 52,52 23,23 9,9 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 85 True A NBPF1 55672 __UNKNOWN__ __UNKNOWN__ 1 16889571 16889572 __UNKNOWN__ 3'UTR INS - - T rs200480425 LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:16889571_16889572insT ENST00000430580.2 - 0 5173_5174 NM_017940.3 NP_060410.2 Q3BBV0 NBPF1_HUMAN neuroblastoma breakpoint family, member 1 NA NA NA cytoplasm (GO:0005737) NA UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179) ATCTCTTCTCCTTTTTGTTGTG 0.356 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 184 166.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.67 AB051480 1p36.13 2013-01-30 ENSG00000219481 ENSG00000219481 55672 "neuroblastoma breakpoint family" 26088 protein-coding gene gene with protein product 610501 NA 11214970, 16079250 Standard NM_017940 NM_017940 NA Approved FLJ20719, KIAA1693 uc001ayw.4 Q3BBV0 OTTHUMG00000002487 ENST00000430580.2:c.*867->A chr1.hg19:g.16889576_16889576dupT 6 7 ref NA False 34 34 PASS 5 PASS ref->het 0 NA 139,148 39,47 7,7 1 1 Q8N4E8|Q9C0H0 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NBPF1-005 NOVEL upstream_uORF|basic|appris_principal protein_coding NA protein_coding OTTHUMT00000106436.3 PASS NA None 184 NA True - T ENST00000430580.2 Unknown 0 __UNKNOWN__ __UNKNOWN__ 1 30043595 30043596 __UNKNOWN__ IGR INS - - T rs201692794|rs149226960|rs371142865 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:30043595_30043596insT NA AL139151.1 (284521 upstream) : AC092265.1 (73795 downstream) NA NA NA NA tctccatgggaaagggctgtta 0.436 NA NA NA NA NA NA NA NA NA -|-|T|insertion 1042 0.208067 0.1861 0.2104 5008 , , NA 20780 0.3343 NA 0.1879 False NA ,,, NA NA NA 2504 0.1268 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 23 24.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr1.hg19:g.30043595_30043596insT 1 3 ref NA False 48 48 PASS 0 PASS ref->hom 0 NA 0,0 20,20 2,2 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 23 NA True T PODN 127435 __UNKNOWN__ __UNKNOWN__ 1 53544366 53544380 __UNKNOWN__ In_Frame_Del DEL TTGGCCGCGAAGACT TTGGCCGCGAAGACT - rs141138245|rs375056345 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:53544366_53544380delTTGGCCGCGAAGACT ENST00000312553.5 + 8 1335_1349 c.1328_1342delTTGGCCGCGAAGACT c.(1327-1344)attggccgcgaagacttt>att p.GREDF444del PODN_ENST00000395871.2_In_Frame_Del_p.GREDF302del|PODN_ENST00000371500.3_In_Frame_Del_p.GREDF425del|RP11-334A14.5_ENST00000447867.1_RNA NM_001199081.1|NM_153703.4 NP_001186010.1|NP_714914.2 Q7Z5L7 PODN_HUMAN podocan 396 NA T -> M (in dbSNP:rs12567021). {ECO:0000269|PubMed:12796502}. NA negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285) cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578) collagen binding (GO:0005518) p.R445H(1) breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1) 33 ATCACAGGCATTGGCCGCGAAGACTTTGCCACCAC 0.647 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 1 Substitution - Missense(1) pancreas(1) NA NA NA NA NA 1115 1060.76 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 1.46 AY313607 CCDS573.1, CCDS55601.1, CCDS55602.1 1p32.3 2008-02-05 ENSG00000174348 ENSG00000174348 127435 "Proteoglycans / Extracellular Matrix : Small leucine-rich repeats" 23174 protein-coding gene gene with protein product "podocan proteoglycan" 608661 NA Standard NM_153703 NM_153703 NA Approved PCAN, PODOCAN, MGC24995, SLRR5A uc010onr.2 Q7Z5L7 OTTHUMG00000008934 ENST00000312553.5:c.1328_1342delTTGGCCGCGAAGACT chr1.hg19:g.53544366_53544380delTTGGCCGCGAAGACT ENSP00000308315:p.Gly444_Phe448del 0 3 ref NA False 182 155 PASS 1 PASS ref->het 0 NA 915,924 240,244 133,126 1 1 B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641 True hg19 CCDS573.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PODN-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000024735.1 PASS NA None 1115 NA True + TTGGCCGCGAAGACT ENST00000312553.5 PODN 127435 __UNKNOWN__ __UNKNOWN__ 1 53544478 53544479 __UNKNOWN__ Frame_Shift_Del DEL GC GC - LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:53544478_53544479delGC ENST00000312553.5 + 8 1447_1448 c.1440_1441delGC c.(1438-1443)ctgcgcfs p.R481fs PODN_ENST00000395871.2_Frame_Shift_Del_p.R339fs|PODN_ENST00000371500.3_Frame_Shift_Del_p.R462fs|RP11-334A14.5_ENST00000447867.1_RNA NM_001199081.1|NM_153703.4 NP_001186010.1|NP_714914.2 Q7Z5L7 PODN_HUMAN podocan 433 NA NA negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285) cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578) collagen binding (GO:0005518) breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1) 33 TGCGCCTGCTGCGCTCGCTGGA 0.634 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 589 640.23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.37 AY313607 CCDS573.1, CCDS55601.1, CCDS55602.1 1p32.3 2008-02-05 ENSG00000174348 ENSG00000174348 127435 "Proteoglycans / Extracellular Matrix : Small leucine-rich repeats" 23174 protein-coding gene gene with protein product "podocan proteoglycan" 608661 NA Standard NM_153703 NM_153703 NA Approved PCAN, PODOCAN, MGC24995, SLRR5A uc010onr.2 Q7Z5L7 OTTHUMG00000008934 ENST00000312553.5:c.1440_1441delGC chr1.hg19:g.53544480_53544481delGC ENSP00000308315:p.Arg481fs 1 2 ref NA False 124 106 PASS 2 PASS ref->het 0 NA 331,336 163,167 87,79 1 1 B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641 True hg19 CCDS573.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PODN-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000024735.1 PASS NA None 589 NA True + GC ENST00000312553.5 UBR3 130507 __UNKNOWN__ __UNKNOWN__ 2 170821510 170821511 __UNKNOWN__ Intron INS - - ATAAGA LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:170821510_170821511insATAAGA ENST00000272793.5 + 24 3684 UBR3_ENST00000418381.1_Intron|UBR3_ENST00000392631.1_Intron Q6ZT12 UBR3_HUMAN ubiquitin protein ligase E3 component n-recognin 3 (putative) NA NA NA embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511) integral component of membrane (GO:0016021) ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270) breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1) 33 CATTTCATTTGTTTATGTTGGC 0.426 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 90 94.91 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.52 AL834144 CCDS2238.2 2q31.1 2008-06-23 2008-06-23 2007-11-29 ENSG00000144357 ENSG00000144357 130507 "Ubiquitin protein ligase E3 component n-recognins" 30467 protein-coding gene gene with protein product 613831 "zinc finger protein 650" ZNF650 NA 17462990 Standard NM_172070 NM_172070 NA Approved KIAA2024, DKFZp434P117, FLJ37422 uc010zdi.2 Q6ZT12 OTTHUMG00000132229 ENST00000272793.5:c.3634+6474->ATAAGA chr2.hg19:g.170821510_170821511insATAAGA 1 6 ref NA False 42 42 PASS 0 PASS ref->het 0 NA 36,36 20,20 7,7 1 1 B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UBR3-001 KNOWN non_canonical_conserved|basic|appris_principal protein_coding NA protein_coding OTTHUMT00000255290.2 PASS NA None 90 NA True + ATAAGA ENST00000272793.5 UBR3 130507 __UNKNOWN__ __UNKNOWN__ 2 170821516 170821529 __UNKNOWN__ Intron DEL GTTGGCCATGGCCA GTTGGCCATGGCCA - LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:170821516_170821529delGTTGGCCATGGCCA ENST00000272793.5 + 24 3684 UBR3_ENST00000418381.1_Intron|UBR3_ENST00000392631.1_Intron Q6ZT12 UBR3_HUMAN ubiquitin protein ligase E3 component n-recognin 3 (putative) NA NA NA embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511) integral component of membrane (GO:0016021) ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270) breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1) 33 ATTTGTTTATGTTGGCCATGGCCACACCACTAGG 0.435 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 61 90.27 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.56 AL834144 CCDS2238.2 2q31.1 2008-06-23 2008-06-23 2007-11-29 ENSG00000144357 ENSG00000144357 130507 "Ubiquitin protein ligase E3 component n-recognins" 30467 protein-coding gene gene with protein product 613831 "zinc finger protein 650" ZNF650 NA 17462990 Standard NM_172070 NM_172070 NA Approved KIAA2024, DKFZp434P117, FLJ37422 uc010zdi.2 Q6ZT12 OTTHUMG00000132229 ENST00000272793.5:c.3634+6480GTTGGCCATGGCCA>- chr2.hg19:g.170821516_170821529delGTTGGCCATGGCCA 0 4 ref NA False 37 37 PASS 1 PASS ref->het 0 NA 39,39 20,20 5,5 1 1 B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UBR3-001 KNOWN non_canonical_conserved|basic|appris_principal protein_coding NA protein_coding OTTHUMT00000255290.2 PASS NA None 61 NA True + GTTGGCCATGGCCA ENST00000272793.5 MFSD1 64747 __UNKNOWN__ __UNKNOWN__ 3 158546742 158546771 __UNKNOWN__ Stop_Codon_Del DEL GTAATTTATTGCGTTATGTTTTGCAGATGA GTAATTTATTGCGTTATGTTTTGCAGATGA - rs375410786|rs368509514 LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:158546742_158546771delGTAATTTATTGCGTTATGTTTTGCAGATGA ENST00000264266.8 + 0 1456_1460 MFSD1_ENST00000392813.4_Stop_Codon_Del|MFSD1_ENST00000415822.2_Stop_Codon_Del Q9H3U5 MFSD1_HUMAN major facilitator superfamily domain containing 1 NA NA NA transmembrane transport (GO:0055085) integral component of membrane (GO:0016021) breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1) 26 Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523) TTCCTCTTTGGTAATTTATTGCGTTATGTTTTGCAGATGAGAAGTTAAAA 0.291 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(62;1186 1654 36636 37908) PASS NA NA NA NA NA 0 NA NA NA NA NA 566 505.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001567 stop_retained_variant 0.01 BC017661 CCDS3185.1, CCDS3185.2, CCDS54666.1 3q25.32 2005-11-17 ENSG00000118855 ENSG00000118855 64747 25874 protein-coding gene gene with protein product NA NA Standard NM_022736 NM_022736 NA Approved FLJ14153, UG0581B09 uc003fcl.2 Q9H3U5 OTTHUMG00000158835 ENST00000264266.8:c.1369_1398delGTAATTTATTGCGTTATGTTTTGCAGATGA chr3.hg19:g.158546742_158546771delGTAATTTATTGCGTTATGTTTTGCAGATGA ENSP00000264266:p.Glu457_*466delinsGluext*7 0 3 ref NA False 56 56 PASS 1 PASS ref->het 0 NA 576,578 37,38 77,76 1 1 B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MFSD1-018 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000470730.1 PASS NA None 566 NA True + GTAATTTATTGCGTTATGTTTTGCAGATGA ENST00000264266.8 PPP1R2 5504 __UNKNOWN__ __UNKNOWN__ 3 195241750 195241756 __UNKNOWN__ 3'UTR DEL AAGAATC AAGAATC - LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:195241750_195241756delAAGAATC ENST00000328432.3 - 0 2916_2922 NM_006241.4 NP_006232.1 P41236 IPP2_HUMAN protein phosphatase 1, regulatory (inhibitor) subunit 2 NA NA NA generation of precursor metabolites and energy (GO:0006091)|glycogen metabolic process (GO:0005977)|negative regulation of catalytic activity (GO:0043086)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of signal transduction (GO:0009966) protein serine/threonine phosphatase inhibitor activity (GO:0004865) endometrium(2)|kidney(1)|large_intestine(1)|urinary_tract(2) 6 all_cancers(143;1.8e-08)|Ovarian(172;0.0634) Epithelial(36;2.64e-22)|all cancers(36;2.69e-20)|OV - Ovarian serous cystadenocarcinoma(49;3.52e-19)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128) GBM - Glioblastoma multiforme(46;9.55e-05) AAAACACAAAAAGAATCAACTGTTTAA 0.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 209 218.79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 3.71 U68111 CCDS3309.1 3q29 2012-04-17 ENSG00000184203 ENSG00000184203 5504 3.1.3.16 "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits" 9288 protein-coding gene gene with protein product 601792 NA 9126490, 8119416 Standard NM_006241 XM_006713682 NA Approved IPP2 uc003fup.3 P41236 OTTHUMG00000155887 ENST00000328432.3:c.*1944GATTCTT>- chr3.hg19:g.195241750_195241756delAAGAATC 0 7 ref NA False 117 104 PASS 1 PASS ref->het 0 NA 128,131 62,64 32,29 1 1 True hg19 CCDS3309.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPP1R2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000342133.1 PASS NA None 209 NA True - AAGAATC ENST00000328432.3 KDM1B 221656 __UNKNOWN__ __UNKNOWN__ 6 18218101 18218102 __UNKNOWN__ Frame_Shift_Ins INS - - T LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:18218101_18218102insT ENST00000297792.5 + 17 1851_1852 c.1674_1675insT c.(1675-1677)tttfs p.F559fs KDM1B_ENST00000397244.1_Frame_Shift_Ins_p.F560fs|KDM1B_ENST00000388870.2_Frame_Shift_Ins_p.F792fs|KDM1B_ENST00000546309.2_Frame_Shift_Ins_p.F82fs Q8NB78 KDM1B_HUMAN lysine (K)-specific demethylase 1B 791 NA NA DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270) breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1) 25 AAGGAACCGTCTTTTTCGCTGG 0.421 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 229 220.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.56 AK125318 CCDS34343.1 6p22.3 2011-07-01 2009-09-29 2009-09-29 ENSG00000165097 ENSG00000165097 221656 "Chromatin-modifying enzymes / K-demethylases" 21577 protein-coding gene gene with protein product 613081 "amine oxidase, flavin containing 1", "chromosome 6 open reading frame 193", "amine oxidase (flavin containing) domain 1" C6orf193, AOF1 NA 19407342, 19727073 Standard NM_153042 NM_153042 NA Approved FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2 uc003ncn.1 Q8NB78 OTTHUMG00000014316 ENST00000297792.5:c.1679dupT chr6.hg19:g.18218106_18218106dupT ENSP00000297792:p.Phe559fs 6 6 ref NA False 33 33 PASS 5 PASS ref->het 0 NA 144,146 60,61 23,21 1 1 A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7 True hg19 CCDS34343.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KDM1B-002 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000277080.1 PASS NA None 229 NA True + T ENST00000297792.5 INTS1 26173 __UNKNOWN__ __UNKNOWN__ 7 1545229 1545229 __UNKNOWN__ Intron DEL C C - rs11338201 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:1545229delC ENST00000389470.4 - 1 58 Q8N201 INT1_HUMAN integrator complex subunit 1 NA NA NA inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474) integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020) autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 62 Ovarian(82;0.0253) UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15) ctgcagccggccgacagagcg 0.537 NA NA NA NA NA NA NA NA NA C|CC|C|insertion 3006 0.60024 0.8283 0.4063 5008 , , NA 16857 0.7143 NA 0.4493 False NA ,,, NA NA NA 2504 0.4673 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 31 40.98 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.02 AB037861 CCDS47526.1 7p22.3 2009-11-06 ENSG00000164880 ENSG00000164880 26173 24555 protein-coding gene gene with protein product 611345 NA 16239144 Standard NM_001080453 NA Approved DKFZp586J0619, KIAA1440, INT1, NET28 uc003skn.2 Q8N201 OTTHUMG00000151449 ENST00000389470.4:c.58+202G>- chr7.hg19:g.1545229delC 1 2 ref NA False 32 32 PASS 2 PASS ref->het 0 NA 1,1 24,24 6,6 1 1 A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA INTS1-201 KNOWN basic protein_coding NA protein_coding PASS NA None 31 NA True - C ENST00000389470.4 DNAH11 8701 __UNKNOWN__ __UNKNOWN__ 7 21907452 21907453 __UNKNOWN__ Intron INS - - T rs5882827|rs550700201 LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:21907452_21907453insT ENST00000409508.3 + 72 11721 DNAH11_ENST00000328843.6_Intron NM_001277115.1 NP_001264044.1 Q96DT5 DYH11_HUMAN dynein, axonemal, heavy chain 11 NA NA NA microtubule-based movement (GO:0007018) cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874) ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777) NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 230 CACTGATCATGTTTTTATATTC 0.366 NA NA NA NA NA NA Kartagener syndrome NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 38 47.61 NA 1108,2394 NA 230,648,873 NA NA NA NA -9.1 0 NA dbSNP_114 31 5825,1969 NA 2227,1371,299 no intron DNAH11 NM_003777.3 2457,2019,1172 A1A1,A1R,RR NA 25.263,31.6391,38.6243 NA 6933,4363 NA NA NA SO:0001627 intron_variant 0.3 Familial Cancer Database Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome U83569 CCDS64602.1 7p21 2008-07-18 2006-09-04 8701 "Axonemal dyneins" 2942 protein-coding gene gene with protein product "dynein, ciliary, heavy chain 11", "dynein, heavy chain beta-like" 603339 "dynein, axonemal, heavy polypeptide 11" NA 9256245 Standard NM_003777 NM_001277115 NA Approved Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL uc031swp.1 Q96DT5 ENST00000409508.3:c.11691-24->T chr7.hg19:g.21907457_21907457dupT 6 6 ref NA False 35 35 PASS 5 PASS ref->het 0 NA 1,1 31,31 6,6 1 1 Q9UJ82 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DNAH11-001 KNOWN basic|appris_candidate protein_coding NA protein_coding OTTHUMT00000326582.6 PASS NA None 38 NA True + T ENST00000409508.3 DDC 1644 __UNKNOWN__ __UNKNOWN__ 7 50560384 50560388 __UNKNOWN__ Intron DEL TTTCC TTTCC - rs386713134|rs62445939 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:50560384_50560388delTTTCC ENST00000426377.1 - 7 779 DDC_ENST00000444124.2_Intron|DDC_ENST00000431062.1_Intron|DDC_ENST00000357936.5_Intron|DDC_ENST00000380984.4_3'UTR NM_001242888.1 NP_001229817 P20711 DDC_HUMAN dopa decarboxylase (aromatic L-amino acid decarboxylase) NA NA NA catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842) axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021) amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170) breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1) 40 Glioma(55;0.08)|all_neural(89;0.245) Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968) ACAAGGAAATTTTCCAAATGGCCTT 0.502 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 23 80.79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 4.26 CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1 7p12.1 2012-08-30 ENSG00000132437 ENSG00000132437 1644 4.1.1.28 2719 protein-coding gene gene with protein product 107930 NA 1612608 Standard NM_001082971 NA Approved AADC uc003tpf.4 P20711 OTTHUMG00000023353 ENST00000426377.1:c.710+2659GGAAA>- chr7.hg19:g.50560384_50560388delTTTCC 0 4 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 3,3 20,20 0,0 1 1 C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6 True hg19 CCDS56485.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DDC-013 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000342604.1 PASS NA None 23 NA True - TTTCC ENST00000426377.1 DDC 1644 __UNKNOWN__ __UNKNOWN__ 7 50560391 50560392 __UNKNOWN__ Intron INS - - CTC rs538192467|rs199887122|rs386713134|rs557877090 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:50560391_50560392insCTC ENST00000426377.1 - 7 779 DDC_ENST00000444124.2_Intron|DDC_ENST00000431062.1_Intron|DDC_ENST00000357936.5_Intron|DDC_ENST00000380984.4_3'UTR NM_001242888.1 NP_001229817 P20711 DDC_HUMAN dopa decarboxylase (aromatic L-amino acid decarboxylase) NA NA NA catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842) axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021) amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170) breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1) 40 Glioma(55;0.08)|all_neural(89;0.245) Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968) AATTTTCCAAATGGCCTTTTCC 0.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 23 91.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 4.26 CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1 7p12.1 2012-08-30 ENSG00000132437 ENSG00000132437 1644 4.1.1.28 2719 protein-coding gene gene with protein product 107930 NA 1612608 Standard NM_001082971 NA Approved AADC uc003tpf.4 P20711 OTTHUMG00000023353 ENST00000426377.1:c.710+2655->GAG chr7.hg19:g.50560391_50560392insCTC 1 3 ref NA False 33 33 PASS 0 PASS ref->het 0 NA 3,3 20,20 0,0 1 1 C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6 True hg19 CCDS56485.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DDC-013 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000342604.1 PASS NA None 23 NA True - CTC ENST00000426377.1 DDC 1644 __UNKNOWN__ __UNKNOWN__ 7 50560393 50560394 __UNKNOWN__ Intron INS - - TCCTCTCT rs540730472|rs386713134|rs578102955 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:50560393_50560394insTCCTCTCT ENST00000426377.1 - 7 779 DDC_ENST00000444124.2_Intron|DDC_ENST00000431062.1_Intron|DDC_ENST00000357936.5_Intron|DDC_ENST00000380984.4_3'UTR NM_001242888.1 NP_001229817 P20711 DDC_HUMAN dopa decarboxylase (aromatic L-amino acid decarboxylase) NA NA NA catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842) axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021) amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170) breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1) 40 Glioma(55;0.08)|all_neural(89;0.245) Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968) TTTTCCAAATGGCCTTTTCCAA 0.505 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 23 93.44 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 4.26 CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1 7p12.1 2012-08-30 ENSG00000132437 ENSG00000132437 1644 4.1.1.28 2719 protein-coding gene gene with protein product 107930 NA 1612608 Standard NM_001082971 NA Approved AADC uc003tpf.4 P20711 OTTHUMG00000023353 ENST00000426377.1:c.710+2653->AGAGAGGA chr7.hg19:g.50560393_50560394insTCCTCTCT 1 2 ref NA False 32 32 PASS 0 PASS ref->het 0 NA 3,3 20,20 0,0 1 1 C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6 True hg19 CCDS56485.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DDC-013 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000342604.1 PASS NA None 23 NA True - TCCTCTCT ENST00000426377.1 CASD1 64921 __UNKNOWN__ __UNKNOWN__ 7 94185519 94185526 __UNKNOWN__ 3'UTR DEL ACTTTCTT ACTTTCTT - LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:94185519_94185526delACTTTCTT ENST00000297273.4 + 0 3130_3137 NM_022900.4 NP_075051.4 Q96PB1 CASD1_HUMAN CAS1 domain containing 1 NA NA NA integral component of membrane (GO:0016021) NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1) 31 all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215) STAD - Stomach adenocarcinoma(171;0.0031) TTCATTGGAAACTTTCTTACTCAAGAAT 0.332 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 104 103.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.03 AF355594 CCDS5636.1 7q22 2006-03-09 ENSG00000127995 ENSG00000127995 64921 16014 protein-coding gene gene with protein product "chromosome 7 open reading frame 12" 611686 NA 11703667, 11528394 Standard NM_022900 NM_022900 NA Approved FLJ21213, FLJ21879, C7orf12 uc003uni.4 Q96PB1 OTTHUMG00000023356 ENST00000297273.4:c.*456ACTTTCTT>- chr7.hg19:g.94185519_94185526delACTTTCTT 0 5 ref NA False 155 80 PASS 1 PASS ref->het 0 NA 13,13 75,75 15,15 1 1 B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770 True hg19 CCDS5636.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CASD1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255216.1 PASS NA None 104 NA True + ACTTTCTT ENST00000297273.4 NEBL 10529 __UNKNOWN__ __UNKNOWN__ 10 21177157 21177157 __UNKNOWN__ Intron DEL A A - rs67288319 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:21177157delA ENST00000417816.2 - 4 711 NEBL_ENST00000377159.4_Intron|NEBL_ENST00000377122.4_Intron|NEBL_ENST00000377119.1_Intron NM_001173484.1|NM_213569.2 NP_001166955.1|NP_998734.1 O76041 NEBL_HUMAN nebulette NA NA NA cardiac muscle thin filament assembly (GO:0071691) extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018) actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523) NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2) 70 AAAAAACAGGAAAAAAATAAA 0.313 NA NA NA NA NA NA NA NA NA AAAAAAA|AAAAAAA|AAAAAA|deletion 2707 0.540535 0.4992 0.6167 5008 , , NA 15248 0.3998 NA 0.6511 False NA ,,, NA NA NA 2504 0.5736 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 43 51.8 NA ,, 2129,2131 NA 558,1013,559 15 14 15 NA ,, -7.5 0 10 dbSNP_130 28 5315,2933 NA 1733,1849,542 no intron,intron,intron NEBL NM_213569.2,NM_006393.2,NM_001173484.1 ,, 2291,2862,1101 A1A1,A1R,RR NA 35.5601,49.9765,40.4861 ,, ,, 21177157 7444,5064 2187 4288 6475 SO:0001627 intron_variant 0.45 Y16241 CCDS7133.1, CCDS7134.1 10p12 2014-09-17 ENSG00000078114 ENSG00000078114 10529 16932 protein-coding gene gene with protein product 605491 NA 9733644, 10470015 Standard NM_006393 NM_213569 NA Approved uc001iqi.3 O76041 OTTHUMG00000017788 ENST00000417816.2:c.357+73443T>- chr10.hg19:g.21177157delA 6 10 ref NA False 54 53 PASS 7 PASS ref->het 0 NA 1,1 36,37 5,4 1 1 B0YJ45|Q2TBD0|Q70I54|Q9UIC4 True hg19 CCDS7133.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NEBL-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000047112.1 PASS NA None 43 NA True - A ENST00000417816.2 PNLIPRP1 5407 __UNKNOWN__ __UNKNOWN__ 10 118352229 118352243 __UNKNOWN__ Intron DEL TGAAGCAACCACATT TGAAGCAACCACATT - LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:118352229_118352243delTGAAGCAACCACATT ENST00000528052.1 + 4 401 PNLIPRP1_ENST00000534537.1_Intron|PNLIPRP1_ENST00000358834.4_Intron|PNLIPRP1_ENST00000442761.1_Intron|PNLIPRP1_ENST00000480870.2_Intron P54315 LIPR1_HUMAN pancreatic lipase-related protein 1 NA NA NA lipid metabolic process (GO:0006629) extracellular region (GO:0005576) calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806) breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1) 38 all cancers(201;0.0161) ATCTGCACACTGAAGCAACCACATTTGCTGTTAGA 0.358 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 262 231.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.67 BC025784 CCDS7595.1 10q26.12 2006-07-04 ENSG00000187021 ENSG00000187021 5407 9156 protein-coding gene gene with protein product 604422 NA 1379598 Standard NM_006229 NM_006229 NA Approved PLRP1 uc001lco.1 P54315 OTTHUMG00000019109 ENST00000528052.1:c.330+176TGAAGCAACCACATT>- chr10.hg19:g.118352229_118352243delTGAAGCAACCACATT 0 3 ref NA False 227 85 PASS 1 PASS ref->het 0 NA 45,45 179,180 44,43 1 1 Q68D83|Q68DR6|Q8TAU2|Q9BS82 True hg19 CCDS7595.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PNLIPRP1-011 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000384633.1 PASS NA None 262 NA True + TGAAGCAACCACATT ENST00000528052.1 CTD-2572N17.1 0 __UNKNOWN__ __UNKNOWN__ 11 42262642 42262656 __UNKNOWN__ lincRNA DEL TCTGGGTCCAGACAA TCTGGGTCCAGACAA - rs549705481 LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:42262642_42262656delTCTGGGTCCAGACAA ENST00000527757.1 - 0 111_125 NA NA NA NA GGAAATATTTTCTGGGTCCAGACAAGCGATCATGG 0.386 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 421 381.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.32 NA NA NA NA NA ENST00000527757.1: chr11.hg19:g.42262642_42262656delTCTGGGTCCAGACAA 0 5 ref NA False 49 49 PASS 1 PASS ref->het 0 NA 328,331 64,64 32,31 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CTD-2572N17.1-001 KNOWN basic lincRNA NA lincRNA OTTHUMT00000389473.1 PASS NA None 421 NA True - TCTGGGTCCAGACAA ENST00000527757.1 PLEKHA5 54477 __UNKNOWN__ __UNKNOWN__ 12 19427634 19427640 __UNKNOWN__ Frame_Shift_Del DEL TTAACAA TTAACAA - rs200553875 LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:19427634_19427640delTTAACAA ENST00000429027.2 + 11 1062_1068 c.1030_1036delTTAACAA c.(1030-1038)ttaacaaaafs p.LTK344fs PLEKHA5_ENST00000510738.2_3'UTR|PLEKHA5_ENST00000299275.6_Frame_Shift_Del_p.LTK338fs|PLEKHA5_ENST00000359180.3_Frame_Shift_Del_p.LTK338fs|PLEKHA5_ENST00000355397.3_Frame_Shift_Del_p.LTK338fs|PLEKHA5_ENST00000424268.1_Frame_Shift_Del_p.LTK230fs|PLEKHA5_ENST00000543806.1_Frame_Shift_Del_p.LTK230fs|PLEKHA5_ENST00000538714.1_Frame_Shift_Del_p.LTK338fs|PLEKHA5_ENST00000317589.4_Frame_Shift_Del_p.LTK338fs|PLEKHA5_ENST00000309364.4_Frame_Shift_Del_p.LTK338fs|PLEKHA5_ENST00000539256.1_Frame_Shift_Del_p.LTK96fs NM_001256470.1 NP_001243399.1 Q9HAU0 PKHA5_HUMAN pleckstrin homology domain containing, family A member 5 338 NA NA reproductive system development (GO:0061458) cytosol (GO:0005829)|membrane (GO:0016020) 1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314) autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 35 Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804) AGATAGACCCTTAACAAAAATTAATAG 0.377 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(196;329 2193 11246 14234 19524) PASS NA NA NA NA NA 0 NA NA NA NA NA 135 151.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 AF302150 CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1 12p12 2013-01-10 ENSG00000052126 ENSG00000052126 54477 "Pleckstrin homology (PH) domain containing" 30036 protein-coding gene gene with protein product 607770 NA 11214970, 11001876 Standard NM_019012 NM_001143821 NA Approved PEPP2, KIAA1686, FLJ10667 uc031qgo.1 Q9HAU0 OTTHUMG00000167921 ENST00000429027.2:c.1030_1036delTTAACAA chr12.hg19:g.19427634_19427640delTTAACAA ENSP00000404296:p.Leu344fs 0 7 ref NA False 66 66 PASS 1 PASS ref->het 0 NA 95,96 38,38 13,13 1 1 A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8 True hg19 CCDS58213.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PLEKHA5-004 NOVEL basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000397012.1 PASS NA None 135 NA True + TTAACAA ENST00000429027.2 TMTC2 160335 __UNKNOWN__ __UNKNOWN__ 12 83290022 83290041 __UNKNOWN__ Frame_Shift_Del DEL CCAGAACTCAGAGACTAAGT CCAGAACTCAGAGACTAAGT - LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:83290022_83290041delCCAGAACTCAGAGACTAAGT ENST00000321196.3 + 3 1787_1806 c.1080_1099delCCAGAACTCAGAGACTAAGT c.(1078-1101)taccagaactcagagactaagtccfs p.QNSETKS361fs TMTC2_ENST00000549919.1_Frame_Shift_Del_p.QNSETKS355fs|TMTC2_ENST00000548305.1_Frame_Shift_Del_p.QNSETKS361fs NM_152588.1 NP_689801.1 Q8N394 TMTC2_HUMAN transmembrane and tetratricopeptide repeat containing 2 361 NA NA calcium ion homeostasis (GO:0055074) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021) breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1) 39 ATGTGGAGTACCAGAACTCAGAGACTAAGTCCAGCTTTGC 0.423 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 379 349.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.55 AK074634 CCDS9025.1 12q21.31 2014-06-09 ENSG00000179104 ENSG00000179104 160335 "Tetratricopeptide (TTC) repeat domain containing" 25440 protein-coding gene gene with protein product 615856 NA 24764305 Standard NM_152588 NM_152588 NA Approved DKFZp762A217 uc001szt.3 Q8N394 OTTHUMG00000169736 ENST00000321196.3:c.1080_1099delCCAGAACTCAGAGACTAAGT chr12.hg19:g.83290022_83290041delCCAGAACTCAGAGACTAAGT ENSP00000322300:p.Gln361fs 0 2 ref NA False 122 95 PASS 1 PASS ref->het 0 NA 204,205 116,116 86,86 1 1 B2RCU7|Q8N2K8 True hg19 CCDS9025.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMTC2-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000405663.1 PASS NA None 379 NA True + CCAGAACTCAGAGACTAAGT ENST00000321196.3 KL 9365 __UNKNOWN__ __UNKNOWN__ 13 33591060 33591077 __UNKNOWN__ In_Frame_Del DEL GCGCGGGCGTCCCCAACC GCGCGGGCGTCCCCAACC - rs371131557|rs387907444 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:33591060_33591077delGCGCGGGCGTCCCCAACC ENST00000380099.3 + 1 490_507 c.482_499delGCGCGGGCGTCCCCAACC c.(481-501)agcgcgggcgtccccaaccgc>agc p.AGVPNR162del KL_ENST00000426690.2_Intron|KL_ENST00000487852.1_3'UTR NM_004795.3 NP_004786.2 Q9UEF7 KLOT_HUMAN klotho 162 Glycosyl hydrolase-1 1. NA NA acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080) extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499) breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5) 41 all_epithelial(80;0.133) Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262) GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05) CCCAATGGCAGCGCGGGCGTCCCCAACCGCGAGGGGCT 0.702 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 166 170.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.39 AB005142 CCDS9347.1 13q12 2008-02-05 ENSG00000133116 ENSG00000133116 9365 6344 protein-coding gene gene with protein product 604824 NA 9464267 Standard NM_004795 NA Approved uc001uus.3 Q9UEF7 OTTHUMG00000017408 ENST00000380099.3:c.482_499delGCGCGGGCGTCCCCAACC chr13.hg19:g.33591060_33591077delGCGCGGGCGTCCCCAACC ENSP00000369442:p.Ala162_Arg167del 0 3 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 154,156 4,4 29,27 1 1 Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0 True hg19 CCDS9347.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KL-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000045987.1 PASS NA None 166 NA True + GCGCGGGCGTCCCCAACC ENST00000380099.3 LHFP 10186 __UNKNOWN__ __UNKNOWN__ 13 39952653 39952654 __UNKNOWN__ In_Frame_Ins INS - - GCT LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:39952653_39952654insGCT ENST00000379589.3 - 3 857_858 c.395_396insAGC c.(394-396)att>atAGCt p.132_133insA NM_005780.2 NP_005771.1 Q9Y693 LHFP_HUMAN lipoma HMGIC fusion partner 132 NA NA integral component of membrane (GO:0016021) DNA binding (GO:0003677) HMGA2/LHFP(2) breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2) 13 Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114) OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105) AGCCAGCACCAATCAACAAGCC 0.485 NA NA TRUE HMGA2 lipoma NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Dom yes NA 13 13q12 10186 lipoma HMGIC fusion partner NA M 0 NA NA NA NA NA 74 86.95 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001652 inframe_insertion 19.54 AF098807 CCDS9369.1 13q12 2008-07-18 ENSG00000183722 ENSG00000183722 10186 6586 protein-coding gene gene with protein product 606710 NA 10329012 Standard NM_005780 NM_005780 NA Approved MGC22429 uc001uxf.3 Q9Y693 OTTHUMG00000016767 ENST00000379589.3:c.395_396insAGC chr13.hg19:g.39952653_39952654insGCT ENSP00000368908:p.Ile132_Gly133insAla 1 2 ref NA False 240 97 PASS 0 PASS ref->het 0 NA 4,4 48,48 4,4 2 1 B2R7M2|Q53FC0|Q96SH5 True hg19 CCDS9369.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LHFP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044619.1 PASS NA None 74 NA True - GCT ENST00000379589.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 13 88547685 88547686 __UNKNOWN__ IGR INS - - G rs35885596|rs397805696|rs397783736|rs386773101 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:88547685_88547686insG NA RP11-471M2.3 (84198 upstream) : RP11-545P6.2 (247435 downstream) NA NA NA NA AAGAAGAATGTGGTGTCTTGCA 0.371 NA NA NA NA NA NA NA NA NA GGG|GG|GGG|deletion 3261 0.651158 0.7474 0.7594 5008 , , NA 19767 0.6677 NA 0.5994 False NA ,,, NA NA NA 2504 0.4806 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 144 141.36 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.13 NA NA NA NA NA chr13.hg19:g.88547687_88547687dupG 3 3 ref NA False 49 48 PASS 2 PASS ref->het 0 NA 2,3 129,131 15,13 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 144 NA True G Unknown 0 __UNKNOWN__ __UNKNOWN__ 13 91214940 91214941 __UNKNOWN__ IGR INS - - ATTA rs10666617|rs57719725|rs35213037 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:91214940_91214941insATTA NA LINC01049 (27606 upstream) : RNU6-75P (219078 downstream) NA NA NA NA aaccttggcacattgagacctg 0.436 NA NA NA NA NA NA NA NA NA 3353 0.669529 0.6309 0.7305 5008 , , NA 19389 0.7252 NA 0.6481 False NA ,,, NA NA NA 2504 0.6431 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 38 37.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr13.hg19:g.91214940_91214941insATTA 1 2 ref NA False 45 43 PASS 0 PASS ref->hom 0 NA 0,0 36,36 2,2 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 38 NA True ATTA Unknown 0 __UNKNOWN__ __UNKNOWN__ 14 23979028 23979029 __UNKNOWN__ IGR INS - - TGAATGTAGATCTCTT rs60810485|rs78137046|rs142350707 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:23979028_23979029insTGAATGTAGATCTCTT NA NGDN (30996 upstream) : RP11-66N24.4 (1939 downstream) NA NA NA NA ACCTGGAAATATGGCAAATCAA 0.441 NA NA NA NA NA NA NA NA NA 1356 0.270767 0.5688 0.1254 5008 , , NA 19840 0.1786 NA 0.1372 False NA ,,, NA NA NA 2504 0.2035 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 51 53.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr14.hg19:g.23979028_23979029insTGAATGTAGATCTCTT 1 4 ref NA False 30 30 PASS 0 PASS ref->het 0 NA 1,1 22,22 27,27 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 51 NA True TGAATGTAGATCTCTT MAX 4149 __UNKNOWN__ __UNKNOWN__ 14 65542130 65542130 __UNKNOWN__ 3'UTR DEL A A - LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:65542130delA ENST00000284165.6 - 0 2944 MAX_ENST00000555932.1_3'UTR|MAX_ENST00000341653.2_Intron|MAX_ENST00000358402.4_3'UTR NM_145113.2 NP_660088.1 P61244 MAX_HUMAN MYC associated factor X NA NA NA cellular response to peptide hormone stimulus (GO:0071375)|cellular response to starvation (GO:0009267)|negative regulation of gene expression (GO:0010629)|neuron apoptotic process (GO:0051402)|protein complex assembly (GO:0006461)|response to axon injury (GO:0048678)|response to insulin (GO:0032868)|retina development in camera-type eye (GO:0060041)|transcription from RNA polymerase II promoter (GO:0006366) cytoplasm (GO:0005737)|dendrite (GO:0030425)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)|PML body (GO:0016605) sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712) breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1) 17 all cancers(60;0.000776)|OV - Ovarian serous cystadenocarcinoma(108;0.00359)|BRCA - Breast invasive adenocarcinoma(234;0.00999) CCAGGACAGTAGGAAAGGAAG 0.502 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 88 91.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.58 CCDS9770.1, CCDS9771.1, CCDS9772.1, CCDS9774.1, CCDS41965.1 14q23 2014-09-17 2005-02-08 ENSG00000125952 ENSG00000125952 4149 "Basic helix-loop-helix proteins" 6913 protein-coding gene gene with protein product 154950 "MAX protein" NA 1557420 Standard NM_197957 NM_002382 NA Approved bHLHd4, bHLHd5, bHLHd6, bHLHd7, bHLHd8 uc001xif.2 P61244 OTTHUMG00000142809 ENST00000284165.6:c.*2391T>- chr14.hg19:g.65542130delA 0 2 ref NA False 226 85 PASS 1 PASS ref->het 0 NA 4,4 70,72 13,12 1 1 A6NH73|A8K265|A8K4G4|A8K824|P25912|P52163|Q14803|Q96CY8 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAX-004 PUTATIVE basic protein_coding NA protein_coding OTTHUMT00000286388.1 PASS NA None 88 NA True - A ENST00000284165.6 TMEM229B 161145 __UNKNOWN__ __UNKNOWN__ 14 67938789 67938805 __UNKNOWN__ 3'UTR DEL TGTGGCAGGGTTAATAC TGTGGCAGGGTTAATAC - rs149619552|rs544303155 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:67938789_67938805delTGTGGCAGGGTTAATAC ENST00000557006.1 - 0 2118_2134 TMEM229B_ENST00000357461.2_3'UTR Q8NBD8 T229B_HUMAN transmembrane protein 229B NA NA NA integral component of membrane (GO:0016021) central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2) 5 TGCCCATGAGTGTGGCAGGGTTAATACTGTTTAAGGA 0.567 NA NA NA NA NA NA NA NA NA 19 0.00379393 8e-04 0 5008 , , NA 24905 0.0159 NA 0 False NA ,,, NA NA NA 2504 0.002 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 93 92.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.05 AK090706 CCDS9783.1 14q23.3-q24.1 2009-09-22 2009-09-22 2009-09-22 ENSG00000198133 ENSG00000198133 161145 20130 protein-coding gene gene with protein product NA "chromosome 14 open reading frame 83" C14orf83 NA Standard NM_182526 NM_182526 NA Approved FLJ33387 uc001xjk.3 Q8NBD8 ENST00000557006.1:c.*1348GTATTAACCCTGCCACA>- chr14.hg19:g.67938789_67938805delTGTGGCAGGGTTAATAC 0 4 ref NA False 52 51 PASS 1 PASS ref->het 0 NA 11,11 67,70 16,16 1 1 True hg19 CCDS9783.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM229B-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000412718.2 PASS NA None 93 NA True - TGTGGCAGGGTTAATAC ENST00000557006.1 SPATA7 55812 __UNKNOWN__ __UNKNOWN__ 14 88881655 88881683 __UNKNOWN__ Intron DEL TCTTTGTCCTTATTGCTGTTGGTTTAAAG TCTTTGTCCTTATTGCTGTTGGTTTAAAG - LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:88881655_88881683delTCTTTGTCCTTATTGCTGTTGGTTTAAAG ENST00000393545.4 + 5 527 SPATA7_ENST00000045347.7_Intron|SPATA7_ENST00000556553.1_Intron|SPATA7_ENST00000356583.5_Intron NM_018418.4 NP_060888.2 Q9P0W8 SPAT7_HUMAN spermatogenesis associated 7 NA NA NA response to stimulus (GO:0050896)|visual perception (GO:0007601) cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1) 18 gtaatgcccatctttgtccttattgctgttggtttaaagtctgttttat 0.389 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 63 53.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF144487 CCDS9883.1, CCDS32132.1 14q31.3 2011-02-17 ENSG00000042317 55812 20423 protein-coding gene gene with protein product 609868 "Leber congenital amaurosis 3" LCA3 NA 9799089, 19268277 Standard NM_018418 NA Approved HSD3 uc001xwq.3 Q9P0W8 ENST00000393545.4:c.239-1372TCTTTGTCCTTATTGCTGTTGGTTTAAAG>- chr14.hg19:g.88881655_88881683delTCTTTGTCCTTATTGCTGTTGGTTTAAAG 0 4 ref NA False 59 59 PASS 1 PASS ref->het 0 NA 8,8 24,24 30,30 1 1 Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7 True hg19 CCDS9883.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SPATA7-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000410172.1 PASS NA None 63 NA True + TCTTTGTCCTTATTGCTGTTGGTTTAAAG ENST00000393545.4 GATM 2628 __UNKNOWN__ __UNKNOWN__ 15 45670901 45670922 __UNKNOWN__ 5'UTR DEL GCTTGCCCTTTTTTAGCCAGCG GCTTGCCCTTTTTTAGCCAGCG - LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:45670901_45670922delGCTTGCCCTTTTTTAGCCAGCG ENST00000396659.3 - 0 69_90 NM_001482.2 NP_001473.1 P50440 GATM_HUMAN glycine amidinotransferase (L-arginine:glycine amidinotransferase) NA NA NA cellular nitrogen compound metabolic process (GO:0034641)|creatine biosynthetic process (GO:0006601)|creatine metabolic process (GO:0006600)|embryo development (GO:0009790)|response to mercury ion (GO:0046689)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246) extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758) glycine amidinotransferase activity (GO:0015068)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines (GO:0016813) biliary_tract(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|urinary_tract(1) 15 all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027) all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06) Glycine(DB00145)|L-Ornithine(DB00129) AGCCTCCGATGCTTGCCCTTTTTTAGCCAGCGGGGCCACTGA 0.685 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 195 185.84 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.61 S68805 CCDS10122.1 15q15.1 2007-12-06 ENSG00000171766 ENSG00000171766 2628 2.1.4.1 4175 protein-coding gene gene with protein product 602360 NA 8313955 Standard NM_001482 NM_001482 NA Approved AGAT uc001zvc.3 P50440 OTTHUMG00000131427 ENST00000396659.3:c.-271CGCTGGCTAAAAAAGGGCAAGC>- chr15.hg19:g.45670901_45670922delGCTTGCCCTTTTTTAGCCAGCG 0 5 ref NA False 189 142 PASS 1 PASS ref->het 0 NA 128,140 52,55 44,37 1 1 B4DH99|B4DPI3|Q53EQ4 True hg19 CCDS10122.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GATM-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254220.2 PASS NA None 195 NA True - GCTTGCCCTTTTTTAGCCAGCG ENST00000396659.3 SCAPER 49855 __UNKNOWN__ __UNKNOWN__ 15 77057766 77057776 __UNKNOWN__ Frame_Shift_Del DEL AGGATGTATTT AGGATGTATTT - LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:77057766_77057776delAGGATGTATTT ENST00000563290.1 - 13 1610_1620 c.1515_1525delAAATACATCCT c.(1513-1527)caaaatacatcctggfs p.NTSW506fs SCAPER_ENST00000538941.2_Frame_Shift_Del_p.NTSW260fs|SCAPER_ENST00000324767.7_Frame_Shift_Del_p.NTSW506fs Q9BY12 SCAPE_HUMAN S-phase cyclin A-associated protein in the ER 506 Glu-rich. NA NA endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634) metal ion binding (GO:0046872) NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2) 39 ATGTCCCCCCAGGATGTATTTTGGCGCCAAG 0.403 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 323 293.55 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.22 AB040887, AF242528 CCDS53961.1, CCDS53962.1 15q24.3 2012-10-05 2009-03-11 2007-08-20 ENSG00000140386 ENSG00000140386 49855 "Zinc fingers, C2H2-type" 13081 protein-coding gene gene with protein product 611611 "zinc finger protein 291" ZNF291 NA 17698606 Standard NM_020843 NM_020843 NA Approved Zfp291 uc002bby.3 Q9BY12 OTTHUMG00000172655 ENST00000563290.1:c.1515_1525delAAATACATCCT chr15.hg19:g.77057766_77057776delAGGATGTATTT ENSP00000454973:p.Asn506fs 0 6 ref NA False 174 119 PASS 1 PASS ref->het 0 NA 209,210 102,105 18,17 1 1 F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274 True hg19 CCDS53962.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SCAPER-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000419698.1 PASS NA None 323 NA True - AGGATGTATTT ENST00000563290.1 ITGAE 3682 __UNKNOWN__ __UNKNOWN__ 17 3664477 3664478 __UNKNOWN__ Intron INS - - ATT rs10687117|rs3830684 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:3664477_3664478insATT ENST00000263087.4 - 6 532 NM_002208.4 NP_002199.3 P38570 ITAE_HUMAN integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide) NA NA NA cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229) external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886) metal ion binding (GO:0046872) NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 41 UCEC - Uterine corpus endometrioid carcinoma (3;0.0813) ATTTTCTTTAAAAACACACATG 0.52 NA NA NA NA NA NA NA NA NA 1354 0.270367 0.1785 0.3314 5008 , , NA 22806 0.1815 NA 0.4513 False NA ,,, NA NA NA 2504 0.2566 NA NA NA NSCLC(182;635 2928 8995 38788) PASS NA NA NA NA NA 0 NA NA NA NA NA 87 84.96 NA 916,3344 NA 92,732,1306 NA NA NA NA 1.2 0.4 NA dbSNP_119 104 3555,4699 NA 761,2033,1333 no intron ITGAE NM_002208.4 853,2765,2639 A1A1,A1R,RR NA 43.07,21.5023,35.728 NA 4471,8043 NA NA NA SO:0001627 intron_variant 0 L25851 CCDS32531.1 17p13 2010-03-23 ENSG00000083457 3682 "CD molecules", "Integrins" 6147 protein-coding gene gene with protein product 604682 NA 8119947 Standard NM_002208 NM_002208 NA Approved CD103, HUMINAE uc002fwo.4 P38570 ENST00000263087.4:c.434-6->AAT chr17.hg19:g.3664477_3664478insATT 1 6 ref NA False 49 48 PASS 0 PASS ref->het 0 NA 4,4 71,72 10,9 1 1 Q17RS6|Q9NZU9 True hg19 CCDS32531.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ITGAE-001 KNOWN upstream_ATG|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000438169.1 PASS NA None 87 NA True - ATT ENST00000263087.4 MAP2K3 5606 __UNKNOWN__ __UNKNOWN__ 17 21215434 21215435 __UNKNOWN__ Intron INS - - C rs538777379|rs113634008|rs35298639|rs67669954 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:21215434_21215435insC ENST00000342679.4 + 10 1023 MAP2K3_ENST00000361818.5_Intron|MAP2K3_ENST00000316920.6_Intron NM_145109.2 NP_659731.1 P46734 MP2K3_HUMAN mitogen-activated protein kinase kinase 3 NA NA NA activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666) cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654) ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713) NA COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553) GGGGCCTCTGACCCCCTGTCCC 0.658 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 102 113.54 NA , 10,2121,2133 NA 0,0,10,0,2121,1 NA NA NA NA , 0.3 0.3 NA dbSNP_130 50 97,4030,4127 NA 0,0,97,0,4030,0 no intron,intron MAP2K3 NM_145109.2,NM_002756.4 , 0,0,107,0,6151,1 A1A1,A1A2,A1R,A2A2,A2R,RR NA 50.0,49.9765,49.992 , , NA 107,6151,6260 NA NA NA SO:0001627 intron_variant 0.01 L36719 CCDS11217.1, CCDS11218.1 17q11.2 2011-06-09 ENSG00000034152 ENSG00000034152 5606 "Mitogen-activated protein kinase cascade / Kinase kinases" 6843 protein-coding gene gene with protein product "MAPK/ERK kinase 3", "MAP kinase kinase 3", "dual specificity mitogen activated protein kinase kinase 3" 602315 PRKMK3 NA 9465908 Standard NM_145109 NM_145109 NA Approved MEK3, MKK3, MAPKK3 uc002gys.3 P46734 OTTHUMG00000134322 ENST00000342679.4:c.775-19->C chr17.hg19:g.21215439_21215439dupC 6 5 ref NA False 30 30 PASS 5 PASS ref->het 0 NA 54,54 39,39 10,10 1 1 B3KSK7|Q99441|Q9UE71|Q9UE72 True hg19 CCDS11217.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAP2K3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000259374.2 PASS NA None 102 NA True + C ENST00000342679.4 ELANE 1991 __UNKNOWN__ __UNKNOWN__ 19 853294 853317 __UNKNOWN__ In_Frame_Del DEL CCCATAACCTCTCGCGGCGGGAGC CCCATAACCTCTCGCGGCGGGAGC - rs143634717 LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:853294_853317delCCCATAACCTCTCGCGGCGGGAGC ENST00000590230.1 + 4 398_421 c.257_280delCCCATAACCTCTCGCGGCGGGAGC c.(256-282)gcccataacctctcgcggcgggagccc>gcc p.HNLSRREP87del ELANE_ENST00000263621.1_In_Frame_Del_p.HNLSRREP87del P08246 ELNE_HUMAN elastase, neutrophil expressed 87 Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}. NA NA acute inflammatory response to antigenic stimulus (GO:0002438)|cellular calcium ion homeostasis (GO:0006874)|collagen catabolic process (GO:0030574)|defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of chemotaxis (GO:0050922)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil mediated killing of fungus (GO:0070947)|phagocytosis (GO:0006909)|positive regulation of immune response (GO:0050778)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)|response to UV (GO:0009411)|response to yeast (GO:0001878) cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|transcriptional repressor complex (GO:0017053) cytokine binding (GO:0019955)|endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|RNA polymerase II transcription corepressor activity (GO:0001106)|serine-type endopeptidase activity (GO:0004252) breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(1)|lung(4)|pancreas(1) 13 Alpha-1-proteinase inhibitor(DB00058)|Filgrastim(DB00099)|Pegfilgrastim(DB00019) GTCCTGGGAGCCCATAACCTCTCGCGGCGGGAGCCCACCCGGCA 0.705 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 120 128.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.65 CCDS12045.1 19p13.3 2014-09-17 2009-05-05 2009-05-05 ENSG00000197561 ENSG00000197561 1991 3.4.21.37 3309 protein-coding gene gene with protein product "neutrophil elastase", "leukocyte elastase", "medullasin" 130130 "elastase 2, neutrophil" ELA2 NA 2902087 Standard NM_001972 XM_005259517 NA Approved NE, HNE, HLE uc002lqb.3 P08246 ENST00000590230.1:c.257_280delCCCATAACCTCTCGCGGCGGGAGC chr19.hg19:g.853294_853317delCCCATAACCTCTCGCGGCGGGAGC ENSP00000466090:p.His87_Pro94del 0 6 ref NA False 76 76 PASS 1 PASS ref->het 0 NA 154,164 8,8 27,18 1 1 P09649|Q6B0D9|Q6LDP5 True hg19 CCDS12045.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ELANE-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000457890.2 PASS NA None 120 NA True + CCCATAACCTCTCGCGGCGGGAGC ENST00000590230.1 ANGPT4 51378 __UNKNOWN__ __UNKNOWN__ 20 853434 853434 __UNKNOWN__ 3'UTR DEL T T - rs68006621|rs541864923|rs370362896 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:853434delT ENST00000381922.3 - 0 1783 ANGPT4_ENST00000546022.1_3'UTR NM_015985.2 NP_057069.1 Q9Y264 ANGP4_HUMAN angiopoietin 4 NA NA NA activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731) extracellular region (GO:0005576)|extracellular space (GO:0005615) receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297) breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1) 27 CGGAGGGGAGTTGGGGGGCAG 0.637 NA NA NA NA NA NA NA NA NA TG|TT|T|complex_deletion 747 0.149161 0.2617 0.0591 5008 , , NA 18799 0.1151 NA 0.0785 False NA ,,, NA NA NA 2504 0.1687 NA NA NA Pancreas(181;481 2077 3259 31286 49856) PASS NA NA NA NA NA 0 NA NA NA NA NA 93 101.21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.94 AF074332 CCDS13009.1 20p13 2013-02-06 ENSG00000101280 ENSG00000101280 51378 "Fibrinogen C domain containing" 487 protein-coding gene gene with protein product 603705 NA 10051567, 10218486 Standard NM_015985 NM_015985 NA Approved uc002wei.3 Q9Y264 OTTHUMG00000031652 ENST00000381922.3:c.*169A>- chr20.hg19:g.853434delT 1 6 ref NA False 37 37 PASS 2 PASS ref->het 0 NA 7,7 71,74 13,10 1 1 B4E3J9|Q5TFF4|Q9H4Z4 True hg19 CCDS13009.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ANGPT4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000077493.1 PASS NA None 93 NA True - T ENST00000381922.3 DDX27 55661 __UNKNOWN__ __UNKNOWN__ 20 47858503 47858504 __UNKNOWN__ Frame_Shift_Ins INS - - A LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:47858503_47858504insA ENST00000371764.4 + 17 2073_2074 c.2064_2065insA c.(2065-2067)aaafs p.K689fs ZNFX1_ENST00000371754.4_Intron|ZNFX1_ENST00000469991.1_Intron|DDX27_ENST00000484427.1_3'UTR NM_017895.7 NP_060365.7 Q96GQ7 DDX27_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 689 NA NA nucleus (GO:0005634) ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822) p.K691fs*4(3) NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1) 45 BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166) TGAAGGATGCCAAAAAAAAGGG 0.485 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 3 Deletion - Frameshift(3) large_intestine(2)|ovary(1) NA NA NA NA NA 507 486.26 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.81 AL049766 CCDS13416.1 20q13.13 2010-07-06 2003-06-13 ENSG00000124228 ENSG00000124228 55661 "DEAD-boxes" 15837 protein-coding gene gene with protein product NA "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27" NA Standard NM_017895 NA Approved dJ686N3.1, DRS1 uc002xuh.3 Q96GQ7 OTTHUMG00000033072 ENST00000371764.4:c.2072dupA chr20.hg19:g.47858511_47858511dupA ENSP00000360828:p.Lys689fs 9 8 ref NA False 55 55 PASS 8 PASS ref->het 0 NA 355,363 75,76 74,67 1 1 A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6 True hg19 CCDS13416.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DDX27-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000080485.1 PASS NA None 507 NA True + A ENST00000371764.4 AC006547.14 0 __UNKNOWN__ __UNKNOWN__ 22 20137434 20137434 __UNKNOWN__ Intron DEL T T - rs368639630 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:20137434delT ENST00000540078.1 - 3 525 NA NA NA NA TGGAGTGCTGTTACGAAGCTT 0.662 NA NA NA NA NA NA NA NA NA T|TT|T|insertion 160 0.0319489 0.003 0.0101 5008 , , NA 12536 0.0317 NA 0.0328 False NA ,,, NA NA NA 2504 0.0859 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 36 35.33 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.75 NA NA NA NA NA ENST00000540078.1:c.525+43A>- chr22.hg19:g.20137434delT 1 3 ref NA False 33 33 PASS 2 PASS ref->hom 0 NA 0,0 30,32 6,4 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AC006547.14-201 KNOWN basic|appris_principal protein_coding NA protein_coding PASS NA None 36 NA True - T ENST00000540078.1 AC006547.14 0 __UNKNOWN__ __UNKNOWN__ 22 20137448 20137448 __UNKNOWN__ Intron DEL C C - rs529592656|rs200146458|rs533547394 byFrequency LTS-016_T LTS-016_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:20137448delC ENST00000540078.1 - 3 525 NA NA NA NA GAAGCTTCCTCCCCCCCCACA 0.667 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 35 36.13 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.61 NA NA NA NA NA ENST00000540078.1:c.525+29G>- chr22.hg19:g.20137448delC 7 10 ref NA False 33 32 PASS 8 PASS ref->hom 0 NA 0,0 30,31 6,5 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AC006547.14-201 KNOWN basic|appris_principal protein_coding NA protein_coding PASS NA None 35 NA True - C ENST00000540078.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ M 303 303 __UNKNOWN__ IGR DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrM:303delC NA None (None upstream) : MT-TF (273 downstream) NA NA NA NA TTCCACCAAACCCCCCCCTCC 0.418 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 131 138.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 2.91 NA NA NA NA NA chrM.hg19:g.303delC 7 14 ref NA False 241 67 PASS 8 PASS ref->het 0 NA 17,20 72,77 46,41 1 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 131 True C VWA1 64856 __UNKNOWN__ __UNKNOWN__ 1 1376817 1376817 __UNKNOWN__ 3'UTR DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:1376817delG ENST00000476993.1 + 0 3066 VWA1_ENST00000404702.3_3'UTR NM_022834.4 NP_073745.2 Q6PCB0 VWA1_HUMAN von Willebrand factor A domain containing 1 NA NA NA behavioral response to pain (GO:0048266)|extracellular matrix organization (GO:0030198) basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interstitial matrix (GO:0005614) NS(1)|breast(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1) 8 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145) GGGTGTCTGTGGGGGGGCCCT 0.652 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 788 749.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 4.99 BC059409 CCDS27.1, CCDS28.1, CCDS28.2 1p36.33 2013-02-11 ENSG00000179403 ENSG00000179403 64856 "Fibronectin type III domain containing" 30910 protein-coding gene gene with protein product 611901 NA 14527666, 12062410 Standard NM_022834 NM_022834 NA Approved FLJ22215, VWA-1, WARP uc001afs.3 Q6PCB0 OTTHUMG00000002975 ENST00000476993.1:c.*1650G>- chr1.hg19:g.1376817delG 6 8 ref NA False 179 154 PASS 7 PASS ref->het 0 NA 512,527 128,130 151,134 1 1 A8K692|B3KUA1|E9PB53|Q7L5D7|Q9H6J5 True hg19 CCDS27.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA VWA1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000008291.1 PASS NA None 788 True + G ENST00000476993.1 CDK11B 984 __UNKNOWN__ __UNKNOWN__ 1 1572010 1572010 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:1572010delC ENST00000407249.3 - 18 1926 CDK11B_ENST00000341832.6_Intron|CDK11B_ENST00000317673.7_Intron|CDK11B_ENST00000340677.5_Intron P21127 CD11B_HUMAN cyclin-dependent kinase 11B NA NA NA apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355) cytoplasm (GO:0005737)|nucleus (GO:0005634) ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674) endometrium(2)|large_intestine(3)|lung(4)|skin(1)|stomach(2) 12 TCCTCCACAACCCCACAGCGC 0.607 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 542 514.05 NA NA 51 55 54 NA NA NA 1 NA NA NA 1572010 2118 4244 6362 SO:0001627 intron_variant 2.66 AK000081 CCDS72682.1, CCDS72683.1, CCDS72684.1 1p36.33 2013-09-24 2009-12-16 2009-12-16 ENSG00000248333 ENSG00000248333 984 "Cyclin-dependent kinases" 1729 protein-coding gene gene with protein product 176873 "cell division cycle 2-like 1 (PITSLRE proteins)" CDC2L1 NA 1774066, 14511641, 19884882 Standard NM_001787 XM_006711061 NA Approved CDK11-p110, CDK11-p58, CDK11-p46 uc001agv.1 P21127 OTTHUMG00000078638 ENST00000407249.3:c.1926+33G>- chr1.hg19:g.1572010delC 3 5 ref NA False 60 60 PASS 4 PASS ref->het 0 NA 423,436 51,53 69,56 1 1 O95265|Q12817|Q12818|Q12819|Q12820|Q12822|Q8N530|Q9NZS5|Q9UBJ0|Q9UBQ1|Q9UBR0|Q9UNY2|Q9UP57|Q9UP58|Q9UP59 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDK11B-204 KNOWN basic|appris_candidate_longest protein_coding NA protein_coding PASS NA None 542 True - C ENST00000407249.3 AJAP1 55966 __UNKNOWN__ __UNKNOWN__ 1 4771947 4771947 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:4771947delC ENST00000378191.4 + 2 410 AJAP1_ENST00000466761.1_Intron|AJAP1_ENST00000378190.3_Intron NM_018836.3 NP_061324.1 Q9UKB5 AJAP1_HUMAN adherens junctions associated protein 1 NA NA NA cell adhesion (GO:0007155) cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1) 24 all_cancers(77;0.071)|Ovarian(185;0.0721) all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215) Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689) TCTCTCCTTTCCCCCCCGCAC 0.667 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 246 242.66 NA , 4,23,4187 NA 0,0,4,9,5,2089 61 81 75 NA , -1.4 0 1 74 13,36,8123 NA 1,0,11,13,10,4051 no intron,intron AJAP1 NM_018836.3,NM_001042478.1 , 1,0,15,22,15,6140 A1A1,A1A2,A1R,A2A2,A2R,RR NA 0.5996,0.6407,0.6136 , , 4771947 17,59,12310 2188 4281 6469 SO:0001627 intron_variant 2.42 AF175409 CCDS54.1 1p36.32 2008-02-05 2008-01-08 ENSG00000196581 ENSG00000196581 55966 30801 protein-coding gene gene with protein product "transmembrane protein SHREW1" 610972 NA 14595118 Standard NM_018836 NM_001042478 NA Approved SHREW1, SHREW-1, MOT8 uc001aln.3 Q9UKB5 OTTHUMG00000000645 ENST00000378191.4:c.30-13C>- chr1.hg19:g.4771947delC 6 8 ref NA False 75 75 PASS 7 PASS ref->het 0 NA 153,166 49,49 49,37 1 1 Q9Y229 True hg19 CCDS54.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AJAP1-001 KNOWN NMD_exception|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000001542.3 PASS NA None 246 True + C ENST00000378191.4 UBXN10 127733 __UNKNOWN__ __UNKNOWN__ 1 20522018 20522018 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:20522018delA ENST00000375099.3 + 0 5048 NM_152376.3 NP_689589.1 Q96LJ8 UBX10_HUMAN UBX domain protein 10 NA NA NA endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|skin(2) 14 TCTTAAGGAGAAAAAAAAGGA 0.453 NA NA NA OREG0013187 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 174 175.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.25 AK058158 CCDS205.1 1p36.13 2008-07-25 2008-07-25 2008-07-25 ENSG00000162543 ENSG00000162543 127733 "UBX domain containing" 26354 protein-coding gene gene with protein product NA "UBX domain containing 3" UBXD3 NA 12477932 Standard NM_152376 NM_152376 NA Approved FLJ25429 uc001bdb.3 Q96LJ8 OTTHUMG00000002708 ENST00000375099.3:c.*4121A>- chr1.hg19:g.20522018delA 7 9 ref 741 False 57 57 PASS 8 PASS ref->het 0 NA 113,120 38,39 24,18 2 2 Q5R386 True hg19 CCDS205.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UBXN10-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000007693.1 PASS NA None 174 True + A ENST00000375099.3 THEMIS2 9473 __UNKNOWN__ __UNKNOWN__ 1 28208686 28208686 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:28208686delA ENST00000373921.3 + 4 855 c.851delA c.(850-852)caafs p.Q284fs THEMIS2_ENST00000328928.7_Intron|THEMIS2_ENST00000373927.3_Intron|THEMIS2_ENST00000373925.1_Intron NM_001105556.1 NP_001099026.1 Q5TEJ8 THMS2_HUMAN thymocyte selection associated family member 2 284 CABIT 2. NA NA cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852) cytoplasm (GO:0005737)|nucleus (GO:0005634) NA GGCTCCTTGCAAAAAGGCCAG 0.647 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 203 207.43 NA NA 30 32 32 NA NA NA 1 NA NA NA 28208686 1930 4133 6063 SO:0001589 frameshift_variant 0.56 AF044896 CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1 1p35.2 2012-07-10 2012-07-10 2012-07-10 ENSG00000130775 ENSG00000130775 9473 16839 protein-coding gene gene with protein product "induced by contact to basement membrane 1" NA "chromosome 1 open reading frame 38" C1orf38 NA 16219472 Standard NM_004848 XM_005246041 NA Approved ICB-1, Icb-1 uc001bpc.4 Q5TEJ8 OTTHUMG00000003735 ENST00000373921.3:c.851delA chr1.hg19:g.28208686delA ENSP00000363031:p.Gln284fs 4 5 ref NA False 80 79 PASS 5 PASS ref->het 0 NA 117,119 63,63 22,20 1 1 A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90 True hg19 CCDS41290.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA THEMIS2-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000011148.1 PASS NA None 203 True + A ENST00000373921.3 FNDC5 252995 __UNKNOWN__ __UNKNOWN__ 1 33330280 33330280 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:33330280delC ENST00000373471.3 - 5 684 c.618delG c.(616-618)gggfs p.G206fs FNDC5_ENST00000481487.1_5'UTR|FNDC5_ENST00000496770.1_Frame_Shift_Del_p.G131fs|FNDC5_ENST00000609187.1_Frame_Shift_Del_p.G131fs NM_001171940.1|NM_153756.2 NP_001165411.2|NP_715637.2 Q8NAU1 FNDC5_HUMAN fibronectin type III domain containing 5 206 NA NA positive regulation of brown fat cell differentiation (GO:0090336)|response to muscle activity (GO:0014850) endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)|plasma membrane (GO:0005886) breast(1)|large_intestine(1)|lung(2)|ovary(1) 5 Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186) TGCGGAGAAGCCCCCCGCCCT 0.587 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 78 73.48 NA NA 133 113 120 NA NA NA 1 NA NA NA 33330280 2203 4300 6503 SO:0001589 frameshift_variant 0 AK092102 CCDS369.1, CCDS369.2, CCDS65483.1 1p34.3 2013-10-16 ENSG00000160097 ENSG00000160097 252995 "Fibronectin type III domain containing" 20240 protein-coding gene gene with protein product "irisin" 611906 NA 12384288, 22237023, 24120943 Standard NM_153756 NM_153756 NA Approved FRCP2 uc001bwg.3 Q8NAU1 OTTHUMG00000004015 ENST00000373471.3:c.618delG chr1.hg19:g.33330280delC ENSP00000362570:p.Gly206fs 5 9 ref NA False 42 42 PASS 6 PASS ref->het 0 NA 47,48 26,26 6,6 2 2 A6NMC9|D3DPQ6|Q6P6D9|Q7Z676 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FNDC5-001 KNOWN non_ATG_start|basic protein_coding NA protein_coding OTTHUMT00000011467.3 PASS NA None 78 True - C ENST00000373471.3 ZMPSTE24 10269 __UNKNOWN__ __UNKNOWN__ 1 40759055 40759055 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:40759055delT ENST00000372759.3 + 0 2307 NM_005857.4 NP_005848.2 O75844 FACE1_HUMAN zinc metallopeptidase STE24 NA NA NA CAAX-box protein processing (GO:0071586)|nuclear envelope organization (GO:0006998)|prenylated protein catabolic process (GO:0030327)|proteolysis (GO:0006508) endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634) metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metalloexopeptidase activity (GO:0008235) endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1) 16 Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;6.3e-18) TGTCTTTATCTTTTTTTCCCA 0.328 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 158 157.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.44 Y13834 CCDS449.1 1p34 2014-09-17 2012-12-10 ENSG00000084073 ENSG00000084073 10269 3.4.24.84 12877 protein-coding gene gene with protein product "Hutchinson-Gilford progeria syndrome", "CAAX prenyl protease 1 homolog" 606480 "zinc metalloproteinase (STE24 homolog, yeast)", "zinc metallopeptidase (STE24 homolog, yeast)", "zinc metallopeptidase STE24 homolog (S. cerevisiae)" NA 10373325, 9700155, 16671095 Standard NM_005857 NA Approved FACE-1, Ste24p, STE24, HGPS, PRO1 uc001cfg.4 O75844 OTTHUMG00000005762 ENST00000372759.3:c.*714T>- chr1.hg19:g.40759055delT 6 8 ref NA False 32 32 PASS 7 PASS ref->het 0 NA 108,108 34,35 17,17 1 1 B3KQI7|D3DPU7|Q8NDZ8|Q9UBQ2 True hg19 CCDS449.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZMPSTE24-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000015766.1 PASS NA None 158 True + T ENST00000372759.3 STIL 6491 __UNKNOWN__ __UNKNOWN__ 1 47717177 47717186 __UNKNOWN__ Frame_Shift_Del DEL ACCAAGCTGT ACCAAGCTGT - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:47717177_47717186delACCAAGCTGT ENST00000371877.3 - 17 3636_3645 c.3489_3498delACAGCTTGGT c.(3487-3498)gaacagcttggtfs p.EQLG1163fs STIL_ENST00000360380.3_Frame_Shift_Del_p.EQLG1162fs|STIL_ENST00000243182.6_Frame_Shift_Del_p.EQLG1162fs|STIL_ENST00000337817.5_Frame_Shift_Del_p.EQLG1162fs|STIL_ENST00000396221.2_Frame_Shift_Del_p.EQLG1145fs Q15468 STIL_HUMAN SCL/TAL1 interrupting locus 1162 NA NA cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224) centrosome (GO:0005813)|cytoplasm (GO:0005737) central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3) 36 Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444) CTTTCTGACCACCAAGCTGTTCAGGTATGG 0.395 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 468 458.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.39 M74558 CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1 1p32 2010-02-09 2005-11-29 2005-11-29 ENSG00000123473 ENSG00000123473 6491 10879 protein-coding gene gene with protein product 181590 "TAL1 (SCL) interrupting locus" SIL NA 2209547 Standard NM_003035 NM_003035 NA Approved MCPH7 uc001crd.1 Q15468 OTTHUMG00000007851 ENST00000371877.3:c.3489_3498delACAGCTTGGT chr1.hg19:g.47717177_47717186delACCAAGCTGT ENSP00000360944:p.Glu1163fs 0 4 ref NA False 76 76 PASS 1 PASS ref->het 0 NA 359,361 91,91 38,37 1 1 Q5T0C5|Q68CN9 True hg19 CCDS41329.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA STIL-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000021652.2 PASS NA None 468 True - ACCAAGCTGT ENST00000371877.3 SCP2 6342 __UNKNOWN__ __UNKNOWN__ 1 53446093 53446102 __UNKNOWN__ Frame_Shift_Del DEL CTGCAAGAAA CTGCAAGAAA - rs185811440 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:53446093_53446102delCTGCAAGAAA ENST00000528311.1 + 9 904_913 c.608_617delCTGCAAGAAA c.(607-618)gctgcaagaaaafs p.AARK203fs SCP2_ENST00000371513.5_Frame_Shift_Del_p.AARK240fs|SCP2_ENST00000473584.1_3'UTR|SCP2_ENST00000371514.3_Frame_Shift_Del_p.AARK284fs|SCP2_ENST00000407246.2_Frame_Shift_Del_p.AARK260fs|SCP2_ENST00000371509.4_Frame_Shift_Del_p.AARK240fs NM_001193617.1 NP_001180546.1 Q9BX26 SYCP2_HUMAN sterol carrier protein 2 0 NA NA female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130) lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795) DNA binding (GO:0003677) p.R286*(1) breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1) 15 AGTAAAGAAGCTGCAAGAAAATGCTATGAG 0.357 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 1 Substitution - Nonsense(1) lung(1) 177 158.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 M75884 CCDS572.1, CCDS30719.1, CCDS41338.1, CCDS44149.1, CCDS44150.1, CCDS53317.1, CCDS53318.1, CCDS53319.1 1p32 2010-08-20 ENSG00000116171 ENSG00000116171 6342 10606 protein-coding gene gene with protein product 184755 NA 1703300, 1718316 Standard NM_002979 NM_001007098 NA Approved uc001cur.2 P22307 OTTHUMG00000008936 ENST00000528311.1:c.608_617delCTGCAAGAAA chr1.hg19:g.53446093_53446102delCTGCAAGAAA ENSP00000434132:p.Ala203fs 0 6 ref NA False 91 86 PASS 1 PASS ref->het 0 NA 83,83 83,84 18,18 1 1 A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27 True hg19 CCDS53319.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SCP2-010 PUTATIVE basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000387558.1 PASS NA None 177 True + CTGCAAGAAA ENST00000528311.1 LEPR 3953 __UNKNOWN__ __UNKNOWN__ 1 66103714 66103714 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:66103714delA ENST00000349533.6 + 0 4699 NM_002303.5 NP_002294.2 O15243 OBRG_HUMAN leptin receptor NA NA NA negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009) endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021) receptor binding (GO:0005102) breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2) 36 OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094) CCATCAATTTAAAAAAACTGA 0.393 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 132 123.76 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.3 U43168 CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1 1p31 2014-09-17 ENSG00000116678 ENSG00000116678 3953 "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing" 6554 protein-coding gene gene with protein product 601007 NA 8548812, 8812446 Standard NM_002303 NM_001003680 NA Approved OBR, CD295 uc001dci.3 P48357 OTTHUMG00000009115 ENST00000349533.6:c.*1016A>- chr1.hg19:g.66103714delA 6 7 ref NA False 42 42 PASS 7 PASS ref->het 0 NA 76,76 36,36 18,19 2 2 Q6FHL5 True hg19 CCDS631.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LEPR-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000025275.1 PASS NA None 132 True + A ENST00000349533.6 SGIP1 84251 __UNKNOWN__ __UNKNOWN__ 1 67109410 67109411 __UNKNOWN__ Intron INS - - TG rs373027734|rs145373755|rs367753809 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:67109410_67109411insTG ENST00000371037.4 + 7 536 SGIP1_ENST00000371039.1_Intron|SGIP1_ENST00000371035.3_Intron|SGIP1_ENST00000371036.3_Intron|SGIP1_ENST00000468286.1_Intron|SGIP1_ENST00000237247.6_Intron NM_032291.2 NP_115667.2 Q9BQI5 SGIP1_HUMAN SH3-domain GRB2-like (endophilin) interacting protein 1 NA NA NA endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021) AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886) microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124) breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1) 71 GTGGTGAGTGTTGTGTGTGTGT 0.406 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 281 258.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.36 AL136561 CCDS30744.1 1p31.3 2008-02-05 ENSG00000118473 ENSG00000118473 84251 25412 protein-coding gene gene with protein product 611540 NA 11230166 Standard NM_032291 NM_032291 NA Approved DKFZp761D221 uc001dcr.3 Q9BQI5 OTTHUMG00000009161 ENST00000371037.4:c.459+8->TG chr1.hg19:g.67109419_67109420dupTG 8 3 ref NA False 81 81 PASS 7 PASS ref->het 0 NA 178,178 48,51 54,51 1 1 A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2 True hg19 CCDS30744.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SGIP1-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000025395.4 PASS NA None 281 True + TG ENST00000371037.4 SGIP1 84251 __UNKNOWN__ __UNKNOWN__ 1 67209806 67209806 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:67209806delA ENST00000371037.4 + 0 3592 SGIP1_ENST00000371039.1_3'UTR|SGIP1_ENST00000435165.2_3'UTR|SGIP1_ENST00000371036.3_3'UTR|SGIP1_ENST00000237247.6_3'UTR NM_032291.2 NP_115667.2 Q9BQI5 SGIP1_HUMAN SH3-domain GRB2-like (endophilin) interacting protein 1 NA NA NA endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021) AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886) microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124) breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1) 71 AATTTTAGGGAAAAAAAAGTC 0.343 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 139 131.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AL136561 CCDS30744.1 1p31.3 2008-02-05 ENSG00000118473 ENSG00000118473 84251 25412 protein-coding gene gene with protein product 611540 NA 11230166 Standard NM_032291 NM_032291 NA Approved DKFZp761D221 uc001dcr.3 Q9BQI5 OTTHUMG00000009161 ENST00000371037.4:c.*1028A>- chr1.hg19:g.67209806delA 7 8 ref NA False 55 55 PASS 8 PASS ref->het 0 NA 89,90 28,28 21,22 1 1 A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2 True hg19 CCDS30744.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SGIP1-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000025395.4 PASS NA None 139 True + A ENST00000371037.4 C1orf141 400757 __UNKNOWN__ __UNKNOWN__ 1 67561988 67561988 __UNKNOWN__ Frame_Shift_Del DEL T T - rs145606616 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:67561988delT ENST00000371007.2 - 6 472 c.363delA c.(361-363)aaafs p.K121fs C1orf141_ENST00000371006.1_Frame_Shift_Del_p.K121fs|C1orf141_ENST00000544837.1_Frame_Shift_Del_p.K121fs NM_001276351.1 NP_001263280.1 Q5JVX7 CA141_HUMAN chromosome 1 open reading frame 141 121 NA NA NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1) 18 GTTTCCTAGGTTTTTTTTCAA 0.249 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 291 271.09 NA 14,4168 NA 0,14,2077 NA NA NA NA -7.5 0 dbSNP_134 31 17,8143 NA 0,17,4063 no frameshift C1orf141 NM_001013674.1 0,31,6140 A1A1,A1R,RR NA 0.2083,0.3348,0.2512 NA 31,12311 NA NA NA SO:0001589 frameshift_variant 0.52 BC090886 CCDS30745.1, CCDS72804.1 1p31.2 2012-07-23 ENSG00000203963 ENSG00000203963 400757 32044 protein-coding gene gene with protein product NA NA Standard NM_001013674 NM_001276351 NA Approved uc001ddm.2 Q5JVX7 OTTHUMG00000009406 ENST00000371007.2:c.363delA chr1.hg19:g.67561988delT ENSP00000360046:p.Lys121fs 7 8 ref NA False 89 89 PASS 8 PASS ref->het 0 NA 189,192 65,66 39,37 1 1 Q0P5P5|Q5JVX5 True hg19 CCDS30745.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C1orf141-004 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000026096.2 PASS NA None 291 True - T ENST00000371007.2 C1orf173 0 __UNKNOWN__ __UNKNOWN__ 1 75072556 75072556 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:75072556delT ENST00000326665.5 - 10 1436 c.1218delA c.(1216-1218)aaafs p.K406fs RP4-612J11.1_ENST00000416017.1_RNA|C1orf173_ENST00000420661.2_Frame_Shift_Del_p.K209fs NM_001002912.4 NP_001002912.4 Q5RHP9 ERIC3_HUMAN 406 NA NA NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5) 184 GCAAAGACGGTTTTTTGTCAA 0.418 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 586 579.58 NA NA 107 104 105 NA NA NA 1 NA NA NA 75072556 2203 4299 6502 SO:0001589 frameshift_variant 0.67 NA NA NA NA NA ENST00000326665.5:c.1218delA chr1.hg19:g.75072556delT ENSP00000322609:p.Lys406fs 5 7 ref NA False 55 55 PASS 6 PASS ref->het 0 NA 454,456 63,63 65,63 1 1 Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41 True hg19 CCDS30755.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C1orf173-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000026516.1 PASS NA None 586 True - T ENST00000326665.5 CYR61 3491 __UNKNOWN__ __UNKNOWN__ 1 86047289 86047289 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:86047289delA ENST00000451137.2 + 2 501 CYR61_ENST00000480413.1_Intron NM_001554.4 NP_001545.2 O00622 CYR61_HUMAN cysteine-rich, angiogenic inducer, 61 NA NA NA anatomical structure morphogenesis (GO:0009653)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|chondroblast differentiation (GO:0060591)|chorio-allantoic fusion (GO:0060710)|extracellular matrix organization (GO:0030198)|intussusceptive angiogenesis (GO:0002041)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of apoptotic process (GO:0043066)|osteoblast differentiation (GO:0001649)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|reactive oxygen species metabolic process (GO:0072593)|regulation of cell growth (GO:0001558)|regulation of ERK1 and ERK2 cascade (GO:0070372)|ventricular septum development (GO:0003281)|wound healing, spreading of cells (GO:0044319) extracellular matrix (GO:0031012)|extracellular region (GO:0005576) extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201) central_nervous_system(1)|endometrium(1)|large_intestine(2)|prostate(1) 5 all cancers(265;0.0216)|Epithelial(280;0.0441) TGGCCCCTTTAAAAAAAATAC 0.493 NA NA NA OREG0013583 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 89 88.58 NA 10,4256 NA 0,10,2123 18 19 18 NA 4.8 1 1 19 20,8234 NA 0,20,4107 no intron CYR61 NM_001554.4 0,30,6230 A1A1,A1R,RR NA 0.2423,0.2344,0.2396 86047289 30,12490 2203 4300 6503 SO:0001627 intron_variant 0 AF031385 CCDS706.1 1p22.3 2008-02-05 ENSG00000142871 ENSG00000142871 3491 2654 protein-coding gene gene with protein product 602369 IGFBP10 NA 9135077 Standard NM_001554 NM_001554 NA Approved GIG1, CCN1 uc001dle.3 O00622 OTTHUMG00000010577 ENST00000451137.2:c.277+28A>- chr1.hg19:g.86047289delA 7 9 ref 1241 False 41 41 PASS 8 PASS ref->het 0 NA 61,64 12,12 14,13 2 2 O14934|O43775|Q9BZL7 True hg19 CCDS706.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CYR61-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000029187.1 PASS NA None 89 True + A ENST00000451137.2 LMO4 8543 __UNKNOWN__ __UNKNOWN__ 1 87811760 87811760 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:87811760delT ENST00000370544.5 + 0 2559 NM_006769.3 NP_006760.1 P61968 LMO4_HUMAN LIM domain only 4 NA NA NA negative regulation of protein complex assembly (GO:0031333)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell activation (GO:0050865)|regulation of cell fate specification (GO:0042659)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron differentiation (GO:0021522)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)|ventral spinal cord interneuron differentiation (GO:0021514)|ventricular septum development (GO:0003281) transcription factor complex (GO:0005667) enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270) NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(1) 9 Lung NSC(277;0.179) all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153) CCCAGAGCTCTTTTTTTATGG 0.393 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 243 249.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.06 U24576 CCDS713.1 1p22.3 2008-02-05 ENSG00000143013 ENSG00000143013 8543 6644 protein-coding gene gene with protein product 603129 NA Standard NM_006769 NM_006769 NA Approved uc001dmi.3 P61968 OTTHUMG00000010248 ENST00000370544.5:c.*1281T>- chr1.hg19:g.87811760delT 6 8 ref NA False 61 61 PASS 7 PASS ref->het 0 NA 180,185 37,37 28,27 2 2 D3DT23|O00158|O88894 True hg19 CCDS713.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LMO4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000028264.2 PASS NA None 243 True + T ENST00000370544.5 AMPD2 271 __UNKNOWN__ __UNKNOWN__ 1 110173500 110173519 __UNKNOWN__ Intron DEL CTTGGGGTGGGGCATGACCC CTTGGGGTGGGGCATGACCC - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:110173500_110173519delCTTGGGGTGGGGCATGACCC ENST00000256578.3 + 18 2790 AMPD2_ENST00000528454.1_Intron|AMPD2_ENST00000342115.4_Intron|AMPD2_ENST00000358729.4_Intron|AMPD2_ENST00000528667.1_Intron|AMPD2_ENST00000393688.3_Intron NM_004037.7 NP_004028.3 Q01433 AMPD2_HUMAN adenosine monophosphate deaminase 2 NA NA NA cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829) AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872) breast(1)|large_intestine(3)|ovary(2)|skin(1) 7 all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244) Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228) CCTGGGATGGCTTGGGGTGGGGCATGACCCCTCAGCACTG 0.623 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 258 275.62 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.89 S47833 CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1 1p13.3 2014-03-03 2010-02-10 ENSG00000116337 ENSG00000116337 271 3.5.4.6 469 protein-coding gene gene with protein product "AMPD isoform L" 102771 "adenosine monophosphate deaminase 2 (isoform L)" NA 1400401, 24482476 Standard NM_004037 NA Approved SPG63 uc009wfh.2 Q01433 OTTHUMG00000011649 ENST00000256578.3:c.2431-46CTTGGGGTGGGGCATGACCC>- chr1.hg19:g.110173500_110173519delCTTGGGGTGGGGCATGACCC 0 5 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 212,219 22,24 54,47 1 1 B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4 True hg19 CCDS805.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AMPD2-011 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000390615.1 PASS NA None 258 True + CTTGGGGTGGGGCATGACCC ENST00000256578.3 PHTF1 10745 __UNKNOWN__ __UNKNOWN__ 1 114255866 114255866 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:114255866delA ENST00000369604.1 - 8 1267 PHTF1_ENST00000357783.2_Intron|PHTF1_ENST00000474926.1_Intron|PHTF1_ENST00000369600.1_Intron|PHTF1_ENST00000369598.1_Intron|PHTF1_ENST00000393357.2_Intron|PHTF1_ENST00000369596.2_Intron|PHTF1_ENST00000447664.2_Intron Q9UMS5 PHTF1_HUMAN putative homeodomain transcription factor 1 NA NA NA transcription, DNA-templated (GO:0006351) cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634) DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700) breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1) 27 Lung SC(450;0.184) all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133) TTACATGGGGAAAAAAACCCC 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 269 274.44 NA NA 93 97 95 NA NA NA 1 NA NA NA 114255866 2203 4300 6503 SO:0001627 intron_variant 0.14 AJ011863 CCDS861.1 1p13-p11 2008-07-18 ENSG00000116793 ENSG00000116793 10745 8939 protein-coding gene gene with protein product 604950 PHTF NA 10395808 Standard NM_006608 NM_006608 NA Approved uc009wgp.1 Q9UMS5 OTTHUMG00000011800 ENST00000369604.1:c.783+34T>- chr1.hg19:g.114255866delA 6 7 ref NA False 48 48 PASS 7 PASS ref->het 0 NA 196,197 45,45 29,28 1 1 Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8 True hg19 CCDS861.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PHTF1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000032666.1 PASS NA None 269 True - A ENST00000369604.1 CSDE1 7812 __UNKNOWN__ __UNKNOWN__ 1 115280554 115280554 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:115280554delA ENST00000530886.1 - 3 600 CSDE1_ENST00000534699.1_Intron|CSDE1_ENST00000438362.2_Intron|CSDE1_ENST00000358528.4_Intron|CSDE1_ENST00000261443.5_Intron|CSDE1_ENST00000339438.6_Intron|CSDE1_ENST00000369530.1_Intron O75534 CSDE1_HUMAN cold shock domain containing E1, RNA-binding NA NA NA male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355) CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886) DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822) NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1) 51 all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211) all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133) GCAGGGCCCTAAAAAAACACA 0.373 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 689 694.06 NA NA 151 147 148 NA NA NA 1 NA NA NA 115280554 2203 4300 6503 SO:0001627 intron_variant 2.12 CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1 1p13.2 2011-11-02 ENSG00000009307 ENSG00000009307 7812 29905 protein-coding gene gene with protein product "upstream of NRAS" 191510 NA 2204029, 10048485 Standard NM_007158 NM_007158 NA Approved D1S155E, UNR uc001efi.3 O75534 OTTHUMG00000012060 ENST00000530886.1:c.12+29T>- chr1.hg19:g.115280554delA 6 8 ref NA False 211 169 PASS 7 PASS ref->het 0 NA 477,482 123,125 100,95 1 1 A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CSDE1-007 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000392607.1 PASS NA None 689 True - A ENST00000530886.1 ADAMTSL4-AS1 574406 __UNKNOWN__ __UNKNOWN__ 1 150533858 150533860 __UNKNOWN__ In_Frame_Del DEL GGA GGA - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:150533858_150533860delGGA ENST00000369035.2 - 1 109_111 c.87_89delTCC c.(85-90)cctcca>cca p.29_30PP>P Q5T5F5 A4AS1_HUMAN ADAMTSL4 antisense RNA 1 29 Pro-rich. NA NA NA CCCTTCCCCTGGAGGAGGAGGAG 0.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 153 169.41 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.58 AK127688 1q21.2 2013-08-29 2013-08-29 2013-08-29 ENSG00000203804 ENSG00000203804 574406 "Long non-coding RNAs" 32041 non-coding RNA RNA, long non-coding NA "chromosome 1 open reading frame 138" C1orf138 NA Standard NR_104133 NA Approved FLJ45786 Q5T5F5 OTTHUMG00000034866 ENST00000369035.2:c.87_89delTCC chr1.hg19:g.150533867_150533869delGGA ENSP00000358031:p.Pro30del 3 4 ref NA False 70 70 PASS 4 PASS ref->het 0 NA 89,92 25,27 38,34 1 1 Q6ZS69 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ADAMTSL4-AS1-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000084401.1 PASS NA None 153 True - GGA ENST00000369035.2 MLLT11 10962 __UNKNOWN__ __UNKNOWN__ 1 151040476 151040476 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:151040476delT ENST00000368921.3 + 0 3578 CDC42SE1_ENST00000439374.2_Intron NM_006818.3 NP_006809.1 Q13015 AF1Q_HUMAN myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11 NA NA NA extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of apoptotic process (GO:0043065)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of transcription, DNA-templated (GO:0045893) intracellular (GO:0005622) upper_aerodigestive_tract(1) 1 Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211) AGTCTCTTGCTTTTTTTTGAT 0.323 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 154 164.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.88 BC006471 CCDS982.1 1q21 2008-02-05 ENSG00000213190 ENSG00000213190 10962 16997 protein-coding gene gene with protein product "ALL1 fused gene from chromosome 1q" 604684 NA 7833468 Standard NM_006818 NM_006818 NA Approved AF1Q uc001ewq.3 Q13015 OTTHUMG00000035160 ENST00000368921.3:c.*503T>- chr1.hg19:g.151040476delT 7 8 ref NA False 48 48 PASS 8 PASS ref->het 0 NA 97,104 30,30 27,24 1 1 True hg19 CCDS982.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MLLT11-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000085103.1 PASS NA None 154 True + T ENST00000368921.3 FLG2 388698 __UNKNOWN__ __UNKNOWN__ 1 152323154 152323154 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:152323154delT ENST00000388718.5 - 3 7180 c.7108delA c.(7108-7110)agcfs p.S2370fs FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA NM_001014342.2 NP_001014364.1 Q5D862 FILA2_HUMAN filaggrin family member 2 2370 NA NA establishment of skin barrier (GO:0061436) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634) calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198) NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5) 188 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) TTACTGATGCTTTTTCTGCTG 0.443 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 507 512.26 NA NA 197 188 191 NA NA NA 1 NA NA NA 152323154 2203 4300 6503 SO:0001589 frameshift_variant 0.79 AY827490 CCDS30861.1 1q21.3 2013-01-10 ENSG00000143520 ENSG00000143520 388698 "EF-hand domain containing" 33276 protein-coding gene gene with protein product NA NA 12477932 Standard NM_001014342 NM_001014342 NA Approved IFPS uc001ezw.4 Q5D862 OTTHUMG00000012245 ENST00000388718.5:c.7108delA chr1.hg19:g.152323154delT ENSP00000373370:p.Ser2370fs 4 6 ref NA False 68 68 PASS 5 PASS ref->het 0 NA 364,372 84,88 56,51 1 1 Q9H4U1 True hg19 CCDS30861.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FLG2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000034018.5 PASS NA None 507 True - T ENST00000388718.5 PMVK 10654 __UNKNOWN__ __UNKNOWN__ 1 154897495 154897495 __UNKNOWN__ 3'UTR DEL C C - rs144182615 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:154897495delC ENST00000368467.3 - 0 994 NM_006556.3 NP_006547.1 Q15126 PMVK_HUMAN phosphomevalonate kinase NA NA NA cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|response to cholesterol (GO:0070723)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|peroxisome (GO:0005777) ATP binding (GO:0005524)|phosphomevalonate kinase activity (GO:0004631) endometrium(1)|kidney(1)|large_intestine(1)|lung(3) 6 all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.142) BRCA - Breast invasive adenocarcinoma(34;0.00034) AGAATCTAGACCCCCCCTGTC 0.592 NA NA NA 27 0.00539137 8e-04 0.0043 5008 , , NA 15129 0 NA 0.0169 False NA ,,, NA NA NA 2504 0.0061 NA NA NA PASS NA NA NA 0 284 272.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 5.01 L77213 CCDS1073.1 1q21.3 2012-09-20 ENSG00000163344 ENSG00000163344 10654 2.7.4.2 9141 protein-coding gene gene with protein product 607622 NA 8663599, 10191291 Standard NM_006556 NM_006556 NA Approved PMK, PMKA, HUMPMKI uc001ffq.3 Q15126 OTTHUMG00000037415 ENST00000368467.3:c.*110G>- chr1.hg19:g.154897495delC 6 7 ref NA False 46 46 PASS 7 PASS ref->het 0 NA 186,198 46,47 50,38 1 1 Q5TZW9 True hg19 CCDS1073.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PMVK-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000091088.1 PASS NA None 284 True - C ENST00000368467.3 ASH1L-AS1 645676 __UNKNOWN__ __UNKNOWN__ 1 155532735 155532735 __UNKNOWN__ RNA DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:155532735delC ENST00000452809.1 + 0 214 ASH1L antisense RNA 1 NA NA NA NA CTCCCACAATCCCCCCCGCGG 0.736 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 117 128.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2.93 BC017347 1q22 2012-10-12 2012-08-15 ENSG00000235919 ENSG00000235919 645676 "Long non-coding RNAs" 44146 non-coding RNA RNA, long non-coding NA "ASH1L antisense RNA 1 (non-protein coding)" NA Standard NR_027023 NR_027023 NA Approved uc010pge.2 OTTHUMG00000014012 ENST00000452809.1: chr1.hg19:g.155532735delC 6 8 ref NA False 45 45 PASS 7 PASS ref->het 0 NA 80,86 17,20 25,17 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ASH1L-AS1-001 KNOWN basic antisense NA processed_transcript OTTHUMT00000039405.2 PASS NA None 117 True + C ENST00000452809.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 1 155556552 155556552 __UNKNOWN__ IGR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:155556552delT NA ASH1L-AS1 (22817 upstream) : RP11-29H23.4 (23014 downstream) NA NA NA NA tttattattatttttttaact 0.463 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 336 343.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.68 NA NA NA NA NA chr1.hg19:g.155556552delT 6 9 ref NA False 73 73 PASS 7 PASS ref->het 0 NA 209,213 68,68 50,48 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 336 True T GON4L 54856 __UNKNOWN__ __UNKNOWN__ 1 155823172 155823172 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:155823172delT ENST00000437809.1 - 2 522 c.400delA c.(400-402)atgfs p.M134fs GON4L_ENST00000271883.5_Frame_Shift_Del_p.M134fs|GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000368331.1_Frame_Shift_Del_p.M134fs|GON4L_ENST00000361040.5_Frame_Shift_Del_p.M134fs NM_001282856.1 NP_001269785.1 Q3T8J9 GON4L_HUMAN gon-4-like (C. elegans) 134 NA NA regulation of transcription, DNA-templated (GO:0006355) nucleus (GO:0005634) chromatin binding (GO:0003682)|DNA binding (GO:0003677) NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1) 45 Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195) CTGAGTGTCATTTTTTTCCCT 0.458 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 419 411.52 NA NA 131 133 132 NA NA NA 1 NA NA NA 155823172 2203 4300 6503 SO:0001589 frameshift_variant 1.19 AB046826 CCDS1121.1, CCDS44242.1, CCDS60296.1 1q22 2013-10-31 2006-11-08 2006-02-16 ENSG00000116580 ENSG00000116580 54856 25973 protein-coding gene gene with protein product 610393 "gon-4 homolog (C.elegans)" GON4 NA 16545939, 21454521 Standard NM_032292 XM_005245283 NA Approved FLJ20203, GON-4 uc001fly.1 Q3T8J9 OTTHUMG00000014106 ENST00000437809.1:c.400delA chr1.hg19:g.155823172delT ENSP00000396117:p.Met134fs 6 7 ref NA False 40 40 PASS 7 PASS ref->het 0 NA 284,287 83,86 52,50 1 1 B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6 True hg19 CCDS44242.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GON4L-019 KNOWN alternative_5_UTR|basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000340937.1 PASS NA None 419 True - T ENST00000437809.1 RAB25 57111 __UNKNOWN__ __UNKNOWN__ 1 156030984 156030984 __UNKNOWN__ 5'UTR DEL C C - rs557037341 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:156030984delC ENST00000361084.5 + 0 34 NM_020387.2 NP_065120.2 P57735 RAB25_HUMAN RAB25, member RAS oncogene family NA NA NA positive regulation of cell proliferation (GO:0008284)|protein transport (GO:0015031)|pseudopodium organization (GO:0031268)|small GTPase mediated signal transduction (GO:0007264) cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143) GTP binding (GO:0005525)|myosin V binding (GO:0031489) endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1) 5 Hepatocellular(266;0.158)|all_neural(408;0.195) CCTTACAGCACCCCCACCTGC 0.612 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 356 360.91 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 2.16 AF083124 CCDS41413.1 1q22 2008-07-03 ENSG00000132698 ENSG00000132698 57111 "RAB, member RAS oncogene" 18238 protein-coding gene gene with protein product 612942 NA 11697911 Standard NM_020387 NA Approved CATX-8 uc001fnc.3 P57735 OTTHUMG00000017457 ENST00000361084.5:c.-208C>- chr1.hg19:g.156030984delC 4 7 ref NA False 82 82 PASS 5 PASS ref->het 0 NA 258,264 57,58 43,38 1 1 Q5VYA2|Q8NG24|Q96GB1|Q9BT12 True hg19 CCDS41413.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RAB25-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000046185.1 PASS NA None 356 True + C ENST00000361084.5 LMNA 4000 __UNKNOWN__ __UNKNOWN__ 1 156106936 156106936 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:156106936delC ENST00000368300.4 + 9 1733 c.1521delC c.(1519-1521)agcfs p.S507fs LMNA_ENST00000347559.2_Frame_Shift_Del_p.S507fs|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000392353.3_Frame_Shift_Del_p.S426fs|LMNA_ENST00000368299.3_Frame_Shift_Del_p.S507fs|LMNA_ENST00000448611.2_Frame_Shift_Del_p.S395fs|LMNA_ENST00000368297.1_Frame_Shift_Del_p.S426fs|LMNA_ENST00000368301.2_Frame_Shift_Del_p.S507fs|LMNA_ENST00000473598.2_Frame_Shift_Del_p.S408fs|LMNA_ENST00000361308.4_Frame_Shift_Del_p.S507fs NM_170707.3 NP_733821.1 P02545 LMNA_HUMAN lamin A/C 507 LTD.|Tail. NA NA activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015) cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471) structural molecule activity (GO:0005198) NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4) 10 Hepatocellular(266;0.158) CCACCCACAGCCCCCCTACCG 0.632 NA NA NA Werner syndrome;Hutchinson-Gilford Progeria Syndrome NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 389 372.14 NA NA 32 35 34 NA NA NA 1 NA NA NA 156106936 2203 4300 6503 SO:0001589 frameshift_variant 1.92 Familial Cancer Database WS, Adult Progeria;HGPS, Progeria BC014507 CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1 1q22 2014-09-17 ENSG00000160789 ENSG00000160789 4000 "Intermediate filaments type V, lamins" 6636 protein-coding gene gene with protein product 150330 "cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1" LMN1, CMD1A, LGMD1B, PRO1, LMNL1 NA 8511676, 8838815, 12702809 Standard NM_170707 NM_005572 NA Approved HGPS uc001fni.3 P02545 OTTHUMG00000013961 ENST00000368300.4:c.1521delC chr1.hg19:g.156106936delC ENSP00000357283:p.Ser507fs 5 6 ref NA False 141 141 PASS 6 PASS ref->het 0 NA 278,289 66,66 43,34 2 1 B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2 True hg19 CCDS1129.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LMNA-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000039200.2 PASS NA None 389 True + C ENST00000368300.4 ARHGEF11 9826 __UNKNOWN__ __UNKNOWN__ 1 156905646 156905647 __UNKNOWN__ 3'UTR INS - - C rs569188325 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:156905646_156905647insC ENST00000368194.3 - 0 5873_5874 ARHGEF11_ENST00000361409.2_3'UTR|ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000315174.8_3'UTR NM_198236.2 NP_937879.1 O15085 ARHGB_HUMAN Rho guanine nucleotide exchange factor (GEF) 11 NA NA NA actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032) cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020) G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089) NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2) 81 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) CATGCGGGTCTCCCCCCGGGCC 0.604 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 473 448.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.99 AB002378 CCDS1162.1, CCDS1163.1 1q21 2011-11-16 ENSG00000132694 ENSG00000132694 9826 "Rho guanine nucleotide exchange factors" 14580 protein-coding gene gene with protein product 605708 NA 10526156, 9205841 Standard NM_198236 NM_014784 NA Approved KIAA0380, GTRAP48, PDZ-RHOGEF uc001fqn.3 O15085 OTTHUMG00000041292 ENST00000368194.3:c.*146->G chr1.hg19:g.156905652_156905652dupC 7 7 ref NA False 75 75 PASS 6 PASS ref->het 0 NA 334,339 75,78 62,55 1 1 D3DVD0|Q5VY40|Q6PFW2 True hg19 CCDS1163.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARHGEF11-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000098930.1 PASS NA None 473 True - C ENST00000368194.3 OR6N2 81442 __UNKNOWN__ __UNKNOWN__ 1 158746538 158746575 __UNKNOWN__ Frame_Shift_Del DEL TTCCTTGTTACGAAGACTGTAGATAATTGGATTGACCA TTCCTTGTTACGAAGACTGTAGATAATTGGATTGACCA - rs199979930|rs373599103|rs144962739 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:158746538_158746575delTTCCTTGTTACGAAGACTGTAGATAATTGGATTGACCA ENST00000339258.1 - 1 850_887 c.851_888delTGGTCAATCCAATTATCTACAGTCTTCGTAACAAGGAA c.(850-888)atggtcaatccaattatctacagtcttcgtaacaaggaafs p.MVNPIIYSLRNKE284fs NM_001005278.1 NP_001005278.1 Q8NGY6 OR6N2_HUMAN olfactory receptor, family 6, subfamily N, member 2 284 NA NA integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984) p.N294K(1)|p.N286S(1) endometrium(3)|large_intestine(6)|lung(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 24 all_hematologic(112;0.0378) CTTTAATGATTTCCTTGTTACGAAGACTGTAGATAATTGGATTGACCATTGGTGTTAG 0.416 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 2 Substitution - Missense(2) lung(1)|endometrium(1) 686 680.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.43 BK004200 CCDS30906.1 1q23.1 2012-08-09 ENSG00000188340 ENSG00000188340 81442 "GPCR / Class A : Olfactory receptors" 15035 protein-coding gene gene with protein product NA NA Standard NM_001005278 NA Approved uc010pir.2 Q8NGY6 OTTHUMG00000022775 ENST00000339258.1:c.851_888delTGGTCAATCCAATTATCTACAGTCTTCGTAACAAGGAA chr1.hg19:g.158746538_158746575delTTCCTTGTTACGAAGACTGTAGATAATTGGATTGACCA ENSP00000344101:p.Met284fs 0 3 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 810,816 12,12 86,81 1 1 Q6IFR2 True hg19 CCDS30906.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OR6N2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000059068.1 PASS NA None 686 True - TTCCTTGTTACGAAGACTGTAGATAATTGGATTGACCA ENST00000339258.1 KCNJ9 3765 __UNKNOWN__ __UNKNOWN__ 1 160058423 160058424 __UNKNOWN__ 3'UTR INS - - AG rs140202927 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:160058423_160058424insAG ENST00000368088.3 + 0 2240_2241 NM_004983.2 NP_004974.2 Q92806 KCNJ9_HUMAN potassium inwardly-rectifying channel, subfamily J, member 9 NA NA NA synaptic transmission (GO:0007268) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) G-protein activated inward rectifier potassium channel activity (GO:0015467) biliary_tract(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|skin(2) 16 all_cancers(52;5.86e-16)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.111) CACAGGCAGGAAGAGAGAGAGA 0.545 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 281 261.26 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.5 U52152 CCDS1194.1 1q23.2 2011-07-05 ENSG00000162728 ENSG00000162728 3765 "Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying" 6270 protein-coding gene gene with protein product 600932 NA 8575783, 16382105 Standard NM_004983 NM_004983 NA Approved Kir3.3, GIRK3 uc001fuy.1 Q92806 OTTHUMG00000024072 ENST00000368088.3:c.*817->AG chr1.hg19:g.160058432_160058433dupAG 8 3 ref NA False 44 44 PASS 7 PASS ref->het 0 NA 175,180 42,42 64,61 1 1 Q5JW75 True hg19 CCDS1194.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KCNJ9-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000060628.1 PASS NA None 281 True + AG ENST00000368088.3 TRMT1L 81627 __UNKNOWN__ __UNKNOWN__ 1 185088283 185088283 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:185088283delA ENST00000367506.5 - 0 3338 TRMT1L_ENST00000367504.3_3'UTR NM_001202423.1|NM_030934.4 NP_001189352.1|NP_112196.3 Q7Z2T5 TRM1L_HUMAN tRNA methyltransferase 1 homolog (S. cerevisiae)-like NA NA NA adult locomotory behavior (GO:0008344) metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049) NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1) 21 AAGCAACAACAAAAAAACAAC 0.323 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 245 241.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.34 AF288399 CCDS1366.1 1q25.2 2012-06-29 2012-06-29 2011-01-24 ENSG00000121486 ENSG00000121486 81627 16782 protein-coding gene gene with protein product "TRM1-like" 611673 "chromosome 1 open reading frame 25", "TRM1 tRNA methyltransferase 1-like" C1orf25 NA 11318611, 17198746 Standard NM_030934 NM_030934 NA Approved uc001grf.4 Q7Z2T5 OTTHUMG00000035389 ENST00000367506.5:c.*868T>- chr1.hg19:g.185088283delA 6 9 ref NA False 96 96 PASS 7 PASS ref->het 0 NA 172,174 45,45 25,25 1 1 Q5TEN0|Q6ZMX0|Q8IWH5|Q8NC68|Q9BZQ1 True hg19 CCDS1366.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRMT1L-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000085787.1 PASS NA None 245 True - A ENST00000367506.5 SWT1 54823 __UNKNOWN__ __UNKNOWN__ 1 185240446 185240447 __UNKNOWN__ Intron INS - - T rs201420919 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:185240446_185240447insT ENST00000367500.4 + 17 2606 SWT1_ENST00000367501.3_Intron NM_017673.6 NP_060143.4 Q5T5J6 SWT1_HUMAN SWT1 RNA endoribonuclease homolog (S. cerevisiae) NA NA NA breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1) 41 TTTTTATTTTATTTTTTAGGAT 0.312 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 195 190.6 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.9 AF288392 CCDS1367.1 1q25 2013-08-29 2011-01-24 2011-01-24 ENSG00000116668 ENSG00000116668 54823 16785 protein-coding gene gene with protein product NA "chromosome 1 open reading frame 26" C1orf26 NA 11318611, 19127978, 23768067 Standard NM_017673 NM_017673 NA Approved FLJ20121, HsSwt1 uc001grg.4 Q5T5J6 OTTHUMG00000035390 ENST00000367500.4:c.2442-8->T chr1.hg19:g.185240452_185240452dupT 7 10 ref NA False 33 33 PASS 6 PASS ref->het 0 NA 148,151 28,28 18,15 2 2 Q8NEK9|Q9BZQ7|Q9NXQ0 True hg19 CCDS1367.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SWT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000085790.1 PASS NA None 195 True + T ENST00000367500.4 C1orf106 55765 __UNKNOWN__ __UNKNOWN__ 1 200877920 200877920 __UNKNOWN__ Frame_Shift_Del DEL C C - rs372625309 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:200877920delC ENST00000413687.2 + 7 998 c.637delC c.(637-639)cccfs p.P213fs C1orf106_ENST00000367342.4_Frame_Shift_Del_p.P298fs NM_001142569.2 NP_001136041.1 Q3KP66 CA106_HUMAN chromosome 1 open reading frame 106 298 NA NA endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2) 21 GCCTCTCCCACCCCAAACCCT 0.602 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 298 276.42 NA NA 70 83 79 NA NA NA 1 NA NA NA 200877920 2203 4300 6503 SO:0001589 frameshift_variant 2.05 AK001763 CCDS44292.1 1q32.1 2011-02-15 ENSG00000163362 ENSG00000163362 55765 25599 protein-coding gene gene with protein product NA NA 14702039 Standard NM_018265 NM_018265 NA Approved FLJ10901 uc001gvo.4 Q3KP66 OTTHUMG00000035789 ENST00000413687.2:c.637delC chr1.hg19:g.200877920delC ENSP00000392105:p.Pro213fs 3 7 ref NA False 50 50 PASS 4 PASS ref->het 0 NA 206,213 55,56 39,31 1 1 B4E1K9|E9PFY0|Q9NV65|Q9NVI0 True hg19 CCDS44292.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C1orf106-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000087058.10 PASS NA None 298 True + C ENST00000413687.2 SERTAD4 56256 __UNKNOWN__ __UNKNOWN__ 1 210412959 210412959 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:210412959delT ENST00000367012.3 + 3 521 SERTAD4_ENST00000490620.1_Intron NM_019605.3 NP_062551.1 Q9NUC0 SRTD4_HUMAN SERTA domain containing 4 NA NA NA nucleus (GO:0005634) endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1) 14 OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127) ATAAAGTATGTTTTTTTAATA 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 229 230.39 NA NA 51 58 56 NA NA NA 1 NA NA NA 210412959 2203 4300 6503 SO:0001627 intron_variant 0.48 BC012083 CCDS1494.1 1q32.1-q41 2008-02-05 ENSG00000082497 ENSG00000082497 56256 25236 protein-coding gene gene with protein product NA NA 12477932 Standard NM_019605 NM_019605 NA Approved DJ667H12.2 uc001hhy.3 Q9NUC0 OTTHUMG00000036391 ENST00000367012.3:c.291+6T>- chr1.hg19:g.210412959delT 6 8 ref NA False 49 49 PASS 7 PASS ref->het 0 NA 160,161 33,33 31,30 1 1 B2RD32 True hg19 CCDS1494.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SERTAD4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000088577.1 PASS NA None 229 True + T ENST00000367012.3 PROX1 5629 __UNKNOWN__ __UNKNOWN__ 1 214185076 214185076 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:214185076delT ENST00000366958.4 + 4 2636 PROX1_ENST00000498508.2_Intron|PROX1_ENST00000261454.4_Intron|PROX1_ENST00000435016.1_Intron NM_001270616.1 NP_001257545.1 Q92786 PROX1_HUMAN prospero homeobox 1 NA NA NA aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412) cytoplasm (GO:0005737)|nucleus (GO:0005634) core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212) autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4) 47 OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219) CTAATCTTTATTTTTTGGTCA 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 153 156.86 NA NA 81 79 79 NA NA NA 1 NA NA NA 214185076 2203 4300 6503 SO:0001627 intron_variant 0.2 U44060 CCDS31021.1 1q41 2011-06-20 2007-06-01 ENSG00000117707 ENSG00000117707 5629 "Homeoboxes / PROS class" 9459 protein-coding gene gene with protein product 601546 "prospero-related homeobox 1" NA 8812486 Standard NM_002763 NM_002763 NA Approved uc001hkg.2 Q92786 OTTHUMG00000036946 ENST00000366958.4:c.2028+18T>- chr1.hg19:g.214185076delT 5 9 ref NA False 31 31 PASS 6 PASS ref->het 0 NA 98,101 31,31 22,21 2 2 A6NK29|A8K2B1|Q5SW76|Q8TB91 True hg19 CCDS31021.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PROX1-001 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000089727.6 PASS NA None 153 True + T ENST00000366958.4 HIST3H2BB 128312 __UNKNOWN__ __UNKNOWN__ 1 228645898 228645900 __UNKNOWN__ In_Frame_Del DEL AGA AGA - rs545229261 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:228645898_228645900delAGA ENST00000369160.2 + 1 91_93 c.68_70delAGA c.(67-72)cagaag>cag p.K25del NM_175055.2 NP_778225.1 Q8N257 H2B3B_HUMAN histone cluster 3, H2bb 25 NA NA chromatin organization (GO:0006325) nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634) DNA binding (GO:0003677) skin(1) 1 Prostate(94;0.183) ACCAAGGCACAGAAGAAGGACGG 0.576 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 557 566.93 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 1.12 AY131981 CCDS1574.1 1q42.13 2011-01-27 2006-10-11 ENSG00000196890 ENSG00000196890 128312 "Histones / Replication-dependent" 20514 protein-coding gene gene with protein product 615046 "histone 3, H2bb" NA 12408966 Standard NM_175055 NM_175055 NA Approved uc001hsz.3 Q8N257 OTTHUMG00000040045 ENST00000369160.2:c.68_70delAGA chr1.hg19:g.228645901_228645903delAGA ENSP00000375736:p.Lys25del 1 4 ref NA False 84 84 PASS 2 PASS ref->het 0 NA 410,422 69,71 74,68 1 1 A4FU05|Q3ZCP6|Q5TA30 True hg19 CCDS1574.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HIST3H2BB-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000096597.1 PASS NA None 557 True + AGA ENST00000369160.2 TARBP1 6894 __UNKNOWN__ __UNKNOWN__ 1 234613897 234613898 __UNKNOWN__ Intron INS - - G LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:234613897_234613898insG ENST00000040877.1 - 1 931 NM_005646.3 NP_005637.3 Q13395 TARB1_HUMAN TAR (HIV-1) RNA binding protein 1 NA NA NA regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396) nucleus (GO:0005634) RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173) NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4) 55 Ovarian(103;0.0339) all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172) OV - Ovarian serous cystadenocarcinoma(106;0.000263) AGCACTAGGCTGGGGGGCAAAG 0.609 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 326 319.98 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.32 CCDS1601.1 1q42.2 2012-06-12 2007-06-26 ENSG00000059588 ENSG00000059588 6894 11568 protein-coding gene gene with protein product "tRNA methyltransferase 3 homolog (S. cerevisiae)" 605052 "Tar (HIV-1) RNA binding protein 1" NA 1936997 Standard NM_005646 NM_005646 NA Approved TRP-185, TRM3 uc001hwd.3 Q13395 OTTHUMG00000037947 ENST00000040877.1:c.931+20->C chr1.hg19:g.234613903_234613903dupG 7 6 ref NA False 67 67 PASS 6 PASS ref->het 0 NA 207,212 62,62 54,49 1 1 Q9H581 True hg19 CCDS1601.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TARBP1-001 NOVEL basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000092616.1 PASS NA None 326 True - G ENST00000040877.1 C1orf229 388759 __UNKNOWN__ __UNKNOWN__ 1 247273909 247273909 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:247273909delA ENST00000408893.2 - 0 1810 NM_207401.1 NP_997284.1 Q6ZS94 CA229_HUMAN chromosome 1 open reading frame 229 NA NA NA NA taatagagacaaaaaaaGGGG 0.547 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 324 309.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 3.99 BC156415 CCDS1630.1 1q44 2012-05-30 ENSG00000221953 ENSG00000221953 388759 33759 protein-coding gene gene with protein product NA NA Standard NM_207401 NM_207401 NA Approved FLJ45717 uc001icg.1 Q6ZS94 OTTHUMG00000165196 ENST00000408893.2:c.*904T>- chr1.hg19:g.247273909delA 6 8 ref NA False 44 44 PASS 7 PASS ref->het 0 NA 249,264 31,31 46,38 1 1 True hg19 CCDS1630.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C1orf229-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000382614.1 PASS NA None 324 True - A ENST00000408893.2 KIDINS220 57498 __UNKNOWN__ __UNKNOWN__ 2 8869715 8869716 __UNKNOWN__ 3'UTR INS - - AT rs145525895 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:8869715_8869716insAT ENST00000256707.3 - 0 6631_6632 KIDINS220_ENST00000418530.1_3'UTR|KIDINS220_ENST00000473731.1_3'UTR|KIDINS220_ENST00000427284.1_3'UTR NM_020738.2 NP_065789.1 Q9ULH0 KDIS_HUMAN kinase D-interacting substrate, 220kDa NA NA NA activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976) cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234) PDZ domain binding (GO:0030165) NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 60 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) CACTTATATAGATATATATATA 0.317 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 121 136.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.83 AK025528 CCDS42650.1 2p24 2013-01-10 ENSG00000134313 ENSG00000134313 57498 "Ankyrin repeat domain containing" 29508 protein-coding gene gene with protein product "ankyrin repeat-rich membrane-spanning protein" 615759 NA 10998417, 10574462 Standard NM_020738 NM_020738 NA Approved ARMS uc002qzc.2 Q9ULH0 OTTHUMG00000151658 ENST00000256707.3:c.*1135->AT chr2.hg19:g.8869724_8869725dupAT 8 2 ref NA False 32 32 PASS 7 PASS ref->het 0 NA 72,74 19,19 28,27 1 1 A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42 True hg19 CCDS42650.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KIDINS220-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000323408.2 PASS NA None 121 True - AT ENST00000256707.3 ZNF513 130557 __UNKNOWN__ __UNKNOWN__ 2 27600281 27600282 __UNKNOWN__ 3'UTR INS - - C rs577733777|rs187524222 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:27600281_27600282insC ENST00000323703.6 - 0 1954_1955 ZNF513_ENST00000407879.1_3'UTR NM_144631.5 NP_653232.3 Q8N8E2 ZN513_HUMAN zinc finger protein 513 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212) endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|ovary(2) 17 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) GTCCATATGGGCCCCCCCGCCC 0.614 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 445 424.11 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.32 AL833946 CCDS1751.1, CCDS56114.1 2p23.3 2014-01-28 ENSG00000163795 ENSG00000163795 130557 "Zinc fingers, C2H2-type" 26498 protein-coding gene gene with protein product 613598 NA 12477932 Standard NM_144631 NM_001201459 NA Approved FLJ32203, RP58 uc002rkk.3 Q8N8E2 OTTHUMG00000097783 ENST00000323703.6:c.*131->G chr2.hg19:g.27600288_27600288dupC 8 10 ref NA False 153 132 PASS 7 PASS ref->het 0 NA 274,282 105,109 69,60 1 1 A8K3S5|B7WP71|Q3ZCU1|Q68CJ1|Q86UZ3|Q8NDL8|Q96ML3 True hg19 CCDS1751.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF513-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000215026.2 PASS NA None 445 True - C ENST00000323703.6 Unknown 0 __UNKNOWN__ __UNKNOWN__ 2 27917862 27917863 __UNKNOWN__ IGR INS - - T rs539063895 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:27917862_27917863insT NA SLC4A1AP (26 upstream) : AC074091.13 (10789 downstream) NA NA NA NA attttattttattttttttaag 0.366 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 165 190.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.91 NA NA NA NA NA chr2.hg19:g.27917870_27917870dupT 9 12 ref NA False 49 49 PASS 8 PASS ref->het 0 NA 77,80 27,27 56,54 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 165 True T NLRC4 58484 __UNKNOWN__ __UNKNOWN__ 2 32449823 32449824 __UNKNOWN__ Frame_Shift_Ins INS - - A LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:32449823_32449824insA ENST00000404025.2 - 10 3281_3282 c.2793_2794insT c.(2791-2796)tttggafs p.G932fs NLRC4_ENST00000402280.1_Frame_Shift_Ins_p.G932fs|NLRC4_ENST00000342905.6_Frame_Shift_Ins_p.G267fs|NLRC4_ENST00000360906.5_Frame_Shift_Ins_p.G932fs Q9NPP4 NLRC4_HUMAN NLR family, CARD domain containing 4 932 NA NA activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269) cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557) ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803) p.G932*(1)|p.G932R(1) breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2) 16 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208) GGGTTCTTTCCAAAAAATGCAC 0.327 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 2 Substitution - Missense(1)|Substitution - Nonsense(1) lung(1)|skin(1) 264 247.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 4.64 AF376061 CCDS33174.1 2p22-p21 2008-08-27 2006-12-08 2006-12-08 ENSG00000091106 ENSG00000091106 58484 "Nucleotide-binding domain and leucine rich repeat containing" 16412 protein-coding gene gene with protein product "nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4", "NOD-like receptor C4" 606831 "caspase recruitment domain family, member 12" CARD12 NA 11374873 Standard NM_021209 NM_021209 NA Approved CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN uc021vfq.1 Q9NPP4 OTTHUMG00000152107 ENST00000404025.2:c.2794dupT chr2.hg19:g.32449829_32449829dupA ENSP00000385090:p.Gly932fs 7 6 ref NA False 127 121 PASS 6 PASS ref->het 0 NA 159,161 59,63 42,36 1 1 A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83 True hg19 CCDS33174.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NLRC4-001 KNOWN non_canonical_other|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000325222.2 PASS NA None 264 True - A ENST00000404025.2 ARHGEF33 100271715 __UNKNOWN__ __UNKNOWN__ 2 39158428 39158428 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:39158428delT ENST00000409978.1 + 7 770 ARHGEF33_ENST00000398800.4_Intron|ARHGEF33_ENST00000536934.1_Intron A8MVX0 ARG33_HUMAN Rho guanine nucleotide exchange factor (GEF) 33 NA NA NA Rho guanyl-nucleotide exchange factor activity (GO:0005089) endometrium(3)|pancreas(1)|prostate(1) 5 TAATCAAGTATTTTTTTCCCA 0.393 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 146 145.8 NA NA 50 43 45 NA NA NA 2 NA NA NA 39158428 692 1591 2283 SO:0001627 intron_variant 0.24 CCDS46263.1, CCDS46263.2 2p22.1 2012-07-24 ENSG00000214694 ENSG00000214694 100271715 "Rho guanine nucleotide exchange factors" 37252 protein-coding gene gene with protein product NA NA Standard NM_001145451 NM_001145451 NA Approved uc021vgd.1 A8MVX0 OTTHUMG00000153540 ENST00000409978.1:c.505+36T>- chr2.hg19:g.39158428delT 6 8 ref NA False 35 35 PASS 7 PASS ref->het 0 NA 83,85 36,36 24,24 2 2 J3KPX2 True hg19 CCDS46263.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARHGEF33-001 PUTATIVE basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000331554.1 PASS NA None 146 True + T ENST00000409978.1 PREPL 9581 __UNKNOWN__ __UNKNOWN__ 2 44550553 44550553 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:44550553delA ENST00000409411.1 - 11 1694 PREPL_ENST00000409957.1_Intron|PREPL_ENST00000378520.3_Intron|PREPL_ENST00000260648.6_Intron|PREPL_ENST00000409936.1_Intron|PREPL_ENST00000410081.1_Intron|PREPL_ENST00000409272.1_Intron|PREPL_ENST00000378511.3_Intron|PREPL_ENST00000541738.1_Intron NM_001171613.1 NP_001165084.1 Q4J6C6 PPCEL_HUMAN prolyl endopeptidase-like NA NA NA cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794) serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008) p.?(2) breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2) 33 all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175) AAAGGTGCCTAAAAAAAAGGC 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 2 Unknown(2) lung(2) 201 196.61 NA NA 70 64 66 NA NA NA 2 NA NA NA 44550553 2203 4300 6503 SO:0001627 intron_variant 0.18 AB007896 CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1 2p22.1 2008-02-05 ENSG00000138078 ENSG00000138078 9581 30228 protein-coding gene gene with protein product 609557 NA 11524703 Standard NM_006036 NM_006036 NA Approved KIAA0436 uc002ruk.2 Q4J6C6 OTTHUMG00000152791 ENST00000409411.1:c.1480-3T>- chr2.hg19:g.44550553delA 7 8 ref NA False 149 96 PASS 8 PASS ref->het 0 NA 78,78 94,95 25,25 1 1 A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7 True hg19 CCDS54353.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PREPL-007 NOVEL alternative_5_UTR|not_organism_supported|basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000327899.6 PASS NA None 201 True - A ENST00000409411.1 C2orf73 129852 __UNKNOWN__ __UNKNOWN__ 2 54586086 54586086 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:54586086delT ENST00000398634.2 + 4 430 C2orf73_ENST00000405749.1_Intron|C2orf73_ENST00000491538.1_Intron NM_001100396.1 NP_001093866.1 Q8N5S3 CB073_HUMAN chromosome 2 open reading frame 73 NA NA NA breast(2) 2 TCACAAAATCTTTTTTTTAGT 0.274 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 76 77.36 NA NA 32 28 29 NA NA NA 2 NA NA NA 54586086 1772 4023 5795 SO:0001627 intron_variant 0 BC031669, AK097617 CCDS46285.1 2p16.2 2008-07-07 ENSG00000177994 ENSG00000177994 129852 26861 protein-coding gene gene with protein product NA NA 14702039 Standard NM_001100396 NM_001100396 NA Approved FLJ40298 uc002rxt.1 Q8N5S3 OTTHUMG00000151826 ENST00000398634.2:c.389-10T>- chr2.hg19:g.54586086delT 7 9 ref NA False 33 33 PASS 8 PASS ref->het 0 NA 57,57 15,15 3,3 1 1 A0AV79|A0AV81|Q8N7V4 True hg19 CCDS46285.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C2orf73-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000324075.2 PASS NA None 76 True + T ENST00000398634.2 COMMD1 150684 __UNKNOWN__ __UNKNOWN__ 2 62322900 62322900 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:62322900delA ENST00000311832.5 + 3 494 AC018462.2_ENST00000421323.1_RNA|COMMD1_ENST00000472729.1_Intron|AC018462.2_ENST00000425966.2_RNA NM_152516.2 NP_689729.1 Q8N668 COMD1_HUMAN copper metabolism (Murr1) domain containing 1 NA NA NA copper ion homeostasis (GO:0055070)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of protein ubiquitination (GO:0031398)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434) Cul2-RING ubiquitin ligase complex (GO:0031462)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634) copper ion binding (GO:0005507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803) large_intestine(1)|liver(2)|lung(5)|ovary(1) 9 Lung NSC(7;0.035)|all_lung(7;0.0691) LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934) TCCTGGAATTAAAAAAAATGG 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 61 60.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 BC022046 CCDS1869.1 2p15 2004-03-02 2004-02-13 2004-02-18 ENSG00000173163 ENSG00000173163 150684 23024 protein-coding gene gene with protein product "copper metabolism gene MURR1" 607238 "chromosome 2 open reading frame 5 (MURR1)" C2orf5 NA 9001233, 11809725 Standard NM_152516 NM_152516 NA Approved MURR1, MGC27155 uc002sbp.3 Q8N668 OTTHUMG00000129445 ENST00000311832.5:c.463-40066A>- chr2.hg19:g.62322900delA 7 8 ref NA False 33 33 PASS 8 PASS ref->het 0 NA 38,39 17,17 7,7 1 1 B4DFQ4|Q96GS0 True hg19 CCDS1869.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COMMD1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251607.2 PASS NA None 61 True + A ENST00000311832.5 SERTAD2 9792 __UNKNOWN__ __UNKNOWN__ 2 64862565 64862567 __UNKNOWN__ 3'UTR DEL GAG GAG - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:64862565_64862567delGAG ENST00000313349.3 - 0 1736_1738 NM_014755.2 NP_055570.1 Q14140 SRTD2_HUMAN SERTA domain containing 2 NA NA NA negative regulation of cell growth (GO:0030308)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleus (GO:0005634) transcription coactivator activity (GO:0003713) breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|skin(1) 12 CAACACTTACGAGGAGTAGTTAA 0.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 50 50.33 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.2 D50917 CCDS33210.1 2p15 2007-05-01 ENSG00000179833 ENSG00000179833 9792 30784 protein-coding gene gene with protein product "transcriptional regulator interacting with the PHS-bromodomain 2" NA NA 8590280, 11331592 Standard NM_014755 NM_014755 NA Approved TRIP-Br2, KIAA0127, Sei-2 uc002sde.2 Q14140 OTTHUMG00000152678 ENST00000313349.3:c.*496CTC>- chr2.hg19:g.64862568_64862570delGAG 1 3 ref NA False 35 35 PASS 2 PASS ref->het 0 NA 32,32 12,12 7,7 1 1 Q53TS2 True hg19 CCDS33210.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SERTAD2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000327322.2 PASS NA None 50 True - GAG ENST00000313349.3 FBXO48 554251 __UNKNOWN__ __UNKNOWN__ 2 68691329 68691329 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:68691329delT ENST00000377957.3 - 0 887 NM_001024680.1 NP_001019851.1 Q5FWF7 FBX48_HUMAN F-box protein 48 NA NA NA endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1) 4 AGATTTGTGATTTTTTTTCCC 0.353 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 525 512.29 NA NA 161 163 162 NA NA NA 2 NA NA NA 68691329 2203 4300 6503 SO:0001624 3_prime_UTR_variant 0.93 BC089423 CCDS33213.1 2p13.3 2011-03-09 ENSG00000204923 ENSG00000204923 554251 "F-boxes / "other"" 33857 protein-coding gene gene with protein product NA NA Standard NM_001024680 XM_005264407 NA Approved uc002seo.3 Q5FWF7 OTTHUMG00000152585 ENST00000377957.3:c.*12A>- chr2.hg19:g.68691329delT 7 8 ref NA False 278 207 PASS 8 PASS ref->het 0 NA 363,372 109,110 58,54 1 1 True hg19 CCDS33213.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FBXO48-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000326900.2 PASS NA None 525 True - T ENST00000377957.3 CNNM4 26504 __UNKNOWN__ __UNKNOWN__ 2 97475532 97475532 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:97475532delT ENST00000377075.2 + 0 2704 NM_020184.3 NP_064569.3 Q6P4Q7 CNNM4_HUMAN cyclin and CBS domain divalent metal cation transport mediator 4 NA NA NA biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) adenyl nucleotide binding (GO:0030554) breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2) 20 GGCTCATCACTTTTTTTTAAA 0.388 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 269 256.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.96 AB046812 CCDS2024.2 2q11.2 2014-08-08 2014-08-07 ENSG00000158158 ENSG00000158158 26504 105 protein-coding gene gene with protein product 607805 "cyclin M4" ACDP4 NA 21393841, 24194943 Standard NM_020184 XM_005263914 NA Approved KIAA1592 uc002swx.3 Q6P4Q7 OTTHUMG00000130532 ENST00000377075.2:c.*278T>- chr2.hg19:g.97475532delT 7 8 ref NA False 68 68 PASS 8 PASS ref->het 0 NA 175,177 61,62 33,30 1 1 B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1 True hg19 CCDS2024.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CNNM4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252954.1 PASS NA None 269 True + T ENST00000377075.2 FAM178B 51252 __UNKNOWN__ __UNKNOWN__ 2 97636577 97636577 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:97636577delA ENST00000490605.2 - 4 843 FAM178B_ENST00000327896.3_Intron|FAM178B_ENST00000417561.3_Intron Q8IXR5 F178B_HUMAN family with sequence similarity 178, member B NA NA NA large_intestine(1)|ovary(1) 2 GAGAAAAAAGAAAAAAAACTA 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 139 140.28 NA NA 29 31 30 NA NA NA 2 NA NA NA 97636577 692 1591 2283 SO:0001627 intron_variant 1.24 AF151068, BC039488 CCDS33252.1, CCDS46366.1, CCDS46366.2 2q11.2 2008-08-08 ENSG00000168754 ENSG00000168754 51252 28036 protein-coding gene gene with protein product NA NA 11042152 Standard NM_016490 NM_001122646 NA Approved LOC51252 uc002sxl.4 Q8IXR5 OTTHUMG00000155257 ENST00000490605.2:c.565-63T>- chr2.hg19:g.97636577delA 7 14 ref NA False 35 35 PASS 8 PASS ref->het 0 NA 83,85 31,31 24,22 1 1 A8MXN2|E9PD86|Q8IUY0|Q9P0P4 True hg19 CCDS46366.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM178B-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000339494.2 PASS NA None 139 True - A ENST00000490605.2 LIPT1 51601 __UNKNOWN__ __UNKNOWN__ 2 99778781 99778781 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:99778781delA ENST00000393473.2 + 3 585 c.361delA c.(361-363)aaafs p.K123fs MRPL30_ENST00000410042.1_Intron|LIPT1_ENST00000393474.3_Frame_Shift_Del_p.K123fs|LIPT1_ENST00000393477.3_Frame_Shift_Del_p.K123fs|LIPT1_ENST00000340066.1_Frame_Shift_Del_p.K123fs|LIPT1_ENST00000393471.2_Frame_Shift_Del_p.K123fs NM_001204830.1|NM_015929.3 NP_001191759.1|NP_057013.1 Q9Y234 LIPT_HUMAN lipoyltransferase 1 123 BPL/LPL catalytic. {ECO:0000255|PROSITE- ProRule:PRU01067}. NA NA cellular protein modification process (GO:0006464)|lipid metabolic process (GO:0006629)|protein lipoylation (GO:0009249) mitochondrion (GO:0005739) transferase activity, transferring acyl groups (GO:0016746) large_intestine(6)|lung(1) 7 Lipoic Acid(DB00166) CTTTACAACCAAAAAAAAGTA 0.388 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(84;665 1268 21657 25485 30647) PASS NA NA NA 0 390 423.04 NA NA 47 46 46 NA NA NA 2 NA NA NA 99778781 2203 4300 6503 SO:0001589 frameshift_variant 0.9 AB017566 CCDS2039.1 2q11.2 2010-11-25 ENSG00000144182 ENSG00000144182 51601 2.3.1.181 29569 protein-coding gene gene with protein product 610284 NA 10103005 Standard NM_015929 NM_145197 NA Approved MGC12290, MGC13378 uc002szq.4 Q9Y234 OTTHUMG00000130640 ENST00000393473.2:c.361delA chr2.hg19:g.99778781delA ENSP00000377115:p.Lys123fs 7 8 ref NA False 36 36 PASS 8 PASS ref->het 0 NA 249,262 70,73 70,63 1 1 Q4ZFZ1 True hg19 CCDS2039.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LIPT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253128.1 PASS NA None 390 True + A ENST00000393473.2 MAP3K2 10746 __UNKNOWN__ __UNKNOWN__ 2 128096511 128096511 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:128096511delT ENST00000409947.1 - 3 402 c.120delA c.(118-120)aaafs p.K40fs MAP3K2_ENST00000344908.5_Frame_Shift_Del_p.K40fs Q9Y2U5 M3K2_HUMAN mitogen-activated protein kinase kinase kinase 2 40 NA NA activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468) cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634) ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674) central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2) 7 Colorectal(110;0.1) BRCA - Breast invasive adenocarcinoma(221;0.0706) Bosutinib(DB06616) TAAATACCTGTTTTTTTGGTG 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 130 136.35 NA NA 63 55 57 NA NA NA 2 NA NA NA 128096511 1799 4061 5860 SO:0001589 frameshift_variant 0.39 AF111105 CCDS46404.1 2q21.1 2011-06-09 ENSG00000169967 ENSG00000169967 10746 "Mitogen-activated protein kinase cascade / Kinase kinase kinases" 6854 protein-coding gene gene with protein product "MAP/ERK kinase kinase 2" 609487 MEKK2 NA 8621389, 10085062 Standard NM_006609 NM_006609 NA Approved MEKK2B uc002toj.2 Q9Y2U5 OTTHUMG00000153397 ENST00000409947.1:c.120delA chr2.hg19:g.128096511delT ENSP00000387246:p.Lys40fs 6 8 ref NA False 54 54 PASS 7 PASS ref->het 0 NA 94,96 25,25 14,12 1 1 B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3 True hg19 CCDS46404.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAP3K2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000331014.1 PASS NA None 130 True - T ENST00000409947.1 CCDC115 84317 __UNKNOWN__ __UNKNOWN__ 2 131095908 131095908 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:131095908delA ENST00000259229.2 - 0 1551 NM_032357.2 NP_115733.2 Q96NT0 CC115_HUMAN coiled-coil domain containing 115 NA NA NA endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020) central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1) 7 Colorectal(110;0.1) ataaaaagtcaaaaaaaataa 0.299 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 204 214.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AK054693 CCDS2159.1 2q21.1 2010-12-24 ENSG00000136710 ENSG00000136710 84317 28178 protein-coding gene gene with protein product 613734 NA 21118521 Standard NM_032357 XM_005263825 NA Approved MGC12981, FLJ30131, ccp1 uc002tqy.1 Q96NT0 OTTHUMG00000131631 ENST00000259229.2:c.*785T>- chr2.hg19:g.131095908delA 7 10 ref NA False 67 66 PASS 8 PASS ref->het 0 NA 118,120 57,57 32,32 1 1 B4DJ47|Q9BR88 True hg19 CCDS2159.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCDC115-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254524.2 PASS NA None 204 True - A ENST00000259229.2 PKP4 8502 __UNKNOWN__ __UNKNOWN__ 2 159481373 159481374 __UNKNOWN__ Intron INS - - C rs374426398 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:159481373_159481374insC ENST00000389759.3 + 7 715 PKP4_ENST00000389757.3_Intron NM_003628.3 NP_003619.2 Q99569 PKP4_HUMAN plakophilin 4 NA NA NA cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337) cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922) breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1) 61 TTCTCTTTTTTCCCCCCCTTTC 0.426 NA NA NA HNSCC(62;0.18) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 357 348.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.81 X81889 CCDS33305.1, CCDS33306.1 2q24.1 2013-02-14 ENSG00000144283 ENSG00000144283 8502 "Armadillo repeat containing" 9026 protein-coding gene gene with protein product 604276 NA 9342840, 8937994 Standard NM_003628 NA Approved p0071 uc002tzv.3 Q99569 OTTHUMG00000153969 ENST00000389759.3:c.604-16->C chr2.hg19:g.159481380_159481380dupC 8 7 ref NA False 69 69 PASS 7 PASS ref->het 0 NA 235,242 74,76 58,55 1 1 Q86W91 True hg19 CCDS33305.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PKP4-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000333250.1 PASS NA None 357 True + C ENST00000389759.3 NOSTRIN 115677 __UNKNOWN__ __UNKNOWN__ 2 169684652 169684652 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:169684652delT ENST00000458381.2 + 8 955 NOSTRIN_ENST00000397209.2_Intron|NOSTRIN_ENST00000444448.2_Intron|NOSTRIN_ENST00000445023.2_Intron|NOSTRIN_ENST00000317647.7_Intron|NOSTRIN_ENST00000397206.2_Intron|NOSTRIN_ENST00000421711.2_Intron NM_001171631.1 NP_001165102.1 Q8IVI9 NOSTN_HUMAN nitric oxide synthase trafficking NA NA NA endocytosis (GO:0006897)|negative regulation of transcription, DNA-templated (GO:0045892)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281) cytoskeleton (GO:0005856)|endocytic vesicle membrane (GO:0030666)|nucleus (GO:0005634)|plasma membrane (GO:0005886) DNA binding (GO:0003677) kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1) 9 TGTTCCCCACTTTTTTTTGCC 0.483 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 304 316.95 NA NA 184 175 178 NA NA NA 2 NA NA NA 169684652 1933 4154 6087 SO:0001627 intron_variant 1.45 AJ532842 CCDS42771.1, CCDS42772.1, CCDS54415.1, CCDS54416.1 2q31.1 2013-08-05 2013-08-05 ENSG00000163072 ENSG00000163072 115677 20203 protein-coding gene gene with protein product 607496 "nitric oxide synthase trafficker" NA 12446846 Standard NM_052946 NM_001171631 NA Approved MGC20702 uc002ueg.3 Q8IVI9 OTTHUMG00000153990 ENST00000458381.2:c.198-16T>- chr2.hg19:g.169684652delT 7 8 ref NA False 49 49 PASS 8 PASS ref->het 0 NA 185,192 71,71 47,42 2 2 A8K2I9|B3KSF5|E7EPT9|Q27HG3|Q53S62|Q96CJ9 True hg19 CCDS54415.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NOSTRIN-002 NOVEL alternative_5_UTR|basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000333357.3 PASS NA None 304 True + T ENST00000458381.2 PPIG 9360 __UNKNOWN__ __UNKNOWN__ 2 170497512 170497512 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:170497512delT ENST00000260970.3 + 0 5964 NM_004792.2 NP_004783.2 Q13427 PPIG_HUMAN peptidylprolyl isomerase G (cyclophilin G) NA NA NA protein folding (GO:0006457)|RNA splicing (GO:0008380) cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822) NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1) 43 L-Proline(DB00172) TGTTTCTGACTTTTTTTCTTT 0.358 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 118 123 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 X99717 CCDS2235.1 2q31.1 2010-07-23 2006-01-12 ENSG00000138398 ENSG00000138398 9360 6.1.1.16 14650 protein-coding gene gene with protein product "SR-related CTD-associated factor 10" 606093 "peptidyl-prolyl isomerase G (cyclophilin G)" NA 8973360, 9153302 Standard NM_004792 NA Approved CARS-Cyp, SRCyp, SCAF10 uc002uez.3 Q13427 OTTHUMG00000132206 ENST00000260970.3:c.*3479T>- chr2.hg19:g.170497512delT 6 10 ref NA False 31 31 PASS 7 PASS ref->het 0 NA 87,87 22,22 9,9 1 1 D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9 True hg19 CCDS2235.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPIG-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255264.2 PASS NA None 118 True + T ENST00000260970.3 FKBP7 51661 __UNKNOWN__ __UNKNOWN__ 2 179328660 179328674 __UNKNOWN__ 3'UTR DEL AGGGAAGGCGATGAA AGGGAAGGCGATGAA - rs573334034 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:179328660_179328674delAGGGAAGGCGATGAA ENST00000424785.2 - 0 2550_2564 NM_001135212.1|NM_181342.2 NP_001128684.1|NP_851939.1 Q9Y680 FKBP7_HUMAN FK506 binding protein 7 NA NA NA chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413) endoplasmic reticulum membrane (GO:0005789) calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755) kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1) 8 OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564) GGTTTTTTTGAGGGAAGGCGATGAAAGAGTAAATG 0.316 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Melanoma(26;682 927 5286 17599 46613) PASS NA NA NA 0 291 287.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.35 AF092137 CCDS2280.1, CCDS46462.1 2q31.2 2013-01-10 2001-11-28 ENSG00000079150 ENSG00000079150 51661 "EF-hand domain containing" 3723 protein-coding gene gene with protein product 607062 "FK506-binding protein 7" NA 9806833 Standard NM_181342 NM_181342 NA Approved FKBP23 uc002umk.3 Q9Y680 OTTHUMG00000132577 ENST00000424785.2:c.*1837TTCATCGCCTTCCCT>- chr2.hg19:g.179328660_179328674delAGGGAAGGCGATGAA 0 7 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 274,277 28,29 28,27 1 1 Q4ZG70|Q6V3B2|Q86U65|Q96DA4|Q9Y6B0 True hg19 CCDS2280.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FKBP7-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000255783.1 PASS NA None 291 True - AGGGAAGGCGATGAA ENST00000424785.2 NUP35 129401 __UNKNOWN__ __UNKNOWN__ 2 184025805 184025805 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:184025805delA ENST00000295119.4 + 9 1030 c.927delA c.(925-927)ccafs p.P309fs NUP35_ENST00000409798.1_Frame_Shift_Del_p.P292fs|NUP35_ENST00000541912.1_Frame_Shift_Del_p.P174fs NM_138285.3 NP_612142.2 Q8NFH5 NUP53_HUMAN nucleoporin 35kDa 309 NA NA carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032) intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|plasma membrane (GO:0005886) breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2) 8 GACAAACGCCAAAAAAAGATG 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 141 131.48 NA NA 81 76 77 NA NA NA 2 NA NA NA 184025805 2203 4300 6503 SO:0001589 frameshift_variant 0.98 AF514993 CCDS2290.1, CCDS74614.1 2q32 2008-02-05 ENSG00000163002 ENSG00000163002 129401 29797 protein-coding gene gene with protein product 608140 NA Standard NM_138285 XM_005246284 NA Approved MP44 uc002upf.3 Q8NFH5 OTTHUMG00000132621 ENST00000295119.4:c.927delA chr2.hg19:g.184025805delA ENSP00000295119:p.Pro309fs 6 8 ref NA False 30 30 PASS 7 PASS ref->het 0 NA 102,104 23,24 16,13 1 1 B4DP57|B4DYB4|Q4ZFZ9|Q53S95|Q8TDJ1 True hg19 CCDS2290.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NUP35-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255865.1 PASS NA None 141 True + A ENST00000295119.4 FSIP2 401024 __UNKNOWN__ __UNKNOWN__ 2 186671156 186671157 __UNKNOWN__ Frame_Shift_Ins INS - - C LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:186671156_186671157insC ENST00000424728.1 + 17 17123_17124 c.17123_17124insC c.(17122-17127)agccccfs p.SP5708fs FSIP2_ENST00000343098.5_Frame_Shift_Ins_p.SP5797fs Q5CZC0 FSIP2_HUMAN fibrous sheath interacting protein 2 5708 NA NA NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2) 69 TATGACCAAAGCCCCCCAGGTG 0.337 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 228 221.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 AK092099 CCDS54426.1 2q32.1 2010-06-18 ENSG00000188738 ENSG00000188738 401024 21675 protein-coding gene gene with protein product 615796 NA 14702039 Standard NM_173651 NM_173651 NA Approved FLJ34780 uc002upl.3 Q5CZC0 OTTHUMG00000153874 ENST00000424728.1:c.17129dupC chr2.hg19:g.186671162_186671162dupC ENSP00000401306:p.Ser5708fs 7 6 ref NA False 51 51 PASS 6 PASS ref->het 0 NA 165,167 39,39 25,25 1 1 Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FSIP2-001 KNOWN basic protein_coding NA protein_coding OTTHUMT00000332778.3 PASS NA None 228 True + C ENST00000424728.1 SLC40A1 30061 __UNKNOWN__ __UNKNOWN__ 2 190426402 190426402 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:190426402delT ENST00000261024.2 - 0 2344 NM_014585.5 NP_055400.1 Q9NP59 S40A1_HUMAN solute carrier family 40 (iron-regulated transporter), member 1 NA NA NA anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085) basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021) iron ion transmembrane transporter activity (GO:0005381) endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 14 OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491) TCTTTTCCAATTTTTTTTCCA 0.338 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 226 223.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.01 AF215636 CCDS2299.1 2q32 2014-09-17 2003-06-04 2003-06-05 ENSG00000138449 ENSG00000138449 30061 "Solute carriers" 10909 protein-coding gene gene with protein product "ferroportin 1" 604653 "solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3" SLC11A3 NA 10828623 Standard NM_014585 NA Approved MTP1, IREG1, FPN1, HFE4 uc002uqp.4 Q9NP59 OTTHUMG00000132662 ENST00000261024.2:c.*202A>- chr2.hg19:g.190426402delT 7 8 ref NA False 38 38 PASS 8 PASS ref->het 0 NA 167,169 32,34 29,27 1 1 Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0 True hg19 CCDS2299.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC40A1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255916.2 PASS NA None 226 True - T ENST00000261024.2 TMEM194B 100131211 __UNKNOWN__ __UNKNOWN__ 2 191370610 191370610 __UNKNOWN__ 3'UTR DEL G G - rs189441647 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:191370610delG ENST00000409150.3 - 0 4625 NM_001142645.1 NP_001136117.1 A6NFY4 T194B_HUMAN transmembrane protein 194B NA NA NA integral component of membrane (GO:0016021) NA ccactggggtggggggtggca 0.473 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 228 237.65 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.33 CCDS46476.1 2q32.2 2008-06-10 ENSG00000189362 ENSG00000189362 100131211 33700 protein-coding gene gene with protein product NA NA Standard XM_001723498 NM_001142645 NA Approved uc010zgf.2 A6NFY4 OTTHUMG00000154454 ENST00000409150.3:c.*3305C>- chr2.hg19:g.191370610delG 5 10 ref NA False 58 58 PASS 6 PASS ref->het 0 NA 143,149 47,47 37,34 2 2 B4DYG6 True hg19 CCDS46476.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM194B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000335299.1 PASS NA None 228 True - G ENST00000409150.3 HECW2 57520 __UNKNOWN__ __UNKNOWN__ 2 197064609 197064609 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:197064609delA ENST00000409111.1 - 0 6057 HECW2_ENST00000260983.3_3'UTR Q9P2P5 HECW2_HUMAN HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2 NA NA NA protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787) cytoplasm (GO:0005737)|nucleus (GO:0005634) ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842) biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2) 113 TGCATCAGTGAAAATGCAGGC 0.338 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 179 166.62 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.12 AL390186 CCDS33354.1 2q32.3 2004-12-13 ENSG00000138411 ENSG00000138411 57520 29853 protein-coding gene gene with protein product NA NA 10718198, 12890487 Standard NM_020760 NM_020760 NA Approved KIAA1301, NEDL2 uc002utm.1 Q9P2P5 OTTHUMG00000154435 ENST00000409111.1:c.*1392T>- chr2.hg19:g.197064609delA 3 4 ref NA False 50 50 PASS 4 PASS ref->het 0 NA 131,132 32,32 14,14 2 2 B8ZZB4|Q17RT5|Q68DF8|Q9NPS9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HECW2-002 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000335314.2 PASS NA None 179 True - A ENST00000409111.1 NOP58 51602 __UNKNOWN__ __UNKNOWN__ 2 203168133 203168133 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:203168133delA ENST00000264279.5 + 15 1790 c.1564delA c.(1564-1566)aaafs p.K524fs NM_015934.3 NP_057018.1 Q9Y2X3 NOP58_HUMAN NOP58 ribonucleoprotein 524 Lys-rich. NA NA cell growth (GO:0016049)|rRNA processing (GO:0006364)|snRNP protein import into nucleus (GO:0006608) box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732) poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515) breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2) 16 gaagaaaaagaaaaaaaagag 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 457 481.28 NA NA 46 52 50 NA NA NA 2 NA NA NA 203168133 2193 4297 6490 SO:0001589 frameshift_variant 1.33 CCDS2353.1 2q33.1 2012-12-10 2012-12-10 ENSG00000055044 ENSG00000055044 51602 29926 protein-coding gene gene with protein product NA "NOP58 ribonucleoprotein homolog (yeast)" NA 10606270, 10925205 Standard NM_015934 NM_015934 NA Approved NOP5, HSPC120 uc002uzb.3 Q9Y2X3 OTTHUMG00000132840 ENST00000264279.5:c.1564delA chr2.hg19:g.203168133delA ENSP00000264279:p.Lys524fs 7 13 ref NA False 92 92 PASS 8 PASS ref->het 0 NA 314,333 73,73 81,75 2 2 Q53SA4|Q6PK08|Q9P036|Q9UFN3 True hg19 CCDS2353.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NOP58-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256313.2 PASS NA None 457 True + A ENST00000264279.5 BMPR2 659 __UNKNOWN__ __UNKNOWN__ 2 203426177 203426177 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:203426177delT ENST00000374574.2 + 0 3386 BMPR2_ENST00000374580.4_3'UTR Q13873 BMPR2_HUMAN bone morphogenetic protein receptor, type II (serine/threonine kinase) NA NA NA activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841) apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886) activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024) autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2) 42 CCTCTGCATGTTTTTTTTAAA 0.244 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 188 184.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.07 Z48923 CCDS33361.1 2q33-q34 2014-09-17 ENSG00000204217 ENSG00000204217 659 1078 protein-coding gene gene with protein product 600799 "primary pulmonary hypertension 1" PPH1 NA 7791754 Standard NM_001204 NM_001204 NA Approved BRK-3, T-ALK, BMPR3, BMPR-II uc002uzf.4 Q13873 OTTHUMG00000133617 ENST00000374574.2:c.*1752T>- chr2.hg19:g.203426177delT 7 9 ref NA False 47 47 PASS 8 PASS ref->het 0 NA 136,139 30,31 22,21 1 1 Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BMPR2-002 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000257744.1 PASS NA None 188 True + T ENST00000374574.2 IKZF2 22807 __UNKNOWN__ __UNKNOWN__ 2 214014889 214014889 __UNKNOWN__ 5'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:214014889delA ENST00000434687.1 - 0 273 IKZF2_ENST00000457361.1_Intron|IKZF2_ENST00000342002.2_Intron|IKZF2_ENST00000442445.1_Intron|IKZF2_ENST00000374319.4_5'UTR Q9UKS7 IKZF2_HUMAN IKAROS family zinc finger 2 (Helios) NA NA NA positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 23 Esophageal squamous(248;0.0559)|Renal(323;0.218) UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792) TCCTTTGATTAAAAAAGATTC 0.393 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 298 305.15 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.09 AF130863 CCDS2395.1, CCDS46507.1 2q13.1 2013-01-08 2006-08-25 2006-08-25 ENSG00000030419 ENSG00000030419 22807 "Zinc fingers, C2H2-type", "IKAROS zinc fingers" 13177 protein-coding gene gene with protein product 606234 "zinc finger protein, subfamily 1A, 2 (Helios)" ZNFN1A2 NA 9512513, 9560339 Standard NM_016260 NM_001079526 NA Approved Helios uc002vem.3 Q9UKS7 OTTHUMG00000133005 ENST00000434687.1:c.-37T>- chr2.hg19:g.214014889delA 5 7 ref NA False 104 104 PASS 6 PASS ref->het 0 NA 209,210 59,60 36,34 1 1 Q53YJ5|Q6PQC5|Q6PQC6|Q6PQC7|Q6PQC8|Q6PQD0|Q6PQD1|Q8N6S1 True hg19 CCDS2395.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IKZF2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256593.3 PASS NA None 298 True - A ENST00000434687.1 CCDC108 255101 __UNKNOWN__ __UNKNOWN__ 2 219892999 219892999 __UNKNOWN__ Frame_Shift_Del DEL G G - rs375880549 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:219892999delG ENST00000341552.5 - 12 1858 c.1775delC c.(1774-1776)cctfs p.P592fs CCDC108_ENST00000409865.3_Frame_Shift_Del_p.P581fs|CCDC108_ENST00000441968.1_Frame_Shift_Del_p.P592fs|CCDC108_ENST00000453220.1_Frame_Shift_Del_p.P592fs|CCDC108_ENST00000410037.1_Frame_Shift_Del_p.P527fs NM_194302.2 NP_919278.2 Q6ZU64 CC108_HUMAN coiled-coil domain containing 108 592 NA NA integral component of membrane (GO:0016021) poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198) autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 80 Renal(207;0.0915) Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942) CAGGATGTCAGGGGGGTAGAG 0.627 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 162 168.18 NA NA 85 89 87 NA NA NA 2 NA NA NA 219892999 2203 4300 6503 SO:0001589 frameshift_variant 1.5 NM_194302, AL833882, AK127189 CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1 2q35 2008-02-05 ENSG00000181378 ENSG00000181378 255101 25325 protein-coding gene gene with protein product 614270 NA 12477932 Standard NM_194302 NM_194302 NA Approved DKFZp434O0527, MGC35338 uc002vjl.2 Q6ZU64 OTTHUMG00000133013 ENST00000341552.5:c.1775delC chr2.hg19:g.219892999delG ENSP00000340776:p.Pro592fs 5 6 ref NA False 30 30 PASS 6 PASS ref->het 0 NA 109,117 28,29 23,15 1 1 A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3 True hg19 CCDS2430.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCDC108-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000256598.4 PASS NA None 162 True - G ENST00000341552.5 UGT1A3 54659 __UNKNOWN__ __UNKNOWN__ 2 234638282 234638283 __UNKNOWN__ Frame_Shift_Ins INS - - T rs45586035|rs544798573 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:234638282_234638283insT ENST00000482026.1 + 1 529_530 c.510_511insT c.(511-513)tttfs p.F171fs UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A1_ENST00000609767.1_Frame_Shift_Ins_p.F171fs|UGT1A5_ENST00000373414.3_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A4_ENST00000373409.3_Intron P35503 UD13_HUMAN UDP glucuronosyltransferase 1 family, polypeptide A3 171 NA NA cellular glucuronidation (GO:0052695)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021) enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|UDP-glycosyltransferase activity (GO:0008194) breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1) 46 Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128) Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599) Atorvastatin(DB01076)|Candesartan(DB00796)|Cyproheptadine(DB00434)|Eltrombopag(DB06210)|Etodolac(DB00749)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Irbesartan(DB01029)|Lamotrigine(DB00555)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Pitavastatin(DB08860)|Simvastatin(DB00641)|Valproic Acid(DB00313) TTCCTACTGTGTTTTTTTTGAG 0.441 NA NA NA TTTTTtTT|TTTTTTTT|TTTTTTTTT|insertion 31 0.0061901 0.0227 0.0014 5008 , , NA 22319 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 298 280.68 NA ,,,,,,,, 49,4217 NA 0,49,2084 NA NA NA NA ,,,,,,,, 0.1 1 dbSNP_127 187 5,8249 NA 0,5,4122 no intron,intron,frameshift,intron,intron,intron,intron,intron,intron UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A3 NM_205862.1,NM_021027.2,NM_019093.2,NM_019078.1,NM_019077.2,NM_019076.4,NM_019075.2,NM_007120.2,NM_001072.3 ,,,,,,,, 0,54,6206 A1A1,A1R,RR NA 0.0606,1.1486,0.4313 ,,,,,,,, ,,,,,,,, NA 54,12466 NA NA NA SO:0001589 frameshift_variant 1.44 M84127 CCDS2509.1 2q37 2010-03-05 2005-07-20 ENSG00000243135 ENSG00000243135 54659 "UDP glucuronosyltransferases" 12535 other complex locus constituent 606428 "UDP glycosyltransferase 1 family, polypeptide A3" NA 9295054, 1339448, 11434514 Standard NM_019093 NM_019093 NA Approved UGT1C P35503 OTTHUMG00000059118 ENST00000482026.1:c.518dupT chr2.hg19:g.234638290_234638290dupT ENSP00000418532:p.Phe171fs 9 9 ref NA False 31 31 PASS 8 PASS ref->het 0 NA 189,190 51,51 54,54 1 1 B8K287 True hg19 CCDS2509.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UGT1A3-001 KNOWN basic|appris_principal|readthrough_transcript|CCDS protein_coding NA protein_coding OTTHUMT00000130983.1 PASS NA None 298 True + T ENST00000482026.1 CXXC11 0 __UNKNOWN__ __UNKNOWN__ 2 242814374 242814375 __UNKNOWN__ Frame_Shift_Ins INS - - C rs35989328 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:242814374_242814375insC ENST00000343216.3 + 2 695_696 c.667_668insC c.(667-669)gccfs p.A223fs NM_173821.2 NP_776182.2 NA NA NA NA TGAGGGCCCTGCCCCCCCTGCG 0.658 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 324 333.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.9 NA NA NA NA NA ENST00000343216.3:c.674dupC chr2.hg19:g.242814381_242814381dupC ENSP00000345374:p.Ala223fs 8 7 ref NA False 38 38 PASS 7 PASS ref->het 0 NA 229,239 41,45 57,45 1 1 True hg19 CCDS42843.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CXXC11-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000322310.1 PASS NA None 324 True + C ENST00000343216.3 SLC6A1 6529 __UNKNOWN__ __UNKNOWN__ 3 11080606 11080606 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:11080606delT ENST00000287766.4 + 0 4175 NM_003042.3 NP_003033.3 P30531 SC6A1_HUMAN solute carrier family 6 (neurotransmitter transporter), member 1 NA NA NA gamma-aminobutyric acid import (GO:0051939)|learning (GO:0007612)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neurotransmitter secretion (GO:0007269)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|protein homooligomerization (GO:0051260)|response to calcium ion (GO:0051592)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to lead ion (GO:0010288)|response to purine-containing compound (GO:0014074)|response to sucrose (GO:0009744)|response to toxic substance (GO:0009636)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810) axon (GO:0030424)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886) gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328) breast(1)|endometrium(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(1) 26 Ovarian(110;0.0392) OV - Ovarian serous cystadenocarcinoma(96;0.00099) Clobazam(DB00349)|Tiagabine(DB00906) TATGTGTAACTTTTTTTTAGT 0.328 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 120 122.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.02 CCDS2603.1 3p25.3 2013-07-19 2013-07-19 ENSG00000157103 ENSG00000157103 6529 "Solute carriers" 11042 protein-coding gene gene with protein product "GABA transporter 1" 137165 "solute carrier family 6 (neurotransmitter transporter, GABA), member 1" NA 8530094 Standard NM_003042 NM_003042 NA Approved GAT1, GABATR, GABATHG uc010hdq.3 P30531 OTTHUMG00000044208 ENST00000287766.4:c.*1954T>- chr3.hg19:g.11080606delT 7 8 ref NA False 33 33 PASS 8 PASS ref->het 0 NA 83,83 22,22 13,14 1 1 Q8N4K8 True hg19 CCDS2603.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC6A1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000102767.2 PASS NA None 120 True + T ENST00000287766.4 HACL1 26061 __UNKNOWN__ __UNKNOWN__ 3 15642796 15642797 __UNKNOWN__ Intron INS - - C LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:15642796_15642797insC ENST00000451445.2 - 1 205 HACL1_ENST00000457447.2_Intron|HACL1_ENST00000321169.5_Intron|HACL1_ENST00000435217.2_Intron|HACL1_ENST00000456194.2_Intron NM_001284416.1 NP_001271345.1 Q9UJ83 HACL1_HUMAN 2-hydroxyacyl-CoA lyase 1 NA NA NA cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281) peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777) carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976) NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1) 16 AAACCCCCCGACCCCCATCGCC 0.574 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 94 119.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.23 AJ131753 CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1 3p24.3 2009-01-14 2006-05-16 2006-05-16 ENSG00000131373 ENSG00000131373 26061 4.1.-.- 17856 protein-coding gene gene with protein product 604300 "2-hydroxyphytanoyl-CoA lyase" HPCL NA 10468558, 15644336 Standard NM_012260 NM_001284416 NA Approved 2-HPCL, PHYH2 uc003caf.3 Q9UJ83 OTTHUMG00000129862 ENST00000451445.2:c.81+92->G chr3.hg19:g.15642801_15642801dupC 6 5 ref NA False 42 42 PASS 5 PASS ref->het 0 NA 61,65 19,21 18,14 1 1 B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HACL1-002 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000342872.1 PASS NA None 94 True - C ENST00000451445.2 MLH1 4292 __UNKNOWN__ __UNKNOWN__ 3 37050358 37050362 __UNKNOWN__ 5'UTR DEL AAGTG AAGTG - rs63749944 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:37050358_37050362delAAGTG ENST00000458205.2 + 0 651_655 MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000539477.1_Intron|MLH1_ENST00000435176.1_Frame_Shift_Del_p.SE72fs|MLH1_ENST00000231790.2_Frame_Shift_Del_p.SE170fs|MLH1_ENST00000492474.1_3'UTR NM_001258274.1 NP_001245203.1 P40692 MLH1_HUMAN mutL homolog 1 NA NA NA ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129) chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795) ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137) p.0?(1) NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2) 127 TAAAAAATCCAAGTGAAGAATATGG 0.371 NA 1 "D, Mis, N, F, S" "colorectal, endometrial, ovarian, CNS" "colorectal, endometrial, ovarian, CNS" NA Mismatch excision repair (MMR) Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS yes Rec yes "Hereditary non-polyposis colorectal cancer, Turcot syndrome" 3 3p21.3 4292 E.coli MutL homolog gene NA "E, O" 1 Whole gene deletion(1) ovary(1) 168 164.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.26 Familial Cancer Database Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III U07418 CCDS2663.1, CCDS54562.1, CCDS54563.1 3p22.3 2014-09-17 2013-09-12 ENSG00000076242 ENSG00000076242 4292 7127 protein-coding gene gene with protein product 120436 "mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)", "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)" COCA2 NA 7903889 Standard NM_000249 NM_000249 NA Approved HNPCC, FCC2, HNPCC2 uc003cgl.3 P40692 OTTHUMG00000130797 ENST00000458205.2:c.-213AAGTG>- chr3.hg19:g.37050358_37050362delAAGTG 0 4 ref NA False 354 136 PASS 1 PASS ref->het 0 NA 64,65 89,92 20,18 1 1 B4DI13|B4DQ11|E9PCU2 True hg19 CCDS54563.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MLH1-004 PUTATIVE basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000341984.3 PASS NA None 168 True + AAGTG ENST00000458205.2 COL7A1 1294 __UNKNOWN__ __UNKNOWN__ 3 48601617 48601617 __UNKNOWN__ 3'UTR DEL C C - rs563231190 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:48601617delC ENST00000328333.8 - 0 9164 COL7A1_ENST00000470076.1_5'UTR|COL7A1_ENST00000454817.1_3'UTR NM_000094.3 NP_000085.1 Q02388 CO7A1_HUMAN collagen, type VII, alpha 1 NA NA NA cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198) basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615) serine-type endopeptidase inhibitor activity (GO:0004867) NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5) 137 BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632) CCCACAGCCACCCCCCCACAG 0.602 NA NA NA CCCCCC|CCCCCCC|CCCCCC|insertion 3 0.000599042 0 0.0014 5008 , , NA 16374 0 NA 0 False NA ,,, NA NA NA 2504 0.002 NA NA NA PASS NA NA NA 0 174 197.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.32 L02870 CCDS2773.1 3p21.1 2014-09-17 2008-08-01 ENSG00000114270 ENSG00000114270 1294 "Collagens", "Fibronectin type III domain containing" 2214 protein-coding gene gene with protein product "collagen VII, alpha-1 polypeptide", "LC collagen" 120120 "epidermolysis bullosa, dystrophic, dominant and recessive" EBDCT, EBD1, EBR1 NA 1871109 Standard NM_000094 NM_000094 NA Approved uc003ctz.2 Q02388 OTTHUMG00000133541 ENST00000328333.8:c.*222G>- chr3.hg19:g.48601617delC 6 9 ref NA False 92 89 PASS 7 PASS ref->het 0 NA 83,88 50,53 41,34 1 1 Q14054|Q16507 True hg19 CCDS2773.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COL7A1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257519.1 PASS NA None 174 True - C ENST00000328333.8 CACNA2D3 55799 __UNKNOWN__ __UNKNOWN__ 3 54919677 54919678 __UNKNOWN__ Intron INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:54919677_54919678insT ENST00000474759.1 + 23 2104 CACNA2D3_ENST00000288197.5_Intron|CACNA2D3_ENST00000490478.1_Intron|CACNA2D3-AS1_ENST00000471265.1_RNA|CACNA2D3_ENST00000415676.2_Intron NM_018398.2 NP_060868.2 Q8IZS8 CA2D3_HUMAN calcium channel, voltage-dependent, alpha 2/delta subunit 3 NA NA NA integral component of membrane (GO:0016021) metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245) NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3) 59 KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327) Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421) AACTCAAAACATTTTTTGGCCT 0.426 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 123 125.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.03 AJ272268 CCDS54598.1 3p21.1 2010-10-05 2008-02-26 ENSG00000157445 ENSG00000157445 55799 "Calcium channel subunits" 15460 protein-coding gene gene with protein product 606399 NA 11245980 Standard XM_005265318 NA Approved HSA272268 uc003dhf.3 Q8IZS8 OTTHUMG00000158580 ENST00000474759.1:c.2056+64->T chr3.hg19:g.54919683_54919683dupT 7 6 ref NA False 55 55 PASS 6 PASS ref->het 0 NA 70,70 34,34 19,19 1 1 B2RPL6|Q9NY16|Q9NY18 True hg19 CCDS54598.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CACNA2D3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000351402.1 PASS NA None 123 True + T ENST00000474759.1 GBE1 2632 __UNKNOWN__ __UNKNOWN__ 3 81630270 81630271 __UNKNOWN__ Intron DEL AG AG - rs555859246 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:81630270_81630271delAG ENST00000429644.2 - 11 2090 GBE1_ENST00000489715.1_Intron NM_000158.3 NP_000149 Q04446 GLGB_HUMAN glucan (1,4-alpha-), branching enzyme 1 NA NA NA carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062) 1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553) breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 18 Lung NSC(201;0.0117) UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247) GGAAGGAGGAAGAGAGAGAGAG 0.337 NA NA NA Glycogen Storage Disease, type IV 24 0.00479233 0.0083 0.0014 5008 , , NA 16456 0 NA 0.002 False NA ,,, NA NA NA 2504 0.0102 NA NA NA PASS NA NA NA 0 136 149.22 NA 223,3341 NA 2,219,1561 NA NA NA NA -3.5 0 48 547,7271 NA 4,539,3366 no intron GBE1 NM_000158.3 6,758,4927 A1A1,A1R,RR NA 6.9967,6.257,6.7651 NA 770,10612 NA NA NA SO:0001627 intron_variant 0.34 Familial Cancer Database Andersen Disease, Brancher deficiency CCDS54612.1 3p12.2 2013-09-20 2008-08-01 ENSG00000114480 ENSG00000114480 2632 2.4.1.18 4180 protein-coding gene gene with protein product "glycogen branching enzyme", "Andersen disease", "glycogen storage disease type IV" 607839 NA 8463281 Standard NM_000158 NA Approved uc021xav.1 Q04446 OTTHUMG00000158978 ENST00000429644.2:c.1446+44CT>- chr3.hg19:g.81630280_81630281delAG 6 3 ref NA False 47 47 PASS 7 PASS ref->het 0 NA 82,87 30,31 26,21 1 1 B3KWV3|Q96EN0 True hg19 CCDS54612.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBE1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000352760.2 PASS NA None 136 True - AG ENST00000429644.2 C3orf38 285237 __UNKNOWN__ __UNKNOWN__ 3 88206665 88206665 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:88206665delA ENST00000318887.3 + 0 2180 NM_173824.3 NP_776185.2 Q5JPI3 CC038_HUMAN chromosome 3 open reading frame 38 NA NA NA apoptotic process (GO:0006915) breast(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|urinary_tract(1) 12 Lung NSC(201;0.17) UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661) CAGAGATGACAAAAAAAACCC 0.318 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 286 266.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.93 AL832398 CCDS2921.1, CCDS2921.2 3p11.1 2011-01-25 ENSG00000179021 ENSG00000179021 285237 28384 protein-coding gene gene with protein product NA NA 12477932 Standard NM_173824 NM_173824 NA Approved MGC26717 uc003dqw.3 Q5JPI3 OTTHUMG00000155752 ENST00000318887.3:c.*880A>- chr3.hg19:g.88206665delA 7 9 ref NA False 96 96 PASS 8 PASS ref->het 0 NA 200,206 51,52 33,30 1 1 B2R8X6|Q8TC85 True hg19 CCDS2921.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C3orf38-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000341513.1 PASS NA None 286 True + A ENST00000318887.3 NXPE3 91775 __UNKNOWN__ __UNKNOWN__ 3 101525973 101525973 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:101525973delA ENST00000491511.2 + 6 1878 NXPE3_ENST00000273347.5_Intron|NXPE3_ENST00000477909.1_Intron|NXPE3_ENST00000422132.1_Intron NM_001134456.1 NP_001127928.1 Q969Y0 NXPE3_HUMAN neurexophilin and PC-esterase domain family, member 3 NA NA NA extracellular region (GO:0005576) NA AATAAAAGGTAAAAAAAAGAA 0.353 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 275 268.18 NA NA 95 98 97 NA NA NA 3 NA NA NA 101525973 2203 4300 6503 SO:0001627 intron_variant 0 AK054664 CCDS2945.1 3q12.3 2012-06-14 2012-06-11 2012-06-11 ENSG00000144815 ENSG00000144815 91775 28238 protein-coding gene gene with protein product NA "family with sequence similarity 55, member C" FAM55C NA 12975309 Standard NM_145037 NM_001134456 NA Approved MGC15606 uc003dvn.3 Q969Y0 OTTHUMG00000159179 ENST00000491511.2:c.922+3A>- chr3.hg19:g.101525973delA 7 10 ref NA False 59 59 PASS 8 PASS ref->het 0 NA 191,191 50,50 29,29 1 1 A8K0X4|D3DN53|Q7Z2S8 True hg19 CCDS2945.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NXPE3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000353711.2 PASS NA None 275 True + A ENST00000491511.2 ZPLD1 131368 __UNKNOWN__ __UNKNOWN__ 3 102197621 102197621 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:102197621delA ENST00000306176.1 + 0 2555 NM_175056.1 NP_778226.1 Q8TCW7 ZPLD1_HUMAN zona pellucida-like domain containing 1 NA NA NA integral component of membrane (GO:0016021) central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3) 35 ATGTTCTTACAAAAAAAATCA 0.328 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 269 271.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.5 AY090780 CCDS2947.1 3q12.3 2009-03-25 ENSG00000170044 ENSG00000170044 131368 27022 protein-coding gene gene with protein product 615915 NA 18632209 Standard NM_175056 NM_175056 NA Approved uc003dvt.1 Q8TCW7 OTTHUMG00000159229 ENST00000306176.1:c.*1159A>- chr3.hg19:g.102197621delA 7 9 ref NA False 45 45 PASS 8 PASS ref->het 0 NA 187,191 46,47 42,42 1 1 Q49AS1|Q8WU36 True hg19 CCDS2947.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZPLD1-003 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000354023.2 PASS NA None 269 True + A ENST00000306176.1 MGLL 11343 __UNKNOWN__ __UNKNOWN__ 3 127434833 127434833 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:127434833delT ENST00000398101.3 - 3 901 MGLL_ENST00000453507.2_Intron|MGLL_ENST00000434178.2_Intron|MGLL_ENST00000265052.5_Intron|MGLL_ENST00000398104.1_Intron Q99685 MGLL_HUMAN monoglyceride lipase NA NA NA acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433) endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202) acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803) cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2) 6 CCTGCATGGCTCCCCCATTGA 0.547 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 149 162.82 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.3 BC000551 CCDS43148.1, CCDS46902.1, CCDS58852.1 3p13-q13.33 2014-03-14 ENSG00000074416 ENSG00000074416 11343 3.1.1.23 17038 protein-coding gene gene with protein product 609699 NA 9495531 Standard NM_007283 NM_007283 NA Approved HU-K5, MGL uc003ejx.4 Q99685 OTTHUMG00000159641 ENST00000398101.3:c.402+5062A>- chr3.hg19:g.127434833delT 0 6 ref NA False 44 44 PASS 1 PASS ref->het 0 NA 94,95 40,43 11,11 1 1 B3KRC2|B7Z9D1|Q6IBG9|Q96AA5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MGLL-004 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000356720.1 PASS NA None 149 True - T ENST00000398101.3 PPP2R3A 5523 __UNKNOWN__ __UNKNOWN__ 3 135825165 135825168 __UNKNOWN__ Splice_Site DEL GTGA GTGA - rs112326792 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:135825165_135825168delGTGA ENST00000264977.3 + 13 3946 c.e13+1 PPP2R3A_ENST00000334546.2_Splice_Site|PPP2R3A_ENST00000490467.1_Splice_Site|PPP2R3A_ENST00000469270.1_Splice_Site NM_001190447.1|NM_002718.4 NP_001177376.1|NP_002709.2 Q06190 P2R3A_HUMAN protein phosphatase 2, regulatory subunit B'', alpha NA NA NA eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244) protein phosphatase type 2A complex (GO:0000159) calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601) breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 31 TCCAGGAAGGGTGAGTAAGTTTCC 0.451 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 219 212.62 NA ,, 0,4266 NA 0,0,2133 NA NA NA NA ,, 6 1 63 1,8253 NA 0,1,4126 no splice-5,splice-5,splice-5 PPP2R3A NM_181897.2,NM_002718.4,NM_001190447.1 ,, 0,1,6259 A1A1,A1R,RR NA 0.0121,0.0,0.0080 ,, ,, NA 1,12519 NA NA NA SO:0001630 splice_region_variant 0.63 L12146 CCDS3087.1, CCDS3088.1, CCDS54642.1 3q22.2-q22.3 2013-01-10 2010-06-18 2002-04-26 ENSG00000073711 ENSG00000073711 5523 3.1.3.16 "Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "EF-hand domain containing" 9307 protein-coding gene gene with protein product 604944 "protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha" PPP2R3 NA 8392071 Standard NM_002718 NM_002718 NA Approved uc003eqv.2 Q06190 OTTHUMG00000159766 ENST00000264977.3:c.3329+1GTGA>- chr3.hg19:g.135825165_135825168delGTGA 0 4 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 170,173 32,32 25,22 1 1 A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5 True hg19 CCDS3087.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPP2R3A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000357232.1 PASS NA None 219 Intron True + GTGA ENST00000264977.3 DZIP1L 199221 __UNKNOWN__ __UNKNOWN__ 3 137787783 137787784 __UNKNOWN__ Intron INS - - AG LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:137787783_137787784insAG ENST00000327532.2 - 13 1978 DZIP1L_ENST00000488595.1_Intron NM_173543.2 NP_775814.2 Q8IYY4 DZI1L_HUMAN DAZ interacting zinc finger protein 1-like NA NA NA cilium assembly (GO:0042384) ciliary basal body (GO:0036064) metal ion binding (GO:0046872) breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1) 35 ATGGGAAGAGAAGAGAGAGAGT 0.436 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 456 448.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.99 AK057406 CCDS3096.1, CCDS54645.1 3q22.3 2013-05-22 2013-05-22 ENSG00000158163 ENSG00000158163 199221 26551 protein-coding gene gene with protein product NA "DAZ interacting protein 1-like" NA 12477932 Standard NM_173543 NM_173543 NA Approved FLJ32844, DZIP2 uc003erq.3 Q8IYY4 OTTHUMG00000159819 ENST00000327532.2:c.1616-574->CT chr3.hg19:g.137787792_137787793dupAG 6 3 ref NA False 45 45 PASS 5 PASS ref->het 0 NA 347,350 60,62 50,46 1 1 C9JUG5|Q96M38 True hg19 CCDS3096.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DZIP1L-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000357548.1 PASS NA None 456 True - AG ENST00000327532.2 A4GNT 51146 __UNKNOWN__ __UNKNOWN__ 3 137843517 137843518 __UNKNOWN__ Frame_Shift_Ins INS - - A LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:137843517_137843518insA ENST00000236709.3 - 3 812_813 c.611_612insT c.(610-612)ttgfs p.L204fs NM_016161.2 NP_057245.1 Q9UNA3 A4GCT_HUMAN alpha-1,4-N-acetylglucosaminyltransferase 204 NA NA carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493) Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020) acetylglucosaminyltransferase activity (GO:0008375) breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7) 16 TGCATTCCCACAAAAAGGGGTG 0.48 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 340 357.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.01 AF141315 CCDS3097.1 3p14.3 2010-12-14 ENSG00000118017 ENSG00000118017 51146 17968 protein-coding gene gene with protein product NA NA 10430883 Standard NM_016161 NM_016161 NA Approved alpha4GnT uc003ers.2 Q9UNA3 OTTHUMG00000159820 ENST00000236709.3:c.612dupT chr3.hg19:g.137843522_137843522dupA ENSP00000236709:p.Leu204fs 6 6 ref NA False 79 79 PASS 5 PASS ref->het 0 NA 248,252 57,57 32,30 1 1 Q0VDK1|Q0VDK2 True hg19 CCDS3097.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA A4GNT-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000357557.1 PASS NA None 340 True - A ENST00000236709.3 MECOM 2122 __UNKNOWN__ __UNKNOWN__ 3 168833257 168833257 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:168833257delT ENST00000464456.1 - 7 3039 c.1839delA c.(1837-1839)aaafs p.K613fs MECOM_ENST00000264674.3_Frame_Shift_Del_p.K678fs|MECOM_ENST00000468789.1_Frame_Shift_Del_p.K613fs|MECOM_ENST00000472280.1_Frame_Shift_Del_p.K614fs|MECOM_ENST00000392736.3_Frame_Shift_Del_p.K613fs|MECOM_ENST00000460814.1_Frame_Shift_Del_p.K613fs|MECOM_ENST00000494292.1_Frame_Shift_Del_p.K801fs|MECOM_ENST00000433243.2_Frame_Shift_Del_p.K614fs NM_001164000.1 NP_001157472.1 Q13465 MDS1_HUMAN MDS1 and EVI1 complex locus 22 NA NA regulation of transcription, DNA-templated (GO:0006355) sequence-specific DNA binding transcription factor activity (GO:0003700) p.G614fs*30(2) NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4) 85 CGTTGCTTCCTTTTTTTCCCC 0.498 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 2 Deletion - Frameshift(2) large_intestine(2) 387 357.68 NA NA 121 110 114 NA NA NA 3 NA NA NA 168833257 2203 4300 6503 SO:0001589 frameshift_variant 0.96 S82592, AF164154 CCDS3205.1, CCDS54669.1, CCDS54670.1 3q26.2 2013-01-08 2009-08-07 2009-08-07 ENSG00000085276 ENSG00000085276 2122 "Zinc fingers, C2H2-type" 3498 protein-coding gene gene with protein product 165215 "myelodysplasia syndrome 1", "ecotropic viral integration site 1" MDS1, EVI1 NA 2115646, 8171026, 8643684 Standard NM_005241, NM_004991 NM_001105077 NA Approved MDS1-EVI1, PRDM3 uc011bpj.1 Q03112 OTTHUMG00000158596 ENST00000464456.1:c.1839delA chr3.hg19:g.168833257delT ENSP00000419770:p.Lys613fs 6 7 ref NA False 60 60 PASS 7 PASS ref->het 0 NA 275,280 61,62 50,50 1 1 Q13466|Q6FH90 True hg19 CCDS54669.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MECOM-020 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000351519.1 PASS NA None 387 True - T ENST00000464456.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 3 169587760 169587761 __UNKNOWN__ IGR INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:169587760_169587761insT NA LRRC31 (42 upstream) : SAMD7 (41598 downstream) NA NA NA NA TTCTTTTTCTGTTTTTTTATTG 0.381 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 415 415.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 2.51 NA NA NA NA NA chr3.hg19:g.169587767_169587767dupT 8 9 ref NA False 34 34 PASS 7 PASS ref->het 0 NA 285,286 55,56 67,67 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 415 True T ZMAT3 64393 __UNKNOWN__ __UNKNOWN__ 3 178741931 178741931 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:178741931delA ENST00000311417.2 - 0 2485 ZMAT3_ENST00000432729.1_3'UTR NM_022470.3 NP_071915.1 zinc finger, matrin-type 3 NA NA NA breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1) 14 all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155) OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527) ACTAGGGGGGAAAAAAGAGGA 0.413 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 173 173 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.46 AK122768 CCDS3224.1, CCDS46962.1 3q26.32 2012-10-05 2010-09-15 ENSG00000172667 ENSG00000172667 64393 "Zinc fingers, matrin-type" 29983 protein-coding gene gene with protein product 606452 NA 9400996, 11689294 Standard NM_152240 NM_022470 NA Approved WIG1, MGC10613, FLJ12296, WIG-1, PAG608 uc003fjg.3 Q9HA38 OTTHUMG00000157290 ENST00000311417.2:c.*874T>- chr3.hg19:g.178741931delA 5 7 ref NA False 31 31 PASS 6 PASS ref->het 0 NA 120,123 31,31 23,22 1 1 True hg19 CCDS3224.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZMAT3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000348336.2 PASS NA None 173 True - A ENST00000311417.2 YEATS2 55689 __UNKNOWN__ __UNKNOWN__ 3 183465510 183465510 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:183465510delT ENST00000305135.5 + 9 1164 NM_018023.4 NP_060493.3 Q9ULM3 YETS2_HUMAN YEATS domain containing 2 NA NA NA chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892) Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686) TBP-class protein binding (GO:0017025) NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3) 49 all_cancers(143;6.55e-10)|Ovarian(172;0.0303) all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22) AGACGGTAGGTTTTTTTCCTA 0.398 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 428 407.77 NA NA 137 127 130 NA NA NA 3 NA NA NA 183465510 1842 4090 5932 SO:0001627 intron_variant 6.15 AB033023 CCDS43175.1 3q27.3 2004-08-18 ENSG00000163872 ENSG00000163872 55689 25489 protein-coding gene gene with protein product 613373 NA 10574462 Standard NM_018023 NM_018023 NA Approved FLJ10201, FLJ12841, FLJ13308, KIAA1197 uc003fly.2 Q9ULM3 OTTHUMG00000156898 ENST00000305135.5:c.969+6T>- chr3.hg19:g.183465510delT 6 7 ref NA False 41 41 PASS 7 PASS ref->het 0 NA 307,317 53,53 69,59 2 2 A7E2B9|D3DNS9|Q641P6|Q9NW96 True hg19 CCDS43175.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA YEATS2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000346507.2 PASS NA None 428 True + T ENST00000305135.5 MAP3K13 9175 __UNKNOWN__ __UNKNOWN__ 3 185195228 185195228 __UNKNOWN__ Intron DEL A A - rs570640959 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:185195228delA ENST00000265026.3 + 12 2835 MAP3K13_ENST00000535426.1_Intron|MAP3K13_ENST00000446828.1_Intron|MAP3K13_ENST00000424227.1_Intron|MAP3K13_ENST00000443863.1_Intron NM_004721.4 NP_004712.1 mitogen-activated protein kinase kinase kinase 13 NA NA NA NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 54 all_cancers(143;7.21e-11)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;1.93e-20) TGGAATGGGGAAAAAAAATCC 0.433 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 474 469.22 NA ,, 59,2,4205 NA 1,0,57,0,2,2073 72 71 71 NA ,, -2.3 0 3 73 266,7,7981 NA 5,0,256,0,7,3859 no intron,intron,intron MAP3K13 NM_004721.4,NM_001242317.1,NM_001242314.1 ,, 6,0,313,0,9,5932 A1A1,A1A2,A1R,A2A2,A2R,RR NA 3.3075,1.4299,2.6677 ,, ,, 185195228 325,9,12186 2203 4300 6503 SO:0001627 intron_variant 1.62 BC031677 CCDS3270.1, CCDS56298.1 3q27 2011-06-09 ENSG00000073803 ENSG00000073803 9175 "Mitogen-activated protein kinase cascade / Kinase kinase kinases" 6852 protein-coding gene gene with protein product "leucine zipper-bearing kinase" 604915 NA 9353328 Standard NM_004721 NM_004721 NA Approved LZK, MEKK13 uc003fpi.3 O43283 OTTHUMG00000156673 ENST00000265026.3:c.2501+44A>- chr3.hg19:g.185195228delA 7 8 ref NA False 65 65 PASS 8 PASS ref->het 0 NA 335,339 70,72 64,60 1 1 True hg19 CCDS3270.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAP3K13-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000345268.1 PASS NA None 474 True + A ENST00000265026.3 EIF4A2 1974 __UNKNOWN__ __UNKNOWN__ 3 186502742 186502742 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:186502742delT ENST00000323963.5 + 4 272 EIF4A2_ENST00000440191.2_Intron|EIF4A2_ENST00000356531.5_Intron Q14240 IF4A2_HUMAN eukaryotic translation initiation factor 4A2 NA NA NA cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032) cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281) ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743) breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1) 28 all_cancers(143;2.68e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;1.07e-20) GBM - Glioblastoma multiforme(93;0.0704) TGTATCCTACTTTTTTTAGGG 0.403 NA NA T BCL6 NHL NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 3 3q27.3 1974 "eukaryotic translation initiation factor 4A, isoform 2" NA L 0 441 461.69 NA NA 160 142 148 NA NA NA 3 NA NA NA 186502742 2203 4300 6503 SO:0001627 intron_variant 1.45 D30655 CCDS3282.1 3q28 2012-02-23 2010-02-10 ENSG00000156976 ENSG00000156976 1974 3.6.1.1 "DEAD-boxes" 3284 protein-coding gene gene with protein product 601102 "eukaryotic translation initiation factor 4A, isoform 2" EIF4F NA 8521730 Standard NM_001967 NM_001967 NA Approved DDX2B, EIF4A, BM-010 uc003fqs.3 Q14240 OTTHUMG00000156564 ENST00000323963.5:c.209-9T>- chr3.hg19:g.186502742delT 6 7 ref NA False 58 58 PASS 7 PASS ref->het 0 NA 318,321 49,50 72,71 1 1 D3DNU9|Q53XJ6|Q96B90|Q96EA8 True hg19 CCDS3282.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EIF4A2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000344609.1 PASS NA None 441 True + T ENST00000323963.5 MASP1 5648 __UNKNOWN__ __UNKNOWN__ 3 186971115 186971116 __UNKNOWN__ Intron DEL GA GA - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:186971115_186971116delGA ENST00000392472.2 - 5 857 MASP1_ENST00000337774.5_Intron|MASP1_ENST00000169293.6_Intron|MASP1_ENST00000392470.2_Intron|MASP1_ENST00000495249.1_Intron|MASP1_ENST00000296280.6_Intron P48740 MASP1_HUMAN mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor) NA NA NA complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916) extracellular region (GO:0005576)|extracellular space (GO:0005615) calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252) NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1) 60 all_cancers(143;5.33e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;3.49e-18) GBM - Glioblastoma multiforme(93;0.0366) TGCAAAATATGAGAGAGAGAGA 0.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 197 190.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.94 D28593 CCDS33907.1, CCDS33908.1, CCDS33909.1 3q27-q28 2014-09-17 2005-08-17 ENSG00000127241 ENSG00000127241 5648 "Serine peptidases / Serine peptidases" 6901 protein-coding gene gene with protein product 600521 "mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)" CRARF, PRSS5 NA 8018603, 8240317 Standard NM_001879 NR_033519 NA Approved MASP uc003fri.3 P48740 OTTHUMG00000156461 ENST00000392472.2:c.406-12TC>- chr3.hg19:g.186971125_186971126delGA 7 2 ref NA False 47 47 PASS 8 PASS ref->het 0 NA 128,128 30,31 38,37 1 1 A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MASP1-005 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000344266.2 PASS NA None 197 True - GA ENST00000392472.2 TPRG1 285386 __UNKNOWN__ __UNKNOWN__ 3 189043010 189043010 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:189043010delA ENST00000345063.3 + 0 5396 NM_198485.3 NP_940887.1 Q6ZUI0 TPRG1_HUMAN tumor protein p63 regulated 1 NA NA NA cytoplasm (GO:0005737) endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|skin(2)|urinary_tract(1) 16 all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925) all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255) Lung(62;6.93e-06) GBM - Glioblastoma multiforme(93;4.77e-14) GCCCAAGACCAAAAAAAATGA 0.408 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 169 166.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.73 AK125682 CCDS3292.1 3q28 2008-02-04 2008-01-16 2008-01-16 ENSG00000188001 ENSG00000188001 285386 24759 protein-coding gene gene with protein product NA "family with sequence similarity 79, member B" FAM79B NA Standard NM_198485 NM_198485 NA Approved FLJ41238, FLJ43694 uc003frw.2 Q6ZUI0 OTTHUMG00000156321 ENST00000345063.3:c.*4401A>- chr3.hg19:g.189043010delA 7 8 ref NA False 35 35 PASS 8 PASS ref->het 0 NA 120,122 27,28 24,22 1 1 True hg19 CCDS3292.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TPRG1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000343931.1 PASS NA None 169 True + A ENST00000345063.3 TMEM207 131920 __UNKNOWN__ __UNKNOWN__ 3 190165586 190165587 __UNKNOWN__ Frame_Shift_Ins INS - - TT rs181974010 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:190165586_190165587insTT ENST00000354905.2 - 2 171_172 c.105_106insAA c.(103-108)gaagatfs p.D36fs NM_207316.1 NP_997199.1 Q6UWW9 TM207_HUMAN transmembrane protein 207 36 NA NA integral component of membrane (GO:0016021) endometrium(1)|large_intestine(2)|lung(4) 7 all_cancers(143;3.61e-10)|Ovarian(172;0.0991) Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05) GBM - Glioblastoma multiforme(93;0.0176) TACATTTCATCTTCTTCGCATG 0.356 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 221 216.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 BC071780 CCDS3297.1 3q28 2008-02-18 ENSG00000198398 ENSG00000198398 131920 33705 protein-coding gene gene with protein product 614786 NA Standard NM_207316 NM_207316 NA Approved uc003fsj.2 Q6UWW9 OTTHUMG00000156213 ENST00000354905.2:c.104_105dupAA chr3.hg19:g.190165587_190165588dupTT ENSP00000346981:p.Asp36fs 4 4 ref NA False 49 49 PASS 2 PASS ref->het 0 NA 159,160 39,39 22,22 1 1 True hg19 CCDS3297.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM207-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000343515.1 PASS NA None 221 True - T ENST00000354905.2 HES1 3280 __UNKNOWN__ __UNKNOWN__ 3 193854390 193854390 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:193854390delT ENST00000232424.3 + 2 344 NM_005524.3 NP_005515.1 P30042 ES1_HUMAN hes family bHLH transcription factor 1 NA NA NA mitochondrion (GO:0005739) endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1) 6 all_cancers(143;7.3e-09)|Ovarian(172;0.0634) OV - Ovarian serous cystadenocarcinoma(49;3.65e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06) GBM - Glioblastoma multiforme(46;1.48e-05) CACAGAACTCTTTTTTTTATT 0.433 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 422 414 NA NA 49 55 53 NA NA NA 3 NA NA NA 193854390 2203 4300 6503 SO:0001627 intron_variant 1.55 L19314 CCDS3305.1 3q28-q29 2013-10-17 2013-10-17 2003-01-10 ENSG00000114315 ENSG00000114315 3280 "Basic helix-loop-helix proteins" 5192 protein-coding gene gene with protein product 139605 "hairy homolog (Drosophila)", "hairy and enhancer of split 1, (Drosophila)" HRY NA 8020957 Standard NM_005524 NA Approved FLJ20408, HES-1, Hes1, bHLHb39 uc003ftq.2 Q14469 OTTHUMG00000155984 ENST00000232424.3:c.109-16T>- chr3.hg19:g.193854390delT 7 11 ref NA False 121 121 PASS 8 PASS ref->het 0 NA 313,316 55,56 51,48 1 1 A6NFJ6|A6NJY7|O00650|O00660|O15011|O15012|P55346|P78474|Q92505|Q92507 True hg19 CCDS3305.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HES1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000342632.1 PASS NA None 422 True + T ENST00000232424.3 PPP1R2 5504 __UNKNOWN__ __UNKNOWN__ 3 195242558 195242559 __UNKNOWN__ 3'UTR INS - - A rs201153201 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:195242558_195242559insA ENST00000328432.3 - 0 2113_2114 NM_006241.4 NP_006232.1 P41236 IPP2_HUMAN protein phosphatase 1, regulatory (inhibitor) subunit 2 NA NA NA generation of precursor metabolites and energy (GO:0006091)|glycogen metabolic process (GO:0005977)|negative regulation of catalytic activity (GO:0043086)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of signal transduction (GO:0009966) protein serine/threonine phosphatase inhibitor activity (GO:0004865) endometrium(2)|kidney(1)|large_intestine(1)|urinary_tract(2) 6 all_cancers(143;1.8e-08)|Ovarian(172;0.0634) Epithelial(36;2.64e-22)|all cancers(36;2.69e-20)|OV - Ovarian serous cystadenocarcinoma(49;3.52e-19)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128) GBM - Glioblastoma multiforme(46;9.55e-05) AAAAAACAAACAAAAAAAACCC 0.307 NA NA NA |||unknown(STR3?) 408 0.0814696 0.0408 0.036 5008 , , NA 20041 0.123 NA 0.0537 False NA ,,, NA NA NA 2504 0.1544 NA NA NA PASS NA NA NA 0 207 222.58 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.44 U68111 CCDS3309.1 3q29 2012-04-17 ENSG00000184203 ENSG00000184203 5504 3.1.3.16 "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits" 9288 protein-coding gene gene with protein product 601792 NA 9126490, 8119416 Standard NM_006241 XM_006713682 NA Approved IPP2 uc003fup.3 P41236 OTTHUMG00000155887 ENST00000328432.3:c.*1136->T chr3.hg19:g.195242566_195242566dupA 9 11 ref NA False 90 90 PASS 8 PASS ref->het 0 NA 129,129 51,51 28,28 2 1 True hg19 CCDS3309.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPP1R2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000342133.1 PASS NA None 207 True - A ENST00000328432.3 TNK2 10188 __UNKNOWN__ __UNKNOWN__ 3 195595228 195595229 __UNKNOWN__ Frame_Shift_Ins INS - - G rs541695993 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:195595228_195595229insG ENST00000333602.6 - 12 2512_2513 c.1895_1896insC c.(1894-1896)ccgfs p.P632fs TNK2_ENST00000381916.2_Frame_Shift_Ins_p.P710fs|TNK2_ENST00000428187.1_Frame_Shift_Ins_p.P664fs|TNK2_ENST00000392400.1_Frame_Shift_Ins_p.P632fs NM_005781.4 NP_005772.3 Q07912 ACK1_HUMAN tyrosine kinase, non-receptor, 2 632 Pro-rich.|Required for interaction with NEDD4. {ECO:0000250}.|Required for interaction with SRC. NA NA Missing (in Ref. 4; AAH08884). {ECO:0000305}. cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264) axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886) ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699) central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1) 29 all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206) Lung NSC(153;0.191) Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05) GBM - Glioblastoma multiforme(46;0.000757) Adenosine triphosphate(DB00171) CATAGGCGGGCGGGGGGGGCAG 0.728 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 586 579.94 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 15.45 L13738 CCDS33927.1, CCDS33928.1 3q29 2013-09-02 ENSG00000061938 ENSG00000061938 10188 19297 protein-coding gene gene with protein product "activated Cdc42-associated kinase 1" 606994 NA 8497321, 14506255 Standard NM_005781 XM_006713460 NA Approved p21cdc42Hs, ACK, ACK1 uc003fvt.1 Q07912 OTTHUMG00000155737 ENST00000333602.6:c.1896dupC chr3.hg19:g.195595236_195595236dupG ENSP00000329425:p.Pro632fs 9 11 ref NA False 63 63 PASS 8 PASS ref->het 0 NA 277,310 74,88 232,186 2 2 Q6ZMQ0|Q8N6U7|Q96H59 True hg19 CCDS33928.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNK2-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000341437.3 PASS NA None 586 True - G ENST00000333602.6 PIGZ 80235 __UNKNOWN__ __UNKNOWN__ 3 196674300 196674301 __UNKNOWN__ Frame_Shift_Ins INS - - C rs200103570 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:196674300_196674301insC ENST00000412723.1 - 3 1613_1614 c.1467_1468insG c.(1465-1470)gggactfs p.T490fs NM_025163.2 NP_079439.2 Q86VD9 PIGZ_HUMAN phosphatidylinositol glycan anchor biosynthesis, class Z 490 NA NA GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021) alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030) breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1) 14 all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838) Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06) GBM - Glioblastoma multiforme(46;0.00603) CAGTCCTCAGTCCCCCCCATGT 0.629 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 630 638.63 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 2.13 BC018804 CCDS3324.1 3q29 2013-02-26 2006-06-28 ENSG00000119227 ENSG00000119227 80235 "Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis" 30596 protein-coding gene gene with protein product "GPI mannosyltransferase 4", "dol-P-Man dependent GPI mannosyltransferase" 611671 "phosphatidylinositol glycan, class Z" NA 15208306 Standard NM_025163 NM_025163 NA Approved FLJ12768, MGC52163, SMP3 uc003fxh.3 Q86VD9 OTTHUMG00000155522 ENST00000412723.1:c.1468dupG chr3.hg19:g.196674307_196674307dupC ENSP00000413405:p.Thr490fs 8 7 ref NA False 47 47 PASS 7 PASS ref->het 0 NA 470,474 81,83 76,73 1 1 Q9H9G6 True hg19 CCDS3324.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PIGZ-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000340486.2 PASS NA None 630 True - C ENST00000412723.1 GRK4 2868 __UNKNOWN__ __UNKNOWN__ 4 3011222 3011234 __UNKNOWN__ Intron DEL CACAGTCCCTGAG CACAGTCCCTGAG - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:3011222_3011234delCACAGTCCCTGAG ENST00000398052.4 + 7 879 GRK4_ENST00000398051.4_Intron|GRK4_ENST00000345167.6_Intron|GRK4_ENST00000504933.1_Intron NM_182982.2 NP_892027.2 P32298 GRK4_HUMAN G protein-coupled receptor kinase 4 NA NA NA G-protein coupled receptor internalization (GO:0002031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032) cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025) ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254) lung(1)|upper_aerodigestive_tract(1) 2 UCEC - Uterine corpus endometrioid carcinoma (64;0.168) TAGAGGGAGCCACAGTCCCTGAGCACAGACACC 0.423 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 191 187.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 5.37 CCDS33946.1, CCDS33947.1, CCDS47002.1, CCDS68656.1 4p16.3 2008-02-05 2004-02-04 2004-02-06 ENSG00000125388 ENSG00000125388 2868 4543 protein-coding gene gene with protein product 137026 "G protein-coupled receptor kinase 2-like (Drosophila)" GPRK2L NA 1338872 Standard NM_005307 NM_182982 NA Approved GPRK4 uc003ggn.1 P32298 OTTHUMG00000159914 ENST00000398052.4:c.537-141CACAGTCCCTGAG>- chr4.hg19:g.3011222_3011234delCACAGTCCCTGAG 0 3 ref NA False 133 98 PASS 1 PASS ref->het 0 NA 108,117 74,80 33,20 1 1 O00641|O00642|Q13293|Q13294|Q13295|Q14453|Q14725|Q15313|Q15314|Q15315|Q15316|Q17RH6|Q53EQ8 True hg19 CCDS33946.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GRK4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000358176.2 PASS NA None 191 True + CACAGTCCCTGAG ENST00000398052.4 LINC00955 285492 __UNKNOWN__ __UNKNOWN__ 4 3591606 3591607 __UNKNOWN__ 3'UTR INS - - ACAC rs139255858|rs551743514|rs35459098 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:3591606_3591607insACAC ENST00000514422.1 + 0 1377_1378 long intergenic non-protein coding RNA 955 NA NA NA NA TACATGGAAATacacacacact 0.401 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 121 122.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 7.89 AK092743 4p16.3 2014-04-09 ENSG00000216560 ENSG00000216560 285492 26644 other unknown NA NA Standard NR_040045 NA Approved FLJ35424 OTTHUMG00000159817 ENST00000514422.1:c.*507->ACAC chr4.hg19:g.3591611_3591614dupACAC 7 4 ref NA False 36 36 PASS 5 PASS ref->het 0 NA 57,58 29,40 36,24 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LINC00955-001 NOVEL basic|appris_principal protein_coding NA protein_coding OTTHUMT00000357538.6 PASS NA None 121 True + AC ENST00000514422.1 NSG1 0 __UNKNOWN__ __UNKNOWN__ 4 4389490 4389491 __UNKNOWN__ Intron INS - - C rs565067471|rs576197176 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:4389490_4389491insC ENST00000504171.1 + 2 224 NSG1_ENST00000506380.1_Intron|NSG1_ENST00000421177.2_Intron|NSG1_ENST00000397958.1_Intron|NSG1_ENST00000513555.1_Intron|NSG1_ENST00000505246.1_Intron|NSG1_ENST00000433139.2_Intron P42857 NSG1_HUMAN NA NA NA clathrin coat assembly (GO:0048268)|dopamine receptor signaling pathway (GO:0007212) cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634) NA GATAAGGTAAGCCCCCCCACGC 0.658 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 380 381.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.97 NA NA NA NA NA ENST00000504171.1:c.129+5->C chr4.hg19:g.4389497_4389497dupC 8 8 ref NA False 81 81 PASS 7 PASS ref->het 0 NA 243,251 49,52 90,80 1 1 B4DXC5|Q49AQ1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSG1-004 NOVEL alternative_5_UTR|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000358777.1 PASS NA None 380 True + C ENST00000504171.1 RAB28 9364 __UNKNOWN__ __UNKNOWN__ 4 13485808 13485808 __UNKNOWN__ 5'UTR DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:13485808delG ENST00000330852.5 - 0 181 RAB28_ENST00000288723.4_5'UTR|RAB28_ENST00000338176.4_5'UTR NM_001017979.2 NP_001017979.1 P51157 RAB28_HUMAN RAB28, member RAS oncogene family NA NA NA GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264) ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886) GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924) endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1) 8 CCCTCGAGGTGGGGGGGGAAG 0.706 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 199 210.05 NA ,, 49,62,3881 NA 1,1,46,0,61,1887 6 5 6 NA ,, 2 0.2 4 6 100,123,7579 NA 4,0,92,1,121,3683 no utr-5,utr-5,utr-5 RAB28 NM_004249.3,NM_001159601.1,NM_001017979.2 ,, 5,1,138,1,182,5570 A1A1,A1A2,A1R,A2A2,A2R,RR NA 2.8582,2.7806,2.8319 ,, ,, 13485808 149,185,11460 2136 4195 6331 SO:0001623 5_prime_UTR_variant 7.79 X94703 CCDS3409.1, CCDS33961.1, CCDS54741.1 4p16.1 2014-04-24 ENSG00000157869 ENSG00000157869 9364 "RAB, member RAS oncogene" 9768 protein-coding gene gene with protein product 612994 NA 8647132 Standard NM_001017979 NM_004249 NA Approved uc003gmu.2 P51157 OTTHUMG00000090543 ENST00000330852.5:c.-34C>- chr4.hg19:g.13485808delG 7 10 ref NA False 102 102 PASS 8 PASS ref->het 0 NA 107,118 31,32 63,52 1 1 G8JLC5|Q8IYR8|Q8NI05 True hg19 CCDS33961.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RAB28-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000207068.2 PASS NA None 199 True - G ENST00000330852.5 LGI2 55203 __UNKNOWN__ __UNKNOWN__ 4 25001499 25001499 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:25001499delT ENST00000382114.4 - 0 5397 NM_018176.3 NP_060646.2 Q8N0V4 LGI2_HUMAN leucine-rich repeat LGI family, member 2 NA NA NA extracellular region (GO:0005576) breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2) 33 Breast(46;0.173) AGGTTTTGAATTTTTCCTTCA 0.468 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 568 549.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.51 AJ487516 CCDS3431.1 4p15.31 2008-07-28 ENSG00000153012 ENSG00000153012 55203 18710 protein-coding gene gene with protein product 608301 NA 12023020, 16014869 Standard NM_018176 NA Approved KIAA1916, FLJ10675 uc003grf.2 Q8N0V4 OTTHUMG00000097749 ENST00000382114.4:c.*3574A>- chr4.hg19:g.25001499delT 4 5 ref NA False 128 76 PASS 5 PASS ref->het 0 NA 357,361 146,148 67,63 1 1 Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4 True hg19 CCDS3431.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LGI2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000214978.1 PASS NA None 568 True - T ENST00000382114.4 PGM2 55276 __UNKNOWN__ __UNKNOWN__ 4 37864493 37864494 __UNKNOWN__ 3'UTR DEL TA TA - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:37864493_37864494delTA ENST00000381967.4 + 0 3199_3200 NM_018290.3 NP_060760.2 Q96G03 PGM2_HUMAN phosphoglucomutase 2 NA NA NA carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062) magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973) breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1) 19 AAGCCATATTTATGTTTATTTT 0.287 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 112 98.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.48 BC010087 CCDS3443.1 4p14 2012-10-02 ENSG00000169299 ENSG00000169299 55276 5.4.2.2 8906 protein-coding gene gene with protein product "phosphopentomutase" 172000 NA 9549096 Standard NM_018290 NM_018290 NA Approved FLJ10983 uc011byb.1 Q96G03 OTTHUMG00000097813 ENST00000381967.4:c.*1261TA>- chr4.hg19:g.37864493_37864494delTA 0 4 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 74,74 22,22 17,18 1 1 B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22 True hg19 CCDS3443.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PGM2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000215079.2 PASS NA None 112 True + TA ENST00000381967.4 TBC1D1 23216 __UNKNOWN__ __UNKNOWN__ 4 38139135 38139136 __UNKNOWN__ 3'UTR INS - - T rs140473695 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:38139135_38139136insT ENST00000261439.4 + 0 4041_4042 TBC1D1_ENST00000407365.1_3'UTR|TBC1D1_ENST00000508802.1_3'UTR NM_001253914.1|NM_001253915.1|NM_015173.3 NP_001240843.1|NP_001240844.1|NP_055988.2 Q86TI0 TBCD1_HUMAN TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1 NA NA NA membrane organization (GO:0061024)|regulation of protein localization (GO:0032880) cytosol (GO:0005829)|nucleus (GO:0005634) Rab GTPase activator activity (GO:0005097) NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1) 36 ATGTCCCAGTGTTTTTTTTGTT 0.45 NA NA NA TTTTTTTTT|TTTTTTTT|TTTTTTTTT|deletion 58 0.0115815 0.0416 0.0029 5008 , , NA 20577 0 NA 0.001 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 168 149.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.62 AB029031 CCDS33972.1, CCDS58897.1 4p14 2013-07-09 ENSG00000065882 ENSG00000065882 23216 11578 protein-coding gene gene with protein product 609850 NA 10965142, 18258599 Standard NM_015173 NM_015173 NA Approved TBC, TBC1, KIAA1108 uc003gtb.3 Q86TI0 OTTHUMG00000150302 ENST00000261439.4:c.*180->T chr4.hg19:g.38139143_38139143dupT 9 10 ref NA False 47 47 PASS 8 PASS ref->het 0 NA 115,116 27,29 23,21 1 1 B7Z3D9|E9PGH8|Q96K82|Q9UPP4 True hg19 CCDS33972.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TBC1D1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000317443.2 PASS NA None 168 True + T ENST00000261439.4 LIMCH1 22998 __UNKNOWN__ __UNKNOWN__ 4 41629001 41629001 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:41629001delA ENST00000514096.1 + 3 714 LIMCH1_ENST00000509277.1_Intron|LIMCH1_ENST00000512946.1_Intron|LIMCH1_ENST00000503057.1_Frame_Shift_Del_p.S334fs|LIMCH1_ENST00000396595.3_Intron|LIMCH1_ENST00000512632.1_Intron|LIMCH1_ENST00000313860.7_Intron|LIMCH1_ENST00000511496.1_Intron|LIMCH1_ENST00000512820.1_Intron|LIMCH1_ENST00000381753.4_Intron|LIMCH1_ENST00000508501.1_Intron|LIMCH1_ENST00000513024.1_Intron Q9UPQ0 LIMC1_HUMAN LIM and calponin homology domains 1 NA NA NA actomyosin structure organization (GO:0031032) zinc ion binding (GO:0008270) central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5) 41 AGGGAATCTCAAAAAAAAGAA 0.438 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 176 166.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.5 AB029025 CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1 4p13 2007-06-14 2008-01-09 ENSG00000064042 ENSG00000064042 22998 29191 protein-coding gene gene with protein product NA NA 10470851 Standard NM_014988 XM_005248057 NA Approved DKFZP686A01247, LIMCH1A, LMO7B uc003gvz.4 Q9UPQ0 OTTHUMG00000160575 ENST00000514096.1:c.494+7544A>- chr4.hg19:g.41629001delA 7 10 ref NA False 42 42 PASS 8 PASS ref->het 0 NA 111,116 26,26 37,34 1 1 A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LIMCH1-014 NOVEL alternative_5_UTR|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000361261.1 PASS NA None 176 True + A ENST00000514096.1 SEPT11 55752 __UNKNOWN__ __UNKNOWN__ 4 77955730 77955731 __UNKNOWN__ Intron DEL TG TG - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:77955730_77955731delTG ENST00000505788.1 + 10 1369 SEPT11_ENST00000512575.1_3'UTR|SEPT11_ENST00000541121.1_3'UTR|SEPT11_ENST00000264893.6_3'UTR|SEPT11_ENST00000510515.1_3'UTR Q9NVA2 SEP11_HUMAN septin 11 NA NA NA cell cycle (GO:0007049)|cell division (GO:0051301)|protein heterooligomerization (GO:0051291) cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|septin complex (GO:0031105)|stress fiber (GO:0001725)|synapse (GO:0045202) GTP binding (GO:0005525) endometrium(2)|kidney(3)|large_intestine(3)|lung(1)|skin(1)|stomach(1) 11 ATCTCTGCCATGTGTGTTCTTT 0.356 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 339 308.93 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.43 AK001711 CCDS34018.1 4q21.1 2013-01-21 ENSG00000138758 ENSG00000138758 55752 "Septins" 25589 protein-coding gene gene with protein product 612887 NA 14999297, 15140406 Standard NM_018243 NM_018243 NA Approved FLJ10849 uc003hkj.3 Q9NVA2 OTTHUMG00000160854 ENST00000505788.1:c.1275-2192TG>- chr4.hg19:g.77955734_77955735delTG 2 2 ref NA False 107 107 PASS 3 PASS ref->het 0 NA 241,243 49,50 44,42 1 1 B7Z7Z6|E9KL32|Q4W5G1|Q7L4N1|Q96SP1|Q9UFY9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SEPT11-002 PUTATIVE basic|appris_candidate_longest|exp_conf protein_coding NA protein_coding OTTHUMT00000362677.1 PASS NA None 339 True + TG ENST00000505788.1 CNOT6L 246175 __UNKNOWN__ __UNKNOWN__ 4 78636847 78636848 __UNKNOWN__ 3'UTR INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:78636847_78636848insT ENST00000504123.1 - 0 6535_6536 CNOT6L_ENST00000264903.4_3'UTR Q96LI5 CNO6L_HUMAN CCR4-NOT transcription complex, subunit 6-like NA NA NA gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351) CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634) metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535) kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1) 9 GAAAGAACTGCTTTTTTTTCTT 0.351 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 193 181.84 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.44 AL133112 CCDS68731.1 4q13.3 2014-06-17 ENSG00000138767 246175 18042 protein-coding gene gene with protein product NA NA Standard NM_144571 NA Approved DKFZp434K098, Ccr4b uc003hks.3 Q96LI5 ENST00000504123.1:c.*4738->A chr4.hg19:g.78636855_78636855dupT 9 11 ref NA False 31 31 PASS 8 PASS ref->het 0 NA 141,144 27,27 23,21 2 2 Q9UF92 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CNOT6L-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000362515.1 PASS NA None 193 True - T ENST00000504123.1 GRID2 2895 __UNKNOWN__ __UNKNOWN__ 4 94693677 94693677 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:94693677delT ENST00000282020.4 + 0 3310 NM_001510.2 NP_001501.2 O43424 GRID2_HUMAN glutamate receptor, ionotropic, delta 2 NA NA NA cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810) cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202) extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110) NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1) 100 Hepatocellular(203;0.114)|all_hematologic(202;0.177) OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191) TCACTGTTTCTTTTTTAGGAC 0.393 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 496 489.98 NA NA 35 34 34 NA NA NA 4 NA NA NA 94693677 2203 4300 6503 SO:0001624 3_prime_UTR_variant 0.39 AF009014 CCDS3637.1, CCDS68758.1 4q22 2012-08-29 ENSG00000152208 ENSG00000152208 2895 "Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors" 4576 protein-coding gene gene with protein product 602368 NA 9465309 Standard NM_001510 NA Approved GluD2, GluR-delta-2 uc011cdt.2 O43424 OTTHUMG00000130975 ENST00000282020.4:c.*28T>- chr4.hg19:g.94693677delT 5 9 ref NA False 197 128 PASS 6 PASS ref->het 0 NA 302,305 141,141 51,49 1 1 E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1 True hg19 CCDS3637.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GRID2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253588.2 PASS NA None 496 True + T ENST00000282020.4 UBE2D3 7323 __UNKNOWN__ __UNKNOWN__ 4 103748142 103748142 __UNKNOWN__ 5'UTR DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:103748142delG ENST00000343106.5 - 0 137 UBE2D3_ENST00000338145.3_Intron|UBE2D3_ENST00000394803.5_Intron|UBE2D3_ENST00000349311.8_Intron|UBE2D3_ENST00000394804.2_Intron|UBE2D3_ENST00000357194.6_Intron|UBE2D3_ENST00000394801.4_Intron|UBE2D3_ENST00000513098.1_5'UTR|UBE2D3_ENST00000321805.7_Intron|UBE2D3_ENST00000453744.2_Intron NM_181892.2 NP_871621.1 P61077 UB2D3_HUMAN ubiquitin-conjugating enzyme E2D 3 NA NA NA apoptotic process (GO:0006915)|BMP signaling pathway (GO:0030509)|cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|DNA repair (GO:0006281)|gene expression (GO:0010467)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type I interferon production (GO:0032480)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ubiquitin-dependent protein catabolic process (GO:0006511) cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886) acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842) kidney(1)|lung(3)|skin(1) 5 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;2.13e-08) AGAAAGGCAAGGGGGGAGGGG 0.632 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 188 194.84 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.57 U39318 CCDS3659.1, CCDS3660.1, CCDS3661.1, CCDS75172.1 4q24 2011-05-19 2011-05-19 ENSG00000109332 ENSG00000109332 7323 "Ubiquitin-conjugating enzymes E2" 12476 protein-coding gene gene with protein product 602963 "ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5)", "ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)" NA 8530467 Standard NM_181893 NM_181886 NA Approved UbcH5C uc003hwl.3 P61077 OTTHUMG00000131119 ENST00000343106.5:c.-477C>- chr4.hg19:g.103748142delG 5 11 ref NA False 98 98 PASS 6 PASS ref->het 0 NA 143,151 18,19 34,26 1 1 A6NJ93|A6NJB1|A6NM99|P47986|Q6IB88|Q6NXS4|Q8N924 True hg19 CCDS3661.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UBE2D3-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000253792.3 PASS NA None 188 True - G ENST00000343106.5 NPNT 255743 __UNKNOWN__ __UNKNOWN__ 4 106848395 106848395 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:106848395delT ENST00000427316.2 + 3 384 NPNT_ENST00000513430.1_Intron|NPNT_ENST00000305572.8_Intron|NPNT_ENST00000453617.2_Intron|NPNT_ENST00000514622.1_Intron|NPNT_ENST00000506666.1_Intron|NPNT_ENST00000379987.2_Intron|RP11-710F7.2_ENST00000512514.1_RNA|RP11-710F7.2_ENST00000511059.1_RNA NM_001184691.1 NP_001171620.1 Q6UXI9 NPNT_HUMAN nephronectin NA NA NA branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|ureteric bud development (GO:0001657) basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485) calcium ion binding (GO:0005509)|integrin binding (GO:0005178) kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1) 21 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;5.41e-07) TAAGTTCTAGTTTTTTTTCTT 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 95 108.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.36 CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1 4q25 2005-10-07 255743 27405 protein-coding gene gene with protein product 610306 NA 15754038 Standard NM_198278 NM_001033047 NA Approved EGFL6L, POEM uc011cfd.2 Q6UXI9 ENST00000427316.2:c.173-98T>- chr4.hg19:g.106848395delT 7 12 ref NA False 34 34 PASS 8 PASS ref->het 0 NA 66,68 17,17 10,9 1 1 A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04 True hg19 CCDS54785.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NPNT-003 NOVEL basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000364085.1 PASS NA None 95 True + T ENST00000427316.2 ELOVL6 79071 __UNKNOWN__ __UNKNOWN__ 4 110969872 110969872 __UNKNOWN__ 3'UTR DEL A A - rs201125372|rs200600528|rs5860996 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:110969872delA ENST00000394607.3 - 0 3583 Q9H5J4 ELOV6_HUMAN ELOVL fatty acid elongase 6 NA NA NA cellular lipid metabolic process (GO:0044255)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty acid biosynthetic process (GO:0042759)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176) transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747) cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1) 8 OV - Ovarian serous cystadenocarcinoma(123;0.00462) gttttgttttAAAAAAAATGT 0.284 NA NA NA ?|AAAAAAAA|AAAAAAA|unsure 2629 0.52496 0.7867 0.438 5008 , , NA 18207 0.5069 NA 0.3797 False NA ,,, NA NA NA 2504 0.4008 NA NA NA PASS NA NA NA 0 171 159.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.24 AK027031 CCDS3690.1 4q25 2011-05-25 2011-05-25 ENSG00000170522 ENSG00000170522 79071 15829 protein-coding gene gene with protein product 611546 "ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)" NA 11567032 Standard NM_024090 NM_024090 NA Approved FLJ23378, MGC5487, LCE uc003hzz.3 Q9H5J4 OTTHUMG00000132547 ENST00000394607.3:c.*2622T>- chr4.hg19:g.110969872delA 7 8 ref NA False 42 42 PASS 8 PASS ref->het 0 NA 123,125 31,31 16,14 1 1 Q4W5L0|Q8NCD1 True hg19 CCDS3690.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ELOVL6-001 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255748.1 PASS NA None 171 True - A ENST00000394607.3 ENPEP 2028 __UNKNOWN__ __UNKNOWN__ 4 111437040 111437041 __UNKNOWN__ Intron INS - - AG rs139525131 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:111437040_111437041insAG ENST00000265162.5 + 8 1851 RP11-380D23.1_ENST00000503998.1_RNA NM_001977.3 NP_001968.3 Q07075 AMPE_HUMAN glutamyl aminopeptidase (aminopeptidase A) NA NA NA angiogenesis (GO:0001525)|angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|glomerulus development (GO:0032835)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081) apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886) aminopeptidase activity (GO:0004177)|metalloaminopeptidase activity (GO:0070006)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270) breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(1) 54 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.0031) gtcctcatagcagagagagaga 0.495 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 82 75.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.06 L12468 CCDS3691.1 4q25 2008-02-05 ENSG00000138792 ENSG00000138792 2028 3.4.11.7 "CD molecules" 3355 protein-coding gene gene with protein product 138297 NA 9268642 Standard NM_001977 NA Approved gp160, CD249 uc003iab.4 Q07075 OTTHUMG00000132546 ENST00000265162.5:c.1509+442->AG chr4.hg19:g.111437049_111437050dupAG 8 2 ref NA False 30 30 PASS 7 PASS ref->het 0 NA 47,53 14,14 22,16 2 2 Q504U2 True hg19 CCDS3691.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENPEP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255747.2 PASS NA None 82 True + AG ENST00000265162.5 RAPGEF2 9693 __UNKNOWN__ __UNKNOWN__ 4 160244596 160244597 __UNKNOWN__ Intron INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:160244596_160244597insT ENST00000264431.4 + 5 926 NM_014247.2 NP_055062.1 Q9Y4G8 RPGF2_HUMAN Rap guanine nucleotide exchange factor (GEF) 2 NA NA NA adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591) cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202) beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699) breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3) 70 all_hematologic(180;0.24) COAD - Colon adenocarcinoma(41;0.0817) CTTTGTCTTTATTTTTTTGGAT 0.376 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 202 188.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.41 AB002311 CCDS43277.1 4q32.1 2004-03-01 2004-03-01 2004-03-01 9693 16854 protein-coding gene gene with protein product "Rap GEP" 609530 "PDZ domain containing guanine nucleotide exchange factor (GEF) 1" PDZGEF1 NA 9205841, 10934204 Standard NM_014247 NM_014247 NA Approved PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313 uc003iqg.4 Q9Y4G8 ENST00000264431.4:c.508-14->T chr4.hg19:g.160244603_160244603dupT 8 10 ref NA False 44 44 PASS 7 PASS ref->het 0 NA 131,131 39,40 32,31 1 1 D3DP27 True hg19 CCDS43277.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RAPGEF2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000364980.2 PASS NA None 202 True + T ENST00000264431.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 4 184369358 184369358 __UNKNOWN__ IGR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:184369358delT NA CDKN2AIP (7 upstream) : RP11-367N14.2 (46732 downstream) NA NA NA NA AGAAGTTGTGTTTTTTTTCTC 0.299 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 71 72.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr4.hg19:g.184369358delT 7 9 ref NA False 38 38 PASS 8 PASS ref->het 0 NA 52,52 15,15 6,6 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 71 True T GDNF 2668 __UNKNOWN__ __UNKNOWN__ 5 37814906 37814907 __UNKNOWN__ 3'UTR DEL TC TC - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:37814906_37814907delTC ENST00000326524.2 - 0 1681_1682 GDNF_ENST00000344622.4_3'UTR NM_000514.3 NP_000505.1 P39905 GDNF_HUMAN glial cell derived neurotrophic factor NA NA NA adult locomotory behavior (GO:0008344)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|enteric nervous system development (GO:0048484)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|metanephros development (GO:0001656)|mRNA stabilization (GO:0048255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|organ induction (GO:0001759)|peristalsis (GO:0030432)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|postganglionic parasympathetic nervous system development (GO:0021784)|postsynaptic membrane organization (GO:0001941)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of morphogenesis of a branching structure (GO:0060688)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|ureteric bud formation (GO:0060676) extracellular region (GO:0005576) protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102) NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(8)|skin(2) 15 all_lung(31;0.00118) GTAACATCTGTCTCTCTGTAAA 0.515 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 280 272.34 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.17 CCDS3922.1, CCDS3923.1, CCDS54845.1, CCDS54846.1, CCDS75237.1 5p13.1-p12 2014-01-30 ENSG00000168621 ENSG00000168621 2668 "Endogenous ligands" 4232 protein-coding gene gene with protein product "astrocyte-derived trophic factor", "glial cell line derived neurotrophic factor", "glial derived neurotrophic factor" 600837 NA 8493557 Standard NM_000514 NM_199231 NA Approved ATF1, ATF2, HFB1-GDNF uc011cpg.2 P39905 OTTHUMG00000090809 ENST00000326524.2:c.*847GA>- chr5.hg19:g.37814910_37814911delTC 2 2 ref NA False 44 44 PASS 3 PASS ref->het 0 NA 206,208 49,50 25,23 1 1 B7WPK7|O95448|O95449|O95986|Q6FH33|Q96L44|Q9UD32|Q9UD33|Q9UMV2|Q9UP67|Q9UP97 True hg19 CCDS3922.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GDNF-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000207606.1 PASS NA None 280 True - TC ENST00000326524.2 SKIV2L2 23517 __UNKNOWN__ __UNKNOWN__ 5 54604005 54604006 __UNKNOWN__ Intron INS - - T rs528498095 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:54604005_54604006insT ENST00000230640.5 + 1 388 SKIV2L2_ENST00000504388.1_Intron|SKIV2L2_ENST00000545714.1_Intron NM_015360.4 NP_056175.3 P42285 SK2L2_HUMAN superkiller viralicidic activity 2-like 2 (S. cerevisiae) NA NA NA maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398) catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634) ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822) NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 41 Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194) TGTTGCTTTTATTTTTTTTCTC 0.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Melanoma(2;92 134 23744 29976 33782) PASS NA NA NA 0 166 173.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.65 D29641 CCDS3967.1 5q11.2 2008-11-25 2005-02-18 2005-02-18 ENSG00000039123 ENSG00000039123 23517 18734 protein-coding gene gene with protein product "functional spliceosome-associated protein 118" NA "KIAA0052" KIAA0052 NA Standard NM_015360 NA Approved Mtr4, Dob1, fSAP118 uc003jpy.4 P42285 OTTHUMG00000097019 ENST00000230640.5:c.134+30->T chr5.hg19:g.54604013_54604013dupT 9 12 ref NA False 98 98 PASS 8 PASS ref->het 0 NA 96,98 44,44 22,21 1 1 Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2 True hg19 CCDS3967.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SKIV2L2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000214108.1 PASS NA None 166 True + T ENST00000230640.5 DDX4 54514 __UNKNOWN__ __UNKNOWN__ 5 55094438 55094438 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:55094438delT ENST00000505374.1 + 18 1707 DDX4_ENST00000511853.1_Intron|DDX4_ENST00000354991.5_Intron|DDX4_ENST00000353507.5_Intron|DDX4_ENST00000514278.2_Intron NM_024415.2 NP_077726.1 Q9NQI0 DDX4_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 NA NA NA male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283) chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547) ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676) endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2) 24 Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223) ATGATTTTGattttttttaat 0.299 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 106 120.24 NA NA 35 36 36 NA NA NA 5 NA NA NA 55094438 2202 4300 6502 SO:0001627 intron_variant 0.22 AF262962 CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1 5p15.2-p13.1 2008-02-05 2003-06-13 ENSG00000152670 ENSG00000152670 54514 "DEAD-boxes" 18700 protein-coding gene gene with protein product 605281 "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4" NA 10920202, 11850529 Standard NM_024415 NM_001142549 NA Approved VASA uc003jqg.4 Q9NQI0 OTTHUMG00000097044 ENST00000505374.1:c.1615+39T>- chr5.hg19:g.55094438delT 7 8 ref NA False 48 48 PASS 8 PASS ref->het 0 NA 62,62 29,30 12,12 1 1 A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1 True hg19 CCDS3969.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DDX4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000214147.2 PASS NA None 106 True + T ENST00000505374.1 WDR41 55255 __UNKNOWN__ __UNKNOWN__ 5 76728856 76728856 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:76728856delA ENST00000296679.4 - 0 1859 WDR41_ENST00000414719.2_3'UTR|WDR41_ENST00000512033.1_5'UTR|WDR41_ENST00000507029.1_3'UTR NM_018268.2 NP_060738.2 Q9HAD4 WDR41_HUMAN WD repeat domain 41 NA NA NA lysosomal membrane (GO:0005765) NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5) 14 all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059) OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40) ATGGACTGACAAAAAAAATTA 0.318 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 179 210.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.54 AF115511 CCDS4038.1 5q14 2013-01-09 ENSG00000164253 ENSG00000164253 55255 "WD repeat domain containing" 25601 protein-coding gene gene with protein product NA NA 12477932 Standard NM_018268 NM_018268 NA Approved FLJ10904 uc003kff.1 Q9HAD4 OTTHUMG00000102169 ENST00000296679.4:c.*104T>- chr5.hg19:g.76728856delA 7 9 ref NA False 78 78 PASS 8 PASS ref->het 0 NA 106,107 49,50 29,28 1 1 B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62 True hg19 CCDS4038.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA WDR41-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000220014.2 PASS NA None 179 True - A ENST00000296679.4 ANKRD34B 340120 __UNKNOWN__ __UNKNOWN__ 5 79853618 79853620 __UNKNOWN__ 3'UTR DEL AAC AAC - rs558213535 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:79853618_79853620delAAC ENST00000338682.3 - 0 2891_2893 NM_001004441.2 NP_001004441.2 A5PLL1 AN34B_HUMAN ankyrin repeat domain 34B NA NA NA cytoplasm (GO:0005737)|nucleus (GO:0005634) NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1) 28 Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113) OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36) ACAGTGCACAAACAACAAGACCC 0.345 NA NA NA 3 0.000599042 0.0023 0 5008 , , NA 15674 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 196 201.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.01 CCDS34194.1 5q14.1 2014-08-12 ENSG00000189127 ENSG00000189127 340120 "Ankyrin repeat domain containing" 33736 protein-coding gene gene with protein product NA NA Standard NM_001004441 NM_001004441 NA Approved DP58 uc003kgw.3 A5PLL1 OTTHUMG00000162541 ENST00000338682.3:c.*676GTT>- chr5.hg19:g.79853621_79853623delAAC 1 5 ref NA False 69 69 PASS 2 PASS ref->het 0 NA 132,133 48,48 20,20 1 1 B2RPH1|Q68D79 True hg19 CCDS34194.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ANKRD34B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000369475.1 PASS NA None 196 True - AAC ENST00000338682.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 5 95159461 95159461 __UNKNOWN__ IGR DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:95159461delC NA GLRX (752 upstream) : AC008592.4 (12185 downstream) NA NA NA NA CTAGTTCCGGCCCCCTCTAGT 0.458 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 59 68.92 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.5 NA NA NA NA NA chr5.hg19:g.95159461delC 4 6 ref NA False 47 47 PASS 5 PASS ref->het 0 NA 33,33 21,22 4,3 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 59 True C CTD-2215E18.1 0 __UNKNOWN__ __UNKNOWN__ 5 96496956 96496956 __UNKNOWN__ Intron DEL A A - rs34671120 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:96496956delA ENST00000509481.1 + 4 573 RIOK2_ENST00000283109.3_3'UTR NA NA NA urinary_tract(1) 1 ACTCCTAGGCAAAAAAAAGTG 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 102 104.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.49 NA NA NA NA NA ENST00000509481.1:c.33-21756A>- chr5.hg19:g.96496956delA 7 8 ref NA False 32 32 PASS 8 PASS ref->het 0 NA 71,72 13,13 14,13 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CTD-2215E18.1-001 PUTATIVE basic|appris_principal|exp_conf protein_coding NA protein_coding OTTHUMT00000370857.1 PASS NA None 102 True + A ENST00000509481.1 DIAPH1 1729 __UNKNOWN__ __UNKNOWN__ 5 140940450 140940450 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:140940450delT ENST00000389054.3 - 17 2614 DIAPH1_ENST00000518047.1_Intron|DIAPH1_ENST00000253811.6_Intron|DIAPH1_ENST00000398562.2_Intron|DIAPH1_ENST00000398566.3_Intron|DIAPH1_ENST00000520569.1_Intron|CTD-2024I7.13_ENST00000502205.2_RNA|DIAPH1_ENST00000389057.5_Intron|DIAPH1_ENST00000398557.4_Intron O60610 DIAP1_HUMAN diaphanous-related formin 1 NA NA NA actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605) cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587) ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102) breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2) 23 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CATACTGCTGTTTTTTTCCCT 0.527 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 91 88.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.44 BC007411 5q31 2013-05-24 2013-05-24 ENSG00000131504 ENSG00000131504 1729 2876 protein-coding gene gene with protein product 602121 "diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)" DFNA1 NA 9360932, 1350680 Standard NM_005219 NM_005219 NA Approved hDIA1, LFHL1 uc003llb.4 O60610 OTTHUMG00000149893 ENST00000389054.3:c.2473+11042A>- chr5.hg19:g.140940450delT 6 8 ref NA False 69 69 PASS 7 PASS ref->het 0 NA 59,62 22,22 9,7 2 2 A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DIAPH1-001 KNOWN basic|appris_candidate protein_coding NA protein_coding OTTHUMT00000313771.3 PASS NA None 91 True - T ENST00000389054.3 FAM114A2 10827 __UNKNOWN__ __UNKNOWN__ 5 153414554 153414554 __UNKNOWN__ Intron DEL T T - rs75714302 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:153414554delT ENST00000351797.4 - 2 63 FAM114A2_ENST00000522858.1_Intron|FAM114A2_ENST00000520667.1_Intron|FAM114A2_ENST00000520313.1_Intron NM_018691.2 NP_061161.2 Q9NRY5 F1142_HUMAN family with sequence similarity 114, member A2 NA NA NA purine nucleotide binding (GO:0017076) NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)|urinary_tract(1) 18 CCAAAAAAAATTTATATAGGC 0.323 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 167 168.65 NA NA 16 17 17 NA NA NA 5 NA NA NA 153414554 2182 4282 6464 SO:0001627 intron_variant 0.59 AF159700 CCDS4323.1 5q31-q33 2008-06-13 2008-06-13 2008-06-13 ENSG00000055147 ENSG00000055147 10827 1333 protein-coding gene gene with protein product NA "chromosome 5 open reading frame 3" C5orf3 NA 10843801 Standard NM_018691 XM_005268359 NA Approved 133K02 uc003lvc.3 Q9NRY5 OTTHUMG00000130147 ENST00000351797.4:c.14-27A>- chr5.hg19:g.153414554delT 2 8 ref NA False 146 107 PASS 3 PASS ref->het 0 NA 88,89 62,63 18,17 1 1 B2R8D8|Q9H7E0 True hg19 CCDS4323.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM114A2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252455.1 PASS NA None 167 True - T ENST00000351797.4 SIRT5 23408 __UNKNOWN__ __UNKNOWN__ 6 13612398 13612398 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:13612398delA ENST00000606117.1 + 0 1530 SIRT5_ENST00000359782.3_3'UTR NM_012241.4 NP_036373.1 sirtuin 5 NA NA NA breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(3)|upper_aerodigestive_tract(1) 11 Breast(50;0.00669)|Ovarian(93;0.0634) all_hematologic(90;0.117) Epithelial(50;0.176) TAGATTGTCTAAAAAAAATAG 0.299 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 213 203.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.96 AF083110 CCDS4526.1, CCDS4527.1, CCDS54966.1, CCDS56398.1 6p23 2010-08-05 2010-06-25 ENSG00000124523 ENSG00000124523 23408 14933 protein-coding gene gene with protein product 604483 "sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 5", "sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae)" NA 10381378 Standard NM_012241 NA Approved uc003nay.3 Q9NXA8 OTTHUMG00000014278 ENST00000606117.1:c.*301A>- chr6.hg19:g.13612398delA 7 9 ref NA False 48 48 PASS 8 PASS ref->het 0 NA 152,155 37,37 25,27 1 1 True hg19 CCDS4526.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SIRT5-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000039908.2 PASS NA None 213 True + A ENST00000606117.1 NOL7 51406 __UNKNOWN__ __UNKNOWN__ 6 13621337 13621338 __UNKNOWN__ 3'UTR INS - - A LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:13621337_13621338insA ENST00000451315.2 + 0 1084_1085 NOL7_ENST00000474485.1_Intron NM_016167.3 NP_057251.2 Q9UMY1 NOL7_HUMAN nucleolar protein 7, 27kDa NA NA NA nucleus (GO:0005634) poly(A) RNA binding (GO:0044822) breast(1)|large_intestine(3)|lung(1) 5 Breast(50;0.00669)|Ovarian(93;0.0634) all_hematologic(90;0.135) Epithelial(50;0.176) AGAGGGGTGGCAAAAATGGCAC 0.391 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 196 185.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.01 AF172066 CCDS4528.1 6p23 2008-05-23 2004-02-10 ENSG00000225921 ENSG00000225921 51406 21040 protein-coding gene gene with protein product 611533 "chromosome 6 open reading frame 90", "polyglutamine binding protein 3" C6orf90, PQBP3 NA 16205646 Standard NM_016167 NM_016167 NA Approved NOP27, RARG-1, dJ223E5.2 uc003naz.3 Q9UMY1 OTTHUMG00000014277 ENST00000451315.2:c.*279->A chr6.hg19:g.13621342_13621342dupA 6 5 ref NA False 35 35 PASS 5 PASS ref->het 0 NA 138,142 31,33 27,25 1 1 Q5T297|Q9Y3U7 True hg19 CCDS4528.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NOL7-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000039904.1 PASS NA None 196 True + A ENST00000451315.2 JARID2 3720 __UNKNOWN__ __UNKNOWN__ 6 15496722 15496722 __UNKNOWN__ Frame_Shift_Del DEL G G - rs554145993 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:15496722delG ENST00000341776.2 + 7 1510 c.1266delG c.(1264-1266)gtgfs p.V422fs JARID2_ENST00000541660.1_Frame_Shift_Del_p.V384fs|JARID2_ENST00000397311.3_Frame_Shift_Del_p.V250fs NM_004973.3 NP_004964.2 Q92833 JARD2_HUMAN jumonji, AT rich interactive domain 2 422 NA NA central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351) histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634) chromatin binding (GO:0003682)|DNA binding (GO:0003677) breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1) 59 Breast(50;0.0142)|Ovarian(93;0.103) all_hematologic(90;0.00612) CTAAGGAGGTGGGGGGGCGGC 0.667 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 202 216.05 NA NA 22 28 26 NA NA NA 6 NA NA NA 15496722 2180 4275 6455 SO:0001589 frameshift_variant 9.91 U57592 CCDS4533.1, CCDS58996.1 6p24-p23 2008-02-05 2006-10-06 2004-01-30 ENSG00000008083 ENSG00000008083 3720 6196 protein-coding gene gene with protein product 601594 "jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2" JMJ NA 8894700 Standard NM_004973 NM_001267040 NA Approved uc003nbj.4 Q92833 OTTHUMG00000014293 ENST00000341776.2:c.1266delG chr6.hg19:g.15496722delG ENSP00000341280:p.Val422fs 6 9 ref NA False 69 69 PASS 7 PASS ref->het 0 NA 120,137 34,36 56,37 1 1 A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63 True hg19 CCDS4533.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA JARID2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000039926.1 PASS NA None 202 True + G ENST00000341776.2 PRSS16 10279 __UNKNOWN__ __UNKNOWN__ 6 27218858 27218858 __UNKNOWN__ Frame_Shift_Del DEL C C - rs368386726 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:27218858delC ENST00000230582.3 + 6 644 c.629delC c.(628-630)gccfs p.A210fs PRSS16_ENST00000421826.2_Intron NM_005865.3 NP_005856.1 Q9NQE7 TSSP_HUMAN protease, serine, 16 (thymus) 210 NA NA protein catabolic process (GO:0030163) cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764) serine-type peptidase activity (GO:0008236) central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1) 26 GCCTCCTCCGCCCCGGTGCGG 0.647 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSCLC(178;1118 2105 17078 23587 44429) PASS NA NA NA 0 551 512.63 NA NA 64 74 71 NA NA NA 6 NA NA NA 27218858 2203 4300 6503 SO:0001589 frameshift_variant 4.53 AF052514 CCDS4623.1 6p21 2010-05-07 ENSG00000112812 ENSG00000112812 10279 "Serine peptidases / Serine peptidases" 9480 protein-coding gene gene with protein product 607169 NA 10527559 Standard NM_005865 NA Approved TSSP uc003nja.3 Q9NQE7 OTTHUMG00000016167 ENST00000230582.3:c.629delC chr6.hg19:g.27218858delC ENSP00000230582:p.Ala210fs 3 6 ref NA False 99 99 PASS 4 PASS ref->het 0 NA 404,417 80,83 71,58 1 1 O75416 True hg19 CCDS4623.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PRSS16-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000043418.2 PASS NA None 551 True + C ENST00000230582.3 OR2J2 26707 __UNKNOWN__ __UNKNOWN__ 6 29141422 29141422 __UNKNOWN__ Frame_Shift_Del DEL A A - rs556940268|rs201438710 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:29141422delA ENST00000377167.2 + 1 112 c.10delA c.(10-12)aaafs p.K5fs NM_030905.2 NP_112167.2 O76002 OR2J2_HUMAN olfactory receptor, family 2, subfamily J, member 2 5 NA NA integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984) endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1) 25 AATGATGATTAAAAAAAATGC 0.358 NA NA NA AAAAAAAA|AAAAAAAA|AAAAAAA|deletion 21 0.00419329 0.0144 0.0014 5008 , , NA 19015 0 NA 0.001 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 584 579.24 NA NA 105 102 103 NA NA NA 6 NA NA NA 29141422 1836 4079 5915 SO:0001589 frameshift_variant 1.29 CCDS43434.1 6p22.2-p21.31 2012-08-09 ENSG00000204700 ENSG00000204700 26707 "GPCR / Class A : Olfactory receptors" 8260 protein-coding gene gene with protein product NA NA Standard NM_030905 NA Approved OR6-8, hs6M1-6, dJ80I19.4 uc011dlm.2 O76002 OTTHUMG00000031091 ENST00000377167.2:c.10delA chr6.hg19:g.29141422delA ENSP00000366372:p.Lys5fs 7 8 ref NA False 64 64 PASS 8 PASS ref->het 0 NA 429,435 92,92 61,59 1 1 A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3 True hg19 CCDS43434.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OR2J2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076131.2 PASS NA None 584 True + A ENST00000377167.2 TNF 7124 __UNKNOWN__ __UNKNOWN__ 6 31543582 31543582 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:31543582delG ENST00000449264.2 + 1 239 c.64delG c.(64-66)gggfs p.G23fs NM_000594.3 NP_000585.2 P01375 TNFA_HUMAN tumor necrosis factor 23 NA NA activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209) cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037) cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164) large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3) 8 Ovarian(999;0.00556) Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041) CAAGAAGACAGGGGGGCCCCA 0.642 NA NA NA Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 688 704.01 NA NA 76 79 78 NA NA NA 6 NA NA NA 31543582 2203 4300 6503 SO:0001589 frameshift_variant 2.16 Familial Cancer Database incl.: Familial Head and Neck Cancer X02910 CCDS4702.1 6p21.3 2013-05-22 2010-05-04 ENSG00000232810 ENSG00000232810 7124 "Tumor necrosis factor (ligand) superfamily" 11892 protein-coding gene gene with protein product "TNF superfamily, member 2" 191160 "tumor necrosis factor (TNF superfamily, member 2)" TNFA NA 2413547, 6392892 Standard NM_000594 NA Approved TNFSF2, DIF, TNF-alpha uc003nui.4 P01375 OTTHUMG00000031194 ENST00000449264.2:c.64delG chr6.hg19:g.31543582delG ENSP00000398698:p.Gly23fs 5 6 ref NA False 138 133 PASS 6 PASS ref->het 0 NA 460,471 136,140 89,74 1 1 O43647|Q9P1Q2|Q9UIV3 True hg19 CCDS4702.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNF-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076390.2 PASS NA None 688 True + G ENST00000449264.2 NOTCH4 4855 __UNKNOWN__ __UNKNOWN__ 6 32190722 32190722 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:32190722delC ENST00000375023.3 - 2 294 NM_004557.3 NP_004548.3 Q99466 NOTC4_HUMAN notch 4 NA NA NA cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367) cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886) calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872) NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1) 100 cctcacctctccccccctgct 0.567 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 361 335.39 NA NA 39 38 39 NA NA NA 6 NA NA NA 32190722 692 1591 2283 SO:0001627 intron_variant 1.87 CCDS34420.1 6p21.3 2013-01-10 2010-06-24 ENSG00000204301 ENSG00000204301 4855 "Ankyrin repeat domain containing" 7884 protein-coding gene gene with protein product 164951 "Notch (Drosophila) homolog 4", "Notch homolog 4 (Drosophila)" INT3 NA 7835890 Standard NM_004557 NA Approved uc003obb.3 Q99466 OTTHUMG00000031044 ENST00000375023.3:c.155+59G>- chr6.hg19:g.32190722delC 6 8 ref NA False 113 112 PASS 7 PASS ref->het 0 NA 240,244 74,76 56,50 1 1 B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0 True hg19 CCDS34420.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NOTCH4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076045.2 PASS NA None 361 True - C ENST00000375023.3 ITPR3 3710 __UNKNOWN__ __UNKNOWN__ 6 33648261 33648261 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:33648261delC ENST00000374316.5 + 33 5410 ITPR3_ENST00000605930.1_Intron Q14573 ITPR3_HUMAN inositol 1,4,5-trisphosphate receptor, type 3 NA NA NA activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281) apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235) inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091) NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 85 Caffeine(DB00201) GTGGGTGAAGCCCCCCAGGAG 0.622 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 215 222.69 NA NA 47 49 48 NA NA NA 6 NA NA NA 33648261 2203 4300 6503 SO:0001627 intron_variant 2.04 D26351 CCDS4783.1 6p21.31 2011-11-24 2011-04-28 ENSG00000096433 ENSG00000096433 3710 "Ion channels / Inositol triphosphate receptors" 6182 protein-coding gene gene with protein product 147267 "inositol 1,4,5-triphosphate receptor, type 3" NA 8081734, 8288584 Standard NM_002224 NM_002224 NA Approved IP3R3 uc021ywr.1 Q14573 OTTHUMG00000014532 ENST00000374316.5:c.4350+30C>- chr6.hg19:g.33648261delC 5 6 ref NA False 61 61 PASS 6 PASS ref->het 0 NA 153,155 35,36 27,26 1 1 Q14649|Q5TAQ2 True hg19 CCDS4783.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ITPR3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000040204.2 PASS NA None 215 True + C ENST00000374316.5 GSTA2 2939 __UNKNOWN__ __UNKNOWN__ 6 52619887 52619887 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:52619887delA ENST00000493422.1 - 4 295 NM_000846.4 NP_000837.3 P09210 GSTA2_HUMAN glutathione S-transferase alpha 2 NA NA NA epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062) glutathione transferase activity (GO:0004364) breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 16 Lung NSC(77;0.118) Azathioprine(DB00993)|Busulfan(DB01008)|Chloroquine(DB00608)|Clofibrate(DB00636)|Ethacrynic acid(DB00903)|Glutathione(DB00143)|Vitamin E(DB00163) TAAGAGGAAGAAAAAAAAGGA 0.368 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 163 154.06 NA NA 93 91 92 NA NA NA 6 NA NA NA 52619887 2203 4300 6503 SO:0001627 intron_variant 0 AL109918 CCDS4944.1 6p12.2 2012-06-21 2008-11-26 ENSG00000244067 ENSG00000244067 2939 2.5.1.18 "Glutathione S-transferases / Soluble" 4627 protein-coding gene gene with protein product 138360 "glutathione S-transferase A2" GST2 NA Standard NM_000846 NM_000846 NA Approved uc003pay.3 P09210 OTTHUMG00000016263 ENST00000493422.1:c.140-14T>- chr6.hg19:g.52619887delA 7 10 ref NA False 37 37 PASS 8 PASS ref->het 0 NA 97,99 49,49 17,17 1 1 Q12759|Q16491|Q9NTY6 True hg19 CCDS4944.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GSTA2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000043589.1 PASS NA None 163 True - A ENST00000493422.1 DST 667 __UNKNOWN__ __UNKNOWN__ 6 56476324 56476324 __UNKNOWN__ Frame_Shift_Del DEL A A - rs35805169 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:56476324delA ENST00000361203.3 - 34 4503 c.4496delT c.(4495-4497)ttgfs p.L1499fs DST_ENST00000370788.2_Frame_Shift_Del_p.L1499fs|DST_ENST00000370769.4_Frame_Shift_Del_p.L1499fs|DST_ENST00000370754.5_Frame_Shift_Del_p.L1677fs|DST_ENST00000244364.6_Frame_Shift_Del_p.L1173fs|DST_ENST00000446842.2_Frame_Shift_Del_p.L1173fs|DST_ENST00000421834.2_Frame_Shift_Del_p.L1499fs|DST_ENST00000312431.6_Frame_Shift_Del_p.L1499fs Q03001 DYST_HUMAN dystonin 1499 NA NA axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090) actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018) calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803) NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3) 105 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) ATGTTTTGCCAAAAAAAGCTG 0.353 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 109 96.5 NA NA 128 121 123 NA NA NA 6 NA NA NA 56476324 1814 4084 5898 SO:0001589 frameshift_variant 0.37 M22942, M69225 CCDS4959.1, CCDS47443.1, CCDS75474.1 6p12.1 2013-01-10 2004-06-25 2004-07-01 ENSG00000151914 ENSG00000151914 667 "EF-hand domain containing" 1090 protein-coding gene gene with protein product 113810 "bullous pemphigoid antigen 1, 230/240kDa" BPAG1 NA 2461961, 2276744 Standard NM_001723 NM_001144770 NA Approved BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2 uc021zba.2 Q03001 OTTHUMG00000014913 ENST00000361203.3:c.4496delT chr6.hg19:g.56476324delA ENSP00000354508:p.Leu1499fs 6 7 ref NA False 54 54 PASS 7 PASS ref->het 0 NA 65,67 28,28 15,13 2 2 B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DST-004 NOVEL not_organism_supported|basic|appris_candidate protein_coding NA protein_coding OTTHUMT00000041021.3 PASS NA None 109 True - A ENST00000361203.3 KCNQ5 56479 __UNKNOWN__ __UNKNOWN__ 6 73766487 73766487 __UNKNOWN__ Intron DEL A A - rs201031713 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:73766487delA ENST00000370398.1 + 3 725 KCNQ5_ENST00000402622.2_Intron|KCNQ5_ENST00000355635.3_Intron|KCNQ5_ENST00000355194.4_Intron|KCNQ5_ENST00000414165.2_Intron|KCNQ5_ENST00000342056.2_Intron|KCNQ5_ENST00000403813.2_Intron|KCNQ5_ENST00000370392.1_Intron NM_019842.3 NP_062816.2 Q9NR82 KCNQ5_HUMAN potassium voltage-gated channel, KQT-like subfamily, member 5 NA NA NA protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268) plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076) delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242) breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1) 57 all_epithelial(107;0.116)|Lung NSC(302;0.219) COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583) Ezogabine(DB04953) GATGTGCAATAAAAAAAAGAa 0.398 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(142;1375 1859 14391 23261 44706) PASS NA NA NA 0 242 213.62 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.46 AF202977 CCDS4976.1, CCDS55034.1 6q14 2012-07-05 ENSG00000185760 ENSG00000185760 56479 "Potassium channels", "Voltage-gated ion channels / Potassium channels" 6299 protein-coding gene gene with protein product 607357 NA 10787416, 10816588, 16382104 Standard NM_019842 NM_019842 NA Approved Kv7.5 uc011dyh.2 Q9NR82 OTTHUMG00000015020 ENST00000370398.1:c.616+14702A>- chr6.hg19:g.73766487delA 7 10 ref NA False 34 34 PASS 8 PASS ref->het 0 NA 166,166 50,50 25,25 1 1 A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6 True hg19 CCDS4976.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KCNQ5-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000041198.3 PASS NA None 242 True + A ENST00000370398.1 KHDC1 80759 __UNKNOWN__ __UNKNOWN__ 6 74001672 74001672 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:74001672delT ENST00000370384.3 - 2 707 RP11-398K22.12_ENST00000441363.1_RNA|KHDC1_ENST00000484801.1_Intron NM_001251874.1 NP_001238803.1 Q4VXA5 KHDC1_HUMAN KH homology domain containing 1 NA NA NA integral component of membrane (GO:0016021) RNA binding (GO:0003723) large_intestine(1)|lung(4)|skin(1) 6 ACAGACTCCCTTTTTTTGGTA 0.423 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 576 540.08 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.55 CCDS43480.1, CCDS59027.1 6q13 2014-05-15 2007-11-13 2007-11-13 ENSG00000135314 ENSG00000135314 80759 21366 protein-coding gene gene with protein product 611688 "chromosome 6 open reading frame 148" C6orf148 NA 17913455 Standard NM_030568 NM_030568 NA Approved MGC10818, bA257K9.4, NDG1 uc003pgn.4 Q4VXA5 OTTHUMG00000015030 ENST00000370384.3:c.206+48A>- chr6.hg19:g.74001672delT 6 7 ref NA False 121 121 PASS 7 PASS ref->het 0 NA 435,438 94,94 50,48 1 1 Q5JSQ7|Q8WTV2|Q96NQ5 True hg19 CCDS59027.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KHDC1-005 PUTATIVE basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000148103.2 PASS NA None 576 True - T ENST00000370384.3 OOEP 441161 __UNKNOWN__ __UNKNOWN__ 6 74104340 74104340 __UNKNOWN__ Intron DEL G G - rs575785933|rs537622156 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:74104340delG ENST00000370363.1 - 1 375 A6NGQ2 OOEP_HUMAN oocyte expressed protein NA NA NA cellular protein complex assembly (GO:0043623)|embryo implantation (GO:0007566)|embryonic pattern specification (GO:0009880)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|protein phosphorylation (GO:0006468) apical part of cell (GO:0045177)|cell cortex (GO:0005938)|protein complex (GO:0043234) RNA binding (GO:0003723) large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1) 8 AATACACAGTGGGGGGGTGGG 0.572 NA NA NA OREG0003901 type=REGULATORY REGION|Gene=DDX43|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay ?|GGGGGGG|GGGGGG|unsure 32 0.00638978 0.0234 0.0014 5008 , , NA 13155 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 114 125.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 4.58 BC024931 CCDS47451.1 6q13 2012-02-22 2012-02-22 2007-11-13 ENSG00000203907 ENSG00000203907 441161 21382 protein-coding gene gene with protein product "KH homology domain containing 2" 611689 "chromosome 6 open reading frame 156", "oocyte expressed protein homolog (dog)" C6orf156 NA 17913455 Standard NM_001080507 NM_001080507 NA Approved Em:AC019205.2, KHDC2 uc003pgu.4 A6NGQ2 OTTHUMG00000150057 ENST00000370363.1:c.117+101C>- chr6.hg19:g.74104340delG 6 13 ref 1150 False 31 31 PASS 7 PASS ref->het 0 NA 50,62 23,27 47,33 1 1 A6NIN5|A9UIB7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OOEP-001 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000041200.1 PASS NA None 114 True - G ENST00000370363.1 ASCC3 10973 __UNKNOWN__ __UNKNOWN__ 6 100956908 100956908 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:100956908delA ENST00000369162.2 - 0 7307 NM_006828.2 NP_006819.2 Q8N3C0 ASCC3_HUMAN activating signal cointegrator 1 complex subunit 3 NA NA NA cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634) ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822) breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 92 all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13) BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199) GGTTTTCCTTAAAAAAAGCAG 0.343 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 77 78.31 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.31 AJ223948 CCDS5046.1, CCDS5047.1, CCDS75497.1 6q16 2008-02-05 2004-07-28 ENSG00000112249 ENSG00000112249 10973 18697 protein-coding gene gene with protein product "RNA helicase family" 614217 "helicase, ATP binding 1" HELIC1 NA 10218103 Standard NM_006828 NM_006828 NA Approved RNAH, ASC1p200, dJ121G13.4, dJ467N11.1 uc003pqk.3 Q8N3C0 OTTHUMG00000015279 ENST00000369162.2:c.*354T>- chr6.hg19:g.100956908delA 6 7 ref NA False 68 68 PASS 7 PASS ref->het 0 NA 42,43 27,27 9,10 2 2 E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0 True hg19 CCDS5046.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ASCC3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041632.2 PASS NA None 77 True - A ENST00000369162.2 HDAC2 3066 __UNKNOWN__ __UNKNOWN__ 6 114255228 114255229 __UNKNOWN__ 3'UTR INS - - A LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:114255228_114255229insA ENST00000519065.1 - 0 8836_8837 Q92769 HDAC2_HUMAN histone deacetylase 2 NA NA NA ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667) chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134) biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2) 27 all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24) all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832) Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546) TTAAATATGAGAAAAAAGTTGA 0.267 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 79 80.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.29 U31814 CCDS43493.1, CCDS43493.2 6q21 2008-08-29 ENSG00000196591 ENSG00000196591 3066 4853 protein-coding gene gene with protein product 605164 NA 9782097 Standard NM_001527 NA Approved RPD3, YAF1 uc003pwd.2 Q92769 OTTHUMG00000015411 ENST00000519065.1:c.*6994->T chr6.hg19:g.114255234_114255234dupA 7 7 ref NA False 51 51 PASS 6 PASS ref->het 0 NA 48,49 21,21 10,10 1 1 B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4 True hg19 CCDS43493.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HDAC2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041909.2 PASS NA None 79 True - A ENST00000519065.1 DSE 29940 __UNKNOWN__ __UNKNOWN__ 6 116575389 116575389 __UNKNOWN__ 5'UTR DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:116575389delC ENST00000540275.1 + 0 54 RP3-486I3.7_ENST00000448740.2_lincRNA Q9UL01 DSE_HUMAN dermatan sulfate epimerase NA NA NA carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281) endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021) chondroitin-glucuronate 5-epimerase activity (GO:0047757) NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1) 35 all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234) Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262) CTTCTTGTCACAAAAAGAATT 0.448 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 146 149.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.31 AF098066 CCDS5107.1 6q22 2008-02-05 2007-01-29 2007-01-29 ENSG00000111817 ENSG00000111817 29940 5.1.3.19 21144 protein-coding gene gene with protein product 605942 "squamous cell carcinoma antigen recognized by T cells 2" SART2 NA 11920522, 16505484 Standard NM_013352 NM_001080976 NA Approved DSEPI uc003pws.3 Q9UL01 OTTHUMG00000015434 ENST00000540275.1:c.-68C>- chr6.hg19:g.116575389delC 0 7 ref NA False 347 128 PASS 1 PASS ref->het 0 NA 44,44 83,85 18,17 1 1 Q5R3K6 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DSE-203 KNOWN basic protein_coding NA protein_coding PASS NA None 146 True + C ENST00000540275.1 GOPC 57120 __UNKNOWN__ __UNKNOWN__ 6 117883069 117883069 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:117883069delA ENST00000052569.6 - 0 2952 DCBLD1_ENST00000296955.8_Intron|GOPC_ENST00000467125.1_Intron|GOPC_ENST00000535237.1_3'UTR|GOPC_ENST00000368498.2_3'UTR NM_001017408.2 NP_001017408.1 Q9HD26 GOPC_HUMAN golgi-associated PDZ and coiled-coil motif containing NA NA NA apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289) cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140) ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083) GOPC/ROS1(14) endometrium(1)|large_intestine(3)|lung(4)|ovary(1) 9 all_cancers(87;0.00844)|all_epithelial(87;0.0242) GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976) TGGGAAAGCCAAAAAAAATGT 0.264 NA NA O ROS1 glioblastoma NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 6 6q21 57120 golgi associated PDZ and coiled-coil motif containing NA O 0 57 61.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF287894 CCDS5117.1, CCDS34523.1 6q21 2010-02-12 2010-02-12 ENSG00000047932 ENSG00000047932 57120 17643 protein-coding gene gene with protein product 606845 NA 11162552, 11520064 Standard NM_020399 NM_020399 NA Approved dJ94G16.2, PIST, FIG, GOPC1, CAL Q9HD26 OTTHUMG00000015457 ENST00000052569.6:c.*1348T>- chr6.hg19:g.117883069delA 7 8 ref NA False 61 61 PASS 8 PASS ref->het 0 NA 24,24 25,26 7,6 1 1 A6NM30|Q59FS4|Q969U8 True hg19 CCDS34523.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GOPC-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041987.1 PASS NA None 57 True - A ENST00000052569.6 FABP7 2173 __UNKNOWN__ __UNKNOWN__ 6 123105136 123105138 __UNKNOWN__ 3'UTR DEL CCT CCT - rs200830892|rs199657149 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:123105136_123105138delCCT ENST00000368444.3 + 0 943_945 NM_001446.3 NP_001437.1 O15540 FABP7_HUMAN fatty acid binding protein 7, brain NA NA NA cell proliferation in forebrain (GO:0021846)|epithelial cell proliferation (GO:0050673)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|prepulse inhibition (GO:0060134) cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|nucleus (GO:0005634) lipid binding (GO:0008289)|transporter activity (GO:0005215) kidney(1)|large_intestine(1)|lung(2)|stomach(1) 5 GBM - Glioblastoma multiforme(226;0.226) Alpha-Linolenic Acid(DB00132)|Dihomo-gamma-linolenic acid(DB00154)|Icosapent(DB00159) TCCCCCCCCCCCTTTTTTTTATA 0.256 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 118 126.23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.7 D88648 CCDS5127.1 6q22-q23 2013-03-01 ENSG00000164434 ENSG00000164434 2173 "Fatty acid binding protein family" 3562 protein-coding gene gene with protein product "brain lipid binding protein" 602965 NA 9375786 Standard NM_001446 NM_001446 NA Approved B-FABP, BLBP uc003pzf.3 O15540 OTTHUMG00000015489 ENST00000368444.3:c.*226CCT>- chr6.hg19:g.123105136_123105138delCCT 0 11 ref NA False 95 95 PASS 1 PASS ref->het 0 NA 75,84 31,31 22,14 1 1 B2R4L1|O14951|Q6IAU7|Q9H047 True hg19 CCDS5127.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FABP7-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000042037.1 PASS NA None 118 True + CCT ENST00000368444.3 BCLAF1 9774 __UNKNOWN__ __UNKNOWN__ 6 136582194 136582195 __UNKNOWN__ 3'UTR INS - - AA rs141067744 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:136582194_136582195insAA ENST00000531224.1 - 0 3068_3069 BCLAF1_ENST00000530767.1_3'UTR|BCLAF1_ENST00000527536.1_3'UTR|BCLAF1_ENST00000031135.9_3'UTR|BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000353331.4_3'UTR|BCLAF1_ENST00000527759.1_3'UTR NM_001077441.1|NM_014739.2 NP_001070909.1|NP_055554.1 Q9NYF8 BCLF1_HUMAN BCL2-associated transcription factor 1 NA NA NA apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634) DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822) haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1) 9 Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331) AAAAATCAGGTAAAAAAAATGG 0.267 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Colon(142;1534 1789 5427 7063 28491) PASS NA NA NA 0 298 275.55 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.58 AF249273 CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1 6q22-q23 2007-03-02 ENSG00000029363 ENSG00000029363 9774 16863 protein-coding gene gene with protein product 612588 NA 8724849, 10330179 Standard NM_014739 NM_001077440 NA Approved KIAA0164, BTF uc003qgx.1 Q9NYF8 OTTHUMG00000033323 ENST00000531224.1:c.*54->TT chr6.hg19:g.136582201_136582202dupAA 10 8 ref NA False 157 156 PASS 8 PASS ref->het 0 NA 190,199 53,62 54,51 1 1 A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0 True hg19 CCDS5177.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BCLAF1-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000042375.2 PASS NA None 298 True - A ENST00000531224.1 IFNGR1 3459 __UNKNOWN__ __UNKNOWN__ 6 137519505 137519506 __UNKNOWN__ Frame_Shift_Del DEL CT CT - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:137519505_137519506delCT ENST00000367739.4 - 7 1253_1254 c.1132_1133delAG c.(1132-1134)agtfs p.S380fs IFNGR1_ENST00000543628.1_Frame_Shift_Del_p.S352fs NM_000416.2 NP_000407.1 P15260 INGR1_HUMAN interferon gamma receptor 1 380 NA NA cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165) dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982) interferon-gamma receptor activity (GO:0004906) central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1) 18 Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389) Interferon gamma-1b(DB00033) AGGTGAAGAACTCTCTCTCTCT 0.431 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 218 215.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.11 CCDS5185.1 6q23-q24 2014-09-17 ENSG00000027697 ENSG00000027697 3459 "Interferons", "CD molecules" 5439 protein-coding gene gene with protein product 107470 IFNGR NA Standard NM_000416 NA Approved CD119 uc003qho.2 P15260 OTTHUMG00000015656 ENST00000367739.4:c.1132_1133delAG chr6.hg19:g.137519515_137519516delCT ENSP00000356713:p.Ser380fs 5 4 ref NA False 109 104 PASS 6 PASS ref->het 0 NA 132,134 60,61 28,28 1 1 B4DFT7|E1P587|Q53Y96 True hg19 CCDS5185.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IFNGR1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000042401.1 PASS NA None 218 True - CT ENST00000367739.4 EIF3B 8662 __UNKNOWN__ __UNKNOWN__ 7 2418994 2418994 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:2418994delC ENST00000360876.4 + 18 2397 EIF3B_ENST00000397011.2_Intron NM_001037283.1 NP_001032360.1 eukaryotic translation initiation factor 3, subunit B NA NA NA breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1) 24 Ovarian(82;0.0253) UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14) TAGGCATGTGCCCCCATGGGT 0.652 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 94 107.3 NA NA 39 35 36 NA NA NA 7 NA NA NA 2418994 2197 4289 6486 SO:0001627 intron_variant 0.05 U62583 CCDS5332.1 7p22 2013-02-12 2007-07-27 2007-07-27 ENSG00000106263 ENSG00000106263 8662 "RNA binding motif (RRM) containing" 3280 protein-coding gene gene with protein product 603917 "eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa" EIF3S9 NA 8995410 Standard NM_001037283 NA Approved PRT1, eIF3b uc003sly.3 P55884 OTTHUMG00000022839 ENST00000360876.4:c.2342-35C>- chr7.hg19:g.2418994delC 4 5 ref NA False 38 38 PASS 5 PASS ref->het 0 NA 54,55 29,29 12,11 1 1 True hg19 CCDS5332.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EIF3B-002 KNOWN alternative_3_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000207006.1 PASS NA None 94 True + C ENST00000360876.4 CAMK2B 816 __UNKNOWN__ __UNKNOWN__ 7 44270576 44270577 __UNKNOWN__ Intron INS - - G rs540063043 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:44270576_44270577insG ENST00000353625.4 - 14 1046 CAMK2B_ENST00000502837.2_Intron|CAMK2B_ENST00000395747.2_Intron|CAMK2B_ENST00000440254.2_Intron|CAMK2B_ENST00000358707.3_Intron|CAMK2B_ENST00000350811.3_Intron|CAMK2B_ENST00000258682.6_Intron|CAMK2B_ENST00000395749.2_Intron|CAMK2B_ENST00000457475.1_Intron|CAMK2B_ENST00000346990.4_Intron|CAMK2B_ENST00000347193.4_Intron NM_172083.2 NP_742080.1 Q13554 KCC2B_HUMAN calcium/calmodulin-dependent protein kinase II beta NA NA NA activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268) cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233) ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803) cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1) 18 CCAAGGCCGCTGGGGGGGCAAG 0.574 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 273 258.6 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.08 U50358 CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1 7p14.3-p14.1 2008-10-30 2008-10-30 ENSG00000058404 ENSG00000058404 816 1461 protein-coding gene gene with protein product "CaM-kinase II beta chain", "calcium/calmodulin-dependent protein kinase type II beta chain", "CaM kinase II beta subunit", "proline rich calmodulin-dependent protein kinase" 607707 "calcium/calmodulin-dependent protein kinase (CaM kinase) II beta" CAMKB NA Standard NM_172084 NM_172079 NA Approved CAM2, CAMK2 uc003tkq.2 Q13554 OTTHUMG00000023491 ENST00000353625.4:c.1036+27->C chr7.hg19:g.44270583_44270583dupG 8 7 ref NA False 47 47 PASS 7 PASS ref->het 0 NA 189,192 41,42 44,44 1 1 A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4 True hg19 CCDS5488.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CAMK2B-006 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251231.1 PASS NA None 273 True - G ENST00000353625.4 GSAP 54103 __UNKNOWN__ __UNKNOWN__ 7 76940794 76940794 __UNKNOWN__ Intron DEL A A - rs531113787 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:76940794delA ENST00000257626.7 - 31 2552 GSAP_ENST00000441833.2_Intron NM_017439.3 NP_059135.2 A4D1B5 GSAP_HUMAN gamma-secretase activating protein NA NA NA positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162) trans-Golgi network (GO:0005802) beta-amyloid binding (GO:0001540) NA GAGGGCAGGGAAAAAGGGTTA 0.388 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 244 247.62 NA NA 51 47 48 NA NA NA 7 NA NA NA 76940794 1851 4087 5938 SO:0001627 intron_variant 0.4 CCDS34672.2 7q11.23 2013-04-05 2013-04-05 2013-04-05 ENSG00000186088 ENSG00000186088 54103 28042 protein-coding gene gene with protein product 613552 "pigeon homolog (Drosophila)" PION NA 20811458 Standard NM_017439 NM_017439 NA Approved LOC54103 uc003ugf.3 A4D1B5 OTTHUMG00000150504 ENST00000257626.7:c.2474-28T>- chr7.hg19:g.76940794delA 4 5 ref NA False 118 104 PASS 5 PASS ref->het 0 NA 136,138 71,71 36,37 1 1 A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9 True hg19 CCDS34672.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GSAP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000318672.2 PASS NA None 244 True - A ENST00000257626.7 PON1 5444 __UNKNOWN__ __UNKNOWN__ 7 94928082 94928082 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:94928082delA ENST00000222381.3 - 0 1473 NM_000446.5 NP_000437.3 P27169 PON1_HUMAN paraoxonase 1 NA NA NA aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636) blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366) aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803) autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2) 27 all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239) STAD - Stomach adenocarcinoma(171;0.0031) Cefazolin(DB01327) GTGTATTCTCAAAAAAAAGCC 0.348 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(119;715 1622 17358 22490 33240) PASS NA NA NA 0 338 347.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.55 AF539592 CCDS5638.1 7q21.3 2014-03-14 ENSG00000005421 ENSG00000005421 5444 3.1.1.2 "Paraoxonases" 9204 protein-coding gene gene with protein product "esterase A", "arylesterase 1" 168820 PON NA 8661009, 15450851 Standard NM_000446 NM_000446 NA Approved ESA uc003uns.3 P27169 OTTHUMG00000153894 ENST00000222381.3:c.*174T>- chr7.hg19:g.94928082delA 7 8 ref NA False 65 65 PASS 8 PASS ref->het 0 NA 224,232 65,68 45,41 1 1 B2RA40|Q16052|Q6B0J6|Q9UCB1 True hg19 CCDS5638.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PON1-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000332865.2 PASS NA None 338 True - A ENST00000222381.3 CUX1 1523 __UNKNOWN__ __UNKNOWN__ 7 101556434 101556434 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:101556434delA ENST00000560541.1 + 0 367 CUX1_ENST00000393824.3_Intron|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000549414.2_Intron|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Intron|CUX1_ENST00000360264.3_Intron|CUX1_ENST00000550008.2_Intron|CUX1_ENST00000292535.7_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000546411.2_Intron P39880 CUX1_HUMAN cut-like homeobox 1 NA NA NA auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301) cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634) chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565) breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5) 70 GTTGTTTTTTAAAAAAATTTT 0.473 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 158 179.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.74 M74099 CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1 7q22.1 2012-10-03 2007-11-07 2007-11-07 ENSG00000257923 ENSG00000257923 1523 "Homeoboxes / CUT class" 2557 protein-coding gene gene with protein product "golgi integral membrane protein 6" 116896 "cut (Drosophila)-like 1 (CCAAT displacement protein)", "cut-like 1, CCAAT displacement protein (Drosophila)" CUTL1 NA 8468066, 9799793, 15004235 Standard NM_001913 NM_001202543 NA Approved CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6 uc003uyx.4 P39880 OTTHUMG00000157129 ENST00000560541.1:c.*364A>- chr7.hg19:g.101556434delA 6 8 ref NA False 37 37 PASS 7 PASS ref->het 0 NA 99,102 38,39 21,19 1 1 B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CUX1-019 KNOWN basic|exp_conf processed_transcript NA protein_coding OTTHUMT00000418419.1 PASS NA None 158 True + A ENST00000560541.1 BCAP29 55973 __UNKNOWN__ __UNKNOWN__ 7 107259330 107259330 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:107259330delT ENST00000005259.4 + 0 1587 BCAP29_ENST00000379119.2_3'UTR|BCAP29_ENST00000379117.2_3'UTR NM_018844.3 NP_061332.2 Q9UHQ4 BAP29_HUMAN B-cell receptor-associated protein 29 NA NA NA apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020) cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1) 14 ATGACCTTAGTTTTTTTTAAG 0.303 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 168 159.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.59 CCDS34730.1, CCDS34731.1 7q22.3 2012-09-20 ENSG00000075790 ENSG00000075790 55973 24131 protein-coding gene gene with protein product NA NA 12477932 Standard NM_018844 NM_018844 NA Approved BAP29, DKFZp686M2086 uc011kma.1 Q9UHQ4 OTTHUMG00000154770 ENST00000005259.4:c.*522T>- chr7.hg19:g.107259330delT 7 8 ref NA False 33 33 PASS 8 PASS ref->het 0 NA 114,118 28,29 21,19 1 1 G5E9L4|O95003 True hg19 CCDS34731.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BCAP29-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000337011.2 PASS NA None 168 True + T ENST00000005259.4 MKLN1 4289 __UNKNOWN__ __UNKNOWN__ 7 131180428 131180428 __UNKNOWN__ 3'UTR DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:131180428delC ENST00000352689.6 + 0 10189 RP11-180C16.1_ENST00000610193.1_RNA NM_013255.4 NP_037387.2 Q9UL63 MKLN1_HUMAN muskelin 1, intracellular mediator containing kelch motifs NA NA NA signal transduction (GO:0007165) cytoplasm (GO:0005737) breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1) 28 Melanoma(18;0.162) AAGCATATGTCCCCCCACCCT 0.388 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 184 180.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.53 AF047489 CCDS34754.1 7q32 2008-07-18 ENSG00000128585 ENSG00000128585 4289 7109 protein-coding gene gene with protein product 605623 NA 10640805 Standard NM_013255 NM_001145354 NA Approved TWA2 uc011kpm.2 Q9UL63 OTTHUMG00000154880 ENST00000352689.6:c.*7941C>- chr7.hg19:g.131180428delC 5 9 ref NA False 69 69 PASS 6 PASS ref->het 0 NA 129,132 40,40 14,12 1 1 A4D1M8|A6NG43|Q9NSK4|Q9NUS8 True hg19 CCDS34754.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MKLN1-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000337473.4 PASS NA None 184 True + C ENST00000352689.6 UBN2 254048 __UNKNOWN__ __UNKNOWN__ 7 138968105 138968106 __UNKNOWN__ Frame_Shift_Ins INS - - A LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:138968105_138968106insA ENST00000473989.3 + 15 2454_2455 c.2454_2455insA c.(2455-2457)aaafs p.K819fs UBN2_ENST00000288561.8_Frame_Shift_Ins_p.K736fs NM_173569.3 NP_775840.3 Q6ZU65 UBN2_HUMAN ubinuclein 2 819 NA NA extracellular space (GO:0005615)|nucleus (GO:0005634) NS(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1) 42 TAGCTACTCCCAAAAAACTAGA 0.446 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 318 336.79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.28 AK098644 CCDS43655.1, CCDS43655.2 7q34 2008-12-08 ENSG00000157741 ENSG00000157741 254048 21931 protein-coding gene gene with protein product 613841 NA 19029251 Standard NM_173569 NM_173569 NA Approved FLJ25778, KIAA2030 uc011kqr.2 Q6ZU65 OTTHUMG00000157623 ENST00000473989.3:c.2460dupA chr7.hg19:g.138968111_138968111dupA ENSP00000418648:p.Lys819fs 7 6 ref NA False 48 48 PASS 6 PASS ref->het 0 NA 226,227 62,62 28,28 1 1 A4D1S2|Q2YDY4|Q6P1K0|Q86XN9|Q8N7D1 True hg19 CCDS43655.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UBN2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000349272.3 PASS NA None 318 True + A ENST00000473989.3 AGK 55750 __UNKNOWN__ __UNKNOWN__ 7 141333648 141333654 __UNKNOWN__ Intron DEL GAGTTCT GAGTTCT - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:141333648_141333654delGAGTTCT ENST00000355413.4 + 10 848 AGK_ENST00000473247.1_Intron|AGK_ENST00000535825.1_Intron NM_018238.3 NP_060708.1 Q53H12 AGK_HUMAN acylglycerol kinase NA NA NA ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205) intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739) acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951) breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3) 17 Melanoma(164;0.0171) TAGATGTAAAGAGTTCTGAGTGATTAT 0.367 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 142 149.34 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.08 BC022777 CCDS5865.1 7q34 2010-05-04 2007-01-11 2007-01-11 ENSG00000006530 ENSG00000006530 55750 2.7.1.94 21869 protein-coding gene gene with protein product 610345 "multiple substrate lipid kinase" MULK NA 15252046, 15939762, 17135245 Standard NM_018238 NM_018238 NA Approved FLJ10842 uc003vwi.2 Q53H12 OTTHUMG00000157499 ENST00000355413.4:c.589-47GAGTTCT>- chr7.hg19:g.141333648_141333654delGAGTTCT 0 4 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 107,107 31,31 13,13 1 1 Q75KN1|Q96GC3|Q9NP48 True hg19 CCDS5865.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AGK-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000348969.1 PASS NA None 142 True + GAGTTCT ENST00000355413.4 TRBV7-7 28591 __UNKNOWN__ __UNKNOWN__ 7 142120214 142120215 __UNKNOWN__ RNA DEL AC AC - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:142120214_142120215delAC ENST00000390377.1 - 0 49 T cell receptor beta variable 7-7 NA NA NA NA acacatgcatacacacacacac 0.436 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 104 103.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1.09 L36092 7q34 2012-02-07 ENSG00000253291 ENSG00000253291 28591 "T cell receptors / TRB locus" 12241 other T cell receptor gene NA NA 8650574 Standard NG_001333 NG_001333 NA Approved TRBV77, TCRBV6S6A2T, TCRBV7S7 OTTHUMG00000158872 ENST00000390377.1: chr7.hg19:g.142120224_142120225delAC 5 2 ref NA False 32 32 PASS 6 PASS ref->het 0 NA 60,62 22,22 23,22 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRBV7-7-001 KNOWN mRNA_end_NF|cds_end_NF|basic|appris_principal TR_V_gene NA TR_V_gene OTTHUMT00000352480.1 PASS NA None 104 True - AC ENST00000390377.1 RARRES2 5919 __UNKNOWN__ __UNKNOWN__ 7 150038081 150038082 __UNKNOWN__ 5'UTR DEL CT CT - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:150038081_150038082delCT ENST00000466675.1 - 0 650_651 RARRES2_ENST00000482669.1_Intron|RARRES2_ENST00000223271.3_Intron Q99969 RARR2_HUMAN retinoic acid receptor responder (tazarotene induced) 2 NA NA NA brown fat cell differentiation (GO:0050873)|chemotaxis (GO:0006935)|embryonic digestive tract development (GO:0048566)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|positive regulation of chemotaxis (GO:0050921)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of protein phosphorylation (GO:0001934)|regulation of lipid catabolic process (GO:0050994)|retinoid metabolic process (GO:0001523) extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062) receptor binding (GO:0005102) endometrium(1)|large_intestine(1)|lung(1)|pancreas(1)|skin(1) 5 OV - Ovarian serous cystadenocarcinoma(82;0.011) CCCGGAGCCCCTCTCTCCTTTC 0.668 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 614 625.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 6.72 U77594 CCDS5902.1 7q36.1 2013-02-25 ENSG00000106538 ENSG00000106538 5919 "Endogenous ligands" 9868 protein-coding gene gene with protein product "chemerin" 601973 NA 9270552, 17767914 Standard NM_002889 NA Approved TIG2, HP10433 uc003wha.3 Q99969 OTTHUMG00000158325 ENST00000466675.1:c.-384AG>- chr7.hg19:g.150038085_150038086delCT 2 5 ref NA False 580 289 PASS 3 PASS ref->het 0 NA 341,350 172,180 102,87 1 1 Q7LE02 True hg19 CCDS5902.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RARRES2-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000350693.1 PASS NA None 614 True - CT ENST00000466675.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 7 152143188 152143189 __UNKNOWN__ IGR INS - - G rs144632479 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:152143188_152143189insG NA FABP5P3 (2916 upstream) : LINC01003 (17681 downstream) NA NA NA NA GCACGCTGCACGGGGGGACACT 0.604 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 188 197.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.57 NA NA NA NA NA chr7.hg19:g.152143194_152143194dupG 7 6 ref NA False 34 34 PASS 6 PASS ref->het 0 NA 130,134 24,24 30,27 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 188 True G RBM33 155435 __UNKNOWN__ __UNKNOWN__ 7 155465545 155465545 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:155465545delT ENST00000392759.3 + 3 297 RBM33_ENST00000401878.3_Intron|RBM33_ENST00000287912.3_Intron Q96EV2 RBM33_HUMAN RNA binding motif protein 33 NA NA NA nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822) breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1) 27 all_neural(206;0.101) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.011) UCEC - Uterine corpus endometrioid carcinoma (81;0.2) GACATGTCTCTTTTTTTTCTC 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 69 61.36 NA 16,3298 NA 4,8,1645 45 45 45 NA -0.3 0 7 45 67,7341 NA 21,25,3658 no intron RBM33 NM_053043.2 25,33,5303 A1A1,A1R,RR NA 0.9044,0.4828,0.7741 155465545 83,10639 1731 3896 5627 SO:0001627 intron_variant 0.25 AL832196 CCDS5941.2 7q36.3 2013-02-12 ENSG00000184863 ENSG00000184863 155435 "RNA binding motif (RRM) containing" 27223 protein-coding gene gene with protein product NA "proline rich 8" PRR8 NA Standard NM_001008408 NM_053043 NA Approved DKFZp686F102, MGC20460, DKFZp434D1319 uc010lqk.1 Q96EV2 OTTHUMG00000150260 ENST00000392759.3:c.123-16T>- chr7.hg19:g.155465545delT 7 9 ref NA False 41 41 PASS 8 PASS ref->het 0 NA 40,43 20,20 10,9 1 1 A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RBM33-005 NOVEL basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000317227.1 PASS NA None 69 True + T ENST00000392759.3 DLGAP2 9228 __UNKNOWN__ __UNKNOWN__ 8 1654892 1654893 __UNKNOWN__ 3'UTR INS - - A LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:1654892_1654893insA ENST00000421627.2 + 0 8382_8383 NM_004745.3 NP_004736.2 Q9P1A6 DLGP2_HUMAN discs, large (Drosophila) homolog-associated protein 2 NA NA NA neuron-neuron synaptic transmission (GO:0007270) cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211) breast(1)|endometrium(6)|lung(31)|prostate(3) 41 Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846) BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171) AATGATGAAGGAAAAAAAATTA 0.426 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 177 185.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AB000275 CCDS47760.1, CCDS75689.1 8p23 2007-12-06 2001-11-28 ENSG00000198010 ENSG00000198010 9228 2906 protein-coding gene gene with protein product 605438 "discs, large (Drosophila) homolog-associated protein 2" NA 9286858, 10854099 Standard NM_004745 NM_004745 NA Approved DAP-2 uc003wpl.4 Q9P1A6 OTTHUMG00000163599 ENST00000421627.2:c.*5321->A chr8.hg19:g.1654900_1654900dupA 9 8 ref NA False 93 93 PASS 8 PASS ref->het 0 NA 118,121 44,44 12,10 1 1 A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7 True hg19 CCDS47760.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DLGAP2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000374478.1 PASS NA None 177 True + A ENST00000421627.2 LGI3 203190 __UNKNOWN__ __UNKNOWN__ 8 22005413 22005414 __UNKNOWN__ 3'UTR INS - - G LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:22005413_22005414insG ENST00000306317.2 - 0 2195_2196 LGI3_ENST00000424267.2_3'UTR NM_139278.2 NP_644807.1 Q8N145 LGI3_HUMAN leucine-rich repeat LGI family, member 3 NA NA NA exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157) cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021) catalytic activity (GO:0003824) endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2) 17 Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999) GCTGCAGAGTAGGGGGGGCCTG 0.644 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 141 146.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.49 AJ487518 CCDS6025.1 8p21.2 2008-07-28 ENSG00000168481 ENSG00000168481 203190 18711 protein-coding gene gene with protein product 608302 NA 12023020, 18628660 Standard NM_139278 NA Approved uc003xav.3 Q8N145 OTTHUMG00000131599 ENST00000306317.2:c.*260->C chr8.hg19:g.22005420_22005420dupG 8 7 ref NA False 57 57 PASS 7 PASS ref->het 0 NA 82,87 38,39 22,19 1 1 A5PLP2|Q86TL4|Q8N296 True hg19 CCDS6025.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LGI3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254482.1 PASS NA None 141 True - G ENST00000306317.2 SORBS3 10174 __UNKNOWN__ __UNKNOWN__ 8 22429367 22429368 __UNKNOWN__ Intron INS - - G rs192331993|rs537010962 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:22429367_22429368insG ENST00000240123.7 + 19 2230 SORBS3_ENST00000428103.1_Intron NM_005775.4 NP_005766.3 O60504 VINEX_HUMAN sorbin and SH3 domain containing 3 NA NA NA actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|muscle contraction (GO:0006936)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of stress fiber assembly (GO:0051496) cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634) structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166) breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9) 18 Prostate(55;0.0421)|Breast(100;0.102) BRCA - Breast invasive adenocarcinoma(99;0.00566)|Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061) TGATCAGACGTGGGGGGGGTCA 0.594 NA NA NA GGGGGG|GGGGGGGG|GGGGGGGGG|cryptic_indel 16 0.00319489 0.0091 0.0014 5008 , , NA 19459 0.003 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 157 177.89 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.75 CCDS6031.1 8p21.3 2008-02-05 ENSG00000120896 ENSG00000120896 10174 30907 protein-coding gene gene with protein product 610795 NA 9885244, 12510380 Standard NM_005775 NM_001018003 NA Approved SCAM-1, SH3D4, vinexin uc003xbv.3 O60504 OTTHUMG00000131728 ENST00000240123.7:c.1847+33->G chr8.hg19:g.22429375_22429375dupG 9 9 ref NA False 68 68 PASS 8 PASS ref->het 0 NA 84,90 36,39 35,30 1 1 Q5BJE4|Q6NX54|Q96FY4|Q9UQE4 True hg19 CCDS6031.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SORBS3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254647.3 PASS NA None 157 True + G ENST00000240123.7 STMN4 81551 __UNKNOWN__ __UNKNOWN__ 8 27093859 27093860 __UNKNOWN__ 3'UTR INS - - CA rs140426507 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:27093859_27093860insCA ENST00000265770.7 - 0 1209_1210 STMN4_ENST00000350889.4_3'UTR|STMN4_ENST00000519997.1_3'UTR Q9H169 STMN4_HUMAN stathmin-like 4 NA NA NA regulation of microtubule polymerization or depolymerization (GO:0031110) cell projection (GO:0042995)|Golgi apparatus (GO:0005794) endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1) 11 Ovarian(32;0.00167) UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142) Lomustine(DB01206) AAATGATGGTTCACACACACAC 0.475 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 279 260.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.68 CCDS6055.1, CCDS64851.1, CCDS64852.1, CCDS64854.1 8p21.2 2006-12-09 ENSG00000015592 ENSG00000015592 81551 16078 protein-coding gene gene with protein product NA NA 11230166 Standard NM_030795 NM_001283054 NA Approved RB3 uc003xfj.3 Q9H169 OTTHUMG00000099461 ENST00000265770.7:c.*504->TG chr8.hg19:g.27093868_27093869dupCA 8 2 ref NA False 91 90 PASS 7 PASS ref->het 0 NA 146,146 77,77 52,52 1 1 B7Z2Z7|B7Z4I9|D3DSS8|D3DSS9|G5EA16|Q2TAB9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA STMN4-006 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000375941.1 PASS NA None 279 True - CA ENST00000265770.7 PLEKHA2 59339 __UNKNOWN__ __UNKNOWN__ 8 38829153 38829154 __UNKNOWN__ 3'UTR DEL TC TC - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:38829153_38829154delTC ENST00000521746.1 + 0 1982_1983 CTD-2544N14.3_ENST00000520863.1_RNA|PLEKHA2_ENST00000420274.1_3'UTR|PLEKHA2_ENST00000388745.4_3'UTR Q9HB19 PKHA2_HUMAN pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 2 NA NA NA positive regulation of cell-matrix adhesion (GO:0001954) cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234) fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|lipid binding (GO:0008289) breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1) 13 all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152) LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235) TACCCATTTATCTCTCTCTCTC 0.421 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 81 75.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.13 AF286164 CCDS75732.1 8p11.21 2013-01-10 2002-01-14 ENSG00000169499 59339 "Pleckstrin homology (PH) domain containing" 14336 protein-coding gene gene with protein product "tandem PH Domain containing protein-2" 607773 "pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 2" NA 11001876 Standard NM_021623 NM_021623 NA Approved TAPP2 uc003xmi.4 Q9HB19 ENST00000521746.1:c.*999TC>- chr8.hg19:g.38829163_38829164delTC 6 4 ref NA False 64 64 PASS 7 PASS ref->het 0 NA 34,34 23,25 28,27 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PLEKHA2-002 PUTATIVE basic protein_coding NA protein_coding OTTHUMT00000377068.1 PASS NA None 81 True + TC ENST00000521746.1 CRH 1392 __UNKNOWN__ __UNKNOWN__ 8 67089076 67089076 __UNKNOWN__ 3'UTR DEL T T - rs544221122|rs149972470 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:67089076delT ENST00000276571.3 - 0 1083 NM_000756.2 NP_000747.1 P06850 CRF_HUMAN corticotropin releasing hormone NA NA NA adrenal gland development (GO:0030325)|associative learning (GO:0008306)|cellular response to cocaine (GO:0071314)|cellular response to dexamethasone stimulus (GO:0071549)|diterpenoid metabolic process (GO:0016101)|feeding behavior (GO:0007631)|female pregnancy (GO:0007565)|ferulate metabolic process (GO:0033494)|glucocorticoid biosynthetic process (GO:0006704)|hormone-mediated apoptotic signaling pathway (GO:0008628)|hypothalamus development (GO:0021854)|inflammatory response (GO:0006954)|ion homeostasis (GO:0050801)|learning or memory (GO:0007611)|locomotory exploration behavior (GO:0035641)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|lung development (GO:0030324)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell death (GO:0060548)|negative regulation of circadian sleep/wake cycle, REM sleep (GO:0042322)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gene expression (GO:0010629)|negative regulation of glucagon secretion (GO:0070093)|negative regulation of luteinizing hormone secretion (GO:0033685)|negative regulation of norepinephrine secretion (GO:0010700)|parturition (GO:0007567)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of corticosterone secretion (GO:2000854)|positive regulation of corticotropin secretion (GO:0051461)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of digestive system process (GO:0060456)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein phosphorylation (GO:0001934)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of serotonin secretion (GO:0014062)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to immobilization stress (GO:0035902)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963) cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|varicosity (GO:0043196) hormone activity (GO:0005179)|neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102) breast(1)|endometrium(1)|lung(2)|urinary_tract(1) 5 all_cancers(86;2.58e-06)|all_epithelial(80;6.27e-09)|all_lung(136;0.000414)|Lung NSC(129;0.0011) Epithelial(68;0.0136)|all cancers(69;0.0507)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904) Corticotropin(DB01285) TTTTTTTAAATTTTTTTTGTG 0.373 NA NA NA OREG0018805 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) TTTTTtT|TTTTTTTT|TTTTTTT|insertion 65 0.0129792 0.0477 0.0029 5008 , , NA 19093 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 365 362.19 NA 213,4043 NA 18,177,1933 15 17 16 NA -2.6 0 8 dbSNP_134 16 72,8152 NA 21,30,4061 no utr-3 CRH NM_000756.2 39,207,5994 A1A1,A1R,RR NA 0.8755,5.0047,2.2837 67089076 285,12195 2200 4291 6491 SO:0001624 3_prime_UTR_variant 2.45 CCDS6188.1 8q13 2013-02-25 ENSG00000147571 1392 "Endogenous ligands" 2355 protein-coding gene gene with protein product "corticotropin-releasing factor", "corticoliberin" 122560 NA Standard NM_000756 NM_000756 NA Approved CRF uc003xvy.2 P06850 ENST00000276571.3:c.*46A>- chr8.hg19:g.67089076delT 7 9 ref 1096 False 58 58 PASS 8 PASS ref->het 0 NA 238,246 52,53 80,72 1 1 B3KQS4 True hg19 CCDS6188.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CRH-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000378926.1 PASS NA None 365 True - T ENST00000276571.3 TRAM1 23471 __UNKNOWN__ __UNKNOWN__ 8 71486093 71486094 __UNKNOWN__ 3'UTR DEL AT AT - rs35679510 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:71486093_71486094delAT ENST00000262213.2 - 0 2367_2368 TRAM1_ENST00000521425.1_3'UTR|AC120194.1_ENST00000391684.1_5'UTR NM_014294.5 NP_055109.1 Q15629 TRAM1_HUMAN translocation associated membrane protein 1 NA NA NA cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|viral process (GO:0016032) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021) receptor activity (GO:0004872) endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1) 17 Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509) AGAGATACaaatatatatatat 0.267 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Ovarian(85;984 1334 5116 12432 40638) PASS NA NA NA 0 78 88.08 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 X63679 CCDS6207.1 8q13.1 2004-01-22 ENSG00000067167 ENSG00000067167 23471 20568 protein-coding gene gene with protein product 605190 NA 1315422 Standard NM_014294 NM_014294 NA Approved TRAM, TRAMP uc003xyo.2 Q15629 OTTHUMG00000164428 ENST00000262213.2:c.*1074AT>- chr8.hg19:g.71486103_71486104delAT 7 4 ref NA False 38 38 PASS 8 PASS ref->het 0 NA 39,39 19,19 21,21 1 1 B4E0K2 True hg19 CCDS6207.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRAM1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000378738.1 PASS NA None 78 True - AT ENST00000262213.2 TRIQK 286144 __UNKNOWN__ __UNKNOWN__ 8 93897075 93897075 __UNKNOWN__ 3'UTR DEL G G - rs531028746 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:93897075delG ENST00000521988.1 - 0 2354 CTD-3239E11.2_ENST00000523197.1_RNA|TRIQK_ENST00000537541.1_3'UTR|TRIQK_ENST00000518748.1_3'UTR|AC117834.1_ENST00000391681.1_Frame_Shift_Del_p.V11fs|CTD-3239E11.2_ENST00000521203.1_RNA NM_001171797.1 NP_001165268.1 Q629K1 TRIQK_HUMAN triple QxxK/R motif containing NA NA NA endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021) endometrium(3) 3 tgatgggagtgggggggtggg 0.403 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 414 446.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.17 AK096398, BC110326, BC031029, BC065838 CCDS55261.1 8q22.1 2012-04-18 2012-04-18 2012-04-18 ENSG00000205133 ENSG00000205133 286144 27828 protein-coding gene gene with protein product NA "chromosome 8 open reading frame 83" C8orf83 NA 18828657 Standard NM_001171795 NM_001171796 NA Approved DKFZp779L1068, PRO0845, LOC286144 uc022aya.1 Q629K1 OTTHUMG00000164162 ENST00000521988.1:c.*1775C>- chr8.hg19:g.93897075delG 6 11 ref NA False 67 67 PASS 7 PASS ref->het 0 NA 272,282 77,77 71,64 1 1 True hg19 CCDS55261.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRIQK-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000377523.3 PASS NA None 414 True - G ENST00000521988.1 EIF3E 3646 __UNKNOWN__ __UNKNOWN__ 8 109254408 109254408 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:109254408delT ENST00000220849.5 - 2 153 EIF3E_ENST00000519030.1_Intron NM_001568.2 NP_001559.1 eukaryotic translation initiation factor 3, subunit E NA NA NA EIF3E/RSPO2(6) NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 30 OV - Ovarian serous cystadenocarcinoma(57;6.84e-10) CATGACCTTATTTTTTATGTG 0.348 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(15;360 410 8460 34179 52246) PASS NA NA NA 0 510 516.71 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.18 U94175 CCDS6308.1 8q22-q23 2010-03-10 2007-07-27 2007-07-27 ENSG00000104408 ENSG00000104408 3646 3277 protein-coding gene gene with protein product 602210 "eukaryotic translation initiation factor 3, subunit 6 48kDa" INT6, EIF3S6 NA 9403073, 9295280 Standard NM_001568 NM_001568 NA Approved eIF3-p48, eIF3e uc003ymu.3 P60228 OTTHUMG00000164858 ENST00000220849.5:c.91-266A>- chr8.hg19:g.109254408delT 5 8 ref NA False 40 40 PASS 6 PASS ref->het 0 NA 399,407 68,68 52,52 2 2 True hg19 CCDS6308.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EIF3E-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000380612.2 PASS NA None 510 True - T ENST00000220849.5 TMEM74 157753 __UNKNOWN__ __UNKNOWN__ 8 109796600 109796600 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:109796600delC ENST00000297459.3 - 2 906 c.728delG c.(727-729)ggcfs p.G243fs TMEM74_ENST00000518838.1_Intron NM_153015.1 NP_694560.1 Q96NL1 TMM74_HUMAN transmembrane protein 74 243 NA NA autophagy (GO:0006914) cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764) breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1) 29 OV - Ovarian serous cystadenocarcinoma(57;3.08e-10) CAGGATGACGCCCCCCAGCGT 0.587 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 846 801.08 NA NA 68 66 67 NA NA NA 8 NA NA NA 109796600 2203 4300 6503 SO:0001589 frameshift_variant 2.8 AK055230 CCDS6310.1 8q23.1 2009-11-06 ENSG00000164841 157753 26409 protein-coding gene gene with protein product 613935 NA 12477932 Standard NM_153015 NM_153015 NA Approved FLJ30668, NET36 uc003ymy.1 Q96NL1 ENST00000297459.3:c.728delG chr8.hg19:g.109796600delC ENSP00000297459:p.Gly243fs 5 7 ref NA False 53 53 PASS 6 PASS ref->het 0 NA 647,664 108,112 90,75 1 1 True hg19 CCDS6310.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM74-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000380755.1 PASS NA None 846 True - C ENST00000297459.3 TRPS1 7227 __UNKNOWN__ __UNKNOWN__ 8 116430693 116430693 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:116430693delA ENST00000395715.3 - 6 3278 TRPS1_ENST00000519076.1_Intron|TRPS1_ENST00000520276.1_Intron|TRPS1_ENST00000220888.5_Intron NM_001282902.1|NM_001282903.1|NM_014112.2 NP_001269831.1|NP_001269832.1|NP_054831.2 Q9UHF7 TRPS1_HUMAN trichorhinophalangeal syndrome I NA NA NA chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178) nucleus (GO:0005634) sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270) autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2) 111 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) GAAACAGGGGAAAAAAACCAA 0.443 NA NA NA Langer-Giedion syndrome NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 154 151.29 NA NA 69 70 69 NA NA NA 8 NA NA NA 116430693 1893 4114 6007 SO:0001627 intron_variant 0.38 Familial Cancer Database Trichorhinophalangeal syndrome type 2, TRPS II AF183810 CCDS6318.2, CCDS64957.1 8q23.3 2014-06-23 ENSG00000104447 ENSG00000104447 7227 "GATA zinc finger domain containing", "Zinc fingers, C2H2-type" 12340 protein-coding gene gene with protein product 604386 NA 8530105, 10615131, 10647898 Standard NM_014112 NM_001282903 NA Approved LGCR uc003yny.3 Q9UHF7 OTTHUMG00000142829 ENST00000395715.3:c.2701-13T>- chr8.hg19:g.116430693delA 6 7 ref NA False 45 45 PASS 7 PASS ref->het 0 NA 106,110 23,23 25,21 2 2 B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6 True hg19 CCDS6318.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRPS1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000286435.3 PASS NA None 154 True - A ENST00000395715.3 KCNQ3 3786 __UNKNOWN__ __UNKNOWN__ 8 133184774 133184775 __UNKNOWN__ Intron DEL AC AC - rs146253351 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:133184774_133184775delAC ENST00000388996.4 - 7 1561 KCNQ3_ENST00000519445.1_Intron|KCNQ3_ENST00000521134.1_Intron NM_004519.3 NP_004510.1 O43525 KCNQ3_HUMAN potassium voltage-gated channel, KQT-like subfamily, member 3 NA NA NA axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268) axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076) delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249) NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 70 Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.000311) Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939) atgcacacatacacacacacac 0.495 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 247 244.58 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.4 AB208890 CCDS34943.1, CCDS56554.1 8q24 2012-07-05 ENSG00000184156 ENSG00000184156 3786 "Potassium channels", "Voltage-gated ion channels / Potassium channels" 6297 protein-coding gene gene with protein product 602232 EBN2 NA 9425900, 16382104 Standard NM_004519 NM_004519 NA Approved Kv7.3 uc003ytj.3 O43525 OTTHUMG00000137472 ENST00000388996.4:c.1140+69GT>- chr8.hg19:g.133184784_133184785delAC 6 2 ref NA False 32 32 PASS 7 PASS ref->het 0 NA 163,164 44,44 47,46 1 1 A2VCT8|B4DJY4|E7EQ89 True hg19 CCDS34943.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KCNQ3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000268621.2 PASS NA None 247 True - AC ENST00000388996.4 TONSL 4796 __UNKNOWN__ __UNKNOWN__ 8 145668452 145668452 __UNKNOWN__ Intron DEL G G - rs541781044 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:145668452delG ENST00000409379.3 - 4 478 NM_013432.4 NP_038460.4 Q96HA7 TONSL_HUMAN tonsoku-like, DNA repair protein NA NA NA cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297) cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634) histone binding (GO:0042393)|transcription corepressor activity (GO:0003714) biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1) 26 AGGAGGCTGCGGGGGTGCTGG 0.627 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 423 459.61 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.97 CCDS34968.2 8q24.3 2013-01-10 2010-12-02 2010-11-30 ENSG00000160949 ENSG00000160949 4796 "Ankyrin repeat domain containing" 7801 protein-coding gene gene with protein product 604546 "nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2" NFKBIL2 NA 7738005, 11246458 Standard NM_013432 NM_013432 NA Approved IKBR uc011llg.2 Q96HA7 OTTHUMG00000153122 ENST00000409379.3:c.448+68C>- chr8.hg19:g.145668452delG 4 6 ref NA False 31 31 PASS 5 PASS ref->het 0 NA 322,333 39,39 79,73 1 1 B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2 True hg19 CCDS34968.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TONSL-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000329668.2 PASS NA None 423 True - G ENST00000409379.3 ERMP1 79956 __UNKNOWN__ __UNKNOWN__ 9 5791180 5791181 __UNKNOWN__ Intron DEL AG AG - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:5791180_5791181delAG ENST00000339450.5 - 14 2476 ERMP1_ENST00000214893.5_Intron|ERMP1_ENST00000543230.1_Intron|ERMP1_ENST00000381506.3_Intron NM_024896.2 NP_079172.2 Q7Z2K6 ERMP1_HUMAN endoplasmic reticulum metallopeptidase 1 NA NA NA endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020) metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237) endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1) 20 Acute lymphoblastic leukemia(23;0.158) GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111) acagagagaaagagagagagag 0.426 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 73 67.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AB058718 CCDS34983.1 9p24 2008-02-05 2007-07-05 2007-07-05 ENSG00000099219 ENSG00000099219 79956 23703 protein-coding gene gene with protein product "Felix-ina" 611156 "KIAA1815" KIAA1815 NA 11347906 Standard NM_024896 XM_005251587 NA Approved FLJ23309, FXNA uc003zjm.1 Q7Z2K6 OTTHUMG00000019508 ENST00000339450.5:c.2387-3587CT>- chr9.hg19:g.5791190_5791191delAG 5 4 ref NA False 57 57 PASS 6 PASS ref->het 0 NA 43,43 20,20 12,12 1 1 B2RNA4|B3KSB1|Q8N5T5|Q9H5M1 True hg19 CCDS34983.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ERMP1-004 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000354877.1 PASS NA None 73 True - AG ENST00000339450.5 ACER2 340485 __UNKNOWN__ __UNKNOWN__ 9 19450832 19450833 __UNKNOWN__ 3'UTR INS - - C rs563612990 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:19450832_19450833insC ENST00000340967.2 + 0 1052_1053 NM_001010887.2 NP_001010887.2 Q5QJU3 ACER2_HUMAN alkaline ceramidase 2 NA NA NA activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to drug (GO:0035690)|ceramide metabolic process (GO:0006672)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of protein glycosylation in Golgi (GO:0090285)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512) Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173) ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633) endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1) 13 AATATTCCCTGCCCCCCTGCAG 0.347 NA NA NA CCCCCC|CCCCCC|CCCCCCC|insertion 10 0.00199681 0.0076 0 5008 , , NA 18507 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 236 243.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AK123581 CCDS34992.1 9p21.3 2013-01-25 2008-12-19 2008-12-19 ENSG00000177076 ENSG00000177076 340485 3.5.1.23 "Alkaline ceramidase" 23675 protein-coding gene gene with protein product 613492 "N-acylsphingosine amidohydrolase 3-like" ASAH3L NA 18945876 Standard XM_294540 XM_005251447 NA Approved FLJ41587 uc003zny.1 Q5QJU3 OTTHUMG00000019644 ENST00000340967.2:c.*199->C chr9.hg19:g.19450838_19450838dupC 7 6 ref NA False 63 63 PASS 6 PASS ref->het 0 NA 144,146 59,61 27,25 1 1 A2A3R8|Q569G5|Q5VZR7|Q71RD2 True hg19 CCDS34992.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACER2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000051864.1 PASS NA None 236 True + C ENST00000340967.2 ELAVL2 1993 __UNKNOWN__ __UNKNOWN__ 9 23692165 23692165 __UNKNOWN__ 3'UTR DEL A A - rs202039694|rs184512831 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:23692165delA ENST00000223951.6 - 0 1699 ELAVL2_ENST00000397312.2_3'UTR|ELAVL2_ENST00000380110.4_3'UTR|ELAVL2_ENST00000544538.1_3'UTR|ELAVL2_ENST00000380117.1_3'UTR NM_001171197.1 NP_001164668.1 Q12926 ELAV2_HUMAN ELAV like neuron-specific RNA binding protein 2 NA NA NA regulation of transcription, DNA-templated (GO:0006355) mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822) breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1) 39 GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19) AAAAGGGGGGAAAAAAAAGAC 0.313 NA NA NA AAAAAAAA|AAAAAAAA|AAAAAAA|deletion 11 0.00219649 8e-04 0 5008 , , NA 15062 0.0069 NA 0.001 False NA ,,, NA NA NA 2504 0.002 NA NA NA PASS NA NA NA 0 107 104.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.22 BC030692 CCDS6515.1, CCDS55298.1 9p21 2013-10-03 2013-10-03 ENSG00000107105 ENSG00000107105 1993 "RNA binding motif (RRM) containing" 3313 protein-coding gene gene with protein product "Hu antigen B" 601673 "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2", "ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)" NA 8812435 Standard NM_004432 NM_004432 NA Approved HuB, HEL-N1 uc003zpu.3 Q12926 OTTHUMG00000019700 ENST00000223951.6:c.*390T>- chr9.hg19:g.23692165delA 7 9 ref NA False 30 30 PASS 8 PASS ref->het 0 NA 77,78 14,16 15,13 1 1 D3DRK3|Q13235|Q59G15|Q8NEM4|Q9H1Q8 True hg19 CCDS55298.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ELAVL2-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000051944.2 PASS NA None 107 True - A ENST00000223951.6 PLAA 9373 __UNKNOWN__ __UNKNOWN__ 9 26905423 26905423 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:26905423delT ENST00000397292.3 - 0 2891 NM_001031689.2 NP_001026859.1 Q9Y263 PLAP_HUMAN phospholipase A2-activating protein NA NA NA inflammatory response (GO:0006954)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165) extracellular vesicular exosome (GO:0070062) phospholipase A2 activator activity (GO:0016005) breast(1)|endometrium(7)|kidney(2)|large_intestine(3)|lung(3)|prostate(1) 17 all_neural(3;3.53e-10)|Glioma(3;2.71e-09) Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011) CCGTATTCTCTTTTTTTAATT 0.343 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Melanoma(175;2670 2735 14091 35526) PASS NA NA NA 0 232 231.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.7 AF083395 CCDS35000.1 9p21 2013-01-10 ENSG00000137055 ENSG00000137055 9373 "WD repeat domain containing" 9043 protein-coding gene gene with protein product "DOA1 homolog (S. cerevisiae)" 603873 NA 9931468, 10644453 Standard NM_001031689 NM_001031689 NA Approved PLAP, PLA2P, FLJ11281, FLJ12699, DOA1 uc003zqd.3 Q9Y263 OTTHUMG00000019708 ENST00000397292.3:c.*86A>- chr9.hg19:g.26905423delT 6 8 ref NA False 154 113 PASS 7 PASS ref->het 0 NA 124,126 71,72 35,33 1 1 Q53EU5|Q5VY33|Q9NUL8|Q9NVE9|Q9UF53|Q9Y5L1 True hg19 CCDS35000.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PLAA-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000051958.2 PASS NA None 232 True - T ENST00000397292.3 CHMP5 51510 __UNKNOWN__ __UNKNOWN__ 9 33265820 33265820 __UNKNOWN__ Intron DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:33265820delG ENST00000223500.8 + 2 206 CHMP5_ENST00000419016.2_Intron NM_016410.5 NP_057494.3 Q9NZZ3 CHMP5_HUMAN charged multivesicular body protein 5 NA NA NA endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of receptor recycling (GO:0001919)|viral life cycle (GO:0019058)|viral process (GO:0016032) cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634) endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1) 10 LUSC - Lung squamous cell carcinoma(29;0.00506) GCAGTGTGGCGGGGGGTAAGA 0.448 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 150 173.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.46 AF132968 CCDS6537.1, CCDS56569.1 9p13.3 2011-09-21 2011-09-21 2005-08-09 ENSG00000086065 ENSG00000086065 51510 "Charged multivesicular body proteins" 26942 protein-coding gene gene with protein product 610900 "chromosome 9 open reading frame 83", "chromatin modifying protein 5" C9orf83, SNF7DC2 NA 15644320, 11559748 Standard NM_016410 NM_016410 NA Approved HSPC177, CGI-34, Vps60 uc003zsm.4 Q9NZZ3 OTTHUMG00000019765 ENST00000223500.8:c.70-188G>- chr9.hg19:g.33265820delG 5 8 ref NA False 49 49 PASS 6 PASS ref->het 0 NA 86,93 40,43 26,16 1 1 B2RD95|B4DIR6|Q5VXW2|Q96AV2|Q9HB68|Q9NYS4|Q9Y323 True hg19 CCDS6537.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CHMP5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000052040.3 PASS NA None 150 True + G ENST00000223500.8 VPS13A 23230 __UNKNOWN__ __UNKNOWN__ 9 79834842 79834842 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:79834842delT ENST00000360280.3 + 11 1014 VPS13A_ENST00000376636.3_Intron|VPS13A_ENST00000357409.5_Intron|VPS13A_ENST00000376634.4_Intron NM_033305.2 NP_150648.2 Q96RL7 VP13A_HUMAN vacuolar protein sorting 13 homolog A (S. cerevisiae) NA NA NA cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176) dense core granule (GO:0031045)|intracellular (GO:0005622) breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1) 104 TATAACTCAGTTTTTTTTCCA 0.348 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 80 84.91 NA ,,, 25,4223 NA 9,7,2108 38 41 40 NA ,,, -7.6 0 9 40 25,8211 NA 6,13,4099 no intron,intron,intron,intron VPS13A NM_033305.2,NM_015186.3,NM_001018038.2,NM_001018037.1 ,,, 15,20,6207 A1A1,A1R,RR NA 0.3035,0.5885,0.4005 ,,, ,,, 79834842 50,12434 2197 4293 6490 SO:0001627 intron_variant 0 AB023203 CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1 9q21 2014-01-30 2006-04-04 2004-02-11 ENSG00000197969 ENSG00000197969 23230 1908 protein-coding gene gene with protein product "chorein" 605978 "chorea acanthocytosis", "vacuolar protein sorting 13A (yeast)" CHAC NA 9382101, 11381253 Standard NM_015186 NM_001018038 NA Approved KIAA0986 uc004akr.3 Q96RL7 OTTHUMG00000020055 ENST00000360280.3:c.755-28T>- chr9.hg19:g.79834842delT 7 8 ref NA False 75 75 PASS 8 PASS ref->het 0 NA 41,41 33,33 6,6 1 1 Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1 True hg19 CCDS6655.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA VPS13A-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000052753.2 PASS NA None 80 True + T ENST00000360280.3 TLE1 7088 __UNKNOWN__ __UNKNOWN__ 9 84202839 84202840 __UNKNOWN__ Intron INS - - TCATCCCGCC rs71699706 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:84202839_84202840insTCATCCCGCC ENST00000376499.3 - 17 2894 NM_005077.3 NP_005068.2 Q04724 TLE1_HUMAN transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila) NA NA NA multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055) cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667) chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134) NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1) 29 gtgtgtgtgtgtgtgtgtgtgt 0.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870) PASS NA NA NA 0 66 104.88 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.87 CCDS6661.1 9q21.32 2013-01-10 2001-11-28 ENSG00000196781 ENSG00000196781 7088 "WD repeat domain containing" 11837 protein-coding gene gene with protein product "enhancer of split groucho 1" 600189 "transducin-like enhancer of split 1, homolog of Drosophila E(sp1)" NA 8365415, 8808280 Standard NM_005077 NM_005077 NA Approved ESG1, GRG1, ESG uc004aly.3 Q04724 OTTHUMG00000021008 ENST00000376499.3:c.1830-96->GGCGGGATGA chr9.hg19:g.84202839_84202840insTCATCCCGCC 1 2 ref NA False 34 34 PASS 0 PASS ref->het 0 NA 46,53 6,7 60,56 1 1 A8K495|Q5T3G4|Q969V9 True hg19 CCDS6661.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TLE1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000055407.1 PASS NA None 66 True - TCATCCCGCC ENST00000376499.3 ZCCHC6 79670 __UNKNOWN__ __UNKNOWN__ 9 88924081 88924081 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:88924081delT ENST00000375963.3 - 21 3833 ZCCHC6_ENST00000375960.2_Intron|ZCCHC6_ENST00000375957.1_Intron|ZCCHC6_ENST00000277141.6_Intron|ZCCHC6_ENST00000375961.2_Intron NM_001185059.1|NM_024617.3 NP_001171988.1|NP_078893.2 Q5VYS8 TUT7_HUMAN zinc finger, CCHC domain containing 6 NA NA NA RNA 3'-end processing (GO:0031123) poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270) breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1) 46 GTATAGCTAATTTTTAGTCAA 0.254 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 48 45.78 NA NA 21 23 23 NA NA NA 9 NA NA NA 88924081 2174 4239 6413 SO:0001627 intron_variant 0 AL832026 CCDS35057.1, CCDS55323.1 9q21 2014-03-05 ENSG00000083223 ENSG00000083223 79670 "Zinc fingers, CCHC domain containing" 25817 protein-coding gene gene with protein product "TUTase7" NA NA 11214970 Standard NM_024617 NM_001185059 NA Approved KIAA1711, FLJ13409, PAPD6, TUT7 uc004aoq.3 Q5VYS8 OTTHUMG00000020137 ENST00000375963.3:c.3660+45A>- chr9.hg19:g.88924081delT 4 5 ref NA False 35 35 PASS 5 PASS ref->het 0 NA 32,35 13,13 5,5 2 2 Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6 True hg19 CCDS35057.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZCCHC6-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000052918.1 PASS NA None 48 True - T ENST00000375963.3 ROR2 4920 __UNKNOWN__ __UNKNOWN__ 9 94486026 94486028 __UNKNOWN__ In_Frame_Del DEL TCC TCC - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:94486026_94486028delTCC ENST00000375708.3 - 9 2946_2948 c.2748_2750delGGA c.(2746-2751)gaggaa>gaa p.916_917EE>E ROR2_ENST00000375715.1_Intron|ROR2_ENST00000550066.1_5'UTR NM_004560.3 NP_004551.2 Q01974 ROR2_HUMAN receptor tyrosine kinase-like orphan receptor 2 916 NA NA cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071) clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147) autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 71 GACAGAGCCTTCCTCCTCCTCCT 0.645 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 195 182.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.45 M97639 CCDS6691.1 9q22 2013-01-11 ENSG00000169071 ENSG00000169071 4920 "Immunoglobulin superfamily / I-set domain containing" 10257 protein-coding gene gene with protein product 602337 NTRKR2, BDB, BDB1 NA 1334494, 10700182 Standard NM_004560 NA Approved uc004arj.2 Q01974 OTTHUMG00000020211 ENST00000375708.3:c.2748_2750delGGA chr9.hg19:g.94486035_94486037delTCC ENSP00000364860:p.Glu917del 3 4 ref NA False 110 110 PASS 4 PASS ref->het 0 NA 125,128 40,40 37,36 1 1 Q59GF5|Q5SPI5|Q9HAY7|Q9HB61 True hg19 CCDS6691.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ROR2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000053040.1 PASS NA None 195 True - TCC ENST00000375708.3 HSD17B3 3293 __UNKNOWN__ __UNKNOWN__ 9 99015211 99015211 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:99015211delT ENST00000375263.3 - 4 325 HSD17B3_ENST00000375262.2_Intron NM_000197.1 NP_000188.1 P37058 DHB3_HUMAN hydroxysteroid (17-beta) dehydrogenase 3 NA NA NA androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370) endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231) testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045) breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 13 Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214) GAGACAACAGTTTTTTTAATG 0.443 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 153 141.43 NA NA 85 83 84 NA NA NA 9 NA NA NA 99015211 2203 4299 6502 SO:0001627 intron_variant 0.09 CCDS6716.1 9q22 2011-09-20 ENSG00000130948 ENSG00000130948 3293 1.1.1.62 "Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3" 5212 protein-coding gene gene with protein product "short chain dehydrogenase/reductase family 12C, member 2" 605573 NA 8075637, 19027726 Standard NM_000197 NM_000197 NA Approved SDR12C2 uc004awa.1 P37058 OTTHUMG00000020292 ENST00000375263.3:c.278-19A>- chr9.hg19:g.99015211delT 6 7 ref NA False 40 40 PASS 7 PASS ref->het 0 NA 108,109 32,32 13,12 1 1 Q5U0Q6 True hg19 CCDS6716.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HSD17B3-005 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000053259.1 PASS NA None 153 True - T ENST00000375263.3 GRIN3A 116443 __UNKNOWN__ __UNKNOWN__ 9 104333784 104333784 __UNKNOWN__ 3'UTR DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:104333784delG ENST00000361820.3 - 0 5620 NM_133445.2 NP_597702.2 Q8TCU5 NMD3A_HUMAN glutamate receptor, ionotropic, N-methyl-D-aspartate 3A NA NA NA calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249) cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202) calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721) breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1) 80 Acute lymphoblastic leukemia(62;0.0568) Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193) CAAATTGGTTGGGGGTGGAAC 0.443 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 122 123.27 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.26 CCDS6758.1 9q31.1 2012-08-29 ENSG00000198785 ENSG00000198785 116443 "Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors" 16767 protein-coding gene gene with protein product 606650 NA Standard NM_133445 NA Approved GluN3A uc004bbp.2 Q8TCU5 OTTHUMG00000020387 ENST00000361820.3:c.*1672C>- chr9.hg19:g.104333784delG 4 7 ref NA False 31 31 PASS 5 PASS ref->het 0 NA 78,80 30,30 15,14 1 1 B3DLF9|Q5VTR3|Q8TF29|Q8WXI6 True hg19 CCDS6758.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GRIN3A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000053453.1 PASS NA None 122 True - G ENST00000361820.3 PALM2-AKAP2 445815 __UNKNOWN__ __UNKNOWN__ 9 112707388 112707388 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:112707388delT ENST00000374530.3 + 6 676 PALM2_ENST00000448454.2_3'UTR|AKAP2_ENST00000555236.1_Intron|PALM2-AKAP2_ENST00000302798.7_Intron|AKAP2_ENST00000510514.5_Intron|PALM2_ENST00000374531.2_3'UTR NM_007203.4|NM_147150.2 NP_009134.1|NP_671492.1 PALM2-AKAP2 readthrough NA NA NA breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1) 44 AATCTATTGCTTTTTTTTAAT 0.269 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 161 163 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.5 AB023137 CCDS35100.1, CCDS35101.1 9q31.3 2010-02-17 ENSG00000157654 ENSG00000157654 445815 33529 other readthrough NA NA 11478809 Standard NM_147150 NA Approved uc004bej.4 OTTHUMG00000156812 ENST00000374530.3:c.496+13080T>- chr9.hg19:g.112707388delT 7 8 ref NA False 57 57 PASS 8 PASS ref->het 0 NA 102,106 39,40 20,19 1 1 True hg19 CCDS35100.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PALM2-AKAP2-001 KNOWN basic|appris_candidate_longest|readthrough_transcript|CCDS protein_coding NA protein_coding OTTHUMT00000053603.1 PASS NA None 161 True + T ENST00000374530.3 SET 6418 __UNKNOWN__ __UNKNOWN__ 9 131451837 131451837 __UNKNOWN__ 5'UTR DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:131451837delC ENST00000322030.8 + 0 333 SET_ENST00000372692.4_Intron|SET_ENST00000409104.3_Intron NM_003011.3 NP_003002.2 Q01105 SET_HUMAN SET nuclear proto-oncogene NA NA NA DNA replication (GO:0006260)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of catalytic activity (GO:0043086)|negative regulation of histone acetylation (GO:0035067)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|nucleosome disassembly (GO:0006337)|regulation of catalytic activity (GO:0050790)|RNA metabolic process (GO:0016070) cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234) DNA binding (GO:0003677)|histone binding (GO:0042393)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 2A regulator activity (GO:0008601) endometrium(2)|kidney(1)|lung(2) 5 Myeloproliferative disorder(178;0.204) GBM - Glioblastoma multiforme(294;3.1e-09) cctccccgctccccccccGAC 0.726 NA NA T NUP214 AML NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 9 9q34 6418 SET translocation NA L 0 40 35.92 NA , 50,58,3238 NA 8,0,34,8,42,1581 NA NA NA NA , 0.4 0.8 4 99,102,6579 NA 11,0,77,6,90,3206 no utr-5,intron SET NM_003011.3,NM_001122821.1 , 19,0,111,14,132,4787 A1A1,A1A2,A1R,A2A2,A2R,RR NA 2.9646,3.2277,3.0516 , , NA 149,160,9817 NA NA NA SO:0001623 5_prime_UTR_variant 1.61 M93651 CCDS6907.1, CCDS48037.1, CCDS59149.1, CCDS59150.1 9q34 2014-06-25 2014-06-25 ENSG00000119335 ENSG00000119335 6418 10760 protein-coding gene gene with protein product "protein phosphatase type 2A inhibitor", "Template-Activating Factor-I, chromatin remodelling factor" 600960 "SET translocation (myeloid leukemia-associated)" NA 1630450, 8626647 Standard NM_001122821 NM_003011 NA Approved PHAPII, 2PP2A, IPP2A2 uc022bol.1 Q01105 OTTHUMG00000020755 ENST00000322030.8:c.-25C>- chr9.hg19:g.131451837delC 7 9 ref NA False 71 71 PASS 8 PASS ref->het 0 NA 22,22 11,13 7,5 1 1 A5A5H4|A6NGV1|B4DUE2|Q15541|Q5VXV1|Q5VXV2|Q6FHZ5 True hg19 CCDS6907.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SET-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000054477.2 PASS NA None 40 True + C ENST00000322030.8 TSC1 7248 __UNKNOWN__ __UNKNOWN__ 9 135766991 135766991 __UNKNOWN__ 3'UTR DEL A A - rs548749114|rs60000611 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:135766991delA ENST00000298552.3 - 0 8347 TSC1_ENST00000440111.2_3'UTR|TSC1_ENST00000545250.1_3'UTR NM_000368.4|NM_001162426.1|NM_001162427.1 NP_000359.1|NP_001155898.1|NP_001155899.1 Q92574 TSC1_HUMAN tuberous sclerosis 1 NA NA NA activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808) cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596) chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485) p.?(1) NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4) 65 OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06) GCAGTCCGTTAAAAAAAATCA 0.363 NA NA "D, Mis, N, F, S" "hamartoma, renal cell" NA Tuberous Sclerosis AAAAAAAA|AAAAAAAA|AAAAAAA|deletion 23 0.00459265 0.0129 0.0058 5008 , , NA 19272 0 NA 0.001 False NA ,,, NA NA NA 2504 0.001 NA NA NA PASS yes Rec Tuberous sclerosis 1 9 9q34 7248 tuberous sclerosis 1 gene NA "E, O" 1 Unknown(1) bone(1) 155 153.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 3.01 Familial Cancer Database TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease AF013168 CCDS6956.1, CCDS55350.1 9q34 2014-09-17 ENSG00000165699 ENSG00000165699 7248 12362 protein-coding gene gene with protein product 605284 TSC NA 9242607, 10806479 Standard NM_000368 NA Approved KIAA0243, LAM, hamartin uc004cca.2 Q92574 OTTHUMG00000020844 ENST00000298552.3:c.*4631T>- chr9.hg19:g.135766991delA 7 8 ref NA False 87 86 PASS 8 PASS ref->het 0 NA 85,87 51,52 21,21 1 1 B7Z897|Q5VVN5 True hg19 CCDS6956.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TSC1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000054799.1 PASS NA None 155 True - A ENST00000298552.3 NELFB 25920 __UNKNOWN__ __UNKNOWN__ 9 140167078 140167078 __UNKNOWN__ Intron DEL G G - rs372024826 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:140167078delG ENST00000343053.4 + 12 1933 NM_015456.3 NP_056271.2 Q8WX92 NELFB_HUMAN negative elongation factor complex member B NA NA NA gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032) cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) NA GTGGGTGCCCGGGGGGGCTGC 0.677 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 116 107.59 NA 15,4195 NA 0,15,2090 10 11 10 NA -4.2 0 9 5 26,8130 NA 3,20,4055 no intron COBRA1 NM_015456.3 3,35,6145 A1A1,A1R,RR NA 0.3188,0.3563,0.3316 140167078 41,12325 2188 4280 6468 SO:0001627 intron_variant 0.81 AF464935 CCDS7040.1 9q34 2013-01-31 2013-01-31 2013-01-31 ENSG00000188986 ENSG00000188986 25920 24324 protein-coding gene gene with protein product 611180 "cofactor of BRCA1" COBRA1 NA 11230166, 10574461, 17910036, 17659869 Standard NM_015456 NM_015456 NA Approved KIAA1182, NELF-B uc004cmm.4 Q8WX92 OTTHUMG00000131778 ENST00000343053.4:c.1596+11G>- chr9.hg19:g.140167078delG 6 7 ref NA False 158 104 PASS 7 PASS ref->het 0 NA 45,47 47,48 24,22 1 1 A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0 True hg19 CCDS7040.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NELFB-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254710.1 PASS NA None 116 True + G ENST00000343053.4 AKR1C2 1646 __UNKNOWN__ __UNKNOWN__ 10 5031514 5031514 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:5031514delA ENST00000380753.4 - 0 1833 NM_205845.2 NP_995317.1 P52895 AK1C2_HUMAN aldo-keto reductase family 1, member C2 NA NA NA cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202) cytoplasm (GO:0005737) alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115) breast(1)|large_intestine(5)|lung(3)|skin(1) 10 Ursodeoxycholic acid(DB01586) TATAATGATCAAAAAAAAGGG 0.398 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 521 460.57 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.42 L32592 CCDS7062.1, CCDS44350.1 10p15-p14 2014-01-29 2012-12-04 ENSG00000151632 ENSG00000151632 1646 1.3.1.20, 1.1.1.213 "Aldo-keto reductases" 385 protein-coding gene gene with protein product "dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III" 600450 "aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)", "testicular 17,20-desmolase deficiency" DDH2, TDD NA 9716498, 21802064 Standard NM_001354 NM_001354 NA Approved DD, BABP, DD2, HAKRD, MCDR2 uc001iht.3 P52895 OTTHUMG00000017584 ENST00000380753.4:c.*674T>- chr10.hg19:g.5031514delA 7 8 ref NA False 87 87 PASS 8 PASS ref->het 0 NA 360,370 109,112 52,51 1 1 A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71 True hg19 CCDS7062.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AKR1C2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000046531.1 PASS NA None 521 True - A ENST00000380753.4 COMMD3-BMI1 100532731 __UNKNOWN__ __UNKNOWN__ 10 22615361 22615362 __UNKNOWN__ Splice_Site INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:22615361_22615362insT ENST00000602390.1 + 6 421_422 c.412_413insT c.(412-414)att>aTtt p.I138fs COMMD3-BMI1_ENST00000463409.2_3'UTR|BMI1_ENST00000376663.3_5'UTR NM_001204062.1 NP_001190991.1 COMMD3-BMI1 readthrough NA NA NA NA GTCTTGCAGGATTTTTTATCAA 0.381 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 471 463.37 NA , 0,4264 NA 0,0,2132 NA NA NA NA , 2.6 1 110 2,8252 NA 0,2,4125 no utr-5,frameshift-near-splice BMI1,COMMD3-BMI1 NM_005180.8,NM_001204062.1 , 0,2,6257 A1A1,A1R,RR NA 0.0242,0.0,0.016 , , NA 2,12516 NA NA NA SO:0001630 splice_region_variant 0 CCDS59213.1 10p12.2 2013-05-08 ENSG00000269897 ENSG00000269897 100532731 48326 other readthrough NA NA Standard NM_001204062 NA Approved OTTHUMG00000184031 ENST00000602390.1:c.411-1->T chr10.hg19:g.22615367_22615367dupT 7 7 ref NA False 180 179 PASS 6 PASS ref->het 0 NA 330,332 77,77 60,60 1 1 True hg19 CCDS59213.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COMMD3-BMI1-001 NOVEL basic|appris_principal|readthrough_transcript|CCDS protein_coding NA protein_coding OTTHUMT00000467824.1 PASS NA None 471 Frame_Shift_Ins True + T ENST00000602390.1 ARHGAP12 94134 __UNKNOWN__ __UNKNOWN__ 10 32098255 32098256 __UNKNOWN__ Intron DEL TG TG - rs374781140 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:32098255_32098256delTG ENST00000375250.5 - 15 2202 ARHGAP12_ENST00000344936.2_Intron|ARHGAP12_ENST00000311380.4_Intron|ARHGAP12_ENST00000375245.4_Intron|ARHGAP12_ENST00000492028.1_Intron|ARHGAP12_ENST00000396144.4_Intron NM_001270696.1|NM_001270698.1 NP_001257625.1|NP_001257627.1 Q8IWW6 RHG12_HUMAN Rho GTPase activating protein 12 NA NA NA morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264) cytosol (GO:0005829) GTPase activator activity (GO:0005096) NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2) 31 Prostate(175;0.0199) AATAATAATTTGTGTGTGTGTG 0.386 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 191 178.65 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.94 AY033594 CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1 10p11.22 2013-01-10 ENSG00000165322 ENSG00000165322 94134 "Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing" 16348 protein-coding gene gene with protein product 610577 NA 11854031 Standard NM_001270695 NA Approved FLJ20737, FLJ10971, FLJ21785 uc001ivz.2 Q8IWW6 OTTHUMG00000017911 ENST00000375250.5:c.1961-20CA>- chr10.hg19:g.32098265_32098266delTG 6 4 ref NA False 70 70 PASS 7 PASS ref->het 0 NA 110,112 30,31 50,50 1 1 B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76 True hg19 CCDS59215.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARHGAP12-008 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000047464.1 PASS NA None 191 True - TG ENST00000375250.5 WDFY4 57705 __UNKNOWN__ __UNKNOWN__ 10 50040562 50040562 __UNKNOWN__ Intron DEL A A - rs3747873 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:50040562delA ENST00000325239.5 + 38 6553 WDFY4_ENST00000413659.2_Intron NM_020945.1 NP_065996.1 Q6ZS81 WDFY4_HUMAN WDFY family member 4 NA NA NA integral component of membrane (GO:0016021) NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1) 48 AGCTAGCTATAAAAATAGTGT 0.507 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 239 245.85 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.73 AK074085 CCDS44385.1 10q11.23 2013-01-10 ENSG00000128815 ENSG00000128815 57705 "WD repeat domain containing" 29323 protein-coding gene gene with protein product 613316 "chromosome 10 open reading frame 64" C10orf64 NA 10997877 Standard XM_033379 NM_020945 NA Approved KIAA1607, Em:AC060234.3, FLJ45748 uc001jha.4 Q6ZS81 OTTHUMG00000018180 ENST00000325239.5:c.6527-56A>- chr10.hg19:g.50040562delA 4 6 ref NA False 36 36 PASS 5 PASS ref->het 0 NA 158,162 56,56 27,25 2 2 B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5 True hg19 CCDS44385.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA WDFY4-201 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding PASS NA None 239 True + A ENST00000325239.5 C10orf40 283025 __UNKNOWN__ __UNKNOWN__ 10 61718326 61718326 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:61718326delA ENST00000521074.1 - 3 1190 c.104delT c.(103-105)ttafs p.L35fs C10orf40_ENST00000430888.1_Frame_Shift_Del_p.L35fs|C10orf40_ENST00000444900.1_Frame_Shift_Del_p.L35fs chromosome 10 open reading frame 40 NA NA NA NA TACGTCCCTTAAAAAAAAGAA 0.378 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 349 362.82 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.42 BC038741 10q21.3 2013-01-15 ENSG00000235931 ENSG00000235931 283025 23524 other unknown NA NA 12477932 Standard NR_024340 NR_024340 NA Approved AC023904.2 uc021prf.1 A4QN01 OTTHUMG00000018285 ENST00000521074.1:c.104delT chr10.hg19:g.61718326delA ENSP00000430990:p.Leu35fs 7 10 ref NA False 46 46 PASS 8 PASS ref->het 0 NA 216,219 71,71 56,55 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C10orf40-002 KNOWN alternative_5_UTR|basic|appris_principal protein_coding NA protein_coding OTTHUMT00000379562.1 PASS NA None 349 True - A ENST00000521074.1 ARID5B 84159 __UNKNOWN__ __UNKNOWN__ 10 63810798 63810799 __UNKNOWN__ Intron INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:63810798_63810799insT ENST00000279873.7 + 5 1256 ARID5B_ENST00000309334.5_Intron NM_032199.2 NP_115575.1 Q14865 ARI5B_HUMAN AT rich interactive domain 5B (MRF1-like) NA NA NA adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212) NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 44 Prostate(12;0.016)|all_hematologic(501;0.215) TTCGTTGCATCTTTTTATTTTT 0.411 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 246 240.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.77 M73837 CCDS31208.1, CCDS58082.1 10q11.22 2013-02-07 ENSG00000150347 ENSG00000150347 84159 "-" 17362 protein-coding gene gene with protein product 608538 NA 11483573, 11478881 Standard XM_084482 NM_032199 NA Approved FLJ21150, MRF2 uc001jlt.2 Q14865 OTTHUMG00000018298 ENST00000279873.7:c.846+39->T chr10.hg19:g.63810803_63810803dupT 6 10 ref NA False 169 156 PASS 5 PASS ref->het 0 NA 169,170 56,56 20,19 1 1 B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786 True hg19 CCDS31208.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARID5B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000048233.1 PASS NA None 246 True + T ENST00000279873.7 RTKN2 219790 __UNKNOWN__ __UNKNOWN__ 10 63956596 63956597 __UNKNOWN__ 3'UTR INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:63956596_63956597insT ENST00000373789.3 - 0 2996_2997 RTKN2_ENST00000315289.2_Intron|RTKN2_ENST00000395265.1_Intron NM_145307.2 NP_660350.2 Q8IZC4 RTKN2_HUMAN rhotekin 2 NA NA NA hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165) plasma membrane (GO:0005886) endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 21 Prostate(12;0.0297)|all_hematologic(501;0.215) cctttaaggtatttttctgcta 0.282 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 121 121.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.35 BC025765 CCDS7263.1, CCDS73140.1 10q21.3 2013-01-10 2007-12-14 2007-12-14 ENSG00000182010 ENSG00000182010 219790 "Pleckstrin homology (PH) domain containing" 19364 protein-coding gene gene with protein product NA "pleckstrin homology domain containing, family K member 1" PLEKHK1 NA 15504364 Standard NM_145307 NM_001282941 NA Approved Em:AC024597.2, bA531F24.1, FLJ39352 uc001jlw.3 Q8IZC4 OTTHUMG00000018299 ENST00000373789.3:c.*1071->A chr10.hg19:g.63956601_63956601dupT 6 6 ref NA False 33 33 PASS 5 PASS ref->het 0 NA 80,82 28,28 15,16 2 2 Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2 True hg19 CCDS7263.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RTKN2-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000091618.1 PASS NA None 121 True - T ENST00000373789.3 ZNF365 22891 __UNKNOWN__ __UNKNOWN__ 10 64160487 64160488 __UNKNOWN__ 3'UTR DEL CT CT - rs143608968 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:64160487_64160488delCT ENST00000395254.3 + 0 2443_2444 ZNF365_ENST00000395255.3_Intron|ZNF365_ENST00000410046.3_Intron|ZNF365_ENST00000466727.1_3'UTR NM_014951.2 NP_055766.2 Q70YC4 TALAN_HUMAN zinc finger protein 365 NA NA NA breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 27 Prostate(12;0.0297)|all_hematologic(501;0.228) GTCAGTGGCCCTCTCTCTCTCT 0.569 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 361 335.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.8 AB020651 CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1 10q21.2 2008-10-28 ENSG00000138311 ENSG00000138311 22891 "Zinc fingers, C2H2-type" 18194 protein-coding gene gene with protein product "Talanin" 607818 NA 10048485, 12740763 Standard NM_014951 NM_199450 NA Approved KIAA0844, UAN uc001jmc.2 Q70YC4 OTTHUMG00000018302 ENST00000395254.3:c.*940CT>- chr10.hg19:g.64160497_64160498delCT 5 4 ref NA False 49 49 PASS 6 PASS ref->het 0 NA 230,235 78,78 54,49 1 1 True hg19 CCDS31209.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF365-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000048238.2 PASS NA None 361 True + CT ENST00000395254.3 LIPM 340654 __UNKNOWN__ __UNKNOWN__ 10 90565660 90565660 __UNKNOWN__ Intron DEL A A - rs139608926 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:90565660delA ENST00000404743.4 + 2 314 LIPM_ENST00000539337.1_5'UTR NM_001128215.1 NP_001121687.1 Q5VYY2 LIPM_HUMAN lipase, family member M NA NA NA lipid catabolic process (GO:0016042) extracellular region (GO:0005576) hydrolase activity, acting on ester bonds (GO:0016788) breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)|skin(1) 7 tacagacttcaaaacagccag 0.428 NA NA NA AAAA|AAAA|AAA|deletion 1961 0.391573 0.2663 0.4035 5008 , , NA 21178 0.5486 NA 0.3519 False NA ,,, NA NA NA 2504 0.4315 NA NA NA PASS NA NA NA 0 116 105.23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS44457.1 10q23.31 2008-02-04 2007-02-27 2007-02-27 ENSG00000173239 ENSG00000173239 340654 23455 protein-coding gene gene with protein product 613923 "lipase-like, ab-hydrolase domain containing 3" LIPL3 NA Standard XM_291663 NM_001128215 NA Approved bA304I5.1 uc009xtm.1 Q5VYY2 OTTHUMG00000018698 ENST00000404743.4:c.148-2395A>- chr10.hg19:g.90565660delA 3 5 ref NA False 75 71 PASS 4 PASS ref->het 0 NA 26,26 83,84 7,7 1 1 A6PVS3|B2RXK7|B5MCR3 True hg19 CCDS44457.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LIPM-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000049261.3 PASS NA None 116 True + A ENST00000404743.4 FAS 355 __UNKNOWN__ __UNKNOWN__ 10 90750678 90750717 __UNKNOWN__ Intron DEL GCCCGGGTGGAGGCTTACCCCGTCTTAGTCCCGGGGATAG GCCCGGGTGGAGGCTTACCCCGTCTTAGTCCCGGGGATAG - rs202165529|rs376591116|rs371701570|rs367885573|rs368294302 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:90750678_90750717delGCCCGGGTGGAGGCTTACCCCGTCTTAGTCCCGGGGATAG ENST00000355279.2 + 1 30 FAS_ENST00000355740.2_Intron|ACTA2_ENST00000458208.1_5'UTR|FAS_ENST00000357339.2_Intron|FAS_ENST00000352159.4_Intron P49327 FAS_HUMAN Fas cell surface death receptor NA NA NA acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767) cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886) 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270) breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2) 18 Colorectal(252;0.0161) Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193) Cerulenin(DB01034)|Orlistat(DB01083) GCCCTCTCCTGCCCGGGTGGAGGCTTACCCCGTCTTAGTCCCGGGGATAGGCAAAGTGGG 0.679 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 314 301.31 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.95 M67454 CCDS7393.1, CCDS7394.1, CCDS7395.1 10q24.1 2014-09-17 2013-05-22 2005-01-07 ENSG00000026103 ENSG00000026103 355 "Tumor necrosis factor receptor superfamily", "CD molecules" 11920 protein-coding gene gene with protein product "TNF receptor superfamily member 6" 134637 "tumor necrosis factor receptor superfamily, member 6", "Fas (TNF receptor superfamily, member 6)" FAS1, APT1, TNFRSF6 NA 1385299, 1385309 Standard NM_000043 NA Approved CD95, APO-1 uc001kfr.3 P25445 OTTHUMG00000018701 ENST00000355279.2:c.30+15GCCCGGGTGGAGGCTTACCCCGTCTTAGTCCCGGGGATAG>- chr10.hg19:g.90750678_90750717delGCCCGGGTGGAGGCTTACCCCGTCTTAGTCCCGGGGATAG 0 3 ref NA False 90 90 PASS 1 PASS ref->het 0 NA 298,310 11,11 50,39 1 1 Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0 True hg19 CCDS7395.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAS-011 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000049280.2 PASS NA None 314 True + GCCCGGGTGGAGGCTTACCCCGTCTTAGTCCCGGGGATAG ENST00000355279.2 IFIT1 3434 __UNKNOWN__ __UNKNOWN__ 10 91162617 91162617 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:91162617delA ENST00000371804.3 + 2 752 c.585delA c.(583-585)acafs p.T195fs IFIT1_ENST00000546318.1_Frame_Shift_Del_p.T164fs|LIPA_ENST00000371837.1_Intron NM_001270927.1|NM_001548.4 NP_001257856.1|NP_001539.3 P09914 IFIT1_HUMAN interferon-induced protein with tetratricopeptide repeats 1 195 NA NA cellular response to exogenous dsRNA (GO:0071360)|cellular response to type I interferon (GO:0071357)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|intracellular transport of viral protein in host cell (GO:0019060)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of helicase activity (GO:0051097)|negative regulation of protein binding (GO:0032091)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337) cytoplasm (GO:0005737)|cytosol (GO:0005829) RNA binding (GO:0003723) breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(2)|prostate(2)|upper_aerodigestive_tract(1) 15 AATTAGCCACAAAAAATCACA 0.473 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 171 176.68 NA NA 181 188 186 NA NA NA 10 NA NA NA 91162617 2203 4300 6503 SO:0001589 frameshift_variant 0.52 M24594 CCDS31243.1, CCDS59220.1 10q23.31 2014-05-22 ENSG00000185745 ENSG00000185745 3434 "Tetratricopeptide (TTC) repeat domain containing" 5407 protein-coding gene gene with protein product 147690 G10P1, IFI56, IFNAI1 NA 1377167, 3360121 Standard NM_001548 NM_001548 NA Approved GARG-16 uc001kgi.4 P09914 OTTHUMG00000018712 ENST00000371804.3:c.585delA chr10.hg19:g.91162617delA ENSP00000360869:p.Thr195fs 5 7 ref NA False 38 38 PASS 6 PASS ref->het 0 NA 111,114 39,41 16,15 1 1 B3KS50|D3DR31|Q5T7J1|Q96QM5 True hg19 CCDS31243.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IFIT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000049302.1 PASS NA None 171 True + A ENST00000371804.3 SORBS1 10580 __UNKNOWN__ __UNKNOWN__ 10 97127476 97127476 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:97127476delA ENST00000361941.3 - 20 1932 SORBS1_ENST00000474353.2_Intron|SORBS1_ENST00000371245.3_Intron|SORBS1_ENST00000393949.1_Intron|SORBS1_ENST00000354106.3_Intron|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000277982.5_Intron|SORBS1_ENST00000371247.2_Intron|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000371246.2_Intron|SORBS1_ENST00000371227.4_Intron NM_001034954.1 NP_001030126 sorbin and SH3 domain containing 1 NA NA NA NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 42 Colorectal(252;0.0429) Epithelial(162;1.7e-06)|all cancers(201;6.52e-05) TCCAAAAAAGAAAAAAAAGAA 0.338 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 140 133.4 NA ,,,,,, 14,6,4244 NA 0,0,14,0,6,2112 33 33 33 NA ,,,,,, -7.6 0 10 33 17,8,8227 NA 0,0,17,0,8,4101 no intron,intron,intron,intron,intron,intron,intron SORBS1 NM_024991.1,NM_015385.2,NM_006434.2,NM_001034957.1,NM_001034956.1,NM_001034955.1,NM_001034954.1 ,,,,,, 0,0,31,0,14,6213 A1A1,A1A2,A1R,A2A2,A2R,RR NA 0.303,0.469,0.3595 ,,,,,, ,,,,,, 97127476 31,14,12471 2203 4298 6501 SO:0001627 intron_variant 0.14 AF136381 CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1 10q23.33 2011-07-25 2002-05-08 ENSG00000095637 ENSG00000095637 10580 14565 protein-coding gene gene with protein product "c-Cbl-associated protein" 605264 "SH3-domain protein 5 (ponsin)" SH3D5 NA 10085297, 11001060 Standard XM_005269405 NA Approved FLJ12406, CAP, sh3p12, ponsin, KIAA1296 uc001kkp.3 Q9BX66 OTTHUMG00000018812 ENST00000361941.3:c.1906-20T>- chr10.hg19:g.97127476delA 7 14 ref NA False 31 31 PASS 8 PASS ref->het 0 NA 77,77 28,29 27,26 1 1 True hg19 CCDS31255.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SORBS1-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000049517.1 PASS NA None 140 True - A ENST00000361941.3 PSD 5662 __UNKNOWN__ __UNKNOWN__ 10 104176574 104176574 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:104176574delG ENST00000020673.5 - 2 748 c.222delC c.(220-222)cccfs p.P74fs PSD_ENST00000406432.1_Frame_Shift_Del_p.P74fs|PSD_ENST00000492902.2_5'UTR NM_001270966.1|NM_002779.4 NP_001257895.1|NP_002770.3 A5PKW4 PSD1_HUMAN pleckstrin and Sec7 domain containing 74 Pro-rich. NA NA neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165) cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871) p.S75fs*127(1) breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 34 Epithelial(162;1.27e-08)|all cancers(201;2.85e-07) CACGGGGTGAGGGGGGGCCAC 0.672 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 1 Insertion - Frameshift(1) ovary(1) 193 194.5 NA NA 38 43 42 NA NA NA 10 NA NA NA 104176574 2192 4282 6474 SO:0001589 frameshift_variant 6.15 X99688 CCDS31272.1, CCDS73187.1 10q24 2013-01-10 2004-04-28 ENSG00000059915 ENSG00000059915 5662 "Pleckstrin homology (PH) domain containing" 9507 protein-coding gene gene with protein product 602327 "pleckstrin and Sec7 domain protein" NA 9417912 Standard NM_002779 NA Approved KIAA2011, TYL, PSD1 uc009xxd.2 A5PKW4 OTTHUMG00000018954 ENST00000020673.5:c.222delC chr10.hg19:g.104176574delG ENSP00000020673:p.Pro74fs 6 8 ref NA False 61 61 PASS 7 PASS ref->het 0 NA 120,126 36,37 39,37 1 1 B1AKX7|D3DR87|Q15673|Q8IVG0 True hg19 CCDS31272.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PSD-004 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000050041.2 PASS NA None 193 True - G ENST00000020673.5 GFRA1 2674 __UNKNOWN__ __UNKNOWN__ 10 117856297 117856297 __UNKNOWN__ Intron DEL G G - rs551851074 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:117856297delG ENST00000355422.6 - 7 1321 GFRA1_ENST00000439649.3_Intron|GFRA1_ENST00000544592.1_Intron|GFRA1_ENST00000369236.1_Intron NM_005264.4 NP_005255.1 P56159 GFRA1_HUMAN GDNF family receptor alpha 1 NA NA NA axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860) anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886) glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102) endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1) 26 Lung NSC(174;0.21) all cancers(201;0.0337) AAAAAGGGGTGGGGGGTGGAA 0.458 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Ovarian(128;329 1725 45498 46808 50759) PASS NA NA NA 0 166 148.34 NA ,, 3,4257 NA 0,3,2127 21 23 22 NA ,, -2.5 0 10 23 5,8249 NA 0,5,4122 no intron,intron,intron GFRA1 NM_145793.3,NM_005264.4,NM_001145453.1 ,, 0,8,6249 A1A1,A1R,RR NA 0.0606,0.0704,0.0639 ,, ,, 117856297 8,12506 2203 4300 6503 SO:0001627 intron_variant 0.5 AF038421 CCDS7593.1, CCDS44481.1 10q25-q26 2011-01-25 ENSG00000151892 ENSG00000151892 2674 4243 protein-coding gene gene with protein product 601496 GDNFRA NA 9465905, 9545641 Standard NM_145793 NM_005264 NA Approved RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1 uc001lcj.3 P56159 OTTHUMG00000019097 ENST00000355422.6:c.771-22C>- chr10.hg19:g.117856297delG 5 10 ref NA False 54 54 PASS 6 PASS ref->het 0 NA 103,107 39,39 22,20 1 1 A8KA21|O15507|O43912 True hg19 CCDS44481.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GFRA1-002 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000050512.2 PASS NA None 166 True - G ENST00000355422.6 CACUL1 143384 __UNKNOWN__ __UNKNOWN__ 10 120445798 120445798 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:120445798delA ENST00000369151.3 - 9 1553 CACUL1_ENST00000544392.1_Intron NM_153810.4 NP_722517.3 Q86Y37 CACL1_HUMAN CDK2-associated, cullin domain 1 NA NA NA G1/S transition of mitotic cell cycle (GO:0000082)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase activity (GO:0045860)|ubiquitin-dependent protein catabolic process (GO:0006511) cullin-RING ubiquitin ligase complex (GO:0031461) protein kinase binding (GO:0019901) NA AAAAAGGCTTAAAAAAAATCC 0.428 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 110 131.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.26 AK097728 CCDS41570.1 10q26.13 2012-06-12 2012-06-12 2012-06-12 ENSG00000151893 ENSG00000151893 143384 23727 protein-coding gene gene with protein product "Cdk-Associated Cullin1" NA "chromosome 10 open reading frame 46" C10orf46 NA 19829063 Standard NM_153810 NM_153810 NA Approved FLJ40409, MGC33215, CAC1 uc001lds.1 Q86Y37 OTTHUMG00000019138 ENST00000369151.3:c.1070-118T>- chr10.hg19:g.120445798delA 7 8 ref NA False 40 40 PASS 8 PASS ref->het 0 NA 54,56 36,37 20,18 1 1 Q5XPL7|Q8IY11|Q8N7S4 True hg19 CCDS41570.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CACUL1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000050612.2 PASS NA None 110 True - A ENST00000369151.3 FAM175B 23172 __UNKNOWN__ __UNKNOWN__ 10 126505229 126505229 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:126505229delA ENST00000298492.5 + 3 245 NM_032182.3 NP_115558.3 Q15018 F175B_HUMAN family with sequence similarity 175, member B NA NA NA cellular response to freezing (GO:0071497) BRISC complex (GO:0070552)|cytoplasm (GO:0005737) polyubiquitin binding (GO:0031593) NS(1) 1 ATTGATTGATAAAAAAAACTA 0.358 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 147 146.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 D63877 CCDS31308.2 10q26.2 2013-01-24 2008-07-02 2008-07-02 ENSG00000165660 ENSG00000165660 23172 28975 protein-coding gene gene with protein product "Abraxas brother" 611144 "KIAA0157" KIAA0157 NA 8590280 Standard NM_032182 NM_032182 NA Approved Em:AC068896.4, ABRO1 uc001lib.4 Q15018 OTTHUMG00000019218 ENST00000298492.5:c.200+48A>- chr10.hg19:g.126505229delA 7 9 ref NA False 50 50 PASS 8 PASS ref->het 0 NA 82,82 46,46 17,17 1 1 B4DKR2|Q96H11 True hg19 CCDS31308.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM175B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000050891.2 PASS NA None 147 True + A ENST00000298492.5 CTBP2 1488 __UNKNOWN__ __UNKNOWN__ 10 126715710 126715710 __UNKNOWN__ Intron DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:126715710delG ENST00000337195.5 - 3 458 CTBP2_ENST00000531469.1_Intron|CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000309035.6_Frame_Shift_Del_p.L207fs|CTBP2_ENST00000494626.2_Intron NM_001329.2 NP_001320.1 P56545 CTBP2_HUMAN C-terminal binding protein 2 NA NA NA negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872) cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053) NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714) breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 25 all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173) Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147) ACCTGGCTGAGGGGGTAGGCA 0.672 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 311 298.62 NA NA 37 41 40 NA NA NA 10 NA NA NA 126715710 2203 4299 6502 SO:0001627 intron_variant 1.06 AF016507 CCDS7643.1, CCDS7644.1 10q26.13 2008-08-01 ENSG00000175029 ENSG00000175029 1488 2495 protein-coding gene gene with protein product 602619 NA 9479502, 11864595 Standard NM_001083914 NM_022802 NA Approved ribeye uc001lie.4 P56545 OTTHUMG00000019224 ENST00000337195.5:c.58+11855C>- chr10.hg19:g.126715710delG 4 6 ref NA False 98 98 PASS 5 PASS ref->het 0 NA 214,223 58,61 39,30 1 1 A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8 True hg19 CCDS7643.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CTBP2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000050900.3 PASS NA None 311 True - G ENST00000337195.5 BCCIP 56647 __UNKNOWN__ __UNKNOWN__ 10 127522431 127522431 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:127522431delA ENST00000278100.6 + 6 702 c.690delA c.(688-690)ggafs p.G230fs BCCIP_ENST00000368759.5_Frame_Shift_Del_p.G230fs|BCCIP_ENST00000429863.2_Frame_Shift_Del_p.G200fs|BCCIP_ENST00000299130.3_Frame_Shift_Del_p.G230fs NM_078468.2 NP_510868.1 Q9P287 BCCIP_HUMAN BRCA2 and CDKN1A interacting protein 230 Interaction with CDKN1A. NA NA G -> E (in Ref. 6; AAH09771). {ECO:0000305}. cell cycle (GO:0007049)|DNA repair (GO:0006281)|neuroendocrine cell differentiation (GO:0061101)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079) nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nucleus (GO:0005634) kinase regulator activity (GO:0019207)|poly(A) RNA binding (GO:0044822) breast(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1) 8 all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936) TGGAAGCAGGAAAAAACAATT 0.408 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 179 164.82 NA NA 100 106 104 NA NA NA 10 NA NA NA 127522431 2203 4300 6503 SO:0001589 frameshift_variant 0 AB040451 CCDS7649.1, CCDS7650.1, CCDS7651.1 10q26.2 2008-05-14 2001-11-29 ENSG00000107949 ENSG00000107949 56647 978 protein-coding gene gene with protein product 611883 "BRCA2 and CDKN1A-interacting protein" NA 11313963, 10878006 Standard NM_016567 NA Approved BCCIPalpha, TOK-1 uc001ljd.4 Q9P287 OTTHUMG00000019237 ENST00000278100.6:c.690delA chr10.hg19:g.127522431delA ENSP00000278100:p.Gly230fs 5 8 ref NA False 44 44 PASS 6 PASS ref->het 0 NA 128,129 34,35 16,16 1 1 B3KP45|Q8ND15|Q96GC4|Q9P288 True hg19 CCDS7651.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BCCIP-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000050941.1 PASS NA None 179 True + A ENST00000278100.6 INPP5A 3632 __UNKNOWN__ __UNKNOWN__ 10 134459538 134459539 __UNKNOWN__ Intron DEL TT TT - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:134459538_134459539delTT ENST00000368594.3 + 3 495 INPP5A_ENST00000368593.3_Intron NM_005539.3 NP_005530.3 Q14642 I5P1_HUMAN inositol polyphosphate-5-phosphatase, 40kDa NA NA NA inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|small molecule metabolic process (GO:0044281) extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886) inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|PH domain binding (GO:0042731) cervix(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 15 all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203) OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326) GGCGGGGGTCTTTTCATGGTAC 0.579 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(63;823 1267 11107 20380 51626) PASS NA NA NA 0 141 136.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.88 X77567 CCDS7669.2 10q26.3 2008-08-07 2002-08-29 ENSG00000068383 ENSG00000068383 3632 3.1.3.56 6076 protein-coding gene gene with protein product "CTCL tumor antigen HD-CL-02", "43 kDa inositol polyphosphate 5-phophatase", "inositol polyphosphate 5-phophatase, 40kDa", "InsP3 5-phosphatase", "type I inositol-1,4,5-trisphosphate 5-phosphatase" 600106 "inositol polyphosphate-5-phosphatase, 40kD" NA 8013665 Standard NM_005539 NM_005539 NA Approved 5PTASE uc001llp.3 Q14642 OTTHUMG00000019293 ENST00000368594.3:c.218+66TT>- chr10.hg19:g.134459540_134459541delTT 2 5 ref NA False 88 84 PASS 4 PASS ref->het 0 NA 53,59 68,68 20,16 1 1 D3DXI3|Q14640|Q5JSF1 True hg19 CCDS7669.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA INPP5A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000051085.1 PASS NA None 141 True + T ENST00000368594.3 C11orf35 0 __UNKNOWN__ __UNKNOWN__ 11 558069 558069 __UNKNOWN__ Intron DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:558069delG ENST00000329451.3 - 5 462 RP11-496I9.1_ENST00000527620.1_RNA NM_173573.2 NP_775844.2 Q8IXW0 LMTD2_HUMAN NA NA NA NS(1)|breast(1)|central_nervous_system(1)|lung(4)|pancreas(1) 8 all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703) GGTTGGTGGTGGGGGGGTGTC 0.697 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 298 292.9 NA 7,4253 NA 2,3,2125 33 37 35 NA -0.7 0 11 35 10,8240 NA 3,4,4118 no intron C11orf35 NM_173573.2 5,7,6243 A1A1,A1R,RR NA 0.1212,0.1643,0.1359 558069 17,12493 2201 4299 6500 SO:0001627 intron_variant 2.51 NA NA NA NA NA ENST00000329451.3:c.400-30C>- chr11.hg19:g.558069delG 6 9 ref NA False 89 89 PASS 7 PASS ref->het 0 NA 198,208 56,56 47,39 1 1 True hg19 CCDS7701.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C11orf35-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254973.2 PASS NA None 298 True - G ENST00000329451.3 PNPLA2 57104 __UNKNOWN__ __UNKNOWN__ 11 825456 825456 __UNKNOWN__ 3'UTR DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:825456delC ENST00000336615.4 + 0 2311 AP006621.8_ENST00000532946.1_RNA NM_020376.3 NP_065109.1 Q96AD5 PLPL2_HUMAN patatin-like phospholipase domain containing 2 NA NA NA acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|negative regulation of sequestering of triglyceride (GO:0010891)|phospholipid metabolic process (GO:0006644)|positive regulation of triglyceride catabolic process (GO:0010898)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433) cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|plasma membrane (GO:0005886) triglyceride lipase activity (GO:0004806) breast(1)|endometrium(2)|lung(4)|prostate(1)|urinary_tract(1) 9 all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;1.63e-25)|Epithelial(43;1.28e-24)|OV - Ovarian serous cystadenocarcinoma(40;7.09e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703) TGCATCCACACCCCCCCCAAT 0.552 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 328 335.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 8.03 AJ278475 CCDS7718.1 11p15.5 2014-03-14 ENSG00000177666 ENSG00000177666 57104 3.1.1.3 "Patatin-like phospholipase domain containing" 30802 protein-coding gene gene with protein product 609059 NA 8619474, 16799181, 19029121 Standard NM_020376 NM_020376 NA Approved desnutrin, TTS-2.2, ATGL, FP17548, iPLA2zeta uc001lrt.3 Q96AD5 OTTHUMG00000133309 ENST00000336615.4:c.*594C>- chr11.hg19:g.825456delC 7 9 ref NA False 74 72 PASS 8 PASS ref->het 0 NA 180,195 69,71 80,63 1 1 O60643|Q5EFF5|Q6XYE5|Q96ET6|Q9NQ61|Q9NQ62 True hg19 CCDS7718.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PNPLA2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257106.1 PASS NA None 328 True + C ENST00000336615.4 BRSK2 9024 __UNKNOWN__ __UNKNOWN__ 11 1483147 1483147 __UNKNOWN__ 3'UTR DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:1483147delG ENST00000308219.9 + 0 3321 BRSK2_ENST00000528710.1_3'UTR NM_001256627.1|NM_003957.3 NP_001243556.1|NP_003948.2 Q8IWQ3 BRSK2_HUMAN BR serine/threonine kinase 2 NA NA NA actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178) centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783) ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321) endometrium(4)|large_intestine(1)|lung(5) 10 all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842) CTCCACCTCTGGGGGGGCTCG 0.607 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 219 214.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 3.97 AF020089 CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1 11p15.5 2008-02-05 2003-09-11 2005-01-27 ENSG00000174672 ENSG00000174672 9024 11405 protein-coding gene gene with protein product "serine/threonine kinase 29" 609236 "chromsosome 11 open reading frame 7" C11orf7, STK29 NA 9852686, 9929968 Standard NM_003957 NM_001256629 NA Approved PEN11B uc001ltm.4 Q8IWQ3 OTTHUMG00000167089 ENST00000308219.9:c.*928G>- chr11.hg19:g.1483147delG 6 7 ref NA False 102 102 PASS 7 PASS ref->het 0 NA 129,137 41,42 49,42 1 1 B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60 True hg19 CCDS41590.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BRSK2-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000393031.1 PASS NA None 219 True + G ENST00000308219.9 TRPM5 29850 __UNKNOWN__ __UNKNOWN__ 11 2434055 2434055 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:2434055delG ENST00000155858.6 - 15 2292 c.2284delC c.(2284-2286)cagfs p.Q762fs TRPM5_ENST00000533060.1_Frame_Shift_Del_p.Q762fs|TRPM5_ENST00000452833.1_Frame_Shift_Del_p.Q764fs|TRPM5_ENST00000528453.1_Frame_Shift_Del_p.Q762fs NM_014555.3 NP_055370.1 transient receptor potential cation channel, subfamily M, member 5 NA NA NA breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2) 23 Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311) BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191) GAGGGGCCCTGGGGGGGCGGC 0.637 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSCLC(1;49 61 17205 18850 43201) PASS NA NA NA 0 353 337.29 NA 15,18,4175 NA 1,0,13,1,16,2073 20 21 21 NA -3.6 0 11 20 29,24,8165 NA 3,0,23,0,24,4059 no codingComplex TRPM5 NM_014555.3 4,0,36,1,40,6132 A1A1,A1A2,A1R,A2A2,A2R,RR NA 0.6449,0.7842,0.6921 2434055 44,42,12340 2187 4297 6484 SO:0001589 frameshift_variant 4.98 AF177473 CCDS31340.1 11p15.5 2011-12-14 ENSG00000070985 ENSG00000070985 29850 "Voltage-gated ion channels / Transient receptor potential cation channels" 14323 protein-coding gene gene with protein product 604600 NA 10607831, 16382100 Standard NM_014555 NM_014555 NA Approved LTRPC5, MTR1 uc001lwm.4 Q9NZQ8 OTTHUMG00000009896 ENST00000155858.6:c.2284delC chr11.hg19:g.2434055delG ENSP00000155858:p.Gln762fs 6 9 ref NA False 77 77 PASS 7 PASS ref->het 0 NA 218,233 53,55 84,67 1 1 True hg19 CCDS31340.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRPM5-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000027378.1 PASS NA None 353 True - G ENST00000155858.6 ZNF214 7761 __UNKNOWN__ __UNKNOWN__ 11 7020822 7020825 __UNKNOWN__ 3'UTR DEL GAAT GAAT - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:7020822_7020825delGAAT ENST00000278314.4 - 0 2404_2407 ZNF214_ENST00000536068.1_3'UTR NM_013249.2 NP_037381.2 Q9UL59 ZN214_HUMAN zinc finger protein 214 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|zinc ion binding (GO:0008270) NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 29 Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081) GAATGAAATAGAATGAAGAGTTTT 0.216 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Ovarian(22;251 657 736 21522 46864) PASS NA NA NA 0 123 113.08 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF056617 CCDS31418.1 11p15.4 2013-01-08 ENSG00000149050 7761 "Zinc fingers, C2H2-type", "-" 13006 protein-coding gene gene with protein product 605015 NA Standard NM_013249 NA Approved uc001mfa.2 Q9UL59 ENST00000278314.4:c.*271ATTC>- chr11.hg19:g.7020822_7020825delGAAT 0 4 ref NA False 64 64 PASS 1 PASS ref->het 0 NA 62,63 47,47 15,15 1 1 B2R8Q1 True hg19 CCDS31418.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF214-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000385349.1 PASS NA None 123 True - GAAT ENST00000278314.4 USP47 55031 __UNKNOWN__ __UNKNOWN__ 11 11977505 11977506 __UNKNOWN__ Intron INS - - G rs3215040|rs397820556 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:11977505_11977506insG ENST00000399455.2 + 29 4073 USP47_ENST00000539466.1_Intron|USP47_ENST00000339865.5_Intron|USP47_ENST00000305481.6_Intron|USP47_ENST00000527733.1_Intron NM_001282659.1 NP_001269588.1 Q96K76 UBP47_HUMAN ubiquitin specific peptidase 47 NA NA NA base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511) cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005) ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987) breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 46 Epithelial(150;0.000339) ATAGAGGTGGAGGGCTCTACTG 0.322 NA NA NA GGG|GGG|GGGG|insertion 636 0.126997 0.0726 0.0418 5008 , , NA 19330 0.3016 NA 0.0567 False NA ,,, NA NA NA 2504 0.1534 NA NA NA PASS NA NA NA 0 34 44.46 NA 240,3274 NA 14,212,1531 NA NA NA NA -6.6 0 dbSNP_126 41 558,7278 NA 18,522,3378 no intron USP47 NM_017944.3 32,734,4909 A1A1,A1R,RR NA 7.121,6.8298,7.0308 NA 798,10552 NA NA NA SO:0001627 intron_variant 0 AK027362 CCDS41619.1, CCDS60725.1 11p15.2 2008-02-05 2005-08-08 ENSG00000170242 ENSG00000170242 55031 "Ubiquitin-specific peptidases" 20076 protein-coding gene gene with protein product 614460 "Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47" NA 12838346 Standard NM_017944 XM_005252997 NA Approved uc001mjr.3 Q96K76 OTTHUMG00000165685 ENST00000399455.2:c.3954-42->G chr11.hg19:g.11977508_11977508dupG 4 5 ref NA False 41 41 PASS 3 PASS ref->het 0 NA 1,1 27,28 7,8 1 1 B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA USP47-003 KNOWN basic|appris_candidate_longest protein_coding NA protein_coding OTTHUMT00000385853.2 PASS NA None 34 True + G ENST00000399455.2 TSG101 7251 __UNKNOWN__ __UNKNOWN__ 11 18548457 18548459 __UNKNOWN__ 5'UTR DEL CGG CGG - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:18548457_18548459delCGG ENST00000536719.1 - 0 39_41 TSG101_ENST00000357193.3_5'UTR|TSG101_ENST00000251968.3_5'UTR Q99816 TS101_HUMAN tumor susceptibility 101 NA NA NA cell cycle arrest (GO:0007050)|cell division (GO:0051301)|cellular protein modification process (GO:0006464)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|keratinocyte differentiation (GO:0030216)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell growth (GO:0001558)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral budding (GO:0046755)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068) cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|nucleolus (GO:0005730)|plasma membrane (GO:0005886) calcium-dependent protein binding (GO:0048306)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transcription corepressor activity (GO:0003714)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625) kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2) 22 ACCCCCAACCCGGCCTCAAACAA 0.675 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(99;1348 1396 8611 26475 50572) PASS NA NA NA 0 548 518.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 5.04 U82130 CCDS7842.1 11p15 2013-08-22 2013-08-22 ENSG00000074319 ENSG00000074319 7251 15971 protein-coding gene gene with protein product 601387 "tumor susceptibility gene 10", "tumor susceptibility gene 101" TSG10 NA 9019400, 9241264 Standard NM_006292 NM_006292 NA Approved VPS23 uc001mor.3 Q99816 OTTHUMG00000167725 ENST00000536719.1:c.-96CCG>- chr11.hg19:g.18548457_18548459delCGG 0 3 ref NA False 668 344 PASS 1 PASS ref->het 0 NA 341,357 158,166 51,28 1 1 Q9BUM5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TSG101-002 PUTATIVE not_organism_supported|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000395905.2 PASS NA None 548 True - CGG ENST00000536719.1 C11orf94 143678 __UNKNOWN__ __UNKNOWN__ 11 45928455 45928456 __UNKNOWN__ Frame_Shift_Ins INS - - G LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:45928455_45928456insG ENST00000449465.1 - 2 175_176 c.139_140insC c.(139-141)ctgfs p.L47fs NM_001080446.2 NP_001073915.2 C9JXX5 CK094_HUMAN chromosome 11 open reading frame 94 47 NA NA extracellular region (GO:0005576) NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|ovary(1)|pancreas(1)|prostate(1) 7 CGAGAGTTCCAGGGGGGCGGAA 0.619 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 220 220.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.85 CCDS44577.1 11p11.2 2012-08-10 ENSG00000234776 ENSG00000234776 143678 37213 protein-coding gene gene with protein product NA NA Standard NM_001080446 NM_001080446 NA Approved uc001nbs.4 C9JXX5 OTTHUMG00000167004 ENST00000449465.1:c.140dupC chr11.hg19:g.45928461_45928461dupG ENSP00000401498:p.Leu47fs 7 8 ref NA False 37 37 PASS 6 PASS ref->het 0 NA 142,145 37,37 36,35 1 1 True hg19 CCDS44577.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C11orf94-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000392395.1 PASS NA None 220 True - G ENST00000449465.1 CKAP5 9793 __UNKNOWN__ __UNKNOWN__ 11 46829683 46829683 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:46829683delT ENST00000529230.1 - 8 922 c.876delA c.(874-876)aaafs p.K292fs CKAP5_ENST00000312055.5_Frame_Shift_Del_p.K292fs|CKAP5_ENST00000354558.3_Frame_Shift_Del_p.K292fs|CKAP5_ENST00000415402.1_Frame_Shift_Del_p.K292fs Q14008 CKAP5_HUMAN cytoskeleton associated protein 5 292 NA NA centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051) centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922) breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 43 TCTCTTGCCATTTTTTTGCCT 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Ovarian(4;85 273 2202 4844 13323) PASS NA NA NA 0 390 366.71 NA NA 163 173 169 NA NA NA 11 NA NA NA 46829683 2201 4299 6500 SO:0001589 frameshift_variant 0.01 CCDS7924.1, CCDS31477.1 11p11.2 2006-09-20 ENSG00000175216 ENSG00000175216 9793 28959 protein-coding gene gene with protein product 611142 NA 7788527, 8536682 Standard NM_014756 NM_014756 NA Approved ch-TOG, KIAA0097, TOG, TOGp uc001ndi.2 Q14008 OTTHUMG00000166599 ENST00000529230.1:c.876delA chr11.hg19:g.46829683delT ENSP00000432768:p.Lys292fs 6 7 ref NA False 104 104 PASS 7 PASS ref->het 0 NA 279,282 64,64 40,40 2 2 Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4 True hg19 CCDS31477.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CKAP5-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000390679.1 PASS NA None 390 True - T ENST00000529230.1 OR5D18 219438 __UNKNOWN__ __UNKNOWN__ 11 55587612 55587613 __UNKNOWN__ Frame_Shift_Del DEL TC TC - rs148481353|rs147698486 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:55587612_55587613delTC ENST00000333976.4 + 1 527_528 c.507_508delTC c.(505-510)tttcatfs p.FH169fs NM_001001952.1 NP_001001952.1 Q8NGL1 OR5DI_HUMAN olfactory receptor, family 5, subfamily D, member 18 169 NA NA integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984) p.H170Y(1) NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 55 all_epithelial(135;0.208) AGTTATGTTTTCATGGTTTCAA 0.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 1 Substitution - Missense(1) skin(1) 409 417.44 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.8 AB065781 CCDS31510.1 11q11 2012-08-09 ENSG00000186119 ENSG00000186119 219438 "GPCR / Class A : Olfactory receptors" 15285 protein-coding gene gene with protein product NA NA Standard NM_001001952 NM_001001952 NA Approved uc010rin.2 Q8NGL1 OTTHUMG00000166811 ENST00000333976.4:c.507_508delTC chr11.hg19:g.55587612_55587613delTC ENSP00000335025:p.Phe169fs 0 5 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 321,325 55,55 45,44 2 2 Q6IF67|Q6IFD3|Q96RB3 True hg19 CCDS31510.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OR5D18-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000391515.1 PASS NA None 409 True + TC ENST00000333976.4 SIPA1 6494 __UNKNOWN__ __UNKNOWN__ 11 65417622 65417623 __UNKNOWN__ Frame_Shift_Del DEL AG AG - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:65417622_65417623delAG ENST00000527525.1 + 15 2803_2804 c.2556_2557delAG c.(2554-2559)ccagagfs p.E853fs SIPA1_ENST00000394224.3_Frame_Shift_Del_p.E955fs|SIPA1_ENST00000394227.3_Frame_Shift_Del_p.E853fs|SIPA1_ENST00000534313.1_Frame_Shift_Del_p.E955fs Q96FS4 SIPA1_HUMAN signal-induced proliferation-associated 1 955 NA NA cell proliferation (GO:0008283)|cellular response to water deprivation (GO:0042631)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|signal transduction (GO:0007165) cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)|transport vesicle (GO:0030133) GTPase activator activity (GO:0005096)|Rap GTPase activator activity (GO:0046582) cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1) 10 AGCCCATCCCAGAGAGTGGAGA 0.609 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 401 381.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 2.02 AH006363, BC010492, BM677738 CCDS8108.1 11q13.3 2008-09-12 2008-09-12 ENSG00000213445 ENSG00000213445 6494 10885 protein-coding gene gene with protein product 602180 NA 9027487 Standard NM_006747 NM_006747 NA Approved SPA1 uc001ofb.2 Q96FS4 OTTHUMG00000166541 ENST00000527525.1:c.2556_2557delAG chr11.hg19:g.65417626_65417627delAG ENSP00000433686:p.Glu853fs 2 3 ref NA False 130 130 PASS 3 PASS ref->het 0 NA 290,298 67,69 40,34 1 1 O14518|O60484|O60618|Q2YD83 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SIPA1-002 NOVEL alternative_5_UTR|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000390355.1 PASS NA None 401 True + AG ENST00000527525.1 CD248 57124 __UNKNOWN__ __UNKNOWN__ 11 66082151 66082151 __UNKNOWN__ 3'UTR DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:66082151delC ENST00000311330.3 - 0 2364 RP11-867G23.13_ENST00000534065.1_RNA NM_020404.2 NP_065137.1 Q9HCU0 CD248_HUMAN CD248 molecule, endosialin NA NA NA anatomical structure regression (GO:0060033)|cell migration (GO:0016477)|lymph node development (GO:0048535)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578) calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|extracellular matrix binding (GO:0050840) breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2) 26 AGCTGGGCAGCCCCCATGGGT 0.652 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 62 64.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.51 AF279142 CCDS8134.1 11q13 2006-04-12 2006-03-28 2005-02-11 ENSG00000174807 ENSG00000174807 57124 "CD molecules" 18219 protein-coding gene gene with protein product "endosialin", "tumor endothelial marker 1" 606064 "CD164 sialomucin-like 1", "CD248 antigen, endosialin" CD164L1 NA 10947988, 11084048 Standard NM_020404 NM_020404 NA Approved TEM1 uc001ohm.1 Q9HCU0 OTTHUMG00000167073 ENST00000311330.3:c.*74G>- chr11.hg19:g.66082151delC 4 5 ref NA False 34 34 PASS 5 PASS ref->het 0 NA 37,39 18,18 7,5 1 1 Q2M2V5|Q3SX55|Q96KB6 True hg19 CCDS8134.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CD248-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000392922.2 PASS NA None 62 True - C ENST00000311330.3 BRMS1 25855 __UNKNOWN__ __UNKNOWN__ 11 66109532 66109533 __UNKNOWN__ Intron INS - - GTGTGG LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:66109532_66109533insGTGTGG ENST00000359957.3 - 2 300 BRMS1_ENST00000425825.2_Intron NM_015399.3 NP_056214.1 Q9HCU9 BRMS1_HUMAN breast cancer metastasis suppressor 1 NA NA NA apoptotic process (GO:0006915)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of anoikis (GO:2000210)|positive regulation of protein deacetylation (GO:0090312)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleus (GO:0005634) NF-kappaB binding (GO:0051059) large_intestine(1)|liver(1)|lung(1)|prostate(1)|skin(1) 5 gggctctgtgtgtgtgtgtgtg 0.574 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(7;55 307 2662 20856 28942) PASS NA NA NA 0 148 199.44 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.48 AF147350 CCDS8135.1, CCDS44654.1 11q13-q13.2 2008-02-05 ENSG00000174744 25855 17262 protein-coding gene gene with protein product 606259 NA 10850410 Standard NM_015399 XM_005273883 NA Approved DKFZP564A063 uc001oho.1 Q9HCU9 ENST00000359957.3:c.139+33->CCACAC chr11.hg19:g.66109532_66109533insGTGTGG 1 2 ref NA False 92 91 PASS 0 PASS ref->het 0 NA 84,88 43,43 49,47 1 1 Q6IAI2 True hg19 CCDS8135.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BRMS1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000392958.2 PASS NA None 148 True - GTGTGG ENST00000359957.3 PITPNM1 9600 __UNKNOWN__ __UNKNOWN__ 11 67261074 67261074 __UNKNOWN__ Intron DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:67261074delG ENST00000534749.1 - 21 3347 PITPNM1_ENST00000436757.2_Intron|PITPNM1_ENST00000356404.3_Intron|PITPNM1_ENST00000526450.1_Intron O00562 PITM1_HUMAN phosphatidylinositol transfer protein, membrane-associated 1 NA NA NA brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031) endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020) metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526) breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3) 18 CCTGTGGGGCGGGGGCAGCGG 0.677 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(28;144 709 4607 5525) PASS NA NA NA 0 170 159.6 NA NA 15 16 16 NA NA NA 11 NA NA NA 67261074 2138 4242 6380 SO:0001627 intron_variant 2.77 X98654 CCDS31620.1, CCDS44659.1 11q13 2008-07-21 2003-05-16 ENSG00000110697 ENSG00000110697 9600 9003 protein-coding gene gene with protein product "PYK2 N-terminal domain-interacting receptor 2", "retinal degeneration B alpha 1" 608794 PITPNM NA 9680295 Standard NM_004910 NM_004910 NA Approved DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB uc001oly.3 O00562 OTTHUMG00000167675 ENST00000534749.1:c.3159-10C>- chr11.hg19:g.67261074delG 4 9 ref NA False 84 84 PASS 5 PASS ref->het 0 NA 104,114 31,33 31,19 1 1 A6NME4|Q6T7X3|Q8TBN3|Q9BZ73 True hg19 CCDS31620.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PITPNM1-002 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000395520.1 PASS NA None 170 True - G ENST00000534749.1 B3GNT6 192134 __UNKNOWN__ __UNKNOWN__ 11 76751890 76751890 __UNKNOWN__ 3'UTR DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:76751890delG ENST00000533140.1 + 0 1433 B3GNT6_ENST00000354301.5_3'UTR O43505 B3GN1_HUMAN UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase) NA NA NA axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281) extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173) N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532) central_nervous_system(1)|kidney(2)|lung(4)|prostate(1) 8 cagctggggtggggggtgtgg 0.527 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 304 292.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.62 AB073740 CCDS53681.1 11q13.4 2013-02-19 ENSG00000198488 ENSG00000198488 192134 "Beta 3-glycosyltransferases" 24141 protein-coding gene gene with protein product 615315 NA 11821425 Standard NM_138706 NM_138706 NA Approved B3Gn-T6 uc021qnp.1 Q6ZMB0 ENST00000533140.1:c.*137G>- chr11.hg19:g.76751890delG 5 10 ref NA False 58 58 PASS 6 PASS ref->het 0 NA 211,219 44,44 52,45 2 2 Q4TTN0 True hg19 CCDS53681.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA B3GNT6-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000382740.2 PASS NA None 304 True + G ENST00000533140.1 DLG2 1740 __UNKNOWN__ __UNKNOWN__ 11 83344443 83344443 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:83344443delC ENST00000532653.1 - 14 1813 DLG2_ENST00000524982.1_Intron|DLG2_ENST00000376106.3_Intron|DLG2_ENST00000280241.8_Intron|DLG2_ENST00000330014.6_Intron|DLG2_ENST00000418306.2_Intron|DLG2_ENST00000530800.1_Intron|DLG2_ENST00000404783.3_Intron|DLG2_ENST00000537455.1_Intron|DLG2_ENST00000543673.1_Intron|DLG2_ENST00000398309.2_Intron|DLG2_ENST00000376104.2_Intron|DLG2_ENST00000426717.2_Intron|DLG2_ENST00000531015.1_Intron|DLG2_ENST00000398304.1_Intron Q14168 MPP2_HUMAN discs, large homolog 2 (Drosophila) NA NA NA nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165) integral component of plasma membrane (GO:0005887)|membrane (GO:0016020) guanylate kinase activity (GO:0004385) breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1) 71 all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036) GCCCAGGCAGCCCCTCACCCA 0.453 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 295 308.6 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.95 U32376 CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1 11q21 2012-04-17 2008-12-15 ENSG00000150672 ENSG00000150672 1740 "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits" 2901 protein-coding gene gene with protein product "protein phosphatase 1, regulatory subunit 58" 603583 "discs, large homolog 2, chapsyn-110 (Drosophila)" NA 8755482, 9806853 Standard NM_001364 NM_001142702 NA Approved PSD-93, PSD93, chapsyn-110, PPP1R58 uc001pak.2 Q15700 OTTHUMG00000134309 ENST00000532653.1:c.1511-75G>- chr11.hg19:g.83344443delC 3 5 ref NA False 149 113 PASS 4 PASS ref->het 0 NA 168,170 89,91 37,35 1 1 B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DLG2-009 NOVEL basic|appris_candidate protein_coding NA protein_coding OTTHUMT00000259253.2 PASS NA None 295 True - C ENST00000532653.1 VSTM5 387804 __UNKNOWN__ __UNKNOWN__ 11 93551641 93551641 __UNKNOWN__ 3'UTR DEL A A - rs530025105 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:93551641delA ENST00000409977.1 - 0 2725 NM_001144871.1 NP_001138343.1 A8MXK1 VSTM5_HUMAN V-set and transmembrane domain containing 5 NA NA NA integral component of membrane (GO:0016021) endometrium(1) 1 AGCTTTTTTTAAAAAAAACAT 0.373 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 80 85.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.77 CCDS44709.1 11q21 2013-01-11 2011-07-01 2011-07-01 ENSG00000214376 ENSG00000214376 387804 "Immunoglobulin superfamily / V-set domain containing" 34443 protein-coding gene gene with protein product NA "chromosome 11 open reading frame 90" C11orf90 NA 16554811 Standard NM_001144871 NM_001144871 NA Approved LOC387804 uc010ruc.1 A8MXK1 OTTHUMG00000154159 ENST00000409977.1:c.*2094T>- chr11.hg19:g.93551641delA 7 9 ref NA False 58 58 PASS 8 PASS ref->het 0 NA 46,49 27,27 9,7 1 1 True hg19 CCDS44709.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA VSTM5-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000334162.1 PASS NA None 80 True - A ENST00000409977.1 FUT4 2526 __UNKNOWN__ __UNKNOWN__ 11 94281281 94281281 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:94281281delT ENST00000358752.2 + 0 4265 RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA NM_002033.3 NP_002024.1 P22083 FUT4_HUMAN fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-specific) NA NA NA carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486) cell periphery (GO:0071944)|cell surface (GO:0009986)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020) alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417) central_nervous_system(2)|endometrium(2)|lung(1)|skin(2)|upper_aerodigestive_tract(1) 8 Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824) TTTGAAAATATTTTTTTGGTT 0.264 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 76 72.98 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 CCDS8301.1 11q21 2013-02-26 ENSG00000196371 ENSG00000196371 2526 "CD molecules", "Fucosyltransferases" 4015 protein-coding gene gene with protein product "ELAM ligand fucosyltransferase", "galactoside 3-L-fucosyltransferase" 104230 CD15, FCT3A, ELFT NA 1702034 Standard NM_002033 NM_002033 NA Approved FUC-TIV uc001pez.3 P22083 OTTHUMG00000167795 ENST00000358752.2:c.*2389T>- chr11.hg19:g.94281281delT 6 8 ref NA False 36 36 PASS 7 PASS ref->het 0 NA 54,54 17,17 5,5 1 1 B2RMS0 True hg19 CCDS8301.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FUT4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000396327.2 PASS NA None 76 True + T ENST00000358752.2 SESN3 143686 __UNKNOWN__ __UNKNOWN__ 11 94924774 94924775 __UNKNOWN__ Intron INS - - A rs182315158|rs150790532 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:94924774_94924775insA ENST00000278499.2 - 3 451 SESN3_ENST00000393234.1_Intron|RP11-712B9.2_ENST00000534891.1_RNA|SESN3_ENST00000537480.1_Intron|SESN3_ENST00000416495.2_Intron|SESN3_ENST00000536441.1_Intron|RP11-712B9.2_ENST00000534864.1_RNA P58005 SESN3_HUMAN sestrin 3 NA NA NA glucose homeostasis (GO:0042593)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)|response to insulin (GO:0032868) nucleus (GO:0005634) endometrium(5)|large_intestine(6)|lung(3)|skin(1)|stomach(1) 16 Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123) BRCA - Breast invasive adenocarcinoma(274;0.234) ACCTTATAACCAAAAAAAACAA 0.342 NA NA NA AAAAAAAA|AAAAAAAA|AAAAAAAAA|insertion 657 0.13119 0.0809 0.0735 5008 , , NA 21704 0.3115 NA 0.0159 False NA ,,, NA NA NA 2504 0.1728 NA NA NA PASS NA NA NA 0 92 103.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.89 AK096300 CCDS8303.1, CCDS60938.1 11q21 2005-09-18 ENSG00000149212 ENSG00000149212 143686 23060 protein-coding gene gene with protein product 607768 NA 12607115 Standard NM_144665 NM_144665 NA Approved SEST3, MGC29667 uc001pfj.4 P58005 OTTHUMG00000167829 ENST00000278499.2:c.90-9->T chr11.hg19:g.94924782_94924782dupA 9 12 ref NA False 69 69 PASS 8 PASS ref->het 0 NA 41,42 27,27 23,22 1 1 B7Z7P9|Q96AD1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SESN3-003 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000396479.1 PASS NA None 92 True - A ENST00000278499.2 CEP57 9702 __UNKNOWN__ __UNKNOWN__ 11 95565448 95565448 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:95565448delA ENST00000325542.5 + 0 2769 CEP57_ENST00000325486.5_3'UTR|CEP57_ENST00000541150.1_3'UTR NM_001243776.1|NM_014679.4 NP_001230705.1|NP_055494.2 Q86XR8 CEP57_HUMAN centrosomal protein 57kDa NA NA NA fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286) centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634) fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803) endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1) 13 Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824) ACAAGCTCTCAAAAAATGCAT 0.333 NA NA NA Mosaic Variegated Aneuploidy Syndrome NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 84 86.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 Familial Cancer Database MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division D42054 CCDS8304.1, CCDS58166.1, CCDS58167.1 11q21 2014-09-17 ENSG00000166037 ENSG00000166037 9702 30794 protein-coding gene gene with protein product 607951 NA 7788527 Standard NM_014679 NM_014679 NA Approved Translokin, TSP57, KIAA0092 uc001pfp.2 Q86XR8 OTTHUMG00000167740 ENST00000325542.5:c.*1028A>- chr11.hg19:g.95565448delA 5 6 ref NA False 72 71 PASS 6 PASS ref->het 0 NA 44,45 27,27 12,12 1 1 A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9 True hg19 CCDS8304.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CEP57-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000395983.1 PASS NA None 84 True + A ENST00000325542.5 DYNC2H1 79659 __UNKNOWN__ __UNKNOWN__ 11 102985880 102985880 __UNKNOWN__ Intron DEL T T - rs370941940 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:102985880delT ENST00000375735.2 + 4 646 DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Intron NM_001080463.1|NM_001377.2 NP_001073932.1|NP_001368.2 Q8NCM8 DYHC2_HUMAN dynein, cytoplasmic 2, heavy chain 1 NA NA NA antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522) apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886) ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774) NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2) 33 Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348) BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785) TTCTATGCCATTTTTTTCCCC 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 79 74.87 NA NA 43 35 38 NA NA NA 11 NA NA NA 102985880 1820 4071 5891 SO:0001627 intron_variant 0.45 AB082528 CCDS44717.1, CCDS53701.1 11q21-q22.1 2011-06-02 2005-11-24 2005-11-24 ENSG00000187240 ENSG00000187240 79659 "Cytoplasmic dyneins" 2962 protein-coding gene gene with protein product 603297 "dynein, cytoplasmic, heavy polypeptide 2" DNCH2 NA 9763680, 9373155 Standard XM_370652 NM_001080463 NA Approved hdhc11, DHC2, DHC1b, DYH1B uc001phn.1 Q8NCM8 OTTHUMG00000165941 ENST00000375735.2:c.503-26T>- chr11.hg19:g.102985880delT 6 7 ref NA False 38 38 PASS 7 PASS ref->het 0 NA 49,50 18,18 12,11 1 1 O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4 True hg19 CCDS53701.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DYNC2H1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000387196.1 PASS NA None 79 True + T ENST00000375735.2 C11orf57 55216 __UNKNOWN__ __UNKNOWN__ 11 111953289 111953289 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:111953289delA ENST00000393047.3 + 6 1084 c.475delA c.(475-477)aaafs p.K161fs C11orf57_ENST00000420986.2_Frame_Shift_Del_p.K160fs|C11orf57_ENST00000532163.1_Frame_Shift_Del_p.K132fs|C11orf57_ENST00000280352.9_Frame_Shift_Del_p.K160fs Q6ZUT1 CK057_HUMAN chromosome 11 open reading frame 57 160 Lys-rich. NA NA autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1) 12 all_cancers(61;9.8e-15)|all_epithelial(67;6.57e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425) Epithelial(105;3.6e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;7.01e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0521) GAAATCCCACAAAAAAAAGCA 0.393 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 174 177.9 NA NA 74 80 78 NA NA NA 11 NA NA NA 111953289 2201 4297 6498 SO:0001589 frameshift_variant 0 BX538107 CCDS8356.2, CCDS41715.1, CCDS73383.1 11q23.1 2006-03-09 ENSG00000150776 ENSG00000150776 55216 25569 protein-coding gene gene with protein product NA NA 12477932 Standard NM_018195 NM_001082970 NA Approved FLJ10726 uc001pmw.4 Q6ZUT1 OTTHUMG00000150213 ENST00000393047.3:c.475delA chr11.hg19:g.111953289delA ENSP00000376767:p.Lys161fs 7 9 ref NA False 145 131 PASS 8 PASS ref->het 0 NA 97,99 41,41 31,31 2 1 Q5RL41|Q6IN53|Q7Z357|Q8N2T3 True hg19 CCDS8356.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C11orf57-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000316853.1 PASS NA None 174 True + A ENST00000393047.3 HMBS 3145 __UNKNOWN__ __UNKNOWN__ 11 118963752 118963752 __UNKNOWN__ Intron DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:118963752delG ENST00000278715.3 + 13 1063 HMBS_ENST00000542729.1_Intron|HMBS_ENST00000543090.1_Intron|HMBS_ENST00000544387.1_Intron|HMBS_ENST00000537841.1_Intron|HMBS_ENST00000392841.1_Intron|HMBS_ENST00000442944.2_Intron NM_000190.3 NP_000181.2 P08397 HEM3_HUMAN hydroxymethylbilane synthase NA NA NA heme biosynthetic process (GO:0006783)|peptidyl-pyrromethane cofactor linkage (GO:0018160)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829) hydroxymethylbilane synthase activity (GO:0004418) central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1) 15 all_hematologic(175;0.0977) Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;7.72e-05) TGGAGGGCGAGGGGGTAATAA 0.517 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 167 167.76 NA NA 76 74 75 NA NA NA 11 NA NA NA 118963752 2200 4295 6495 SO:0001627 intron_variant 0.23 X04808 CCDS8409.1, CCDS41726.1, CCDS58186.1, CCDS58187.1 11q23.3 2013-07-10 ENSG00000256269 ENSG00000256269 3145 2.5.1.61 4982 protein-coding gene gene with protein product 609806 "uroporphyrinogen I synthase", "porphobilinogen deaminase", "porphyria, acute; Chester type" PBGD, UPS, PORC NA 8432552, 17298217 Standard NM_000190 NM_001258208 NA Approved uc001puz.1 P08397 OTTHUMG00000168295 ENST00000278715.3:c.912+21G>- chr11.hg19:g.118963752delG 4 6 ref NA False 106 105 PASS 5 PASS ref->het 0 NA 97,99 43,44 25,22 1 1 A8K2L0|G3V1P4|G5EA58|P08396|Q16012 True hg19 CCDS8409.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HMBS-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000399188.1 PASS NA None 167 True + G ENST00000278715.3 C2CD2L 9854 __UNKNOWN__ __UNKNOWN__ 11 118988881 118988882 __UNKNOWN__ 3'UTR INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:118988881_118988882insT ENST00000336702.3 + 0 4398_4399 NM_014807.3 NP_055622.3 O14523 C2C2L_HUMAN C2CD2-like NA NA NA integral component of membrane (GO:0016021) NS(1)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1) 13 gaagtctgggctttttttagtg 0.396 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 155 169.13 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AK025223 CCDS8413.1 11q23.3 2008-04-22 2008-04-22 2008-04-22 ENSG00000172375 9854 29000 protein-coding gene gene with protein product NA "transmembrane protein 24" TMEM24 NA 15289880 Standard NM_014807 XM_005271738 NA Approved KIAA0285 uc001pvn.3 O14523 ENST00000336702.3:c.*1916->T chr11.hg19:g.118988888_118988888dupT 8 7 ref NA False 83 83 PASS 7 PASS ref->het 0 NA 102,105 38,39 16,16 2 2 Q86UT7|Q86V04|Q8N522|Q8TBN4|Q96G10 True hg19 CCDS8413.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C2CD2L-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000388197.2 PASS NA None 155 True + T ENST00000336702.3 CACNA2D4 93589 __UNKNOWN__ __UNKNOWN__ 12 1965331 1965331 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:1965331delT ENST00000382722.5 - 21 2417 CACNA2D4_ENST00000588077.1_Intron|CACNA2D4_ENST00000585708.1_Intron|CACNA2D4_ENST00000539048.2_Intron|CACNA2D4_ENST00000586184.1_Intron|CACNA2D4_ENST00000585732.1_Intron|CACNA2D4_ENST00000587995.1_Intron NM_172364.4 NP_758952.4 Q7Z3S7 CA2D4_HUMAN calcium channel, voltage-dependent, alpha 2/delta subunit 4 NA NA NA calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908) voltage-gated calcium channel complex (GO:0005891) metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245) endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1) 39 Ovarian(42;0.107) Myeloproliferative disorder(1001;0.206) OV - Ovarian serous cystadenocarcinoma(31;0.00113) Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451) CTCCCTCCCATTTTTTACTCC 0.517 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Colon(2;101 179 21030 23310 28141) PASS NA NA NA 0 225 211.41 NA NA 131 137 135 NA NA NA 12 NA NA NA 1965331 1977 4145 6122 SO:0001627 intron_variant 0.44 AF516695 CCDS44785.1 12p13.33 2003-03-05 ENSG00000151062 ENSG00000151062 93589 "Calcium channel subunits" 20202 protein-coding gene gene with protein product 608171 NA 12181424 Standard NM_172364 NA Approved uc021qsx.1 Q7Z3S7 OTTHUMG00000168111 ENST00000382722.5:c.2054+18A>- chr12.hg19:g.1965331delT 5 6 ref NA False 36 36 PASS 6 PASS ref->het 0 NA 185,185 26,27 13,13 1 1 Q7Z3S8|Q86XZ5|Q8IZS9 True hg19 CCDS44785.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CACNA2D4-001 KNOWN non_canonical_U12|basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000398230.2 PASS NA None 225 True - T ENST00000382722.5 STYK1 55359 __UNKNOWN__ __UNKNOWN__ 12 10780338 10780338 __UNKNOWN__ Intron DEL A A - rs12319401 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:10780338delA ENST00000075503.3 - 7 1154 NM_018423.2 NP_060893.2 Q6J9G0 STYK1_HUMAN serine/threonine/tyrosine kinase 1 NA NA NA integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715) breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3) 26 AGAGACAGGGAAAAAAAGCCA 0.368 NA NA NA HNSCC(73;0.22) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 179 193.35 NA NA 92 73 80 NA NA NA 12 NA NA NA 10780338 2203 4300 6503 SO:0001627 intron_variant 0.69 AF251059 CCDS8629.1 12p13.2 2005-01-21 55359 18889 protein-coding gene gene with protein product 611433 NA 12841579 Standard NM_018423 NM_018423 NA Approved SuRTK106, DKFZp761P1010, NOK uc001qys.2 Q6J9G0 ENST00000075503.3:c.634-15T>- chr12.hg19:g.10780338delA 6 7 ref NA False 51 51 PASS 7 PASS ref->het 0 NA 102,103 44,44 30,29 1 1 B2R9T2|Q52LR3|Q9BXY2|Q9NSH1 True hg19 CCDS8629.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA STYK1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000399622.1 PASS NA None 179 True - A ENST00000075503.3 ERGIC2 51290 __UNKNOWN__ __UNKNOWN__ 12 29523198 29523198 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:29523198delA ENST00000360150.4 - 3 182 NM_016570.2 NP_057654.2 Q96RQ1 ERGI2_HUMAN ERGIC and golgi 2 NA NA NA vesicle-mediated transport (GO:0016192) endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730) endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)|urinary_tract(1) 10 Lung NSC(12;2.02e-08)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)|Lung SC(9;0.184) TTAAAACAATAAAAAAAGCAA 0.264 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 62 63.88 NA NA 23 20 21 NA NA NA 12 NA NA NA 29523198 1765 4008 5773 SO:0001627 intron_variant 0 AF216751 CCDS41765.1 12p11.22 2006-02-08 51290 30208 protein-coding gene gene with protein product 612236 NA 11445006, 12932305 Standard NM_016570 NM_016570 NA Approved PTX1, Erv41 uc001riv.3 Q96RQ1 ENST00000360150.4:c.107-43T>- chr12.hg19:g.29523198delA 6 9 ref NA False 68 68 PASS 7 PASS ref->het 0 NA 28,29 28,28 6,6 2 1 A6NHH6|Q53GY2|Q8N2Q9|Q9BVV9|Q9NZA3 True hg19 CCDS41765.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ERGIC2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000403489.1 PASS NA None 62 True - A ENST00000360150.4 H3F3C 440093 __UNKNOWN__ __UNKNOWN__ 12 31944622 31944622 __UNKNOWN__ 3'UTR DEL A A - rs541802300 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:31944622delA ENST00000340398.3 - 0 553 NM_001013699.2 NP_001013721.2 Q6NXT2 H3C_HUMAN H3 histone, family 3C NA NA NA positive regulation of cell growth (GO:0030307) nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786) nucleosomal DNA binding (GO:0031492) endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|skin(2)|upper_aerodigestive_tract(2) 18 AATTTCTTACAAAAAAAGTCA 0.368 NA NA NA HNSCC(67;0.2) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 418 411.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.88 BC066906 CCDS31769.1 12p11.21 2012-02-15 ENSG00000188375 ENSG00000188375 440093 "Histones / Replication-independent" 33164 protein-coding gene gene with protein product NA NA 21274551 Standard NM_001013699 NM_001013699 NA Approved H3.5 uc001rkr.3 Q6NXT2 OTTHUMG00000157811 ENST00000340398.3:c.*71T>- chr12.hg19:g.31944622delA 6 8 ref NA False 145 117 PASS 7 PASS ref->het 0 NA 255,257 109,109 49,47 2 1 E9P281 True hg19 CCDS31769.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA H3F3C-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000349653.1 PASS NA None 418 True - A ENST00000340398.3 ALG10B 144245 __UNKNOWN__ __UNKNOWN__ 12 38714473 38714473 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:38714473delT ENST00000308742.4 + 3 1196 c.880delT c.(880-882)tttfs p.F295fs ALG10B_ENST00000551464.1_Intron NM_001013620.3 NP_001013642.1 Q5I7T1 AG10B_HUMAN ALG10B, alpha-1,2-glucosyltransferase 295 NA NA cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) transferase activity, transferring hexosyl groups (GO:0016758) breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1) 25 Esophageal squamous(101;0.187) Lung NSC(34;0.204)|all_lung(34;0.235) ACTATTCTACTTTTTTTCATT 0.343 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 395 417.56 NA NA 131 137 135 NA NA NA 12 NA NA NA 38714473 2203 4299 6502 SO:0001589 frameshift_variant 0.02 AY845858 CCDS31772.1 12q12 2013-03-04 2013-03-04 ENSG00000175548 ENSG00000175548 144245 2.4.1.256 31088 protein-coding gene gene with protein product "potassium channel regulator 1", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase" NA "asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)" NA Standard NM_001013620 NM_001013620 NA Approved KCR1 uc001rln.4 Q5I7T1 OTTHUMG00000169298 ENST00000308742.4:c.880delT chr12.hg19:g.38714473delT ENSP00000310120:p.Phe295fs 6 7 ref NA False 59 59 PASS 7 PASS ref->het 0 NA 287,292 55,56 53,53 1 1 B2RPF4 True hg19 CCDS31772.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ALG10B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000403349.1 PASS NA None 395 True + T ENST00000308742.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 12 43962682 43962682 __UNKNOWN__ IGR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:43962682delA NA ADAMTS20 (16958 upstream) : RP11-350F4.2 (150113 downstream) NA NA NA NA GAGATGTGGGAAAAAAACAGG 0.388 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 173 159.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.45 NA NA NA NA NA chr12.hg19:g.43962682delA 6 8 ref NA False 33 33 PASS 7 PASS ref->het 0 NA 105,110 48,49 20,17 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 173 True A CACNB3 784 __UNKNOWN__ __UNKNOWN__ 12 49218524 49218524 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:49218524delC ENST00000301050.2 + 5 671 CACNB3_ENST00000536187.2_Intron|CACNB3_ENST00000540990.1_Intron|CACNB3_ENST00000547230.1_Intron|CACNB3_ENST00000547392.1_Intron NM_000725.3 NP_000716.2 P54284 CACB3_HUMAN calcium channel, voltage-dependent, beta 3 subunit NA NA NA axon guidance (GO:0007411)|calcium ion transport (GO:0006816)|membrane depolarization (GO:0051899)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|transport (GO:0006810) apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|membrane (GO:0016020)|voltage-gated calcium channel complex (GO:0005891) voltage-gated calcium channel activity (GO:0005245) autonomic_ganglia(1)|breast(1)|large_intestine(5)|lung(4)|prostate(1) 12 Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661) TAGGTAGCCTCCCCCCAACCC 0.562 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 475 472.38 NA NA 45 46 45 NA NA NA 12 NA NA NA 49218524 2203 4300 6503 SO:0001627 intron_variant 1.3 CCDS8769.1, CCDS55821.1, CCDS55822.1, CCDS55823.1 12q13 2008-05-02 ENSG00000167535 784 "Calcium channel subunits" 1403 protein-coding gene gene with protein product 601958 CACNLB3 NA 8119293 Standard NM_000725 NA Approved uc010sly.2 P54284 ENST00000301050.2:c.472+8C>- chr12.hg19:g.49218524delC 5 8 ref NA False 117 115 PASS 6 PASS ref->het 0 NA 303,309 106,110 66,58 1 1 A8K0Z4|B7Z4Q1|B7Z973|B7ZAK8|F5GZW7|F5H2P6|F8VSG3|Q13913 True hg19 CCDS8769.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CACNB3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000408886.1 PASS NA None 475 True + C ENST00000301050.2 KRT84 3890 __UNKNOWN__ __UNKNOWN__ 12 52774315 52774316 __UNKNOWN__ Frame_Shift_Ins INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:52774315_52774316insT ENST00000257951.3 - 7 1321_1322 c.1255_1256insA c.(1255-1257)accfs p.T419fs RP3-416H24.4_ENST00000547174.1_RNA NM_033045.3 NP_149034.2 Q9NSB2 KRT84_HUMAN keratin 84 419 Coil 2.|Rod. NA NA hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616) extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095) structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280) breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3) 27 all_hematologic(5;0.12) BRCA - Breast invasive adenocarcinoma(357;0.189) ATCACTGAGGGTCGCCTCGCCC 0.644 NA NA NA OREG0021848 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 189 174.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.56 Y19209 CCDS8825.1 12q13 2013-06-25 2006-07-17 2006-07-17 ENSG00000161849 ENSG00000161849 3890 "-", "Intermediate filaments type II, keratins (basic)" 6461 protein-coding gene gene with protein product "hard keratin type II 4" 602766 "keratin, hair, basic, 4" KRTHB4 NA 2431943, 16831889 Standard NM_033045 NM_033045 NA Approved Hb-4 uc001sah.1 Q9NSB2 OTTHUMG00000169634 ENST00000257951.3:c.1256dupA chr12.hg19:g.52774316_52774316dupT ENSP00000257951:p.Thr419fs 2 4 ref 987 False 240 110 PASS 1 PASS ref->het 0 NA 71,72 97,97 19,18 1 1 B2RA43|Q6ISB0|Q701L6 True hg19 CCDS8825.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KRT84-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000405187.1 PASS NA None 189 True - T ENST00000257951.3 HOXC4 3221 __UNKNOWN__ __UNKNOWN__ 12 54422130 54422130 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:54422130delT ENST00000303406.4 + 1 484 RP11-834C11.12_ENST00000513209.1_Intron|RP11-834C11.14_ENST00000512206.1_RNA|HOXC6_ENST00000394331.3_Intron NM_014620.4 NP_055435.2 P09017 HXC4_HUMAN homeobox C4 NA NA NA multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700) cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1) 13 GCAGAAGCGATTTTTTTCCCC 0.403 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 241 238.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.16 CCDS8873.1 12q13.13 2011-06-20 2005-12-22 ENSG00000198353 ENSG00000198353 3221 "Homeoboxes / ANTP class : HOXL subclass" 5126 protein-coding gene gene with protein product 142974 "homeo box C4" HOX3, HOX3E NA 1973146, 1358459 Standard NM_014620 NA Approved uc001sex.3 P09017 OTTHUMG00000160036 ENST00000303406.4:c.-124+10932T>- chr12.hg19:g.54422130delT 6 7 ref NA False 104 103 PASS 7 PASS ref->het 0 NA 161,163 60,63 23,20 1 1 True hg19 CCDS8873.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HOXC4-001 PUTATIVE basic|appris_principal|readthrough_transcript|CCDS protein_coding NA protein_coding OTTHUMT00000358964.1 PASS NA None 241 True + T ENST00000303406.4 PA2G4 5036 __UNKNOWN__ __UNKNOWN__ 12 56507054 56507054 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:56507054delT ENST00000303305.6 + 0 1986 PA2G4_ENST00000552766.1_Intron|RP11-603J24.17_ENST00000548595.1_RNA NM_006191.2 NP_006182.2 Q9UQ80 PA2G4_HUMAN proliferation-associated 2G4, 38kDa NA NA NA cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of translation (GO:0006417)|rRNA processing (GO:0006364)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529) DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625) NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1) 12 OV - Ovarian serous cystadenocarcinoma(18;0.0739) CTCAGCCGAATTTTTTTATAC 0.403 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 145 139.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 U59435, BC007561 CCDS8902.1 12q13.2 2008-09-05 2002-08-29 ENSG00000170515 ENSG00000170515 5036 8550 protein-coding gene gene with protein product 602145 "proliferation-associated 2G4, 38kD" NA 9345902 Standard NM_006191 NM_006191 NA Approved uc001sjm.3 Q9UQ80 OTTHUMG00000170173 ENST00000303305.6:c.*382T>- chr12.hg19:g.56507054delT 6 8 ref NA False 61 61 PASS 7 PASS ref->het 0 NA 96,97 35,36 13,12 1 1 O43846|Q9UM59 True hg19 CCDS8902.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PA2G4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000407767.1 PASS NA None 145 True + T ENST00000303305.6 LRP1 4035 __UNKNOWN__ __UNKNOWN__ 12 57603940 57603940 __UNKNOWN__ Frame_Shift_Del DEL C C - rs368578321 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:57603940delC ENST00000243077.3 + 81 13034 c.12568delC c.(12568-12570)cccfs p.P4192fs NM_002332.2 NP_002323.2 Q07954 LRP1_HUMAN low density lipoprotein receptor-related protein 1 4192 NA NA aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523) clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235) apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872) NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5) 184 BRCA - Breast invasive adenocarcinoma(357;0.0103) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) CTCTCCAACGCCCCCCCCAGA 0.637 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 644 652.95 NA NA 69 63 65 NA NA NA 12 NA NA NA 57603940 2203 4300 6503 SO:0001589 frameshift_variant 3.49 X13916 CCDS8932.1 12q13.3 2013-05-28 2010-01-26 ENSG00000123384 ENSG00000123384 4035 "CD molecules", "Low density lipoprotein receptors" 6692 protein-coding gene gene with protein product 107770 "alpha-2-macroglobulin receptor" APR, A2MR NA 2548950 Standard NM_002332 NM_002332 NA Approved LRP, CD91, LRP1A, APOER uc001snd.3 Q07954 OTTHUMG00000044412 ENST00000243077.3:c.12568delC chr12.hg19:g.57603940delC ENSP00000243077:p.Pro4192fs 7 9 ref NA False 53 53 PASS 8 PASS ref->het 0 NA 489,504 65,67 95,82 1 1 Q2PP12|Q86SW0|Q8IVG8 True hg19 CCDS8932.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LRP1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000412772.2 PASS NA None 644 True + C ENST00000243077.3 LRIG3 121227 __UNKNOWN__ __UNKNOWN__ 12 59279691 59279691 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:59279691delA ENST00000320743.3 - 10 1459 LRIG3_ENST00000379141.4_Intron NM_153377.4 NP_700356.2 Q6UXM1 LRIG3_HUMAN leucine-rich repeats and immunoglobulin-like domains 3 NA NA NA otolith morphogenesis (GO:0032474) cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) LRIG3/ROS1(2) breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 48 GBM - Glioblastoma multiforme(1;1.17e-18) TATCCTGGGGAAAAAAATTAC 0.363 NA NA T ROS1 NSCLC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 12 12q14.1 121227 leucine-rich repeats and immunoglobulin-like domains 3 NA E 0 166 159.43 NA NA 100 115 110 NA NA NA 12 NA NA NA 59279691 2203 4300 6503 SO:0001627 intron_variant 0.89 AY505340 CCDS8960.1, CCDS44933.1 12q13.2 2013-01-11 ENSG00000139263 121227 "Immunoglobulin superfamily / I-set domain containing" 30991 protein-coding gene gene with protein product 608870 NA Standard NM_153377 NM_153377 NA Approved FLJ90440, KIAA3016 uc001sqr.4 Q6UXM1 OTTHUMG00000169940 ENST00000320743.3:c.1173-7T>- chr12.hg19:g.59279691delA 6 7 ref NA False 56 56 PASS 7 PASS ref->het 0 NA 114,114 37,37 15,15 1 1 Q6UXL7|Q8NC72 True hg19 CCDS8960.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LRIG3-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000406623.1 PASS NA None 166 True - A ENST00000320743.3 MDM2 4193 __UNKNOWN__ __UNKNOWN__ 12 69237601 69237601 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:69237601delT ENST00000544125.1 + 0 280 MDM2_ENST00000462284.1_3'UTR|MDM2_ENST00000428863.2_3'UTR|MDM2_ENST00000356290.4_3'UTR|MDM2_ENST00000258149.5_3'UTR|MDM2_ENST00000540827.1_3'UTR Q00987 MDM2_HUMAN MDM2 proto-oncogene, E3 ubiquitin protein ligase NA NA NA cellular response to acid chemical (GO:0071229)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to estrogen stimulus (GO:0071391)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to UV-C (GO:0071494)|cellular response to vitamin B1 (GO:0071301)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of protein localization (GO:0045184)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein processing (GO:0010955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-lysine modification (GO:0018205)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein export from nucleus (GO:0046827)|protein complex assembly (GO:0006461)|protein destabilization (GO:0031648)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of protein catabolic process (GO:0042176)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ether (GO:0045472)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to morphine (GO:0043278)|synaptic transmission (GO:0007268)|traversing start control point of mitotic cell cycle (GO:0007089)|viral process (GO:0016032) cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202) enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270) central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(8)|prostate(1)|urinary_tract(1) 19 all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684) all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143) GCAGAATCTCTTTTTTTTGGA 0.368 NA NA A "sarcoma, glioma, colorectal, other" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 12 12q15 4193 Mdm2 p53 binding protein homolog NA "M, O, E, L" 0 624 619.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.69 CCDS8986.2, CCDS61189.1 12q13-q14 2014-06-26 2014-06-26 ENSG00000135679 ENSG00000135679 4193 6973 protein-coding gene gene with protein product 164785 "mouse double minute 2, human homolog of; p53-binding protein", "Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse)", "Mdm2 p53 binding protein homolog (mouse)" NA 1614537, 16905769 Standard NM_006880 NM_002392 NA Approved HDM2, MGC5370 uc001sui.4 Q00987 OTTHUMG00000142827 ENST00000544125.1:c.*277T>- chr12.hg19:g.69237601delT 7 9 ref NA False 180 145 PASS 8 PASS ref->het 0 NA 400,406 143,145 81,75 1 1 A6NL51|A8K2S6|Q13226|Q13297|Q13298|Q13299|Q13300|Q13301|Q53XW0|Q71TW9|Q8WYJ1|Q8WYJ2|Q9UGI3|Q9UMT8 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MDM2-043 PUTATIVE basic|exp_conf processed_transcript NA protein_coding OTTHUMT00000402676.1 PASS NA None 624 True + T ENST00000544125.1 NAV3 89795 __UNKNOWN__ __UNKNOWN__ 12 78388636 78388636 __UNKNOWN__ Frame_Shift_Del DEL A A - rs35319232 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:78388636delA ENST00000536525.2 + 6 898 c.725delA c.(724-726)caafs p.Q242fs NAV3_ENST00000266692.7_Frame_Shift_Del_p.Q242fs|NAV3_ENST00000228327.6_Frame_Shift_Del_p.Q242fs|NAV3_ENST00000397909.2_Frame_Shift_Del_p.Q242fs NM_014903.4 NP_055718.4 Q8IVL0 NAV3_HUMAN neuron navigator 3 242 NA NA membrane (GO:0016020)|nuclear envelope (GO:0005635) NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1) 236 GCAACCAGTCAAAAAAAGCCT 0.323 NA NA NA HNSCC(70;0.22) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 182 171.36 NA NA 126 119 121 NA NA NA 12 NA NA NA 78388636 1816 4087 5903 SO:0001589 frameshift_variant 0.27 AB023155 CCDS41815.1, CCDS66432.1 12q14.3 2008-08-05 ENSG00000067798 89795 15998 protein-coding gene gene with protein product "pore membrane and/or filament interacting like protein 1", "steerin 3" 611629 NA 12079279, 12062803 Standard NM_001024383 XM_005269215 NA Approved KIAA0938, POMFIL1 uc001syo.3 Q8IVL0 OTTHUMG00000170001 ENST00000536525.2:c.725delA chr12.hg19:g.78388636delA ENSP00000446132:p.Gln242fs 6 7 ref NA False 32 32 PASS 7 PASS ref->het 0 NA 130,131 26,27 24,22 1 1 Q8NFW7|Q9Y2E7 True hg19 CCDS41815.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NAV3-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000406811.1 PASS NA None 182 True + A ENST00000536525.2 TMTC3 160418 __UNKNOWN__ __UNKNOWN__ 12 88589306 88589306 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:88589306delA ENST00000266712.6 + 14 2845 c.2625delA c.(2623-2625)ggafs p.G875fs NM_181783.3 NP_861448.2 Q6ZXV5 TMTC3_HUMAN transmembrane and tetratricopeptide repeat containing 3 876 NA NA bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468) integral component of membrane (GO:0016021) NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1) 31 AACAATTAGGAAAAAATGGAG 0.323 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 85 91 NA NA 71 73 72 NA NA NA 12 NA NA NA 88589306 2203 4299 6502 SO:0001589 frameshift_variant 0 CCDS9032.1 12q21.32 2014-09-04 ENSG00000139324 ENSG00000139324 160418 "Tetratricopeptide (TTC) repeat domain containing" 26899 protein-coding gene gene with protein product NA NA Standard NM_181783 NM_181783 NA Approved FLJ90492, SMILE uc001tau.3 Q6ZXV5 OTTHUMG00000169887 ENST00000266712.6:c.2625delA chr12.hg19:g.88589306delA ENSP00000266712:p.Gly875fs 5 6 ref NA False 31 31 PASS 6 PASS ref->het 0 NA 59,61 20,20 7,7 2 2 Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50 True hg19 CCDS9032.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMTC3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000406421.1 PASS NA None 85 True + A ENST00000266712.6 HNF1A 6927 __UNKNOWN__ __UNKNOWN__ 12 121432117 121432118 __UNKNOWN__ Frame_Shift_Ins INS - - C rs56348580 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:121432117_121432118insC ENST00000257555.6 + 4 1090_1091 c.864_865insC c.(865-867)cccfs p.P289fs HNF1A_ENST00000541395.1_Frame_Shift_Ins_p.P289fs|HNF1A_ENST00000543427.1_Frame_Shift_Ins_p.P172fs|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000544413.1_Frame_Shift_Ins_p.P289fs|HNF1A_ENST00000402929.1_Frame_Shift_Ins_p.P289fs|HNF1A_ENST00000400024.2_Frame_Shift_Ins_p.P289fs P20823 HNF1A_HUMAN HNF1 homeobox A 289 NA NA glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623) cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234) DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212) breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1) 221 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) CGTACAGCGGGCCCCCCCCAGG 0.663 NA NA NA Hepatic Adenoma, Familial Clustering of NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 GRCh37 CI064741|CM067044|CM082856 HNF1A I|M rs56348580 429 419.11 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 2.09 Familial Cancer Database incl. Maturity-Onset Diabetes of the Young type 3, MODY3 M57732 CCDS9209.1 12q24.31 2014-09-17 2007-08-24 2007-08-24 ENSG00000135100 ENSG00000135100 6927 "Homeoboxes / HNF class" 11621 protein-coding gene gene with protein product 142410 "transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor" MODY3, TCF1 NA 1535333, 7795649 Standard NM_000545 NM_000545 NA Approved HNF1, LFB1 uc001tzg.3 P20823 OTTHUMG00000151015 ENST00000257555.6:c.872dupC chr12.hg19:g.121432125_121432125dupC ENSP00000257555:p.Pro289fs 9 8 ref NA False 103 90 PASS 8 PASS ref->het 0 NA 274,283 78,81 74,63 1 1 A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861 True hg19 CCDS9209.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HNF1A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000320957.5 PASS NA None 429 True + C ENST00000257555.6 NCOR2 9612 __UNKNOWN__ __UNKNOWN__ 12 124848228 124848228 __UNKNOWN__ Frame_Shift_Del DEL G G - rs12321697 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:124848228delG ENST00000405201.1 - 21 2925 c.2925delC c.(2923-2925)cccfs p.P975fs NCOR2_ENST00000397355.1_Frame_Shift_Del_p.P958fs|NCOR2_ENST00000404621.1_Frame_Shift_Del_p.P957fs|NCOR2_ENST00000429285.2_Frame_Shift_Del_p.P957fs|NCOR2_ENST00000356219.3_Frame_Shift_Del_p.P975fs|NCOR2_ENST00000404121.2_Frame_Shift_Del_p.P528fs Q9Y618 NCOR2_HUMAN nuclear receptor corepressor 2 975 NA NA cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179) membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053) chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714) breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2) 69 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) CACTCACGATGGGGGGGATGG 0.652 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 193 191.73 NA NA 63 84 77 NA NA NA 12 NA NA NA 124848228 1997 4147 6144 SO:0001589 frameshift_variant 2.71 U37146 CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1 12q24 2010-06-10 2010-06-10 ENSG00000196498 ENSG00000196498 9612 7673 protein-coding gene gene with protein product 600848 "nuclear receptor co-repressor 2" NA 7566127, 8813722 Standard NM_006312 NM_001077261 NA Approved SMRT, SMRTE, TRAC-1, CTG26, TNRC14 uc010tbb.2 Q9Y618 OTTHUMG00000150455 ENST00000405201.1:c.2925delC chr12.hg19:g.124848228delG ENSP00000384018:p.Pro975fs 6 7 ref NA False 122 119 PASS 7 PASS ref->het 0 NA 118,128 43,44 41,31 1 1 O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0 True hg19 CCDS41858.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NCOR2-005 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000318173.2 PASS NA None 193 True - G ENST00000405201.1 FBRSL1 57666 __UNKNOWN__ __UNKNOWN__ 12 133158015 133158015 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:133158015delC ENST00000434748.2 + 14 2983 FBRSL1_ENST00000261673.6_Intron NM_001142641.1 NP_001136113.1 Q9HCM7 FBSL_HUMAN fibrosin-like 1 NA NA NA poly(A) RNA binding (GO:0044822) central_nervous_system(2)|endometrium(1)|stomach(1) 4 AACCTGGCTGCCCCCCCCAGG 0.632 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 155 166.08 NA 34,54,2240 NA 6,0,22,15,24,1097 24 30 28 NA -3 0 12 28 70,116,4562 NA 6,1,57,36,43,2231 no intron FBRSL1 NM_001142641.1 12,1,79,51,67,3328 A1A1,A1A2,A1R,A2A2,A2R,RR NA 3.9174,3.7801,3.8722 133158015 104,170,6802 692 1591 2283 SO:0001627 intron_variant 0.8 CCDS45010.1 12q24.33 2008-12-09 ENSG00000112787 ENSG00000112787 57666 29308 protein-coding gene gene with protein product NA NA 10997877 Standard NM_001142641 NA Approved KIAA1545 uc001ukf.3 Q9HCM7 OTTHUMG00000167991 ENST00000434748.2:c.1964-10C>- chr12.hg19:g.133158015delC 7 8 ref NA False 55 55 PASS 8 PASS ref->het 0 NA 111,112 33,33 15,14 1 1 Q86XQ1 True hg19 CCDS45010.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FBRSL1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000397404.2 PASS NA None 155 True + C ENST00000434748.2 P2RX2 22953 __UNKNOWN__ __UNKNOWN__ 12 133198204 133198204 __UNKNOWN__ Splice_Site DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:133198204delG ENST00000389110.3 + 11 1099 c.e11-1 P2RX2_ENST00000350048.5_Splice_Site|P2RX2_ENST00000449132.2_Splice_Site|P2RX2_ENST00000343948.4_Frame_Shift_Del_p.Q380fs|P2RX2_ENST00000352418.4_Splice_Site|P2RX2_ENST00000348800.5_Splice_Site|P2RX2_ENST00000351222.4_Splice_Site NM_170682.2|NM_170683.2|NM_174873.1 NP_733782.1|NP_733783.1|NP_777362.1 Q9UBL9 P2RX2_HUMAN purinergic receptor P2X, ligand-gated ion channel, 2 NA NA NA behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of hypoxic conditions in blood by carotid body chemoreceptor signaling (GO:0003029)|ion transmembrane transport (GO:0034220)|neuromuscular junction development (GO:0007528)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to hypoxia (GO:0001666)|sensory perception of sound (GO:0007605)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|urinary bladder smooth muscle contraction (GO:0014832) apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)|terminal bouton (GO:0043195) ATP binding (GO:0005524)|cadmium ion binding (GO:0046870)|cobalt ion binding (GO:0050897)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|ligand-gated ion channel activity (GO:0015276)|mercury ion binding (GO:0045340)|nickel cation binding (GO:0016151)|phosphatidylinositol binding (GO:0035091)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270) NS(1)|breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(8)|ovary(1)|prostate(3) 20 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0767) OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06) GCTGGCCCCAGGGCTCCTTCC 0.582 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 242 245.81 NA NA 55 59 58 NA NA NA 12 NA NA NA 133198204 2203 4300 6503 SO:0001630 splice_region_variant 1.31 AF109387 CCDS31930.1, CCDS31931.1, CCDS31932.1, CCDS31933.1, CCDS31934.1, CCDS31935.1, CCDS61286.1, CCDS73548.1 12q24.33 2013-03-22 ENSG00000187848 ENSG00000187848 22953 "Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic" 15459 protein-coding gene gene with protein product 600844 "deafness, autosomal dominant 41" DFNA41 NA 10570044, 7523952, 23345450 Standard XM_005266154 NA Approved P2X2 uc001ukk.1 Q9UBL9 OTTHUMG00000168018 ENST00000389110.3:c.1063-1G>- chr12.hg19:g.133198204delG 2 4 ref NA False 45 45 PASS 3 PASS ref->het 0 NA 164,167 54,55 24,21 1 1 A6NGB4|A6NH93|A6NHC2|A6NHU3|A6NIG9|Q6V9R6|Q9NR37|Q9NR38|Q9UHD5|Q9UHD6|Q9UHD7|Q9Y637|Q9Y638 True hg19 CCDS31931.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA P2RX2-006 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000397542.1 PASS NA None 242 Intron True + G ENST00000389110.3 TPTE2 93492 __UNKNOWN__ __UNKNOWN__ 13 20000633 20000636 __UNKNOWN__ Frame_Shift_Del DEL TGTC TGTC - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:20000633_20000636delTGTC ENST00000382978.1 - 17 1246_1249 c.1204_1207delGACA c.(1204-1209)gacaaafs p.DK402fs TPTE2_ENST00000457266.2_Frame_Shift_Del_p.DK331fs|TPTE2_ENST00000382977.4_Frame_Shift_Del_p.DK442fs|TPTE2_ENST00000255310.6_Frame_Shift_Del_p.DK365fs|TPTE2_ENST00000400103.2_Frame_Shift_Del_p.DK331fs|TPTE2_ENST00000400230.2_Frame_Shift_Del_p.DK442fs|TPTE2_ENST00000382975.4_Frame_Shift_Del_p.DK402fs|TPTE2_ENST00000390680.2_Frame_Shift_Del_p.DK365fs Q6XPS3 TPTE2_HUMAN transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 442 C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}. NA NA phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281) endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021) ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138) NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 65 all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089) ATTAATATTTTGTCTGTTTCAATG 0.343 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 315 307.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.55 AJ421032 CCDS9285.1, CCDS45013.1, CCDS45014.1 13q12.11 2012-12-10 ENSG00000132958 ENSG00000132958 93492 "Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs" 17299 protein-coding gene gene with protein product 606791 NA 11716755, 12717346, 15057823 Standard NM_199254 NM_130785 NA Approved TPIP uc001umd.3 Q6XPS3 OTTHUMG00000016493 ENST00000382978.1:c.1204_1207delGACA chr13.hg19:g.20000633_20000636delTGTC ENSP00000372438:p.Asp402fs 0 5 ref NA False 57 57 PASS 1 PASS ref->het 0 NA 226,229 47,47 41,43 1 1 A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TPTE2-001 NOVEL basic protein_coding NA protein_coding OTTHUMT00000044022.1 PASS NA None 315 True - TGTC ENST00000382978.1 RNF6 6049 __UNKNOWN__ __UNKNOWN__ 13 26788241 26788241 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:26788241delA ENST00000381588.4 - 5 2530 c.1778delT c.(1777-1779)ttafs p.L594fs RNF6_ENST00000399762.2_Frame_Shift_Del_p.L238fs|RNF6_ENST00000346166.3_Frame_Shift_Del_p.L594fs|RNF6_ENST00000468480.1_Intron|RNF6_ENST00000381570.3_Frame_Shift_Del_p.L594fs NM_005977.3 NP_005968.1 Q9Y252 RNF6_HUMAN ring finger protein (C3H2C3 type) 6 594 NA NA negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511) axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605) androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270) breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2) 23 Colorectal(5;0.000442) Lung SC(185;0.0156)|Breast(139;0.147) all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245) TTCATTTAGTAAAAAAAAGTG 0.403 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 255 256.55 NA NA 134 130 132 NA NA NA 13 NA NA NA 26788241 2203 4300 6503 SO:0001589 frameshift_variant 1.5 AJ010346 CCDS9316.1 13q12.2 2013-01-09 ENSG00000127870 ENSG00000127870 6049 "RING-type (C3HC4) zinc fingers" 10069 protein-coding gene gene with protein product "RING-H2 protein RNF-6" 604242 NA 10331950 Standard NM_005977 NM_005977 NA Approved DKFZp686P0776 uc001uqq.3 Q9Y252 OTTHUMG00000016614 ENST00000381588.4:c.1778delT chr13.hg19:g.26788241delA ENSP00000371000:p.Leu594fs 7 8 ref NA False 79 79 PASS 8 PASS ref->het 0 NA 157,159 59,60 37,37 1 1 B4DDP0|Q5W0H0|Q9BZP5|Q9UF41 True hg19 CCDS9316.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RNF6-006 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044246.2 PASS NA None 255 True - A ENST00000381588.4 FLT3 2322 __UNKNOWN__ __UNKNOWN__ 13 28601256 28601256 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:28601256delA ENST00000241453.7 - 17 2257 c.2176delT c.(2176-2178)tacfs p.Y726fs FLT3_ENST00000380982.4_Frame_Shift_Del_p.Y726fs|FLT3_ENST00000537084.1_Frame_Shift_Del_p.Y726fs NM_004119.2 NP_004110.2 P36888 FLT3_HUMAN fms-related tyrosine kinase 3 726 Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}. NA NA B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084) endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887) ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021) NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 12390 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0156)|Ovarian(182;0.0392) Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105) OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212) Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268) AAAGTGGGGTAAAAACTGAAA 0.388 NA NA "Mis, O" "AML, ALL" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 13 13q12 2322 fms-related tyrosine kinase 3 NA L 0 142 133.25 NA NA 176 180 179 NA NA NA 13 NA NA NA 28601256 2203 4300 6503 SO:0001589 frameshift_variant 0 U02687 CCDS31953.1 13q12 2014-09-17 ENSG00000122025 ENSG00000122025 2322 2.7.10.1 "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing" 3765 protein-coding gene gene with protein product 136351 NA 8394751 Standard NM_004119 NA Approved STK1, FLK2, CD135 uc001urw.3 P36888 OTTHUMG00000016646 ENST00000241453.7:c.2176delT chr13.hg19:g.28601256delA ENSP00000241453:p.Tyr726fs 4 5 ref NA False 34 34 PASS 5 PASS ref->het 0 NA 105,105 24,24 11,11 1 1 A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414 True hg19 CCDS31953.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FLT3-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000044319.2 PASS NA None 142 True - A ENST00000241453.7 RXFP2 122042 __UNKNOWN__ __UNKNOWN__ 13 32367197 32367197 __UNKNOWN__ Frame_Shift_Del DEL C C - rs376914410 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:32367197delC ENST00000298386.2 + 16 1829 c.1758delC c.(1756-1758)agcfs p.S586fs RXFP2_ENST00000380314.1_Frame_Shift_Del_p.S562fs NM_130806.3 NP_570718.1 Q8WXD0 RXFP2_HUMAN relaxin/insulin-like family peptide receptor 2 586 NA NA adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500) cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1) 33 Lung SC(185;0.0262) all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535) ATATTGGAAGCAAAGGGTATT 0.303 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 125 120.2 NA NA 36 40 38 NA NA NA 13 NA NA NA 32367197 2198 4298 6496 SO:0001589 frameshift_variant 0 AF403384 CCDS9342.1, CCDS53862.1 13q12.3 2012-08-08 2006-05-09 2006-05-09 ENSG00000133105 ENSG00000133105 122042 "GPCR / Class A : Relaxin family peptide receptors" 17318 protein-coding gene gene with protein product 606655 "leucine-rich repeat-containing G protein-coupled receptor 8" LGR8 NA 12217959, 12970298, 15956688, 16507880 Standard NM_130806 NM_130806 NA Approved GREAT, GPR106, INSL3R, RXFPR2 uc001utt.3 Q8WXD0 OTTHUMG00000016690 ENST00000298386.2:c.1758delC chr13.hg19:g.32367197delC ENSP00000298386:p.Ser586fs 0 3 ref NA False 55 55 PASS 1 PASS ref->het 0 NA 45,45 70,70 7,7 1 1 B1ALE9|Q3KU23 True hg19 CCDS9342.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RXFP2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000044399.1 PASS NA None 125 True + C ENST00000298386.2 NBEA 26960 __UNKNOWN__ __UNKNOWN__ 13 35619419 35619421 __UNKNOWN__ Intron DEL TTC TTC - rs74051223 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:35619419_35619421delTTC ENST00000379939.2 + 4 788 NBEA_ENST00000400445.3_Intron|NBEA_ENST00000310336.4_Intron|NBEA_ENST00000540320.1_Intron Q8NFP9 NBEA_HUMAN neurobeachin NA NA NA protein localization (GO:0008104) cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802) NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3) 108 Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207) all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199) ACAATGACATTTCTTTCTTTTAT 0.305 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 195 202.85 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF467288 CCDS45026.1, CCDS55894.1 13q13 2014-09-17 ENSG00000172915 ENSG00000172915 26960 "A-kinase anchor proteins", "WD repeat domain containing" 7648 protein-coding gene gene with protein product 604889 NA 10501977 Standard NM_015678 NM_015678 NA Approved KIAA1544, BCL8B, FLJ10197 uc021ric.1 Q8NFP9 OTTHUMG00000016724 ENST00000379939.2:c.628-22TTC>- chr13.hg19:g.35619419_35619421delTTC 0 7 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 146,150 43,44 13,13 1 1 B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NBEA-001 KNOWN basic|appris_candidate protein_coding NA protein_coding OTTHUMT00000044460.1 PASS NA None 195 True + TTC ENST00000379939.2 COL4A2 1284 __UNKNOWN__ __UNKNOWN__ 13 111091058 111091059 __UNKNOWN__ Intron INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:111091058_111091059insT ENST00000360467.5 + 15 1218 NM_001846.2 NP_001837.2 P08572 CO4A2_HUMAN collagen, type IV, alpha 2 NA NA NA angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351) collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231) extracellular matrix structural constituent (GO:0005201) NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1) 80 all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922) Breast(118;0.212) BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151) GTTTGGTTTGGTTtttttcagt 0.446 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 262 252.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.84 AK025912 CCDS41907.1 13q34 2013-09-05 ENSG00000134871 ENSG00000134871 1284 "Collagens" 2203 protein-coding gene gene with protein product "canstatin", "collagen type IV alpha 2" 120090 NA 2439508, 3025878 Standard NM_001846 NM_001846 NA Approved FLJ22259, DKFZp686I14213 uc001vqx.3 P08572 OTTHUMG00000017344 ENST00000360467.5:c.912+43->T chr13.hg19:g.111091065_111091065dupT 8 7 ref NA False 107 106 PASS 7 PASS ref->het 0 NA 161,163 63,64 40,40 1 1 Q14052|Q548C3|Q5VZA9|Q66K23 True hg19 CCDS41907.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COL4A2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000045761.2 PASS NA None 262 True + T ENST00000360467.5 ING1 3621 __UNKNOWN__ __UNKNOWN__ 13 111371664 111371665 __UNKNOWN__ Frame_Shift_Del DEL GC GC - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:111371664_111371665delGC ENST00000333219.7 + 2 1097_1098 c.225_226delGC c.(223-228)cagcgcfs p.R76fs ING1_ENST00000464141.1_3'UTR|ING1_ENST00000338450.7_Frame_Shift_Del_p.R32fs|ING1_ENST00000375775.3_Frame_Shift_Del_p.R7fs|ING1_ENST00000375774.3_Frame_Shift_Del_p.R219fs NM_001267728.1|NM_198219.2 NP_001254657.1|NP_937862.1 Q9UK53 ING1_HUMAN inhibitor of growth family, member 1 219 NA NA cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941) nucleus (GO:0005634) methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270) endometrium(4)|large_intestine(6)|lung(1)|ovary(1) 12 all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148) BRCA - Breast invasive adenocarcinoma(86;0.188) ACTGTGTGCAGCGCGCGCTGAT 0.644 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 534 570.93 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 3.15 CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1 13q34 2013-01-28 ENSG00000153487 ENSG00000153487 3621 "Zinc fingers, PHD-type" 6062 protein-coding gene gene with protein product "inhibitor of growth 1", "tumor suppressor ING1", "growth inhibitor ING1", "growth inhibitory protein ING1" 601566 NA 8944021, 9186514 Standard NM_005537 NM_198219 NA Approved p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a uc001vri.3 Q9UK53 OTTHUMG00000017346 ENST00000333219.7:c.225_226delGC chr13.hg19:g.111371670_111371671delGC ENSP00000328436:p.Arg76fs 3 2 ref NA False 110 110 PASS 4 PASS ref->het 0 NA 353,371 65,69 111,95 1 1 O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52 True hg19 CCDS9516.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ING1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000045767.1 PASS NA None 534 True + GC ENST00000333219.7 PCID2 55795 __UNKNOWN__ __UNKNOWN__ 13 113839723 113839724 __UNKNOWN__ Intron INS - - AT LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:113839723_113839724insAT ENST00000337344.4 - 8 620 PCID2_ENST00000246505.5_Intron|PCID2_ENST00000375457.2_Intron|PCID2_ENST00000375479.2_Intron|PCID2_ENST00000375459.1_Intron|PCID2_ENST00000493650.1_Intron|PCID2_ENST00000375477.1_Intron NM_001127202.2 NP_001120674.1 Q5JVF3 PCID2_HUMAN PCI domain containing 2 NA NA NA negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mRNA stability (GO:0043488)|spleen development (GO:0048536) breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10) 20 Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_lung(25;0.216)|all_epithelial(44;0.234) all cancers(43;0.104) GAGGCTAGCTGATATATATATG 0.401 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 258 250.34 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.97 AK002167 CCDS9532.2, CCDS58301.1, CCDS58302.1 13q34 2006-03-31 ENSG00000126226 ENSG00000126226 55795 25653 protein-coding gene gene with protein product 613713 NA 12477932 Standard NM_018386 NM_001127203 NA Approved FLJ11305 uc031qnm.1 Q5JVF3 OTTHUMG00000017385 ENST00000337344.4:c.543+74->AT chr13.hg19:g.113839732_113839733dupAT 6 2 ref NA False 41 41 PASS 5 PASS ref->het 0 NA 173,173 47,47 38,38 1 1 A6NK09|Q3ZCX1|Q5TC57|Q5TC58|Q9H7K1|Q9HBZ7|Q9NUK6|Q9NVY1|Q9NW44|Q9NWH3 True hg19 CCDS9532.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PCID2-002 KNOWN alternative_3_UTR|non_canonical_U12|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000045897.1 PASS NA None 258 True - AT ENST00000337344.4 HECTD1 25831 __UNKNOWN__ __UNKNOWN__ 14 31609023 31609023 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:31609023delT ENST00000399332.1 - 19 3468 HECTD1_ENST00000553700.1_Intron NM_015382.2 NP_056197.2 Q9ULT8 HECD1_HUMAN HECT domain containing E3 ubiquitin protein ligase 1 NA NA NA neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787) cytoplasm (GO:0005737)|nucleus (GO:0005634) ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842) breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3) 70 Hepatocellular(127;0.0877)|Breast(36;0.176) LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173) GBM - Glioblastoma multiforme(265;0.00617) AAGAAAATAATTTTTTTTAAA 0.299 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 65 69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AB032957 CCDS41939.1 14q12 2013-01-10 2012-02-23 ENSG00000092148 ENSG00000092148 25831 "Ankyrin repeat domain containing" 20157 protein-coding gene gene with protein product NA "HECT domain containing 1" NA 10574461 Standard XM_005267502 NA Approved KIAA1131 uc001wrc.1 Q9ULT8 OTTHUMG00000170670 ENST00000399332.1:c.2979+74A>- chr14.hg19:g.31609023delT 7 8 ref NA False 45 45 PASS 8 PASS ref->het 0 NA 35,36 23,23 7,7 2 2 D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7 True hg19 CCDS41939.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HECTD1-201 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000409942.1 PASS NA None 65 True - T ENST00000399332.1 SRP54 6729 __UNKNOWN__ __UNKNOWN__ 14 35498327 35498327 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:35498327delT ENST00000556994.1 + 17 1881 c.1484delT c.(1483-1485)atgfs p.M495fs SRP54_ENST00000546080.1_Frame_Shift_Del_p.M446fs|SRP54_ENST00000216774.6_Frame_Shift_Del_p.M495fs|SRP54_ENST00000555557.1_Frame_Shift_Del_p.M431fs P61011 SRP54_HUMAN signal recognition particle 54kDa 495 M-domain. NA NA cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO:0006617)|SRP-dependent cotranslational protein targeting to membrane, translocation (GO:0006616)|translation (GO:0006412) cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786) 7S RNA binding (GO:0008312)|drug binding (GO:0008144)|endoplasmic reticulum signal peptide binding (GO:0030942)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021) NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1) 14 Breast(36;0.0545)|Hepatocellular(127;0.158) LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243) GBM - Glioblastoma multiforme(112;0.0396) GCTGGCAACATGAAAGGCATG 0.403 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 194 187.6 NA NA 99 97 97 NA NA NA 14 NA NA NA 35498327 2203 4300 6503 SO:0001589 frameshift_variant 0 X86373 CCDS9652.1, CCDS53893.1 14q13.2 2014-06-02 2002-08-29 ENSG00000100883 ENSG00000100883 6729 11301 protein-coding gene gene with protein product 604857 "signal recognition particle 54kD" NA 8722571 Standard NM_003136 NM_003136 NA Approved uc001wso.3 P61011 OTTHUMG00000140214 ENST00000556994.1:c.1484delT chr14.hg19:g.35498327delT ENSP00000451818:p.Met495fs 0 3 ref NA False 112 103 PASS 1 PASS ref->het 0 NA 114,116 59,59 18,18 1 1 B2R759|B4DUW6|P13624 True hg19 CCDS9652.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SRP54-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000276643.2 PASS NA None 194 True + T ENST00000556994.1 RP11-407N17.3 0 __UNKNOWN__ __UNKNOWN__ 14 39782670 39782671 __UNKNOWN__ Intron INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:39782670_39782671insT ENST00000553728.1 + 18 3113 CTAGE5_ENST00000341749.3_Intron|CTAGE5_ENST00000396165.4_Intron|CTAGE5_ENST00000557038.1_Intron|RP11-407N17.3_ENST00000603904.1_Intron|CTAGE5_ENST00000553352.1_Intron|CTAGE5_ENST00000556148.1_Intron|CTAGE5_ENST00000348007.3_Intron|CTAGE5_ENST00000280083.3_Intron|CTAGE5_ENST00000396158.2_Intron|CTAGE5_ENST00000341502.5_Intron NA NA NA NA TTTCTGGTTTCTTTTTTGGAAT 0.317 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 54 52.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA NA NA NA ENST00000553728.1:c.2900+25->T chr14.hg19:g.39782676_39782676dupT 7 9 ref NA False 40 40 PASS 6 PASS ref->het 0 NA 30,30 12,13 11,10 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-407N17.3-001 NOVEL not_organism_supported|basic|appris_principal|readthrough_transcript protein_coding NA protein_coding OTTHUMT00000410208.1 PASS NA None 54 True + T ENST00000553728.1 FBXO33 254170 __UNKNOWN__ __UNKNOWN__ 14 39868111 39868112 __UNKNOWN__ 3'UTR INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:39868111_39868112insT ENST00000298097.7 - 0 2613_2614 NM_203301.3 NP_976046.1 Q7Z6M2 FBX33_HUMAN F-box protein 33 NA NA NA protein ubiquitination (GO:0016567) endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1) 9 Hepatocellular(127;0.213) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169) GBM - Glioblastoma multiforme(112;0.0425) ACGTAAATGCATTTTTTTTAAA 0.257 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 147 153.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.23 BI460761 CCDS9677.1 14q13.3 2004-08-24 2004-06-15 ENSG00000165355 ENSG00000165355 254170 "F-boxes / "other"" 19833 protein-coding gene gene with protein product 609103 "F-box only protein 33" NA Standard NM_203301 NA Approved Fbx33 uc001wvk.3 Q7Z6M2 OTTHUMG00000140257 ENST00000298097.7:c.*609->A chr14.hg19:g.39868119_39868119dupT 9 8 ref NA False 65 65 PASS 8 PASS ref->het 0 NA 94,95 30,31 23,22 1 1 Q6PIR2|Q86TR2|Q86YE0 True hg19 CCDS9677.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FBXO33-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000276769.2 PASS NA None 147 True - T ENST00000298097.7 VCPKMT 79609 __UNKNOWN__ __UNKNOWN__ 14 50582633 50582633 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:50582633delA ENST00000395860.2 - 3 382 VCPKMT_ENST00000395859.2_Intron NM_024558.2 NP_078834.2 Q9H867 MT21D_HUMAN valosin containing protein lysine (K) methyltransferase NA NA NA peptidyl-lysine trimethylation (GO:0018023) cytoplasm (GO:0005737) protein-lysine N-methyltransferase activity (GO:0016279) NA TTCCCCCCTTAAAAATGCCAA 0.373 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 99 97.47 NA NA 65 65 65 NA NA NA 14 NA NA NA 50582633 2203 4300 6503 SO:0001627 intron_variant 0.27 AK023982 CCDS9696.2, CCDS41951.1 14q21.3 2013-09-30 2013-09-30 2013-09-30 ENSG00000100483 ENSG00000100483 79609 20352 protein-coding gene gene with protein product 615260 "chromosome 14 open reading frame 138", "methyltransferase like 21D" C14orf138, METTL21D NA 22948820 Standard NM_024558 NR_049738 NA Approved VCP-KMT uc001wxo.1 Q9H867 OTTHUMG00000029531 ENST00000395860.2:c.378-4T>- chr14.hg19:g.50582633delA 4 5 ref NA False 42 42 PASS 5 PASS ref->het 0 NA 75,76 15,15 9,8 2 2 B7ZLA3|B7ZLA4|Q2M2X3|Q86T12 True hg19 CCDS9696.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA VCPKMT-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000276877.1 PASS NA None 99 True - A ENST00000395860.2 SAMD4A 23034 __UNKNOWN__ __UNKNOWN__ 14 55227159 55227159 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:55227159delC ENST00000555192.1 + 2 346 c.230delC c.(229-231)gccfs p.A77fs SAMD4A_ENST00000251091.5_Frame_Shift_Del_p.A398fs|SAMD4A_ENST00000554335.1_Frame_Shift_Del_p.A486fs|SAMD4A_ENST00000357634.3_Frame_Shift_Del_p.A485fs|SAMD4A_ENST00000392067.3_Frame_Shift_Del_p.A486fs NM_001161577.1 NP_001155049.1 Q9UPU9 SMAG1_HUMAN sterile alpha motif domain containing 4A 486 NA NA negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727) cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202) poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371) breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1) 29 CTGGCCGTCGCCCCCCTGCCA 0.687 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 164 163.74 NA NA 4 6 5 NA NA NA 14 NA NA NA 55227159 1978 3900 5878 SO:0001589 frameshift_variant 1.26 AB028976 CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2 14q22.2 2013-01-10 2006-01-27 2006-01-27 ENSG00000020577 ENSG00000020577 23034 "Sterile alpha motif (SAM) domain containing" 23023 protein-coding gene gene with protein product "smaug homolog (Drosophila)" 610747 "sterile alpha motif domain containing 4" SAMD4 NA 16221671 Standard NM_015589 NM_001161577 NA Approved KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1 uc001xbb.4 Q9UPU9 OTTHUMG00000170999 ENST00000555192.1:c.230delC chr14.hg19:g.55227159delC ENSP00000450808:p.Ala77fs 5 7 ref NA False 149 130 PASS 6 PASS ref->het 0 NA 95,97 43,47 25,22 1 1 A8MPZ5|Q0VA96|Q6PEW4 True hg19 CCDS55918.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SAMD4A-006 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000411193.1 PASS NA None 164 True + C ENST00000555192.1 CHURC1 91612 __UNKNOWN__ __UNKNOWN__ 14 65400017 65400017 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:65400017delA ENST00000552002.2 + 0 1480 CHURC1_ENST00000549115.1_3'UTR|CHURC1-FNTB_ENST00000549987.1_Intron|FNTB_ENST00000542227.1_Intron|CHURC1_ENST00000359118.2_3'UTR|CHURC1_ENST00000607599.1_3'UTR|FNTB_ENST00000447296.2_Intron Q8WUH1 CHUR_HUMAN churchill domain containing 1 NA NA NA multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351) zinc ion binding (GO:0008270) breast(1)|pancreas(1) 2 all cancers(60;0.00119)|OV - Ovarian serous cystadenocarcinoma(108;0.0056)|BRCA - Breast invasive adenocarcinoma(234;0.00976) ccacgaaaagaaaaaaaggtc 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 85 86.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF060510 CCDS32101.1, CCDS32101.2, CCDS55921.1, CCDS55922.1 14q23.3 2011-09-28 2004-05-05 2004-05-07 ENSG00000258289 ENSG00000258289 91612 20099 protein-coding gene gene with protein product 608577 C14orf52 NA Standard NM_145165 NM_145165 NA Approved My015, FLJ33064 Q8WUH1 OTTHUMG00000170218 ENST00000552002.2:c.*1069A>- chr14.hg19:g.65400017delA 6 11 ref NA False 51 51 PASS 7 PASS ref->het 0 NA 50,51 31,31 5,5 1 1 B3KQ81|G3V1X3|G3V214|Q9H3K7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CHURC1-011 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000470736.1 PASS NA None 85 True + A ENST00000552002.2 SRSF5 6430 __UNKNOWN__ __UNKNOWN__ 14 70237833 70237833 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:70237833delT ENST00000553635.1 + 7 656 SRSF5_ENST00000556587.1_Intron|SRSF5_ENST00000557154.1_Intron|SRSF5_ENST00000553521.1_Intron|SRSF5_ENST00000394366.2_Intron Q13243 SRSF5_HUMAN serine/arginine-rich splicing factor 5 NA NA NA gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366) cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822) large_intestine(1)|liver(1) 2 GTATCTCTAATTTTTTAAAGT 0.318 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 99 94.5 NA NA 58 64 62 NA NA NA 14 NA NA NA 70237833 2203 4298 6501 SO:0001627 intron_variant 0 AF020307 CCDS32109.1 14q24 2013-02-12 2010-06-22 2010-06-22 ENSG00000100650 ENSG00000100650 6430 "Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing" 10787 protein-coding gene gene with protein product "SR splicing factor 5" 600914 "splicing factor, arginine/serine-rich 5" SFRS5 NA 7686911, 20516191 Standard NM_001039465 XM_005267998 NA Approved SRP40, HRS uc001xlp.3 Q13243 ENST00000553635.1:c.542+11T>- chr14.hg19:g.70237833delT 5 6 ref NA False 79 79 PASS 6 PASS ref->het 0 NA 59,59 29,29 11,11 1 1 O14797|Q16662|Q49AD6|Q6FGE0 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SRSF5-004 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000412460.1 PASS NA None 99 True + T ENST00000553635.1 SMOC1 64093 __UNKNOWN__ __UNKNOWN__ 14 70478176 70478176 __UNKNOWN__ Intron DEL C C - rs61674022|rs71305856|rs116375526|rs386778578 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:70478176delC ENST00000361956.3 + 9 1120 SMOC1_ENST00000381280.4_Intron Q9H4F8 SMOC1_HUMAN SPARC related modular calcium binding 1 NA NA NA cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|eye development (GO:0001654)|limb development (GO:0060173)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of osteoblast differentiation (GO:0045667)|signal transduction (GO:0007165) basement membrane (GO:0005604) calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840) breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 21 all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028) CCCCTCCCAACCCCCCCCATA 0.557 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 138 130.19 NA , 10,400,3854 NA 0,0,10,24,352,1746 43 44 44 NA , -1.6 0 14 dbSNP_130 44 18,2494,5742 NA 0,3,15,375,1741,1993 no intron,intron SMOC1 NM_022137.5,NM_001034852.2 , 0,3,25,399,2093,3739 A1A1,A1A2,A1R,A2A2,A2R,RR NA 30.4337,9.6154,23.3424 , , 70478176 28,2894,9596 2203 4300 6503 SO:0001627 intron_variant 0.69 AJ249900 CCDS9798.1, CCDS32110.1 14q24.1 2010-08-05 ENSG00000198732 ENSG00000198732 64093 20318 protein-coding gene gene with protein product 608488 NA 12130637 Standard NM_001034852 NA Approved uc001xlt.2 Q9H4F8 ENST00000361956.3:c.858-26C>- chr14.hg19:g.70478176delC 7 8 ref NA False 88 88 PASS 8 PASS ref->het 0 NA 84,84 43,44 11,10 1 1 A8K1S3|B2R7P5|Q96F78 True hg19 CCDS32110.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SMOC1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000412466.1 PASS NA None 138 True + C ENST00000361956.3 MLH3 27030 __UNKNOWN__ __UNKNOWN__ 14 75509021 75509022 __UNKNOWN__ Intron INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:75509021_75509022insT ENST00000556740.1 - 2 3415 MLH3_ENST00000355774.2_Intron|MLH3_ENST00000238662.7_Intron|MLH3_ENST00000380968.2_Intron|MLH3_ENST00000544985.1_Intron|MLH3_ENST00000556257.1_Intron|MLH3_ENST00000555671.1_Intron Q9UHC1 MLH3_HUMAN mutL homolog 3 NA NA NA ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130) chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795) ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697) breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 44 BRCA - Breast invasive adenocarcinoma(234;0.00688) AGCCTGCTTTGTTTTTTGAGTT 0.495 NA NA NA Mismatch excision repair (MMR) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 88 89.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF195657 CCDS9837.1, CCDS32123.1 14q24.3 2014-09-17 2013-09-12 ENSG00000119684 27030 7128 protein-coding gene gene with protein product 604395 "mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)" NA 10615123 Standard NM_014381 XR_245681 NA Approved uc001xrd.1 Q9UHC1 ENST00000556740.1:c.3379+59->A chr14.hg19:g.75509027_75509027dupT 7 9 ref NA False 55 55 PASS 6 PASS ref->het 0 NA 48,48 29,29 10,10 1 1 P49751|Q56DK9|Q9P292|Q9UHC0 True hg19 CCDS32123.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MLH3-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000415006.1 PASS NA None 88 True - T ENST00000556740.1 RPS6KA5 9252 __UNKNOWN__ __UNKNOWN__ 14 91526786 91526786 __UNKNOWN__ 5'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:91526786delT ENST00000261991.3 - 0 166 RPS6KA5_ENST00000418736.2_5'UTR NM_004755.2 NP_004746.2 O75582 KS6A5_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 5 NA NA NA axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666) cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674) endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2) 24 all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146) Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201) CATCTTCTCCTTTTTTTCCGA 0.721 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 314 279.58 NA NA 11 13 12 NA NA NA 14 NA NA NA 91526786 2153 4169 6322 SO:0001623 5_prime_UTR_variant 1.23 AF074393 CCDS9893.1, CCDS45149.1 14q31-q32.1 2011-04-05 2002-08-29 ENSG00000100784 9252 10434 protein-coding gene gene with protein product 603607 "ribosomal protein S6 kinase, 90kD, polypeptide 5" NA 9687510, 10702687 Standard NM_004755 NM_004755 NA Approved MSK1, RLPK uc001xys.2 O75582 ENST00000261991.3:c.-8A>- chr14.hg19:g.91526786delT 6 7 ref NA False 331 302 PASS 7 PASS ref->het 0 NA 199,211 62,67 52,37 1 1 O95316|Q96AF7 True hg19 CCDS9893.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPS6KA5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000411442.2 PASS NA None 314 True - T ENST00000261991.3 BTBD7 55727 __UNKNOWN__ __UNKNOWN__ 14 93706221 93706222 __UNKNOWN__ 3'UTR INS - - G rs146274327|rs573515870|rs200783356|rs183661722 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:93706221_93706222insG ENST00000334746.5 - 0 6103_6104 NM_001002860.2 NP_001002860.2 Q9P203 BTBD7_HUMAN BTB (POZ) domain containing 7 NA NA NA multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693) nucleus (GO:0005634) breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1) 35 all_cancers(154;0.08) Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223) CTAACATTTGCGGGGGGGGAAG 0.426 NA NA NA ?|GGGGGGGG|GGGGGGGGG|unsure 113 0.0225639 0.0023 0 5008 , , NA 17781 0.0446 NA 0.004 False NA ,,, NA NA NA 2504 0.0624 NA NA NA PASS NA NA NA 0 229 235.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.1 AB040958 CCDS32146.1, CCDS32147.1, CCDS73684.1 14q32.13 2013-01-08 ENSG00000011114 ENSG00000011114 55727 "BTB/POZ domain containing" 18269 protein-coding gene gene with protein product 610386 NA 10819331, 11527404 Standard NM_001002860 NM_001289133 NA Approved FLJ10648, FUP1 uc001ybo.3 Q9P203 OTTHUMG00000171269 ENST00000334746.5:c.*2398->C chr14.hg19:g.93706229_93706229dupG 9 9 ref NA False 61 61 PASS 8 PASS ref->het 0 NA 128,129 41,45 53,50 1 1 A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0 True hg19 CCDS32146.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BTBD7-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000412701.1 PASS NA None 229 True - G ENST00000334746.5 BCL11B 64919 __UNKNOWN__ __UNKNOWN__ 14 99636599 99636599 __UNKNOWN__ 3'UTR DEL T T - rs545826280 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:99636599delT ENST00000357195.3 - 0 6583 BCL11B_ENST00000345514.2_3'UTR NM_001282237.1|NM_138576.2 NP_001269166.1|NP_612808.1 Q9C0K0 BC11B_HUMAN B-cell CLL/lymphoma 11B (zinc finger protein) NA NA NA alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538) nucleus (GO:0005634) metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077) NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2) 34 Melanoma(154;0.0866)|all_epithelial(191;0.241) COAD - Colon adenocarcinoma(157;0.103) CCCTCCCCCCTTTTTTTTAAC 0.473 NA NA T TLX3 T-ALL NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 14 14q32.1 64919 B-cell CLL/lymphoma 11B (CTIP2) NA L 0 182 179.95 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.95 AJ404614 CCDS9949.1, CCDS9950.1 14q32 2013-01-08 ENSG00000127152 ENSG00000127152 64919 "Zinc fingers, C2H2-type" 13222 protein-coding gene gene with protein product 606558 ZNF856B NA 11719382, 16950772 Standard NM_138576 NM_138576 NA Approved CTIP-2, CTIP2, hRIT1-alpha uc001yga.3 Q9C0K0 OTTHUMG00000028967 ENST00000357195.3:c.*3889A>- chr14.hg19:g.99636599delT 7 9 ref NA False 45 45 PASS 8 PASS ref->het 0 NA 115,122 41,41 28,21 1 1 Q9H162 True hg19 CCDS9950.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BCL11B-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000072332.2 PASS NA None 182 True - T ENST00000357195.3 PPP2R5C 5527 __UNKNOWN__ __UNKNOWN__ 14 102231708 102231708 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:102231708delT ENST00000556260.2 + 0 335 PPP2R5C_ENST00000328724.5_Intron|PPP2R5C_ENST00000554442.1_Intron|PPP2R5C_ENST00000422945.2_Intron|PPP2R5C_ENST00000556068.1_Intron Q13362 2A5G_HUMAN protein phosphatase 2, regulatory subunit B', gamma NA NA NA DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165) chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159) protein phosphatase type 2A regulator activity (GO:0008601) breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 20 TTTATTATTGTTTTTTTTCCC 0.373 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 425 431.6 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.46 L42375 CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1 14q32.31 2010-06-18 2010-04-14 ENSG00000078304 ENSG00000078304 5527 "Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits" 9311 protein-coding gene gene with protein product 601645 "protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform" NA 7592815 Standard NM_002719 NM_002719 NA Approved B56G, PR61G uc001ykk.3 Q13362 ENST00000556260.2:c.*104T>- chr14.hg19:g.102231708delT 7 10 ref NA False 104 103 PASS 8 PASS ref->het 0 NA 251,256 78,79 81,77 1 1 B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPP2R5C-014 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000414361.2 PASS NA None 425 True + T ENST00000556260.2 CTD-3051D23.1 0 __UNKNOWN__ __UNKNOWN__ 14 105309250 105309250 __UNKNOWN__ lincRNA DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:105309250delT ENST00000556430.1 + 0 251 NA NA NA NA TCTGTAATCCTTTTTTACCAA 0.403 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 517 487.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2.13 NA NA NA NA NA ENST00000556430.1: chr14.hg19:g.105309250delT 5 6 ref NA False 151 140 PASS 6 PASS ref->het 0 NA 350,354 108,109 59,54 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CTD-3051D23.1-001 KNOWN basic lincRNA NA lincRNA OTTHUMT00000410286.1 PASS NA None 517 True + T ENST00000556430.1 AHNAK2 113146 __UNKNOWN__ __UNKNOWN__ 14 105403604 105403606 __UNKNOWN__ 3'UTR DEL TTC TTC - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:105403604_105403606delTTC ENST00000557457.1 - 0 3419_3421 Q8IVF2 AHNK2_HUMAN AHNAK nucleoprotein 2 NA NA NA costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018) cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3) 33 all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183) all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116) ATGCAGCACTTTCTTTATTGCCC 0.562 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 239 230.71 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.86 AB095939 CCDS45177.1 14q32.33 2010-04-01 2007-03-26 2007-03-26 ENSG00000185567 ENSG00000185567 113146 20125 protein-coding gene gene with protein product 608570 "chromosome 14 open reading frame 78" C14orf78 NA 15007166 Standard NM_138420 NM_138420 NA Approved uc010axc.1 Q8IVF2 ENST00000557457.1:c.*796GAA>- chr14.hg19:g.105403604_105403606delTTC 0 6 ref NA False 68 68 PASS 1 PASS ref->het 0 NA 170,174 47,47 27,23 1 1 Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AHNAK2-003 PUTATIVE basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000410299.1 PASS NA None 239 True - TTC ENST00000557457.1 UBR1 197131 __UNKNOWN__ __UNKNOWN__ 15 43236144 43236144 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:43236144delA ENST00000290650.4 - 0 6711 UBR1_ENST00000382177.2_3'UTR NM_174916.2 NP_777576.1 Q8IWV7 UBR1_HUMAN ubiquitin protein ligase E3 component n-recognin 1 NA NA NA cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511) cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151) leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270) NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1) 58 all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215) GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214) TAAAAGTACCAAAAAAATCTA 0.343 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 169 160.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.42 CCDS10091.1 15q13 2008-06-23 ENSG00000159459 ENSG00000159459 197131 "Ubiquitin protein ligase E3 component n-recognins" 16808 protein-coding gene gene with protein product 605981 NA 9653112 Standard NM_174916 NM_174916 NA Approved uc001zqq.3 Q8IWV7 OTTHUMG00000130702 ENST00000290650.4:c.*1383T>- chr15.hg19:g.43236144delA 6 7 ref NA False 94 93 PASS 7 PASS ref->het 0 NA 105,106 49,49 15,14 1 2 O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4 True hg19 CCDS10091.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UBR1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253202.1 PASS NA None 169 True - A ENST00000290650.4 DUT 1854 __UNKNOWN__ __UNKNOWN__ 15 48634180 48634180 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:48634180delA ENST00000455976.2 + 6 587 DUT_ENST00000331200.3_Intron|DUT_ENST00000558813.1_Intron|DUT_ENST00000559416.1_Intron|DUT_ENST00000559540.1_3'UTR NM_001948.3 NP_001939.1 P33316 DUT_HUMAN deoxyuridine triphosphatase NA NA NA DNA replication (GO:0006260)|dUMP biosynthetic process (GO:0006226)|dUTP catabolic process (GO:0046081)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotrimerization (GO:0070207)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of protein heterodimerization activity (GO:0043497)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) dUTP diphosphatase activity (GO:0004170)|poly(A) RNA binding (GO:0044822)|pyrimidine deoxyribonucleotide binding (GO:0032556)|receptor inhibitor activity (GO:0030547) kidney(2) 2 all_lung(180;0.00265) all cancers(107;2.66e-09)|GBM - Glioblastoma multiforme(94;6.76e-07) AGAGGCTCTTAAAAAAAACTG 0.378 NA NA NA Modulation of nucleotide pools NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 216 214.97 NA NA 56 62 60 NA NA NA 15 NA NA NA 48634180 2196 4297 6493 SO:0001627 intron_variant 0 M89913 CCDS32231.1, CCDS45255.1, CCDS45256.1 15q21.1 2010-06-24 2007-12-17 ENSG00000128951 ENSG00000128951 1854 3.6.1.23 3078 protein-coding gene gene with protein product 601266 "dUTP pyrophosphatase" NA 1325640, 9070952 Standard XM_005254211 NA Approved dUTPase uc001zws.3 P33316 ENST00000455976.2:c.439-39A>- chr15.hg19:g.48634180delA 7 8 ref NA False 170 124 PASS 8 PASS ref->het 0 NA 121,123 68,68 29,28 2 1 A8K650|B4DPR5|O14785|Q16708|Q16860|Q6FHN1|Q6NSA3|Q96Q81 True hg19 CCDS45255.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DUT-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000417144.2 PASS NA None 216 True + A ENST00000455976.2 USP8 9101 __UNKNOWN__ __UNKNOWN__ 15 50776588 50776588 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:50776588delA ENST00000425032.3 + 9 1765 USP8_ENST00000433963.1_Intron|USP8_ENST00000396444.3_Intron|USP8_ENST00000307179.4_Intron NM_001283049.1 NP_001269978.1 P40818 UBP8_HUMAN ubiquitin specific peptidase 8 NA NA NA cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511) acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634) cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843) central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 35 all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771) AAAAAACTGGAAAAAAAAGCC 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 26 30.03 NA NA 31 32 31 NA NA NA 15 NA NA NA 50776588 2195 4287 6482 SO:0001627 intron_variant 0 D29956 CCDS10137.1, CCDS61632.1 15q21.1 2014-03-03 2005-08-08 ENSG00000138592 ENSG00000138592 9101 "Ubiquitin-specific peptidases" 12631 protein-coding gene gene with protein product 603158 "ubiquitin specific protease 8" NA 12838346, 9582025, 24482476 Standard NM_005154 NM_005154 NA Approved HumORF8, KIAA0055, UBPY, SPG59 uc001zyl.4 P40818 OTTHUMG00000131645 ENST00000425032.3:c.1572+2326A>- chr15.hg19:g.50776588delA 7 8 ref NA False 33 33 PASS 8 PASS ref->het 0 NA 12,12 12,12 3,3 1 1 B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA USP8-002 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000418317.1 PASS NA None 26 True + A ENST00000425032.3 TRPM7 54822 __UNKNOWN__ __UNKNOWN__ 15 50862222 50862222 __UNKNOWN__ Intron DEL A A - rs373487160 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:50862222delA ENST00000313478.7 - 38 5642 TRPM7_ENST00000560955.1_Intron|TRPM7_ENST00000561443.1_Intron NM_017672.4 NP_060142.3 Q96QT4 TRPM7_HUMAN transient receptor potential cation channel, subfamily M, member 7 NA NA NA actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726) ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674) breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3) 52 all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045) AAAAAACAACAAAAAAAAGGG 0.299 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 64 65.51 NA 8,17,3425 NA 0,0,8,7,3,1707 51 48 49 NA -0.7 0 15 4 8,26,7746 NA 0,0,8,9,8,3865 no intron TRPM7 NM_017672.4 0,0,16,16,11,5572 A1A1,A1A2,A1R,A2A2,A2R,RR NA 0.437,0.7246,0.5254 50862222 16,43,11171 1775 4055 5830 SO:0001627 intron_variant 0 AF346629 CCDS42035.1, CCDS73725.1 15q21 2011-12-14 ENSG00000092439 54822 "Voltage-gated ion channels / Transient receptor potential cation channels" 17994 protein-coding gene gene with protein product 605692 NA 11161216, 11385574, 16382100 Standard NM_017672 XM_005254486 NA Approved CHAK1, LTRPC7, TRP-PLIK uc001zyt.4 Q96QT4 ENST00000313478.7:c.5361-32T>- chr15.hg19:g.50862222delA 7 10 ref NA False 62 62 PASS 8 PASS ref->het 0 NA 27,27 24,24 13,14 1 1 Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2 True hg19 CCDS42035.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRPM7-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000418604.1 PASS NA None 64 True - A ENST00000313478.7 MYO5C 55930 __UNKNOWN__ __UNKNOWN__ 15 52564923 52564923 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:52564923delA ENST00000261839.7 - 6 768 MYO5C_ENST00000541028.1_Intron|MYO5C_ENST00000443683.2_Intron NM_018728.3 NP_061198.2 Q9NQX4 MYO5C_HUMAN myosin VC NA NA NA extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459) ATP binding (GO:0005524)|motor activity (GO:0003774) breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 66 all cancers(107;0.0137) CCAACGGCCTAAAAAAAATAA 0.358 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 150 143.77 NA NA 78 69 72 NA NA NA 15 NA NA NA 52564923 1806 4067 5873 SO:0001627 intron_variant 1.08 AF272390 CCDS42036.1 15q21 2011-09-27 ENSG00000128833 55930 "Myosins / Myosin superfamily : Class V" 7604 protein-coding gene gene with protein product "myosin 5C" 610022 NA 11870218 Standard NM_018728 NM_018728 NA Approved MGC74969 uc010bff.3 Q9NQX4 ENST00000261839.7:c.607-3T>- chr15.hg19:g.52564923delA 7 10 ref NA False 53 53 PASS 8 PASS ref->het 0 NA 92,94 37,38 18,15 1 1 Q6P1W8 True hg19 CCDS42036.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MYO5C-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000419562.1 PASS NA None 150 True - A ENST00000261839.7 SMAD6 4091 __UNKNOWN__ __UNKNOWN__ 15 66995566 66995566 __UNKNOWN__ 5'UTR DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:66995566delC ENST00000288840.5 + 0 1001 SMAD6_ENST00000457357.2_5'UTR NM_005585.4 NP_005576.3 O43541 SMAD6_HUMAN SMAD family member 6 NA NA NA BMP signaling pathway (GO:0030509)|cell-substrate adhesion (GO:0031589)|fat cell differentiation (GO:0045444)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|response to estrogen (GO:0043627)|response to laminar fluid shear stress (GO:0034616)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352) cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667) chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity (GO:0030617)|type I activin receptor binding (GO:0070698)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625) lung(1)|skin(1) 2 GAGACCGCCTCCCCCCCACCC 0.706 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(179;72 2004 22333 39628 47290) PASS NA NA NA 0 83 89.62 NA 12,2858 NA 3,6,1426 3 3 3 NA 2.8 1 15 3 32,5836 NA 8,16,2910 no utr-5 SMAD6 NM_005585.4 11,22,4336 A1A1,A1R,RR NA 0.5453,0.4181,0.5035 66995566 44,8694 1607 3287 4894 SO:0001623 5_prime_UTR_variant 0.57 BC012986 CCDS10221.1 15q22.31 2014-09-11 2006-11-06 2004-05-26 ENSG00000137834 ENSG00000137834 4091 "SMADs" 6772 protein-coding gene gene with protein product 602931 "MAD, mothers against decapentaplegic homolog 6 (Drosophila)", "SMAD, mothers against DPP homolog 6 (Drosophila)" MADH7, MADH6 NA 9256479 Standard NM_005585 NR_027654 NA Approved HsT17432 uc002aqf.3 O43541 OTTHUMG00000133218 ENST00000288840.5:c.-31C>- chr15.hg19:g.66995566delC 6 11 ref NA False 41 41 PASS 7 PASS ref->het 0 NA 59,61 14,14 11,9 1 1 A9J6M5|O43654|Q15799|Q7Z7L4|Q96E31|Q9UKZ3 True hg19 CCDS10221.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SMAD6-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256953.2 PASS NA None 83 True + C ENST00000288840.5 PML 5371 __UNKNOWN__ __UNKNOWN__ 15 74287226 74287226 __UNKNOWN__ Frame_Shift_Del DEL C C - rs376726233 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:74287226delC ENST00000268058.3 + 1 169 c.73delC c.(73-75)cccfs p.P26fs PML_ENST00000268059.6_Frame_Shift_Del_p.P26fs|PML_ENST00000569477.1_Frame_Shift_Del_p.P26fs|PML_ENST00000395135.3_Frame_Shift_Del_p.P26fs|PML_ENST00000354026.6_Frame_Shift_Del_p.P26fs|PML_ENST00000435786.2_Frame_Shift_Del_p.P26fs|PML_ENST00000563500.1_Frame_Shift_Del_p.P26fs|PML_ENST00000395132.2_Frame_Shift_Del_p.P26fs|PML_ENST00000436891.3_Frame_Shift_Del_p.P26fs|PML_ENST00000565898.1_Frame_Shift_Del_p.P26fs|PML_ENST00000567543.1_Frame_Shift_Del_p.P26fs|PML_ENST00000569965.1_Frame_Shift_Del_p.P26fs|PML_ENST00000359928.4_Frame_Shift_Del_p.P26fs|PML_ENST00000564428.1_Frame_Shift_Del_p.P26fs NM_033238.2 NP_150241.2 P29590 PML_HUMAN promyelocytic leukemia 26 Pro-rich. NA NA activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032) cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605) cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270) breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 31 CACCATGCCTCCCCCCGAGAC 0.652 NA NA T "RARA, PAX5" "APL, ALL" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 15 15q22 5371 promyelocytic leukemia NA L 0 138 159.2 NA NA 3 4 3 NA NA NA 15 NA NA NA 74287226 1957 3899 5856 SO:0001589 frameshift_variant 0.67 AB208950 CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1 15q24.1 2011-04-21 ENSG00000140464 ENSG00000140464 5371 "Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers" 9113 protein-coding gene gene with protein product 102578 NA Standard NM_002675 NM_033244 NA Approved MYL, TRIM19, RNF71 uc002awv.3 P29590 OTTHUMG00000137607 ENST00000268058.3:c.73delC chr15.hg19:g.74287226delC ENSP00000268058:p.Pro26fs 5 8 ref NA False 100 100 PASS 6 PASS ref->het 0 NA 77,84 26,31 34,22 1 1 E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3 True hg19 CCDS10255.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PML-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000269021.3 PASS NA None 138 True + C ENST00000268058.3 SNX33 257364 __UNKNOWN__ __UNKNOWN__ 15 75950761 75950761 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:75950761delT ENST00000308527.5 + 0 4127 NM_153271.1 NP_695003.1 Q8WV41 SNX33_HUMAN sorting nexin 33 NA NA NA cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|macropinocytosis (GO:0044351)|membrane tubulation (GO:0097320)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|negative regulation of endocytosis (GO:0045806)|negative regulation of protein localization to cell surface (GO:2000009)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein localization to cell surface (GO:2000010)|protein import (GO:0017038) cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020) identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091) breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|soft_tissue(1)|urinary_tract(2) 19 GGGCCCCTGCTCCCCGTCAGG 0.607 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 283 268.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.07 AK091291 CCDS10283.1 15q23 2008-04-18 2008-03-25 2008-03-25 ENSG00000173548 ENSG00000173548 257364 28468 protein-coding gene gene with protein product NA "SH3 and PX domain containing 3" SH3PX3 NA 16374509, 16782399, 18353773 Standard NM_153271 NM_153271 NA Approved MGC32065, SH3PXD3C, SNX30 uc002bau.3 Q8WV41 OTTHUMG00000142835 ENST00000308527.5:c.*1205T>- chr15.hg19:g.75950761delT 0 5 ref NA False 54 54 PASS 1 PASS ref->het 0 NA 224,225 31,32 31,30 1 1 B1NM17 True hg19 CCDS10283.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SNX33-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000286471.1 PASS NA None 283 True + T ENST00000308527.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ 15 83006768 83006769 __UNKNOWN__ IGR INS - - TC LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:83006768_83006769insTC NA RP11-152F13.7 (32478 upstream) : RP13-996F3.4 (4609 downstream) NA NA NA NA TAGCTATAAATTCTCTCTcaca 0.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 86 79.21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 2.11 NA NA NA NA NA chr15.hg19:g.83006775_83006776dupTC 5 3 ref NA False 51 51 PASS 4 PASS ref->het 0 NA 41,56 21,27 25,26 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 86 True TC Unknown 0 __UNKNOWN__ __UNKNOWN__ 15 88407901 88407901 __UNKNOWN__ IGR DEL T T - rs564774006 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:88407901delT NA RP11-648K4.2 (160818 upstream) : NTRK3 (10328 downstream) NA NA NA NA TCTCCTTGTATTTTTTAGAGC 0.378 NA NA NA TTTTTT|TTTTTT|TTTTT|deletion 12 0.00239617 0.0083 0.0014 5008 , , NA 19223 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 127 123.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr15.hg19:g.88407901delT 5 7 ref NA False 42 42 PASS 6 PASS ref->het 0 NA 81,82 34,34 12,12 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 127 True T IQGAP1 8826 __UNKNOWN__ __UNKNOWN__ 15 90969312 90969312 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:90969312delT ENST00000268182.5 + 3 279 IQGAP1_ENST00000560738.1_Intron NM_003870.3 NP_003861.1 P46940 IQGA1_HUMAN IQ motif containing GTPase activating protein 1 NA NA NA cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281) actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057) calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099) breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 59 Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488) BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194) CTTCCCTTTCTTTTTTTGCAT 0.448 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 141 127.14 NA NA 39 38 39 NA NA NA 15 NA NA NA 90969312 2198 4298 6496 SO:0001627 intron_variant 0.75 D29640 CCDS10362.1 15q26.1 2008-07-18 ENSG00000140575 ENSG00000140575 8826 6110 protein-coding gene gene with protein product "RasGAP-like with IQ motifs" 603379 NA 8051149, 8670801 Standard NM_003870 XM_005254984 NA Approved p195, KIAA0051, SAR1, HUMORFA01 uc002bpl.1 P46940 OTTHUMG00000149832 ENST00000268182.5:c.156-30T>- chr15.hg19:g.90969312delT 6 10 ref NA False 124 101 PASS 7 PASS ref->het 0 NA 77,79 53,53 13,12 1 1 A7MBM3 True hg19 CCDS10362.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IQGAP1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000313493.1 PASS NA None 141 True + T ENST00000268182.5 CACNA1H 8912 __UNKNOWN__ __UNKNOWN__ 16 1270880 1270880 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:1270880delC ENST00000565831.1 + 33 6930 c.6930delC c.(6928-6930)gacfs p.D2310fs CACNA1H_ENST00000358590.4_Frame_Shift_Del_p.D2310fs|CACNA1H_ENST00000348261.5_Frame_Shift_Del_p.D2316fs O95180 CAC1H_HUMAN calcium channel, voltage-dependent, T type, alpha 1H subunit 2316 NA NA aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810) caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891) low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110) breast(4)|endometrium(5)|kidney(2)|lung(23) 34 Hepatocellular(780;0.00369) Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909) CCGTCGGTGACCCCCCAGAGA 0.652 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 523 487.86 NA NA 61 68 66 NA NA NA 16 NA NA NA 1270880 1845 4083 5928 SO:0001589 frameshift_variant 3.9 AL031703 CCDS45375.1, CCDS45376.1 16p13.3 2012-03-07 2007-02-16 8912 "Calcium channel subunits", "Voltage-gated ion channels / Calcium channels" 1395 protein-coding gene gene with protein product 607904 NA 9670923, 16382099 Standard NM_001005407 NM_021098 NA Approved Cav3.2 uc002cks.3 O95180 ENST00000565831.1:c.6930delC chr16.hg19:g.1270880delC ENSP00000455840:p.Asp2310fs 5 6 ref NA False 94 92 PASS 6 PASS ref->het 0 NA 322,330 127,130 69,60 1 1 B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5 True hg19 CCDS45376.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CACNA1H-002 KNOWN non_canonical_U12|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000421602.2 PASS NA None 523 True + C ENST00000565831.1 UBE2I 7329 __UNKNOWN__ __UNKNOWN__ 16 1370937 1370937 __UNKNOWN__ Intron DEL G G - rs573816014 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:1370937delG ENST00000355803.4 + 6 964 UBE2I_ENST00000402301.1_3'UTR|UBE2I_ENST00000397515.2_Intron|LA16c-358B7.3_ENST00000567829.1_RNA|UBE2I_ENST00000566587.1_Intron|LA16c-358B7.3_ENST00000568106.1_RNA|UBE2I_ENST00000397514.3_Intron|UBE2I_ENST00000325437.5_Intron|UBE2I_ENST00000406620.1_Intron|UBE2I_ENST00000403747.2_Intron NM_194260.2 NP_919236.1 P63279 UBC9_HUMAN ubiquitin-conjugating enzyme E2I NA NA NA cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intracellular steroid hormone receptor signaling pathway (GO:0033145)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein sumoylation (GO:0016925)|regulation of receptor activity (GO:0010469)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032) cytoplasm (GO:0005737)|dendrite (GO:0030425)|fibrillar center (GO:0001650)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|synapse (GO:0045202)|synaptonemal complex (GO:0000795) ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RING-like zinc finger domain binding (GO:0071535)|SUMO ligase activity (GO:0019789)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842) breast(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1) 5 Hepatocellular(780;0.00369) TTCCTTCTGTGGGGGGGCCCA 0.662 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 138 137.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.93 D45050 CCDS10433.1 16p13.3 2011-05-19 2011-05-19 ENSG00000103275 ENSG00000103275 7329 6.3.2.19 "Ubiquitin-conjugating enzymes E2" 12485 protein-coding gene gene with protein product 601661 "ubiquitin-conjugating enzyme E2I (homologous to yeast UBC9)", "ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast)" NA 8565643 Standard NM_003345 NM_003345 NA Approved UBC9 uc002cld.2 P63279 OTTHUMG00000047845 ENST00000355803.4:c.413+419G>- chr16.hg19:g.1370937delG 6 8 ref NA False 36 36 PASS 7 PASS ref->het 0 NA 89,94 22,23 25,19 1 1 D3DU69|P50550|Q15698|Q59GX1|Q86VB3 True hg19 CCDS10433.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UBE2I-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250317.2 PASS NA None 138 True + G ENST00000355803.4 MEFV 4210 __UNKNOWN__ __UNKNOWN__ 16 3299821 3299822 __UNKNOWN__ Intron INS - - A LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:3299821_3299822insA ENST00000339854.4 - 3 410 MEFV_ENST00000541159.1_Intron|MEFV_ENST00000536379.1_Intron|MEFV_ENST00000219596.1_Intron O15553 MEFV_HUMAN Mediterranean fever NA NA NA inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056) cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634) actin binding (GO:0003779)|zinc ion binding (GO:0008270) NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6) 50 ATGGCAAACCCAAGTTGCTTAC 0.574 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 197 189.62 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.33 AF018080 CCDS10498.1, CCDS55981.1 16p13.3 2014-09-17 ENSG00000103313 ENSG00000103313 4210 "Tripartite motif containing / Tripartite motif containing" 6998 protein-coding gene gene with protein product "pyrin" 608107 MEF NA 9288094 Standard NM_000243 NM_000243 NA Approved FMF, TRIM20 uc002cun.1 O15553 OTTHUMG00000129324 ENST00000339854.4:c.371-41->T chr16.hg19:g.3299823_3299823dupA 3 3 ref NA False 106 96 PASS 2 PASS ref->het 0 NA 106,107 68,68 21,21 1 1 D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MEFV-010 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000398510.1 PASS NA None 197 True - A ENST00000339854.4 SOCS1 8651 __UNKNOWN__ __UNKNOWN__ 16 11348273 11348274 __UNKNOWN__ 3'UTR DEL TA TA - rs76979931|rs199732720|rs35739545|rs8060459 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:11348273_11348274delTA ENST00000332029.2 - 0 1212_1213 RMI2_ENST00000572173.1_Intron NM_003745.1 NP_003736.1 O15524 SOCS1_HUMAN suppressor of cytokine signaling 1 NA NA NA cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337) cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634) insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860) p.0?(1) breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3) 71 tatttttttttaaaaaaaaaaC 0.376 NA NA "F, O" "Hodgkin Lymphoma, PMBL" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Colon(177;456 3548 27231) PASS Rec yes 16 16p13.13 8651 suppressor of cytokine signaling 1  NA L 1 Whole gene deletion(1) haematopoietic_and_lymphoid_tissue(1) 14 19.36 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 U88326 CCDS10546.1 16p13.13 2013-02-14 ENSG00000185338 ENSG00000185338 8651 "Suppressors of cytokine signaling", "SH2 domain containing" 19383 protein-coding gene gene with protein product 603597 NA 7796808, 9266833 Standard NM_003745 NA Approved SOCS-1, SSI-1, JAB, TIP3, Cish1 uc002dar.1 O15524 OTTHUMG00000129792 ENST00000332029.2:c.*427TA>- chr16.hg19:g.11348273_11348274delTA 0 11 ref NA False 50 50 PASS 1 PASS ref->het 0 NA 6,6 7,7 2,2 1 1 O15097|Q9NSA7 True hg19 CCDS10546.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SOCS1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252018.1 PASS NA None 14 True - TA ENST00000332029.2 AKTIP 64400 __UNKNOWN__ __UNKNOWN__ 16 53525747 53525748 __UNKNOWN__ 3'UTR INS - - A rs576554175|rs540969796 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:53525747_53525748insA ENST00000394657.7 - 0 1629_1630 AKTIP_ENST00000300245.4_3'UTR NM_001012398.1|NM_022476.2 NP_001012398.1|NP_071921.1 Q9H8T0 AKTIP_HUMAN AKT interacting protein NA NA NA apoptotic process (GO:0006915)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|protein transport (GO:0015031) FHF complex (GO:0070695)|plasma membrane (GO:0005886) acid-amino acid ligase activity (GO:0016881) large_intestine(1)|lung(2)|prostate(2) 5 all_cancers(37;0.14) GTAATTTGCTTAAAAAAAACAA 0.332 NA NA NA AAAAAAAA|AAAAAAAA|AAAAAAAAA|insertion 6 0.00119808 0.0023 0.0014 5008 , , NA 18408 0.001 NA 0 False NA ,,, NA NA NA 2504 0.001 NA NA NA PASS NA NA NA 0 662 627.73 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 6.29 AK023320 CCDS10749.1 16q12.2 2010-01-14 2007-01-16 2007-01-16 ENSG00000166971 ENSG00000166971 64400 "Ubiquitin-conjugating enzymes E2" 16710 protein-coding gene gene with protein product 608483 "fused toes (mouse) homolog", "fused toes homolog (mouse)" FTS NA 7818539, 8626685 Standard NM_022476 XM_005256094 NA Approved FLJ13258 uc002ehl.3 Q9H8T0 OTTHUMG00000133199 ENST00000394657.7:c.*577->T chr16.hg19:g.53525755_53525755dupA 9 10 ref NA False 232 172 PASS 8 PASS ref->het 0 NA 416,434 150,154 97,81 1 1 Q503B1|Q53H38 True hg19 CCDS10749.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AKTIP-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000256909.4 PASS NA None 662 True - A ENST00000394657.7 CKLF-CMTM1 100529251 __UNKNOWN__ __UNKNOWN__ 16 66611099 66611100 __UNKNOWN__ Frame_Shift_Ins INS - - G rs140837467 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:66611099_66611100insG ENST00000527729.1 + 2 274_275 c.171_172insG c.(172-174)gggfs p.G58fs CMTM1_ENST00000336328.6_Frame_Shift_Ins_p.G59fs|CMTM1_ENST00000457188.2_Frame_Shift_Ins_p.G112fs|CMTM1_ENST00000533953.1_Frame_Shift_Ins_p.G181fs|CMTM1_ENST00000332695.7_Frame_Shift_Ins_p.G65fs|CMTM1_ENST00000379500.2_Frame_Shift_Ins_p.G229fs|CMTM1_ENST00000533666.1_Intron|CMTM1_ENST00000529506.1_Frame_Shift_Ins_p.G13fs|CMTM1_ENST00000528324.1_Frame_Shift_Ins_p.G112fs|CMTM1_ENST00000328020.6_Frame_Shift_Ins_p.G229fs|CMTM1_ENST00000531885.1_Frame_Shift_Ins_p.G59fs NM_001202509.1 NP_001189438.1 CKLF-CMTM1 readthrough NA NA NA NA TACTCTATGTCGGGGGGGTAAG 0.401 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 544 500.65 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.79 CCDS56000.1, CCDS73898.1, CCDS73899.1 16q22.1 2011-04-19 ENSG00000254788 ENSG00000254788 100529251 39977 other readthrough NA NA Standard NM_001202509 NA Approved OTTHUMG00000167106 ENST00000527729.1:c.177dupG chr16.hg19:g.66611106_66611106dupG ENSP00000433998:p.Gly58fs 8 7 ref NA False 115 115 PASS 7 PASS ref->het 0 NA 392,399 64,67 83,76 1 1 True hg19 CCDS56000.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CKLF-CMTM1-002 KNOWN basic|appris_principal|readthrough_transcript|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000393191.1 PASS NA None 544 True + G ENST00000527729.1 ZFHX3 463 __UNKNOWN__ __UNKNOWN__ 16 72817190 72817190 __UNKNOWN__ 3'UTR DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:72817190delC ENST00000268489.5 - 0 15657 RP5-991G20.1_ENST00000563328.2_RNA|ZFHX3_ENST00000397992.5_3'UTR NM_006885.3 NP_008816.3 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 NA NA NA brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366) mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667) enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270) NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11) 153 Ovarian(137;0.13) TTGCCCCCCTCCCCCCTGAAG 0.393 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 152 139.79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.36 D10250 CCDS10908.1, CCDS54035.1 16q22.3 2012-03-09 2007-08-09 2007-08-09 ENSG00000140836 ENSG00000140836 463 "Zinc fingers, C2H2-type", "Homeoboxes / ZF class" 777 protein-coding gene gene with protein product 104155 "AT-binding transcription factor 1" ATBF1 NA 1719379, 7592926 Standard NM_006885 NM_006885 NA Approved ZNF927 uc002fck.3 Q15911 OTTHUMG00000137599 ENST00000268489.5:c.*3873G>- chr16.hg19:g.72817190delC 5 12 ref NA False 50 50 PASS 6 PASS ref->het 0 NA 111,112 29,29 10,9 1 1 D3DWS8|O15101|Q13719 True hg19 CCDS10908.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZFHX3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000269008.1 PASS NA None 152 True - C ENST00000268489.5 CBFA2T3 863 __UNKNOWN__ __UNKNOWN__ 16 88967931 88967931 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:88967931delG ENST00000268679.4 - 2 681 c.285delC c.(283-285)cccfs p.P95fs CBFA2T3_ENST00000448839.1_Intron|CBFA2T3_ENST00000436887.2_Frame_Shift_Del_p.P95fs|CBFA2T3_ENST00000360302.2_Frame_Shift_Del_p.P34fs|CBFA2T3_ENST00000327483.5_Frame_Shift_Del_p.P34fs NM_005187.5 NP_005178.4 O75081 MTG16_HUMAN core-binding factor, runt domain, alpha subunit 2; translocated to, 3 95 Mediates interaction with PDE7A (in isoform 2).|Mediates localization to the nucleus. {ECO:0000250}.|Pro-rich.|Required for nucleolar targeting (in isoform 1). NA NA cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351) Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634) chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1) 17 BRCA - Breast invasive adenocarcinoma(80;0.0275) GCGTGAAGGAGGGGGGGCGTG 0.677 NA NA T RUNX1 AML NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 16 16q24 863 "core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (MTG-16)" NA L 0 105 112.32 NA NA 18 23 21 NA NA NA 16 NA NA NA 88967931 2178 4284 6462 SO:0001589 frameshift_variant 1.59 AF052213 CCDS10972.1, CCDS10973.1 16q24 2013-10-16 ENSG00000129993 ENSG00000129993 863 "Zinc fingers, MYND-type", "A-kinase anchor proteins" 1537 protein-coding gene gene with protein product "myeloid translocation gene 8 and 16b" 603870 NA 9790752, 20150326 Standard NM_005187 NM_005187 NA Approved MTGR2, ZMYND4, MTG16 uc002fmm.2 O75081 OTTHUMG00000137864 ENST00000268679.4:c.285delC chr16.hg19:g.88967931delG ENSP00000268679:p.Pro95fs 6 9 ref NA False 35 35 PASS 7 PASS ref->het 0 NA 61,64 24,25 23,19 1 1 D3DX78|O60615|O60616|O60617|O75082|O75107|O75108|Q0P5Z6|Q6P5W6 True hg19 CCDS10972.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CBFA2T3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000269545.2 PASS NA None 105 True - G ENST00000268679.4 SMG6 23293 __UNKNOWN__ __UNKNOWN__ 17 2201092 2201092 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:2201092delA ENST00000263073.6 - 3 2091 SMG6_ENST00000544865.1_Intron NM_017575.4 NP_060045.4 Q86US8 EST1A_HUMAN SMG6 nonsense mediated mRNA decay factor NA NA NA gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723) chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697) endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162) NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 45 TTCAGGTAGTAAAAATCCATC 0.413 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Melanoma(59;28 1088 11621 25887 46638 50814) PASS NA NA NA 0 123 131.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.33 AB018275 CCDS11016.1, CCDS58498.1 17p13.3 2013-07-02 2013-07-02 2006-02-16 ENSG00000070366 ENSG00000070366 23293 17809 protein-coding gene gene with protein product "EST1 telomerase component homolog A (S. cerevisiae)" 610963 "chromosome 17 open reading frame 31", "smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)" C17orf31 NA 12676087, 12699629 Standard NM_017575 NA Approved KIAA0732, SMG-6, EST1A uc002fub.1 Q86US8 OTTHUMG00000177578 ENST00000263073.6:c.2040+64T>- chr17.hg19:g.2201092delA 4 5 ref NA False 34 34 PASS 5 PASS ref->het 0 NA 83,85 31,31 9,9 2 2 B7Z874|O94837|Q86VH6|Q9UF60 True hg19 CCDS11016.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SMG6-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000437826.3 PASS NA None 123 True - A ENST00000263073.6 PAFAH1B1 5048 __UNKNOWN__ __UNKNOWN__ 17 2541639 2541639 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:2541639delA ENST00000397195.5 + 2 483 PAFAH1B1_ENST00000572915.2_Intron NM_000430.3 NP_000421.1 platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa) NA NA NA endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|skin(1) 11 TTTGTGCTTTAAAAAAAATCT 0.353 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 46 40.07 NA NA 66 63 64 NA NA NA 17 NA NA NA 2541639 2203 4300 6503 SO:0001627 intron_variant 0.29 L25107 CCDS32528.1 17p13.3 2014-04-04 2010-02-10 ENSG00000007168 ENSG00000007168 5048 "WD repeat domain containing" 8574 protein-coding gene gene with protein product "lissencephaly-1" 601545 "platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit (45kD)", "Miller-Dieker syndrome chromosome region", "platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa", "platelet-activating factor acetylhydrolase, isoform Ib, subunit 1 (45kDa)" MDCR, MDS NA 8355785, 9063735 Standard NM_000430 NM_000430 NA Approved LIS1, PAFAH uc002fuw.4 P43034 OTTHUMG00000177574 ENST00000397195.5:c.32+25A>- chr17.hg19:g.2541639delA 7 8 ref NA False 33 33 PASS 8 PASS ref->het 0 NA 23,24 17,17 6,5 1 1 True hg19 CCDS32528.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PAFAH1B1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000437797.2 PASS NA None 46 True + A ENST00000397195.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ 17 6644177 6644177 __UNKNOWN__ IGR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:6644177delT NA SLC13A5 (27291 upstream) : XAF1 (14978 downstream) NA NA NA NA tcatggcatattttttttcca 0.423 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 116 103.48 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr17.hg19:g.6644177delT 7 9 ref NA False 34 34 PASS 8 PASS ref->het 0 NA 69,69 34,34 12,12 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 116 True T MYOCD 93649 __UNKNOWN__ __UNKNOWN__ 17 12669293 12669294 __UNKNOWN__ 3'UTR INS - - A LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:12669293_12669294insA ENST00000425538.1 + 0 5493_5494 RP11-1090M7.1_ENST00000584772.1_RNA NM_001146312.1|NM_153604.2 NP_001139784.1|NP_705832.1 Q8IZQ8 MYCD_HUMAN myocardin NA NA NA cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012) nucleus (GO:0005634) core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134) breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1) 70 UCEC - Uterine corpus endometrioid carcinoma (92;0.0969) TCATCAGAACCAAAAAAATCCA 0.317 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 153 149.84 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.65 AF532596 CCDS11163.1, CCDS54091.1 17p11.2 2004-03-01 ENSG00000141052 ENSG00000141052 93649 16067 protein-coding gene gene with protein product 606127 NA 11439182, 12397177 Standard NM_153604 XM_005256863 NA Approved MYCD uc002gno.2 Q8IZQ8 OTTHUMG00000058767 ENST00000425538.1:c.*2333->A chr17.hg19:g.12669300_12669300dupA 8 7 ref NA False 61 61 PASS 7 PASS ref->het 0 NA 97,99 40,40 16,16 1 1 Q5UBU5|Q8N7Q1 True hg19 CCDS54091.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MYOCD-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000129947.2 PASS NA None 153 True + A ENST00000425538.1 MPRIP 23164 __UNKNOWN__ __UNKNOWN__ 17 17046886 17046886 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:17046886delC ENST00000395811.5 + 9 1141 c.1052delC c.(1051-1053)gccfs p.A351fs MPRIP_ENST00000395804.3_Frame_Shift_Del_p.A351fs|MPRIP_ENST00000444976.1_Intron|MPRIP_ENST00000341712.4_Frame_Shift_Del_p.A351fs NM_015134.3|NM_201274.3 NP_055949.2|NP_958431.2 Q6WCQ1 MPRIP_HUMAN myosin phosphatase Rho interacting protein 351 Interaction with F-actin. {ECO:0000250}. NA NA actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925) biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 31 ACCAATGAAGCCCCCCCAGCT 0.652 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 288 286.16 NA NA 54 48 50 NA NA NA 17 NA NA NA 17046886 2202 4300 6502 SO:0001589 frameshift_variant 1.13 BC014102 CCDS32578.1, CCDS42268.1 17p11.2 2013-01-10 ENSG00000133030 ENSG00000133030 23164 "Pleckstrin homology (PH) domain containing" 30321 protein-coding gene gene with protein product "Rho interacting protein 3" 612935 NA 10048485 Standard NM_015134 NM_201274 NA Approved RHOIP3, M-RIP, p116Rip uc002gqy.2 Q6WCQ1 OTTHUMG00000059276 ENST00000395811.5:c.1052delC chr17.hg19:g.17046886delC ENSP00000379156:p.Ala351fs 6 7 ref NA False 366 153 PASS 7 PASS ref->het 0 NA 132,136 121,122 34,30 1 1 Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40 True hg19 CCDS42268.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MPRIP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000131586.2 PASS NA None 288 True + C ENST00000395811.5 CDRT15L2 256223 __UNKNOWN__ __UNKNOWN__ 17 20483454 20483454 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:20483454delT ENST00000399044.1 + 2 285 NM_001190790.1 NP_001177719.1 A8MXV6 CD15L_HUMAN CMT1A duplicated region transcript 15-like 2 NA NA NA integral component of membrane (GO:0016021) central_nervous_system(1) 1 CCCTTTCTCCTTTTTCAGCTC 0.557 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 101 96.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.57 CCDS54096.1 17p11.2 2008-10-30 ENSG00000214819 ENSG00000214819 256223 34075 protein-coding gene gene with protein product NA NA Standard XM_170840 NM_001190790 NA Approved uc021tsn.1 A8MXV6 OTTHUMG00000059557 ENST00000399044.1:c.266-8T>- chr17.hg19:g.20483454delT 4 5 ref NA False 34 34 PASS 5 PASS ref->het 0 NA 66,68 20,21 16,13 1 1 True hg19 CCDS54096.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDRT15L2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000132432.3 PASS NA None 101 True + T ENST00000399044.1 IFT20 90410 __UNKNOWN__ __UNKNOWN__ 17 26655405 26655405 __UNKNOWN__ 3'UTR DEL A A - rs76925317 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:26655405delA ENST00000579419.1 - 0 733 IFT20_ENST00000357896.3_3'UTR|IFT20_ENST00000585089.1_3'UTR|IFT20_ENST00000585313.1_3'UTR|IFT20_ENST00000395418.3_3'UTR|TMEM97_ENST00000226230.6_3'UTR NM_001267777.1 NP_001254706.1 Q8IY31 IFT20_HUMAN intraflagellar transport 20 NA NA NA cardiac muscle cell differentiation (GO:0055007)|centrosome localization (GO:0051642)|cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)|kidney development (GO:0001822)|neural precursor cell proliferation (GO:0061351)|opsin transport (GO:0036372)|photoreceptor cell outer segment organization (GO:0035845)|protein localization to cilium (GO:0061512)|protein localization to Golgi apparatus (GO:0034067)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cilium assembly (GO:1902017)|smoothened signaling pathway (GO:0007224)|visual learning (GO:0008542) centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750) lung(2) 2 all_lung(13;0.000294)|Lung NSC(42;0.000964) UCEC - Uterine corpus endometrioid carcinoma (53;0.153) GTGAATTTACAAAAAAAAGGA 0.378 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 62 61.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.45 AF070643 CCDS32593.1, CCDS58533.1, CCDS58534.1, CCDS58535.1, CCDS74017.1 17q11.2 2014-07-03 2014-07-03 ENSG00000109083 90410 "Intraflagellar transport homologs" 30989 protein-coding gene gene with protein product 614394 "intraflagellar transport 20 homolog (Chlamydomonas)" NA Standard NM_174887 NM_001267774 NA Approved uc002hau.2 Q8IY31 ENST00000579419.1:c.*251T>- chr17.hg19:g.26655405delA 7 9 ref NA False 40 40 PASS 8 PASS ref->het 0 NA 23,24 30,31 9,8 1 1 J3QL09|Q5GLZ2|Q9BUG5 True hg19 CCDS58533.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IFT20-016 PUTATIVE alternative_5_UTR|basic|appris_candidate|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000446185.2 PASS NA None 62 True - A ENST00000579419.1 PIGS 94005 __UNKNOWN__ __UNKNOWN__ 17 26887048 26887048 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:26887048delA ENST00000308360.7 - 7 1195 PIGS_ENST00000395346.2_Intron|PIGS_ENST00000543734.1_Intron|PIGS_ENST00000465444.1_Intron NM_033198.3 NP_149975.1 Q96S52 PIGS_HUMAN phosphatidylinositol glycan anchor biosynthesis, class S NA NA NA attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687) endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020) GPI-anchor transamidase activity (GO:0003923) breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1) 16 Lung NSC(42;0.00431) AGGACTCCTCAACTTGCTCCC 0.493 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 107 97.31 NA NA 45 45 45 NA NA NA 17 NA NA NA 26887048 2203 4300 6503 SO:0001627 intron_variant 0.11 CCDS11235.1 17p13.2 2013-02-26 2006-06-28 ENSG00000087111 ENSG00000087111 94005 "Phosphatidylinositol glycan anchor biosynthesis" 14937 protein-coding gene gene with protein product "GPI transamidase subunit" 610271 "phosphatidylinositol glycan, class S" NA Standard NM_033198 NM_033198 NA Approved uc002hbo.2 Q96S52 OTTHUMG00000132604 ENST00000308360.7:c.819+18T>- chr17.hg19:g.26887048delA 1 3 ref NA False 57 57 PASS 2 PASS ref->het 0 NA 65,65 30,31 12,11 1 1 Q6UVX6 True hg19 CCDS11235.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PIGS-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255833.3 PASS NA None 107 True - A ENST00000308360.7 TRAF4 9618 __UNKNOWN__ __UNKNOWN__ 17 27074842 27074842 __UNKNOWN__ Intron DEL C C - rs368079949 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:27074842delC ENST00000262395.5 + 3 324 TRAF4_ENST00000444415.3_Intron|TRAF4_ENST00000262396.6_Intron NM_004295.3 NP_004286.2 Q9BUZ4 TRAF4_HUMAN TNF receptor-associated factor 4 NA NA NA activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein kinase activity (GO:0045860)|regulation of apoptotic process (GO:0042981)|respiratory gaseous exchange (GO:0007585)|respiratory tube development (GO:0030323)|signal transduction (GO:0007165) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923) DNA binding (GO:0003677)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|WW domain binding (GO:0050699)|zinc ion binding (GO:0008270) endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1) 10 Lung NSC(42;0.01) Epithelial(11;3.26e-05)|all cancers(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.235) CTGGCCAGTTCCCCCATCCCT 0.612 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 122 122 NA 1,4263 NA 0,1,2131 35 31 33 NA -6.8 0 17 32 2,8250 NA 1,0,4125 no intron TRAF4 NM_004295.3 1,1,6256 A1A1,A1R,RR NA 0.0242,0.0235,0.024 27074842 3,12513 2203 4299 6502 SO:0001627 intron_variant 1.1 X80200 CCDS11243.1 17q11-q21.3 2013-01-09 ENSG00000076604 ENSG00000076604 9618 "RING-type (C3HC4) zinc fingers" 12034 protein-coding gene gene with protein product 602464 NA 7592751, 7490069 Standard NM_145751 NM_004295 NA Approved CART1, MLN62, RNF83 uc002hcs.3 Q9BUZ4 OTTHUMG00000132677 ENST00000262395.5:c.196-19C>- chr17.hg19:g.27074842delC 4 5 ref NA False 113 92 PASS 5 PASS ref->het 0 NA 57,61 54,54 14,10 1 1 O75615|Q14848|Q2KJU4|Q2PJN8 True hg19 CCDS11243.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRAF4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255944.2 PASS NA None 122 True + C ENST00000262395.5 SEZ6 124925 __UNKNOWN__ __UNKNOWN__ 17 27296914 27296914 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:27296914delC ENST00000317338.12 - 4 1343 c.915delG c.(913-915)gggfs p.G305fs SEZ6_ENST00000442608.3_Frame_Shift_Del_p.G305fs|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000360295.9_Frame_Shift_Del_p.G305fs|SEZ6_ENST00000335960.6_Frame_Shift_Del_p.G305fs Q53EL9 SEZ6_HUMAN seizure related 6 homolog (mouse) 305 NA NA adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|negative regulation of dendrite development (GO:2000171)|positive regulation of dendrite development (GO:1900006)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074) apical dendrite (GO:0097440)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886) breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1) 29 Lung NSC(42;0.0137) Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111) GTGGGTCAGGCCCCCCCAGGC 0.612 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 173 174.11 NA NA 26 32 30 NA NA NA 17 NA NA NA 27296914 1894 4105 5999 SO:0001589 frameshift_variant 1.35 AY038048 CCDS45638.1, CCDS45639.1 17q11.2 2008-03-06 2001-11-28 ENSG00000063015 ENSG00000063015 124925 15955 protein-coding gene gene with protein product NA "seizure related gene 6 (mouse) homolog" NA 17086543 Standard NM_178860 NA Approved uc002hdp.2 Q53EL9 OTTHUMG00000168010 ENST00000317338.12:c.915delG chr17.hg19:g.27296914delC ENSP00000312942:p.Gly305fs 6 7 ref NA False 85 85 PASS 7 PASS ref->het 0 NA 114,117 40,41 20,16 1 1 B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3 True hg19 CCDS45639.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SEZ6-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000397475.3 PASS NA None 173 True - C ENST00000317338.12 CCL11 6356 __UNKNOWN__ __UNKNOWN__ 17 32614094 32614094 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:32614094delT ENST00000305869.3 + 2 217 NM_002986.2 NP_002977.1 P51671 CCL11_HUMAN chemokine (C-C motif) ligand 11 NA NA NA actin filament organization (GO:0007015)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|chronic inflammatory response (GO:0002544)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|inflammatory response (GO:0006954)|mammary duct terminal end bud growth (GO:0060763)|mast cell chemotaxis (GO:0002551)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of Rac GTPase activity (GO:0032855)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|response to interleukin-4 (GO:0070670)|response to radiation (GO:0009314)|response to virus (GO:0009615)|signal transduction (GO:0007165) extracellular region (GO:0005576)|extracellular space (GO:0005615) chemokine activity (GO:0008009) breast(1)|lung(1)|prostate(1) 3 Breast(3;0.00224) Breast(31;0.151)|Ovarian(249;0.17) BRCA - Breast invasive adenocarcinoma(366;0.155) TCTCTGTTCATTTTTTTTCCC 0.428 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 171 169.76 NA 1,22,4241 NA 0,0,1,8,6,2117 60 67 64 NA -2.7 0.1 17 64 5,36,8213 NA 0,0,5,14,8,4100 no intron CCL11 NM_002986.2 0,0,6,22,14,6217 A1A1,A1A2,A1R,A2A2,A2R,RR NA 0.4967,0.5394,0.5113 32614094 6,58,12454 2203 4300 6503 SO:0001627 intron_variant 0.98 AB063614 CCDS11279.1 17q21.1-q21.2 2013-02-25 2002-08-22 2002-08-23 ENSG00000172156 ENSG00000172156 6356 "Chemokine ligands", "Endogenous ligands" 10610 protein-coding gene gene with protein product "eotaxin-1" 601156 "small inducible cytokine subfamily A (Cys-Cys), member 11 (eotaxin)" SCYA11 NA 9169149 Standard NM_002986 NM_002986 NA Approved eotaxin, MGC22554 uc002hia.1 P51671 OTTHUMG00000132884 ENST00000305869.3:c.77-21T>- chr17.hg19:g.32614094delT 7 8 ref NA False 81 81 PASS 8 PASS ref->het 0 NA 105,107 44,44 23,23 1 1 P50877|Q92490|Q92491 True hg19 CCDS11279.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCL11-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256377.2 PASS NA None 171 True + T ENST00000305869.3 CDK12 51755 __UNKNOWN__ __UNKNOWN__ 17 37690523 37690524 __UNKNOWN__ 3'UTR DEL TG TG - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:37690523_37690524delTG ENST00000447079.4 + 0 7460_7461 NM_015083.1|NM_016507.2 NP_055898.1|NP_057591.2 Q9NYV4 CDK12_HUMAN cyclin-dependent kinase 12 NA NA NA mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380) cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634) ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353) NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3) 70 ACCACTTGTATGTGTGTGTGTA 0.381 NA NA "Mis, N, F" serous ovarian NA TCGA Ovarian(9;0.13) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Rec yes 17 17q12 51755 cyclin-dependent kinase 12 NA E 0 123 117.09 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF227198 CCDS11337.1, CCDS45666.1 17q12 2011-10-25 2009-12-16 2009-12-16 ENSG00000167258 ENSG00000167258 51755 "Cyclin-dependent kinases" 24224 protein-coding gene gene with protein product "CDC2 related protein kinase 7" 615514 "Cdc2-related kinase, arginine/serine-rich" CRKRS NA 10048485, 11683387, 19884882 Standard NM_016507 XM_005257456 NA Approved CRK7, CRKR, KIAA0904 uc010cvv.3 Q9NYV4 OTTHUMG00000133214 ENST00000447079.4:c.*2955TG>- chr17.hg19:g.37690531_37690532delTG 4 2 ref NA False 31 31 PASS 5 PASS ref->het 0 NA 67,68 36,37 20,20 1 1 A7E2B2|B4DYX4|B9EIQ6|O94978 True hg19 CCDS11337.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDK12-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000256941.4 PASS NA None 123 True + TG ENST00000447079.4 TNS4 84951 __UNKNOWN__ __UNKNOWN__ 17 38637248 38637248 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:38637248delC ENST00000254051.6 - 9 1831 NM_032865.5 NP_116254.4 Q8IZW8 TENS4_HUMAN tensin 4 NA NA NA apoptotic process (GO:0006915)|protein localization (GO:0008104) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925) NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1) 30 Breast(137;0.000496) STAD - Stomach adenocarcinoma(5;5.91e-05) CCCCTCCTCGCCCCCCCACCT 0.522 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 190 226.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.85 AF417488 CCDS11368.1 17q21.2 2013-02-14 ENSG00000131746 ENSG00000131746 84951 "SH2 domain containing" 24352 protein-coding gene gene with protein product "C terminal tensin like" 608385 NA 12154022, 12711115 Standard NM_032865 NM_032865 NA Approved CTEN uc010cxb.3 Q8IZW8 OTTHUMG00000133330 ENST00000254051.6:c.1673-228G>- chr17.hg19:g.38637248delC 6 9 ref NA False 56 56 PASS 7 PASS ref->het 0 NA 105,107 49,50 30,27 1 1 A6NMJ7|Q71RB7|Q8WV64|Q96JV4 True hg19 CCDS11368.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNS4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257154.3 PASS NA None 190 True - C ENST00000254051.6 FKBP10 60681 __UNKNOWN__ __UNKNOWN__ 17 39973299 39973300 __UNKNOWN__ Intron INS - - C LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:39973299_39973300insC ENST00000321562.4 + 2 349 NM_021939.3 NP_068758.3 Q96AY3 FKB10_HUMAN FK506 binding protein 10, 65 kDa NA NA NA chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413) endoplasmic reticulum membrane (GO:0005789) calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755) cervix(1)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1) 14 Breast(137;0.00122) BRCA - Breast invasive adenocarcinoma(366;0.148) CATCTGTCCCTCCCCCCCCAGC 0.609 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 374 381.55 NA 30,4234 NA 0,30,2102 NA NA NA NA -6.8 0 83 17,8237 NA 0,17,4110 no intron FKBP10 NM_021939.3 0,47,6212 A1A1,A1R,RR NA 0.206,0.7036,0.3755 NA 47,12471 NA NA NA SO:0001627 intron_variant 3.41 AB045981 CCDS11409.1 17q21.2 2014-09-17 2002-08-29 ENSG00000141756 ENSG00000141756 60681 "EF-hand domain containing" 18169 protein-coding gene gene with protein product 607063 "FK506 binding protein 10 (65 kDa)" NA 11071917, 18786928 Standard NM_021939 NM_021939 NA Approved hFKBP65, FLJ22041, FKBP6, FLJ20683, FLJ23833 uc002hxv.2 Q96AY3 OTTHUMG00000133497 ENST00000321562.4:c.246-10->C chr17.hg19:g.39973307_39973307dupC 9 11 ref NA False 86 86 PASS 8 PASS ref->het 0 NA 250,258 65,66 70,62 1 1 Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89 True hg19 CCDS11409.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FKBP10-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257410.2 PASS NA None 374 True + C ENST00000321562.4 WNK4 65266 __UNKNOWN__ __UNKNOWN__ 17 40939870 40939870 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:40939870delG ENST00000246914.5 + 8 1837 c.1816delG c.(1816-1818)gggfs p.G607fs WNK4_ENST00000587705.1_Intron NM_032387.4 NP_115763.2 Q96J92 WNK4_HUMAN WNK lysine deficient protein kinase 4 607 NA NA chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294) cytoplasm (GO:0005737)|tight junction (GO:0005923) ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674) NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1) 35 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0749) TCAGCCCCCTGGGGGGGTGCC 0.637 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(6;201 374 4964 23855 42828) PASS NA NA NA 0 348 364.34 NA NA 36 39 38 NA NA NA 17 NA NA NA 40939870 2156 4214 6370 SO:0001589 frameshift_variant 1.17 AJ309861 CCDS11439.1 17q21-q22 2005-01-19 2005-01-19 2005-01-19 ENSG00000126562 65266 14544 protein-coding gene gene with protein product 601844 "protein kinase, lysine deficient 4" PRKWNK4 NA Standard NM_032387 NA Approved uc002ibj.3 Q96J92 ENST00000246914.5:c.1816delG chr17.hg19:g.40939870delG ENSP00000246914:p.Gly607fs 6 8 ref NA False 97 96 PASS 7 PASS ref->het 0 NA 214,217 62,64 74,71 1 1 B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5 True hg19 CCDS11439.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA WNK4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000452389.1 PASS NA None 348 True + G ENST00000246914.5 BECN1 8678 __UNKNOWN__ __UNKNOWN__ 17 40963789 40963789 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:40963789delC ENST00000361523.4 - 11 1200 c.1068delG c.(1066-1068)gggfs p.G356fs BECN1_ENST00000590099.1_Frame_Shift_Del_p.G356fs|BECN1_ENST00000438274.3_Intron NM_003766.3 NP_003757.1 Q14457 BECN1_HUMAN beclin 1, autophagy related 356 NA NA autophagic vacuole assembly (GO:0000045)|beta-amyloid metabolic process (GO:0050435)|cellular defense response (GO:0006968)|cellular response to aluminum ion (GO:0071275)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokinesis (GO:0000910)|defense response to virus (GO:0051607)|lysosome organization (GO:0007040)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|positive regulation of macroautophagy (GO:0016239)|regulation of catalytic activity (GO:0050790)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to vitamin E (GO:0033197)|viral process (GO:0016032) dendrite (GO:0030425)|membrane (GO:0016020)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802) haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1) 13 Breast(137;0.00104) BRCA - Breast invasive adenocarcinoma(366;0.0745) AAAACCGCAACCCCCCAGAAC 0.493 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 239 232.61 NA NA 125 117 120 NA NA NA 17 NA NA NA 40963789 2203 4300 6503 SO:0001589 frameshift_variant 0.54 AF077301 CCDS11441.1 17q21 2014-02-12 2008-01-14 ENSG00000126581 ENSG00000126581 8678 1034 protein-coding gene gene with protein product "ATG6 autophagy related 6 homolog (S. cerevisiae)" 604378 "beclin 1 (coiled-coil, moesin-like BCL2 interacting protein)" NA 9765397 Standard NM_003766 NM_003766 NA Approved ATG6, VPS30 uc002ibn.2 Q14457 ENST00000361523.4:c.1068delG chr17.hg19:g.40963789delC ENSP00000355231:p.Gly356fs 5 6 ref NA False 45 45 PASS 6 PASS ref->het 0 NA 168,172 35,36 35,33 2 2 B2R6N7|O75595|Q9UNA8 True hg19 CCDS11441.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BECN1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000452405.1 PASS NA None 239 True - C ENST00000361523.4 PRAC2 360205 __UNKNOWN__ __UNKNOWN__ 17 46801724 46801725 __UNKNOWN__ RNA INS - - G rs3110599|rs372079370|rs369888513 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:46801724_46801725insG ENST00000422730.2 + 0 181_182 PRAC2_ENST00000432056.1_RNA NR_036150.1 prostate cancer susceptibility candidate 2 NA NA NA NA AAAGTGTGTGTGGGGGGGTCCA 0.45 NA NA NA OREG0024525 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 26 0.00519169 0.0189 0 5008 , , NA 19234 0 NA 0.001 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 382 345.57 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1.18 AF532777, BX106051 CCDS74099.1, CCDS74100.1 17q21.3 2014-08-13 2013-08-29 2013-08-29 ENSG00000229637 ENSG00000229637 360205 30143 protein-coding gene gene with protein product "prostate, rectum and colon 2" 610787 "chromosome 17 open reading frame 93", "non-protein coding RNA 253", "HOXB13 antisense RNA 1 (non-protein coding)", "HOXB cluster antisense RNA 5 (non-protein coding)", "HOXB cluster antisense RNA 5" C17orf93, NCRNA00253, HOXB13-AS1, HOXB-AS5 NA 12746837 Standard NM_001282275 NA Approved uc002inz.2 OTTHUMG00000132085 ENST00000422730.2: chr17.hg19:g.46801731_46801731dupG 8 8 ref 942 False 147 136 PASS 7 PASS ref->het 0 NA 264,265 73,76 48,45 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PRAC2-001 KNOWN basic antisense NA antisense OTTHUMT00000255115.1 PASS NA None 382 True + G ENST00000422730.2 DDX5 1655 __UNKNOWN__ __UNKNOWN__ 17 62498057 62498076 __UNKNOWN__ Intron DEL TAAACTTTCTTTAAAAAAGT TAAACTTTCTTTAAAAAAGT - rs551784484 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:62498057_62498076delTAAACTTTCTTTAAAAAAGT ENST00000578804.1 - 11 1383 DDX5_ENST00000225792.5_Intron|DDX5_ENST00000450599.2_Intron P17844 DDX5_HUMAN DEAD (Asp-Glu-Ala-Asp) box helicase 5 NA NA NA cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351) catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529) androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713) breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2) 19 Breast(5;2.15e-14) BRCA - Breast invasive adenocarcinoma(8;8.6e-12) AAGAAAGCAATAAACTTTCTTTAAAAAAGTTAAATGGAGA 0.418 NA NA T ETV4 prostate NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSCLC(22;406 813 4871 19580 40307) PASS Dom yes 17 17q21 1655 DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 NA E 0 101 107.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.1 AF015812 CCDS11659.1 17q21 2012-07-27 2012-02-23 ENSG00000108654 ENSG00000108654 1655 "DEAD-boxes" 2746 protein-coding gene gene with protein product 180630 "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 5" HLR1, G17P1 NA 22156369, 18698352 Standard NM_004396 NM_004396 NA Approved p68 uc002jek.2 P17844 OTTHUMG00000178936 ENST00000578804.1:c.1216+51ACTTTTTTAAAGAAAGTTTA>- chr17.hg19:g.62498057_62498076delTAAACTTTCTTTAAAAAAGT 0 5 ref NA False 60 60 PASS 1 PASS ref->het 0 NA 102,107 24,24 14,13 2 2 B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DDX5-005 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000444032.1 PASS NA None 101 True - TAAACTTTCTTTAAAAAAGT ENST00000578804.1 HGS 9146 __UNKNOWN__ __UNKNOWN__ 17 79653297 79653297 __UNKNOWN__ Intron DEL T T - rs374471960 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:79653297delT ENST00000329138.4 + 3 257 NM_004712.4 NP_004703.1 O14964 HGS_HUMAN hepatocyte growth factor-regulated tyrosine kinase substrate NA NA NA endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165) cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141) metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904) endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1) 12 all_neural(118;0.0878)|all_lung(278;0.23) BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955) GCTGAGACTATTTTTTTCCCG 0.453 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 180 200.18 NA NA 73 67 69 NA NA NA 17 NA NA NA 79653297 2199 4299 6498 SO:0001627 intron_variant 0.3 D84064 CCDS11784.1 17q25 2009-04-29 ENSG00000185359 9146 "Zinc fingers, FYVE domain containing" 4897 protein-coding gene gene with protein product 604375 NA 9407053, 9630564 Standard NM_004712 NM_004712 NA Approved Hrs, ZFYVE8, Vps27 uc002kbg.3 O14964 ENST00000329138.4:c.123-45T>- chr17.hg19:g.79653297delT 6 8 ref NA False 55 55 PASS 7 PASS ref->het 0 NA 132,134 33,34 17,16 1 1 Q9NR36 True hg19 CCDS11784.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HGS-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000440541.1 PASS NA None 180 True + T ENST00000329138.4 MIB1 57534 __UNKNOWN__ __UNKNOWN__ 18 19445444 19445444 __UNKNOWN__ 3'UTR DEL A A - rs530377795 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:19445444delA ENST00000261537.6 + 0 4102 NM_020774.2 NP_065825.1 Q86YT6 MIB1_HUMAN mindbomb E3 ubiquitin protein ligase 1 NA NA NA blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756) centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069) ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270) breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5) 27 STAD - Stomach adenocarcinoma(5;0.212) CAGTGTTTTTAAAAAAAATCT 0.353 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 186 187.98 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.97 AB037744 CCDS11871.1 18q11.2 2014-09-17 2012-02-23 ENSG00000101752 ENSG00000101752 57534 "Zinc fingers, ZZ-type", "Ankyrin repeat domain containing" 21086 protein-coding gene gene with protein product 608677 "mindbomb homolog 1 (Drosophila)" NA Standard NM_020774 NM_020774 NA Approved DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6 uc002ktq.3 Q86YT6 OTTHUMG00000131753 ENST00000261537.6:c.*817A>- chr18.hg19:g.19445444delA 7 8 ref NA False 52 52 PASS 8 PASS ref->het 0 NA 122,122 37,38 27,28 1 1 B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3 True hg19 CCDS11871.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MIB1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254675.1 PASS NA None 186 True + A ENST00000261537.6 OSBPL1A 114876 __UNKNOWN__ __UNKNOWN__ 18 21894285 21894288 __UNKNOWN__ Frame_Shift_Del DEL GAAG GAAG - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:21894285_21894288delGAAG ENST00000319481.3 - 12 1100_1103 c.894_897delCTTC c.(892-897)ctcttcfs p.LF298fs NM_080597.3 NP_542164.2 Q9BXW6 OSBL1_HUMAN oxysterol binding protein-like 1A 298 PH. {ECO:0000255|PROSITE- ProRule:PRU00145}. NA NA antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634) cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543) breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1) 36 all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17) ATTTAATAAAGAAGAGGCAGCTAT 0.353 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 219 205.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.38 AF392449, AF274714 CCDS11884.1, CCDS11885.1, CCDS56056.1 18q11.2 2014-06-03 2014-06-03 2014-06-03 ENSG00000141447 ENSG00000141447 114876 "Oxysterol binding proteins", "Ankyrin repeat domain containing" 16398 protein-coding gene gene with protein product 606730 "oxysterol binding protein-like 1B" OSBPL1B NA 11279184, 10588946 Standard NM_080597 NM_080597 NA Approved ORP-1, ORP1 uc002kve.3 Q9BXW6 OTTHUMG00000131944 ENST00000319481.3:c.894_897delCTTC chr18.hg19:g.21894285_21894288delGAAG ENSP00000320291:p.Leu298fs 0 5 ref NA False 58 58 PASS 1 PASS ref->het 0 NA 150,151 41,41 18,18 1 1 B7Z7D3|Q9BZF5|Q9NW87 True hg19 CCDS11884.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OSBPL1A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254902.1 PASS NA None 219 True - GAAG ENST00000319481.3 C18orf54 162681 __UNKNOWN__ __UNKNOWN__ 18 51905296 51905296 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:51905296delT ENST00000300091.5 + 0 2131 C18orf54_ENST00000382911.4_3'UTR NM_173529.4 NP_775800.3 Q8IYD9 LAS2_HUMAN chromosome 18 open reading frame 54 NA NA NA extracellular region (GO:0005576) breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1) 15 Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186) TTTCCAAACCTTTTTTTGGAG 0.313 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 155 148.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.25 AK126503 CCDS11956.1, CCDS74223.1 18q21 2012-10-24 ENSG00000166845 ENSG00000166845 162681 13796 protein-coding gene gene with protein product "lung adenoma susceptibility protein 2" 613258 NA Standard NM_173529 XM_005258201 NA Approved MGC33382, LAS2 uc031rij.1 Q8IYD9 OTTHUMG00000132703 ENST00000300091.5:c.*680T>- chr18.hg19:g.51905296delT 6 7 ref NA False 101 88 PASS 7 PASS ref->het 0 NA 61,62 73,75 22,22 1 1 I7HFJ6|Q6MZU3|Q6ZTL6 True hg19 CCDS11956.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C18orf54-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256001.1 PASS NA None 155 True + T ENST00000300091.5 KIAA1468 57614 __UNKNOWN__ __UNKNOWN__ 18 59954566 59954566 __UNKNOWN__ Intron DEL T T - rs571403916 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:59954566delT ENST00000398130.2 + 26 3485 KIAA1468_ENST00000256858.6_Intron NM_020854.3 NP_065905.2 Q9P260 K1468_HUMAN KIAA1468 NA NA NA autonomic_ganglia(1)|breast(4)|endometrium(4)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 47 Colorectal(73;0.186) AATTTAACCCTTTTTTTTCTG 0.303 NA NA NA ?|TTTTTTTT|TTTTTTT|unsure 8 0.00159744 0.0061 0 5008 , , NA 18277 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 159 169.12 NA 18,4246 NA 4,10,2118 94 90 91 NA -9.4 0 18 91 13,8239 NA 6,1,4119 no intron KIAA1468 NM_020854.3 10,11,6237 A1A1,A1R,RR NA 0.1575,0.4221,0.2477 59954566 31,12485 2203 4299 6502 SO:0001627 intron_variant 0.22 BC011992 CCDS11979.2 18q21.33 2005-11-03 ENSG00000134444 ENSG00000134444 57614 29289 protein-coding gene gene with protein product NA NA 11973628 Standard NM_020854 NM_020854 NA Approved HsT885, HsT3308, FLJ33841 uc002lil.3 Q9P260 OTTHUMG00000132780 ENST00000398130.2:c.3254-18T>- chr18.hg19:g.59954566delT 7 9 ref NA False 41 41 PASS 8 PASS ref->het 0 NA 108,108 34,34 17,17 1 1 True hg19 CCDS11979.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KIAA1468-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256187.1 PASS NA None 159 True + T ENST00000398130.2 TMEM259 91304 __UNKNOWN__ __UNKNOWN__ 19 1010455 1010455 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:1010455delG ENST00000356663.3 - 11 1878 c.1757delC c.(1756-1758)ccgfs p.P586fs TMEM259_ENST00000333175.5_3'UTR NM_001033026.1 NP_001028198.1 Q4ZIN3 MBRL_HUMAN transmembrane protein 259 586 NA NA cytoplasm (GO:0005737)|integral component of membrane (GO:0016021) NA GGAGTCACTCGGGGGGACACT 0.746 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 140 128.92 NA NA 3 4 4 NA NA NA 19 NA NA NA 1010455 1930 3941 5871 SO:0001589 frameshift_variant 1 BC008957 CCDS12052.1, CCDS32862.1 19p13.3 2013-02-06 2013-02-06 2013-02-06 ENSG00000182087 ENSG00000182087 91304 17039 protein-coding gene gene with protein product "membralin", "aspecific BCL2 ARE-binding protein 1" 611011 "chromosome 19 open reading frame 6" C19orf6 NA 12638133, 16084606 Standard NM_033420 XM_005259675 NA Approved MGC4022, ASBABP1, MBRL uc002lqr.1 Q4ZIN3 ENST00000356663.3:c.1757delC chr19.hg19:g.1010455delG ENSP00000349087:p.Pro586fs 5 6 ref NA False 108 108 PASS 6 PASS ref->het 0 NA 89,94 30,30 21,16 1 1 O60392|Q8NF79|Q96H30 True hg19 CCDS32862.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM259-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000458236.1 PASS NA None 140 True - G ENST00000356663.3 MUM1 84939 __UNKNOWN__ __UNKNOWN__ 19 1366238 1366238 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:1366238delA ENST00000415183.3 + 7 1313 MUM1_ENST00000311401.5_Intron|MUM1_ENST00000344663.3_Intron|MUM1_ENST00000591806.1_Intron Q2TAK8 MUM1_HUMAN melanoma associated antigen (mutated) 1 NA NA NA chromatin organization (GO:0006325)|DNA repair (GO:0006281) nucleus (GO:0005634) nucleosome binding (GO:0031491) breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 18 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) GTGATGTCACAAAAAAATATT 0.468 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 132 131.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AK075241 CCDS12062.1 19p13.3 2008-02-05 ENSG00000160953 84939 29641 protein-coding gene gene with protein product NA NA 11042152, 7644523 Standard NM_032853 NM_032853 NA Approved MUM-1 uc002lrz.2 Q2TAK8 ENST00000415183.3:c.1288-66A>- chr19.hg19:g.1366238delA 6 8 ref NA False 57 57 PASS 7 PASS ref->het 0 NA 87,88 30,30 14,14 1 1 A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MUM1-016 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000449510.1 PASS NA None 132 True + A ENST00000415183.3 CAMSAP3 57662 __UNKNOWN__ __UNKNOWN__ 19 7670255 7670255 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:7670255delC ENST00000446248.2 + 2 393 c.292delC c.(292-294)cccfs p.P99fs CAMSAP3_ENST00000160298.4_Frame_Shift_Del_p.P99fs NM_001080429.2 NP_001073898.1 Q9P1Y5 CAMP3_HUMAN calmodulin regulated spectrin-associated protein family, member 3 99 NA NA epithelial cell-cell adhesion (GO:0090136)|microtubule anchoring (GO:0034453)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of organelle organization (GO:0033043)|zonula adherens maintenance (GO:0045218) cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)|zonula adherens (GO:0005915) microtubule minus-end binding (GO:0051011) cervix(1)|endometrium(7)|kidney(3)|lung(6)|urinary_tract(2) 19 GCTTGAAACACCCCCCAACCC 0.697 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 472 456.15 NA NA 51 59 56 NA NA NA 19 NA NA NA 7670255 1979 4138 6117 SO:0001589 frameshift_variant 6.55 AB040976 CCDS42489.1, CCDS45947.1 19p13.3-p13.2 2014-06-12 2011-08-18 2011-08-18 ENSG00000076826 57662 29307 protein-coding gene gene with protein product "protein phosphatase 1, regulatory subunit 80" 612685 "KIAA1543" KIAA1543 NA 11318610, 10819331, 19041755, 19508979 Standard XM_048362 NM_001080429 NA Approved Nezha, PPP1R80 uc002mgu.4 Q9P1Y5 ENST00000446248.2:c.292delC chr19.hg19:g.7670255delC ENSP00000416797:p.Pro99fs 5 7 ref NA False 286 124 PASS 6 PASS ref->het 0 NA 276,283 137,140 61,51 1 1 Q8NDF1 True hg19 CCDS45947.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CAMSAP3-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000459301.2 PASS NA None 472 True + C ENST00000446248.2 EVI5L 115704 __UNKNOWN__ __UNKNOWN__ 19 7927000 7927000 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:7927000delC ENST00000538904.2 + 15 1644 EVI5L_ENST00000270530.4_Intron NM_001159944.1 NP_001153416.1 Q96CN4 EVI5L_HUMAN ecotropic viral integration site 5-like NA NA NA negative regulation of cilium assembly (GO:1902018)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851) Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137) breast(1)|lung(9)|ovary(1)|upper_aerodigestive_tract(1) 12 CTCGGCTTCACCCCCCAGGCC 0.746 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 196 203.6 NA NA 3 4 3 NA NA NA 19 NA NA NA 7927000 1867 3826 5693 SO:0001627 intron_variant 3.41 BC014111 CCDS12188.1, CCDS54209.1 19p13 2013-07-09 ENSG00000142459 115704 30464 protein-coding gene gene with protein product NA NA 23669355 Standard NM_145245 NM_001159944 NA Approved uc010xjz.2 Q96CN4 ENST00000538904.2:c.1645-8C>- chr19.hg19:g.7927000delC 5 7 ref NA False 75 75 PASS 6 PASS ref->het 0 NA 132,141 33,33 39,31 1 1 B9A6I9 True hg19 CCDS54209.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EVI5L-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000461348.1 PASS NA None 196 True + C ENST00000538904.2 CTD-2192J16.22 0 __UNKNOWN__ __UNKNOWN__ 19 12757294 12757294 __UNKNOWN__ Intron DEL A A - rs532181914 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:12757294delA ENST00000597692.1 - 4 722 NA NA NA NA AATAACAGACAAAAAAAACCC 0.517 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 147 154.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.94 NA NA NA NA NA ENST00000597692.1:c.592+12T>- chr19.hg19:g.12757294delA 7 9 ref NA False 97 92 PASS 8 PASS ref->het 0 NA 74,79 49,51 25,19 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CTD-2192J16.22-001 KNOWN mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript nonsense_mediated_decay NA protein_coding OTTHUMT00000462694.1 PASS NA None 147 True - A ENST00000597692.1 NCAN 1463 __UNKNOWN__ __UNKNOWN__ 19 19338278 19338279 __UNKNOWN__ Frame_Shift_Ins INS - - C LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:19338278_19338279insC ENST00000252575.6 + 8 1948_1949 c.1849_1850insC c.(1849-1851)gccfs p.A617fs NCAN_ENST00000538881.1_Frame_Shift_Ins_p.A68fs NM_004386.2 NP_004377.2 O14594 NCAN_HUMAN neurocan 617 NA NA axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281) extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202) calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540) breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1) 64 Epithelial(12;0.00544) Hyaluronan(DB08818) TCCCAGCCCTGCCCCCTGGGAG 0.644 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 376 378.26 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.72 AF026547 CCDS12397.1 19p12 2014-01-30 2007-02-15 2007-02-15 ENSG00000130287 ENSG00000130287 1463 "Immunoglobulin superfamily / V-set domain containing", "Proteoglycans / Extracellular Matrix : Hyalectans", "Endogenous ligands" 2465 protein-coding gene gene with protein product "neurocan proteoglycan" 600826 "chondroitin sulfate proteoglycan 3" CSPG3 NA 1326557, 21353194 Standard NM_004386 NM_004386 NA Approved uc002nlz.3 O14594 ENST00000252575.6:c.1854dupC chr19.hg19:g.19338283_19338283dupC ENSP00000252575:p.Ala617fs 6 5 ref NA False 31 31 PASS 5 PASS ref->het 0 NA 284,291 41,42 46,41 1 1 Q9UPK6 True hg19 CCDS12397.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NCAN-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000460111.2 PASS NA None 376 True + C ENST00000252575.6 NDUFA13 51079 __UNKNOWN__ __UNKNOWN__ 19 19638549 19638551 __UNKNOWN__ In_Frame_Del DEL CAT CAT - rs376885809 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:19638549_19638551delCAT ENST00000503283.1 + 4 296_298 c.285_287delCAT c.(283-288)gccatc>gcc p.I97del NDUFA13_ENST00000252576.5_In_Frame_Del_p.I180del|NDUFA13_ENST00000428459.2_In_Frame_Del_p.I97del|NDUFA13_ENST00000512771.3_In_Frame_Del_p.I97del|CTC-260F20.3_ENST00000555938.1_In_Frame_Del_p.I97del|YJEFN3_ENST00000608404.1_In_Frame_Del_p.I97del|NDUFA13_ENST00000507754.4_In_Frame_Del_p.I97del|CTC-260F20.3_ENST00000586674.1_3'UTR Q9P0J0 NDUAD_HUMAN NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13 97 NA NA apoptotic signaling pathway (GO:0097190)|cellular metabolic process (GO:0044237)|cellular response to interferon-beta (GO:0035458)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of peptidase activity (GO:0010952)|positive regulation of protein catabolic process (GO:0045732)|protein import into mitochondrial inner membrane (GO:0045039)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654) ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954) endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1) 12 AGGAGGAGGCCATCATCATGAAG 0.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 120 115.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.02 AF261134 CCDS12404.1, CCDS12404.2 19p13.11 2011-07-04 ENSG00000186010 ENSG00000186010 51079 "Mitochondrial respiratory chain complex / Complex I" 17194 protein-coding gene gene with protein product "complex I B16.6 subunit" 609435 NA 12837546, 10924506, 15367666 Standard NM_015965 NM_015965 NA Approved CGI-39, CDA016, GRIM-19, GRIM19, B16.6 Q9P0J0 OTTHUMG00000162211 ENST00000503283.1:c.285_287delCAT chr19.hg19:g.19638555_19638557delCAT ENSP00000468317:p.Ile97del 2 2 ref NA False 67 67 PASS 3 PASS ref->het 0 NA 77,77 28,28 17,17 1 1 B4DF76|K7EK58|Q6PKI0|Q9H2L3|Q9Y327 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NDUFA13-002 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000367917.4 PASS NA None 120 True + CAT ENST00000503283.1 ZNF675 171392 __UNKNOWN__ __UNKNOWN__ 19 23869793 23869793 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:23869793delC ENST00000359788.4 - 1 172 ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000600313.1_Intron|ZNF675_ENST00000599168.1_Intron|ZNF675_ENST00000601010.1_Intron NM_138330.2 NP_612203.2 Q8TD23 ZN675_HUMAN zinc finger protein 675 NA NA NA bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471) DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270) endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1) 27 all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206) TTCCAACCAGCCCCTTCCCCC 0.597 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 342 324.03 NA NA 74 70 71 NA NA NA 19 NA NA NA 23869793 2203 4300 6503 SO:0001627 intron_variant 2.63 CCDS32981.1 19p12 2013-01-08 171392 "Zinc fingers, C2H2-type", "-" 30768 protein-coding gene gene with protein product "TRAF6 inhibitory zinc finger" NA NA 11751921 Standard NM_138330 NM_138330 NA Approved TIZ, TBZF uc002nri.3 Q8TD23 ENST00000359788.4:c.3+39G>- chr19.hg19:g.23869793delC 3 4 ref NA False 75 75 PASS 4 PASS ref->het 0 NA 246,254 51,52 45,36 1 1 Q8N211 True hg19 CCDS32981.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF675-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000466433.1 PASS NA None 342 True - C ENST00000359788.4 ACTN4 81 __UNKNOWN__ __UNKNOWN__ 19 39220096 39220096 __UNKNOWN__ 3'UTR DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:39220096delC ENST00000252699.2 + 0 2836 ACTN4_ENST00000497637.1_3'UTR NM_004924.4 NP_004915.2 O43707 ACTN4_HUMAN actinin, alpha 4 NA NA NA actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830) cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018) actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803) NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3) 30 all_cancers(60;1.57e-05)|Ovarian(47;0.103) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) TGACCCAACACCCCCGACGGC 0.657 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Colon(168;199 1940 10254 46213 46384) PASS NA NA NA 0 406 361.4 NA NA 21 22 22 NA NA NA 19 NA NA NA 39220096 2200 4296 6496 SO:0001624 3_prime_UTR_variant 1.79 D89980 CCDS12518.1 19q13 2013-01-10 ENSG00000130402 ENSG00000130402 81 "EF-hand domain containing" 166 protein-coding gene gene with protein product 604638 "focal segmental glomerulosclerosis 1" FSGS1 NA 9461087, 10700177 Standard NM_004924 NA Approved uc002oja.2 O43707 OTTHUMG00000137382 ENST00000252699.2:c.*24C>- chr19.hg19:g.39220096delC 4 6 ref NA False 79 79 PASS 5 PASS ref->het 0 NA 309,313 48,51 57,52 1 1 A4K467|D6PXK4|O76048 True hg19 CCDS12518.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACTN4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000268091.1 PASS NA None 406 True + C ENST00000252699.2 SUPT5H 6829 __UNKNOWN__ __UNKNOWN__ 19 39964877 39964891 __UNKNOWN__ In_Frame_Del DEL CAACACAGACCAGTT CAACACAGACCAGTT - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:39964877_39964891delCAACACAGACCAGTT ENST00000599117.1 + 28 3022_3036 c.2655_2669delCAACACAGACCAGTT c.(2653-2670)tacaacacagaccagttc>tac p.NTDQF886del SUPT5H_ENST00000359191.6_In_Frame_Del_p.NTDQF882del|SUPT5H_ENST00000432763.2_In_Frame_Del_p.NTDQF886del|SUPT5H_ENST00000402194.2_In_Frame_Del_p.NTDQF882del|SUPT5H_ENST00000598725.1_In_Frame_Del_p.NTDQF886del O00267 SPT5H_HUMAN suppressor of Ty 5 homolog (S. cerevisiae) 886 10 X 8 AA approximate tandem repeats of P-[TS]-P-S-P-[QA]-[SG]-Y, motif CTR2.|Pro-rich. NA NA 7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032) DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982) breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1) 51 all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159) Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657) TCTGCAGGTACAACACAGACCAGTTCTCTCCCTAT 0.619 NA NA NA OREG0025462 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 909 866.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 4.47 U56402 CCDS12536.1, CCDS46072.1 19q13 2008-07-22 2001-11-28 ENSG00000196235 6829 11469 protein-coding gene gene with protein product 602102 "suppressor of Ty (S.cerevisiae) 5 homolog" NA 8975720 Standard NM_003169 NM_003169 NA Approved SPT5H, SPT5, FLJ34157 uc002olp.4 O00267 ENST00000599117.1:c.2655_2669delCAACACAGACCAGTT chr19.hg19:g.39964877_39964891delCAACACAGACCAGTT ENSP00000470252:p.Asn886_Phe890del 0 3 ref 889 False 128 128 PASS 1 PASS ref->het 0 NA 835,857 52,53 91,72 1 1 O43279|Q59G52|Q99639 True hg19 CCDS12536.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SUPT5H-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000464918.1 PASS NA None 909 True + CAACACAGACCAGTT ENST00000599117.1 HIF3A 64344 __UNKNOWN__ __UNKNOWN__ 19 46800433 46800433 __UNKNOWN__ Intron DEL G G - rs3826795|rs534395516 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:46800433delG ENST00000377670.4 + 1 57 NM_152795.3 NP_690008.2 Q9Y2N7 HIF3A_HUMAN hypoxia inducible factor 3, alpha subunit NA NA NA cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366) cytosol (GO:0005829)|nucleoplasm (GO:0005654) DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714) breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1) 33 Ovarian(192;0.00965)|all_neural(266;0.0887) OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136) CTGGATTGTTGGGGGGGGTGG 0.677 NA NA NA ?|GGGGGGGG|GGGGGGG|unsure 88 0.0175719 0.0053 0.0576 5008 , , NA 10369 0.0387 NA 0 False NA ,,, NA NA NA 2504 0.002 NA NA NA PASS NA NA NA 0 80 83.97 NA 30,25,2591 NA 1,0,28,2,21,1271 2 2 2 NA NA 0 19 2 50,34,5854 NA 4,0,42,2,30,2891 no intron HIF3A NM_152795.3 5,0,70,4,51,4162 A1A1,A1A2,A1R,A2A2,A2R,RR NA 1.4146,2.0786,1.6193 46800433 80,59,8445 476 1206 1682 SO:0001627 intron_variant 6.6 AK027725 CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2 19q13 2013-05-21 ENSG00000124440 ENSG00000124440 64344 "Basic helix-loop-helix proteins" 15825 protein-coding gene gene with protein product 609976 NA 11573933, 11734856 Standard NM_152794 NA Approved IPAS, MOP7, PASD7, bHLHe17 uc002peh.3 Q9Y2N7 OTTHUMG00000141296 ENST00000377670.4:c.26+74G>- chr19.hg19:g.46800433delG 7 12 ref NA False 34 34 PASS 8 PASS ref->het 0 NA 31,47 11,13 45,27 1 1 B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2 True hg19 CCDS12681.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HIF3A-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000280556.3 PASS NA None 80 True + G ENST00000377670.4 CDC42EP5 148170 __UNKNOWN__ __UNKNOWN__ 19 54976341 54976341 __UNKNOWN__ Frame_Shift_Del DEL G G - rs150839818 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:54976341delG ENST00000301200.2 - 3 732 c.391delC c.(391-393)cagfs p.Q131fs NM_145057.2 NP_659494.2 Q6NZY7 BORG3_HUMAN CDC42 effector protein (Rho GTPase binding) 5 131 NA NA JNK cascade (GO:0007254)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886) GTP-Rho binding (GO:0017049) lung(1)|skin(1) 2 Ovarian(34;0.19) GBM - Glioblastoma multiforme(193;0.138) CAGCGGGCCTGGGGGGGCTGC 0.751 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 108 114.78 NA NA 3 4 4 NA NA NA 19 NA NA NA 54976341 1599 3128 4727 SO:0001589 frameshift_variant 1.5 BC024327 CCDS12896.1 19q13.42 2008-02-05 ENSG00000167617 ENSG00000167617 148170 17408 protein-coding gene gene with protein product 609171 NA Standard NM_145057 NM_145057 NA Approved CEP5, Borg3 uc002qfz.1 Q6NZY7 OTTHUMG00000065699 ENST00000301200.2:c.391delC chr19.hg19:g.54976341delG ENSP00000301200:p.Gln131fs 6 7 ref NA False 43 43 PASS 7 PASS ref->het 0 NA 76,86 11,11 20,11 1 1 B0VJZ2|Q8TB51 True hg19 CCDS12896.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDC42EP5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000140804.1 PASS NA None 108 True - G ENST00000301200.2 ZIM3 114026 __UNKNOWN__ __UNKNOWN__ 19 57647126 57647126 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:57647126delT ENST00000269834.1 - 5 964 c.579delA c.(577-579)aaafs p.K193fs NM_052882.1 NP_443114.1 Q96PE6 ZIM3_HUMAN zinc finger, imprinted 3 193 NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1) 52 Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243) UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026) ATTCAAAGGGTTTTTGACAGG 0.428 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 429 436.32 NA NA 162 156 158 NA NA NA 19 NA NA NA 57647126 2203 4300 6503 SO:0001589 frameshift_variant 0.73 AF365931 CCDS33125.1 19q13.4 2013-01-08 ENSG00000141946 114026 "Zinc fingers, C2H2-type", "-" 16366 protein-coding gene gene with protein product NA NA Standard NM_052882 NA Approved ZNF657 uc002qnz.1 Q96PE6 ENST00000269834.1:c.579delA chr19.hg19:g.57647126delT ENSP00000269834:p.Lys193fs 4 5 ref NA False 49 49 PASS 5 PASS ref->het 0 NA 321,322 64,64 44,45 1 1 Q14CA6 True hg19 CCDS33125.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZIM3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000465078.1 PASS NA None 429 True - T ENST00000269834.1 PANK2 80025 __UNKNOWN__ __UNKNOWN__ 20 3897554 3897554 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:3897554delT ENST00000316562.4 + 5 1418 PANK2_ENST00000497424.1_Intron|PANK2_ENST00000610179.1_Intron|PANK2_ENST00000464452.1_Intron NM_153638.2 NP_705902.2 Q9BZ23 PANK2_HUMAN pantothenate kinase 2 NA NA NA aerobic respiration (GO:0009060)|cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|mitochondrion morphogenesis (GO:0070584)|pantothenate metabolic process (GO:0015939)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767) cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758) ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594) breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 15 AGCAATGGGATTTTTTTTCCC 0.408 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 373 357.98 NA NA 52 49 50 NA NA NA 20 NA NA NA 3897554 2203 4300 6503 SO:0001627 intron_variant 0.92 AK021791 CCDS13071.2, CCDS13072.1 20p13 2008-07-31 2008-07-31 2002-09-06 ENSG00000125779 ENSG00000125779 80025 2.7.1.33 15894 protein-coding gene gene with protein product "Hallervorden-Spatz syndrome" 606157 "neurodegeneration with brain iron accumulation 1 (Hallervorden-Spatz syndrome)" C20orf48, NBIA1 NA 8944032, 11479594 Standard NM_024960 XM_005260835 NA Approved HSS, FLJ11729, PKAN, HARP uc002wkc.3 Q9BZ23 OTTHUMG00000031768 ENST00000316562.4:c.1413-20T>- chr20.hg19:g.3897554delT 7 8 ref NA False 63 63 PASS 8 PASS ref->het 0 NA 278,283 47,48 50,46 1 1 B1AK33|B2Z3X0|D3DVZ0|Q5T7I2|Q5T7I4|Q7RTX5|Q8N7Q4|Q8TCR5|Q9BYW5|Q9HAF2 True hg19 CCDS13071.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PANK2-007 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000077793.2 PASS NA None 373 True + T ENST00000316562.4 MAPRE1 22919 __UNKNOWN__ __UNKNOWN__ 20 31436657 31436659 __UNKNOWN__ 3'UTR DEL TCT TCT - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:31436657_31436659delTCT ENST00000375571.5 + 0 1069_1071 RP5-1085F17.4_ENST00000565572.1_RNA NM_012325.2 NP_036457.1 Q15691 MARE1_HUMAN microtubule-associated protein, RP/EB family, member 1 NA NA NA cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of microtubule plus-end binding (GO:1903033)|protein localization to microtubule (GO:0035372) cell projection membrane (GO:0031253)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule plus-end (GO:0035371) microtubule plus-end binding (GO:0051010)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022) endometrium(2)|large_intestine(1)|lung(3)|prostate(2) 8 AAAAAGTACCTCTTCTTAAAGTG 0.374 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 335 339.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.5 U24166 CCDS13208.1 20q11.1-q11.3 2013-01-17 ENSG00000101367 ENSG00000101367 22919 6890 protein-coding gene gene with protein product "adenomatous polyposis coli-binding protein EB1" 603108 NA 7606712, 9724749, 11470413 Standard NM_012325 NM_012325 NA Approved EB1 uc002wyh.3 Q15691 OTTHUMG00000032228 ENST00000375571.5:c.*125TCT>- chr20.hg19:g.31436660_31436662delTCT 1 4 ref NA False 53 53 PASS 2 PASS ref->het 0 NA 231,234 63,64 42,40 1 1 B2R6I7|E1P5M8|Q3KQS8 True hg19 CCDS13208.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAPRE1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000078647.2 PASS NA None 335 True + TCT ENST00000375571.5 ACTL10 170487 __UNKNOWN__ __UNKNOWN__ 20 32256055 32256055 __UNKNOWN__ 3'UTR DEL G G - rs73261831 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:32256055delG ENST00000330271.4 + 0 1752 NECAB3_ENST00000375238.4_Intron|NECAB3_ENST00000246190.6_Intron NM_001024675.1 NP_001019846.1 Q5JWF8 ACL10_HUMAN actin-like 10 NA NA NA NA AGGCTGGACTGGGGGGGGTGG 0.597 NA NA NA OREG0025871 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 525 485.82 NA ,, 43,29,4080 NA 2,0,39,0,29,2006 27 32 30 NA ,, -3.4 0 20 30 35,72,7967 NA 1,0,33,1,70,3932 no intron,intron,utr-3 NECAB3,C20orf134 NM_031232.3,NM_031231.3,NM_001024675.1 ,, 3,0,72,1,99,5938 A1A1,A1A2,A1R,A2A2,A2R,RR NA 1.3252,1.7341,1.4641 ,, ,, 32256055 78,101,12047 2175 4241 6416 SO:0001624 3_prime_UTR_variant 7.62 AL121906 CCDS33463.1 20q11.22 2011-11-24 2011-11-24 2011-11-24 ENSG00000182584 ENSG00000182584 170487 16127 protein-coding gene gene with protein product NA "chromosome 20 open reading frame 134" C20orf134 NA Standard NM_001024675 NA Approved uc002wzt.3 Q5JWF8 OTTHUMG00000032262 ENST00000330271.4:c.*14G>- chr20.hg19:g.32256055delG 7 10 ref 831 False 97 97 PASS 8 PASS ref->het 0 NA 363,388 56,58 112,88 1 1 B9EH76 True hg19 CCDS33463.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACTL10-001 PUTATIVE basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000078713.1 PASS NA None 525 True + G ENST00000330271.4 SDC4 6385 __UNKNOWN__ __UNKNOWN__ 20 43976853 43976853 __UNKNOWN__ Intron DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:43976853delG ENST00000372733.3 - 1 100 SDC4_ENST00000537976.1_Intron NM_002999.3 NP_002990.2 P31431 SDC4_HUMAN syndecan 4 NA NA NA carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stress fiber assembly (GO:0051496)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|ureteric bud development (GO:0001657) cell surface (GO:0009986)|costamere (GO:0043034)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886) thrombospondin receptor activity (GO:0070053) SDC4/ROS1(7) NS(1)|breast(1)|endometrium(1)|large_intestine(2) 5 Myeloproliferative disorder(115;0.0122) GTGTCCGGTTGGGGGTAGCGT 0.706 NA NA T ROS1 NSCLC NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 20 20q12 6385 syndecan 4 NA E 0 149 144.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.58 X67016, D13292 CCDS13350.1 20q12 2010-03-25 2007-02-15 ENSG00000124145 ENSG00000124145 6385 "Proteoglycans / Cell Surface : Syndecans" 10661 protein-coding gene gene with protein product "syndecan proteoglycan 4" 600017 "syndecan 4 (amphiglycan, ryudocan)" NA 7916598, 1500433 Standard NM_002999 NM_002999 NA Approved SYND4, amphiglycan, ryudocan uc002xnu.3 P31431 OTTHUMG00000033083 ENST00000372733.3:c.60+111C>- chr20.hg19:g.43976853delG 4 5 ref NA False 45 45 PASS 5 PASS ref->het 0 NA 101,108 19,20 26,19 1 1 O00773|Q16833|Q53FN9|Q6FGN3 True hg19 CCDS13350.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SDC4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000080515.1 PASS NA None 149 True - G ENST00000372733.3 EYA2 2139 __UNKNOWN__ __UNKNOWN__ 20 45644794 45644794 __UNKNOWN__ Intron DEL T T - rs567374244 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:45644794delT ENST00000327619.5 + 5 672 EYA2_ENST00000317304.6_Intron|EYA2_ENST00000357410.3_Intron NM_005244.4 NP_005235.3 O00167 EYA2_HUMAN EYA transcriptional coactivator and phosphatase 2 NA NA NA DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|histone dephosphorylation (GO:0016576)|mesodermal cell fate specification (GO:0007501)|mitochondrial outer membrane permeabilization (GO:0097345)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of transcription, DNA-templated (GO:0006355)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351) centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634) magnesium ion binding (GO:0000287)|protein tyrosine phosphatase activity (GO:0004725) NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1) 32 Myeloproliferative disorder(115;0.0241) TCCTTGGTCCTTTTTTTTCCC 0.483 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(120;56 1725 18501 25218 43520) PASS NA NA NA 0 191 189.18 NA , 3,4261 NA 1,1,2130 134 130 132 NA , 1.3 0.9 20 132 2,8252 NA 1,0,4126 no intron,intron EYA2 NM_172110.3,NM_005244.4 , 2,1,6256 A1A1,A1R,RR NA 0.0242,0.0704,0.0399 , , 45644794 5,12513 2203 4300 6503 SO:0001627 intron_variant 0.96 CCDS13403.1, CCDS54471.1 20q13.1 2014-06-19 2014-06-19 ENSG00000064655 ENSG00000064655 2139 "Protein tyrosine phosphatases / Asp-based PTPs" 3520 protein-coding gene gene with protein product 601654 "eyes absent (Drosophila) homolog 2", "eyes absent homolog 2 (Drosophila)" NA 9020840 Standard NM_005244 NM_005244 NA Approved EAB1 uc002xsm.3 O00167 OTTHUMG00000033041 ENST00000327619.5:c.299-26T>- chr20.hg19:g.45644794delT 7 8 ref NA False 65 65 PASS 8 PASS ref->het 0 NA 120,121 47,49 26,23 1 1 Q5JSW8|Q86U84|Q96CV6|Q96H97|Q99503|Q99812|Q9BWF6|Q9H4S3|Q9H4S9|Q9NPZ4|Q9UIX7 True hg19 CCDS13403.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EYA2-005 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000080326.2 PASS NA None 191 True + T ENST00000327619.5 NCOA3 8202 __UNKNOWN__ __UNKNOWN__ 20 46279814 46279815 __UNKNOWN__ In_Frame_Ins INS - - GCA rs72645299|rs3830810 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:46279814_46279815insGCA ENST00000371998.3 + 20 3931_3932 c.3740_3741insGCA c.(3739-3744)atgcag>atGCAgcag p.1276_1277insQ NCOA3_ENST00000371997.3_In_Frame_Ins_p.1267_1268insQ|NCOA3_ENST00000341724.6_In_Frame_Ins_p.1202_1203insQ|NCOA3_ENST00000372004.3_In_Frame_Ins_p.1272_1273insQ Q9Y6Q9 NCOA3_HUMAN nuclear receptor coactivator 3 1276 Acetyltransferase.|Poly-Gln. NA NA androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068) cytoplasm (GO:0005737)|nucleus (GO:0005634) androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713) breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 52 GCTATGATGATgcagcagcagc 0.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 269 277.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001652 inframe_insertion 1.36 AF012108 CCDS13406.1, CCDS13407.1, CCDS54472.1 20q12 2011-07-01 ENSG00000124151 ENSG00000124151 8202 "Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins" 7670 protein-coding gene gene with protein product "receptor-associated coactivator 3", "thyroid hormone receptor activator molecule 1" 601937 NA 9252329, 9346901 Standard NM_006534 NM_181659 NA Approved RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3 uc002xtk.3 Q9Y6Q9 OTTHUMG00000033061 ENST00000371998.3:c.3759_3761dupGCA chr20.hg19:g.46279821_46279823dupGCA ENSP00000361066:p.Gln1277_Gln1278dup 8 1 ref NA False 40 40 PASS 7 PASS ref->het 0 NA 140,144 39,39 86,83 1 1 A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7 True hg19 CCDS13407.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NCOA3-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000080405.1 PASS NA None 269 True + GCA ENST00000371998.3 PMEPA1 56937 __UNKNOWN__ __UNKNOWN__ 20 56226596 56226597 __UNKNOWN__ 3'UTR INS - - T LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:56226596_56226597insT ENST00000341744.3 - 0 1695_1696 PMEPA1_ENST00000395816.3_3'UTR|PMEPA1_ENST00000347215.4_3'UTR|PMEPA1_ENST00000265626.4_3'UTR NM_020182.4 NP_064567.2 Q969W9 PMEPA_HUMAN prostate transmembrane protein, androgen induced 1 NA NA NA androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179) early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699) breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1) 16 AAAAATTGCCATTTTTTTCCTC 0.307 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 150 143.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.8 AF224278 CCDS13462.1, CCDS13463.1, CCDS13464.1 20q13.31-q13.33 2008-04-03 2008-04-03 2008-04-03 ENSG00000124225 ENSG00000124225 56937 14107 protein-coding gene gene with protein product "solid tumor-associated 1" 606564 "transmembrane, prostate androgen induced RNA" TMEPAI NA 10873380 Standard NM_020182 NM_020182 NA Approved STAG1 uc002xyq.4 Q969W9 OTTHUMG00000032831 ENST00000341744.3:c.*513->A chr20.hg19:g.56226603_56226603dupT 8 7 ref NA False 33 33 PASS 7 PASS ref->het 0 NA 101,102 18,20 33,31 1 1 Q5TDR6|Q8NER4|Q96B72|Q9UJD3 True hg19 CCDS13463.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PMEPA1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000079858.2 PASS NA None 150 True - T ENST00000341744.3 URB1 9875 __UNKNOWN__ __UNKNOWN__ 21 33683727 33683727 __UNKNOWN__ 3'UTR DEL C C - rs545361408 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:33683727delC ENST00000382751.3 - 0 10433 MRAP_ENST00000399784.2_Intron|MRAP_ENST00000399786.3_Intron|MRAP_ENST00000303645.5_Intron|MRAP_ENST00000339944.4_Intron|MRAP_ENST00000497833.1_Intron NM_014825.2 NP_055640.2 O60287 NPA1P_HUMAN URB1 ribosome biogenesis 1 homolog (S. cerevisiae) NA NA NA nucleolus (GO:0005730) poly(A) RNA binding (GO:0044822) NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1) 19 CCACCCCCCACCCCCCCCATC 0.507 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 213 208.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.7 AB011111 CCDS46645.1 21q22.11 2006-11-28 2006-11-28 2006-11-28 ENSG00000142207 ENSG00000142207 9875 17344 protein-coding gene gene with protein product nucleolar preribosomal-associated protein 1 608865 "chromosome 21 open reading frame 108" C21orf108 NA 9628581 Standard NM_014825 NA Approved KIAA0539, NPA1 uc002ypn.2 O60287 OTTHUMG00000064919 ENST00000382751.3:c.*3502G>- chr21.hg19:g.33683727delC 7 14 ref NA False 57 57 PASS 8 PASS ref->het 0 NA 107,119 56,59 53,44 1 1 D3DSE5|Q96NX1|Q9NYQ1 True hg19 CCDS46645.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA URB1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000139400.2 PASS NA None 213 True - C ENST00000382751.3 IFNGR2 3460 __UNKNOWN__ __UNKNOWN__ 21 34799292 34799292 __UNKNOWN__ Frame_Shift_Del DEL T T - rs375419913 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:34799292delT ENST00000290219.6 + 4 1162 c.514delT c.(514-516)tttfs p.F173fs IFNGR2_ENST00000405436.1_Frame_Shift_Del_p.F94fs|IFNGR2_ENST00000381995.1_Frame_Shift_Del_p.F192fs NM_005534.3 NP_005525.2 P38484 INGR2_HUMAN interferon gamma receptor 2 (interferon gamma transducer 1) 173 Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}. NA NA cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615) endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) interferon-gamma receptor activity (GO:0004906) NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1) 13 Interferon gamma-1b(DB00033) CTCCACGGCCTTTTTTTGTTA 0.458 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 278 267.92 NA NA 226 232 230 NA NA NA 21 NA NA NA 34799292 2203 4300 6503 SO:0001589 frameshift_variant 0.55 CCDS33544.1 21q22.1 2014-09-17 ENSG00000159128 ENSG00000159128 3460 "Interferons", "Fibronectin type III domain containing" 5440 protein-coding gene gene with protein product 147569 IFNGT1 NA 3136170 Standard NM_005534 NA Approved AF-1 uc002yrp.4 P38484 OTTHUMG00000065188 ENST00000290219.6:c.514delT chr21.hg19:g.34799292delT ENSP00000290219:p.Phe173fs 6 9 ref NA False 114 113 PASS 7 PASS ref->het 0 NA 191,193 53,53 36,34 1 1 Q9BTL5 True hg19 CCDS33544.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IFNGR2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000139916.1 PASS NA None 278 True + T ENST00000290219.6 RUNX1 861 __UNKNOWN__ __UNKNOWN__ 21 36170259 36170259 __UNKNOWN__ Intron DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:36170259delC ENST00000300305.3 - 7 1412 RUNX1_ENST00000437180.1_Intron|RUNX1_ENST00000399240.1_Intron|RUNX1_ENST00000325074.5_Intron|RUNX1_ENST00000344691.4_Intron Q01196 RUNX1_HUMAN runt-related transcription factor 1 NA NA NA behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351) basement membrane (GO:0005604)|nucleus (GO:0005634) ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134) breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 452 tcaggacagaccccccccaac 0.468 NA NA T "RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4" "AML, preB- ALL, T-ALL" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 21 21q22.3 861 runt-related transcription factor 1 (AML1) NA L 0 129 136.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.1 X79549 CCDS13639.1, CCDS42922.1, CCDS46646.1 21q22.3 2014-09-17 2008-07-29 ENSG00000159216 ENSG00000159216 861 10471 protein-coding gene gene with protein product "aml1 oncogene" 151385 "acute myeloid leukemia 1" AML1, CBFA2 NA 1427868, 7835892 Standard NM_001001890 NA Approved PEBP2A2, AMLCR1 uc010gmv.3 Q01196 OTTHUMG00000086299 ENST00000300305.3:c.967+1338G>- chr21.hg19:g.36170259delC 7 8 ref NA False 48 48 PASS 8 PASS ref->het 0 NA 63,64 37,37 29,28 1 1 A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479 True hg19 CCDS13639.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RUNX1-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000194231.1 PASS NA None 129 True - C ENST00000300305.3 TSPEAR 54084 __UNKNOWN__ __UNKNOWN__ 21 45987773 45987773 __UNKNOWN__ 5'UTR DEL G G - rs587631627 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:45987773delG ENST00000397916.1 - 0 153 TSPEAR_ENST00000323084.4_Frame_Shift_Del_p.R67fs Q8WU66 TSEAR_HUMAN thrombospondin-type laminin G domain and EAR repeats NA NA NA sensory perception of sound (GO:0007605) cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420) breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2) 37 CTCATGGTGCGGGGGGCGGCT 0.562 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 263 259.49 NA NA 65 66 66 NA NA NA 21 NA NA NA 45987773 2203 4300 6503 SO:0001623 5_prime_UTR_variant 1.49 AJ487962 CCDS13712.1, CCDS74801.1 21q22.3 2012-10-30 2011-01-25 2011-01-25 ENSG00000175894 ENSG00000175894 54084 1268 protein-coding gene gene with protein product 612920 "chromosome 21 open reading frame 29", "deafness, autosomal recessive 98" C21orf29, DFNB98 NA 12095917, 22678063 Standard NM_144991 NM_144991 NA Approved MGC11251, TSP-EAR uc002zfe.1 Q8WU66 OTTHUMG00000041215 ENST00000397916.1:c.-6C>- chr21.hg19:g.45987773delG 5 8 ref NA False 104 97 PASS 6 PASS ref->het 0 NA 148,152 87,87 28,24 2 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TSPEAR-002 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000195865.1 PASS NA None 263 True - G ENST00000397916.1 S100B 6285 __UNKNOWN__ __UNKNOWN__ 21 48019047 48019047 __UNKNOWN__ 3'UTR DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:48019047delG ENST00000367071.4 - 0 798 S100B_ENST00000291700.4_3'UTR P04271 S100B_HUMAN S100 calcium binding protein B NA NA NA astrocyte differentiation (GO:0048708)|axonogenesis (GO:0007409)|cell proliferation (GO:0008283)|cellular response to hypoxia (GO:0071456)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of cell shape (GO:0008360)|regulation of neuronal synaptic plasticity (GO:0048168)|response to glucocorticoid (GO:0051384)|response to methylmercury (GO:0051597) cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726) calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RAGE receptor binding (GO:0050786)|S100 protein binding (GO:0044548)|tau protein binding (GO:0048156)|zinc ion binding (GO:0008270) endometrium(1)|large_intestine(2)|lung(1)|skin(1) 5 Breast(49;0.247) Lung NSC(3;0.245) OV - Ovarian serous cystadenocarcinoma(3;1.84e-06)|Epithelial(3;4.45e-06)|all cancers(3;2.07e-05)|Colorectal(79;0.241) Olopatadine(DB00768) AAGAGTCCCTGGGGCCAGTCA 0.493 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 105 97.61 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 M59488 CCDS13736.1 21q22.3 2013-01-10 2006-09-11 ENSG00000160307 ENSG00000160307 6285 "S100 calcium binding proteins", "EF-hand domain containing" 10500 protein-coding gene gene with protein product 176990 "S100 calcium binding protein, beta (neural)" NA 2394738, 1998503 Standard NM_006272 NM_006272 NA Approved S100beta uc002zju.1 P04271 OTTHUMG00000090715 ENST00000367071.4:c.*317C>- chr21.hg19:g.48019047delG 3 4 ref NA False 55 55 PASS 4 PASS ref->het 0 NA 61,63 33,33 14,12 1 1 D3DSN6 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA S100B-002 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000207428.1 PASS NA None 105 True - G ENST00000367071.4 UBE2L3 7332 __UNKNOWN__ __UNKNOWN__ 22 21977187 21977187 __UNKNOWN__ 3'UTR DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:21977187delT ENST00000342192.4 + 0 1892 NM_003347.3 NP_003338.1 P68036 UB2L3_HUMAN ubiquitin-conjugating enzyme E2L 3 NA NA NA cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein K11-linked ubiquitination (GO:0070979)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151) acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)|ubiquitin-protein transferase activity (GO:0004842) UBE2L3/KRAS(2) large_intestine(4) 4 Colorectal(54;0.105) TTTGACTGCCTTTTTTTGTAG 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 132 143.62 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.93 AJ000519 CCDS13790.1, CCDS58795.1, CCDS58796.1 22q11.2 2007-02-05 ENSG00000185651 ENSG00000185651 7332 "Ubiquitin-conjugating enzymes E2" 12488 protein-coding gene gene with protein product 603721 NA 8672131, 9693040 Standard NM_198157 NM_001256356 NA Approved UBCH7 uc031rxe.1 P68036 OTTHUMG00000150823 ENST00000342192.4:c.*1229T>- chr22.hg19:g.21977187delT 6 8 ref NA False 35 35 PASS 7 PASS ref->het 0 NA 87,89 27,28 18,15 1 1 B2R4A7|B4DDG1|B4DSZ4|E7EWS7|P51966|P70653|Q9HAV1 True hg19 CCDS13790.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UBE2L3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000320219.1 PASS NA None 132 True + T ENST00000342192.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 22 22584300 22584301 __UNKNOWN__ IGR INS - - A rs34937605|rs567095191|rs386394996 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:22584300_22584301insA NA IGLV10-54 (14640 upstream) : VPREB1 (14785 downstream) NA NA NA NA CATTTGTAAGTAAGCATCCTTG 0.421 NA NA NA aaa|AA|AAA|deletion 2504 0.5 0.5469 0.4424 5008 , , NA 18421 0.4425 NA 0.3698 False NA ,,, NA NA NA 2504 0.6708 NA NA NA PASS NA NA NA 0 72 66.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr22.hg19:g.22584302_22584302dupA 3 2 ref NA False 38 37 PASS 2 PASS ref->het 0 NA 5,5 58,59 8,7 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 72 True A GUCD1 83606 __UNKNOWN__ __UNKNOWN__ 22 24937927 24937928 __UNKNOWN__ 3'UTR INS - - A LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:24937927_24937928insA ENST00000407471.3 - 0 1959_1960 GUCD1_ENST00000490922.1_Intron|GUCD1_ENST00000435822.1_3'UTR NM_001284251.1 NP_001271180.1 Q96NT3 GUCD1_HUMAN guanylyl cyclase domain containing 1 NA NA NA NA CCAACCTCCCCAAAAAAGAGGA 0.431 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 74 71.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AK054681 CCDS33621.1, CCDS63426.1, CCDS63427.1, CCDS74831.1, CCDS74832.1, CCDS74833.1 22q11.2 2012-11-13 2012-11-13 2012-11-13 ENSG00000138867 ENSG00000138867 83606 14237 protein-coding gene gene with protein product NA "chromosome 22 open reading frame 13" C22orf13 NA 12477932 Standard NM_031444 XM_005261761 NA Approved MGC1842, LLN4 uc003aah.2 Q96NT3 OTTHUMG00000150728 ENST00000407471.3:c.*1047->T chr22.hg19:g.24937933_24937933dupA 7 7 ref NA False 48 48 PASS 6 PASS ref->het 0 NA 41,41 19,20 14,14 1 1 B5MCB8|B5MCL7|Q96Q79|Q9BU32 True hg19 CCDS33621.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GUCD1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000319819.1 PASS NA None 74 True - A ENST00000407471.3 SEC14L3 266629 __UNKNOWN__ __UNKNOWN__ 22 30867267 30867268 __UNKNOWN__ Intron INS - - A LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:30867267_30867268insA ENST00000215812.4 - 1 145 SEC14L3_ENST00000403066.1_Intron|SEC14L3_ENST00000402286.1_Intron|SEC14L3_ENST00000401751.1_Intron|SEC14L3_ENST00000539629.1_Intron NM_174975.4 NP_777635.1 Q9UDX4 S14L3_HUMAN SEC14-like 3 (S. cerevisiae) NA NA NA extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622) lipid binding (GO:0008289)|transporter activity (GO:0005215) NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1) 19 Vitamin E(DB00163) gactccatctcaaaaaaaagaa 0.465 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(108;290 1516 3584 23771 37333) PASS NA NA NA 0 52 49.83 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.39 AY158086 CCDS13877.1, CCDS58800.1, CCDS58801.1 22q12.2 2013-09-23 ENSG00000100012 ENSG00000100012 266629 18655 protein-coding gene gene with protein product 612824 NA Standard NM_174975 NM_174975 NA Approved TAP2 uc003ahy.3 Q9UDX4 OTTHUMG00000151259 ENST00000215812.4:c.54+623->T chr22.hg19:g.30867275_30867275dupA 9 10 ref NA False 54 54 PASS 8 PASS ref->het 0 NA 30,30 17,17 5,5 1 1 E7EN74|E9PE57|Q495V8|Q495W0|Q495W1 True hg19 CCDS13877.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SEC14L3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000321950.4 PASS NA None 52 True - A ENST00000215812.4 SMTN 6525 __UNKNOWN__ __UNKNOWN__ 22 31485922 31485922 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:31485922delC ENST00000358743.1 + 7 927 c.709delC c.(709-711)cccfs p.P238fs SMTN_ENST00000333137.7_Frame_Shift_Del_p.P238fs|SMTN_ENST00000347557.2_Frame_Shift_Del_p.P238fs NM_134270.2 NP_599032.2 P53814 SMTN_HUMAN smoothelin 238 Pro-rich. NA NA muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939) actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634) actin binding (GO:0003779)|structural constituent of muscle (GO:0008307) breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3) 25 CCCAGAGCCACCCCCCAGCCC 0.652 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 97 110.92 NA NA 30 30 30 NA NA NA 22 NA NA NA 31485922 2197 4298 6495 SO:0001589 frameshift_variant 0.36 AY061972 CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1 22q12 2006-01-27 ENSG00000183963 ENSG00000183963 6525 11126 protein-coding gene gene with protein product 602127 NA 9244445, 8707825 Standard NM_134270 NM_006932 NA Approved uc011ale.2 P53814 OTTHUMG00000151203 ENST00000358743.1:c.709delC chr22.hg19:g.31485922delC ENSP00000351593:p.Pro238fs 5 8 ref NA False 103 101 PASS 6 PASS ref->het 0 NA 53,55 28,29 17,16 1 1 O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2 True hg19 CCDS13887.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SMTN-003 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000321768.1 PASS NA None 97 True + C ENST00000358743.1 APOL3 80833 __UNKNOWN__ __UNKNOWN__ 22 36546032 36546033 __UNKNOWN__ Intron INS - - T rs187435085|rs200989786 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:36546032_36546033insT ENST00000349314.2 - 2 261 APOL3_ENST00000361710.2_Intron|APOL3_ENST00000424878.2_Intron|APOL3_ENST00000397287.2_Intron|APOL3_ENST00000397293.2_Intron|APOL3_ENST00000487423.1_Intron NM_145640.2 NP_663615.1 O95236 APOL3_HUMAN apolipoprotein L, 3 NA NA NA inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165) cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020) lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|signal transducer activity (GO:0004871) endometrium(2)|large_intestine(1)|lung(1)|stomach(1) 5 ttaaaaaaaaattttttttaga 0.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 89 86.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF305227 CCDS13922.1, CCDS13924.1 22q13.1 2013-01-24 ENSG00000128284 ENSG00000128284 80833 "Apolipoproteins" 14868 protein-coding gene gene with protein product 607253 NA 11374903 Standard NM_145641 NM_145640 NA Approved CG12-1, APOLIII uc003aot.3 O95236 OTTHUMG00000150632 ENST00000349314.2:c.224-4385->A chr22.hg19:g.36546040_36546040dupT 9 9 ref NA False 66 66 PASS 8 PASS ref->het 0 NA 42,42 24,25 22,21 1 1 B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3 True hg19 CCDS13922.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA APOL3-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000319268.1 PASS NA None 89 True - T ENST00000349314.2 ELFN2 114794 __UNKNOWN__ __UNKNOWN__ 22 37769104 37769104 __UNKNOWN__ 3'UTR DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:37769104delG ENST00000402918.2 - 0 3256 RP1-63G5.5_ENST00000430883.1_RNA NM_052906.3 NP_443138.2 Q5R3F8 PPR29_HUMAN extracellular leucine-rich repeat and fibronectin type III domain containing 2 NA NA NA negative regulation of phosphatase activity (GO:0010923) extracellular space (GO:0005615)|integral component of membrane (GO:0016021) phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864) NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1) 35 Melanoma(58;0.0574) CAGGGAGGAAGGGGGGGGTCA 0.667 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 149 151.85 NA NA 35 34 34 NA NA NA 22 NA NA NA 37769104 2203 4299 6502 SO:0001624 3_prime_UTR_variant 0.46 BC041596 CCDS33642.1 22q13.1 2013-02-11 2011-10-27 2011-10-27 ENSG00000166897 ENSG00000166897 114794 "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Fibronectin type III domain containing" 29396 protein-coding gene gene with protein product NA "leucine rich repeat containing 62", "extracellular leucine-rich repeat and fibronectin type III containing 2", "extracellular leucine-rich repeat and fibronectin type III domain containing 2", "protein phosphatase 1, regulatory subunit 29" LRRC62, PPP1R29 NA 17868438 Standard NM_052906 XR_244427 NA Approved dJ63G5.3, KIAA1904 uc003asq.4 Q5R3F8 OTTHUMG00000150558 ENST00000402918.2:c.*8C>- chr22.hg19:g.37769104delG 7 8 ref NA False 38 38 PASS 8 PASS ref->het 0 NA 82,85 38,39 30,27 1 1 Q96PY3 True hg19 CCDS33642.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ELFN2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000318900.2 PASS NA None 149 True - G ENST00000402918.2 RANGAP1 5905 __UNKNOWN__ __UNKNOWN__ 22 41650190 41650190 __UNKNOWN__ Intron DEL C C - rs7364221|rs113585453 byFrequency LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:41650190delC ENST00000455915.2 - 10 2730 RANGAP1_ENST00000407260.4_Intron|RANGAP1_ENST00000405486.1_Intron|RANGAP1_ENST00000356244.3_Intron P46060 RAGP1_HUMAN Ran GTPase activating protein 1 NA NA NA mitotic cell cycle (GO:0000278)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear pore (GO:0005643)|perinuclear region of cytoplasm (GO:0048471) Ran GTPase activator activity (GO:0005098) breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1) 19 ATCATGCAATCAAAAAAAAAT 0.393 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 111 119.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.38 X82260 CCDS14012.1 22q13 2013-01-17 ENSG00000100401 ENSG00000100401 5905 9854 protein-coding gene gene with protein product 602362 "segregation distorter homolog (Drosophila)" SD NA 7878053 Standard NM_002883 NM_002883 NA Approved Fug1, KIAA1835 uc003azu.3 P46060 OTTHUMG00000150940 ENST00000455915.2:c.1260+121G>- chr22.hg19:g.41650190delC 0 9 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 51,56 41,43 24,18 1 1 Q96JJ2 True hg19 CCDS14012.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RANGAP1-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000320606.1 PASS NA None 111 True - C ENST00000455915.2 MAPK8IP2 23542 __UNKNOWN__ __UNKNOWN__ 22 51049832 51049832 __UNKNOWN__ 3'UTR DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:51049832delG ENST00000399908.2 + 0 3018 MAPK8IP2_ENST00000329492.3_3'UTR|MAPK8IP2_ENST00000341339.4_3'UTR|MAPK8IP2_ENST00000008876.5_3'UTR|MAPK8IP2_ENST00000442429.2_3'UTR|MAPK8IP2_ENST00000399912.1_3'UTR NM_016431.3 NP_057515.1 Q13387 JIP2_HUMAN mitogen-activated protein kinase 8 interacting protein 2 NA NA NA behavioral fear response (GO:0001662)|dendrite morphogenesis (GO:0048813)|MAPK cascade (GO:0000165)|nonassociative learning (GO:0046958)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of signal transduction (GO:0009967)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of JNK cascade (GO:0046328)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of receptor activity (GO:0010469)|regulation of synaptic transmission, glutamatergic (GO:0051966)|signal complex assembly (GO:0007172)|social behavior (GO:0035176) cytoplasm (GO:0005737)|neuronal postsynaptic density (GO:0097481) beta-amyloid binding (GO:0001540)|kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198) central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2) 7 all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) OV - Ovarian serous cystadenocarcinoma(4;1.28e-70)|Epithelial(4;3.46e-65)|GBM - Glioblastoma multiforme(4;4.83e-06)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) GCTGCTAGGAGGGGGGGCCCT 0.662 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 118 110.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.49 AL021708 CCDS74886.1 22q13.33 2010-04-06 ENSG00000008735 ENSG00000008735 23542 6883 protein-coding gene gene with protein product "islet-brain 2", "JNK-interacting protein 2" 607755 "PRKM8 interacting protein-like" PRKM8IPL NA 10490659 Standard NM_012324 NM_012324 NA Approved IB2, JIP2 uc003bmy.3 Q13387 OTTHUMG00000150181 ENST00000399908.2:c.*625G>- chr22.hg19:g.51049832delG 6 9 ref NA False 95 94 PASS 7 PASS ref->het 0 NA 63,64 34,37 23,19 1 1 Q96G62|Q99771|Q9NZ59|Q9UKQ4 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAPK8IP2-002 KNOWN basic protein_coding NA protein_coding OTTHUMT00000316731.2 PASS NA None 118 True + G ENST00000399908.2 TAB3 257397 __UNKNOWN__ __UNKNOWN__ X 30845957 30845957 __UNKNOWN__ 3'UTR DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:30845957delA ENST00000378933.1 - 0 5903 TAB3_ENST00000378930.3_3'UTR NM_152787.3 NP_690000.2 Q8N5C8 TAB3_HUMAN TGF-beta activated kinase 1/MAP3K7 binding protein 3 NA NA NA activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666) cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886) zinc ion binding (GO:0008270) NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1) 27 ATAATACAGGAAAAAAAGTCT 0.328 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(164;1598 1985 29022 43301 49529) PASS NA NA NA 0 77 75.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.27 AY331591 CCDS14226.1 Xp21.2 2010-02-05 2010-02-05 2010-02-05 ENSG00000157625 ENSG00000157625 257397 30681 protein-coding gene gene with protein product "TAK1 binding protein 3" 300480 "mitogen-activated protein kinase kinase kinase 7 interacting protein 3" MAP3K7IP3 NA 14633987, 14670075 Standard NM_152787 XM_005274482 NA Approved uc004dcj.3 Q8N5C8 OTTHUMG00000021329 ENST00000378933.1:c.*3587T>- chrX.hg19:g.30845957delA 6 7 ref NA False 55 55 PASS 7 PASS ref->het 0 NA 32,32 30,30 13,13 1 1 A6NDD9|Q6VQR0 True hg19 CCDS14226.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TAB3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000056173.1 PASS NA None 77 True - A ENST00000378933.1 SYN1 6853 __UNKNOWN__ __UNKNOWN__ X 47446861 47446861 __UNKNOWN__ Intron DEL A A - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:47446861delA ENST00000295987.7 - 6 899 MIR4769_ENST00000584126.1_RNA|SYN1_ENST00000340666.4_Intron NM_006950.3 NP_008881.2 P17600 SYN1_HUMAN synapsin I NA NA NA neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268) cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021) ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215) breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1) 21 GGTATGAGCTAAAAATCCCCA 0.552 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 124 116.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.4 CCDS14280.1, CCDS35233.1 Xp11.2 2012-10-02 ENSG00000008056 ENSG00000008056 6853 11494 protein-coding gene gene with protein product 313440 NA Standard NM_006950 NM_133499 NA Approved uc004die.3 P17600 OTTHUMG00000021454 ENST00000295987.7:c.775-9961T>- chrX.hg19:g.47446861delA 4 5 ref NA False 44 44 PASS 5 PASS ref->het 0 NA 78,78 34,35 11,10 1 1 B1AJQ1|O75825|Q5H9A9 True hg19 CCDS14280.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SYN1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000056445.1 PASS NA None 124 True - A ENST00000295987.7 AF196779.12 0 __UNKNOWN__ __UNKNOWN__ X 48932580 48932580 __UNKNOWN__ Intron DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:48932580delG ENST00000376358.3 - 6 675 WDR45_ENST00000553851.1_Intron|WDR45_ENST00000356463.3_Intron|WDR45_ENST00000396681.4_Intron|WDR45_ENST00000322995.8_Intron|WDR45_ENST00000473974.1_Intron|WDR45_ENST00000376368.2_Intron|WDR45_ENST00000485908.1_Intron|WDR45_ENST00000376372.3_Intron NA NA NA NA GGCTGGGGGAGGGGGGGTGGT 0.567 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 135 126.1 NA NA 34 36 35 NA NA NA X NA NA NA 48932580 2203 4300 6503 SO:0001627 intron_variant 0.41 NA NA NA NA NA ENST00000376358.3:c.521+442C>- chrX.hg19:g.48932580delG 6 12 ref NA False 75 75 PASS 7 PASS ref->het 0 NA 66,71 34,35 36,30 2 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AF196779.12-001 PUTATIVE basic|appris_principal|readthrough_transcript protein_coding NA protein_coding OTTHUMT00000367506.1 PASS NA None 135 True - G ENST00000376358.3 TAF9B 51616 __UNKNOWN__ __UNKNOWN__ X 77385903 77385905 __UNKNOWN__ 3'UTR DEL TAT TAT - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:77385903_77385905delTAT ENST00000341864.5 - 0 2052_2054 NM_015975.4 NP_057059.2 Q9HBM6 TAF9B_HUMAN TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa NA NA NA DNA-templated transcription, initiation (GO:0006352)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell growth (GO:0030307)|programmed cell death (GO:0012501)|protein stabilization (GO:0050821)|response to organic cyclic compound (GO:0014070) transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276) transcription corepressor activity (GO:0003714) central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1) 14 AACATTACAGTATTATTGGGAAA 0.345 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 103 103.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF220509 CCDS35340.1 Xq13.1-q21.1 2010-08-16 2006-01-04 2006-01-04 ENSG00000187325 ENSG00000187325 51616 17306 protein-coding gene gene with protein product 300754 "TAF9-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa" TAF9L NA 15899866 Standard NM_015975 XM_005262142 NA Approved TAFII31L, DN-7, DN7, TFIID-31 uc004eda.3 Q9HBM6 OTTHUMG00000021887 ENST00000341864.5:c.*1204ATA>- chrX.hg19:g.77385906_77385908delTAT 1 4 ref NA False 38 38 PASS 2 PASS ref->het 0 NA 60,60 36,36 8,8 1 1 B2RUZ9|Q9Y2S3 True hg19 CCDS35340.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TAF9B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000057308.1 PASS NA None 103 True - TAT ENST00000341864.5 ARMCX4 100131755 __UNKNOWN__ __UNKNOWN__ X 100747237 100747237 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:100747237delG ENST00000423738.3 + 2 3863 c.3661delG c.(3661-3663)gggfs p.G1222fs NM_001256155.1 NP_001243084.1 Q5H9R4 ARMX4_HUMAN armadillo repeat containing, X-linked 4 0 NA NA integral component of membrane (GO:0016021) lung(1) 1 CCAGGCCAGTGGGGGGTCTTG 0.672 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 111 116.04 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.01 AK096955 CCDS59170.1 Xq22 2014-03-21 2009-11-26 ENSG00000196440 ENSG00000196440 100131755 "Armadillo repeat containing" 28615 protein-coding gene gene with protein product NA "chromosome X open reading frame 35", "armadillo repeat containing, X-linked 4 pseudogene" CXorf35 NA 16221301, 22569362 Standard NM_001256155 NR_028407 NA Approved MGC40053, GASP4 uc031tkc.1 Q5H9R4 OTTHUMG00000022030 ENST00000423738.3:c.3661delG chrX.hg19:g.100747237delG ENSP00000404304:p.Gly1222fs 5 7 ref NA False 88 87 PASS 6 PASS ref->het 0 NA 68,70 34,34 12,12 1 1 A8K928|B3KXA4|Q5H9K8|Q8N8D6 True hg19 CCDS59170.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARMCX4-010 PUTATIVE upstream_ATG|upstream_uORF|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000370455.2 PASS NA None 111 True + G ENST00000423738.3 UTP14A 10813 __UNKNOWN__ __UNKNOWN__ X 129058758 129058758 __UNKNOWN__ Intron DEL T T - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:129058758delT ENST00000394422.3 + 12 1376 UTP14A_ENST00000371042.3_Intron|UTP14A_ENST00000371051.5_Intron|RP4-537K23.4_ENST00000432062.1_RNA|UTP14A_ENST00000425117.2_Intron NM_006649.3 NP_006640.2 Q9BVJ6 UT14A_HUMAN UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast) NA NA NA rRNA processing (GO:0006364) nucleus (GO:0005634)|small-subunit processome (GO:0032040) poly(A) RNA binding (GO:0044822) breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(16)|ovary(3)|urinary_tract(1) 32 GTTTTCATTCTTTTTTCCCCC 0.423 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 290 266 NA NA 137 147 144 NA NA NA X NA NA NA 129058758 2200 4295 6495 SO:0001627 intron_variant 1.02 AF039694 CCDS14615.1, CCDS55489.1 Xq26.1 2009-01-15 2004-06-01 2004-06-01 ENSG00000156697 ENSG00000156697 10813 10665 protein-coding gene gene with protein product 300508 "serologically defined colon cancer antigen 16" SDCCAG16 NA 9610721, 16354793 Standard NM_006649 NM_006649 NA Approved NY-CO-16 uc004euz.3 Q9BVJ6 OTTHUMG00000022378 ENST00000394422.3:c.1349-13T>- chrX.hg19:g.129058758delT 5 8 ref NA False 134 123 PASS 6 PASS ref->het 0 NA 188,189 72,72 30,29 1 1 A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1 True hg19 CCDS14615.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UTP14A-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000058221.1 PASS NA None 290 True + T ENST00000394422.3 GPR112 139378 __UNKNOWN__ __UNKNOWN__ X 135431423 135431425 __UNKNOWN__ In_Frame_Del DEL CTC CTC - rs371035719 LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:135431423_135431425delCTC ENST00000394143.1 + 6 5849_5851 c.5558_5560delCTC c.(5557-5562)tctcct>tct p.P1856del GPR112_ENST00000287534.4_In_Frame_Del_p.P1793del|GPR112_ENST00000412101.1_In_Frame_Del_p.P1651del|GPR112_ENST00000370652.1_In_Frame_Del_p.P1856del|GPR112_ENST00000394141.1_In_Frame_Del_p.P1651del NM_153834.3 NP_722576.3 Q8IZF6 GP112_HUMAN G protein-coupled receptor 112 1856 NA NA G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) G-protein coupled receptor activity (GO:0004930) NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2) 199 Acute lymphoblastic leukemia(192;0.000127) CCAAAGACCTCTCCTCCTCCCAC 0.453 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 330 348.05 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.29 AY140954 CCDS35409.1 Xq26.3 2014-08-08 ENSG00000156920 ENSG00000156920 139378 "-", "GPCR / Class B : Orphans" 18992 protein-coding gene gene with protein product NA NA 12435584 Standard XM_005262367 NA Approved RP1-299I16, PGR17 uc004ezu.1 Q8IZF6 OTTHUMG00000022508 ENST00000394143.1:c.5558_5560delCTC chrX.hg19:g.135431429_135431431delCTC ENSP00000377699:p.Pro1856del 2 4 ref NA False 119 105 PASS 3 PASS ref->het 0 NA 206,206 92,92 31,31 1 1 A2A2J1|A2A2J2|Q5EGP2|Q86SM6 True hg19 CCDS35409.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GPR112-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000286639.1 PASS NA None 330 True + CTC ENST00000394143.1 MCF2 4168 __UNKNOWN__ __UNKNOWN__ X 138678778 138678779 __UNKNOWN__ Frame_Shift_Ins INS - - A LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:138678778_138678779insA ENST00000519895.1 - 23 2599_2600 c.2434_2435insT c.(2434-2436)tgcfs p.C812fs MCF2_ENST00000338585.6_Frame_Shift_Ins_p.C752fs|MCF2_ENST00000370576.4_Frame_Shift_Ins_p.C736fs|MCF2_ENST00000536274.1_Frame_Shift_Ins_p.C697fs|MCF2_ENST00000370573.4_Frame_Shift_Ins_p.C736fs|MCF2_ENST00000370578.4_Frame_Shift_Ins_p.C881fs|MCF2_ENST00000520602.1_Frame_Shift_Ins_p.C796fs|MCF2_ENST00000414978.1_Frame_Shift_Ins_p.C796fs NM_001171876.1 NP_001165347.1 P10911 MCF2_HUMAN MCF.2 cell line derived transforming sequence 736 NA NA apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264) cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020) Rho guanyl-nucleotide exchange factor activity (GO:0005089) NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1) 62 Acute lymphoblastic leukemia(192;0.000127) ACGCCTTTTGCAAAAAACAATG 0.391 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 262 260.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.39 CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1 Xq26.3-q27.1 2012-07-24 ENSG00000101977 ENSG00000101977 4168 "Rho guanine nucleotide exchange factors" 6940 protein-coding gene gene with protein product "Oncogene MCF2 (oncogene DBL)" 311030 NA 2577874, 1611909 Standard NM_005369 NM_001099855 NA Approved DBL, ARHGEF21 uc011mwo.1 P10911 OTTHUMG00000022537 ENST00000519895.1:c.2435dupT chrX.hg19:g.138678784_138678784dupA ENSP00000430276:p.Cys812fs 7 8 ref NA False 49 49 PASS 6 PASS ref->het 0 NA 215,217 27,28 19,16 1 1 B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3 True hg19 CCDS55517.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MCF2-008 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000377602.1 PASS NA None 262 True - A ENST00000519895.1 LDOC1 23641 __UNKNOWN__ __UNKNOWN__ X 140271045 140271045 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-017_T LTS-017_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:140271045delG ENST00000370526.2 - 1 265 c.162delC c.(160-162)cccfs p.P54fs LDOC1_ENST00000460721.1_Intron NM_012317.2 NP_036449.1 O95751 LDOC1_HUMAN leucine zipper, down-regulated in cancer 1 54 NA NA negative regulation of cell proliferation (GO:0008285) nucleus (GO:0005634) endometrium(6)|large_intestine(1)|lung(6)|ovary(1) 14 Acute lymphoblastic leukemia(192;7.65e-05) TAAACGTTTCGGGGAAGGGCA 0.622 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 141 156.91 NA NA 39 36 37 NA NA NA X NA NA NA 140271045 2203 4300 6503 SO:0001589 frameshift_variant 0.54 AB019527 CCDS14672.1 Xq27 2008-02-05 ENSG00000182195 ENSG00000182195 23641 6548 protein-coding gene gene with protein product 300402 BCUR1 NA 10403563, 15716091, 16093683 Standard NM_012317 NM_012317 NA Approved Mar7, Mart7 uc004fbj.3 O95751 OTTHUMG00000022558 ENST00000370526.2:c.162delC chrX.hg19:g.140271045delG ENSP00000359557:p.Pro54fs 3 4 ref NA False 118 111 PASS 4 PASS ref->het 0 NA 81,81 41,43 16,14 1 1 Q6IAR6 True hg19 CCDS14672.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LDOC1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000058592.1 PASS NA None 141 True - G ENST00000370526.2 SMG5 23381 __UNKNOWN__ __UNKNOWN__ 1 156247666 156247667 __UNKNOWN__ Intron DEL TG TG - LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:156247666_156247667delTG ENST00000361813.5 - 3 442 NA NA NA SMG5_ENST00000368267.5_Intron NM_015327.2 NP_056142.2 Q9UPR3 SMG5_HUMAN SMG5 nonsense mediated mRNA decay factor NA NA NA NA NA gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070) cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634) protein phosphatase 2A binding (GO:0051721) NA NS(1)|breast(3)|endometrium(8)|kidney(2)|large_intestine(7)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1) 48 Hepatocellular(266;0.158) CTTTCCTAGCTGTCTCTTCCTT 0.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 563 532.93 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.14 NA NA AB029012 CCDS1137.1 1q21 2013-07-02 2013-07-02 ENSG00000198952 ENSG00000198952 23381 NA 24644 protein-coding gene gene with protein product "EST1 telomerase component homolog B (S. cerevisiae)" 610962 "smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)" NA 12676087, 12699629 Standard NM_015327 NM_015327 NA Approved KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5, EST1B uc001foc.4 Q9UPR3 OTTHUMG00000017491 ENST00000361813.5:c.297+48CA>- chr1.hg19:g.156247666_156247667delTG NA 0 2 ref NA False 92 92 PASS 1 PASS ref->het 0 NA 440,444 88,88 40,38 1 1 D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7 True hg19 CCDS1137.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SMG5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000046308.1 PASS NA None 563 NA True - TG ENST00000361813.5 ZFP36L2 678 __UNKNOWN__ __UNKNOWN__ 2 43453563 43453564 __UNKNOWN__ 5'UTR INS - - G rs186704920 byFrequency LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:43453563_43453564insG ENST00000282388.3 - 0 184_185 NA NA NA THADA_ENST00000330266.7_Intron NM_006887.4 NP_008818.3 P47974 TISD_HUMAN ZFP36 ring finger protein-like 2 NA NA NA NA NA cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077) cytoplasm (GO:0005737)|nucleus (GO:0005634) AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1) 15 Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824) AGGGGCGGGGAGGGGCCGAAAG 0.757 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 37 41.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.57 NA NA X78992 CCDS1811.1 2p22.3-p21 2012-11-27 2012-11-27 2001-11-23 ENSG00000152518 ENSG00000152518 678 NA "RING-type (C3HC4) zinc fingers" 1108 protein-coding gene gene with protein product 612053 "zinc finger protein 36, C3H type-like 1", "zinc finger protein 36, C3H type-like 2" BRF2 NA 7835719, 8545129, 14981510, 17172869 Standard NM_006887 NM_006887 NA Approved ERF2, RNF162C, TIS11D uc002rsv.4 P47974 OTTHUMG00000128642 ENST00000282388.3:c.-110->C chr2.hg19:g.43453567_43453567dupG NA 5 8 ref NA False 30 30 PASS 4 PASS ref->het 0 NA 19,19 9,9 9,10 1 1 Q53TB4|Q9BSJ3 True hg19 CCDS1811.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZFP36L2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250513.2 PASS NA None 37 NA True - G ENST00000282388.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 26157347 26157348 __UNKNOWN__ IGR DEL CT CT - rs882792|rs375226891 LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:26157347_26157348delCT NA NA NA NA HIST1H1E (4 upstream) : HIST1H2BD (1000 downstream) NA NA NA NA NA NA NA CCACCCACCGCTCTCAGTAAAA 0.554 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 597 567.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.32 NA NA NA NA NA NA NA NA chr6.hg19:g.26157349_26157350delCT NA 1 3 ref NA False 516 222 PASS 2 PASS ref->het 0 NA 330,333 196,198 64,60 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 597 NA True CT PXDNL 137902 __UNKNOWN__ __UNKNOWN__ 8 52233299 52233300 __UNKNOWN__ Intron INS - - AGG rs3217441|rs57356169|rs201871468 byFrequency LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:52233299_52233300insAGG ENST00000356297.4 - 22 4361 NA NA NA RP11-401H2.1_ENST00000521294.1_RNA|PXDNL_ENST00000543296.1_Intron NM_144651.4 NP_653252 A1KZ92 PXDNL_HUMAN peroxidasin homolog (Drosophila)-like NA NA NA NA NA hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114) cytoplasm (GO:0005737)|extracellular space (GO:0005615) endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601) NA NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2) 48 all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015) ACTGGCTGGCTAGAAGTGAAAT 0.416 NA NA NA NA NA NA NA NA NA 2262 0.451677 0.8676 0.2795 5008 , , NA 18612 0.3294 NA 0.2803 False NA ,,, NA NA NA 2504 0.3139 NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 178 181.81 NA NA 2685,875 NA 1052,581,147 NA NA NA NA NA -1.9 0 NA dbSNP_106 51 2100,5732 NA 347,1406,2163 no intron PXDNL NM_144651.4 NA 1399,1987,2310 A1A1,A1R,RR NA 26.8131,24.5787,42.0032 NA NA NA 4785,6607 NA NA NA SO:0001627 intron_variant 4.33 NA NA CCDS47855.1 8q11.21-q11.22 2013-02-18 2007-01-12 ENSG00000147485 ENSG00000147485 137902 NA "Immunoglobulin superfamily / I-set domain containing" 26359 protein-coding gene gene with protein product "polysomal ribonuclease 1 homolog (Xenopus)" 615904 "peroxidasin homolog-like (Drosophila)" NA 22543864 Standard NM_144651 NM_144651 NA Approved FLJ25471, PMR1 uc003xqu.4 A1KZ92 OTTHUMG00000164244 ENST00000356297.4:c.4260+43->CCT chr8.hg19:g.52233299_52233300insAGG NA 1 3 ref NA False 33 33 PASS 0 PASS ref->het 0 NA 34,34 125,129 19,16 1 1 B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9 True hg19 CCDS47855.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PXDNL-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000377905.1 PASS NA None 178 NA True - AGG ENST00000356297.4 PXDNL 137902 __UNKNOWN__ __UNKNOWN__ 8 52233308 52233309 __UNKNOWN__ Intron INS - - AC rs376521581|rs372879555 byFrequency LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:52233308_52233309insAC ENST00000356297.4 - 22 4361 NA NA NA RP11-401H2.1_ENST00000521294.1_RNA|PXDNL_ENST00000543296.1_Intron NM_144651.4 NP_653252 A1KZ92 PXDNL_HUMAN peroxidasin homolog (Drosophila)-like NA NA NA NA NA hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114) cytoplasm (GO:0005737)|extracellular space (GO:0005615) endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601) NA NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2) 48 all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015) CTAGAAGTGAAATGGGGAGTTG 0.416 NA NA NA NA NA NA NA NA NA 1608 0.321086 0.6346 0.2291 5008 , , NA 18551 0.1429 NA 0.2386 False NA ,,, NA NA NA 2504 0.2311 NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 173 204.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 4.32 NA NA CCDS47855.1 8q11.21-q11.22 2013-02-18 2007-01-12 ENSG00000147485 ENSG00000147485 137902 NA "Immunoglobulin superfamily / I-set domain containing" 26359 protein-coding gene gene with protein product "polysomal ribonuclease 1 homolog (Xenopus)" 615904 "peroxidasin homolog-like (Drosophila)" NA 22543864 Standard NM_144651 NM_144651 NA Approved FLJ25471, PMR1 uc003xqu.4 A1KZ92 OTTHUMG00000164244 ENST00000356297.4:c.4260+34->GT chr8.hg19:g.52233308_52233309insAC NA 1 3 ref NA False 39 39 PASS 0 PASS ref->het 0 NA 36,36 128,131 7,5 1 1 B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9 True hg19 CCDS47855.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PXDNL-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000377905.1 PASS NA None 173 NA True - AC ENST00000356297.4 FREM1 158326 __UNKNOWN__ __UNKNOWN__ 9 14845934 14845935 __UNKNOWN__ Intron INS - - G LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:14845934_14845935insG ENST00000380880.3 - 8 2177 NA NA NA FREM1_ENST00000380881.4_Intron|FREM1_ENST00000422223.2_Intron Q5H8C1 FREM1_HUMAN FRAS1 related extracellular matrix 1 NA NA NA NA NA cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094) basement membrane (GO:0005604)|integral component of membrane (GO:0016021) carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872) NA breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1) 100 GBM - Glioblastoma multiforme(50;3.53e-06) ATTCTTTGCTAGGTTACCAAGT 0.411 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 195 176.83 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.1 NA NA AK058190 CCDS47952.1, CCDS55293.1 9p22.3 2010-06-04 2004-12-15 2004-12-15 ENSG00000164946 ENSG00000164946 158326 NA 23399 protein-coding gene gene with protein product 608944 "chromosome 9 open reading frame 154" C9orf154 NA 12838346, 15345741 Standard NM_144966 NM_144966 NA Approved FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR uc003zlm.3 Q5H8C1 OTTHUMG00000019575 ENST00000380880.3:c.1393+22->C chr9.hg19:g.14845936_14845936dupG NA 3 2 ref NA False 47 47 PASS 2 PASS ref->het 0 NA 124,124 44,44 25,25 1 1 B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3 True hg19 CCDS47952.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FREM1-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000339474.2 PASS NA None 195 NA True - G ENST00000380880.3 COL15A1 1306 __UNKNOWN__ __UNKNOWN__ 9 101706106 101706107 __UNKNOWN__ 5'UTR INS - - GCGCCGCCGCTGCCCGAGGTGGG rs58585775|rs146258595 byFrequency LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:101706106_101706107insGCGCCGCCGCTGCCCGAGGTGGG ENST00000375001.3 + 0 186_187 NA NA NA COL15A1_ENST00000467052.1_Intron NM_001855.3 NP_001846.3 P39059 COFA1_HUMAN collagen, type XV, alpha 1 NA NA NA NA NA angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165) collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021) extracellular matrix structural constituent (GO:0005201) NA NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1) 107 Acute lymphoblastic leukemia(62;0.0562) CGGGCGTGAGTGCGCAGCGCGC 0.802 NA NA NA NA NA NA NA NA NA 1124 0.224441 0.1604 0.2392 5008 , , NA 10047 0.2192 NA 0.2833 False NA ,,, NA NA NA 2504 0.2454 NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 24 33.93 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 NA NA L25286 CCDS35081.1 9q21-q22 2013-01-16 ENSG00000204291 ENSG00000204291 1306 NA "Proteoglycans / Extracellular Matrix : Collagen proteoglycans", "Collagens" 2192 protein-coding gene gene with protein product "collagen type XV proteoglycan" 120325 NA 1427836 Standard NM_001855 NM_001855 NA Approved uc004azb.2 P39059 OTTHUMG00000020351 ENST00000375001.3:c.-237->GCGCCGCCGCTGCCCGAGGTGGG chr9.hg19:g.101706106_101706107insGCGCCGCCGCTGCCCGAGGTGGG NA 1 2 ref NA False 48 48 PASS 0 PASS ref->het 0 NA 3,3 6,6 15,16 1 1 Q5T6J4|Q9UDC5|Q9Y4W4 True hg19 CCDS35081.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COL15A1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000053386.3 PASS NA None 24 NA True + GCGCCGCCGCTGCCCGAGGTGGG ENST00000375001.3 IGF1R 3480 __UNKNOWN__ __UNKNOWN__ 15 99506761 99506762 __UNKNOWN__ 3'UTR INS - - CGTTCGG LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:99506761_99506762insCGTTCGG ENST00000558762.1 + 0 10729_10730 NA NA NA RP11-654A16.3_ENST00000559468.1_RNA|IGF1R_ENST00000268035.6_3'UTR P08069 IGF1R_HUMAN insulin-like growth factor 1 receptor NA NA NA NA NA axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165) caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235) ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713) NA NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1) 63 all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163) Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261) """Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)" GTGCATGGCACCGTTCGGCATC 0.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 214 205.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.68 NA NA M69229 CCDS10378.1, CCDS73785.1 15q26.3 2013-02-11 ENSG00000140443 ENSG00000140443 3480 NA "CD molecules", "Fibronectin type III domain containing" 5465 protein-coding gene gene with protein product 147370 NA 1316909 Standard NM_000875 XM_006720486 NA Approved JTK13, CD221, IGFIR, MGC18216, IGFR uc002bul.3 P08069 OTTHUMG00000149851 ENST00000558762.1:c.*6091->CGTTCGG chr15.hg19:g.99506762_99506768dupCGTTCGG NA 2 3 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 161,164 15,15 37,34 1 1 B1B5Y2|Q14CV2|Q9UCC0 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IGF1R-002 NOVEL NAGNAG_splice_site|basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000415271.1 PASS NA None 214 NA True + CGTTCGG ENST00000558762.1 CIITA 4261 __UNKNOWN__ __UNKNOWN__ 16 11012270 11012271 __UNKNOWN__ Intron INS - - C LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:11012270_11012271insC ENST00000324288.8 + 16 3195 NA NA NA CIITA_ENST00000381835.5_Intron NM_000246.3 NP_000237 P33076 C2TA_HUMAN class II, major histocompatibility complex, transactivator NA NA NA NA NA aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351) cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605) activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746) NA central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2) 12 TTGGTCCTGAGCCCTCCCCCTC 0.569 NA NA TRUE "FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6" "PMBL, Hodgkin Lymphona, " NA NA NA NA NA OREG0023606 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Dom yes NA 16 16p13 4261 "class II, major histocompatibility complex, transactivator" NA L 0 NA NA NA NA NA NA NA 305 282.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.8 NA NA U18259 CCDS10544.1, CCDS66943.1, CCDS73826.1 16p13 2014-09-17 2005-08-12 2005-08-12 ENSG00000179583 ENSG00000179583 4261 NA "Nucleotide-binding domain and leucine rich repeat containing" 7067 protein-coding gene gene with protein product "NLR family, acid domain containing", "nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing" 600005 "MHC class II transactivator" MHC2TA NA 8402893 Standard NM_000246 NM_000246 NA Approved C2TA, NLRA uc002dai.4 P33076 OTTHUMG00000129753 ENST00000324288.8:c.3063-26->C chr16.hg19:g.11012273_11012273dupC NA 4 8 ref 669 False 284 144 PASS 3 PASS ref->het 0 NA 164,167 115,118 24,20 1 1 A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4 True hg19 CCDS10544.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CIITA-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251966.2 PASS NA None 305 NA True + C ENST00000324288.8 ASCC2 84164 __UNKNOWN__ __UNKNOWN__ 22 30223796 30223797 __UNKNOWN__ Intron INS - - CTC rs5844870|rs148580571 byFrequency LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:30223796_30223797insCTC ENST00000397771.2 - 4 259 NA NA NA ASCC2_ENST00000307790.3_Intron|ASCC2_ENST00000542393.1_Intron Q9H1I8 ASCC2_HUMAN activating signal cointegrator 1 complex subunit 2 NA NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) NA endometrium(3)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(1) 18 OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259) ggctactcattctgacacacac 0.495 NA NA NA NA NA NA NA NA NA 2651 0.529353 0.7171 0.4121 5008 , , NA 12278 0.6518 NA 0.5209 False NA ,,, NA NA NA 2504 0.2413 NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 30 28.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.45 NA NA AY013289 CCDS13869.1, CCDS56226.1 22q12.1 2004-07-27 ENSG00000100325 ENSG00000100325 84164 NA 24103 protein-coding gene gene with protein product "ASC 1 complex subunit P100" 614216 NA 12077347, 9847074 Standard NM_032204 NM_032204 NA Approved ASC1p100, FLJ21588, DKFZp586O0223 uc003agr.3 Q9H1I8 OTTHUMG00000067658 ENST00000397771.2:c.82-2027->GAG chr22.hg19:g.30223796_30223797insCTC NA 1 3 ref NA False 39 39 PASS 0 PASS ref->hom 0 NA 0,0 23,24 7,7 1 1 B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6 True hg19 CCDS13869.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ASCC2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000322127.1 PASS NA None 30 NA True - CTC ENST00000397771.2 PDGFB 5155 __UNKNOWN__ __UNKNOWN__ 22 39621582 39621597 __UNKNOWN__ Intron DEL GGACCAAGGCTCAGAG GGACCAAGGCTCAGAG - rs73163483|rs372771307|rs376341574 byFrequency LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:39621582_39621597delGGACCAAGGCTCAGAG ENST00000331163.6 - 6 1542 NA NA NA PDGFB_ENST00000381551.4_Intron NM_002608.2 NP_002599.1 P01127 PDGFB_HUMAN platelet-derived growth factor beta polypeptide NA NA NA NA NA actin cytoskeleton organization (GO:0030036)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|branching involved in salivary gland morphogenesis (GO:0060445)|cell chemotaxis (GO:0060326)|cell growth (GO:0016049)|cell projection assembly (GO:0030031)|cellular response to growth factor stimulus (GO:0071363)|cellular response to mycophenolic acid (GO:0071506)|DNA replication (GO:0006260)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|metanephric glomerular endothelium development (GO:0072264)|metanephric glomerular mesangial cell development (GO:0072255)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|monocyte chemotaxis (GO:0002548)|negative regulation of cell migration (GO:0030336)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|paracrine signaling (GO:0038001)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of DNA replication (GO:0045740)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of metanephric mesenchymal cell migration (GO:2000591)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to wounding (GO:0009611)|substrate-dependent cell migration (GO:0006929)|transforming growth factor beta receptor signaling pathway (GO:0007179) basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093) chemoattractant activity (GO:0042056)|collagen binding (GO:0005518)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|superoxide-generating NADPH oxidase activator activity (GO:0016176) NA COL1A1/PDGFB(429) central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2) 7 Melanoma(58;0.04) TGGACAGGGAGGACCAAGGCTCAGAGGCTGGATTTT 0.574 NA NA TRUE COL1A1 DFSP NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Dom yes NA 22 22q12.3-q13.1 5155 platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog) NA M 0 NA NA NA NA NA NA NA 139 158.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.13 NA NA CCDS13987.1, CCDS33650.1 22q13.1 2012-10-02 2011-05-19 ENSG00000100311 ENSG00000100311 5155 NA 8800 protein-coding gene gene with protein product "oncogene SIS", "becaplermin" 190040 "platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)" SIS NA 2991848, 1661670 Standard NM_002608 NM_002608 NA Approved SSV uc003axf.3 P01127 OTTHUMG00000151029 ENST00000331163.6:c.723+102CTCTGAGCCTTGGTCC>- chr22.hg19:g.39621582_39621597delGGACCAAGGCTCAGAG NA 0 5 ref NA False 69 69 PASS 1 PASS ref->het 0 NA 112,115 42,42 21,19 1 1 G3XAG8|P78431|Q15354|Q6FHE7|Q9UF23 True hg19 CCDS13987.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PDGFB-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000321043.1 PASS NA None 139 NA True - GGACCAAGGCTCAGAG ENST00000331163.6 RBMX 27316 __UNKNOWN__ __UNKNOWN__ X 135956028 135956028 __UNKNOWN__ 3'UTR DEL G G - rs377294279 LTS-018_T LTS-018_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:135956028delG ENST00000320676.7 - 0 1603 NA NA NA RBMX_ENST00000570135.1_3'UTR|RBMX_ENST00000496459.2_5'UTR|RBMX_ENST00000431446.3_Intron NM_002139.3 NP_002130.2 P38159 RBMX_HUMAN RNA binding motif protein, X-linked NA NA NA NA NA cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366) catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530) chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723) NA NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1) 33 Acute lymphoblastic leukemia(192;0.000127) GTGGCCTTTAGGGGATACTTT 0.348 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 456 451.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.76 NA NA CCDS14661.1, CCDS55510.1 Xq26 2013-05-23 2003-09-12 ENSG00000147274 ENSG00000147274 27316 NA "RNA binding motif (RRM) containing" 9910 protein-coding gene gene with protein product "heterogeneous nuclear ribonucleoprotein G" 300199 "RNA binding motif protein, X chromosome" NA 10391206, 10391207 Standard NM_002139 NM_002139 NA Approved RNMX, hnRNP-G, HNRNPG uc004fae.2 P38159 OTTHUMG00000022517 ENST00000320676.7:c.*273C>- chrX.hg19:g.135956028delG NA 3 4 ref NA False 37 37 PASS 4 PASS ref->het 0 NA 351,356 58,106 47,47 1 1 B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3 True hg19 CCDS14661.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RBMX-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000058507.1 PASS NA None 456 NA True - G ENST00000320676.7 ACVR1C 130399 __UNKNOWN__ __UNKNOWN__ 2 158389379 158389380 __UNKNOWN__ 3'UTR INS - - A LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:158389379_158389380insA ENST00000243349.8 - 0 2892_2893 NM_001111032.1|NM_145259.2 NP_001104502.1|NP_660302.2 activin A receptor, type IC NA NA NA NA NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1) 42 AGTGTGTATGTACAAAGGAAAT 0.292 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 126 134.89 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.57 BC022530 CCDS2205.1, CCDS46432.1, CCDS46433.1, CCDS46434.1 2q24.2 2008-02-05 ENSG00000123612 ENSG00000123612 130399 NA 18123 protein-coding gene gene with protein product 608981 NA Standard NM_145259 NM_145259 NA Approved ALK7, ACVRLK7 uc002tzk.4 Q8NER5 OTTHUMG00000131964 ENST00000243349.8:c.*1051->T chr2.hg19:g.158389380_158389380dupA 2 4 ref NA False 37 37 PASS 1 PASS ref->het 0 NA 75,75 32,34 18,18 1 1 True hg19 CCDS2205.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACVR1C-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254924.2 PASS NA None 126 NA True - A ENST00000243349.8 PCMTD1 115294 __UNKNOWN__ __UNKNOWN__ 8 52731064 52731070 __UNKNOWN__ 3'UTR DEL ACTAGGT ACTAGGT - LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:52731064_52731070delACTAGGT ENST00000360540.5 - 0 3321_3327 PCMTD1_ENST00000544451.1_3'UTR NM_052937.2 NP_443169.2 Q96MG8 PCMD1_HUMAN protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1 NA NA NA cytoplasm (GO:0005737) protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719) NA NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1) 37 Lung NSC(129;0.0795)|all_lung(136;0.144) ATTCAAGGTAACTAGGTACTTCAAAAG 0.329 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 332 332.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 11.28 CCDS6148.1, CCDS69480.1 8q11.23 2010-08-05 ENSG00000168300 ENSG00000168300 115294 NA 30483 protein-coding gene gene with protein product NA NA Standard NM_052937 XM_005251146 NA Approved FLJ10883 uc003xqx.4 Q96MG8 OTTHUMG00000164246 ENST00000360540.5:c.*1847ACCTAGT>- chr8.hg19:g.52731064_52731070delACTAGGT 0 2 ref NA False 47 47 PASS 1 PASS ref->het 0 NA 294,300 11,27 50,43 1 1 Q96FK9 True hg19 CCDS6148.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PCMTD1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000377909.2 PASS NA None 332 NA True - ACTAGGT ENST00000360540.5 MIR548A3 693127 __UNKNOWN__ __UNKNOWN__ 8 105496636 105496645 __UNKNOWN__ RNA DEL ATTGAAAGTA ATTGAAAGTA - rs71297276|rs139528851 byFrequency LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:105496636_105496645delATTGAAAGTA ENST00000385297.1 - 0 48_57 NR_030330.1 microRNA 548a-3 NA NA NA NA NA cagttttgccattgaaagtaatggtaaaac 0.395 NA NA NA NA NA NA 308 0.0615016 0.0855 0.0389 5008 , , NA 12636 0.0337 NA 0.0736 False NA ,,, NA NA NA 2504 0.0613 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 80 82.31 NA NA 313,3639 NA 22,269,1685 NA NA NA NA NA -0.8 0.1 NA dbSNP_134 47 565,6909 NA 37,491,3209 no intergenic NA NA NA 59,760,4894 A1A1,A1R,RR NA 7.5595,7.92,7.6842 NA NA NA 878,10548 NA NA NA 0.21 8q22.3 2011-09-12 2008-12-18 ENSG00000208032 ENSG00000208032 693127 NA "ncRNAs / Micro RNAs" 32798 non-coding RNA RNA, micro NA MIRN548A3 NA Standard NR_030330 NR_030330 NA Approved hsa-mir-548a-3 uc021xbz.1 ENST00000385297.1: chr8.hg19:g.105496636_105496645delATTGAAAGTA 0 2 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 13,13 59,60 8,7 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MIR548A3-201 KNOWN basic miRNA NA miRNA PASS NA None 80 NA True - ATTGAAAGTA ENST00000385297.1 TMEM65 157378 __UNKNOWN__ __UNKNOWN__ 8 125324365 125324366 __UNKNOWN__ 3'UTR INS - - C rs200762629 LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:125324365_125324366insC ENST00000297632.6 - 0 3092_3093 NM_194291.2 NP_919267.2 Q6PI78 TMM65_HUMAN transmembrane protein 65 NA NA NA integral component of membrane (GO:0016021)|mitochondrion (GO:0005739) NA cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|prostate(1) 6 Lung NSC(37;1.18e-11)|Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108) STAD - Stomach adenocarcinoma(47;0.00288) ACCCCACCCTTCCCCCCCCAAA 0.361 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 189 193.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.37 BC032396 CCDS6348.1 8q24.13 2006-11-24 ENSG00000164983 ENSG00000164983 157378 NA 25203 protein-coding gene gene with protein product NA NA 12477932 Standard NM_194291 NM_194291 NA Approved uc010mdl.3 Q6PI78 OTTHUMG00000165021 ENST00000297632.6:c.*1836->G chr8.hg19:g.125324373_125324373dupC 9 8 ref NA False 85 85 PASS 8 PASS ref->het 0 NA 104,106 49,50 39,37 1 1 Q8N5G8|Q8WVK5 True hg19 CCDS6348.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM65-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000381464.1 PASS NA None 189 NA True - C ENST00000297632.6 CNTRL 11064 __UNKNOWN__ __UNKNOWN__ 9 123927250 123927262 __UNKNOWN__ Frame_Shift_Del DEL AAATGGAGCAATC AAATGGAGCAATC - LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:123927250_123927262delAAATGGAGCAATC ENST00000373855.1 + 35 5713_5725 c.5453_5465delAAATGGAGCAATC c.(5452-5466)aaaatggagcaatcafs p.KMEQS1818fs CNTRL_ENST00000238341.5_Frame_Shift_Del_p.KMEQS1818fs|CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000373850.1_Frame_Shift_Del_p.KMEQS1266fs Q7Z7A1 CNTRL_HUMAN centriolin 1818 NA NA cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278) centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020) NA haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3) 20 GAAAATAGCAAAATGGAGCAATCAAACTTAGAA 0.399 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 268 298.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.77 AF513978 CCDS35118.1 9q33.2 2014-02-20 2011-05-23 2011-05-23 ENSG00000119397 ENSG00000119397 11064 NA 1858 protein-coding gene gene with protein product 605496 "centrosomal protein 1", "centrosomal protein 110kDa" CEP1, CEP110 NA 10688839 Standard NM_007018 XM_005251679 NA Approved uc004bkx.1 Q7Z7A1 OTTHUMG00000020581 ENST00000373855.1:c.5453_5465delAAATGGAGCAATC chr9.hg19:g.123927250_123927262delAAATGGAGCAATC ENSP00000362962:p.Lys1818fs 0 4 ref NA False 48 48 PASS 1 PASS ref->het 0 NA 226,229 65,66 31,31 1 1 A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489 True hg19 CCDS35118.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CNTRL-010 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250216.1 PASS NA None 268 NA True + AAATGGAGCAATC ENST00000373855.1 SPTAN1 6709 __UNKNOWN__ __UNKNOWN__ 9 131344178 131344178 __UNKNOWN__ Intron DEL C C - LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:131344178delC ENST00000372731.4 + 12 1682 SPTAN1_ENST00000372739.3_Intron|SPTAN1_ENST00000358161.5_Intron NM_001195532.1|NM_003127.3 NP_001182461.1|NP_003118.2 Q13813 SPTN1_HUMAN spectrin, alpha, non-erythrocytic 1 NA NA NA actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921) cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018) actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200) NA NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 87 TACAGTAAGACCCCTTCTTGT 0.423 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSCLC(120;833 1744 2558 35612 37579) PASS NA NA NA 0 NA NA NA NA NA 339 329.78 NA NA NA 104 104 104 NA NA NA NA 9 NA NA NA NA NA NA NA NA 131344178 2203 4300 6503 SO:0001627 intron_variant 0.93 M19725 CCDS6905.1, CCDS48036.1, CCDS75914.1 9q34.11 2013-01-10 2012-06-15 ENSG00000197694 ENSG00000197694 6709 NA "EF-hand domain containing" 11273 protein-coding gene gene with protein product "alpha-fodrin" 182810 NA 3336352 Standard NM_003127 NM_003127 NA Approved uc004bvm.4 Q13813 OTTHUMG00000020754 ENST00000372731.4:c.1572+7C>- chr9.hg19:g.131344178delC 3 4 ref NA False 133 109 PASS 4 PASS ref->het 0 NA 209,213 98,99 35,34 1 1 Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0 True hg19 CCDS6905.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SPTAN1-004 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000054472.1 PASS NA None 339 NA True + C ENST00000372731.4 CLEC2B 9976 __UNKNOWN__ __UNKNOWN__ 12 10005684 10005685 __UNKNOWN__ 3'UTR INS - - AA rs370105265 LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:10005684_10005685insAA ENST00000228438.2 - 0 1597_1598 NM_005127.2 NP_005118.2 Q92478 CLC2B_HUMAN C-type lectin domain family 2, member B NA NA NA integral component of plasma membrane (GO:0005887) carbohydrate binding (GO:0030246) NA endometrium(1)|large_intestine(3)|lung(1) 5 aagaaagaaagagagagagaga 0.366 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 67 71.85 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.5 X96719 CCDS8605.1 12p13-p12 2005-02-09 2005-02-09 2005-02-09 ENSG00000110852 9976 NA "C-type lectin domain containing" 2053 protein-coding gene gene with protein product 603242 "C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 2 (activation-induced)" CLECSF2 NA 9038101 Standard NM_005127 NM_005127 NA Approved AICL, HP10085 uc001qwn.3 Q92478 ENST00000228438.2:c.*215->TT chr12.hg19:g.10005684_10005685insAA 3 4 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 48,60 10,11 18,21 1 1 B2R9U1|Q8IZE9|Q9BS74|Q9UQB4 True hg19 CCDS8605.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CLEC2B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000399881.1 PASS NA None 67 NA True - A ENST00000228438.2 NACA 4666 __UNKNOWN__ __UNKNOWN__ 12 57112878 57112897 __UNKNOWN__ Intron DEL CTTCTTGGTTGGAGGTCTTT CTTCTTGGTTGGAGGTCTTT - LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:57112878_57112897delCTTCTTGGTTGGAGGTCTTT ENST00000356769.3 - 3 2007 NACA_ENST00000454682.1_Frame_Shift_Del_p.KRPPTKK806fs|NACA_ENST00000548563.1_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000550952.1_Intron|NACA_ENST00000552540.1_Intron NM_001113202.1 NP_001106673.1 E9PAV3 NACAM_HUMAN nascent polypeptide-associated complex alpha subunit NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleus (GO:0005634) DNA binding (GO:0003677) NA breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1) 10 CAGCAGAACCCTTCTTGGTTGGAGGTCTTTTAGTCTGAGG 0.468 NA NA T BCL6 NHL NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 12 12q23-q24.1 4666 nascent-polypeptide-associated complex alpha polypeptide NA L 0 NA NA NA NA NA 222 220.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.62 X80909 CCDS31837.1, CCDS44925.1, CCDS44925.2 12q23-q24.1 2008-09-05 2007-04-20 ENSG00000196531 ENSG00000196531 4666 NA 7629 protein-coding gene gene with protein product 601234 "nascent-polypeptide-associated complex alpha polypeptide" NA 8047162 Standard NM_005594 NM_001113202 NA Approved NACA1 uc001sma.2 E9PAV3 ENST00000356769.3:c.71-4407AAAGACCTCCAACCAAGAAG>- chr12.hg19:g.57112878_57112897delCTTCTTGGTTGGAGGTCTTT 0 5 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 163,167 48,49 16,15 1 1 True hg19 CCDS31837.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NACA-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000406953.1 PASS NA None 222 NA True - CTTCTTGGTTGGAGGTCTTT ENST00000356769.3 SCNN1G 6340 __UNKNOWN__ __UNKNOWN__ 16 23226707 23226721 __UNKNOWN__ In_Frame_Del DEL CCGCCCCCCAAATAC CCGCCCCCCAAATAC - rs72647542 LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:23226707_23226721delCCGCCCCCCAAATAC ENST00000300061.2 + 13 2010_2024 c.1867_1881delCCGCCCCCCAAATAC c.(1867-1881)ccgccccccaaatacdel p.PPPKY623del NM_001039.3 NP_001030.2 P51170 SCNNG_HUMAN sodium channel, non-voltage-gated 1, gamma subunit 623 NA NA excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085) external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706) ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699) NA NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2) 34 GBM - Glioblastoma multiforme(48;0.0366) Amiloride(DB00594)|Triamterene(DB00384) GCCCGGCACACCGCCCCCCAAATACAATACCTTGC 0.558 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 658 620.63 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 1.67 U48937 CCDS10608.1 16p12 2012-02-28 2012-02-28 ENSG00000166828 ENSG00000166828 6340 NA "Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels" 10602 protein-coding gene gene with protein product 600761 "sodium channel, nonvoltage-gated 1, gamma", "sodium channel, non-voltage-gated 1, gamma" NA 7490094 Standard NM_001039 NM_001039 NA Approved ENaCgamma, SCNEG uc002dlm.1 P51170 OTTHUMG00000131609 ENST00000300061.2:c.1867_1881delCCGCCCCCCAAATAC chr16.hg19:g.23226707_23226721delCCGCCCCCCAAATAC ENSP00000300061:p.Pro623_Tyr627del 0 8 ref NA False 94 94 PASS 1 PASS ref->het 0 NA 449,456 133,136 58,48 1 1 P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2 True hg19 CCDS10608.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SCNN1G-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254496.1 PASS NA None 658 NA True + CCGCCCCCCAAATAC ENST00000300061.2 TP53 7157 __UNKNOWN__ __UNKNOWN__ 17 7578503 7578504 __UNKNOWN__ Frame_Shift_Ins INS - - A rs587782620 LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:7578503_7578504insA ENST00000269305.4 - 5 615_616 c.426_427insT c.(424-429)cctgtgfs p.V143fs TP53_ENST00000359597.4_Frame_Shift_Ins_p.V143fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.V143fs|TP53_ENST00000455263.2_Frame_Shift_Ins_p.V143fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.V143fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.V143fs NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 143 Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A. NA V -> A (in sporadic cancers; somatic mutation; strong DNA binding ability at 32.5 degrees Celsius; strong reduction of transcriptional activity at 37.5 degrees Celsius; severely represses interaction with ZNF385A).|V -> E (in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> M (in sporadic cancers; somatic mutation). NA apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032) chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657) ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270) p.V143M(19)|p.0?(8)|p.V143L(4)|p.P142P(3)|p.V143fs*27(2)|p.V11M(1)|p.L137_W146del10(1)|p.V143fs*29(1)|p.P142_Q144delPVQ(1)|p.K139fs*4(1)|p.A138_V143delAKTCPV(1)|p.V50M(1)|p.V143_S149del(1)|p.C141fs*5(1) NA NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) Acetylsalicylic acid(DB00945) CACAGCTGCACAGGGCAGGTCT 0.584 NA 111 "Mis, N, F" "breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types" "breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types" NA Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(47;798 1329 9957 10801) PASS yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 NA "L, E, M, O" 45 Substitution - Missense(25)|Whole gene deletion(8)|Deletion - In frame(4)|Deletion - Frameshift(4)|Substitution - coding silent(3)|Insertion - Frameshift(1) haematopoietic_and_lymphoid_tissue(9)|breast(6)|upper_aerodigestive_tract(4)|bone(4)|central_nervous_system(3)|urinary_tract(3)|lung(3)|ovary(3)|salivary_gland(2)|large_intestine(2)|oesophagus(2)|prostate(2)|cervix(1)|stomach(1) NA NA NA NA NA 282 281.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.31 Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; AF307851 CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1 17p13.1 2014-09-17 2008-01-16 ENSG00000141510 ENSG00000141510 7157 NA 11998 protein-coding gene gene with protein product "Li-Fraumeni syndrome" 191170 NA 6396087, 3456488, 2047879 Standard NM_000546 NM_001126115 NA Approved p53, LFS1 uc002gij.3 P04637 OTTHUMG00000162125 ENST00000269305.4:c.427dupT chr17.hg19:g.7578504_7578504dupA ENSP00000269305:p.Val143fs 2 3 ref NA False 366 122 PASS 1 PASS ref->het 0 NA 87,89 166,171 26,21 1 1 Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61 True hg19 CCDS11118.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TP53-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000367397.1 PASS NA None 282 NA True - A ENST00000269305.4 ZNF566 84924 __UNKNOWN__ __UNKNOWN__ 19 36940848 36940871 __UNKNOWN__ 5'UTR DEL TTCATAAATTTCTTTCTTCAGAAA TTCATAAATTTCTTTCTTCAGAAA - rs150149081 LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:36940848_36940871delTTCATAAATTTCTTTCTTCAGAAA ENST00000493391.1 - 0 476_499 ZNF566_ENST00000454319.1_In_Frame_Del_p.FLKKEIYE90del|ZNF566_ENST00000424129.2_In_Frame_Del_p.FLKKEIYE89del|ZNF566_ENST00000392170.2_In_Frame_Del_p.FLKKEIYE90del|ZNF566_ENST00000434377.2_In_Frame_Del_p.FLKKEIYE89del Q969W8 ZN566_HUMAN zinc finger protein 566 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) NA breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1) 24 Esophageal squamous(110;0.162) TTGATTCTATTTCATAAATTTCTTTCTTCAGAAATAATTTCTTG 0.335 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 276 266.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.39 AK074497 CCDS12494.1, CCDS46061.1, CCDS74346.1 19q13.12 2013-01-08 84924 NA "Zinc fingers, C2H2-type", "-" 25919 protein-coding gene gene with protein product NA NA 12477932 Standard NM_032838 NM_001145343 NA Approved FLJ14779, MGC12515 uc010xtf.2 Q969W8 ENST00000493391.1:c.-48TTTCTGAAGAAAGAAATTTATGAA>- chr19.hg19:g.36940848_36940871delTTCATAAATTTCTTTCTTCAGAAA 0 5 ref NA False 62 62 PASS 1 PASS ref->het 0 NA 183,184 48,49 58,58 1 1 B7ZL95|Q2M3J1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF566-003 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000341055.2 PASS NA None 276 NA True - TTCATAAATTTCTTTCTTCAGAAA ENST00000493391.1 NLRP13 126204 __UNKNOWN__ __UNKNOWN__ 19 56435941 56435941 __UNKNOWN__ Intron DEL A A - rs191058419 LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:56435941delA ENST00000342929.3 - 3 457 NLRP13_ENST00000588751.1_Intron NM_176810.2 NP_789780.2 Q86W25 NAL13_HUMAN NLR family, pyrin domain containing 13 NA NA NA ATP binding (GO:0005524) NA NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1) 109 Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218) GBM - Glioblastoma multiforme(193;0.0642) ATTATCAACCAAGTAATGTAC 0.383 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 469 433.62 NA NA NA 258 179 206 NA NA NA NA 19 NA NA NA NA NA NA NA NA 56435941 2203 4300 6503 SO:0001627 intron_variant 0.65 AY154468 CCDS33119.1 19q13.43 2008-02-05 2006-12-08 2006-12-08 ENSG00000173572 ENSG00000173572 126204 NA "Nucleotide-binding domain and leucine rich repeat containing" 22937 protein-coding gene gene with protein product "nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13" 609660 "NACHT, leucine rich repeat and PYD containing 13" NALP13 NA 12563287 Standard NM_176810 NM_176810 NA Approved NOD14, PAN13, CLR19.7 uc010ygg.2 Q86W25 OTTHUMG00000167839 ENST00000342929.3:c.457+14T>- chr19.hg19:g.56435941delA 1 2 ref NA False 84 83 PASS 2 PASS ref->het 0 NA 279,280 138,141 55,53 1 1 Q7RTR5 True hg19 CCDS33119.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NLRP13-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000396560.1 PASS NA None 469 NA True - A ENST00000342929.3 FRG1B 284802 __UNKNOWN__ __UNKNOWN__ 20 29614292 29614296 __UNKNOWN__ 5'UTR DEL AAAAG AAAAG - rs376619640|rs373374584 LTS-019_T LTS-019_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:29614292_29614296delAAAAG ENST00000278882.3 + 0 285_289 FRG1B_ENST00000439954.2_5'UTR|FRG1B_ENST00000358464.4_5'UTR Q9BZ01 FRG1B_HUMAN FSHD region gene 1 family, member B NA NA NA NA endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9) 53 taagaagagaaaaagagaagatgaa 0.288 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 154 140.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.57 20q11.1 2013-03-18 2007-10-11 2007-10-11 ENSG00000149531 ENSG00000149531 284802 NA 15792 other unknown NA "chromosome 20 open reading frame 80" C20orf80 NA Standard NR_003579 NR_003579 NA Approved bA348I14.2 uc010ztl.1 Q9BZ01 OTTHUMG00000032157 ENST00000278882.3:c.-92AAAAG>- chr20.hg19:g.29614292_29614296delAAAAG 0 6 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 125,141 7,17 26,13 1 1 C4AME5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FRG1B-001 KNOWN not_best_in_genome_evidence|basic|appris_principal protein_coding NA protein_coding OTTHUMT00000078494.2 PASS NA None 154 NA True + AAAAG ENST00000278882.3 TNFRSF1B 7133 __UNKNOWN__ __UNKNOWN__ 1 12267417 12267424 __UNKNOWN__ 3'UTR DEL TTTGTTTG TTTGTTTG - LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:12267417_12267424delTTTGTTTG ENST00000376259.3 + 0 1815_1822 TNFRSF1B_ENST00000492361.1_3'UTR NM_001066.2 NP_001057.1 P20333 TNR1B_HUMAN tumor necrosis factor receptor superfamily, member 1B NA NA NA NA NA aging (GO:0007568)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lipopolysaccharide (GO:0071222)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of inflammatory response (GO:0050728)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|RNA destabilization (GO:0050779)|tumor necrosis factor-mediated signaling pathway (GO:0033209) extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|varicosity (GO:0043196) tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625) NA central_nervous_system(1)|liver(1)|lung(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 10 Ovarian(185;0.249) Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284) Etanercept(DB00005) CCTTGGgttttttgtttgtttgtttgtt 0.577 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 52 50.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA M32315 CCDS145.1 1p36.22 2008-02-05 ENSG00000028137 ENSG00000028137 7133 "Tumor necrosis factor receptor superfamily", "CD molecules" 11917 protein-coding gene gene with protein product 191191 TNFR2 NA 2158863, 8702885 Standard NM_001066 NM_001066 NA Approved TNFBR, TNFR80, TNF-R75, TNF-R-II, p75, CD120b uc001att.3 P20333 OTTHUMG00000001829 ENST00000376259.3:c.*347TTTGTTTG>- chr1.hg19:g.12267425_12267432delTTTGTTTG 5 9 ref NA False 31 31 PASS 7 PASS ref->het 0 NA 3,3 18,18 30,30 1 1 B1AJZ3|Q16042|Q6YI29|Q9UIH1 True hg19 CCDS145.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNFRSF1B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000005133.1 PASS NA None 52 NA True + TTTG ENST00000376259.3 EFCAB14 9813 __UNKNOWN__ __UNKNOWN__ 1 47181981 47182001 __UNKNOWN__ In_Frame_Del DEL TCCTTGAGGGCATCCAGATCC TCCTTGAGGGCATCCAGATCC - LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:47181981_47182001delTCCTTGAGGGCATCCAGATCC ENST00000371933.3 - 2 1276_1296 c.300_320delGGATCTGGATGCCCTCAAGGA c.(298-321)gaggatctggatgccctcaaggaa>gaa p.100_107EDLDALKE>E EFCAB14_ENST00000544071.1_In_Frame_Del_p.100_107EDLDALKE>E NM_014774.2 NP_055589.1 O75071 EFC14_HUMAN EF-hand calcium binding domain 14 100 NA NA NA NA calcium ion binding (GO:0005509) NA NA TCGAAATTTTTCCTTGAGGGCATCCAGATCCTCCTTGAGAG 0.443 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 149 149.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 2.49 NA NA AB007963 CCDS30706.1 1p33 2013-01-10 2012-11-29 2012-11-29 ENSG00000159658 ENSG00000159658 9813 "EF-hand domain containing" 29051 protein-coding gene gene with protein product NA "KIAA0494" KIAA0494 NA 9455484 Standard NM_014774 NM_014774 NA Approved uc001cqk.4 O75071 OTTHUMG00000007992 ENST00000371933.3:c.300_320delGGATCTGGATGCCCTCAAGGA chr1.hg19:g.47181981_47182001delTCCTTGAGGGCATCCAGATCC ENSP00000361001:p.Glu100_Lys106del 0 5 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 174,192 6,6 30,24 1 1 D3DQ23|Q5SXB8 True hg19 CCDS30706.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EFCAB14-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000021931.1 PASS NA None 149 NA True - TCCTTGAGGGCATCCAGATCC ENST00000371933.3 EOGT 285203 __UNKNOWN__ __UNKNOWN__ 3 69025850 69025853 __UNKNOWN__ 3'UTR DEL ACAA ACAA - rs372276999 LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:69025850_69025853delACAA ENST00000383701.3 - 0 3242_3245 EOGT_ENST00000295571.5_3'UTR NM_001278689.1 NP_001265618.1 Q5NDL2 EOGT_HUMAN EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase NA NA NA NA NA protein O-linked glycosylation (GO:0006493) endoplasmic reticulum (GO:0005783) protein N-acetylglucosaminyltransferase activity (GO:0016262) NA NA CTTTCCTACCACAAACAGTGTTAT 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 87 87.26 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.66 NA NA AK091089 CCDS2908.1, CCDS63684.1 3p14.1 2013-10-11 2012-05-21 2012-05-21 ENSG00000163378 ENSG00000163378 285203 2.4.1.255 28526 protein-coding gene gene with protein product "AER61 glycosyltransferase" 614789 "chromosome 3 open reading frame 64" C3orf64 NA 22310717 Standard NM_173654 NM_001278689 NA Approved AER61, FLJ33770 uc003dnk.3 Q5NDL2 OTTHUMG00000156279 ENST00000383701.3:c.*919TTGT>- chr3.hg19:g.69025850_69025853delACAA 0 4 ref NA False 55 55 PASS 1 PASS ref->het 0 NA 51,57 25,30 20,19 1 1 A8K2U1|B4DFH5|L7X1M5|Q6MZY0|Q6P985|Q6ZTV0 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EOGT-002 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000343722.1 PASS NA None 87 NA True - ACAA ENST00000383701.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 5 153913531 153913532 __UNKNOWN__ IGR INS - - ATCTGC rs397803370|rs149563726|rs3052444 byFrequency LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:153913531_153913532insATCTGC NA CTB-158E9.1 (48042 upstream) : MIR3141 (62039 downstream) NA NA NA NA NA NA NA aacctcaggtgatctgcctgcc 0.53 NA NA NA NA NA NA NA NA NA NA NA NA 1612 0.321885 0.3472 0.2594 5008 , , NA 13463 0.3165 NA 0.3181 False NA ,,, NA NA NA 2504 0.3415 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 15 17.75 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.21 NA NA NA NA NA NA NA chr5.hg19:g.153913532_153913537dupATCTGC 2 3 ref NA False 37 37 PASS 1 PASS ref->het 0 NA 1,1 14,16 1,1 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 15 NA True ATCTGC CREB5 9586 __UNKNOWN__ __UNKNOWN__ 7 28758342 28758349 __UNKNOWN__ Intron DEL TGTTTGTT TGTTTGTT - rs373664679 LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:28758342_28758349delTGTTTGTT ENST00000357727.2 + 6 854 CREB5_ENST00000396300.2_Intron|CREB5_ENST00000396299.2_Intron|CREB5_ENST00000396298.2_Intron|CREB5_ENST00000409603.1_Intron NM_182898.2 NP_878901.2 Q02930 CREB5_HUMAN cAMP responsive element binding protein 5 NA NA NA NA NA adipose tissue development (GO:0060612)|fat cell differentiation (GO:0045444)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366) extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634) metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(13)|prostate(1)|skin(3) 32 CCAGGAATCATGTTTGTTTGTTTTTTTC 0.529 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 204 196.04 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA L05515 CCDS5417.1, CCDS5418.1, CCDS43562.1, CCDS43563.1 7p15 2013-01-10 ENSG00000146592 ENSG00000146592 9586 "basic leucine zipper proteins" 16844 protein-coding gene gene with protein product "cAMP response element binding protein CRE-Bpa" NA NA 8378084, 8440710 Standard NM_004904 XM_005249906 NA Approved H_GS165L15.1, CRE-BPA uc003szr.3 Q02930 OTTHUMG00000097081 ENST00000357727.2:c.465-21TGTTTGTT>- chr7.hg19:g.28758342_28758349delTGTTTGTT 1 10 ref NA False 36 36 PASS 3 PASS ref->het 0 NA 165,168 26,26 25,25 1 1 A8KA51|B4DU13|B5BUH3|C9JK47|Q05886|Q06246|Q75N02|Q86UJ9 True hg19 CCDS5417.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CREB5-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000214204.4 PASS NA None 204 NA True + TGTT ENST00000357727.2 POT1 25913 __UNKNOWN__ __UNKNOWN__ 7 124475422 124475438 __UNKNOWN__ Frame_Shift_Del DEL ACTATTAAACTTGTTCG ACTATTAAACTTGTTCG - rs146643991 LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:124475422_124475438delACTATTAAACTTGTTCG ENST00000357628.3 - 15 1998_2014 c.1400_1416delCGAACAAGTTTAATAGT c.(1399-1416)tcgaacaagtttaatagtfs p.SNKFNS467fs POT1_ENST00000393329.1_Frame_Shift_Del_p.SNKFNS336fs NM_015450.2 NP_056265.2 Q9NUX5 POTE1_HUMAN protection of telomeres 1 467 NA NA NA NA DNA duplex unwinding (GO:0032508)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of DNA strand elongation (GO:0060383)|positive regulation of helicase activity (GO:0051096)|positive regulation of telomerase activity (GO:0051973)|positive regulation of telomere maintenance via telomerase (GO:0032212)|telomere capping (GO:0016233)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004) chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) DEAD/H-box RNA helicase binding (GO:0017151)|single-stranded telomeric DNA binding (GO:0043047)|telomerase inhibitor activity (GO:0010521) NA NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1) 47 CAGGAATTACACTATTAAACTTGTTCGAGAGTTTGCA 0.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 169 149.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 NA NA AK022580 CCDS5793.1 7q31.33 2013-01-21 2013-01-21 ENSG00000128513 ENSG00000128513 25913 17284 protein-coding gene gene with protein product 606478 "protection of telomeres 1 homolog (S. pombe)" NA 11349150, 12391173 Standard NR_003102 NA Approved hPot1, DKFZp586D211 uc003vlm.3 Q9NUX5 OTTHUMG00000157194 ENST00000357628.3:c.1400_1416delCGAACAAGTTTAATAGT chr7.hg19:g.124475422_124475438delACTATTAAACTTGTTCG ENSP00000350249:p.Ser467fs 0 2 ref NA False 52 52 PASS 1 PASS ref->het 0 NA 120,121 42,42 14,15 1 1 O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95 True hg19 CCDS5793.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA POT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000347861.1 PASS NA None 169 NA True - ACTATTAAACTTGTTCG ENST00000357628.3 RUNX1T1 862 __UNKNOWN__ __UNKNOWN__ 8 92971405 92971405 __UNKNOWN__ 3'UTR DEL T T - rs34269950 byFrequency LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:92971405delT ENST00000523629.1 - 0 3334 RUNX1T1_ENST00000396218.1_3'UTR|RUNX1T1_ENST00000265814.3_3'UTR NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2 NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1 Q06455 MTG8_HUMAN runt-related transcription factor 1; translocated to, 1 (cyclin D-related) NA NA NA NA NA fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351) nuclear matrix (GO:0016363) DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2) 86 BRCA - Breast invasive adenocarcinoma(11;0.0141) GAACTACTAGTTTTTAATTAA 0.338 NA NA NA NA NA NA NA NA NA NA NA NA TTTTT|TTTTT|TTTT|deletion 2697 0.538538 0.5749 0.4207 5008 , , NA 12325 0.6944 NA 0.328 False NA ,,, NA NA NA 2504 0.6288 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 63 65.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA D43638 CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1 8q22 2007-01-29 2005-01-20 2005-01-22 ENSG00000079102 ENSG00000079102 862 "Zinc fingers, MYND-type" 1535 protein-coding gene gene with protein product 133435 "core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related" AML1T1, CBFA2T1 NA 1391946, 9790752 Standard NM_004349, NM_175635 NM_004349 NA Approved CDR, ETO, MTG8, ZMYND2 uc011lgi.2 Q06455 OTTHUMG00000164066 ENST00000523629.1:c.*1065A>- chr8.hg19:g.92971405delT 4 5 ref NA False 59 57 PASS 5 PASS ref->het 0 NA 7,7 50,51 6,6 1 1 B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0 True hg19 CCDS6256.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RUNX1T1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000377045.3 PASS NA None 63 NA True - T ENST00000523629.1 C10orf111 221060 __UNKNOWN__ __UNKNOWN__ 10 15138895 15138909 __UNKNOWN__ Intron DEL AGAGACAGAGGGCTA AGAGACAGAGGGCTA - rs375634446 LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:15138895_15138909delAGAGACAGAGGGCTA ENST00000378207.3 - 2 233 NM_153244.1 NP_694976.1 Q8N326 CJ111_HUMAN chromosome 10 open reading frame 111 NA NA NA NA NA integral component of membrane (GO:0016021) NA lung(5)|upper_aerodigestive_tract(1) 6 AAAAGCGAATAGAGACAGAGGGCTAAGATTCCAAA 0.567 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 124 116.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA BC029034 CCDS7107.1 10p13 2004-04-20 ENSG00000176236 ENSG00000176236 221060 28582 protein-coding gene gene with protein product NA NA 12477932 Standard NM_153244 NM_153244 NA Approved MGC35468, bA455B2.4 uc001inw.3 Q8N326 OTTHUMG00000017727 ENST00000378207.3:c.41-31TAGCCCTCTGTCTCT>- chr10.hg19:g.15138895_15138909delAGAGACAGAGGGCTA 0 3 ref NA False 66 66 PASS 1 PASS ref->het 0 NA 93,94 24,24 11,13 1 1 B2RAC4 True hg19 CCDS7107.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C10orf111-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000046975.1 PASS NA None 124 NA True - AGAGACAGAGGGCTA ENST00000378207.3 ASAH2 56624 __UNKNOWN__ __UNKNOWN__ 10 51946841 51946842 __UNKNOWN__ 3'UTR INS - - CTGCACATTCAT LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:51946841_51946842insCTGCACATTCAT ENST00000395526.4 - 0 2575_2576 NM_019893.2 NP_063946.2 Q9NR71 ASAH2_HUMAN N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2 NA NA NA NA NA apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665) integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886) ceramidase activity (GO:0017040) NA large_intestine(1)|lung(9)|urinary_tract(1) 11 TATATGGGACAAACctctctct 0.485 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 172 122.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.21 NA NA AF250847 CCDS7239.2, CCDS44398.1 10q11.23 2008-08-11 ENSG00000188611 ENSG00000188611 56624 18860 protein-coding gene gene with protein product 611202 NA 10781606 Standard NM_019893 NM_019893 NA Approved uc001jjd.3 Q9NR71 OTTHUMG00000018223 ENST00000395526.4:c.*234->ATGAATGTGCAG chr10.hg19:g.51946841_51946842insCTGCACATTCAT 1 4 ref NA False 33 33 PASS 0 PASS ref->het 0 NA 156,211 4,4 13,12 2 2 Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6 True hg19 CCDS7239.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ASAH2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000048061.3 PASS NA None 172 NA True - CTGCACATTCAT ENST00000395526.4 PROZ 8858 __UNKNOWN__ __UNKNOWN__ 13 113814588 113814589 __UNKNOWN__ Intron INS - - C rs35691399|rs397697994 byFrequency LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:113814588_113814589insC ENST00000342783.4 + 3 307 PROZ_ENST00000375547.2_Intron NM_001256134.1 NP_001243063.1 P22891 PROZ_HUMAN protein Z, vitamin K-dependent plasma glycoprotein NA NA NA NA NA blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508) endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796) calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252) NA NS(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(2)|skin(2) 16 all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163) all_lung(25;0.216) all cancers(43;0.104) Menadione(DB00170) TAATTAattagcctatttactt 0.431 NA NA NA NA NA NA NA NA NA NA NA NA CC|CC|CCC|insertion 1183 0.236222 0.0855 0.2205 5008 , , NA 17384 0.3036 NA 0.172 False NA ,,, NA NA NA 2504 0.4479 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 49 54.92 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA M55670 CCDS9531.1, CCDS58300.1 13q34 2008-07-18 ENSG00000126231 ENSG00000126231 8858 9460 protein-coding gene gene with protein product 176895 NA 2244898, 2403355 Standard NM_003891 NM_001256134 NA Approved PZ uc010agr.2 P22891 OTTHUMG00000017376 ENST00000342783.4:c.300+97->C chr13.hg19:g.113814590_113814590dupC 3 2 ref NA False 38 38 PASS 2 PASS ref->het 0 NA 6,6 36,36 6,6 1 1 A6NMB4|Q15213|Q5JVF5|Q5JVF6 True hg19 CCDS58300.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PROZ-002 NOVEL basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000045846.1 PASS NA None 49 NA True + C ENST00000342783.4 RP11-44L9.1 0 __UNKNOWN__ __UNKNOWN__ 16 73517269 73517275 __UNKNOWN__ lincRNA DEL TTCCTCA TTCCTCA - LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:73517269_73517275delTTCCTCA ENST00000557393.1 + 0 54_60 NA NA NA NA NA NA NA agagagagagTTCCTCAAGAGAGCCGG 0.531 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 132 118.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1.21 NA NA NA NA NA NA NA ENST00000557393.1: chr16.hg19:g.73517269_73517275delTTCCTCA 0 3 ref NA False 55 55 PASS 1 PASS ref->het 0 NA 125,133 4,5 12,9 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-44L9.1-001 KNOWN basic|exp_conf lincRNA NA lincRNA OTTHUMT00000410605.1 PASS NA None 132 NA True + TTCCTCA ENST00000557393.1 RAI1 10743 __UNKNOWN__ __UNKNOWN__ 17 17701059 17701077 __UNKNOWN__ Frame_Shift_Del DEL GCGGGTGGAGAAGCGAGAC GCGGGTGGAGAAGCGAGAC - LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:17701059_17701077delGCGGGTGGAGAAGCGAGAC ENST00000353383.1 + 3 5266_5284 c.4797_4815delGCGGGTGGAGAAGCGAGAC c.(4795-4815)gtgcgggtggagaagcgagacfs p.VRVEKRD1599fs RAI1_ENST00000261641.6_Intron NM_030665.3 NP_109590.3 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 1599 NA NA NA NA circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501) cytoplasm (GO:0005737)|nucleus (GO:0005634) enhancer binding (GO:0035326)|zinc ion binding (GO:0008270) p.R1600L(1) NA breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7) 48 READ - Rectum adenocarcinoma(1115;0.0276) CACCCTTCGTGCGGGTGGAGAAGCGAGACGCGTTCACCA 0.607 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 1 Substitution - Missense(1) lung(1) NA NA NA NA NA 149 144.94 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 NA NA AJ230819 CCDS11188.1 17p11.2 2011-02-08 ENSG00000108557 ENSG00000108557 10743 9834 protein-coding gene gene with protein product 607642 "Smith-Magenis syndrome chromosome region" SMCR NA 10036180 Standard NM_030665 NM_030665 NA Approved DKFZP434A139, SMS, KIAA1820, MGC12824 uc002grm.3 Q7Z5J4 OTTHUMG00000059314 ENST00000353383.1:c.4797_4815delGCGGGTGGAGAAGCGAGAC chr17.hg19:g.17701059_17701077delGCGGGTGGAGAAGCGAGAC ENSP00000323074:p.Val1599fs 0 4 ref NA False 66 66 PASS 1 PASS ref->het 0 NA 113,113 36,36 20,21 1 1 Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69 True hg19 CCDS11188.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RAI1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000131775.1 PASS NA None 149 NA True + GCGGGTGGAGAAGCGAGAC ENST00000353383.1 PSME3 10197 __UNKNOWN__ __UNKNOWN__ 17 40986486 40986493 __UNKNOWN__ Intron DEL ACCTTCCC ACCTTCCC - LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:40986486_40986493delACCTTCCC ENST00000545225.1 + 5 731 PSME3_ENST00000293362.3_Intron|PSME3_ENST00000592169.1_Intron|PSME3_ENST00000592578.1_Intron|PSME3_ENST00000590720.1_Intron|PSME3_ENST00000441946.2_Intron|PSME3_ENST00000541124.1_Intron P61289 PSME3_HUMAN proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki) NA NA NA NA NA anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032) cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome activator complex (GO:0008537)|proteasome complex (GO:0000502) endopeptidase activator activity (GO:0061133)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039) NA NS(1)|cervix(1)|large_intestine(3)|lung(1) 6 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.156) agagagagagaCCTTCCCACAGATATTA 0.389 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 154 132.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.5 NA NA U11292 CCDS11442.1, CCDS45689.1, CCDS59290.1 17q12-q21 2004-02-17 ENSG00000131467 10197 "Proteasome (prosome, macropain) subunits" 9570 protein-coding gene gene with protein product 605129 NA 7951316 Standard NM_176863 NM_005789 NA Approved Ki, PA28-gamma, REG-GAMMA, PA28G uc002ibq.4 P61289 ENST00000545225.1:c.-108-39ACCTTCCC>- chr17.hg19:g.40986486_40986493delACCTTCCC 0 4 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 149,157 4,4 15,11 2 2 A8K9A3|O35563|P97373|Q12920|Q13172|Q9BQD9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PSME3-006 PUTATIVE alternative_5_UTR|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000452428.1 PASS NA None 154 NA True + ACCTTCCC ENST00000545225.1 MKS1 54903 __UNKNOWN__ __UNKNOWN__ 17 56289718 56289720 __UNKNOWN__ Intron DEL GCA GCA - rs3217067|rs200080801 byFrequency LTS-021_T LTS-021_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:56289718_56289720delGCA ENST00000313863.6 - 9 917 MKS1_ENST00000546108.1_Intron|MKS1_ENST00000537529.2_Intron|MKS1_ENST00000337050.7_Intron|MKS1_ENST00000393119.2_Intron Q9NXB0 MKS1_HUMAN Meckel syndrome, type 1 NA NA NA NA NA branching morphogenesis of an epithelial tube (GO:0048754)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271) centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038) NA endometrium(5)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 26 TCACAGTGCTGCAGGAAGCCAAG 0.488 NA NA NA NA NA NA NA NA NA NA NA NA 431 0.0860623 0.034 0.0591 5008 , , NA 21537 0.1151 NA 0.1064 False NA ,,, NA NA NA 2504 0.1247 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 66 66.23 NA , 183,3751 NA 12,159,1796 NA NA NA NA , 1.2 0 NA dbSNP_106 87 795,7265 NA 43,709,3278 no intron,intron MKS1 NM_017777.3,NM_001165927.1 , 55,868,5074 A1A1,A1R,RR NA 9.8635,4.6518,8.1541 , , NA 978,11016 NA NA NA SO:0001627 intron_variant 0 NA NA DQ185029 CCDS11603.2, CCDS54148.1 17q21-q24 2014-09-17 ENSG00000011143 ENSG00000011143 54903 7121 protein-coding gene gene with protein product "POC12 centriolar protein homolog (Chlamydomonas)" 609883 MKS NA 7550354, 16415886, 18327255 Standard NM_017777 NM_017777 NA Approved FLJ20345, POC12, BBS13 uc002ivr.2 Q9NXB0 OTTHUMG00000133714 ENST00000313863.6:c.915+18TGC>- chr17.hg19:g.56289718_56289720delGCA 0 2 ref NA False 37 37 PASS 1 PASS ref->het 0 NA 14,14 46,46 5,6 1 1 B7WNX4|F5H885|Q284T0|Q96G13 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MKS1-002 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000258014.2 PASS NA None 66 NA True - GCA ENST00000313863.6 MOB3C 148932 __UNKNOWN__ __UNKNOWN__ 1 47080919 47080928 __UNKNOWN__ 5'UTR DEL CCCACCTCCC CCCACCTCCC - LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:47080919_47080928delCCCACCTCCC ENST00000371940.1 - 0 1209_1218 MOB3C_ENST00000477318.1_Intron|MKNK1_ENST00000545730.1_Intron|MOB3C_ENST00000319928.3_Intron Q70IA8 MOB3C_HUMAN MOB kinase activator 3C NA NA NA metal ion binding (GO:0046872) NA TGCCCCACTTCCCACCTCCCCACACCAACC 0.571 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 153 149.26 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.31 NA NA AK091808 CCDS539.1, CCDS540.1 1p34.1 2011-09-28 2011-09-28 2011-09-28 ENSG00000142961 ENSG00000142961 148932 "MOB kinase activators" 29800 protein-coding gene gene with protein product NA "MOB1, Mps One Binder kinase activator-like 2C (yeast)" MOBKL2C NA 12477932 Standard NM_145279 NM_145279 NA Approved MOB1E uc001cqe.4 Q70IA8 OTTHUMG00000007989 ENST00000371940.1:c.-1866GGGAGGTGGG>- chr1.hg19:g.47080919_47080928delCCCACCTCCC 0 6 ref NA False 48 48 PASS 1 PASS ref->het 0 NA 144,149 4,4 29,31 2 2 D3DQ22|Q0VA98|Q5TC10|Q5TC11|Q8NAZ2|Q8NF28 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MOB3C-002 KNOWN basic protein_coding NA protein_coding OTTHUMT00000021926.1 PASS NA None 153 True - CCCACCTCCC ENST00000371940.1 FER1L5 90342 __UNKNOWN__ __UNKNOWN__ 2 97351796 97351816 __UNKNOWN__ RNA DEL AGGACATGGTGGCCACAGCGG AGGACATGGTGGCCACAGCGG - rs118112723 byFrequency LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:97351796_97351816delAGGACATGGTGGCCACAGCGG ENST00000457909.1 + 0 554_574 A0AVI2 FR1L5_HUMAN fer-1-like family member 5 NA NA NA integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2) 38 GCCAAGCCCAAGGACATGGTGGCCACAGCGGAGGACTGGCT 0.647 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 244 219.13 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 NA NA BC126368 2q11.2 2014-06-27 2014-06-27 ENSG00000249715 ENSG00000249715 90342 19044 protein-coding gene gene with protein product NA "fer-1-like 5 (C. elegans)" NA Standard NM_001077400 XM_006712826 NA Approved DKFZp434I0121 uc010fia.3 A0AVI2 OTTHUMG00000154929 ENST00000457909.1: chr2.hg19:g.97351796_97351816delAGGACATGGTGGCCACAGCGG 0 4 ref NA False 60 60 PASS 1 PASS ref->het 0 NA 188,190 40,40 39,39 1 1 Q17RH2|Q6ZU24 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FER1L5-001 KNOWN basic|exp_conf retained_intron NA pseudogene OTTHUMT00000339030.1 PASS NA None 244 True + AGGACATGGTGGCCACAGCGG ENST00000457909.1 CNNM4 26504 __UNKNOWN__ __UNKNOWN__ 2 97463937 97463938 __UNKNOWN__ Intron INS - - C LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:97463937_97463938insC ENST00000377075.2 + 3 1779 CNNM4_ENST00000496186.1_Intron|CNNM4_ENST00000540067.1_Intron NM_020184.3 NP_064569.3 Q6P4Q7 CNNM4_HUMAN cyclin and CBS domain divalent metal cation transport mediator 4 NA NA NA biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) adenyl nucleotide binding (GO:0030554) breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2) 20 accactgcactcagcctgggcc 0.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 74 75.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.32 NA NA AB046812 CCDS2024.2 2q11.2 2014-08-08 2014-08-07 ENSG00000158158 ENSG00000158158 26504 105 protein-coding gene gene with protein product 607805 "cyclin M4" ACDP4 NA 21393841, 24194943 Standard NM_020184 XM_005263914 NA Approved KIAA1592 uc002swx.3 Q6P4Q7 OTTHUMG00000130532 ENST00000377075.2:c.1681+553->C chr2.hg19:g.97463938_97463938dupC 2 2 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 56,57 7,9 10,8 1 1 B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1 True hg19 CCDS2024.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CNNM4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252954.1 PASS NA None 74 True + C ENST00000377075.2 ZEB2 9839 __UNKNOWN__ __UNKNOWN__ 2 145145743 145145758 __UNKNOWN__ 3'UTR DEL AGAAAGTGGAATTTTC AGAAAGTGGAATTTTC - LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:145145743_145145758delAGAAAGTGGAATTTTC ENST00000558170.2 - 0 6089_6104 ZEB2_ENST00000539609.3_3'UTR|ZEB2_ENST00000409487.3_3'UTR|ZEB2_ENST00000303660.4_3'UTR NM_014795.3 NP_055610.1 O60315 ZEB2_HUMAN zinc finger E-box binding homeobox 2 NA NA NA cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208) breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3) 107 BRCA - Breast invasive adenocarcinoma(221;0.112) AACAAGATGAAGAAAGTGGAATTTTCAGTCGAAAAT 0.264 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Melanoma(33;1235 1264 5755 16332) PASS NA NA NA NA NA 0 NA NA NA NA NA 61 58.92 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA AB011141 CCDS2186.1, CCDS54403.1 2q22.3 2013-01-08 2007-02-15 2007-02-15 ENSG00000169554 ENSG00000169554 9839 "Zinc fingers, C2H2-type", "Homeoboxes / ZF class" 14881 protein-coding gene gene with protein product "SMAD interacting protein 1" 605802 "zinc finger homeobox 1b" ZFHX1B NA Standard NM_014795 NM_014795 NA Approved KIAA0569, SIP-1, SIP1 uc002tvu.3 O60315 OTTHUMG00000131834 ENST00000558170.2:c.*1275GAAAATTCCACTTTCT>- chr2.hg19:g.145145743_145145758delAGAAAGTGGAATTTTC 0 5 ref NA False 67 67 PASS 1 PASS ref->het 0 NA 31,31 18,18 14,14 1 1 A0JP09|B7Z2P2|F5H814|Q9UED1 True hg19 CCDS2186.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZEB2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254778.5 PASS NA None 61 True - AGAAAGTGGAATTTTC ENST00000558170.2 HNRNPA3 220988 __UNKNOWN__ __UNKNOWN__ 2 178077260 178077291 __UNKNOWN__ 5'UTR DEL CCCTGACGCGAACGGCGGCAAAGGCCCTCTTC CCCTGACGCGAACGGCGGCAAAGGCCCTCTTC - rs565665485|rs114778780|rs186188372|rs539364511|rs190993250 byFrequency LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:178077260_178077291delCCCTGACGCGAACGGCGGCAAAGGCCCTCTTC ENST00000392524.2 + 0 0_1 AC079305.8_ENST00000455416.1_RNA P51991 ROA3_HUMAN heterogeneous nuclear ribonucleoprotein A3 NA NA NA gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380) catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529) nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723) breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|urinary_tract(1) 16 CCGGAACTCGCCCTGACGCGAACGGCGGCAAAGGCCCTCTTCCCCTGAAAGC 0.698 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 203 172.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.45 NA NA AF517524 CCDS2273.1 2q31.2 2013-02-12 2008-04-18 ENSG00000170144 ENSG00000170144 220988 "RNA binding motif (RRM) containing" 24941 protein-coding gene gene with protein product 605372 HNRPA3 NA 11886857, 15776420 Standard NM_194247 XM_005246380 NA Approved uc002ulc.1 P51991 OTTHUMG00000132529 ENST00000392524.2:c.-237CCCTGACGCGAACGGCGGCAAAGGCCCTCTTC>- chr2.hg19:g.178077260_178077291delCCCTGACGCGAACGGCGGCAAAGGCCCTCTTC 0 4 ref NA False 158 158 PASS 1 PASS ref->het 0 NA 168,173 20,20 56,51 1 1 D3DPF4|Q53RW7|Q6URK5 True hg19 CCDS2273.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HNRNPA3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000255729.3 PASS NA None 203 True + CCCTGACGCGAACGGCGGCAAAGGCCCTCTTC ENST00000392524.2 ABI2 10152 __UNKNOWN__ __UNKNOWN__ 2 204276045 204276076 __UNKNOWN__ Intron DEL AACTCCTCAGTTACCTTTAATGGGATTTGTGG AACTCCTCAGTTACCTTTAATGGGATTTGTGG - rs149356092 LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:204276045_204276076delAACTCCTCAGTTACCTTTAATGGGATTTGTGG ENST00000422511.2 + 10 1124 ABI2_ENST00000261016.6_Intron|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000424558.1_Intron|ABI2_ENST00000261017.5_Frame_Shift_Del_p.TPQLPLMGFVA344fs|ABI2_ENST00000295851.5_Intron|ABI2_ENST00000430418.1_Intron|ABI2_ENST00000261018.7_Intron|ABI2_ENST00000430574.1_Intron Q9NYB9 ABI2_HUMAN abl-interactor 2 NA NA NA actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209) cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625) breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1) 15 TCCTACAGGTAACTCCTCAGTTACCTTTAATGGGATTTGTGGCCAGAGTCCA 0.392 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 126 113.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF260261 CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1 2q33 2010-09-20 2009-07-23 ENSG00000138443 ENSG00000138443 10152 24011 protein-coding gene gene with protein product 606442 NA 7590236, 10964520 Standard NM_005759 XM_005246217 NA Approved ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2 uc002uzz.3 Q9NYB9 OTTHUMG00000132879 ENST00000422511.2:c.1094-5555AACTCCTCAGTTACCTTTAATGGGATTTGTGG>- chr2.hg19:g.204276045_204276076delAACTCCTCAGTTACCTTTAATGGGATTTGTGG 0 3 ref NA False 46 46 PASS 1 PASS ref->het 0 NA 106,110 17,18 8,8 1 1 B4DSN1|Q13147|Q13249|Q13801|Q9BV70 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ABI2-007 NOVEL not_organism_supported|basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000336179.2 PASS NA None 126 True + AACTCCTCAGTTACCTTTAATGGGATTTGTGG ENST00000422511.2 AAMP 14 __UNKNOWN__ __UNKNOWN__ 2 219134942 219134952 __UNKNOWN__ 5'UTR DEL CGGCCGTTCGG CGGCCGTTCGG - rs13419763 byFrequency LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:219134942_219134952delCGGCCGTTCGG ENST00000248450.4 - 0 28_38 Q13685 AAMP_HUMAN angio-associated, migratory cell protein NA NA NA angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|positive regulation of endothelial cell migration (GO:0010595)|smooth muscle cell migration (GO:0014909) cell surface (GO:0009986)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886) heparin binding (GO:0008201) haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(4)|ovary(2)|skin(1) 11 Renal(207;0.0474) Epithelial(149;7.19e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942) GGAAGAGCGACGGCCGTTCGGCCAATAGCTA 0.664 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 180 186.01 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.51 NA NA AB209790 CCDS33378.1 2q 2013-01-10 ENSG00000127837 ENSG00000127837 14 "WD repeat domain containing" 18 protein-coding gene gene with protein product 603488 NA 7743515 Standard NM_001087 XM_005246325 NA Approved uc002vhk.3 Q13685 OTTHUMG00000155202 ENST00000248450.4:c.-143CCGAACGGCCG>- chr2.hg19:g.219134942_219134952delCGGCCGTTCGG 0 2 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 174,177 4,6 22,20 1 1 Q8WUJ9|Q96H92 True hg19 CCDS33378.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AAMP-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000338756.1 PASS NA None 180 True - CGGCCGTTCGG ENST00000248450.4 ZNF330 27309 __UNKNOWN__ __UNKNOWN__ 4 142155187 142155204 __UNKNOWN__ 3'UTR DEL TGTGTGTGCTTGATGAAT TGTGTGTGCTTGATGAAT - rs571407617 byFrequency LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:142155187_142155204delTGTGTGTGCTTGATGAAT ENST00000262990.4 + 0 1235_1252 ZNF330_ENST00000421169.2_3'UTR NM_014487.4 NP_055302.1 Q9Y3S2 ZN330_HUMAN zinc finger protein 330 NA NA NA chromosome, centromeric region (GO:0000775)|midbody (GO:0030496)|nucleolus (GO:0005730) metal ion binding (GO:0046872)|zinc ion binding (GO:0008270) kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(2) 14 all_hematologic(180;0.162) CAGGAGTGAGTGTGTGTGCTTGATGAATTGTGTGTGGT 0.463 NA NA NA NA NA NA NA NA NA NA 15 0.00299521 0.0106 0 5008 , , NA 22211 0 NA 0.001 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 133 127.84 NA NA 20,4244 NA 0,20,2112 NA NA NA NA NA -9 0 NA NA 49 2,8248 NA 0,2,4123 no utr-3 ZNF330 NM_014487.4 NA 0,22,6235 A1A1,A1R,RR NA 0.0242,0.469,0.1758 NA NA NA 22,12492 NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA AJ006591 CCDS3754.1 4q31.21 2008-05-15 ENSG00000109445 ENSG00000109445 27309 "Zinc fingers, C2H2-type" 15462 protein-coding gene gene with protein product 609550 NA 11528117, 10593942 Standard NM_014487 NM_001292002 NA Approved NOA36, HSA6591 uc003iiq.4 Q9Y3S2 OTTHUMG00000133413 ENST00000262990.4:c.*61TGTGTGTGCTTGATGAAT>- chr4.hg19:g.142155187_142155204delTGTGTGTGCTTGATGAAT 0 3 ref NA False 52 52 PASS 1 PASS ref->het 0 NA 123,128 4,4 24,24 1 1 B2RDA3 True hg19 CCDS3754.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF330-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257271.2 PASS NA None 133 True + TGTGTGTGCTTGATGAAT ENST00000262990.4 NUDT1 4521 __UNKNOWN__ __UNKNOWN__ 7 2281871 2281871 __UNKNOWN__ 5'UTR DEL C C - LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:2281871delC ENST00000356714.1 + 0 15 NUDT1_ENST00000397049.1_5'UTR NM_002452.3 NP_002443.3 P36639 8ODP_HUMAN nudix (nucleoside diphosphate linked moiety X)-type motif 1 NA NA NA ATP catabolic process (GO:0006200)|dATP catabolic process (GO:0046061)|dGTP catabolic process (GO:0006203)|DNA protection (GO:0042262)|DNA repair (GO:0006281)|GTP catabolic process (GO:0006184)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleotide catabolic process (GO:0006195)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281) cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634) 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity (GO:0035539)|8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity (GO:0008413)|ATP diphosphatase activity (GO:0047693)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|snoRNA binding (GO:0030515) large_intestine(3)|lung(8)|urinary_tract(1) 12 Ovarian(82;0.0253)|Melanoma(862;0.155) UCEC - Uterine corpus endometrioid carcinoma (27;0.0822)|OV - Ovarian serous cystadenocarcinoma(56;2.8e-14)|BRCA - Breast invasive adenocarcinoma(126;0.15) AGAGGCCACGCCCCCGGAAGC 0.726 NA NA NA NA NA Modulation of nucleotide pools NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 125 129.14 NA NA NA 5 13 10 NA NA NA NA 7 NA NA NA NA NA NA NA 2281871 643 1519 2162 SO:0001623 5_prime_UTR_variant 0.49 NA NA D16581 CCDS5329.1, CCDS5330.1 7p22 2008-07-18 ENSG00000106268 ENSG00000106268 4521 "Nudix motif containing" 8048 protein-coding gene gene with protein product "mutT human homolog 1", "nudix motif 1", "8-oxo-7,8-dihydrodeoxyguanosine triphosphatase", "8-oxo-dGTPase", "7,8-dihydro-8-oxoguanine triphosphatase", "8-oxo-7,8-dihydroguanosine triphosphatase", "nucleoside diphosphate-linked moiety X-type motif 1" 600312 MTH1 NA 7713494, 8226881 Standard NM_002452 NM_002452 NA Approved uc003slp.1 P36639 OTTHUMG00000023072 ENST00000356714.1:c.-33C>- chr7.hg19:g.2281871delC 4 6 ref NA False 66 66 PASS 5 PASS ref->het 0 NA 79,82 25,26 18,15 1 1 A4D205|Q6LES7|Q6P0Y6|Q7Z7N6|Q8IV95|Q9UBM0|Q9UBM9 True hg19 CCDS5330.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NUDT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000059393.2 PASS NA None 125 True + C ENST00000356714.1 HDAC9 9734 __UNKNOWN__ __UNKNOWN__ 7 18631123 18631124 __UNKNOWN__ Intron INS - - GATGGG LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:18631123_18631124insGATGGG ENST00000524023.1 + 4 518 HDAC9_ENST00000401921.1_Intron|HDAC9_ENST00000405010.3_Intron|HDAC9_ENST00000406072.1_Intron|HDAC9_ENST00000441542.2_Intron|HDAC9_ENST00000417496.2_Intron|HDAC9_ENST00000428307.2_Intron|HDAC9_ENST00000432645.2_Intron|HDAC9_ENST00000406451.4_Intron|HDAC9_ENST00000456174.2_Intron NM_001204147.1 NP_001191076.1 Q9UKV0 HDAC9_HUMAN histone deacetylase 9 NA NA NA B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667) histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134) breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 82 all_lung(11;0.187) Valproic Acid(DB00313) tgtgtgtgtgtgtgtgtgtATT 0.416 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 50 46.71 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF124924 CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1 7p21.1 2008-05-15 ENSG00000048052 ENSG00000048052 9734 14065 protein-coding gene gene with protein product 606543 NA 10523670, 10487760 Standard NM_178425 NA Approved KIAA0744, HDAC, MITR, HD7, HDAC7B uc003sui.3 Q9UKV0 OTTHUMG00000152487 ENST00000524023.1:c.314-15->GATGGG chr7.hg19:g.18631123_18631124insGATGGG 1 2 ref NA False 47 47 PASS 0 PASS ref->het 0 NA 34,45 3,3 14,8 1 1 A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3 True hg19 CCDS56468.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HDAC9-022 PUTATIVE basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000376089.1 PASS NA None 50 True + GATGGG ENST00000524023.1 HOXA7 3204 __UNKNOWN__ __UNKNOWN__ 7 27193472 27193484 __UNKNOWN__ 3'UTR DEL CATTGGACCTCCC CATTGGACCTCCC - rs17500918 LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:27193472_27193484delCATTGGACCTCCC ENST00000242159.3 - 0 1870_1882 HOXA-AS3_ENST00000518947.2_RNA NM_006896.3 NP_008827.2 P31268 HXA7_HUMAN homeobox A7 NA NA NA angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134) endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1) 16 TTGCGGAGGGCATTGGACCTCCCCACCCACTAC 0.502 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 95 95.6 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.02 NA NA CCDS5408.1 7p15.2 2011-06-20 2005-12-22 ENSG00000122592 ENSG00000122592 3204 "Homeoboxes / ANTP class : HOXL subclass" 5108 protein-coding gene gene with protein product 142950 "homeo box A7" HOX1A, HOX1 NA 1973146, 1358459 Standard NM_006896 NA Approved uc003sys.3 P31268 OTTHUMG00000023217 ENST00000242159.3:c.*1056GGGAGGTCCAATG>- chr7.hg19:g.27193472_27193484delCATTGGACCTCCC 0 7 ref NA False 140 132 PASS 1 PASS ref->het 0 NA 63,64 28,28 10,9 1 1 A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1 True hg19 CCDS5408.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HOXA7-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000358695.1 PASS NA None 95 True - CATTGGACCTCCC ENST00000242159.3 CNOT7 29883 __UNKNOWN__ __UNKNOWN__ 8 17092263 17092275 __UNKNOWN__ Frame_Shift_Del DEL CATAAATGACAGG CATAAATGACAGG - LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:17092263_17092275delCATAAATGACAGG ENST00000361272.4 - 5 866_878 c.568_580delCCTGTCATTTATG c.(568-582)cctgtcatttatgatfs p.PVIYD190fs CNOT7_ENST00000523917.1_Frame_Shift_Del_p.PVIYD190fs NM_013354.5 NP_037486.2 Q9UIV1 CNOT7_HUMAN CCR4-NOT transcription complex, subunit 7 190 NA NA carbohydrate metabolic process (GO:0005975)|cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|gene silencing by miRNA (GO:0035195)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of cell proliferation (GO:0008285)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351) CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634) 3'-5'-exoribonuclease activity (GO:0000175)|exoribonuclease activity (GO:0004532)|metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871) central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6) 11 Colorectal(111;0.0523)|COAD - Colon adenocarcinoma(73;0.209) TACTTCACATCATAAATGACAGGAAAAAACAAT 0.404 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 71 71.05 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.08 NA NA L46722 CCDS6000.2, CCDS55202.1 8p22-p21.3 2008-08-07 ENSG00000198791 ENSG00000198791 29883 14101 protein-coding gene gene with protein product "BTG1 binding factor 1" 604913 CAF1 NA 10637334, 1538749, 17264152 Standard NM_013354 XM_005273481 NA Approved uc003wxg.1 Q9UIV1 OTTHUMG00000096971 ENST00000361272.4:c.568_580delCCTGTCATTTATG chr8.hg19:g.17092263_17092275delCATAAATGACAGG ENSP00000355279:p.Pro190fs 0 8 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 66,66 3,3 6,6 1 1 A8MZM5|B3KMP1|B3KN35|D3DSP6|G3V108|Q7Z530 True hg19 CCDS6000.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CNOT7-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000214038.1 PASS NA None 71 True - CATAAATGACAGG ENST00000361272.4 B4GALT1 2683 __UNKNOWN__ __UNKNOWN__ 9 33166839 33166844 __UNKNOWN__ In_Frame_Del DEL GGGCCA GGGCCA - LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:33166839_33166844delGGGCCA ENST00000379731.4 - 1 510_515 c.324_329delTGGCCC c.(322-330)cctggcccc>ccc p.108_110PGP>P B4GALT1_ENST00000535206.1_In_Frame_Del_p.108_110PGP>P NM_001497.3 NP_001488.2 P15291 B4GT1_HUMAN UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 108 NA NA SSQPRPGGDSSPVVDSGPGPASNLT -> GKHAKSSFKQFL LQIKELSNPIDLD (in Ref. 6; AAA68219). {ECO:0000305}. acute inflammatory response (GO:0002526)|angiogenesis involved in wound healing (GO:0060055)|binding of sperm to zona pellucida (GO:0007339)|branching morphogenesis of an epithelial tube (GO:0048754)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|development of secondary sexual characteristics (GO:0045136)|epithelial cell development (GO:0002064)|extracellular matrix organization (GO:0030198)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|lactose biosynthetic process (GO:0005989)|leukocyte migration (GO:0050900)|mammary gland development (GO:0030879)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|oligosaccharide biosynthetic process (GO:0009312)|penetration of zona pellucida (GO:0007341)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of acrosome reaction (GO:0060046)|regulation of cellular component movement (GO:0051270)|single fertilization (GO:0007338)|small molecule metabolic process (GO:0044281) basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|desmosome (GO:0030057)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|glycocalyx (GO:0030112)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886) alpha-tubulin binding (GO:0043014)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|beta-tubulin binding (GO:0048487)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|manganese ion binding (GO:0030145)|N-acetyllactosamine synthase activity (GO:0003945)|protein homodimerization activity (GO:0042803)|UDP-galactosyltransferase activity (GO:0035250) endometrium(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1) 14 LUSC - Lung squamous cell carcinoma(29;0.0084) GBM - Glioblastoma multiforme(74;0.121) N-Acetyl-D-glucosamine(DB00141) GTTGCTAGCGGGGCCAGGGCCAGAAT 0.733 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 239 243.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 1.5 NA NA X14085 CCDS6535.1 9p13 2013-02-19 ENSG00000086062 ENSG00000086062 2683 2.4.1.22 "Beta 4-glycosyltransferases" 924 protein-coding gene gene with protein product 137060 GGTB2 NA 9597550 Standard NM_001497 NM_001497 NA Approved beta4Gal-T1 uc003zsg.2 P15291 OTTHUMG00000019764 ENST00000379731.4:c.324_329delTGGCCC chr9.hg19:g.33166845_33166850delGGGCCA ENSP00000369055:p.Pro108_Gly109del 1 5 ref NA False 87 87 PASS 2 PASS ref->het 0 NA 201,207 9,9 33,29 1 1 B2R710|D3DRL2|Q12909|Q12910|Q12911|Q14456|Q14509|Q14523 True hg19 CCDS6535.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA B4GALT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000052039.1 PASS NA None 239 True - GGGCCA ENST00000379731.4 SLC22A12 116085 __UNKNOWN__ __UNKNOWN__ 11 64369072 64369091 __UNKNOWN__ 3'UTR DEL GTTCTCTGGAGAAGGCAGGA GTTCTCTGGAGAAGGCAGGA - rs139851336 byFrequency LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:64369072_64369091delGTTCTCTGGAGAAGGCAGGA ENST00000377567.2 + 0 1851_1870 SLC22A12_ENST00000377572.1_3'UTR|SLC22A12_ENST00000473690.1_3'UTR|SLC22A12_ENST00000377574.1_3'UTR Q96S37 S22AC_HUMAN solute carrier family 22 (organic anion/urate transporter), member 12 NA NA NA cellular homeostasis (GO:0019725)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747) apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) PDZ domain binding (GO:0030165)|urate transmembrane transporter activity (GO:0015143) central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1) 27 Losartan(DB00678)|Probenecid(DB01032) GACTTCTTCTGTTCTCTGGAGAAGGCAGGAGGAAAGCAAA 0.595 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 174 157.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.67 NA NA AB071863 CCDS8075.1, CCDS60835.1, CCDS60836.1 11q13.1 2013-05-22 2008-01-11 ENSG00000197891 ENSG00000197891 116085 "Solute carriers" 17989 protein-coding gene gene with protein product 607096 "solute carrier family 22 (organic anion/cation transporter), member 12" NA 12024214 Standard NM_144585 NM_144585 NA Approved OAT4L, RST, URAT1 uc009yps.2 Q96S37 OTTHUMG00000045213 ENST00000377567.2:c.*68GTTCTCTGGAGAAGGCAGGA>- chr11.hg19:g.64369072_64369091delGTTCTCTGGAGAAGGCAGGA 0 4 ref NA False 73 73 PASS 1 PASS ref->het 0 NA 72,73 64,65 41,42 1 1 B7WPG1|G3XAN7|Q19PF7|Q19PF8|Q19PF9|Q19PG0|Q6UXW3|Q96DT2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC22A12-002 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000141957.2 PASS NA None 174 True + GTTCTCTGGAGAAGGCAGGA ENST00000377567.2 LHFP 10186 __UNKNOWN__ __UNKNOWN__ 13 39917776 39917777 __UNKNOWN__ 3'UTR INS - - TACCTGCA LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:39917776_39917777insTACCTGCA ENST00000379589.3 - 0 1361_1362 NM_005780.2 NP_005771.1 Q9Y693 LHFP_HUMAN lipoma HMGIC fusion partner NA NA NA integral component of membrane (GO:0016021) DNA binding (GO:0003677) HMGA2/LHFP(2) breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2) 13 Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114) OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105) gtgtgtgtgtgtgtgtgtgtgt 0.376 NA NA TRUE HMGA2 lipoma NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Dom yes NA 13 13q12 10186 lipoma HMGIC fusion partner NA M 0 NA NA NA NA NA 91 88.62 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 3.05 NA NA AF098807 CCDS9369.1 13q12 2008-07-18 ENSG00000183722 ENSG00000183722 10186 6586 protein-coding gene gene with protein product 606710 NA 10329012 Standard NM_005780 NM_005780 NA Approved MGC22429 uc001uxf.3 Q9Y693 OTTHUMG00000016767 ENST00000379589.3:c.*297->TGCAGGTA chr13.hg19:g.39917776_39917777insTACCTGCA 1 2 ref NA False 40 40 PASS 0 PASS ref->het 0 NA 74,88 4,4 22,15 1 1 B2R7M2|Q53FC0|Q96SH5 True hg19 CCDS9369.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LHFP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044619.1 PASS NA None 91 True - TACCTGCA ENST00000379589.3 MORF4L1 10933 __UNKNOWN__ __UNKNOWN__ 15 79142281 79142282 __UNKNOWN__ Intron INS - - GA rs397817735|rs200606667|rs57917383|rs151239462 byFrequency LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:79142281_79142282insGA ENST00000379535.4 + 2 679 Q9UBU8 MO4L1_HUMAN mortality factor 4 like 1 NA NA NA cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|double-strand break repair via homologous recombination (GO:0000724)|histone deacetylation (GO:0016575)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|Sin3 complex (GO:0016580) chromatin binding (GO:0003682)|protein N-terminus binding (GO:0047485) breast(1)|large_intestine(3)|lung(4)|prostate(1)|urinary_tract(1) 10 ccagcctgggtgagagtgagac 0.505 NA NA NA NA NA NA NA NA NA NA 3053 0.609625 0.5651 0.6801 5008 , , NA 16338 0.7639 NA 0.6133 False NA ,,, NA NA NA 2504 0.4571 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 15 16.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF100615 CCDS10307.1, CCDS32304.1, CCDS58393.1 15q25.1 2009-07-13 ENSG00000185787 ENSG00000185787 10933 16989 protein-coding gene gene with protein product "MORF-related gene on chromosome 15", "Esa1p-associated factor 3 homolog (S. cerevisiae)" 607303 NA 8619474, 9110174 Standard NM_006791 NM_006791 NA Approved MRG15, MORFRG15, HsT17725, Eaf3, MEAF3 uc002bel.4 Q9UBU8 OTTHUMG00000143865 ENST00000379535.4:c.115+9264->GA chr15.hg19:g.79142284_79142285dupGA 3 4 ref NA False 31 31 PASS 2 PASS ref->hom 0 NA 0,0 14,15 1,2 1 1 B4DKN6|B7Z6R1|D3DW88|O95899|Q5QTS1|Q6NVX8|Q86YT7|Q9HBP6|Q9NSW5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MORF4L1-007 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000417833.1 PASS NA None 15 True + GA ENST00000379535.4 MEF2A 4205 __UNKNOWN__ __UNKNOWN__ 15 100254577 100254591 __UNKNOWN__ 3'UTR DEL GGGGAAAATAATCAT GGGGAAAATAATCAT - LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:100254577_100254591delGGGGAAAATAATCAT ENST00000354410.5 + 0 3730_3744 MEF2A_ENST00000449277.2_3'UTR|MEF2A_ENST00000453228.2_3'UTR|MEF2A_ENST00000557942.1_3'UTR|MEF2A_ENST00000338042.6_3'UTR NM_005587.2 NP_005578.2 Q02078 MEF2A_HUMAN myocyte enhancer factor 2A NA NA NA apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005) cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332) endometrium(2)|large_intestine(2)|lung(7)|ovary(1) 12 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00085) TAAATGATTAGGGGAAAATAATCATGGGGAAAGGG 0.358 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 89 80.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.48 NA NA CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1 15q26 2008-02-05 2007-04-24 ENSG00000068305 4205 "Myocyte enhancer factors" 6993 protein-coding gene gene with protein product 600660 NA 1516833 Standard NM_005587 NA Approved RSRFC4, RSRFC9 uc002bvf.3 Q02078 ENST00000354410.5:c.*1615GGGGAAAATAATCAT>- chr15.hg19:g.100254577_100254591delGGGGAAAATAATCAT 0 4 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 84,84 3,3 10,10 1 1 B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14 True hg19 CCDS45362.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MEF2A-001 KNOWN overlapping_uORF|basic|CCDS protein_coding NA protein_coding OTTHUMT00000415980.1 PASS NA None 89 True + GGGGAAAATAATCAT ENST00000354410.5 UNKL 64718 __UNKNOWN__ __UNKNOWN__ 16 1420336 1420361 __UNKNOWN__ Splice_Site DEL AGAGCCGGCCAGCGACCTGGGACCTG AGAGCCGGCCAGCGACCTGGGACCTG - rs566933782|rs138288642 byFrequency LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:1420336_1420361delAGAGCCGGCCAGCGACCTGGGACCTG ENST00000508903.2 - 12 1357_1379 c.1358_1380delCAGGTCCCAGGTCGCTGGCCGGCTCT c.(1357-1380)gcaggtcccaggtcgctggccggc>g p.AGPRSLAG453fs UNKL_ENST00000397464.1_5'UTR|UNKL_ENST00000402641.2_5'UTR|UNKL_ENST00000248104.7_5'UTR|UNKL_ENST00000389221.4_Splice_Site_p.AGPRSLAG450fs|UNKL_ENST00000403703.1_5'UTR Q9H9P5 UNKL_HUMAN unkempt family zinc finger-like 450 Ser-rich. NA NA protein ubiquitination (GO:0016567) cytoplasm (GO:0005737)|nucleus (GO:0005634) ligase activity (GO:0016874)|zinc ion binding (GO:0008270) autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(1) 4 Hepatocellular(780;0.0893) CGACAGGTGCAGAGCCGGCCAGCGACCTGGGACCTGGCGGGGGCGG 0.699 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 146 141.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0.96 NA NA BC011924 CCDS32359.1, CCDS53980.1, CCDS61787.1 16p13.3 2014-03-10 2013-10-17 ENSG00000059145 ENSG00000059145 64718 "Zinc fingers, CCCH-type domain containing" 14184 protein-coding gene gene with protein product NA "chromosome 16 open reading frame 28", "unkempt homolog (Drosophila)-like" C16orf28 NA 20148946 Standard NM_001037125 NM_001193389 NA Approved ZC3HDC5L, ZC3H5L, FLJ23360 uc031qup.1 Q9H9P5 OTTHUMG00000128553 ENST00000508903.2:c.1358-1CAGGTCCCAGGTCGCTGGCCGGCTCT>- chr16.hg19:g.1420336_1420361delAGAGCCGGCCAGCGACCTGGGACCTG 0 7 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 91,91 26,26 11,11 1 1 B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UNKL-002 NOVEL basic|appris_principal protein_coding NA protein_coding OTTHUMT00000362481.2 PASS NA None 146 Frame_Shift_Del True - AGAGCCGGCCAGCGACCTGGGACCTG ENST00000508903.2 MYH2 4620 __UNKNOWN__ __UNKNOWN__ 17 10435024 10435037 __UNKNOWN__ Intron DEL TTGCCTCTGACTTG TTGCCTCTGACTTG - LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:10435024_10435037delTTGCCTCTGACTTG ENST00000532183.2 - 16 2243 MYH2_ENST00000245503.5_Frame_Shift_Del_p.KSEAK871fs|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Frame_Shift_Del_p.KSEAK871fs|RP11-799N11.1_ENST00000399342.2_RNA Q9UKX2 MYH2_HUMAN myosin, heavy chain 2, skeletal muscle, adult NA NA NA Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823) A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017) ATP binding (GO:0005524)|microfilament motor activity (GO:0000146) NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4) 176 TCCTTCCTTTTTGCCTCTGACTTGGCAAGTTCGT 0.421 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 72 76.13 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.76 NA NA CCDS11156.1 17p13.1 2014-02-04 2006-09-29 ENSG00000125414 ENSG00000125414 4620 "Myosins / Myosin superfamily : Class II" 7572 protein-coding gene gene with protein product 160740 "myosin, heavy polypeptide 2, skeletal muscle, adult", "inclusion body myopathy 3, autosomal dominant" IBM3 NA 7545970, 11889243 Standard NM_017534 NM_001100112 NA Approved MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A uc010coi.3 Q9UKX2 OTTHUMG00000130363 ENST00000532183.2:c.1974+4809CAAGTCAGAGGCAA>- chr17.hg19:g.10435024_10435037delTTGCCTCTGACTTG 0 5 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 65,69 4,4 9,8 1 1 A0AVL4|Q14322|Q16229|Q567P6|Q86T56 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MYH2-006 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000394461.43 PASS NA None 72 True - TTGCCTCTGACTTG ENST00000532183.2 TRPM4 54795 __UNKNOWN__ __UNKNOWN__ 19 49671595 49671619 __UNKNOWN__ Frame_Shift_Del DEL CCAGCACTGGGGGCACCAAGGTGGT CCAGCACTGGGGGCACCAAGGTGGT - rs200075383|rs566398496 LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:49671595_49671619delCCAGCACTGGGGGCACCAAGGTGGT ENST00000252826.5 + 5 653_677 c.527_551delCCAGCACTGGGGGCACCAAGGTGGT c.(526-552)gccagcactgggggcaccaaggtggtgfs p.ASTGGTKVV176fs TRPM4_ENST00000427978.2_Frame_Shift_Del_p.ASTGGTKVV176fs|TRPM4_ENST00000355712.5_Intron NM_017636.3 NP_060106.2 Q8TD43 TRPM4_HUMAN transient receptor potential cation channel, subfamily M, member 4 176 NA NA calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310) endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262) breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2) 49 all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15) all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751) CATCAGATGGCCAGCACTGGGGGCACCAAGGTGGTGGCCATGGGT 0.631 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 162 142.27 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 NA NA AK000048 CCDS33073.1, CCDS56098.1 19q13.3 2011-12-14 ENSG00000130529 54795 "Voltage-gated ion channels / Transient receptor potential cation channels" 17993 protein-coding gene gene with protein product 606936 NA 11535825, 16382100 Standard NM_017636 NM_017636 NA Approved FLJ20041 uc002pmw.3 Q8TD43 ENST00000252826.5:c.527_551delCCAGCACTGGGGGCACCAAGGTGGT chr19.hg19:g.49671595_49671619delCCAGCACTGGGGGCACCAAGGTGGT ENSP00000252826:p.Ala176fs 0 4 ref NA False 78 78 PASS 1 PASS ref->het 0 NA 92,93 38,39 7,6 1 1 A2RU25|Q7Z5D9|Q96L84|Q9NXV1 True hg19 CCDS33073.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRPM4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000465543.2 PASS NA None 162 True + CCAGCACTGGGGGCACCAAGGTGGT ENST00000252826.5 CELSR1 9620 __UNKNOWN__ __UNKNOWN__ 22 46929869 46929893 __UNKNOWN__ Frame_Shift_Del DEL GGACCTCAAAGTCCAGCTCCACCAT GGACCTCAAAGTCCAGCTCCACCAT - rs144782066 LTS-022_T LTS-022_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:46929869_46929893delGGACCTCAAAGTCCAGCTCCACCAT ENST00000262738.3 - 1 3174_3198 c.3175_3199delATGGTGGAGCTGGACTTTGAGGTCC c.(3175-3201)atggtggagctggactttgaggtccggfs p.MVELDFEVR1059fs CELSR1_ENST00000395964.1_Frame_Shift_Del_p.MVELDFEVR1059fs|CELSR1_ENST00000497509.1_5'UTR NM_014246.1 NP_055061.1 Q9NYQ6 CELR1_HUMAN cadherin, EGF LAG seven-pass G-type receptor 1 1059 Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}. NA NA anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060) integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886) calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888) p.L1062M(1) breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3) 95 Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766) UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171) TACTCCCGCCGGACCTCAAAGTCCAGCTCCACCATGGCACGCAGG 0.604 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 1 Substitution - Missense(1) endometrium(1) NA NA NA NA NA 124 117.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.09 NA NA AF231024 CCDS14076.1 22q13.31 2014-08-08 2013-02-18 ENSG00000075275 ENSG00000075275 9620 "Cadherins / Major cadherins", "-", "GPCR / Class B : Orphans" 1850 protein-coding gene gene with protein product "flamingo homolog 2 (Drosophila)" 604523 "cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog" NA 9339365 Standard NM_014246 XM_006724383 NA Approved ME2, HFMI2, FMI2, CDHF9 uc003bhw.1 Q9NYQ6 OTTHUMG00000150423 ENST00000262738.3:c.3175_3199delATGGTGGAGCTGGACTTTGAGGTCC chr22.hg19:g.46929869_46929893delGGACCTCAAAGTCCAGCTCCACCAT ENSP00000262738:p.Met1059fs 0 5 ref NA False 129 108 PASS 1 PASS ref->het 0 NA 74,75 38,39 24,24 1 1 O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526 True hg19 CCDS14076.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CELSR1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000318037.1 PASS NA None 124 True - GGACCTCAAAGTCCAGCTCCACCAT ENST00000262738.3 MORN1 79906 __UNKNOWN__ __UNKNOWN__ 1 2290000 2290003 __UNKNOWN__ Intron DEL GAAC GAAC - rs558147721 LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:2290000_2290003delGAAC ENST00000378529.3 - 9 1043 MORN1_ENST00000606372.1_Intron|MORN1_ENST00000378531.3_Intron Q5T089 MORN1_HUMAN MORN repeat containing 1 NA NA NA breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(1)|ovary(2) 9 all_cancers(77;0.000194)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634) all_epithelial(116;3.3e-15)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217) Epithelial(90;2.21e-37)|OV - Ovarian serous cystadenocarcinoma(86;5.01e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00137)|BRCA - Breast invasive adenocarcinoma(365;0.00488)|STAD - Stomach adenocarcinoma(132;0.00665)|KIRC - Kidney renal clear cell carcinoma(229;0.0203)|Lung(427;0.212) AACAAACTCAGAACTAACTCATTG 0.417 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 606 573.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.81 AK024003 CCDS40.1, CCDS72688.1 1p36.33-p36.32 2008-02-05 ENSG00000116151 ENSG00000116151 79906 25852 protein-coding gene gene with protein product NA NA 12477932 Standard NM_024848 XM_005244798 NA Approved FLJ13941 uc001ajb.1 Q5T089 OTTHUMG00000001402 ENST00000378529.3:c.869+27GTTC>- chr1.hg19:g.2290000_2290003delGAAC 0 3 ref NA False 59 59 PASS 1 PASS ref->het 0 NA 401,405 157,159 47,43 1 1 A6NKZ6|Q8WW30|Q9H852 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MORN1-002 PUTATIVE basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000004056.1 PASS NA None 606 NA True - GAAC ENST00000378529.3 PTBP2 58155 __UNKNOWN__ __UNKNOWN__ 1 97215236 97215238 __UNKNOWN__ Intron DEL TAA TAA - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:97215236_97215238delTAA ENST00000426398.2 + 3 82 PTBP2_ENST00000370198.1_Intron|PTBP2_ENST00000609116.1_Intron|PTBP2_ENST00000482253.1_Intron|PTBP2_ENST00000370197.1_Intron|PTBP2_ENST00000541987.1_Intron|PTBP2_ENST00000394184.3_In_Frame_Del_p.N24del NM_021190.2 NP_067013.1 Q9UKA9 PTBP2_HUMAN polypyrimidine tract binding protein 2 NA NA NA mRNA splice site selection (GO:0006376)|negative regulation of RNA splicing (GO:0033119)|regulation of neural precursor cell proliferation (GO:2000177) spliceosomal complex (GO:0005681) mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822) central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|skin(1) 26 all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171) all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202) ATGTAACAGTTAATAACGTAATT 0.389 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 123 128.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.13 AB051232 CCDS754.1, CCDS72828.1, CCDS72829.1, CCDS72830.1 1p21.3 2013-07-16 ENSG00000117569 ENSG00000117569 58155 "RNA binding motif (RRM) containing" 17662 protein-coding gene gene with protein product 608449 NA 11003644 Standard XM_005271084 NA Approved brPTB, nPTB, PTB, PTBLP uc001drq.3 Q9UKA9 OTTHUMG00000010685 ENST00000426398.2:c.40-1743TAA>- chr1.hg19:g.97215239_97215241delTAA 1 4 ref NA False 42 42 PASS 2 PASS ref->het 0 NA 61,61 52,52 12,12 1 1 Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76 True hg19 CCDS754.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PTBP2-002 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000029453.1 PASS NA None 123 NA True + TAA ENST00000426398.2 FLG 2312 __UNKNOWN__ __UNKNOWN__ 1 152280742 152280756 __UNKNOWN__ In_Frame_Del DEL CCTGAGTGCCTAGAG CCTGAGTGCCTAGAG - rs375983095|rs531670104 LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:152280742_152280756delCCTGAGTGCCTAGAG ENST00000368799.1 - 3 6641_6655 c.6606_6620delCTCTAGGCACTCAGG c.(6604-6621)ggctctaggcactcaggg>ggg p.2202_2207GSRHSG>G FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA NM_002016.1 NP_002007.1 P20930 FILA_HUMAN filaggrin 2202 Ser-rich. NA NA establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275) cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634) calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198) p.G2207A(1) autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12) 424 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) ATGATGCGACCCTGAGTGCCTAGAGCCATCTCCTG 0.572 NA NA NA NA NA Ichthyosis NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 1 Substitution - Missense(1) lung(1) NA NA NA NA NA 923 856.05 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 1.58 Familial Cancer Database X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris XM_048104 CCDS30860.1 1q21.3 2013-01-10 ENSG00000143631 ENSG00000143631 2312 "EF-hand domain containing" 3748 protein-coding gene gene with protein product 135940 NA 2740331, 2248957, 16444271 Standard NM_002016 NM_002016 NA Approved uc001ezu.1 P20930 OTTHUMG00000012202 ENST00000368799.1:c.6606_6620delCTCTAGGCACTCAGG chr1.hg19:g.152280742_152280756delCCTGAGTGCCTAGAG ENSP00000357789:p.Gly2202_Ser2206del 0 3 ref NA False 50 50 PASS 1 PASS ref->het 0 NA 582,594 236,241 141,127 1 1 Q01720|Q5T583|Q9UC71 True hg19 CCDS30860.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FLG-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000033742.1 PASS NA None 923 NA True - CCTGAGTGCCTAGAG ENST00000368799.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 1 168341246 168341247 __UNKNOWN__ IGR DEL TG TG - rs3831823|rs71793871 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:168341246_168341247delTG NA TBX19 (57582 upstream) : MIR557 (3514 downstream) NA NA NA NA aggcctggcatgtgtatccaca 0.495 NA NA NA NA NA 1828 0.365016 0.6112 0.2046 5008 , , NA 21614 0.2768 NA 0.2276 False NA ,,, NA NA NA 2504 0.3783 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 158 162.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.77 NA NA NA NA NA chr1.hg19:g.168341248_168341249delTG 1 2 ref NA False 62 61 PASS 2 PASS ref->het 0 NA 29,30 106,107 23,21 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 158 NA True TG LAMC1 3915 __UNKNOWN__ __UNKNOWN__ 1 183100595 183100598 __UNKNOWN__ Intron DEL TATT TATT - rs67028115|rs56123159|rs55657301|rs4047797|rs566368469|rs2333619|rs138728349 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:183100595_183100598delTATT ENST00000258341.4 + 20 3823 NM_002293.3 NP_002284.3 P11047 LAMC1_HUMAN laminin, gamma 1 (formerly LAMB2) NA NA NA axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446) basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260) extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208) NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3) 76 tgtgtgtgtgtATTGTCTTATCCC 0.402 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 115 126.44 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 6.6 J03202 CCDS1351.1 1q31 2013-03-01 ENSG00000135862 ENSG00000135862 3915 "Laminins" 6492 protein-coding gene gene with protein product 150290 LAMB2 NA 3234037 Standard NM_002293 NM_002293 NA Approved uc001gpy.4 P11047 OTTHUMG00000035418 ENST00000258341.4:c.3566+82TATT>- chr1.hg19:g.183100595_183100598delTATT 0 3 ref NA False 46 46 PASS 1 PASS ref->het 0 NA 9,17 73,76 57,50 2 2 Q5VYE7 True hg19 CCDS1351.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LAMC1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000085954.2 PASS NA None 115 NA True + TATT ENST00000258341.4 TTC27 55622 __UNKNOWN__ __UNKNOWN__ 2 33045922 33045930 __UNKNOWN__ In_Frame_Del DEL GAATTAGCT GAATTAGCT - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:33045922_33045930delGAATTAGCT ENST00000317907.4 + 20 2680_2688 c.2449_2457delGAATTAGCT c.(2449-2457)gaattagctdel p.ELA817del NM_001193509.1|NM_017735.4 NP_001180438.1|NP_060205.3 Q6P3X3 TTC27_HUMAN tetratricopeptide repeat domain 27 817 NA NA breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 38 aatgtccagggaattagctgatgacataa 0.354 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 325 320.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 1.43 BC063791, AK000279 CCDS33176.1 2p22.3 2013-01-10 ENSG00000018699 ENSG00000018699 55622 "Tetratricopeptide (TTC) repeat domain containing" 25986 protein-coding gene gene with protein product NA NA Standard NM_017735 NM_001193509 NA Approved FLJ20272 uc002rom.3 Q6P3X3 OTTHUMG00000152134 ENST00000317907.4:c.2449_2457delGAATTAGCT chr2.hg19:g.33045922_33045930delGAATTAGCT ENSP00000313953:p.Glu817_Ala819del 0 3 ref NA False 153 96 PASS 1 PASS ref->het 0 NA 157,161 147,150 37,31 1 1 A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4 True hg19 CCDS33176.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TTC27-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000325395.1 PASS NA None 325 NA True + GAATTAGCT ENST00000317907.4 HHLA2 11148 __UNKNOWN__ __UNKNOWN__ 3 108081299 108081301 __UNKNOWN__ Intron DEL AGA AGA - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:108081299_108081301delAGA ENST00000357759.5 + 7 1522 HHLA2_ENST00000491820.1_Intron|HHLA2_ENST00000467562.1_Intron|HHLA2_ENST00000467761.1_Intron|HHLA2_ENST00000489514.2_Intron NM_007072.2 NP_009003.1 Q9UM44 HHLA2_HUMAN HERV-H LTR-associating 2 NA NA NA positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295) integral component of membrane (GO:0016021) endometrium(2)|large_intestine(1)|lung(14)|ovary(1) 18 CAGAGGTAATAGAAGAATTTGGG 0.419 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 246 249.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.17 AF126162 CCDS46883.1, CCDS63713.1, CCDS74975.1 3q13.13 2013-01-11 ENSG00000114455 ENSG00000114455 11148 "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing" 4905 protein-coding gene gene with protein product 604371 NA 10444326 Standard NM_007072 NM_007072 NA Approved B7H7 uc003dwz.3 Q9UM44 OTTHUMG00000159224 ENST00000357759.5:c.1108+6AGA>- chr3.hg19:g.108081302_108081304delAGA 1 4 ref NA False 39 39 PASS 2 PASS ref->het 0 NA 143,145 70,70 28,27 1 1 B4DKN2|D3DN60|Q9NWQ6 True hg19 CCDS46883.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HHLA2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000353924.1 PASS NA None 246 NA True + AGA ENST00000357759.5 RNF13 11342 __UNKNOWN__ __UNKNOWN__ 3 149619799 149619800 __UNKNOWN__ Intron INS - - AGTT rs368358458|rs201293440 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:149619799_149619800insAGTT ENST00000344229.3 + 7 1111 RNF13_ENST00000361785.6_Intron|RNF13_ENST00000392894.3_Intron NM_007282.4 NP_009213.1 O43567 RNF13_HUMAN ring finger protein 13 NA NA NA protein autoubiquitination (GO:0051865) endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634) ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270) breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(2) 11 all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255) LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066) ATTATGAAGAAAAGTTGATTAT 0.272 NA NA NA NA NA 135 0.0269569 0.034 0.0159 5008 , , NA 15268 0.004 NA 0.0328 False NA ,,, NA NA NA 2504 0.0429 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 125 126.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.27 AF037204 CCDS3146.1 3q25.1 2013-01-09 ENSG00000082996 ENSG00000082996 11342 "RING-type (C3HC4) zinc fingers" 10057 protein-coding gene gene with protein product 609247 NA Standard NM_183384 NM_183381 NA Approved RZF uc003exp.4 O43567 OTTHUMG00000150338 ENST00000344229.3:c.410-59->AGTT chr3.hg19:g.149619799_149619800insAGTT 1 6 ref NA False 36 36 PASS 0 PASS ref->het 0 NA 32,32 86,88 9,7 1 1 A6NC87|B3KR12|Q05D66|Q6IBJ9 True hg19 CCDS3146.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RNF13-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000356876.1 PASS NA None 125 NA True + AGTT ENST00000344229.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 4 15657976 15657979 __UNKNOWN__ IGR DEL AGAG AGAG - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:15657976_15657979delAGAG NA FBXL5 (941 upstream) : FBXL5 (3374 downstream) NA NA NA NA CTGGACAGATAGAGAAATAGGAGA 0.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 364 364.36 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.55 NA NA NA NA NA chr4.hg19:g.15657976_15657979delAGAG 0 4 ref NA False 64 64 PASS 2 PASS ref->het 0 NA 242,244 68,69 52,50 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 364 NA True AG UGT2A3 79799 __UNKNOWN__ __UNKNOWN__ 4 69798563 69798564 __UNKNOWN__ Intron DEL TT TT - rs60549305 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:69798563_69798564delTT ENST00000251566.4 - 3 895 UGT2A3_ENST00000420231.2_Intron NM_024743.3 NP_079019.3 Q6UWM9 UD2A3_HUMAN UDP glucuronosyltransferase 2 family, polypeptide A3 NA NA NA cellular glucuronidation (GO:0052695) integral component of membrane (GO:0016021) glucuronosyltransferase activity (GO:0015020) NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 36 AAATAAATACTTGAGAAATTAT 0.272 NA NA NA NA NA 367 0.0732827 0.1717 0.0562 5008 , , NA 16700 0.0565 NA 0.002 False NA ,,, NA NA NA 2504 0.0429 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 54 52.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS3525.1 4q13.2 2010-12-14 ENSG00000135220 ENSG00000135220 79799 "UDP glucuronosyltransferases" 28528 protein-coding gene gene with protein product NA NA Standard NM_024743 NM_024743 NA Approved FLJ21934 uc003hef.2 Q6UWM9 OTTHUMG00000129408 ENST00000251566.4:c.865-86AA>- chr4.hg19:g.69798563_69798564delTT 0 2 ref NA False 56 53 PASS 2 PASS ref->het 0 NA 1,1 41,42 9,8 1 1 Q9H6S4 True hg19 CCDS3525.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UGT2A3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251564.1 PASS NA None 54 NA True - T ENST00000251566.4 RASGEF1B 153020 __UNKNOWN__ __UNKNOWN__ 4 82355155 82355156 __UNKNOWN__ Intron INS - - A rs111822559 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:82355155_82355156insA ENST00000264400.2 - 12 1352 RASGEF1B_ENST00000335927.7_Intron|RASGEF1B_ENST00000509081.1_Intron NM_152545.1 NP_689758.1 Q0VAM2 RGF1B_HUMAN RasGEF domain family, member 1B NA NA NA positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264) endosome (GO:0005768) Ras guanyl-nucleotide exchange factor activity (GO:0005088) endometrium(2)|kidney(5)|large_intestine(4)|lung(13)|prostate(1)|skin(1) 26 AAGGTGATCATAAAAAAATAAT 0.342 NA NA NA NA NA AAAAAAA|AAAAAAA|AAAAAAAA|insertion 241 0.048123 0.174 0.0144 5008 , , NA 19282 0 NA 0.001 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 109 125.06 NA 542,3724 NA 32,478,1623 NA NA NA NA 0.8 0 dbSNP_132 60 8,8246 NA 0,8,4119 no intron RASGEF1B NM_152545.1 32,486,5742 A1A1,A1R,RR NA 0.0969,12.7051,4.393 NA 550,11970 NA NA NA SO:0001627 intron_variant 1.09 AK056257 CCDS34022.1, CCDS75151.1, CCDS75152.1 4q21.21 2013-09-24 ENSG00000138670 153020 24881 protein-coding gene gene with protein product 614532 NA 12488504 Standard NM_152545 XM_005262776 NA Approved GPIG4, FLJ31695 uc003hmi.1 Q0VAM2 ENST00000264400.2:c.1201-38->T chr4.hg19:g.82355162_82355162dupA 8 9 ref NA False 48 47 PASS 7 PASS ref->het 0 NA 6,6 86,87 15,15 1 1 Q0VAM1|Q4W5L7|Q4W5M3|Q96MY8 True hg19 CCDS34022.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RASGEF1B-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000362830.1 PASS NA None 109 NA True - A ENST00000264400.2 HELQ 113510 __UNKNOWN__ __UNKNOWN__ 4 84368226 84368249 __UNKNOWN__ Intron DEL CATTGTGGCCAATGCCTGTAATCC CATTGTGGCCAATGCCTGTAATCC - rs202018096|rs67003132|rs113900798|rs11272773 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:84368226_84368249delCATTGTGGCCAATGCCTGTAATCC ENST00000510985.1 - 4 1321 HELQ_ENST00000295488.3_Intron Q8TDG4 HELQ_HUMAN helicase, POLQ-like NA NA NA double-strand break repair via homologous recombination (GO:0000724) nucleolus (GO:0005730)|nucleus (GO:0005634) ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676) breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2) 38 ATTggccaggcattgtggccaatgcctgtaatcccagtaccttg 0.424 NA NA NA NA NA Other identified genes with known or suspected DNA repair function 2593 0.517772 0.292 0.6081 5008 , , NA 18919 0.6786 NA 0.4861 False NA ,,, NA NA NA 2504 0.6258 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 35 39.46 NA 881,3147 NA 198,485,1331 NA NA NA NA 1 0 dbSNP_120 10 3022,4756 NA 851,1320,1718 no intron HELQ NM_133636.2 1049,1805,3049 A1A1,A1R,RR NA 38.8532,21.8719,33.0595 NA 3903,7903 NA NA NA SO:0001627 intron_variant 0.1 AF436845 CCDS3603.1, CCDS75158.1 4q21.23 2009-02-26 ENSG00000163312 ENSG00000163312 113510 18536 protein-coding gene gene with protein product 606769 NA 11751861 Standard NM_133636 XM_005262711 NA Approved Hel308 uc003hom.3 Q8TDG4 OTTHUMG00000130423 ENST00000510985.1:c.1192-987GGATTACAGGCATTGGCCACAATG>- chr4.hg19:g.84368226_84368249delCATTGTGGCCAATGCCTGTAATCC 0 3 ref NA False 34 34 PASS 1 PASS ref->hom 0 NA 0,0 18,18 14,14 1 1 Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HELQ-002 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000363955.1 PASS NA None 35 NA True - CATTGTGGCCAATGCCTGTAATCC ENST00000510985.1 SMARCAD1 56916 __UNKNOWN__ __UNKNOWN__ 4 95194900 95194901 __UNKNOWN__ Intron INS - - G LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:95194900_95194901insG ENST00000509418.1 + 4 769 SMARCAD1_ENST00000457823.2_Intron|SMARCAD1_ENST00000354268.4_Intron NM_001254949.1 NP_001241878.1 Q9H4L7 SMRCD_HUMAN SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 NA NA NA ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018) heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861) ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676) breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 44 OV - Ovarian serous cystadenocarcinoma(123;4.33e-08) GTATTTAACTTTATCATGTTTT 0.376 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 298 289.13 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.38 AB032948 CCDS3639.1, CCDS47101.1, CCDS58914.1 4q22-q23 2008-02-05 ENSG00000163104 ENSG00000163104 56916 18398 protein-coding gene gene with protein product 612761 NA 11031099 Standard NM_020159 NM_001128430 NA Approved ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015 uc003htb.4 Q9H4L7 OTTHUMG00000130971 ENST00000509418.1:c.382+33->G chr4.hg19:g.95194900_95194901insG 1 4 ref NA False 82 82 PASS 0 PASS ref->het 0 NA 207,211 64,64 25,24 1 1 B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7 True hg19 CCDS58914.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SMARCAD1-006 PUTATIVE basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000362981.2 PASS NA None 298 NA True + G ENST00000509418.1 KIAA0922 23240 __UNKNOWN__ __UNKNOWN__ 4 154504516 154504520 __UNKNOWN__ Intron DEL TTTAA TTTAA - rs111303446 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:154504516_154504520delTTTAA ENST00000409959.3 + 10 1000 KIAA0922_ENST00000409663.3_Intron|KIAA0922_ENST00000440693.1_Intron NM_001131007.1 NP_001124479.1 A2VDJ0 T131L_HUMAN KIAA0922 NA NA NA integral component of membrane (GO:0016021) breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 63 all_hematologic(180;0.093) Renal(120;0.118) tcttttttgctttaatttaagccca 0.366 NA NA NA NA NA 510 0.101837 0.3563 0.0288 5008 , , NA 20704 0 NA 0.0139 False NA ,,, NA NA NA 2504 0.0051 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 76 75.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AK096538 CCDS3783.2, CCDS47148.1 4q31.3 2008-02-05 ENSG00000121210 ENSG00000121210 23240 29146 protein-coding gene gene with protein product NA NA 10231032, 11230166 Standard NM_015196 NM_015196 NA Approved DKFZp586H1322, TMEM131L uc010ipp.3 A2VDJ0 OTTHUMG00000153244 ENST00000409959.3:c.951+116TTTAA>- chr4.hg19:g.154504521_154504525delTTTAA 1 3 ref NA False 75 62 PASS 2 PASS ref->het 0 NA 2,2 58,59 14,14 1 1 B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7 True hg19 CCDS47148.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KIAA0922-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000330369.1 PASS NA None 76 NA True + TTTAA ENST00000409959.3 SLC12A7 10723 __UNKNOWN__ __UNKNOWN__ 5 1051516 1051520 __UNKNOWN__ 3'UTR DEL GGGGA GGGGA - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:1051516_1051520delGGGGA ENST00000264930.5 - 0 4250_4254 NM_006598.2 NP_006589.2 Q9Y666 S12A7_HUMAN solute carrier family 12 (potassium/chloride transporter), member 7 NA NA NA cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810) integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901) breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2) 32 Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09) Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165) Potassium Chloride(DB00761) ggggtggggtggggagggCAGTCCT 0.659 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 68 72.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.75 AF105365 CCDS34129.1 5p15 2013-07-18 2013-07-18 ENSG00000113504 ENSG00000113504 10723 "Solute carriers" 10915 protein-coding gene gene with protein product 604879 NA 10347194 Standard NM_006598 NM_006598 NA Approved KCC4, DKFZP434F076 uc003jbu.3 Q9Y666 OTTHUMG00000161931 ENST00000264930.5:c.*959TCCCC>- chr5.hg19:g.1051516_1051520delGGGGA 0 8 ref NA False 92 72 PASS 1 PASS ref->het 0 NA 6,6 46,48 15,13 1 1 A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2 True hg19 CCDS34129.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC12A7-001 KNOWN non_canonical_TEC|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000366446.2 PASS NA None 68 NA True - GGGGA ENST00000264930.5 ITGA2 3673 __UNKNOWN__ __UNKNOWN__ 5 52365923 52365924 __UNKNOWN__ Intron INS - - TT rs398108915|rs3212565|rs10649391 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:52365923_52365924insTT ENST00000296585.5 + 17 2226 NM_002203.3 NP_002194.2 P17301 ITA2_HUMAN integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) NA NA NA axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032) axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886) collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618) breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 47 Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181) TTTCTTTATGATTTTTTTTATC 0.307 NA NA NA NA NA 522 0.104233 0.2035 0.0663 5008 , , NA 21880 0.0317 NA 0.0885 False NA ,,, NA NA NA 2504 0.0879 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 52 57.73 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS3957.1 5q11.2 2010-03-23 ENSG00000164171 ENSG00000164171 3673 "CD molecules", "Integrins" 6137 protein-coding gene gene with protein product 192974 CD49B NA Standard NM_002203 NM_002203 NA Approved CD49b uc003joy.3 P17301 OTTHUMG00000131165 ENST00000296585.5:c.2084-15->TT chr5.hg19:g.52365930_52365931dupTT 10 9 ref NA False 34 34 PASS 8 PASS ref->het 0 NA 7,7 36,37 8,7 1 1 Q14595 True hg19 CCDS3957.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ITGA2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253857.2 PASS NA None 52 NA True + T ENST00000296585.5 F2RL2 2151 __UNKNOWN__ __UNKNOWN__ 5 75911569 75911597 __UNKNOWN__ 3'UTR DEL TACAGGAATATAATGGGTATTAATAACAA TACAGGAATATAATGGGTATTAATAACAA - rs139687205|rs2069694 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:75911569_75911597delTACAGGAATATAATGGGTATTAATAACAA ENST00000296641.4 - 0 3138_3166 IQGAP2_ENST00000379730.3_Intron|IQGAP2_ENST00000274364.6_Intron|IQGAP2_ENST00000502745.1_Intron|IQGAP2_ENST00000396234.3_Intron NM_004101.3 NP_004092.1 O00254 PAR3_HUMAN coagulation factor II (thrombin) receptor-like 2 NA NA NA blood coagulation (GO:0007596)|metabolic process (GO:0008152)|platelet activation (GO:0030168)|response to wounding (GO:0009611) apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) phosphatidylinositol phospholipase C activity (GO:0004435)|thrombin receptor activity (GO:0015057) central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(3) 32 all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129) all cancers(79;4.43e-43) GTCATTTACTTACAGGAATATAATGGGTATTAATAACAAAATTCCATTT 0.336 NA NA NA NA NA 1278 0.255192 0.1725 0.2133 5008 , , NA 22205 0.1637 NA 0.3012 False NA ,,, NA NA NA 2504 0.4438 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 125 115.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 U92971 CCDS4031.1, CCDS58959.1 5q13 2012-08-08 ENSG00000164220 ENSG00000164220 2151 "GPCR / Class A : Protease activated receptors" 3539 protein-coding gene gene with protein product "proteinase-activated receptor-3" 601919 NA 9087410, 9722561 Standard NM_004101 NA Approved PAR3 uc003kem.4 O00254 OTTHUMG00000102119 ENST00000296641.4:c.*1838TTGTTATTAATACCCATTATATTCCTGTA>- chr5.hg19:g.75911569_75911597delTACAGGAATATAATGGGTATTAATAACAA 0 6 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 21,21 48,49 7,7 1 1 B2R754|B4DQ13|Q52M68|Q7Z3W3 True hg19 CCDS4031.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA F2RL2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000219958.3 PASS NA None 125 NA True - TACAGGAATATAATGGGTATTAATAACAA ENST00000296641.4 AP3S1 1176 __UNKNOWN__ __UNKNOWN__ 5 115249647 115249647 __UNKNOWN__ 3'UTR DEL G G - rs145060439 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:115249647delG ENST00000316788.7 + 0 1599 NM_001284.2 NP_001275.1 Q92572 AP3S1_HUMAN adaptor-related protein complex 3, sigma 1 subunit NA NA NA anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transport (GO:0006886) AP-3 adaptor complex (GO:0030123)|AP-type membrane coat adaptor complex (GO:0030119)|Golgi apparatus (GO:0005794)|transport vesicle (GO:0030133) protein transporter activity (GO:0008565)|transporter activity (GO:0005215) cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1) 12 all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245) OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05) TTTTCTCTTAGTTTAAATAAA 0.333 NA NA NA NA NA G|G|-|deletion 1219 0.243411 0.2685 0.2089 5008 , , NA 21725 0.2063 NA 0.2604 False NA ,,, NA NA NA 2504 0.2546 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 278 294.23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.63 D63643 CCDS4123.1 5q22 2010-06-29 ENSG00000177879 ENSG00000177879 1176 2013 protein-coding gene gene with protein product 601507 CLAPS3 NA 8697810, 9118953 Standard NM_001284 NA Approved uc003krl.3 Q92572 OTTHUMG00000128887 ENST00000316788.7:c.*460G>- chr5.hg19:g.115249647delG 0 3 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 169,169 82,100 24,21 1 1 O00647|O00676|O00721|O00727|Q53XL4|Q6ICQ2 True hg19 CCDS4123.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AP3S1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250847.2 PASS NA None 278 NA True + G ENST00000316788.7 CANX 821 __UNKNOWN__ __UNKNOWN__ 5 179135305 179135315 __UNKNOWN__ Frame_Shift_Del DEL TCTCGGGCCAA TCTCGGGCCAA - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:179135305_179135315delTCTCGGGCCAA ENST00000247461.4 + 5 570_580 c.370_380delTCTCGGGCCAA c.(370-381)tctcgggccaagfs p.SRAK124fs CANX_ENST00000503126.1_3'UTR|CANX_ENST00000415618.2_Frame_Shift_Del_p.SRAK159fs|CANX_ENST00000512607.2_Frame_Shift_Del_p.SRAK16fs|CANX_ENST00000504734.1_Frame_Shift_Del_p.SRAK124fs|CANX_ENST00000452673.2_Frame_Shift_Del_p.SRAK124fs NM_001746.3 NP_001737.1 P27824 CALX_HUMAN calnexin 124 NA NA aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|clathrin-mediated endocytosis (GO:0072583)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein secretion (GO:0009306)|synaptic vesicle endocytosis (GO:0048488) axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|ER-mitochondrion membrane contact site (GO:0044233)|extracellular vesicular exosome (GO:0070062)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ribosome (GO:0005840) calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|poly(A) RNA binding (GO:0044822) p.R125L(1) breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3) 22 all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218) all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) Antihemophilic Factor(DB00025)|Tenecteplase(DB00031) TGTGTTGATGTCTCGGGCCAAGCATCATGCC 0.436 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 1 Substitution - Missense(1) lung(1) NA NA NA NA NA 685 643.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 3.1 L18887 CCDS4447.1 5q35 2008-07-18 ENSG00000127022 ENSG00000127022 821 1473 protein-coding gene gene with protein product "major histocompatibility complex class I antigen-binding protein p88" 114217 NA 1326756, 8136357 Standard NM_001024649 NM_001746 NA Approved CNX, IP90, P90 uc003mkl.3 P27824 OTTHUMG00000130910 ENST00000247461.4:c.370_380delTCTCGGGCCAA chr5.hg19:g.179135305_179135315delTCTCGGGCCAA ENSP00000247461:p.Ser124fs 0 2 ref NA False 39 39 PASS 1 PASS ref->het 0 NA 611,624 19,19 86,74 1 1 B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3 True hg19 CCDS4447.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CANX-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253500.2 PASS NA None 685 NA True + TCTCGGGCCAA ENST00000247461.4 MARCKS 4082 __UNKNOWN__ __UNKNOWN__ 6 114183421 114183434 __UNKNOWN__ 3'UTR DEL TGTGTTTCAAAAAT TGTGTTTCAAAAAT - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:114183421_114183434delTGTGTTTCAAAAAT ENST00000368635.4 + 0 3046_3059 NM_002356.5 NP_002347.5 P29966 MARCS_HUMAN myristoylated alanine-rich protein kinase C substrate NA NA NA energy reserve metabolic process (GO:0006112)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281) actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|germinal vesicle (GO:0042585)|plasma membrane (GO:0005886) actin filament binding (GO:0051015)|calmodulin binding (GO:0005516) breast(1)|kidney(1)|large_intestine(1)|lung(1) 4 all_cancers(87;7.65e-05)|all_epithelial(87;0.000296)|all_hematologic(75;0.0172)|Colorectal(196;0.0317)|all_lung(197;0.198) Epithelial(106;1.59e-07)|all cancers(137;9.85e-07)|OV - Ovarian serous cystadenocarcinoma(136;0.000322) TGTGACCAAATGTGTTTCAAAAATTGATGGTGTA 0.332 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 348 356.27 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.59 M68956 CCDS5101.1 6q21 2014-04-10 2001-12-17 2001-12-20 ENSG00000155130 ENSG00000277443 4082 6759 protein-coding gene gene with protein product 177061 "myristoylated alanine-rich protein kinase C substrate (MARCKS, 80K-L)" MACS NA 1560845, 8420923 Standard NM_002356 NM_002356 NA Approved PKCSL, 80K-L uc003pvy.4 P29966 OTTHUMG00000188327 ENST00000368635.4:c.*1679TGTGTTTCAAAAAT>- chr6.hg19:g.114183421_114183434delTGTGTTTCAAAAAT 0 5 ref NA False 76 76 PASS 1 PASS ref->het 0 NA 259,265 53,59 62,57 1 1 E1P560|Q2LA83|Q5TDB7 True hg19 CCDS5101.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MARCKS-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041903.1 PASS NA None 348 NA True + TGTGTTTCAAAAAT ENST00000368635.4 MARCKS 4082 __UNKNOWN__ __UNKNOWN__ 6 114183573 114183573 __UNKNOWN__ 3'UTR DEL T T - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:114183573delT ENST00000368635.4 + 0 3198 NM_002356.5 NP_002347.5 P29966 MARCS_HUMAN myristoylated alanine-rich protein kinase C substrate NA NA NA energy reserve metabolic process (GO:0006112)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281) actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|germinal vesicle (GO:0042585)|plasma membrane (GO:0005886) actin filament binding (GO:0051015)|calmodulin binding (GO:0005516) breast(1)|kidney(1)|large_intestine(1)|lung(1) 4 all_cancers(87;7.65e-05)|all_epithelial(87;0.000296)|all_hematologic(75;0.0172)|Colorectal(196;0.0317)|all_lung(197;0.198) Epithelial(106;1.59e-07)|all cancers(137;9.85e-07)|OV - Ovarian serous cystadenocarcinoma(136;0.000322) TTCATGGGCCTTTAGCATAGT 0.299 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 296 270.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 12.21 M68956 CCDS5101.1 6q21 2014-04-10 2001-12-17 2001-12-20 ENSG00000155130 ENSG00000277443 4082 6759 protein-coding gene gene with protein product 177061 "myristoylated alanine-rich protein kinase C substrate (MARCKS, 80K-L)" MACS NA 1560845, 8420923 Standard NM_002356 NM_002356 NA Approved PKCSL, 80K-L uc003pvy.4 P29966 OTTHUMG00000188327 ENST00000368635.4:c.*1818T>- chr6.hg19:g.114183573delT 2 3 ref NA False 130 128 PASS 3 PASS ref->het 0 NA 176,201 55,63 66,42 1 1 E1P560|Q2LA83|Q5TDB7 True hg19 CCDS5101.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MARCKS-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041903.1 PASS NA None 296 NA True + T ENST00000368635.4 CEP85L 387119 __UNKNOWN__ __UNKNOWN__ 6 118812400 118812403 __UNKNOWN__ Intron DEL ACAT ACAT - rs368541896|rs9481816 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:118812400_118812403delACAT ENST00000368491.3 - 6 2059 CEP85L_ENST00000368488.5_Intron NM_001042475.2 NP_001035940.1 Q5SZL2 CE85L_HUMAN centrosomal protein 85kDa-like NA NA NA centrosome (GO:0005813)|cytoplasm (GO:0005737) NA acacacacacacaTATGCATGCAT 0.358 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 39 42.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.58 AF308284 CCDS5119.2, CCDS43498.1, CCDS55052.1 6q22.31 2011-11-25 2011-11-25 2011-11-25 ENSG00000111860 ENSG00000111860 387119 21638 protein-coding gene gene with protein product NA "chromosome 6 open reading frame 204" C6orf204 NA Standard NM_001042475 NM_206921 NA Approved NY-BR-15, bA57K17.2 uc003pya.2 Q5SZL2 OTTHUMG00000015465 ENST00000368491.3:c.1437+445ATGT>- chr6.hg19:g.118812400_118812403delACAT 0 2 ref NA False 46 45 PASS 1 PASS ref->hom 0 NA 0,0 22,23 18,17 1 1 A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289 True hg19 CCDS43498.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CEP85L-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041996.2 PASS NA None 39 NA True - ACAT ENST00000368491.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 121974926 121974926 __UNKNOWN__ IGR DEL T T - rs77718609|rs201153988 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:121974926delT NA RNU2-8P (73259 upstream) : RNU1-18P (557867 downstream) NA NA NA NA GCCCAGTCCCTTCTGGCAGCA 0.547 NA NA NA NA NA TT|TT|T|deletion 694 0.138578 0.0968 0.0778 5008 , , NA 15755 0.3175 NA 0.1093 False NA ,,, NA NA NA 2504 0.0838 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 23 21.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.39 NA NA NA NA NA chr6.hg19:g.121974926delT 1 3 ref NA False 67 66 PASS 2 PASS ref->hom 0 NA 0,0 18,21 5,2 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 23 NA True T Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 123105222 123105224 __UNKNOWN__ IGR DEL TTG TTG - rs375914971|rs71541214 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:123105222_123105224delTTG NA FABP7 (3 upstream) : SMPDL3A (5090 downstream) NA NA NA NA ACGTGAAATTTTGTTGTTGTTTC 0.256 NA NA NA NA NA 1216 0.242812 0.0991 0.3127 5008 , , NA 13122 0.3304 NA 0.1501 False NA ,,, NA NA NA 2504 0.3926 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 76 78.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.77 NA NA NA NA NA chr6.hg19:g.123105228_123105230delTTG 2 6 ref NA False 73 62 PASS 3 PASS ref->het 0 NA 3,4 56,57 16,17 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 76 NA True TTG NKAIN2 154215 __UNKNOWN__ __UNKNOWN__ 6 125112514 125112528 __UNKNOWN__ In_Frame_Del DEL TGTGAAATGTATAAC TGTGAAATGTATAAC - rs550796318|rs182153928 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:125112514_125112528delTGTGAAATGTATAAC ENST00000368417.1 + 5 564_578 c.504_518delTGTGAAATGTATAAC c.(502-519)gttgtgaaatgtataact>gtt p.VKCIT169del NKAIN2_ENST00000546092.1_In_Frame_Del_p.VKCIT102del|NKAIN2_ENST00000545433.1_In_Frame_Del_p.VKCIT154del NM_001040214.1 NP_001035304.1 Q5VXU1 NKAI2_HUMAN Na+/K+ transporting ATPase interacting 2 169 NA NA integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) cervix(1)|endometrium(1)|large_intestine(3)|lung(12)|skin(2) 19 GBM - Glioblastoma multiforme(226;0.104) CCTGTTATGTTGTGAAATGTATAACTGAAGAAGAG 0.419 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 303 302.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.41 AB070452 CCDS34526.1 6q21 2008-02-05 2007-10-04 2007-10-04 ENSG00000188580 ENSG00000188580 154215 "Na+/K+ transporting ATPase interacting" 16443 protein-coding gene gene with protein product 609758 "T-cell lymphoma breakpoint associated target 1" TCBA1 NA 17606467 Standard NM_001040214 XM_005266833 NA Approved FAM77B uc003pzo.3 Q5VXU1 OTTHUMG00000015500 ENST00000368417.1:c.504_518delTGTGAAATGTATAAC chr6.hg19:g.125112514_125112528delTGTGAAATGTATAAC ENSP00000357402:p.Val169_Thr173del 0 3 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 154,155 140,143 38,35 1 1 Q8IYR4|Q8TF67 True hg19 CCDS34526.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NKAIN2-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000042057.1 PASS NA None 303 NA True + TGTGAAATGTATAAC ENST00000368417.1 COX19 90639 __UNKNOWN__ __UNKNOWN__ 7 1006956 1006972 __UNKNOWN__ 3'UTR DEL AGTTACCTTTGTACGTT AGTTACCTTTGTACGTT - rs116884794|rs542574946|rs553807536 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:1006956_1006972delAGTTACCTTTGTACGTT ENST00000344111.3 - 0 2404_2420 NM_001031617.2 NP_001026788.1 Q49B96 COX19_HUMAN cytochrome c oxidase assembly homolog 19 (S. cerevisiae) NA NA NA cytoplasm (GO:0005737) endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3) 5 Ovarian(82;0.0112) UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;2.15e-15) TTCTCTATCCAGTTACCTTTGTACGTTAGAAAAGCAG 0.516 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 151 173.48 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.34 AY957566 CCDS34582.1 7p22.3 2012-10-15 2012-10-15 ENSG00000240230 ENSG00000240230 90639 "Mitochondrial respiratory chain complex assembly factors" 28074 protein-coding gene gene with protein product 610429 "COX19 cytochrome c oxidase assembly homolog (S. cerevisiae)" NA 15596615, 16212937 Standard NM_001031617 NM_001031617 NA Approved MGC104475 uc003sjp.1 Q49B96 OTTHUMG00000151476 ENST00000344111.3:c.*2058AACGTACAAAGGTAACT>- chr7.hg19:g.1006956_1006972delAGTTACCTTTGTACGTT 0 5 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 103,104 47,48 25,25 1 1 A4FTX0 True hg19 CCDS34582.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COX19-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000322812.1 PASS NA None 151 NA True - AGTTACCTTTGTACGTT ENST00000344111.3 CCT6A 908 __UNKNOWN__ __UNKNOWN__ 7 56131579 56131580 __UNKNOWN__ 3'UTR DEL TC TC - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:56131579_56131580delTC ENST00000275603.4 + 0 2616_2617 CCT6A_ENST00000335503.3_3'UTR NM_001762.3 NP_001753.1 P40227 TCPZ_HUMAN chaperonin containing TCP1, subunit 6A (zeta 1) NA NA NA 'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457) acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199) ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082) breast(1)|cervix(2)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)|upper_aerodigestive_tract(1) 15 Breast(14;0.214) Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099) AGTTGGTCTATCTCTGCAGTCC 0.391 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 220 207.26 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.64 M94083 CCDS5523.1, CCDS34640.1 7p11.2 2011-09-02 ENSG00000146731 ENSG00000146731 908 "Heat Shock Proteins / Chaperonins" 1620 protein-coding gene gene with protein product 104613 CCT6 NA 1352881, 8034610 Standard NM_001762 NM_001762 NA Approved TTCP20, TCPZ, Cctz, HTR3, TCP20 uc003trl.1 P40227 OTTHUMG00000022842 ENST00000275603.4:c.*802TC>- chr7.hg19:g.56131581_56131582delTC 1 2 ref NA False 109 108 PASS 2 PASS ref->het 0 NA 140,142 50,52 34,32 1 1 A6NCD2|Q3KP28|Q75LP4|Q96S46 True hg19 CCDS5523.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCT6A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251526.2 PASS NA None 220 NA True + TC ENST00000275603.4 MCM7 4176 __UNKNOWN__ __UNKNOWN__ 7 99699303 99699303 __UNKNOWN__ 5'UTR DEL T T - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:99699303delT ENST00000303887.5 - 0 260 AP4M1_ENST00000429084.1_5'UTR|MCM7_ENST00000343023.6_5'UTR|AP4M1_ENST00000478501.1_3'UTR|AP4M1_ENST00000359593.4_5'UTR|AP4M1_ENST00000421755.1_5'UTR NM_005916.3 NP_005907.3 P33993 MCM7_HUMAN minichromosome maintenance complex component 7 NA NA NA cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493) chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697) endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1) 17 Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439) CAGGCCCGACTTTCGCCGTCT 0.602 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 115 118.78 NA NA 48 55 53 NA NA NA 7 NA NA NA 99699303 2203 4300 6503 SO:0001623 5_prime_UTR_variant 0.32 CCDS5683.1, CCDS5684.1 7q21.3-q22.1 2014-06-12 2007-04-04 ENSG00000166508 ENSG00000166508 4176 6950 protein-coding gene gene with protein product "protein phosphatase 1, regulatory subunit 104" 600592 "minichromosome maintenance deficient (S. cerevisiae) 7", "MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)" MCM2 NA 7842741 Standard NM_005916 NA Approved CDC47, PPP1R104 uc003usw.1 P33993 OTTHUMG00000154671 ENST00000303887.5:c.-386A>- chr7.hg19:g.99699303delT 2 3 ref NA False 401 134 PASS 3 PASS ref->het 0 NA 25,25 72,75 19,16 1 1 A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1 True hg19 CCDS5683.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MCM7-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000336534.3 PASS NA None 115 NA True - T ENST00000303887.5 SLC26A3 1811 __UNKNOWN__ __UNKNOWN__ 7 107418553 107418554 __UNKNOWN__ Intron INS - - G LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:107418553_107418554insG ENST00000340010.5 - 13 1699 SLC26A3_ENST00000422236.2_Intron NM_000111.2 NP_000102.1 P40879 S26A3_HUMAN solute carrier family 26 (anion exchanger), member 3 NA NA NA anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085) apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225) anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215) breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1) 46 GCCAGTGACATTTTTTTTCCTC 0.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 73 73.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 L02785 CCDS5748.1 7q31 2014-09-17 2013-07-18 ENSG00000091138 ENSG00000091138 1811 "Solute carriers" 3018 protein-coding gene gene with protein product 126650 "congenital chloride diarrhea", "solute carrier family 26, member 3" DRA, CLD NA 8020951, 11087667 Standard NM_000111 NM_000111 NA Approved uc003ver.2 P40879 OTTHUMG00000154812 ENST00000340010.5:c.1514+65->C chr7.hg19:g.107418553_107418554insG 1 8 ref NA False 41 41 PASS 0 PASS ref->het 0 NA 33,35 36,36 4,4 2 2 True hg19 CCDS5748.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC26A3-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000337190.1 PASS NA None 73 NA True - G ENST00000340010.5 FAM3C 10447 __UNKNOWN__ __UNKNOWN__ 7 121000084 121000085 __UNKNOWN__ Intron INS - - AAGTTTT rs57188306|rs111415936 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:121000084_121000085insAAGTTTT ENST00000359943.3 - 8 681 NM_001040020.1|NM_014888.2 NP_001035109.1|NP_055703.1 Q92520 FAM3C_HUMAN family with sequence similarity 3, member C NA NA NA multicellular organismal development (GO:0007275) cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794) cytokine activity (GO:0005125) kidney(1)|lung(8) 9 all_neural(327;0.117) AAAGTTCTGTAAAGTTTACATA 0.307 NA NA NA NA NA 1191 0.237819 0.4629 0.1902 5008 , , NA 15608 0.0516 NA 0.1899 False NA ,,, NA NA NA 2504 0.2086 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 64 75.4 NA , 1795,2461 NA 397,1001,730 NA NA NA NA , -0.6 0 dbSNP_132 26 1487,6757 NA 150,1187,2785 no intron,intron FAM3C NM_014888.2,NM_001040020.1 , 547,2188,3515 A1A1,A1R,RR NA 18.0374,42.1758,26.256 , , NA 3282,9218 NA NA NA SO:0001627 intron_variant 0.04 D87120 CCDS5782.1 7q22.1-q31.1 2014-08-14 ENSG00000196937 ENSG00000196937 10447 18664 protein-coding gene gene with protein product "predicted osteoblast protein", "interleukin-like EMT inducer", "interleukin-like epithelial-mesenchymal transition inducer" 608618 NA 12160727 Standard NM_001040020 NM_014888 NA Approved GS3876, ILEI uc010lkm.3 Q92520 OTTHUMG00000156979 ENST00000359943.3:c.467+11->AAAACTT chr7.hg19:g.121000084_121000085insAAGTTTT 1 3 ref NA False 33 33 PASS 0 PASS ref->het 0 NA 10,10 44,46 11,10 1 1 A6NDN2|A8K3R7 True hg19 CCDS5782.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM3C-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000346945.1 PASS NA None 64 NA True - AAGTTTT ENST00000359943.3 TRBV29-1 28558 __UNKNOWN__ __UNKNOWN__ 7 142448200 142448207 __UNKNOWN__ RNA DEL GGTGGAAA GGTGGAAA - rs56831387|rs112413030|rs76614416 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:142448200_142448207delGGTGGAAA ENST00000422143.2 + 0 101 T cell receptor beta variable 29-1 NA NA NA NA GTTAACACTGGGTGGAAAGGTGGAAAGA 0.457 NA NA NA NA NA 1983 0.395966 0.3812 0.5187 5008 , , NA 21381 0.2222 NA 0.5974 False NA ,,, NA NA NA 2504 0.3006 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 166 161.88 NA 1374,2160 NA 346,682,739 NA NA NA NA 1.6 0 dbSNP_129 48 4141,3571 NA 1278,1585,993 no intergenic 1624,2267,1732 A1A1,A1R,RR NA 46.3045,38.8795,49.0397 NA 5515,5731 NA NA NA 0.33 L36092 7q34 2012-02-07 ENSG00000232869 ENSG00000232869 28558 "T cell receptors / TRB locus" 12210 other T cell receptor gene NA NA 8650574 Standard NG_001333 NG_001333 NA Approved TRBV291, TCRBV29S1, TCRBV4S1A1T OTTHUMG00000158898 ENST00000422143.2: chr7.hg19:g.142448208_142448215delGGTGGAAA 1 5 ref NA False 67 59 PASS 2 PASS ref->het 0 NA 3,3 122,125 41,40 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRBV29-1-001 KNOWN mRNA_end_NF|cds_end_NF|basic|appris_principal TR_V_gene NA TR_V_gene OTTHUMT00000352510.1 PASS NA None 166 NA True + GGTGGAAA ENST00000422143.2 DPP6 1804 __UNKNOWN__ __UNKNOWN__ 7 154645603 154645604 __UNKNOWN__ Intron DEL GA GA - rs148495479 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:154645603_154645604delGA ENST00000377770.3 + 17 1855 DPP6_ENST00000332007.3_Intron|DPP6_ENST00000404039.1_Intron|DPP6_ENST00000427557.1_Intron|RP11-476H24.1_ENST00000448767.1_RNA P42658 DPP6_HUMAN dipeptidyl-peptidase 6 NA NA NA cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381) extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021) dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236) NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1) 71 all_neural(206;0.181) all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204) OV - Ovarian serous cystadenocarcinoma(82;0.0562) AACACTCTATGAGATCAGCTGG 0.426 NA NA NA NA NA 60 0.0119808 0.0424 0.0058 5008 , , NA 22245 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA NSCLC(125;1384 1783 2490 7422 34254) PASS NA NA NA NA NA 0 NA NA NA NA NA 106 109.47 NA ,, 108,3568 NA 5,98,1735 NA NA NA NA ,, -2.5 0 dbSNP_134 58 3,7905 NA 1,1,3952 no intron,intron,intron DPP6 NM_130797.2,NM_001936.3,NM_001039350.1 ,, 6,99,5687 A1A1,A1R,RR NA 0.0379,2.938,0.9582 ,, ,, NA 111,11473 NA NA NA SO:0001627 intron_variant 0 M96859 CCDS75682.1, CCDS75683.1, CCDS75684.1 7q36.2 2006-08-07 2006-01-12 ENSG00000130226 ENSG00000130226 1804 3010 protein-coding gene gene with protein product 126141 "dipeptidylpeptidase VI", "dipeptidylpeptidase 6" NA 1729689 Standard NM_130797 XM_006715871 NA Approved DPPX uc003wlk.3 P42658 OTTHUMG00000151511 ENST00000377770.3:c.1714+66GA>- chr7.hg19:g.154645605_154645606delGA 1 2 ref NA False 34 32 PASS 2 PASS ref->het 0 NA 8,8 88,88 9,10 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DPP6-003 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000322932.1 PASS NA None 106 NA True + GA ENST00000377770.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 8 42195907 42195909 __UNKNOWN__ IGR DEL CTC CTC - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:42195907_42195909delCTC NA IKBKB (6352 upstream) : POLB (63 downstream) NA NA NA NA CGAGTTCTCTCTCCTCACCTGCC 0.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 252 241.34 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 5.93 NA NA NA NA NA chr8.hg19:g.42195910_42195912delCTC 1 3 ref NA False 113 110 PASS 2 PASS ref->het 0 NA 144,165 58,64 49,25 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 252 NA True CTC Unknown 0 __UNKNOWN__ __UNKNOWN__ 8 108509484 108509487 __UNKNOWN__ IGR DEL ACTT ACTT - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:108509484_108509487delACTT NA ANGPT1 (160734 upstream) : RNA5SP275 (387234 downstream) NA NA NA NA GAAAGCAATCACTTACTTTTTGCA 0.417 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 378 382.04 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.02 NA NA NA NA NA chr8.hg19:g.108509488_108509491delACTT 1 2 ref NA False 35 35 PASS 2 PASS ref->het 0 NA 276,279 80,80 36,34 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 378 NA True ACTT PHF20L1 51105 __UNKNOWN__ __UNKNOWN__ 8 133837466 133837506 __UNKNOWN__ Intron DEL AGGATCAGTCGTGATTGCTAAAGTATTCACTTTTATCTTTT AGGATCAGTCGTGATTGCTAAAGTATTCACTTTTATCTTTT - rs373959531|rs370897409 LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:133837466_133837506delAGGATCAGTCGTGATTGCTAAAGTATTCACTTTTATCTTTT ENST00000395386.2 + 14 1935 PHF20L1_ENST00000395390.2_Intron|PHF20L1_ENST00000220847.7_Intron NM_016018.4 NP_057102.4 A8MW92 P20L1_HUMAN PHD finger protein 20-like 1 NA NA NA zinc ion binding (GO:0008270) breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2) 15 all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;4.46e-05) GGAACAACTCAGGATCAGTCGTGATTGCTAAAGTATTCACTTTTATCTTTTAGGTaagaga 0.349 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 950 852.76 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.64 AF230666 CCDS6367.2, CCDS6368.1, CCDS75791.1 8q24.22 2014-03-24 ENSG00000129292 ENSG00000129292 51105 "Tudor domain containing", "Zinc fingers, PHD-type" 24280 protein-coding gene gene with protein product "tudor domain containing 20B" NA NA 10810093, 24492612 Standard NM_016018 NM_016018 NA Approved CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B uc003ytt.3 A8MW92 OTTHUMG00000148656 ENST00000395386.2:c.1637-3AGGATCAGTCGTGATTGCTAAAGTATTCACTTTTATCTTTT>- chr8.hg19:g.133837466_133837506delAGGATCAGTCGTGATTGCTAAAGTATTCACTTTTATCTTTT 0 5 ref NA False 47 47 PASS 1 PASS ref->het 0 NA 774,787 38,39 244,235 1 1 A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381 True hg19 CCDS6367.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PHF20L1-008 PUTATIVE basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000308949.3 PASS NA None 950 NA True + AGGATCAGTCGTGATTGCTAAAGTATTCACTTTTATCTTTT ENST00000395386.2 BRD3 8019 __UNKNOWN__ __UNKNOWN__ 9 136918621 136918622 __UNKNOWN__ 5'UTR DEL TC TC - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:136918621_136918622delTC ENST00000303407.7 - 0 163_164 BRD3_ENST00000371834.2_5'UTR|BRD3_ENST00000357885.2_5'UTR NM_007371.3 NP_031397.1 Q15059 BRD3_HUMAN bromodomain containing 3 NA NA NA chromatin modification (GO:0016568)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577) BRD3/C15orf55(3) kidney(1)|skin(1)|stomach(4) 6 OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07) TCACTCACTTTCTGTCACAGCA 0.683 NA NA TRUE C15orf55 lethal midline carcinoma of young people NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Dom yes NA 9 9q34 8019 bromodomain containing 3 NA E 0 NA NA NA NA NA 316 315.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 3.14 CCDS6980.1 9q34 2010-12-23 2002-01-14 ENSG00000169925 ENSG00000169925 8019 1104 protein-coding gene gene with protein product "RING3-like" 601541 "bromodomain-containing 3" NA 7584044, 8781126 Standard NM_007371 NM_007371 NA Approved RING3L, ORFX, KIAA0043 uc004cew.3 Q15059 OTTHUMG00000021004 ENST00000303407.7:c.-23GA>- chr9.hg19:g.136918621_136918622delTC 0 4 ref NA False 372 95 PASS 1 PASS ref->het 0 NA 42,43 237,253 35,18 1 1 B1APD9|Q4G5Y3|Q5T1R7|Q8N5M3|Q92645 True hg19 CCDS6980.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BRD3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000055390.4 PASS NA None 316 NA True - TC ENST00000303407.7 OTUD1 220213 __UNKNOWN__ __UNKNOWN__ 10 23728611 23728613 __UNKNOWN__ In_Frame_Del DEL CTC CTC - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:23728611_23728613delCTC ENST00000376495.3 + 1 414_416 c.225_227delCTC c.(223-228)ttctcc>ttc p.S77del NM_001145373.2 NP_001138845.1 Q5VV17 OTUD1_HUMAN OTU deubiquitinase 1 77 Ala-rich. NA NA protein K63-linked deubiquitination (GO:0070536) ubiquitin-specific protease activity (GO:0004843) breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2) 5 tgcccgccttctcctcctgcttc 0.813 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 70 63.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 1.68 AK096389 CCDS44366.1 10p12.31 2014-02-24 2014-02-24 ENSG00000165312 ENSG00000165312 220213 "OTU domain containing" 27346 protein-coding gene gene with protein product 612022 "OTU domain containing 1" OTDC1 NA 23827681 Standard XM_166659 NM_001145373 NA Approved DUBA7 uc001irr.2 Q5VV17 OTTHUMG00000017819 ENST00000376495.3:c.225_227delCTC chr10.hg19:g.23728614_23728616delCTC ENSP00000365678:p.Ser77del 1 4 ref NA False 30 30 PASS 2 PASS ref->het 0 NA 48,50 6,8 17,14 1 1 True hg19 CCDS44366.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OTUD1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000047215.1 PASS NA None 70 NA True + CTC ENST00000376495.3 SVIL 6840 __UNKNOWN__ __UNKNOWN__ 10 29813396 29813396 __UNKNOWN__ Intron DEL C C - rs138330085 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:29813396delC ENST00000355867.4 - 14 3339 SVIL_ENST00000375398.2_Intron|SVIL_ENST00000375400.3_Intron NM_021738.2 NP_068506.2 O95425 SVIL_HUMAN supervillin NA NA NA cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519) actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886) actin filament binding (GO:0051015) breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2) 112 Breast(68;0.103) CTATAGCACACCCACCTGCTC 0.468 NA NA NA NA NA CCC|CCC|CC|deletion 147 0.029353 0.0545 0.0029 5008 , , NA 19238 0 NA 0 False NA ,,, NA NA NA 2504 0.0746 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 100 105.95 NA , 178,4086 NA 4,170,1958 137 139 138 NA , 4.7 0.4 10 dbSNP_134 140 1,8253 NA 0,1,4126 no intron,intron SVIL NM_021738.2,NM_003174.3 , 4,171,6084 A1A1,A1R,RR NA 0.0121,4.1745,1.4299 , , 29813396 179,12339 2203 4300 6503 SO:0001627 intron_variant 0.07 AF051851 CCDS7163.1, CCDS7164.1 10p11.2 2008-07-29 ENSG00000197321 ENSG00000197321 6840 11480 protein-coding gene gene with protein product "archvillin" 604126 NA 9382871 Standard NM_003174 NA Approved uc001iut.1 O95425 OTTHUMG00000017882 ENST00000355867.4:c.2586+4G>- chr10.hg19:g.29813396delC 2 5 ref NA False 72 49 PASS 3 PASS ref->hom 0 NA 0,0 91,95 9,5 1 1 D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7 True hg19 CCDS7164.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SVIL-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000047395.1 PASS NA None 100 NA True - C ENST00000355867.4 PARD3 56288 __UNKNOWN__ __UNKNOWN__ 10 34739095 34739095 __UNKNOWN__ Intron DEL A A - rs138785690 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:34739095delA ENST00000374789.3 - 5 1040 PARD3_ENST00000545260.1_Intron|PARD3_ENST00000346874.4_Intron|PARD3_ENST00000374790.3_Intron|PARD3_ENST00000350537.4_Intron|PARD3_ENST00000374794.3_Intron|PARD3_ENST00000374788.3_Intron|PARD3_ENST00000374773.1_Intron|PARD3_ENST00000374776.1_Intron|PARD3_ENST00000545693.1_Intron|PARD3_ENST00000340077.5_Intron NM_019619.3 NP_062565.2 Q8TEW0 PARD3_HUMAN par-3 family cell polarity regulator NA NA NA apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319) apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923) phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546) NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2) 63 Breast(68;0.0707) TATGTTAGATAAACTCTGACA 0.348 NA NA NA NA NA AAA|AAA|AA|deletion 107 0.0213658 0.0749 0.0115 5008 , , NA 20818 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 84 85.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.1 AF252293 CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1 10p11.22 2014-06-13 2013-08-28 ENSG00000148498 ENSG00000148498 56288 16051 protein-coding gene gene with protein product "atypical PKC isotype-specific interacting protein", "par-3 family cell polarity regulator alpha", "protein phosphatase 1, regulatory subunit 118" 606745 "par-3 (partitioning defective 3, C.elegans) homolog", "par-3 partitioning defective 3 homolog (C. elegans)" NA 10934474 Standard NM_019619 NM_001184790 NA Approved PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118 uc010qej.2 Q8TEW0 OTTHUMG00000017948 ENST00000374789.3:c.714+149T>- chr10.hg19:g.34739095delA 2 4 ref NA False 38 38 PASS 3 PASS ref->het 0 NA 10,10 63,65 11,10 1 1 F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6 True hg19 CCDS7178.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PARD3-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000047527.1 PASS NA None 84 NA True - A ENST00000374789.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 10 115268837 115268839 __UNKNOWN__ IGR DEL ATT ATT - rs370879698 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:115268837_115268839delATT NA RNU7-165P (155594 upstream) : HABP2 (41756 downstream) NA NA NA NA aattttaaaaattgtcattttgg 0.394 NA NA NA NA NA 37 0.00738818 0.0234 0.0086 5008 , , NA 22003 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 30 26.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr10.hg19:g.115268837_115268839delATT 0 5 ref NA False 31 31 PASS 1 PASS ref->hom 0 NA 0,0 26,26 3,3 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 30 NA True ATT MMP21 118856 __UNKNOWN__ __UNKNOWN__ 10 127463057 127463060 __UNKNOWN__ Intron DEL AGAC AGAC - rs201423894 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:127463057_127463060delAGAC ENST00000368808.3 - 2 162 NM_147191.1 NP_671724.1 Q8N119 MMP21_HUMAN matrix metallopeptidase 21 NA NA NA hematopoietic progenitor cell differentiation (GO:0002244) extracellular matrix (GO:0031012)|extracellular region (GO:0005576) calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270) endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1) 16 all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936) Marimastat(DB00786) agaagcagagagacagacagggag 0.549 NA NA NA NA NA 188 0.0375399 0.0378 0.0072 5008 , , NA 14399 0.1111 NA 0.001 False NA ,,, NA NA NA 2504 0.0204 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 27 31.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF331526 CCDS7647.1 10q26.3 2008-07-28 2005-08-08 ENSG00000154485 ENSG00000154485 118856 14357 protein-coding gene gene with protein product 608416 "matrix metalloproteinase 21" NA 11255011 Standard NM_147191 NA Approved uc001liu.3 Q8N119 OTTHUMG00000019235 ENST00000368808.3:c.163-123GTCT>- chr10.hg19:g.127463061_127463064delAGAC 1 2 ref NA False 38 38 PASS 2 PASS ref->hom 0 NA 0,0 23,23 4,5 1 1 Q5VZP9|Q8NG02 True hg19 CCDS7647.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MMP21-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000050928.1 PASS NA None 27 NA True - AGAC ENST00000368808.3 FAM111B 374393 __UNKNOWN__ __UNKNOWN__ 11 58894295 58894305 __UNKNOWN__ 3'UTR DEL AAGCAGTTGGG AAGCAGTTGGG - rs2154626 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:58894295_58894305delAAGCAGTTGGG ENST00000343597.3 + 0 2916_2926 FAM111B_ENST00000411426.1_3'UTR NM_198947.3 NP_945185.1 Q6SJ93 F111B_HUMAN family with sequence similarity 111, member B NA NA NA catalytic activity (GO:0003824) endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1) 40 ccattgtggaaagcagttgggtgatttctaa 0.374 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 354 354.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.97 BC062456 CCDS7972.1, CCDS44611.1 11q12.1 2014-03-13 ENSG00000189057 ENSG00000189057 374393 24200 protein-coding gene gene with protein product 615584 NA 24268661 Standard NM_198947 NM_198947 NA Approved CANP uc001nnl.3 Q6SJ93 OTTHUMG00000167279 ENST00000343597.3:c.*530AAGCAGTTGGG>- chr11.hg19:g.58894295_58894305delAAGCAGTTGGG 0 4 ref NA False 51 51 PASS 1 PASS ref->het 0 NA 343,347 20,20 38,35 1 1 B4E2G2|Q6P661 True hg19 CCDS7972.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM111B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000393974.1 PASS NA None 354 NA True + AAGCAGTTGGG ENST00000343597.3 PPP6R3 55291 __UNKNOWN__ __UNKNOWN__ 11 68305521 68305522 __UNKNOWN__ Intron INS - - T rs397700502|rs11403965 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:68305521_68305522insT ENST00000534534.1 + 3 231 PPP6R3_ENST00000524904.1_Intron|PPP6R3_ENST00000393800.2_Intron|PPP6R3_ENST00000524845.1_Intron|PPP6R3_ENST00000265636.5_Intron|PPP6R3_ENST00000265637.4_Intron|PPP6R3_ENST00000393799.2_Intron|PPP6R3_ENST00000393801.3_Intron|PPP6R3_ENST00000529710.1_Intron|PPP6R3_ENST00000527403.2_Intron Q5H9R7 PP6R3_HUMAN protein phosphatase 6, regulatory subunit 3 NA NA NA regulation of phosphoprotein phosphatase activity (GO:0043666) cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886) protein phosphatase binding (GO:0019903) breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 37 CATTCTAGCAGTAAGTCCAGGG 0.406 NA NA NA NA NA T|T|TT|insertion 3282 0.655351 0.4039 0.7104 5008 , , NA 19658 0.7798 NA 0.665 False NA ,,, NA NA NA 2504 0.818 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 80 86.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.35 AF264779 CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1 11q13 2012-04-17 2010-06-28 2010-06-28 ENSG00000110075 ENSG00000110075 55291 "Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits" 1173 protein-coding gene gene with protein product "sporulation-induced transcript 4-associated protein" 610879 "chromosome 11 open reading frame 23", "SAPS domain family, member 3" C11orf23, SAPS3 NA 11401438, 16769727 Standard NM_018312 NM_018312 NA Approved SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712 uc001onv.3 Q5H9R7 ENST00000534534.1:c.-46-6784->T chr11.hg19:g.68305522_68305522dupT 2 2 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 6,6 68,70 7,6 1 1 Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPP6R3-008 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000395280.1 PASS NA None 80 NA True + T ENST00000534534.1 RPS3 6188 __UNKNOWN__ __UNKNOWN__ 11 75113552 75113552 __UNKNOWN__ Intron DEL T T - rs201507842|rs17886478|rs397844185 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:75113552delT ENST00000278572.6 + 4 416 RPS3_ENST00000531188.1_Intron|RPS3_ENST00000526608.1_Intron|RPS3_ENST00000530164.1_3'UTR|RPS3_ENST00000524851.1_Intron|RPS3_ENST00000527446.1_Intron|RPS3_ENST00000534440.1_Intron|RPS3_ENST00000529285.1_Intron P23396 RS3_HUMAN ribosomal protein S3 NA NA NA cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic translation (GO:0002181)|DNA catabolic process, endonucleolytic (GO:0000737)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of DNA repair (GO:0045738)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of DNA N-glycosylase activity (GO:1902546)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083) cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ruffle membrane (GO:0032587) damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|enzyme binding (GO:0019899)|iron-sulfur cluster binding (GO:0051536)|mRNA binding (GO:0003729)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735) endometrium(1)|kidney(1)|large_intestine(2)|lung(2) 6 ATGTCTGCCATTTGTTAATTT 0.443 NA NA NA NA NA ttt|TTT|TT|deletion 583 0.116414 0.0348 0.0937 5008 , , NA 23143 0.1875 NA 0.0656 False NA ,,, NA NA NA 2504 0.2219 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 72 71.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.01 CCDS8236.1, CCDS58161.1 11q13.3-q13.5 2011-04-05 ENSG00000149273 6188 "S ribosomal proteins" 10420 protein-coding gene gene with protein product "IMR-90 ribosomal protein S3", "40S ribosomal protein S3" 600454 NA 1712897, 7789996 Standard NM_001005 NM_001005 NA Approved FLJ26283, FLJ27450, MGC87870, S3 uc031qcs.1 P23396 ENST00000278572.6:c.398+62T>- chr11.hg19:g.75113552delT 2 5 ref NA False 39 38 PASS 3 PASS ref->het 0 NA 2,2 59,60 11,10 1 1 B2R7N5|J3KN86|Q498B5|Q8NI95 True hg19 CCDS58161.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPS3-014 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000384310.1 PASS NA None 72 NA True + T ENST00000278572.6 DLG2 1740 __UNKNOWN__ __UNKNOWN__ 11 83167762 83167762 __UNKNOWN__ 3'UTR DEL A A - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:83167762delA ENST00000398309.2 - 0 6182 DLG2_ENST00000426717.2_3'UTR NM_001364.3 NP_001355.2 Q14168 MPP2_HUMAN discs, large homolog 2 (Drosophila) NA NA NA nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165) integral component of plasma membrane (GO:0005887)|membrane (GO:0016020) guanylate kinase activity (GO:0004385) breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1) 71 all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036) aaagaatgagaaaaaaaGTAG 0.483 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 87 86.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.3 U32376 CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1 11q21 2012-04-17 2008-12-15 ENSG00000150672 ENSG00000150672 1740 "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits" 2901 protein-coding gene gene with protein product "protein phosphatase 1, regulatory subunit 58" 603583 "discs, large homolog 2, chapsyn-110 (Drosophila)" NA 8755482, 9806853 Standard NM_001364 NM_001142702 NA Approved PSD-93, PSD93, chapsyn-110, PPP1R58 uc001pak.2 Q15700 OTTHUMG00000134309 ENST00000398309.2:c.*3099T>- chr11.hg19:g.83167762delA 6 8 ref NA False 43 43 PASS 7 PASS ref->het 0 NA 37,41 38,38 13,9 1 1 B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2 True hg19 CCDS41696.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DLG2-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000259243.3 PASS NA None 87 NA True - A ENST00000398309.2 TAF1D 79101 __UNKNOWN__ __UNKNOWN__ 11 93466291 93466312 __UNKNOWN__ Intron DEL TAGAAAGTACCAATTAAAGATT TAGAAAGTACCAATTAAAGATT - rs546053184 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:93466291_93466312delTAGAAAGTACCAATTAAAGATT ENST00000546088.1 - 4 1319 NR_002973.1 Q9H5J8 TAF1D_HUMAN TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa NA NA NA gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361) microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) DNA binding (GO:0003677) large_intestine(1)|lung(3)|prostate(1)|skin(2) 7 TTCATTCCTATAGAAAGTACCAATTAAAGATTTAGAAAGGAT 0.27 NA NA NA NA NA 19 0.00379393 0.0121 0.0014 5008 , , NA 20598 0.001 NA 0.001 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 46 44.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS8293.1 11q21 2012-05-30 2008-09-30 2008-09-30 ENSG00000166012 ENSG00000166012 79101 28759 protein-coding gene gene with protein product 612823 "Josephin domain containing 3" JOSD3 NA 15520167, 17318177 Standard NM_024116 NM_024116 NA Approved MGC5306, TAF(I)41 uc001pec.3 Q9H5J8 OTTHUMG00000167451 ENST00000546088.1:c.410-4AATCTTTAATTGGTACTTTCTA>- chr11.hg19:g.93466291_93466312delTAGAAAGTACCAATTAAAGATT 0 3 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 2,2 31,32 13,12 1 1 Q6I9Y6 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TAF1D-015 KNOWN basic processed_transcript NA protein_coding OTTHUMT00000394650.1 PASS NA None 46 NA True - TAGAAAGTACCAATTAAAGATT ENST00000546088.1 USP28 57646 __UNKNOWN__ __UNKNOWN__ 11 113669340 113669343 __UNKNOWN__ 3'UTR DEL TGAG TGAG - rs142451643 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:113669340_113669343delTGAG ENST00000003302.4 - 0 3921_3924 USP28_ENST00000260188.5_3'UTR|USP28_ENST00000544967.1_3'UTR NM_020886.2 NP_065937.1 Q96RU2 UBP28_HUMAN ubiquitin specific peptidase 28 NA NA NA cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511) nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234) ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843) breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1) 59 all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425) BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104) CACTGAGGACTGAGTATGAGGTTT 0.363 NA NA NA NA NA 62 0.0123802 0.0461 0.0014 5008 , , NA 19232 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765) PASS NA NA NA NA NA 0 NA NA NA NA NA 137 125.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.06 AB040948 CCDS31680.1, CCDS73394.1 11q23 2008-04-11 2005-08-08 ENSG00000048028 ENSG00000048028 57646 "Ubiquitin-specific peptidases" 12625 protein-coding gene gene with protein product 610748 "ubiquitin specific protease 28" NA 12838346, 11597335 Standard XM_005271630 NA Approved KIAA1515 uc001poh.3 Q96RU2 OTTHUMG00000168205 ENST00000003302.4:c.*622CTCA>- chr11.hg19:g.113669340_113669343delTGAG 0 2 ref NA False 88 65 PASS 1 PASS ref->het 0 NA 4,5 116,118 16,15 1 1 B0YJC0|B0YJC1|Q9P213 True hg19 CCDS31680.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA USP28-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000398789.1 PASS NA None 137 NA True - TGAG ENST00000003302.4 CEP290 80184 __UNKNOWN__ __UNKNOWN__ 12 88454594 88454595 __UNKNOWN__ Intron INS - - A rs11405846|rs386377279|rs386377278|rs370841656 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:88454594_88454595insA ENST00000552810.1 - 47 6866 CEP290_ENST00000309041.7_Intron|CEP290_ENST00000397838.3_Intron|CEP290_ENST00000547691.2_Intron NM_025114.3 NP_079390.3 O15078 CE290_HUMAN centrosomal protein 290kDa NA NA NA cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041) centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038) breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1) 73 ATGATCACATTAAAAAAAATTA 0.257 NA NA NA NA NA AAAAAAAA|AAAAAAAA|AAAAAAAAA|insertion 3814 0.761581 0.3268 0.8761 5008 , , NA 13724 0.9573 NA 0.9225 False NA ,,, NA NA NA 2504 0.9008 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 71 77.64 NA 1383,1929 NA 354,675,627 NA NA NA NA 0 0 dbSNP_120 43 6909,667 NA 3191,527,70 no intron CEP290 NM_025114.3 3545,1202,697 A1A1,A1R,RR NA 8.8041,41.7572,23.8428 NA 8292,2596 NA NA NA SO:0001627 intron_variant 0.01 AB002371 CCDS55858.1 12q21.33 2014-09-17 ENSG00000198707 80184 29021 protein-coding gene gene with protein product "Joubert syndrome 5", "nephrocystin-6", "cancer/testis antigen 87", "POC3 centriolar protein homolog (Chlamydomonas)", "Meckel syndrome, type 4" 610142 NA 15474516, 16682973, 16632484 Standard NM_025114 NM_025114 NA Approved KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3 uc001tar.3 O15078 ENST00000552810.1:c.6522+11->T chr12.hg19:g.88454602_88454602dupA 9 8 ref NA False 67 53 PASS 8 PASS ref->het 0 NA 6,6 54,55 11,10 1 1 Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0 True hg19 CCDS55858.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CEP290-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000406344.1 PASS NA None 71 NA True - A ENST00000552810.1 C12orf75 387882 __UNKNOWN__ __UNKNOWN__ 12 105697261 105697273 __UNKNOWN__ Intron DEL TCACAGAGCTTCC TCACAGAGCTTCC - rs147697665 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:105697261_105697273delTCACAGAGCTTCC ENST00000548458.2 + 2 67 Q8TAD7 OCC1_HUMAN chromosome 12 open reading frame 75 NA NA NA NA atcattgaaatcacagagcttccaagtgttttt 0.427 NA NA NA NA NA 91 0.0181709 0.0681 0.0014 5008 , , NA 23321 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 21 17.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AK056999 CCDS55879.1 12q23.3 2013-07-03 ENSG00000235162 ENSG00000235162 387882 35164 protein-coding gene gene with protein product "adipogenesis down-regulated 3", "overexpressed in colon carcinoma 1" NA NA 19531736 Standard NM_001145199 NM_001145199 NA Approved OCC-1, OCC1, AGD3 uc001tlh.4 Q8TAD7 OTTHUMG00000150129 ENST00000548458.2:c.68-23475TCACAGAGCTTCC>- chr12.hg19:g.105697261_105697273delTCACAGAGCTTCC 0 3 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 1,1 14,14 2,2 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C12orf75-004 KNOWN basic processed_transcript NA protein_coding OTTHUMT00000406306.2 PASS NA None 21 NA True + TCACAGAGCTTCC ENST00000548458.2 FICD 11153 __UNKNOWN__ __UNKNOWN__ 12 108919410 108919410 __UNKNOWN__ 3'UTR DEL A A - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:108919410delA ENST00000546448.1 + 0 254 SART3_ENST00000431469.2_Intron|SART3_ENST00000228284.3_Intron Q9BVA6 FICD_HUMAN FIC domain containing NA NA NA negative regulation of Rho GTPase activity (GO:0034259)|protein adenylylation (GO:0018117) integral component of membrane (GO:0016021) ATP binding (GO:0005524)|protein adenylyltransferase activity (GO:0070733) NS(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|upper_aerodigestive_tract(2) 15 GAAGACAGAGAAAAACCATGA 0.522 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 883 831.56 NA NA 81 77 79 NA NA NA 12 NA NA NA 108919410 2203 4300 6503 SO:0001624 3_prime_UTR_variant 3.12 AF049611 CCDS9116.1 12q24.1 2007-12-05 ENSG00000198855 11153 18416 protein-coding gene gene with protein product "huntingtin interacting protein 13", "fic S-phase protein cell division homolog (E. coli)" NA NA 9700202 Standard NM_007076 NM_007076 NA Approved HYPE, HIP13 uc001tmx.1 Q9BVA6 ENST00000546448.1:c.*251A>- chr12.hg19:g.108919410delA 4 6 ref NA False 165 120 PASS 5 PASS ref->het 0 NA 549,554 212,213 117,111 1 1 O75406 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FICD-005 PUTATIVE basic|exp_conf processed_transcript NA protein_coding OTTHUMT00000404846.1 PASS NA None 883 NA True + A ENST00000546448.1 SALL2 6297 __UNKNOWN__ __UNKNOWN__ 14 22005064 22005065 __UNKNOWN__ 5'UTR DEL AG AG - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:22005064_22005065delAG ENST00000327430.3 - 0 285_286 SALL2_ENST00000317492.5_5'UTR NM_005407.1 NP_005398.1 Q9Y467 SALL2_HUMAN spalt-like transcription factor 2 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2) 43 all_cancers(95;0.000662) GBM - Glioblastoma multiforme(265;0.0151) ATTCCCGGGTAGAGAGTTGGGA 0.619 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 425 395.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 3.07 AB002358 CCDS32045.1 14q11.1-q12.1 2013-10-17 2013-10-17 ENSG00000165821 ENSG00000165821 6297 "Zinc fingers, C2H2-type" 10526 protein-coding gene gene with protein product 602219 "sal (Drosophila)-like 2", "sal-like 2 (Drosophila)" NA 8975705 Standard NM_005407 XM_005267983 NA Approved KIAA0360, Hsal2, ZNF795 uc001wbe.3 Q9Y467 OTTHUMG00000168826 ENST00000327430.3:c.-10CT>- chr14.hg19:g.22005068_22005069delAG 2 3 ref NA False 56 56 PASS 3 PASS ref->het 0 NA 270,285 96,98 65,51 2 2 B2RMX6|B9EGK8|Q8N656|Q9Y4G1 True hg19 CCDS32045.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SALL2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000401242.1 PASS NA None 425 NA True - AG ENST00000327430.3 YLPM1 56252 __UNKNOWN__ __UNKNOWN__ 14 75264886 75264888 __UNKNOWN__ Intron DEL AGG AGG - rs374231863 LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:75264886_75264888delAGG ENST00000552421.1 + 5 2406 YLPM1_ENST00000325680.7_In_Frame_Del_p.G964del|YLPM1_ENST00000238571.3_In_Frame_Del_p.G769del P49750 YLPM1_HUMAN YLP motif containing 1 NA NA NA regulation of telomere maintenance (GO:0032204) nucleus (GO:0005634) poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078) breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1) 62 KIRC - Kidney renal clear cell carcinoma(43;0.238) BRCA - Breast invasive adenocarcinoma(234;0.00162) CTTCAAAAACAGGGGGGATGGAG 0.438 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 383 375.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.11 AK090435 CCDS45135.1 14q24.3 2014-06-13 2004-07-15 2004-07-15 ENSG00000119596 ENSG00000119596 56252 17798 protein-coding gene gene with protein product "protein phosphatase 1, regulatory subunit 169" NA "chromosome 14 open reading frame 170" C14orf170 NA 7596406 Standard NM_019589 NM_019589 NA Approved ZAP, PPP1R169 uc001xqj.4 P49750 OTTHUMG00000172503 ENST00000552421.1:c.2283-4371AGG>- chr14.hg19:g.75264886_75264888delAGG 0 6 ref NA False 142 96 PASS 1 PASS ref->het 0 NA 180,182 154,156 37,34 1 1 P49752|Q96I64|Q9P1V7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA YLPM1-008 NOVEL not_organism_supported|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000404450.1 PASS NA None 383 NA True + AGG ENST00000552421.1 PPIB 5479 __UNKNOWN__ __UNKNOWN__ 15 64455072 64455074 __UNKNOWN__ In_Frame_Del DEL CTT CTT - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:64455072_64455074delCTT ENST00000300026.3 - 1 330_332 c.112_114delAAG c.(112-114)aagdel p.K38del PPIB_ENST00000558492.1_5'UTR NM_000942.4 NP_000933.1 P23284 PPIB_HUMAN peptidylprolyl isomerase B (cyclophilin B) 38 NA NA bone development (GO:0060348)|chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|positive regulation of multicellular organism growth (GO:0040018)|protein peptidyl-prolyl isomerization (GO:0000413)|protein stabilization (GO:0050821) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634) peptide binding (GO:0042277)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|unfolded protein binding (GO:0051082) kidney(2)|large_intestine(2)|lung(6) 10 L-Proline(DB00172) CTTTGGGCCCCTTCTTCTTCTCA 0.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(105;399 1481 32889 33051 36637) PASS NA NA NA NA NA 0 NA NA NA NA NA 77 77.04 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0 CCDS10191.1 15q21-q22 2014-09-17 ENSG00000166794 ENSG00000166794 5479 5.2.1.8 9255 protein-coding gene gene with protein product 123841 NA 2000394, 20089953 Standard NM_000942 NA Approved CYPB, OI9 uc002and.3 P23284 OTTHUMG00000133018 ENST00000300026.3:c.112_114delAAG chr15.hg19:g.64455078_64455080delCTT ENSP00000300026:p.Lys38del 2 4 ref NA False 96 95 PASS 3 PASS ref->het 0 NA 44,45 24,26 12,9 1 1 A8K534|Q6IBH5|Q9BVK5 True hg19 CCDS10191.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPIB-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256604.1 PASS NA None 77 NA True - CTT ENST00000300026.3 LRRC49 54839 __UNKNOWN__ __UNKNOWN__ 15 71186952 71186954 __UNKNOWN__ Intron DEL ACA ACA - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:71186952_71186954delACA ENST00000560369.1 + 2 389 LRRC49_ENST00000443425.2_Intron|LRRC49_ENST00000260382.5_Intron|LRRC49_ENST00000544974.2_Intron Q8IUZ0 LRC49_HUMAN leucine rich repeat containing 49 NA NA NA cytoplasm (GO:0005737)|microtubule (GO:0005874) breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3) 34 GTCTCAAGACACAACATGATTTT 0.345 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 560 507.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.17 CCDS32282.1, CCDS55971.1, CCDS58376.1, CCDS61694.1 15q23 2005-08-09 ENSG00000137821 54839 25965 protein-coding gene gene with protein product NA NA 12477932 Standard NM_017691 NM_001199017 NA Approved FLJ20156 uc010ukf.2 Q8IUZ0 ENST00000560369.1:c.120+958ACA>- chr15.hg19:g.71186955_71186957delACA 1 3 ref NA False 327 147 PASS 2 PASS ref->het 0 NA 314,316 212,215 38,34 1 1 B3KVX1|B7Z366|F5H1J4|G5E9T5|H0YLN4|Q9NXM6 True hg19 CCDS58376.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LRRC49-005 NOVEL basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000417208.1 PASS NA None 560 NA True + ACA ENST00000560369.1 HOMER2 9455 __UNKNOWN__ __UNKNOWN__ 15 83561531 83561533 __UNKNOWN__ In_Frame_Del DEL TTC TTC - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:83561531_83561533delTTC ENST00000304231.8 - 2 258_260 c.66_68delGAA c.(64-69)aagaac>aac p.K22del HOMER2_ENST00000399166.2_In_Frame_Del_p.K22del|HOMER2_ENST00000450735.2_In_Frame_Del_p.K22del|HOMER2_ENST00000426485.1_In_Frame_Del_p.K22del NM_199330.2 NP_955362.1 Q9NSB8 HOME2_HUMAN homer homolog 2 (Drosophila) 22 WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}. NA NA behavioral response to cocaine (GO:0048148)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|chemical homeostasis within a tissue (GO:0048875)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277) apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211) cervix(1)|endometrium(2)|lung(6) 9 AGGCATCCAGTTCTTCTTGGTGT 0.522 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 513 477.98 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 3.36 AF093264 CCDS45334.1, CCDS45336.1 15q24.3 2008-02-05 ENSG00000103942 9455 17513 protein-coding gene gene with protein product 604799 NA 9808459, 9808458 Standard NM_199330 NA Approved CPD, Cupidin, Vesl-2, HOMER-2B, HOMER-2, HOMER-2A uc002bjg.3 Q9NSB8 ENST00000304231.8:c.66_68delGAA chr15.hg19:g.83561534_83561536delTTC ENSP00000305632:p.Lys22del 1 4 ref NA False 77 76 PASS 2 PASS ref->het 0 NA 303,310 162,167 63,53 1 1 O95269|O95349|Q9NSB6|Q9NSB7|Q9UNT7 True hg19 CCDS45334.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HOMER2-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000418689.1 PASS NA None 513 NA True - TTC ENST00000304231.8 POLG 5428 __UNKNOWN__ __UNKNOWN__ 15 89864316 89864317 __UNKNOWN__ Intron INS - - CTAC rs68075517|rs58584025|rs199540650|rs2307433 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:89864316_89864317insCTAC ENST00000268124.5 - 17 3068 POLG_ENST00000442287.2_Intron NM_001126131.1|NM_002693.2 NP_001119603.1|NP_002684.1 P54098 DPOG1_HUMAN polymerase (DNA directed), gamma NA NA NA aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264) extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739) chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020) breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2) 33 Lung NSC(78;0.0472)|all_lung(78;0.089) STAD - Stomach adenocarcinoma(125;0.165) CTGTCAATATGCTGAGGGGCTG 0.569 NA NA NA NA NA DNA polymerases (catalytic subunits) 2796 0.558307 0.8396 0.4784 5008 , , NA 18136 0.4315 NA 0.4692 False NA ,,, NA NA NA 2504 0.4571 NA NA NA Colon(73;648 1203 11348 18386 27782) PASS NA NA NA NA NA 0 NA NA NA NA NA 204 196.93 NA , 3320,942 NA 1307,706,118 NA NA NA NA , 1.9 0 dbSNP_100 85 3881,4373 NA 900,2081,1146 no intron,intron POLG NM_002693.2,NM_001126131.1 , 2207,2787,1264 A1A1,A1R,RR NA 47.0196,22.1023,42.4656 , , NA 7201,5315 NA NA NA SO:0001627 intron_variant 0.46 X98093 CCDS10350.1 15q24 2014-09-17 ENSG00000140521 ENSG00000140521 5428 "DNA polymerases" 9179 protein-coding gene gene with protein product 174763 NA 9465903 Standard NM_002693 NM_002693 NA Approved POLG1, POLGA uc002bnr.4 P54098 OTTHUMG00000149646 ENST00000268124.5:c.2734+38->GTAG chr15.hg19:g.89864316_89864317insCTAC 1 1 ref NA False 31 31 PASS 0 PASS ref->het 0 NA 58,58 122,123 20,20 1 1 Q8NFM2|Q92515 True hg19 CCDS10350.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA POLG-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000312854.2 PASS NA None 204 NA True - CTAC ENST00000268124.5 NDUFB10 4716 __UNKNOWN__ __UNKNOWN__ 16 2011473 2011474 __UNKNOWN__ Intron DEL CT CT - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:2011473_2011474delCT ENST00000569148.1 + 3 309 NDUFB10_ENST00000543683.2_Intron|NDUFB10_ENST00000268668.6_Intron O96000 NDUBA_HUMAN NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10, 22kDa NA NA NA cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281) extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747) NADH dehydrogenase (ubiquinone) activity (GO:0008137) lung(1)|urinary_tract(1) 2 TGTGATTAGCCTCTCTTGCTCC 0.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 340 323.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.88 AF044954 CCDS10451.1 16p13.3 2011-07-04 2002-08-29 ENSG00000140990 ENSG00000140990 4716 "Mitochondrial respiratory chain complex / Complex I" 7696 protein-coding gene gene with protein product "complex I PDSW subunit" 603843 "NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10 (22kD, PDSW)" NA 9763677, 9878551 Standard NM_004548 NM_004548 NA Approved PDSW uc002cni.2 O96000 OTTHUMG00000128709 ENST00000569148.1:c.237-24CT>- chr16.hg19:g.2011477_2011478delCT 2 3 ref NA False 52 52 PASS 3 PASS ref->het 0 NA 256,257 59,61 25,22 1 1 Q96II6 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NDUFB10-004 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000434026.1 PASS NA None 340 NA True + CT ENST00000569148.1 ZC3H7A 29066 __UNKNOWN__ __UNKNOWN__ 16 11846617 11846619 __UNKNOWN__ In_Frame_Del DEL GGA GGA - rs145286621 LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:11846617_11846619delGGA ENST00000396516.2 - 21 2829_2831 c.2632_2634delTCC c.(2632-2634)tccdel p.S878del ZC3H7A_ENST00000575984.1_In_Frame_Del_p.S74del|ZC3H7A_ENST00000355758.4_In_Frame_Del_p.S878del Q8IWR0 Z3H7A_HUMAN zinc finger CCCH-type containing 7A 878 NA NA nucleus (GO:0005634) metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822) breast(2)|endometrium(3)|kidney(5)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(2) 25 TGTGCTTCTCGGAGGAGATGTGG 0.498 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 212 216.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.06 AF161540 CCDS10550.1 16p13-p12 2013-01-11 2005-06-02 2005-06-08 ENSG00000122299 ENSG00000122299 29066 "Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing" 30959 protein-coding gene gene with protein product NA "zinc finger CCCH-type domain containing 7", "zinc finger CCCH-type containing 7" ZC3HDC7, ZC3H7 NA 11042152 Standard NM_014153 NM_014153 NA Approved HSPC055, FLJ20318 uc002dbl.3 Q8IWR0 OTTHUMG00000129825 ENST00000396516.2:c.2632_2634delTCC chr16.hg19:g.11846620_11846622delGGA ENSP00000379773:p.Ser878del 1 4 ref NA False 106 97 PASS 2 PASS ref->het 0 NA 114,114 68,71 34,31 1 1 D3DUG5|Q9NPE9 True hg19 CCDS10550.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZC3H7A-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000437066.1 PASS NA None 212 NA True - GGA ENST00000396516.2 MIEF2 125170 __UNKNOWN__ __UNKNOWN__ 17 18169001 18169003 __UNKNOWN__ 3'UTR DEL CCT CCT - rs80026520|rs398058632|rs202029692 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:18169001_18169003delCCT ENST00000323019.4 + 0 2499_2501 MIEF2_ENST00000395706.2_3'UTR|MIEF2_ENST00000395704.4_3'UTR NM_001144900.1|NM_139162.3 NP_001138372.1|NP_631901.2 Q96C03 MID49_HUMAN mitochondrial elongation factor 2 NA NA NA mitochondrion organization (GO:0007005)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein targeting to membrane (GO:0090314) integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739) NA CCCAAGTGACCCTCCTCCTGCCT 0.458 NA NA NA NA NA 1043 0.208267 0.1248 0.2334 5008 , , NA 19963 0.3185 NA 0.2435 False NA ,,, NA NA NA 2504 0.1534 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 115 106.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.83 BC014973 CCDS11193.1, CCDS45624.1, CCDS45625.1 17p11.2 2013-09-23 2013-09-23 2013-09-23 ENSG00000177427 ENSG00000177427 125170 17920 protein-coding gene gene with protein product 615498 "Smith-Magenis syndrome chromosome region, candidate 7" SMCR7 NA 11997338, 21508961 Standard NM_139162 NM_001144900 NA Approved MGC23130, MiD49 uc010vxq.2 Q96C03 OTTHUMG00000059392 ENST00000323019.4:c.*925CCT>- chr17.hg19:g.18169007_18169009delCCT 2 5 ref NA False 78 63 PASS 3 PASS ref->het 0 NA 5,6 94,95 16,14 1 1 J3KPT3|Q6ZRD4|Q96N07 True hg19 CCDS11193.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MIEF2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000132060.2 PASS NA None 115 NA True + CCT ENST00000323019.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 17 31340061 31340064 __UNKNOWN__ IGR DEL GAGA GAGA - rs141990016 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:31340061_31340064delGAGA NA SPACA3 (15166 upstream) : ASIC2 (40 downstream) NA NA NA NA GCCCCGGAGGGAGAGAGACTCGGA 0.426 NA NA NA NA NA 44 0.00878594 0.0295 0.0072 5008 , , NA 16620 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 46 43.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.01 NA NA NA NA NA chr17.hg19:g.31340065_31340068delGAGA 2 5 ref NA False 45 45 PASS 4 PASS ref->het 0 NA 5,5 34,34 8,8 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 46 NA True GA KRT222 125113 __UNKNOWN__ __UNKNOWN__ 17 38811363 38811364 __UNKNOWN__ Intron DEL GA GA - rs200057667 LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:38811363_38811364delGA ENST00000476049.1 - 6 1010 Q8N1A0 KT222_HUMAN keratin 222 NA NA NA intermediate filament (GO:0005882) structural molecule activity (GO:0005198) breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(2)|skin(1) 15 gaagagagaggagagagagaga 0.297 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 26 27.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AK092967 CCDS11371.1 17q21.2 2013-06-25 2009-08-25 2009-08-25 ENSG00000213424 ENSG00000213424 125113 "-" 28695 protein-coding gene gene with protein product NA "keratin 222 pseudogene" KRT222P NA 16831889 Standard NM_152349 NM_152349 NA Approved KA21, MGC45562 uc002hvc.2 Q8N1A0 OTTHUMG00000133374 ENST00000476049.1:c.885+1209TC>- chr17.hg19:g.38811373_38811374delGA 6 3 ref NA False 42 42 PASS 7 PASS ref->het 0 NA 13,13 12,12 2,2 1 1 Q7Z368 True hg19 CCDS11371.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KRT222-001 KNOWN basic|appris_principal|readthrough_transcript|CCDS nonsense_mediated_decay NA protein_coding OTTHUMT00000447539.1 PASS NA None 26 NA True - GA ENST00000476049.1 TMEM92 162461 __UNKNOWN__ __UNKNOWN__ 17 48357536 48357536 __UNKNOWN__ 3'UTR DEL C C - rs139366122 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:48357536delC ENST00000300433.3 + 0 1457 NM_001168215.1 NP_001161687.1 Q6UXU6 TMM92_HUMAN transmembrane protein 92 NA NA NA integral component of membrane (GO:0016021) NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(1) 7 CAGGAAGCAGCCCTGGGACAG 0.592 NA NA NA NA NA CCC|CCC|CC|deletion 187 0.0373403 0.1354 0.0086 5008 , , NA 17115 0.001 NA 0.001 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 64 71.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 CCDS11562.1 17q21.33 2005-12-13 162461 26579 protein-coding gene gene with protein product NA NA 12975309 Standard NM_153229 NM_153229 NA Approved FLJ33318 uc002iqn.2 Q6UXU6 ENST00000300433.3:c.*867C>- chr17.hg19:g.48357536delC 2 3 ref NA False 44 35 PASS 3 PASS ref->het 0 NA 3,3 48,51 12,10 1 1 Q8NBF0 True hg19 CCDS11562.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM92-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000367053.2 PASS NA None 64 NA True + C ENST00000300433.3 QRICH2 84074 __UNKNOWN__ __UNKNOWN__ 17 74283143 74283170 __UNKNOWN__ Intron DEL ACACACACACACACACACACACACACAT ACACACACACACACACACACACACACAT - rs560629023|rs11271405|rs199704726|rs8072808 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:74283143_74283170delACACACACACACACACACACACACACAT ENST00000262765.5 - 7 3693 NM_032134.1 NP_115510.1 Q9H0J4 QRIC2_HUMAN glutamine rich 2 NA NA NA breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4) 62 acacacacacacacacacacacacacacacacacacaTGATGGGAGGG 0.57 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 36 21.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.02 AK058102 CCDS32741.1 17q25.1 2009-03-19 ENSG00000129646 ENSG00000129646 84074 25326 protein-coding gene gene with protein product NA NA Standard NM_032134 NM_032134 NA Approved DKFZP434P0316 uc002jrd.1 Q9H0J4 OTTHUMG00000167578 ENST00000262765.5:c.3513+102ATGTGTGTGTGTGTGTGTGTGTGTGTGT>- chr17.hg19:g.74283143_74283170delACACACACACACACACACACACACACAT 0 2 ref NA False 35 35 PASS 1 PASS ref->hom 0 NA 0,0 30,32 5,4 1 1 A2RRE1|Q96LM3 True hg19 CCDS32741.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA QRICH2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000395140.1 PASS NA None 36 NA True - ACACACACACACACACACACACACACAT ENST00000262765.5 MFSD11 79157 __UNKNOWN__ __UNKNOWN__ 17 74734318 74734346 __UNKNOWN__ 5'UTR DEL CTCCTGCATCTGCCTTCTCCACTCACCAT CTCCTGCATCTGCCTTCTCCACTCACCAT - rs572209182|rs237054 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:74734318_74734346delCTCCTGCATCTGCCTTCTCCACTCACCAT ENST00000588460.1 + 0 1926_1954 MFSD11_ENST00000593181.1_Intron|RP11-318A15.7_ENST00000587459.1_Intron|MFSD11_ENST00000590393.1_5'UTR|MFSD11_ENST00000355954.3_Intron|MFSD11_ENST00000586622.1_Intron|MFSD11_ENST00000590514.1_Intron|MFSD11_ENST00000336509.4_Intron|MFSD11_ENST00000591864.1_Intron NM_001242534.1 NP_001229463.1 O43934 MFS11_HUMAN major facilitator superfamily domain containing 11 NA NA NA integral component of membrane (GO:0016021) endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1) 17 GGCTGCCTGGCTCCTGCATCTGCCTTCTCCACTCACCATCTCATTTCTT 0.576 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 42 36.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.6 BC002753 CCDS11750.1, CCDS56045.1 17q25.1 2012-03-09 ENSG00000092931 ENSG00000092931 79157 25458 protein-coding gene gene with protein product NA NA 9358160 Standard NM_024311 NM_001242532 NA Approved FLJ22196, FLJ20226 uc002jte.3 O43934 ENST00000588460.1:c.-89CTCCTGCATCTGCCTTCTCCACTCACCAT>- chr17.hg19:g.74734318_74734346delCTCCTGCATCTGCCTTCTCCACTCACCAT 0 3 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 6,6 23,23 13,13 1 1 O43442|Q9NXI5 True hg19 CCDS11750.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MFSD11-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000451516.1 PASS NA None 42 NA True + CTCCTGCATCTGCCTTCTCCACTCACCAT ENST00000588460.1 EPB41L3 23136 __UNKNOWN__ __UNKNOWN__ 18 5419888 5419889 __UNKNOWN__ Intron DEL AT AT - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:5419888_5419889delAT ENST00000341928.2 - 12 1680 EPB41L3_ENST00000342933.3_Intron|EPB41L3_ENST00000400111.3_Frame_Shift_Del_p.M461fs|EPB41L3_ENST00000540638.2_Frame_Shift_Del_p.M461fs|EPB41L3_ENST00000544123.1_Frame_Shift_Del_p.M461fs|EPB41L3_ENST00000542652.2_5'UTR NM_012307.2 NP_036439.2 Q9Y2J2 E41L3_HUMAN erythrocyte membrane protein band 4.1-like 3 NA NA NA apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360) axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886) structural constituent of cytoskeleton (GO:0005200) breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1) 105 TGCAGCAGACATAGAATCCTTC 0.411 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 243 226.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.49 AB023204 CCDS11838.1, CCDS62381.1, CCDS62382.1 18p11.32 2006-06-28 ENSG00000082397 ENSG00000082397 23136 3380 protein-coding gene gene with protein product 605331 NA 9828140, 9892180 Standard NM_012307 NM_012307 NA Approved DAL1, KIAA0987, 4.1B uc002kmt.1 Q9Y2J2 OTTHUMG00000131562 ENST00000341928.2:c.1340-12AT>- chr18.hg19:g.5419888_5419889delAT 0 3 ref NA False 66 66 PASS 1 PASS ref->het 0 NA 120,121 99,100 23,21 1 1 B7Z4I5|F5GX05|O95713|Q9BRP5 True hg19 CCDS11838.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EPB41L3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000254424.1 PASS NA None 243 NA True - AT ENST00000341928.2 MAPRE2 10982 __UNKNOWN__ __UNKNOWN__ 18 32711893 32711894 __UNKNOWN__ Intron INS - - TC rs556702999 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:32711893_32711894insTC ENST00000589699.1 + 6 745 MAPRE2_ENST00000300249.5_Intron|MAPRE2_ENST00000538170.2_Intron|MAPRE2_ENST00000413393.1_Intron|MAPRE2_ENST00000436190.2_Intron Q15555 MARE2_HUMAN microtubule-associated protein, RP/EB family, member 2 NA NA NA cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165) cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371) central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1) 9 TTATTTCTGCTTCTCTCTCTCT 0.441 NA NA NA NA NA 30 0.00599042 0.0197 0.0058 5008 , , NA 20736 0 NA 0 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 81 86.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.38 X94232 CCDS11910.1, CCDS45850.1, CCDS45851.1, CCDS58619.1 18q12.1 2013-01-17 ENSG00000166974 ENSG00000166974 10982 6891 protein-coding gene gene with protein product "APC-binding protein EB1" 605789 NA 9233623, 12475954 Standard NM_014268 NM_001143826 NA Approved RP1, EB1, EB2 uc010xcc.3 Q15555 OTTHUMG00000132551 ENST00000589699.1:c.622-102->TC chr18.hg19:g.32711902_32711903dupTC 9 3 ref NA False 49 48 PASS 8 PASS ref->het 0 NA 2,2 65,67 14,12 1 1 B2RE21|B3KR39|B4DJV4|B7Z2L3|E9PHR3|F5H1V8|G5E9I6|Q9UQ33 True hg19 CCDS45851.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAPRE2-005 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000442242.1 PASS NA None 81 NA True + TC ENST00000589699.1 CDH20 28316 __UNKNOWN__ __UNKNOWN__ 18 59206197 59206198 __UNKNOWN__ Intron INS - - T rs398120544|rs5825446 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:59206197_59206198insT ENST00000262717.4 + 9 1806 CDH20_ENST00000536675.2_Intron|CDH20_ENST00000538374.1_Intron Q9HBT6 CAD20_HUMAN cadherin 20, type 2 NA NA NA homophilic cell adhesion (GO:0007156) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) calcium ion binding (GO:0005509) breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3) 61 Colorectal(73;0.186) AACCATTACTCTTTTTTTTCTT 0.47 NA NA NA NA NA ?|TTTTTTTT|TTTTTTTTT|unsure 4078 0.814297 0.6884 0.9207 5008 , , NA 18794 0.8879 NA 0.8986 False NA ,,, NA NA NA 2504 0.7464 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 112 120.61 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.21 AF217289 CCDS11977.1 18q21.33 2010-01-26 ENSG00000101542 ENSG00000101542 28316 "Cadherins / Major cadherins" 1760 protein-coding gene gene with protein product 605807 NA 10995570 Standard NM_031891 NM_031891 NA Approved CDH7L3, Cdh7 uc010dps.1 Q9HBT6 OTTHUMG00000132768 ENST00000262717.4:c.1409-59->T chr18.hg19:g.59206205_59206205dupT 9 12 ref NA False 36 31 PASS 8 PASS ref->het 0 NA 5,5 85,86 22,21 1 1 Q495S3 True hg19 CCDS11977.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDH20-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256141.2 PASS NA None 112 NA True + T ENST00000262717.4 MYADM 91663 __UNKNOWN__ __UNKNOWN__ 19 54376929 54376940 __UNKNOWN__ In_Frame_Del DEL TGGCCTTCTCGC TGGCCTTCTCGC - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:54376929_54376940delTGGCCTTCTCGC ENST00000391769.2 + 3 426_437 c.146_157delTGGCCTTCTCGC c.(145-159)gtggccttctcgctg>gtg p.AFSL50del MYADM_ENST00000391768.2_In_Frame_Del_p.AFSL50del|MYADM_ENST00000391771.1_In_Frame_Del_p.AFSL50del|MYADM_ENST00000336967.3_In_Frame_Del_p.AFSL50del|MYADM_ENST00000391770.4_In_Frame_Del_p.AFSL50del NM_001020821.1 NP_001018657.1 Q96S97 MYADM_HUMAN myeloid-associated differentiation marker 50 MARVEL 1. {ECO:0000255|PROSITE- ProRule:PRU00581}. NA NA establishment of endothelial barrier (GO:0061028)|membrane raft organization (GO:0031579)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of gene expression (GO:0010629)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of protein kinase C signaling (GO:0090038)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cell migration (GO:0030335)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein targeting to plasma membrane (GO:0072661) cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|ruffle (GO:0001726) central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1) 12 Ovarian(34;0.19) GBM - Glioblastoma multiforme(134;0.0488) TCTACCTGCGTGGCCTTCTCGCTGGTGGCTAG 0.646 NA NA NA NA NA OREG0003650 type=REGULATORY REGION|Gene=MYADM|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 863 889.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 6.3 AF087882 CCDS12866.1 19q13.33-q13.4 2004-07-23 ENSG00000179820 ENSG00000179820 91663 7544 protein-coding gene gene with protein product 609959 NA 10733104, 12075932 Standard NM_138373 NM_001020818 NA Approved uc002qcl.3 Q96S97 OTTHUMG00000060775 ENST00000391769.2:c.146_157delTGGCCTTCTCGC chr19.hg19:g.54376929_54376940delTGGCCTTCTCGC ENSP00000375649:p.Ala50_Leu53del 0 3 ref 999 False 33 33 PASS 1 PASS ref->het 0 NA 657,684 100,105 164,136 1 1 B2RE58|Q542Z1|Q7Z507|Q8N9R4|Q96CS6|Q96SK9 True hg19 CCDS12866.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MYADM-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000134337.1 PASS NA None 863 NA True + TGGCCTTCTCGC ENST00000391769.2 BCAS4 55653 __UNKNOWN__ __UNKNOWN__ 20 49434829 49434830 __UNKNOWN__ Intron INS - - GCCTGGAAGGCGTGGGTTTAG rs376032771|rs11283878 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:49434829_49434830insGCCTGGAAGGCGTGGGTTTAG ENST00000358791.5 + 2 352 BCAS4_ENST00000609336.1_Intron|BCAS4_ENST00000262591.5_Intron|BCAS4_ENST00000485049.1_Intron|BCAS4_ENST00000371608.2_Intron NM_017843.3 NP_060313.3 Q8TDM0 BCAS4_HUMAN breast carcinoma amplified sequence 4 NA NA NA cytoplasm (GO:0005737) large_intestine(2)|lung(2)|pancreas(1)|upper_aerodigestive_tract(1) 6 GGTGAGTGGCTGCCTGGAAGGC 0.569 NA NA NA NA NA OREG0026033 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 369 360.65 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.35 AK000502 CCDS13432.2, CCDS33487.1 20q13 2008-07-03 ENSG00000124243 ENSG00000124243 55653 14367 protein-coding gene gene with protein product 607471 NA 12378525 Standard NM_017843 NM_001010974 NA Approved FLJ20495, CNOL uc002xvq.3 Q8TDM0 OTTHUMG00000032735 ENST00000358791.5:c.252+10->GCCTGGAAGGCGTGGGTTTAG chr20.hg19:g.49434829_49434830insGCCTGGAAGGCGTGGGTTTAG 2 2 ref 962 False 44 44 PASS 1 PASS ref->het 0 NA 4,5 39,39 320,319 1 1 Q5TD52|Q5TD53|Q5TD54|Q5U5K7|Q5XKE8|Q8IXI7|Q8NEZ6|Q8TDL9|Q9NX13|Q9Y511 True hg19 CCDS33487.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BCAS4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000079700.1 PASS NA None 369 NA True + GCCTGGAAGGCGTGGGTTTAG ENST00000358791.5 ADNP 23394 __UNKNOWN__ __UNKNOWN__ 20 49509654 49509676 __UNKNOWN__ Frame_Shift_Del DEL TCCGCATGTGTGCGGCCATCTTT TCCGCATGTGTGCGGCCATCTTT - rs376577810|rs146843778|rs369537762 LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:49509654_49509676delTCCGCATGTGTGCGGCCATCTTT ENST00000396029.3 - 5 2142_2164 c.1575_1597delAAAGATGGCCGCACACATGCGGA c.(1573-1599)gaaaagatggccgcacacatgcggatgfs p.EKMAAHMRM525fs ADNP_ENST00000349014.3_Frame_Shift_Del_p.EKMAAHMRM525fs|ADNP_ENST00000371602.4_Frame_Shift_Del_p.EKMAAHMRM525fs|ADNP_ENST00000396032.3_Frame_Shift_Del_p.EKMAAHMRM525fs NM_001282531.1|NM_015339.2 NP_001269460.1|NP_056154.1 Q9H2P0 ADNP_HUMAN activity-dependent neuroprotector homeobox 525 NA NA negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) extracellular space (GO:0005615)|nucleus (GO:0005634) chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872) NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2) 39 ATGTGAACCATCCGCATGTGTGCGGCCATCTTTTCCACATCAT 0.417 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 1091 1069.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 4.48 AF250860 CCDS13433.1 20q13.13 2011-06-20 2007-07-17 ENSG00000101126 ENSG00000101126 23394 "Homeoboxes / ZF class" 15766 protein-coding gene gene with protein product "ADNP homeobox 1" 611386 "activity-dependent neuroprotector" NA 9872452, 11013255 Standard NM_181442 NM_015339 NA Approved KIAA0784, ADNP1 uc002xvu.1 Q9H2P0 OTTHUMG00000032737 ENST00000396029.3:c.1575_1597delAAAGATGGCCGCACACATGCGGA chr20.hg19:g.49509654_49509676delTCCGCATGTGTGCGGCCATCTTT ENSP00000379346:p.Glu525fs 0 5 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 1062,1073 99,100 143,135 1 1 E1P5Y2|O94881|Q5BKU2|Q9UG34 True hg19 CCDS13433.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ADNP-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000079705.2 PASS NA None 1091 NA True - TCCGCATGTGTGCGGCCATCTTT ENST00000396029.3 MYO18B 84700 __UNKNOWN__ __UNKNOWN__ 22 26346484 26346485 __UNKNOWN__ Intron INS - - TGTGTGTGTATGTGTGTG rs373462917|rs112952110|rs59002655|rs143993522 LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:26346484_26346485insTGTGTGTGTATGTGTGTG ENST00000407587.2 + 37 6004 MYO18B_ENST00000335473.7_Intron|MYO18B_ENST00000536101.1_Intron Q8IUG5 MY18B_HUMAN myosin XVIIIB NA NA NA cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461) ATP binding (GO:0005524)|motor activity (GO:0003774) NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2) 146 aactaataggatgtgtgtgtgt 0.396 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 46 46.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.6 AJ310931 CCDS54507.1 22q12.1 2011-09-27 ENSG00000133454 ENSG00000133454 84700 "Myosins / Myosin superfamily : Class XVIII" 18150 protein-coding gene gene with protein product 607295 NA 12209013, 12547197 Standard NM_032608 NM_032608 NA Approved BK125H2.1 uc003abz.1 Q8IUG5 OTTHUMG00000151129 ENST00000407587.2:c.5835+68->TGTGTGTGTATGTGTGTG chr22.hg19:g.26346484_26346485insTGTGTGTGTATGTGTGTG 1 2 ref NA False 33 33 PASS 0 PASS ref->hom 0 NA 0,0 27,29 18,18 1 1 B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MYO18B-006 NOVEL non_canonical_conserved|basic|appris_candidate_longest|exp_conf protein_coding NA protein_coding OTTHUMT00000400691.1 PASS NA None 46 NA True + TGTGTGTGTATGTGTGTG ENST00000407587.2 EIF4ENIF1 56478 __UNKNOWN__ __UNKNOWN__ 22 31846079 31846080 __UNKNOWN__ Intron INS - - T rs144780466 byFrequency LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:31846079_31846080insT ENST00000344710.5 - 9 1217 EIF4ENIF1_ENST00000397525.1_Intron|EIF4ENIF1_ENST00000330125.5_Intron|EIF4ENIF1_ENST00000397523.1_Intron|EIF4ENIF1_ENST00000382180.2_Intron NM_001164502.1 NP_001157974.1 Q9NRA8 4ET_HUMAN eukaryotic translation initiation factor 4E nuclear import factor 1 NA NA NA cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634) poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565) autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 36 ACTTTGTCAACTTTTTTAGCCA 0.441 NA NA NA NA NA TTTTTT|TTTTTT|TTTTTTT|insertion 1726 0.344649 0.4054 0.3242 5008 , , NA 21831 0.0843 NA 0.4871 False NA ,,, NA NA NA 2504 0.3988 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 66 73.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.32 AF240775 CCDS13898.1, CCDS54520.1 22q11.2 2007-01-16 ENSG00000184708 ENSG00000184708 56478 16687 protein-coding gene gene with protein product 607445 NA 10856257 Standard NM_019843 NM_019843 NA Approved 4E-T, FLJ21601, Clast4, 2610509L04Rik uc003akz.2 Q9NRA8 OTTHUMG00000030793 ENST00000344710.5:c.1059+194->A chr22.hg19:g.31846085_31846085dupT 7 6 ref NA False 39 39 PASS 6 PASS ref->het 0 NA 2,2 60,61 4,3 1 1 B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708 True hg19 CCDS54520.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EIF4ENIF1-001 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000127925.1 PASS NA None 66 NA True - T ENST00000344710.5 BMP15 9210 __UNKNOWN__ __UNKNOWN__ X 50659210 50659211 __UNKNOWN__ In_Frame_Ins INS - - TCT rs531409392|rs371124071|rs111889793 LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:50659210_50659211insTCT ENST00000252677.3 + 2 782_783 c.782_783insTCT c.(781-786)tctctt>tcTCTtctt p.263_264insL NM_005448.2 NP_005439.2 O95972 BMP15_HUMAN bone morphogenetic protein 15 263 NA L -> LL (no or minor deleterious effect detected). {ECO:0000269|PubMed:16464940, ECO:0000269|PubMed:16508750, ECO:0000269|PubMed:16645022, ECO:0000269|PubMed:19263482}. NA female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893) cytoplasm (GO:0005737)|extracellular space (GO:0005615) NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1) 26 Ovarian(276;0.236) GAAAGGGAATCTCTTCTCCGGA 0.465 NA NA NA NA NA 696 0.184371 0.3918 0.0591 3775 , , NA 13145 0.0605 NA 0.003 False NA ,,, NA NA NA 2504 0.0746 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 146 155.76 NA 1671,2050 NA 330,777,234,485,303 NA NA NA NA 2.3 0 dbSNP_132 65 35,6448 NA 0,30,5,2327,1764 no coding BMP15 NM_005448.2 330,807,239,2812,2067 A1A1,A1R,A1,RR,R NA 0.5399,44.9073,16.7189 NA 1706,8498 NA NA NA SO:0001652 inframe_insertion 0.42 AF082349 CCDS14334.1 Xp11.2 2013-02-06 ENSG00000130385 ENSG00000130385 9210 "Bone morphogenetic proteins" 1068 protein-coding gene gene with protein product 300247 NA 9849956 Standard NM_005448 NM_005448 NA Approved GDF9B uc011mnw.2 O95972 OTTHUMG00000021525 ENST00000252677.3:c.786_788dupTCT chrX.hg19:g.50659214_50659216dupTCT ENSP00000252677:p.Leu263_Leu263dup 3 3 ref NA False 80 66 PASS 2 PASS ref->het 0 NA 13,13 113,116 21,18 1 1 Q17RM6|Q5JST1|Q9UMS1 True hg19 CCDS14334.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BMP15-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000056572.1 PASS NA None 146 NA True + TCT ENST00000252677.3 PAK3 5063 __UNKNOWN__ __UNKNOWN__ X 110439050 110439050 __UNKNOWN__ Intron DEL T T - LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:110439050delT ENST00000372010.1 + 16 1597 PAK3_ENST00000446737.1_Intron|PAK3_ENST00000417227.1_Intron|PAK3_ENST00000360648.4_Intron|PAK3_ENST00000425146.1_Intron|PAK3_ENST00000519681.1_Intron|PAK3_ENST00000372007.5_Intron|PAK3_ENST00000262836.4_Intron|PAK3_ENST00000518291.1_Intron O75914 PAK3_HUMAN p21 protein (Cdc42/Rac)-activated kinase 3 NA NA NA activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808) cytoplasm (GO:0005737) ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674) breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4) 41 TAATTAGAACTTTTTTTTCTG 0.303 NA NA NA NA NA TSP Lung(19;0.15) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 83 86.01 NA NA 51 52 51 NA NA NA X NA NA NA 110439050 2201 4297 6498 SO:0001627 intron_variant 1.8 AF068864 CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1 Xq22.3 2008-06-17 2008-06-17 ENSG00000077264 ENSG00000077264 5063 8592 protein-coding gene gene with protein product 300142 "mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3" MRX30, MRX47 NA 8826460, 9731525 Standard NM_002578 NM_002578 NA Approved hPAK3, bPAK uc010npv.1 O75914 OTTHUMG00000022202 ENST00000372010.1:c.1156-20T>- chrX.hg19:g.110439050delT 7 9 ref NA False 40 40 PASS 8 PASS ref->het 0 NA 32,37 41,42 10,7 2 2 A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8 True hg19 CCDS48153.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PAK3-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000057918.1 PASS NA None 83 NA True + T ENST00000372010.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ Y 59004466 59004467 __UNKNOWN__ IGR DEL AG AG - rs369360827 LTS-023_T LTS-023_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrY:59004466_59004467delAG NA None (None upstream) : SPRY3 (96012 downstream) NA NA NA NA atctccaaaaagaaagaaagaa 0.391 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA 19 18.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.5 NA NA NA NA NA chrY.hg19:g.59004466_59004467delAG 0 8 ref NA False 47 47 PASS 1 PASS ref->het 0 NA 9,10 9,9 1,1 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 19 NA True AG VAV3 10451 __UNKNOWN__ __UNKNOWN__ 1 108115411 108115412 __UNKNOWN__ 3'UTR DEL TT TT - LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:108115411_108115412delTT ENST00000370056.4 - 0 3359_3360 VAV3_ENST00000527011.1_3'UTR NM_006113.4 NP_006104.4 Q9UKW4 VAV3_HUMAN vav 3 guanine nucleotide exchange factor NA NA NA NA angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886) GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070) NA NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1) 58 all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594) Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204) GGTAAAAGTGTTTGCCGGGCAA 0.406 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 124 119.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.26 NA NA AF118886 CCDS785.1, CCDS44181.1 1p13.3 2013-02-14 2007-07-25 ENSG00000134215 ENSG00000134215 10451 "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing" 12659 protein-coding gene gene with protein product 605541 "vav 3 oncogene" NA Standard NM_006113 NM_001079874 NA Approved uc001dvk.1 Q9UKW4 OTTHUMG00000010995 ENST00000370056.4:c.*542AA>- chr1.hg19:g.108115411_108115412delTT 1 4 ref NA False 59 59 PASS 3 PASS ref->het 0 NA 64,65 41,42 18,16 1 1 B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8 True hg19 CCDS785.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA VAV3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000030242.2 PASS NA None 124 NA True - T ENST00000370056.4 LAMC1 3915 __UNKNOWN__ __UNKNOWN__ 1 183100595 183100598 __UNKNOWN__ Intron DEL TATT TATT - rs67028115|rs56123159|rs55657301|rs4047797|rs566368469|rs2333619|rs138728349 byFrequency LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:183100595_183100598delTATT ENST00000258341.4 + 20 3823 NM_002293.3 NP_002284.3 P11047 LAMC1_HUMAN laminin, gamma 1 (formerly LAMB2) NA NA NA NA axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446) basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260) extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208) NA NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3) 76 tgtgtgtgtgtATTGTCTTATCCC 0.402 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 160 164.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 5.22 NA NA J03202 CCDS1351.1 1q31 2013-03-01 ENSG00000135862 ENSG00000135862 3915 "Laminins" 6492 protein-coding gene gene with protein product 150290 LAMB2 NA 3234037 Standard NM_002293 NM_002293 NA Approved uc001gpy.4 P11047 OTTHUMG00000035418 ENST00000258341.4:c.3566+82TATT>- chr1.hg19:g.183100595_183100598delTATT 0 3 ref NA False 40 40 PASS 1 PASS ref->het 0 NA 58,66 28,28 69,70 1 1 Q5VYE7 True hg19 CCDS1351.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LAMC1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000085954.2 PASS NA None 160 NA True + TATT ENST00000258341.4 PRKCE 5581 __UNKNOWN__ __UNKNOWN__ 2 46414109 46414113 __UNKNOWN__ 3'UTR DEL TTAAT TTAAT - LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:46414109_46414113delTTAAT ENST00000306156.3 + 0 4630_4634 NM_005400.2 NP_005391.1 Q02156 KPCE_HUMAN protein kinase C, epsilon NA NA NA NA activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669) cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886) actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871) NA MBOAT2/PRKCE(2) breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2) 34 all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209) LUSC - Lung squamous cell carcinoma(58;0.171) Tamoxifen(DB00675) GAACATGAGATTAATTTAATTTATC 0.307 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 237 244.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.48 NA NA CCDS1824.1 2p21 2009-07-10 ENSG00000171132 ENSG00000171132 5581 2.7.11.1 9401 protein-coding gene gene with protein product 176975 NA 1382605, 7877991 Standard NM_005400 NA Approved uc002rut.3 Q02156 OTTHUMG00000128817 ENST00000306156.3:c.*2093TTAAT>- chr2.hg19:g.46414114_46414118delTTAAT 1 3 ref NA False 34 34 PASS 2 PASS ref->het 0 NA 214,218 7,7 34,33 1 1 B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81 True hg19 CCDS1824.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PRKCE-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250751.2 PASS NA None 237 NA True + TTAAT ENST00000306156.3 PTPRG 5793 __UNKNOWN__ __UNKNOWN__ 3 61989040 61989042 __UNKNOWN__ In_Frame_Del DEL GAC GAC - rs189356599 LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:61989040_61989042delGAC ENST00000474889.1 + 4 765_767 c.388_390delGAC c.(388-390)gacdel p.D131del PTPRG_ENST00000295874.10_In_Frame_Del_p.D131del NM_002841.3 NP_002832.3 P23470 PTPRG_HUMAN protein tyrosine phosphatase, receptor type, G 131 Alpha-carbonic anhydrase. NA NA NA brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169) extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887) identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001) NA NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 62 BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065) CCTTCTGAAAGACGACTATTTTG 0.438 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 164 158.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0 NA NA L09247 CCDS2895.1 3p21-p14 2013-02-11 ENSG00000144724 ENSG00000144724 5793 "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing" 9671 protein-coding gene gene with protein product 176886 PTPG NA 1711217 Standard NM_002841 NM_002841 NA Approved RPTPG uc003dlb.3 P23470 OTTHUMG00000158660 ENST00000474889.1:c.388_390delGAC chr3.hg19:g.61989043_61989045delGAC ENSP00000418112:p.Asp131del 1 4 ref NA False 50 50 PASS 2 PASS ref->het 0 NA 109,112 44,47 16,11 1 1 B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5 True hg19 CCDS2895.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PTPRG-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000351674.1 PASS NA None 164 NA True + GAC ENST00000474889.1 JARID2 3720 __UNKNOWN__ __UNKNOWN__ 6 15468723 15468729 __UNKNOWN__ Intron DEL GGGTGAG GGGTGAG - rs200915872|rs139217003|rs147212247|rs375348963|rs79097145 byFrequency LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:15468723_15468729delGGGTGAG ENST00000341776.2 + 5 737 JARID2_ENST00000541660.1_Intron|JARID2_ENST00000397311.3_Intron NM_004973.3 NP_004964.2 Q92833 JARD2_HUMAN jumonji, AT rich interactive domain 2 NA NA NA NA central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351) histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634) chromatin binding (GO:0003682)|DNA binding (GO:0003677) NA breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1) 59 Breast(50;0.0142)|Ovarian(93;0.103) all_hematologic(90;0.00612) CTTCTGGAAAGGGTGAGGGTCAAGGCC 0.435 NA NA NA NA NA NA NA NA NA NA NA NA 2182 0.435703 0.4554 0.4481 5008 , , NA 17254 0.4216 NA 0.3499 False NA ,,, NA NA NA 2504 0.5031 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 44 44.8 NA NA 1951,2311 NA 453,1045,633 NA NA NA NA NA 3 0 NA dbSNP_130 44 2808,5438 NA 510,1788,1825 no intron JARID2 NM_004973.2 NA 963,2833,2458 A1A1,A1R,RR NA 34.0529,45.7766,38.0476 NA NA NA 4759,7749 NA NA NA SO:0001627 intron_variant 0.23 NA NA U57592 CCDS4533.1, CCDS58996.1 6p24-p23 2008-02-05 2006-10-06 2004-01-30 ENSG00000008083 ENSG00000008083 3720 6196 protein-coding gene gene with protein product 601594 "jumonji (mouse) homolog", "Jumonji, AT rich interactive domain 2" JMJ NA 8894700 Standard NM_004973 NM_001267040 NA Approved uc003nbj.4 Q92833 OTTHUMG00000014293 ENST00000341776.2:c.494-44GGGTGAG>- chr6.hg19:g.15468723_15468729delGGGTGAG 0 4 ref NA False 39 38 PASS 1 PASS ref->het 0 NA 4,4 31,31 7,7 1 1 A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63 True hg19 CCDS4533.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA JARID2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000039926.1 PASS NA None 44 NA True + GGGTGAG ENST00000341776.2 LY6G5C 80741 __UNKNOWN__ __UNKNOWN__ 6 31644512 31644513 __UNKNOWN__ 5'UTR DEL AA AA - LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:31644512_31644513delAA ENST00000474395.1 - 0 799_800 LY6G5C_ENST00000375860.2_3'UTR|LY6G5C_ENST00000375858.3_3'UTR Q5SRR4 LY65C_HUMAN lymphocyte antigen 6 complex, locus G5C NA NA NA NA extracellular region (GO:0005576) NA endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1) 7 ACTAGGGGACAAGAGAGGAAAC 0.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 135 128.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.94 NA NA CCDS34401.1, CCDS34401.2 6p21 2010-02-17 2002-07-29 2002-08-01 ENSG00000204428 ENSG00000204428 80741 13932 protein-coding gene gene with protein product 610434 "chromosome 6 open reading frame 20" C6orf20 NA 12079290 Standard NM_025262 NA Approved G5c, NG33 uc003nvu.2 Q5SRR4 OTTHUMG00000031228 ENST00000474395.1:c.-37TT>- chr6.hg19:g.31644512_31644513delAA 0 3 ref NA False 80 80 PASS 2 PASS ref->het 0 NA 76,80 43,44 17,14 1 1 A6NCW4|B0UXB3|B0UXB4|B0UZ69|B0UZQ0|B1B0L9|O95871|Q5SQ59|Q8NDY0|Q8NDY1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LY6G5C-008 KNOWN basic processed_transcript NA protein_coding OTTHUMT00000127866.2 PASS NA None 135 NA True - A ENST00000474395.1 ZNF890P 645700 __UNKNOWN__ __UNKNOWN__ 7 5172045 5172046 __UNKNOWN__ RNA INS - - G rs71811672|rs79186458|rs200698976 LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:5172045_5172046insG ENST00000422060.2 - 0 477 NR_034163.1 zinc finger protein 890, pseudogene NA NA NA NA NA NA aaatccctgctaaaaagggcag 0.515 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 28 28.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 3.55 NA NA 7p22.1 2011-05-24 ENSG00000159904 ENSG00000159904 645700 38691 pseudogene pseudogene NA NA Standard NR_034163 NR_034163 NA Approved uc003snu.1 OTTHUMG00000166790 ENST00000422060.2: chr7.hg19:g.5172045_5172046insG 1 5 ref NA False 39 39 PASS 0 PASS ref->het 0 NA 9,9 13,21 6,4 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF890P-002 KNOWN basic processed_transcript NA pseudogene OTTHUMT00000391474.1 PASS NA None 28 NA True - G ENST00000422060.2 TMEM176B 28959 __UNKNOWN__ __UNKNOWN__ 7 150490798 150490801 __UNKNOWN__ Intron DEL GACA GACA - rs72471023|rs34960382 byFrequency LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:150490798_150490801delGACA ENST00000447204.2 - 4 688 TMEM176B_ENST00000429904.2_Intron|TMEM176B_ENST00000450753.2_Intron|TMEM176B_ENST00000326442.5_Intron|TMEM176B_ENST00000492607.1_Intron|TMEM176B_ENST00000434545.1_Intron NM_014020.3 NP_054739.3 Q3YBM2 T176B_HUMAN transmembrane protein 176B NA NA NA NA cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887) integral component of membrane (GO:0016021)|nucleus (GO:0005634) NA cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3) 19 OV - Ovarian serous cystadenocarcinoma(82;0.0121) UCEC - Uterine corpus endometrioid carcinoma (81;0.168) GGATCCCAGGGACAGACAAAGAAC 0.49 NA NA NA NA NA NA NA NA NA NA NA NA 2040 0.407348 0.292 0.3357 5008 , , NA 18517 0.5308 NA 0.4155 False NA ,,, NA NA NA 2504 0.4785 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 107 102.79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.83 NA NA AF115384 CCDS5908.1, CCDS47746.1 7q36.1 2006-09-04 ENSG00000106565 ENSG00000106565 28959 29596 protein-coding gene gene with protein product 610385 NA 9922225 Standard NM_014020 NM_014020 NA Approved LR8 uc003whu.4 Q3YBM2 OTTHUMG00000157577 ENST00000447204.2:c.316-110TGTC>- chr7.hg19:g.150490802_150490805delGACA 1 3 ref NA False 47 46 PASS 2 PASS ref->het 0 NA 7,7 74,78 22,20 1 1 B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609 True hg19 CCDS5908.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM176B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000349204.1 PASS NA None 107 NA True - GACA ENST00000447204.2 NPFFR1 64106 __UNKNOWN__ __UNKNOWN__ 10 72026052 72026057 __UNKNOWN__ In_Frame_Del DEL AGGAGG AGGAGG - LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:72026052_72026057delAGGAGG ENST00000277942.6 - 2 97_102 c.98_103delCCTCCT c.(97-105)tcctcctac>tac p.SS33del NM_022146.4 NP_071429.1 Q9GZQ6 NPFF1_HUMAN neuropeptide FF receptor 1 33 NA NA NA neuropeptide signaling pathway (GO:0007218) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188) NA endometrium(2)|lung(1) 3 TGCTGATAGTAGGAGGAGAAGGTGAG 0.578 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 175 181.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.44 NA NA AB040104 CCDS53539.1 10q21-q22 2012-08-10 2006-02-15 2006-02-15 ENSG00000148734 ENSG00000148734 64106 "GPCR / Class A : Neuropeptide receptors : FF/AF", "GPCR / Class A : RF amide peptide receptors" 17425 protein-coding gene gene with protein product "neuropeptide FF 1" 607448 "G protein-coupled receptor 147" GPR147 NA 11024015 Standard NM_022146 NM_022146 NA Approved OT7T022, NPFF1R1 uc021psj.1 Q9GZQ6 OTTHUMG00000018404 ENST00000277942.6:c.98_103delCCTCCT chr10.hg19:g.72026052_72026057delAGGAGG ENSP00000277942:p.Ser33_Ser34del 0 4 ref NA False 90 87 PASS 2 PASS ref->het 0 NA 97,100 63,65 25,22 1 1 A2RRF0|Q8NGR0|Q96RN3 True hg19 CCDS53539.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NPFFR1-001 NOVEL basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000048504.2 PASS NA None 175 NA True - AGG ENST00000277942.6 APPL2 55198 __UNKNOWN__ __UNKNOWN__ 12 105629953 105629954 __UNKNOWN__ 5'UTR INS - - CCCGCCGGCCCTCCTCCCGGCCCT rs71069799|rs571636317 byFrequency LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:105629953_105629954insCCCGCCGGCCCTCCTCCCGGCCCT ENST00000258530.3 - 0 62_63 C12orf75_ENST00000548458.2_Intron NM_001251904.1|NM_018171.3 NP_001238833.1|NP_060641.2 Q06481 APLP2_HUMAN adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2 NA NA NA NA cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967) extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886) DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914) NA breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 33 gccgccgcctgcccgccggccc 0.767 NA NA NA NA NA NA NA NA NA NA NA NA 3157 0.630391 0.8396 0.621 5008 , , NA 7846 0.5476 NA 0.5467 False NA ,,, NA NA NA 2504 0.5256 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 22 40.88 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.14 NA NA AY113704 CCDS9101.1, CCDS58275.1, CCDS58276.1 12q23.3 2014-08-12 ENSG00000136044 ENSG00000136044 55198 "Pleckstrin homology (PH) domain containing" 18242 protein-coding gene gene with protein product 606231 NA 11431708, 17030088 Standard NM_018171 NM_001251904 NA Approved FLJ10659, DIP13B uc010swu.1 Q8NEU8 OTTHUMG00000169853 ENST00000258530.3:c.-164->AGGGCCGGGAGGAGGGCCGGCGGG chr12.hg19:g.105629953_105629954insCCCGCCGGCCCTCCTCCCGGCCCT 1 5 ref NA False 39 39 PASS 0 PASS ref->het 0 NA 3,3 6,6 15,15 1 1 B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36 True hg19 CCDS9101.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA APPL2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000406238.3 PASS NA None 22 NA True - CCCGCCGGCCCTCCTCCCGGCCCT ENST00000258530.3 OAS3 4940 __UNKNOWN__ __UNKNOWN__ 12 113376543 113376544 __UNKNOWN__ Intron INS - - CAAAGGG rs3038120|rs368497670|rs397734704|rs34992537 byFrequency LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:113376543_113376544insCAAAGGG ENST00000228928.7 + 1 356 RP1-71H24.1_ENST00000552784.1_RNA|OAS3_ENST00000548514.1_Intron|OAS3_ENST00000546638.1_Intron|OAS3_ENST00000551007.1_Intron NM_006187.2 NP_006178.2 Q9Y6K5 OAS3_HUMAN 2'-5'-oligoadenylate synthetase 3, 100kDa NA NA NA NA cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337) cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886) 2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872) NA breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2) 27 CTTTATGTGTCCAAAGGGGAGT 0.594 NA NA NA NA NA NA NA NA NA NA NA NA 3932 0.785144 0.9864 0.7738 5008 , , NA 16657 0.746 NA 0.6342 False NA ,,, NA NA NA 2504 0.7168 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 49 49.46 NA NA 2782,302 NA 1328,126,88 NA NA NA NA NA -4.3 0 NA dbSNP_114 4 4139,2883 NA 1566,1007,938 no intron OAS3 NM_006187.2 NA 2894,1133,1026 A1A1,A1R,RR NA 41.0567,9.7925,31.5159 NA NA NA 6921,3185 NA NA NA SO:0001627 intron_variant 0.04 NA NA AF063613 CCDS44981.1 12q24.2 2008-05-02 2002-08-29 ENSG00000111331 4940 8088 protein-coding gene gene with protein product 603351 "2'-5'-oligoadenylate synthetase 3 (100 kD)" NA 9790745 Standard NM_006187 NA Approved uc001tug.3 Q9Y6K5 OTTHUMG00000169795 ENST00000228928.7:c.177+31->CAAAGGG chr12.hg19:g.113376544_113376550dupCAAAGGG 2 3 ref NA False 50 49 PASS 1 PASS ref->het 0 NA 3,3 33,34 14,13 1 1 Q2HJ14|Q9H3P5 True hg19 CCDS44981.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OAS3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000405920.1 PASS NA None 49 NA True + CAAAGGG ENST00000228928.7 TAOK3 51347 __UNKNOWN__ __UNKNOWN__ 12 118587766 118587766 __UNKNOWN__ 3'UTR DEL T T - rs545580962 LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:118587766delT ENST00000392533.3 - 0 4223 TAOK3_ENST00000543709.1_5'UTR|TAOK3_ENST00000419821.2_3'UTR NM_016281.3 NP_057365.3 Q9H2K8 TAOK3_HUMAN TAO kinase 3 NA NA NA NA cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468) cytoplasm (GO:0005737)|plasma membrane (GO:0005886) ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740) NA central_nervous_system(1)|lung(5)|skin(1) 7 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) AAATACACAGTTTGAAAGTGT 0.308 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 208 210.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.17 NA NA AF135158 CCDS9188.1 12q 2007-08-03 ENSG00000135090 51347 18133 protein-coding gene gene with protein product NA NA 10559204, 10924369 Standard NM_016281 NM_016281 NA Approved JIK, DPK, MAP3K18 uc001twy.4 Q9H2K8 ENST00000392533.3:c.*1036A>- chr12.hg19:g.118587766delT 2 3 ref NA False 42 42 PASS 3 PASS ref->het 0 NA 135,139 37,38 33,28 1 1 Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7 True hg19 CCDS9188.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TAOK3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000401456.2 PASS NA None 208 NA True - T ENST00000392533.3 SCARB1 949 __UNKNOWN__ __UNKNOWN__ 12 125279525 125279525 __UNKNOWN__ Intron DEL G G - rs201907136|rs397897150|rs5801571 byFrequency LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:125279525delG ENST00000261693.6 - 9 1329 SCARB1_ENST00000535005.1_Intron|SCARB1_ENST00000546215.1_Intron|SCARB1_ENST00000376788.1_Intron|SCARB1_ENST00000339570.5_Intron|SCARB1_ENST00000415380.2_Intron|SCARB1_ENST00000541205.1_Intron|SCARB1_ENST00000544327.1_Intron|SCARB1_ENST00000540495.1_Intron NM_005505.4 NP_005496.4 Q8WTV0 SCRB1_HUMAN scavenger receptor class B, member 1 NA NA NA NA adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060) caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886) 1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215) NA endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1) 17 all_neural(191;0.101)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395) Phosphatidylserine(DB00144) GTGGTGTTCTGGGGAAGGAAT 0.493 NA NA NA NA NA NA NA NA NA NA NA NA GGGG|GGGG|GGG|deletion 1014 0.202476 0.3026 0.1614 5008 , , NA 20336 0.4196 NA 0.0308 False NA ,,, NA NA NA 2504 0.0491 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 42 45.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.04 NA NA Z22555 CCDS9259.1, CCDS45008.1 12q24.32 2008-08-05 2002-09-06 2002-09-06 ENSG00000073060 ENSG00000073060 949 1664 protein-coding gene gene with protein product 601040 "CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1" CD36L1 NA 7689561 Standard NM_005505 NM_001082959 NA Approved SRB1, CLA-1, CLA1, SR-BI uc001ugm.4 Q8WTV0 OTTHUMG00000168544 ENST00000261693.6:c.1202+215C>- chr12.hg19:g.125279525delG 3 4 ref NA False 62 58 PASS 4 PASS ref->het 0 NA 1,1 36,37 5,5 1 1 F8W8N0|Q14016|Q52LZ5|Q6KFX4 True hg19 CCDS9259.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SCARB1-004 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000400166.1 PASS NA None 42 NA True - G ENST00000261693.6 ZFHX3 463 __UNKNOWN__ __UNKNOWN__ 16 72830931 72830931 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:72830931delC ENST00000268489.5 - 9 6322 c.5650delG c.(5650-5652)gaafs p.E1884fs ZFHX3_ENST00000397992.5_Frame_Shift_Del_p.E970fs NM_006885.3 NP_008816.3 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 1884 NA NA NA brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366) mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667) enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270) NA NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11) 153 Ovarian(137;0.13) TTTTCCTTTTCTTTGATGACC 0.547 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 185 180.92 NA NA NA 82 86 84 NA NA NA NA 16 NA NA NA NA NA NA 72830931 2198 4300 6498 SO:0001589 frameshift_variant 0.33 NA NA D10250 CCDS10908.1, CCDS54035.1 16q22.3 2012-03-09 2007-08-09 2007-08-09 ENSG00000140836 ENSG00000140836 463 "Zinc fingers, C2H2-type", "Homeoboxes / ZF class" 777 protein-coding gene gene with protein product 104155 "AT-binding transcription factor 1" ATBF1 NA 1719379, 7592926 Standard NM_006885 NM_006885 NA Approved ZNF927 uc002fck.3 Q15911 OTTHUMG00000137599 ENST00000268489.5:c.5650delG chr16.hg19:g.72830931delC ENSP00000268489:p.Glu1884fs 0 7 ref NA False 145 101 PASS 1 PASS ref->het 0 NA 85,85 69,71 29,27 1 1 D3DWS8|O15101|Q13719 True hg19 CCDS10908.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZFHX3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000269008.1 PASS NA None 185 NA True - C ENST00000268489.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ Y 13801135 13801136 __UNKNOWN__ IGR INS - - TTGATATCAT LTS-024_T LTS-024_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrY:13801135_13801136insTTGATATCAT NA SLC9B1P1 (276418 upstream) : AC011293.1 (146306 downstream) NA NA NA NA NA NA aatggaatggaatggaatggaa 0.366 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 296 230.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 31.85 NA NA NA NA NA NA NA chrY.hg19:g.13801135_13801136insTTGATATCAT 1 2 ref NA False 56 56 PASS 0 PASS ref->het 0 NA 106,511 7,9 181,129 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 296 NA True TTGATATCAT Unknown 0 __UNKNOWN__ __UNKNOWN__ 1 156040327 156040330 __UNKNOWN__ IGR DEL CCTC CCTC - LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:156040327_156040330delCCTC NA RAB25 (32 upstream) : MEX3A (1473 downstream) NA NA NA NA NA NA NA CCCGTCTGTTCCTCCCTCTTCTCC 0.525 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 196 199.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.82 NA NA NA NA NA NA NA chr1.hg19:g.156040331_156040334delCCTC 1 5 ref NA False 152 102 PASS 2 PASS ref->het 0 NA 93,96 77,78 26,25 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 196 True CCTC Unknown 0 __UNKNOWN__ __UNKNOWN__ 1 248085359 248085364 __UNKNOWN__ IGR DEL TGTGTG TGTGTG - rs193012120 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:248085359_248085364delTGTGTG NA OR2T8 (101 upstream) : OR2AJ1 (11706 downstream) NA NA NA NA NA NA NA CTGTTGTCTCTGTGTGTGTGTGTGTT 0.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 206 232.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.95 NA NA NA NA NA NA NA chr1.hg19:g.248085365_248085370delTGTGTG 4 2 ref NA False 47 47 PASS 7 PASS ref->het 0 NA 79,82 80,81 45,42 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 206 True TG DBI 1622 __UNKNOWN__ __UNKNOWN__ 2 120128308 120128327 __UNKNOWN__ Splice_Site DEL TGTTTAAGAACGGCCCGGGA TGTTTAAGAACGGCCCGGGA - rs199499255|rs146343693|rs374134739|rs144004233 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:120128308_120128327delTGTTTAAGAACGGCCCGGGA ENST00000393103.2 + 3 373_385 c.130_142delTGTTTAAGAACGGCCCGGGA c.(130-144)tgtttaagaacggcc>cc p.CLRTA44fs DBI_ENST00000355857.3_Splice_Site_p.CLRTA43fs|DBI_ENST00000542275.1_Splice_Site_p.CLRTA104fs|DBI_ENST00000311521.4_Splice_Site_p.CLRTA60fs|DBI_ENST00000535617.1_Splice_Site_p.CLRTA85fs|DBI_ENST00000535757.1_Splice_Site_p.CLRTA60fs|DBI_ENST00000460901.1_3'UTR|DBI_ENST00000409094.1_Splice_Site_p.CLRTA60fs NM_001079863.1 NP_001073332.1 P07108 ACBP_HUMAN diazepam binding inhibitor (GABA receptor modulator, acyl-CoA binding protein) 43 ACB. {ECO:0000255|PROSITE- ProRule:PRU00573}. NA NA NA hair follicle development (GO:0001942)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|transport (GO:0006810)|triglyceride metabolic process (GO:0006641) endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear endoplasmic reticulum (GO:0097038) benzodiazepine receptor binding (GO:0030156)|lipid binding (GO:0008289)|long-chain fatty acyl-CoA binding (GO:0036042)|protein dimerization activity (GO:0046983) NA NA kidney(1)|lung(4)|skin(1) 6 TTTCTTCCCTTGTTTAAGAACGGCCCGGGATGTTGGACTT 0.427 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 142 130.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 1.28 NA NA L76366 CCDS2126.1, CCDS42740.1, CCDS42741.1, CCDS74568.1 2q12-q21 2010-10-20 2010-04-30 ENSG00000155368 ENSG00000155368 1622 2690 protein-coding gene gene with protein product "endozepine" 125950 "diazepam binding inhibitor (GABA receptor modulator, acyl-Coenzyme A binding protein)" NA 1440058 Standard NM_020548 NM_001079863 NA Approved ACBP, ACBD1 uc021vnj.1 P07108 OTTHUMG00000131403 ENST00000393103.2:c.131-1TGTTTAAGAACGGCCCGGGA>- chr2.hg19:g.120128308_120128327delTGTTTAAGAACGGCCCGGGA 0 5 ref NA False 175 95 PASS 1 PASS ref->het 0 NA 43,45 68,68 39,37 1 1 B8ZWD2|B8ZWD6|B8ZWD7|P08869|Q4VWZ6|Q53SQ7|Q6IB48|Q9UCI8 True hg19 CCDS42741.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DBI-003 PUTATIVE basic|appris_candidate_longest|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000330592.1 PASS NA None 142 Frame_Shift_Del True + TGTTTAAGAACGGCCCGGGA ENST00000393103.2 MAP2 4133 __UNKNOWN__ __UNKNOWN__ 2 210594717 210594718 __UNKNOWN__ Intron INS - - T rs11389149 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:210594717_210594718insT ENST00000360351.4 + 14 5774 MAP2_ENST00000447185.1_Intron|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000392194.1_Intron NM_002374.3 NP_002365.3 P11137 MTAP2_HUMAN microtubule-associated protein 2 NA NA NA NA axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175) cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399) dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198) NA NA breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1) 124 Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202) UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18) Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229) CCAATCTTGTCTTTTTAAAAAA 0.376 NA NA NA NA NA NA NA NA NA NA ?|TTTTT|TTTTTT|unsure 3721 0.743011 0.4221 0.9049 5008 , , NA 19862 0.8006 NA 0.8867 False NA ,,, NA NA NA 2504 0.8548 NA NA NA Pancreas(27;423 979 28787 29963) PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 158 175.34 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.07 NA NA CCDS2384.1, CCDS2385.1, CCDS33369.1 2q34-q35 2008-05-27 ENSG00000078018 ENSG00000078018 4133 "A-kinase anchor proteins" 6839 protein-coding gene gene with protein product 157130 NA 3103857, 7479905 Standard NM_001039538 XM_005246554 NA Approved MAP2A, MAP2B, MAP2C uc002vde.1 P11137 OTTHUMG00000132962 ENST00000360351.4:c.5268+31->T chr2.hg19:g.210594722_210594722dupT 6 6 ref NA False 36 36 PASS 5 PASS ref->hom 0 NA 0,0 127,130 27,25 1 1 Q17S04|Q8IUX2|Q99975|Q99976 True hg19 CCDS2384.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAP2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000256521.2 PASS NA None 158 True + T ENST00000360351.4 GABRA2 2555 __UNKNOWN__ __UNKNOWN__ 4 46263862 46263863 __UNKNOWN__ Intron INS - - G rs369237541|rs35496835|rs397799090 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:46263862_46263863insG ENST00000507069.1 - 8 1066 GABRA2_ENST00000514090.1_Intron|GABRA2_ENST00000510861.1_Intron|GABRA2_ENST00000515082.1_3'UTR|GABRA2_ENST00000540012.1_Intron|GABRA2_ENST00000356504.1_Intron|GABRA2_ENST00000381620.4_Intron P47869 GBRA2_HUMAN gamma-aminobutyric acid (GABA) A receptor, alpha 2 NA NA NA NA gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085) axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211) benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890) NA NA NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1) 56 Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198) CTTTAATGTCAGTTTTTAGAAA 0.302 NA NA NA NA NA NA NA NA NA NA G|G|GG|insertion 2557 0.510583 0.2731 0.4899 5008 , , NA 19004 0.5218 NA 0.5746 False NA ,,, NA NA NA 2504 0.7689 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 95 112.27 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.97 NA NA CCDS3471.1 4p12 2012-06-22 ENSG00000151834 ENSG00000151834 2555 "GABA receptors", "Ligand-gated ion channels / GABA(A) receptors" 4076 protein-coding gene gene with protein product "GABA(A) receptor, alpha 2" 137140 NA Standard NM_000807 NA Approved uc010igc.2 P47869 OTTHUMG00000044266 ENST00000507069.1:c.1059+79->C chr4.hg19:g.46263863_46263863dupG 2 5 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 9,9 76,79 10,8 1 1 A8K0U7|B7Z1H8|Q59G14 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GABRA2-013 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000363658.1 PASS NA None 95 True - G ENST00000507069.1 F2RL2 2151 __UNKNOWN__ __UNKNOWN__ 5 75911569 75911597 __UNKNOWN__ 3'UTR DEL TACAGGAATATAATGGGTATTAATAACAA TACAGGAATATAATGGGTATTAATAACAA - rs139687205|rs2069694 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:75911569_75911597delTACAGGAATATAATGGGTATTAATAACAA ENST00000296641.4 - 0 3138_3166 IQGAP2_ENST00000274364.6_Intron|IQGAP2_ENST00000502745.1_Intron|IQGAP2_ENST00000396234.3_Intron|IQGAP2_ENST00000379730.3_Intron NM_004101.3 NP_004092.1 O00254 PAR3_HUMAN coagulation factor II (thrombin) receptor-like 2 NA NA NA NA blood coagulation (GO:0007596)|metabolic process (GO:0008152)|platelet activation (GO:0030168)|response to wounding (GO:0009611) apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) phosphatidylinositol phospholipase C activity (GO:0004435)|thrombin receptor activity (GO:0015057) NA NA central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(3) 32 all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129) all cancers(79;4.43e-43) GTCATTTACTTACAGGAATATAATGGGTATTAATAACAAAATTCCATTT 0.336 NA NA NA NA NA NA NA NA NA NA 1278 0.255192 0.1725 0.2133 5008 , , NA 22205 0.1637 NA 0.3012 False NA ,,, NA NA NA 2504 0.4438 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 127 120.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.14 NA NA U92971 CCDS4031.1, CCDS58959.1 5q13 2012-08-08 ENSG00000164220 ENSG00000164220 2151 "GPCR / Class A : Protease activated receptors" 3539 protein-coding gene gene with protein product "proteinase-activated receptor-3" 601919 NA 9087410, 9722561 Standard NM_004101 NA Approved PAR3 uc003kem.4 O00254 OTTHUMG00000102119 ENST00000296641.4:c.*1838TTGTTATTAATACCCATTATATTCCTGTA>- chr5.hg19:g.75911569_75911597delTACAGGAATATAATGGGTATTAATAACAA 0 6 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 17,18 55,55 7,6 2 2 B2R754|B4DQ13|Q52M68|Q7Z3W3 True hg19 CCDS4031.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA F2RL2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000219958.3 PASS NA None 127 True - TACAGGAATATAATGGGTATTAATAACAA ENST00000296641.4 F2R 2149 __UNKNOWN__ __UNKNOWN__ 5 76012180 76012210 __UNKNOWN__ Frame_Shift_Del DEL CGGCCCGCTGTTGTCTGCCCGCACCCGGGCC CGGCCCGCTGTTGTCTGCCCGCACCCGGGCC - rs112841414 LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:76012180_76012210delCGGCCCGCTGTTGTCTGCCCGCACCCGGGCC ENST00000319211.4 + 1 313_343 c.48_78delCGGCCCGCTGTTGTCTGCCCGCACCCGGGCC c.(46-78)tgcggcccgctgttgtctgcccgcacccgggccfs p.CGPLLSARTRA16fs F2R_ENST00000505600.1_Frame_Shift_Del_p.CGPLLSARTRA16fs NM_001992.3 NP_001983.2 P25116 PAR1_HUMAN coagulation factor II (thrombin) receptor 16 NA NA NA activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPKK activity (GO:0000186)|anatomical structure morphogenesis (GO:0009653)|blood coagulation (GO:0007596)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|G-protein coupled receptor signaling pathway (GO:0007186)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of renin secretion into blood stream (GO:1900134)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of blood coagulation (GO:0030194)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood coagulation (GO:0030193)|regulation of interleukin-1 beta production (GO:0032651)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|STAT protein import into nucleus (GO:0007262)|tyrosine phosphorylation of STAT protein (GO:0007260) caveola (GO:0005901)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|platelet dense tubular network (GO:0031094)|postsynaptic membrane (GO:0045211) G-protein alpha-subunit binding (GO:0001965)|G-protein beta-subunit binding (GO:0031681)|G-protein coupled receptor activity (GO:0004930)|receptor binding (GO:0005102)|thrombin receptor activity (GO:0015057) NA NA NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(7)|ovary(3) 16 all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129) all cancers(79;4.43e-43) Streptokinase(DB00086) TCAGTCTGTGCGGCCCGCTGTTGTCTGCCCGCACCCGGGCCCGCAGGCCAG 0.749 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 84 71.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.21 NA NA M62424 CCDS4032.1 5q13 2012-08-08 ENSG00000181104 ENSG00000181104 2149 "GPCR / Class A : Protease activated receptors" 3537 protein-coding gene gene with protein product 187930 NA 8395910 Standard NM_001992 NA Approved TR, CF2R, PAR1, PAR-1 uc003ken.4 P25116 OTTHUMG00000131299 ENST00000319211.4:c.48_78delCGGCCCGCTGTTGTCTGCCCGCACCCGGGCC chr5.hg19:g.76012180_76012210delCGGCCCGCTGTTGTCTGCCCGCACCCGGGCC ENSP00000321326:p.Cys16fs 0 4 ref NA False 88 83 PASS 1 PASS ref->het 0 NA 29,30 37,37 26,25 1 1 Q53XV0|Q96RF7|Q9BUN4 True hg19 CCDS4032.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA F2R-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254068.2 PASS NA None 84 True + CGGCCCGCTGTTGTCTGCCCGCACCCGGGCC ENST00000319211.4 FBN2 2201 __UNKNOWN__ __UNKNOWN__ 5 127855153 127855157 __UNKNOWN__ Intron DEL TTAAA TTAAA - rs3059402|rs200994520|rs112355068|rs140146961|rs200025815 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:127855153_127855157delTTAAA ENST00000508053.1 - 11 1507 FBN2_ENST00000508989.1_Intron|FBN2_ENST00000262464.4_Intron P35556 FBN2_HUMAN fibrillin 2 NA NA NA NA anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583) extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578) calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201) NA NA NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1) 197 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) GGATCTTATGTTAAATTATAGTACA 0.298 NA NA NA NA NA NA NA NA NA NA 1675 0.334465 0.4917 0.2565 5008 , , NA 17342 0.2222 NA 0.2863 False NA ,,, NA NA NA 2504 0.3425 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 72 74.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.06 NA NA U03272 CCDS34222.1 5q23-q31 2008-08-01 2008-08-01 ENSG00000138829 2201 3604 protein-coding gene gene with protein product "fibrillin 5" 612570 "congenital contractural arachnodactyly" CCA NA 1852206, 8120105 Standard NM_001999 NM_001999 NA Approved DA9 uc003kuu.3 P35556 ENST00000508053.1:c.533-92TTTAA>- chr5.hg19:g.127855153_127855157delTTAAA 0 3 ref NA False 49 49 PASS 1 PASS ref->het 0 NA 10,10 47,47 11,11 1 1 B4DU01|Q59ES6 True hg19 CCDS34222.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FBN2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000371618.2 PASS NA None 72 True - TTAAA ENST00000508053.1 ATP10B 23120 __UNKNOWN__ __UNKNOWN__ 5 160018024 160018030 __UNKNOWN__ Intron DEL TCTCTGC TCTCTGC - rs199688799|rs554018271 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:160018024_160018030delTCTCTGC ENST00000327245.5 - 23 4492 NM_025153.2 NP_079429.2 O94823 AT10B_HUMAN ATPase, class V, type 10B NA NA NA NA phospholipid translocation (GO:0045332) cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021) ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012) NA NA NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1) 75 Renal(175;0.00196) Medulloblastoma(196;0.0377)|all_neural(177;0.121) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) GACCAGTTCTTCTCTGCAATTTATGTG 0.435 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 84 154 NA 28,3550 NA 0,28,1761 NA NA NA NA -7.3 0 NA NA 65 250,7580 NA 5,240,3670 no intron ATP10B NM_025153.2 5,268,5431 A1A1,A1R,RR NA 3.1928,0.7826,2.4369 NA 278,11130 NA NA NA SO:0001627 intron_variant 29.85 NA NA AB018258 CCDS43394.1 5q34 2010-04-20 2007-09-19 ENSG00000118322 ENSG00000118322 23120 "ATPases / P-type" 13543 protein-coding gene gene with protein product NA "ATPase, Class V, type 10B" NA 9872452, 11015572 Standard NM_025153 NM_025153 NA Approved ATPVB, KIAA0715, FLJ21477 uc003lym.1 O94823 OTTHUMG00000163551 ENST00000327245.5:c.3645+35GCAGAGA>- chr5.hg19:g.160018024_160018030delTCTCTGC 0 4 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 13,13 66,68 5,3 1 1 Q9H725 True hg19 CCDS43394.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ATP10B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000374127.1 PASS NA None 84 True - TCTCTGC ENST00000327245.5 ZNF354C 30832 __UNKNOWN__ __UNKNOWN__ 5 178509351 178509352 __UNKNOWN__ 3'UTR INS - - TCTT rs386695574|rs145972880|rs398072665|rs34059723|rs75956529 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:178509351_178509352insTCTT ENST00000315475.6 + 0 4224_4225 NM_014594.1 NP_055409.1 Q86Y25 Z354C_HUMAN zinc finger protein 354C NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA NA endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3) 30 all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309) all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) all cancers(165;0.247) atttaattaaatcttttgtcta 0.356 NA NA NA NA NA NA NA NA NA NA 1559 0.311302 0.2352 0.2378 5008 , , NA 14850 0.4286 NA 0.3052 False NA ,,, NA NA NA 2504 0.3517 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 104 111.72 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.15 NA NA CCDS4443.1 5q35 2013-01-08 ENSG00000177932 ENSG00000177932 30832 "Zinc fingers, C2H2-type", "-" 16736 protein-coding gene gene with protein product NA NA 10786630 Standard NM_014594 NA Approved KID3 uc003mju.3 Q86Y25 OTTHUMG00000130888 ENST00000315475.6:c.*2254->TCTT chr5.hg19:g.178509352_178509355dupTCTT 2 5 ref NA False 40 39 PASS 1 PASS ref->het 0 NA 4,4 84,84 14,14 1 1 Q6P4P9|Q8NFX1 True hg19 CCDS4443.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF354C-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253473.2 PASS NA None 104 True + TCTT ENST00000315475.6 ITPR3 3710 __UNKNOWN__ __UNKNOWN__ 6 33625601 33625601 __UNKNOWN__ Intron DEL T T - rs3831079 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:33625601delT ENST00000374316.5 + 5 1342 ITPR3_ENST00000605930.1_Intron Q14573 ITPR3_HUMAN inositol 1,4,5-trisphosphate receptor, type 3 NA NA NA NA activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281) apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235) inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091) NA NA NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 85 Caffeine(DB00201) ACtgtgtgtgtgtgtgtgtgt 0.587 NA NA NA NA NA NA NA NA NA NA |||unknown(STR2?) 2167 0.432708 0.4781 0.3127 5008 , , NA 17396 0.4851 NA 0.3042 False NA ,,, NA NA NA 2504 0.5348 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 195 204.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.03 NA NA D26351 CCDS4783.1 6p21.31 2011-11-24 2011-04-28 ENSG00000096433 ENSG00000096433 3710 "Ion channels / Inositol triphosphate receptors" 6182 protein-coding gene gene with protein product 147267 "inositol 1,4,5-triphosphate receptor, type 3" NA 8081734, 8288584 Standard NM_002224 NM_002224 NA Approved IP3R3 uc021ywr.1 Q14573 OTTHUMG00000014532 ENST00000374316.5:c.283-108T>- chr6.hg19:g.33625601delT 0 2 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 36,37 135,142 22,16 1 1 Q14649|Q5TAQ2 True hg19 CCDS4783.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ITPR3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000040204.2 PASS NA None 195 True + T ENST00000374316.5 MTRF1L 54516 __UNKNOWN__ __UNKNOWN__ 6 153310937 153310937 __UNKNOWN__ 3'UTR DEL A A - rs368338572 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:153310937delA ENST00000367233.5 - 0 1235 MTRF1L_ENST00000367230.1_3'UTR|MTRF1L_ENST00000464135.1_5'UTR|MTRF1L_ENST00000367231.5_3'UTR NM_019041.5 NP_061914.3 Q9UGC7 RF1ML_HUMAN mitochondrial translational release factor 1-like NA NA NA NA mitochondrion (GO:0005739) translation release factor activity, codon specific (GO:0016149) NA NA endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1) 10 Ovarian(120;0.125) OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888) GTGTTAACTCAACGTTTTTCA 0.313 NA NA NA NA NA NA NA NA NA NA A|AA|A|insertion 116 0.0231629 0.0212 0.036 5008 , , NA 16324 0.0139 NA 0.0129 False NA ,,, NA NA NA 2504 0.0368 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 64 97.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.14 NA NA BC011873 CCDS5243.1, CCDS47502.1, CCDS75540.1 6q25-q26 2008-02-05 ENSG00000112031 ENSG00000112031 54516 21051 protein-coding gene gene with protein product 613542 NA Standard NM_019041 NM_019041 NA Approved uc003qpi.4 Q9UGC7 OTTHUMG00000015857 ENST00000367233.5:c.*93T>- chr6.hg19:g.153310937delA 1 2 ref NA False 72 72 PASS 2 PASS ref->het 0 NA 35,42 18,23 9,15 1 1 B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40 True hg19 CCDS5243.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MTRF1L-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000042764.1 PASS NA None 64 True - A ENST00000367233.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 169115612 169115613 __UNKNOWN__ IGR INS - - GAG rs377163352|rs374346674|rs374680858 LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:169115612_169115613insGAG NA SMOC2 (41628 upstream) : RP1-125N5.2 (1131 downstream) NA NA NA NA NA NA NA aagataatgatgaggaggacaa 0.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 22 22.75 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 3.91 NA NA NA NA NA NA NA chr6.hg19:g.169115616_169115618dupGAG 3 3 ref NA False 42 42 PASS 2 PASS ref->hom 0 NA 0,0 18,18 4,4 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 22 True GAG Unknown 0 __UNKNOWN__ __UNKNOWN__ 8 128100029 128100030 __UNKNOWN__ IGR INS - - A rs372333255|rs551191707|rs57532727 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:128100029_128100030insA NA PCAT2 (5563 upstream) : RP11-255B23.4 (97849 downstream) NA NA NA NA NA NA NA TATTTTAAGCCAAAAAAAATTC 0.347 NA NA NA NA NA NA NA NA NA NA aaaaaaa|AAAAAAAA|AAAAAAAAA|cryptic_indel 593 0.118411 0.1634 0.0634 5008 , , NA 17340 0.1597 NA 0.1103 False NA ,,, NA NA NA 2504 0.0624 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 148 192.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.6 NA NA NA NA NA NA NA chr8.hg19:g.128100037_128100037dupA 9 8 ref NA False 42 42 PASS 8 PASS ref->het 0 NA 42,43 79,144 30,35 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 148 True A Unknown 0 __UNKNOWN__ __UNKNOWN__ 9 6675477 6675478 __UNKNOWN__ IGR INS - - C rs57829573|rs141774351|rs76369813 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:6675477_6675478insC NA RP11-390F4.6 (4842 upstream) : RP11-390F4.10 (28992 downstream) NA NA NA NA NA NA NA AGCAAACCAAAAAAACCAGAGT 0.441 NA NA NA NA NA NA NA NA NA NA C|-|C|deletion 3982 0.795128 0.9115 0.8674 5008 , , NA 18318 0.6597 NA 0.7763 False NA ,,, NA NA NA 2504 0.7454 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 21 21.34 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.45 NA NA NA NA NA NA NA chr9.hg19:g.6675477_6675478insC 1 7 ref NA False 42 42 PASS 0 PASS ref->hom 0 NA 0,0 19,19 1,1 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 21 True C OR1J2 26740 __UNKNOWN__ __UNKNOWN__ 9 125273385 125273386 __UNKNOWN__ Frame_Shift_Ins INS - - T rs145911830 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:125273385_125273386insT ENST00000335302.5 + 1 305_306 c.305_306insT c.(304-309)tattttfs p.YF102fs NM_054107.1 NP_473448.1 Q8NGS2 OR1J2_HUMAN olfactory receptor, family 1, subfamily J, member 2 102 NA NA NA integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984) NA NA NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1) 26 TCTCAGATGTATTTTTTTATAT 0.401 NA NA NA NA NA NA NA NA NA NA TTTTTTT|TTTTTTT|TTTTTTTT|insertion 273 0.0545128 0.0681 0.0591 5008 , , NA 23759 0.002 NA 0.0974 False NA ,,, NA NA NA 2504 0.0429 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 122 141.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.01 NA NA CCDS35121.1 9q33.2 2013-09-20 ENSG00000197233 ENSG00000197233 26740 "GPCR / Class A : Olfactory receptors" 8209 protein-coding gene gene with protein product NA OR1J3, OR1J5 NA Standard XM_005251920 NA Approved OST044 uc011lyv.2 Q8NGS2 OTTHUMG00000020604 ENST00000335302.5:c.312dupT chr9.hg19:g.125273392_125273392dupT ENSP00000335575:p.Tyr102fs 8 8 ref NA False 38 38 PASS 7 PASS ref->het 0 NA 15,15 93,97 14,12 1 1 A3KFL9|Q6IF14|Q96R90|Q9NZP1 True hg19 CCDS35121.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OR1J2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000053932.1 PASS NA None 122 True + T ENST00000335302.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ 10 42364804 42364805 __UNKNOWN__ IGR INS - - GGAAG rs74213537 LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:42364804_42364805insGGAAG NA None (None upstream) : AL031601.1 (365545 downstream) NA NA NA NA NA NA NA cattccattccattccattcca 0.411 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 521 398.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 59.75 NA NA NA NA NA NA NA chr10.hg19:g.42364804_42364805insGGAAG 1 2 ref NA False 51 51 PASS 0 PASS ref->het 0 NA 241,843 9,28 263,129 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 521 True GGAAG Unknown 0 __UNKNOWN__ __UNKNOWN__ 10 42379894 42379895 __UNKNOWN__ IGR INS - - ATTCT rs377697180 LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:42379894_42379895insATTCT NA None (None upstream) : AL031601.1 (350455 downstream) NA NA NA NA NA NA NA cattccattccattccattccc 0.416 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 36 28.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 3.62 NA NA NA NA NA NA NA chr10.hg19:g.42379894_42379895insATTCT 1 2 ref NA False 104 104 PASS 0 PASS ref->het 0 NA 15,70 5,8 19,14 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 36 True ATTCT ADO 84890 __UNKNOWN__ __UNKNOWN__ 10 64568141 64568145 __UNKNOWN__ 3'UTR DEL TGGGA TGGGA - LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:64568141_64568145delTGGGA ENST00000373783.1 + 0 3626_3630 NM_032804.5 NP_116193.2 Q96SZ5 AEDO_HUMAN 2-aminoethanethiol (cysteamine) dioxygenase NA NA NA NA mitochondrion (GO:0005739) cysteamine dioxygenase activity (GO:0047800)|metal ion binding (GO:0046872) NA NA lung(2) 2 Prostate(12;0.0297)|all_hematologic(501;0.228) ATAACAACTGTGGGATAAAAGTTAT 0.346 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 243 252.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.41 NA NA BC028589 CCDS7266.2 10q21.3 2007-08-28 2007-08-28 2007-08-28 ENSG00000181915 ENSG00000181915 84890 1.13.11.19 23506 protein-coding gene gene with protein product "cysteamine dioxygenase" 611392 "chromosome 10 open reading frame 22" C10orf22 NA 17581819 Standard NM_032804 NM_032804 NA Approved FLJ14547 uc001jmg.3 Q96SZ5 OTTHUMG00000018306 ENST00000373783.1:c.*2513TGGGA>- chr10.hg19:g.64568141_64568145delTGGGA 0 5 ref NA False 64 64 PASS 1 PASS ref->het 0 NA 90,91 124,125 30,30 1 1 B1AL29 True hg19 CCDS7266.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ADO-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000048243.2 PASS NA None 243 True + TGGGA ENST00000373783.1 TRIM66 9866 __UNKNOWN__ __UNKNOWN__ 11 8644563 8644566 __UNKNOWN__ Intron DEL CATA CATA - rs397731807|rs34386713|rs10533257|rs398054970|rs71452476 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:8644563_8644566delCATA ENST00000402157.2 - 15 3019 TRIM66_ENST00000299550.6_Intron O15016 TRI66_HUMAN tripartite motif containing 66 NA NA NA NA aggresome (GO:0016235)|nucleus (GO:0005634) zinc ion binding (GO:0008270) NA NA autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2) 9 TATAGTCATTCATACATAGTGGTG 0.426 NA NA NA NA NA NA NA NA NA NA 2596 0.518371 0.4932 0.5821 5008 , , NA 22809 0.4038 NA 0.6292 False NA ,,, NA NA NA 2504 0.5112 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 224 227.26 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.99 NA NA AB002296 11p15.4 2013-01-28 2011-01-25 ENSG00000166436 ENSG00000166436 9866 "Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type" 29005 protein-coding gene gene with protein product 612000 "chromosome 11 open reading frame 29", "tripartite motif-containing 66" C11orf29 NA 9205841 Standard XM_084529 NM_014818 NA Approved KIAA0298, TIF1D uc010rbo.2 O15016 OTTHUMG00000150481 ENST00000402157.2:c.2579-140TATG>- chr11.hg19:g.8644567_8644570delCATA 1 2 ref NA False 48 47 PASS 2 PASS ref->het 0 NA 18,18 171,172 31,30 1 1 Q9BQQ4 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRIM66-001 NOVEL not_organism_supported|basic|appris_candidate_longest protein_coding NA protein_coding OTTHUMT00000318299.2 PASS NA None 224 True - CATA ENST00000402157.2 BIRC2 329 __UNKNOWN__ __UNKNOWN__ 11 102234397 102234397 __UNKNOWN__ Splice_Site DEL A A - LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:102234397delA ENST00000532672.1 + 6 1348 c.e6-1 BIRC2_ENST00000227758.2_Splice_Site|BIRC2_ENST00000530675.1_Splice_Site|BIRC2_ENST00000527910.1_Splice_Site Q13490 BIRC2_HUMAN baculoviral IAP repeat containing 2 NA NA NA NA apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666) CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634) ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270) NA NA breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 26 all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227) Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093) Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151) BRCA - Breast invasive adenocarcinoma(274;0.0144) CTTGTTTCATAGCTGTTGTCA 0.299 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 229 208.96 NA NA 119 108 112 NA NA NA 11 NA NA NA NA 102234397 2203 4299 6502 SO:0001630 splice_region_variant 0.6 NA NA L49431 CCDS8316.1, CCDS58169.1 11q22 2011-01-25 2011-01-25 ENSG00000110330 ENSG00000110330 329 "Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers" 590 protein-coding gene gene with protein product "NFR2-TRAF signalling complex protein", "apoptosis inhibitor 1" 601712 "baculoviral IAP repeat-containing 2" API1 NA 8552191, 8548810 Standard NM_001166 NM_001166 NA Approved cIAP1, hiap-2, MIHB, RNF48, c-IAP1 uc010ruq.3 Q13490 OTTHUMG00000167325 ENST00000532672.1:c.1012-1A>- chr11.hg19:g.102234397delA 0 2 ref NA False 63 63 PASS 1 PASS ref->het 0 NA 145,145 66,67 18,18 1 1 B4E026|Q16516|Q4TTG0 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BIRC2-003 PUTATIVE not_organism_supported|basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000394171.1 PASS NA None 229 Intron True + A ENST00000532672.1 IFT46 56912 __UNKNOWN__ __UNKNOWN__ 11 118416627 118416630 __UNKNOWN__ Intron DEL CTCT CTCT - LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:118416627_118416630delCTCT ENST00000264021.3 - 10 1091 TMEM25_ENST00000354284.4_Intron|IFT46_ENST00000530872.1_Intron|IFT46_ENST00000264020.2_Intron|TMEM25_ENST00000442938.2_Intron NM_001168618.1 NP_001162089.1 Q9NQC8 IFT46_HUMAN intraflagellar transport 46 NA NA NA NA cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)|protein stabilization (GO:0050821)|smoothened signaling pathway (GO:0007224) centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512) protein C-terminus binding (GO:0008022) NA NA central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4) 9 CCCAGAACCACTCTCTCTCTCTGA 0.485 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 85 84.34 NA ,,, 1,32,4231 NA 0,0,1,0,32,2099 NA NA NA NA ,,, 0.2 0 NA NA 63 17,1,8236 NA 8,0,1,0,1,4117 no intron,intron,intron,intron IFT46,TMEM25 NM_020153.3,NM_001168618.1,NM_001144038.1,NM_001144037.1 ,,, 8,0,2,0,33,6216 A1A1,A1A2,A1R,A2A2,A2R,RR NA 0.2181,0.7739,0.4074 ,,, ,,, NA 18,33,12467 NA NA NA SO:0001627 intron_variant 0.22 NA NA AL136934 CCDS8399.1, CCDS53718.1 11q23.3 2014-07-18 2014-07-03 2010-04-22 ENSG00000118096 ENSG00000118096 56912 "Intraflagellar transport homologs" 26146 protein-coding gene gene with protein product "cilia and flagella associated protein 32" NA "chromosome 11 open reading frame 60", "intraflagellar transport 46 homolog (Chlamydomonas)" C11orf60 NA 10873569, 19253336 Standard NM_020153 NM_020153 NA Approved C11orf2, FLJ21827, CFAP32 uc001pto.2 Q9NQC8 OTTHUMG00000166408 ENST00000264021.3:c.673-59AGAG>- chr11.hg19:g.118416635_118416638delCTCT 4 3 ref NA False 68 62 PASS 6 PASS ref->het 0 NA 7,7 67,69 12,11 1 1 A8K0F6|Q9H6V5 True hg19 CCDS53718.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IFT46-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000389627.1 PASS NA None 85 True - CT ENST00000264021.3 NCAPD3 23310 __UNKNOWN__ __UNKNOWN__ 11 134021739 134021740 __UNKNOWN__ Intron INS - - ATCA rs376491806|rs374731582|rs10665918 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:134021739_134021740insATCA ENST00000526787.2 - 2 761 JAM3_ENST00000299106.4_3'UTR P42695 CNDD3_HUMAN non-SMC condensin II complex, subunit D3 NA NA NA NA mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076) germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654) methylated histone binding (GO:0035064) NA NA NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 71 all_hematologic(175;0.127) all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227) CTAAAAATGCTATCAATCACCC 0.495 NA NA NA NA NA NA NA NA NA NA 1766 0.352636 0.0802 0.5159 5008 , , NA 20199 0.5972 NA 0.2972 False NA ,,, NA NA NA 2504 0.41 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 156 145.6 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.24 NA NA AK124878 CCDS31723.1 11q25 2008-02-04 ENSG00000151503 ENSG00000151503 23310 28952 protein-coding gene gene with protein product 609276 NA 7584044, 8619474, 14532007 Standard NM_015261 NM_015261 NA Approved hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6 uc001qhd.1 P42695 OTTHUMG00000167172 ENST00000526787.2:c.466-1261->TGAT chr11.hg19:g.134021744_134021747dupATCA 3 2 ref NA False 38 36 PASS 2 PASS ref->het 0 NA 18,18 108,110 33,32 1 1 A6NFS2|Q4KMQ9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NCAPD3-016 PUTATIVE basic|exp_conf processed_transcript NA protein_coding OTTHUMT00000393573.2 PASS NA None 156 True - ATCA ENST00000526787.2 AKAP11 11215 __UNKNOWN__ __UNKNOWN__ 13 42894406 42894413 __UNKNOWN__ 3'UTR DEL TTTGTTTG TTTGTTTG - rs9594726|rs141184519 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:42894406_42894413delTTTGTTTG ENST00000025301.2 + 0 6923_6930 NM_016248.3 NP_057332.1 Q9UKA4 AKA11_HUMAN A kinase (PRKA) anchor protein 11 NA NA NA NA intracellular signal transduction (GO:0035556) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856) protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157) NA NA breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2) 56 Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114) OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19) TGGTGTtttttttgtttgtttgtttgtt 0.346 NA NA NA NA NA NA NA NA NA NA 1059 0.211462 0.0159 0.2478 5008 , , NA 8600 0.371 NA 0.2555 False NA ,,, NA NA NA 2504 0.2403 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 50 50.23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.72 NA NA AB014529 CCDS9383.1 13q 2012-04-17 ENSG00000023516 ENSG00000023516 11215 "A-kinase anchor proteins", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits" 369 protein-coding gene gene with protein product "AKAP 220", "A-kinase anchoring protein, 220kDa", "protein kinase A anchoring protein 11", "protein phosphatase 1, regulatory subunit 44" 604696 NA 9734811, 8621616 Standard NM_016248 NM_016248 NA Approved KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44 uc001uys.2 Q9UKA4 OTTHUMG00000016805 ENST00000025301.2:c.*1049TTTGTTTG>- chr13.hg19:g.42894414_42894421delTTTGTTTG 3 11 ref NA False 34 34 PASS 5 PASS ref->het 0 NA 3,3 27,28 18,17 1 1 O75124|Q9NUK7 True hg19 CCDS9383.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AKAP11-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044700.2 PASS NA None 50 True + TTTG ENST00000025301.2 NPEPPS 9520 __UNKNOWN__ __UNKNOWN__ 17 45700384 45700385 __UNKNOWN__ 3'UTR INS - - CTA rs71712895|rs3065062 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:45700384_45700385insCTA ENST00000322157.4 + 0 4095_4096 RP11-580I16.2_ENST00000582066.1_RNA|RP11-580I16.2_ENST00000584391.1_RNA|RP11-580I16.2_ENST00000582389.1_RNA NM_006310.3 NP_006301.3 P55786 PSA_HUMAN aminopeptidase puromycin sensitive NA NA NA NA antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634) aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270) NA NA breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 27 AACAGTATATCCTAATAAGCCT 0.332 NA NA NA NA NA NA NA NA NA NA 2876 0.574281 0.4803 0.6599 5008 , , NA 16815 0.6667 NA 0.5378 False NA ,,, NA NA NA 2504 0.5828 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 81 92.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.04 NA NA Y07701 CCDS45721.1 17q12-q21 2008-07-18 ENSG00000141279 ENSG00000141279 9520 3.4.11.2 7900 protein-coding gene gene with protein product "puromycin-sensitive aminopeptidase", "metalloproteinase MP100" 606793 NA 9048733, 10329370 Standard NM_006310 NM_006310 NA Approved PSA, MP100 uc002ilr.4 P55786 OTTHUMG00000165471 ENST00000322157.4:c.*1099->CTA chr17.hg19:g.45700385_45700387dupCTA 2 2 ref NA False 48 48 PASS 1 PASS ref->het 0 NA 5,5 71,74 9,8 1 1 B7Z463|Q6P145|Q9NP16|Q9UEM2 True hg19 CCDS45721.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NPEPPS-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000384269.1 PASS NA None 81 True + CTA ENST00000322157.4 TRIM65 201292 __UNKNOWN__ __UNKNOWN__ 17 73887808 73887828 __UNKNOWN__ Intron DEL GCACACACACACGTGCTCACA GCACACACACACGTGCTCACA - rs11270925|rs374771847|rs535885010|rs556434171 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:73887808_73887828delGCACACACACACGTGCTCACA ENST00000269383.3 - 5 1051 NM_001256124.1|NM_173547.3 NP_001243053.1|NP_775818.2 Q6PJ69 TRI65_HUMAN tripartite motif containing 65 NA NA NA NA intracellular (GO:0005622) zinc ion binding (GO:0008270) NA NA endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 12 Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154) atacgaacatgcacacacacacgtgctcacagcacacacag 0.575 NA NA NA NA NA NA NA NA NA NA 1045 0.208666 0.3238 0.1715 5008 , , NA 25172 0.13 NA 0.1928 False NA ,,, NA NA NA 2504 0.1769 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 43 44.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.04 NA NA BC006138 CCDS11732.1 17q25.1 2013-01-09 2011-01-25 ENSG00000141569 ENSG00000141569 201292 "Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers" 27316 protein-coding gene gene with protein product NA "tripartite motif-containing 65" NA 12477932 Standard NM_173547 NM_173547 NA Approved uc002jpx.4 Q6PJ69 OTTHUMG00000132127 ENST00000269383.3:c.985+65TGTGAGCACGTGTGTGTGTGC>- chr17.hg19:g.73887808_73887828delGCACACACACACGTGCTCACA 0 2 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 3,4 32,33 11,10 1 1 Q4G0F0|Q6DKJ6|Q9BRP6 True hg19 CCDS11732.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRIM65-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255170.2 PASS NA None 43 True - GCACACACACACGTGCTCACA ENST00000269383.3 KCNQ2 3785 __UNKNOWN__ __UNKNOWN__ 20 62065086 62065086 __UNKNOWN__ Intron DEL A A - LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:62065086delA ENST00000360480.3 - 8 1293 KCNQ2_ENST00000359125.2_Intron|KCNQ2_ENST00000482957.1_5'UTR|KCNQ2_ENST00000370224.1_Intron|KCNQ2_ENST00000344462.4_Intron|KCNQ2_ENST00000357249.2_Intron|KCNQ2_ENST00000359689.1_Intron|KCNQ2_ENST00000354587.3_Intron|KCNQ2_ENST00000344425.5_3'UTR NM_004518.4 NP_004509.2 O43526 KCNQ2_HUMAN potassium voltage-gated channel, KQT-like subfamily, member 2 NA NA NA NA axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226) axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076) ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249) NA NA biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1) 65 all_cancers(38;1.24e-11) BRCA - Breast invasive adenocarcinoma(10;1.04e-05) Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939) AATGAACAACAAAAAGTGGGG 0.408 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 293 291.8 NA NA 51 60 57 NA NA NA 20 NA NA NA NA 62065086 2203 4299 6502 SO:0001627 intron_variant 1.47 NA NA AF033348 CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1 20q13.33 2012-07-05 ENSG00000075043 ENSG00000075043 3785 "Potassium channels", "Voltage-gated ion channels / Potassium channels" 6296 protein-coding gene gene with protein product 602235 EBN, EBN1 NA 9425895, 16382104 Standard NM_172109 NM_172107 NA Approved Kv7.2, ENB1, BFNC, KCNA11, HNSPC uc002yex.3 O43526 OTTHUMG00000033049 ENST00000360480.3:c.1118+75T>- chr20.hg19:g.62065086delA 4 7 ref NA False 61 61 PASS 5 PASS ref->het 0 NA 167,169 106,110 26,22 1 1 O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454 True hg19 CCDS13518.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KCNQ2-011 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000354354.1 PASS NA None 293 True - A ENST00000360480.3 PDE9A 5152 __UNKNOWN__ __UNKNOWN__ 21 44180867 44180868 __UNKNOWN__ Intron DEL CC CC - rs34765923|rs397867031|rs540381503|rs55905735|rs398061782|rs397866542 byFrequency LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:44180867_44180868delCC ENST00000335512.4 + 12 887 PDE9A_ENST00000398224.3_Intron|PDE9A_ENST00000291539.6_Intron|PDE9A_ENST00000335440.6_Intron|PDE9A_ENST00000398232.3_Intron|PDE9A_ENST00000380328.2_Intron|PDE9A_ENST00000539837.1_Intron|PDE9A_ENST00000398229.3_Intron|PDE9A_ENST00000398234.3_Intron|PDE9A_ENST00000398236.3_Intron|PDE9A_ENST00000349112.3_Intron|PDE9A_ENST00000398225.3_Intron|PDE9A_ENST00000398227.3_Intron|PDE9A_ENST00000328862.6_Intron|PDE9A_ENST00000470987.1_Intron NM_001001567.1 NP_001001567.1 O76083 PDE9A_HUMAN phosphodiesterase 9A NA NA NA NA blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165) cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886) 3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872) NA NA breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1) 27 Caffeine(DB00201) cccaattccaccccccctcacc 0.589 NA NA NA NA NA NA NA NA NA NA 2175 0.434305 0.6241 0.3631 5008 , , NA 13452 0.3958 NA 0.5467 False NA ,,, NA NA NA 2504 0.1524 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 55 56.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.03 NA NA AF048837 CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1 21q22.3 2005-11-29 ENSG00000160191 ENSG00000160191 5152 3.1.4.17 "Phosphodiesterases" 8795 protein-coding gene gene with protein product 602973 NA 9624146 Standard NM_001001584 NA Approved uc002zbm.3 O76083 OTTHUMG00000086825 ENST00000335512.4:c.823-67CC>- chr21.hg19:g.44180871_44180872delCC 5 9 ref NA True 36 36 PASS 7 PASS ref->het 0 NA 4,4 47,48 3,3 1 1 B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0 True hg19 CCDS33568.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PDE9A-008 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000195458.1 PASS NA None 55 True + C ENST00000335512.4 MN1 4330 __UNKNOWN__ __UNKNOWN__ 22 28144936 28144945 __UNKNOWN__ 3'UTR DEL AATACGGTCA AATACGGTCA - LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:28144936_28144945delAATACGGTCA ENST00000302326.4 - 0 6875_6884 NM_002430.2 NP_002421.3 Q10571 MN1_HUMAN meningioma (disrupted in balanced translocation) 1 NA NA NA NA intramembranous ossification (GO:0001957) NA NA NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1) 45 TCTTGCCCAGAATACGGTCAACTCTCCCAC 0.486 NA NA TRUE ETV6 "AML, meningioma" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Dom yes NA 22 22q13 4330 meningioma (disrupted in balanced translocation) 1 NA "L, O" 0 NA NA NA NA NA NA NA 265 253.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.99 NA NA X82209 CCDS42998.1 22q12.1 2010-09-29 ENSG00000169184 ENSG00000169184 4330 7180 protein-coding gene gene with protein product "probable tumor suppressor protein MN1" 156100 "meningioma chromosome region" MGCR NA 7731706, 12569362 Standard NM_002430 NM_002430 NA Approved MGCR1-PEN, MGCR1 uc003adj.3 Q10571 OTTHUMG00000150975 ENST00000302326.4:c.*1967TGACCGTATT>- chr22.hg19:g.28144936_28144945delAATACGGTCA 0 3 ref NA False 39 39 PASS 1 PASS ref->het 0 NA 240,242 14,14 37,35 1 1 A9Z1V9 True hg19 CCDS42998.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MN1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000320737.1 PASS NA None 265 True - AATACGGTCA ENST00000302326.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ X 8270601 8270602 __UNKNOWN__ IGR INS - - AA LTS-025_T LTS-025_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:8270601_8270602insAA NA VCX2 (131293 upstream) : VCX3B (162268 downstream) NA NA NA NA NA NA NA aagaaagaaagaaagaaagaaa 0.332 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 94 137.89 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.19 NA NA NA NA NA NA NA chrX.hg19:g.8270602_8270603dupAA 5 6 ref NA False 31 31 PASS 3 PASS ref->het 0 NA 82,84 10,13 66,67 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 94 True A INPP5B 3633 __UNKNOWN__ __UNKNOWN__ 1 38332075 38332082 __UNKNOWN__ Intron DEL CTCTCACA CTCTCACA - rs74067338|rs28420743|rs369317709|rs139686587|rs57582108|rs149926262|rs4653333 byFrequency LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:38332075_38332082delCTCTCACA ENST00000373024.3 - 21 2474 INPP5B_ENST00000373023.2_Intron|INPP5B_ENST00000373027.1_Intron|INPP5B_ENST00000373026.1_Intron P32019 I5P2_HUMAN inositol polyphosphate-5-phosphatase, 75kDa NA NA NA NA in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283) cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886) inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439) NA breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1) 15 Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197) Myeloproliferative disorder(586;0.0255) ctctctctctctctcacacacacacaca 0.399 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 86 104.09 NA NA 352,865,2451 NA 22,53,255,34,744,726 NA NA NA NA NA -3 0 NA dbSNP_134 69 792,1460,5622 NA 15,157,605,11,1281,1868 no intron INPP5B NM_005540.2 NA 37,210,860,45,2025,2594 A1A1,A1A2,A1R,A2A2,A2R,RR NA 28.6005,33.1788,30.0554 NA NA NA 1144,2325,8073 NA NA NA SO:0001627 intron_variant 0.82 NA NA M74161 CCDS41306.1, CCDS72760.1 1p34 2008-02-05 2002-08-29 ENSG00000204084 ENSG00000204084 3633 3.1.3.56 6077 protein-coding gene gene with protein product 147264 "inositol polyphosphate-5-phosphatase, 75kD" NA 1718960 Standard NM_005540 NM_005540 NA Approved uc001ccg.1 P32019 OTTHUMG00000004436 ENST00000373024.3:c.2386+48TGTGAGAG>- chr1.hg19:g.38332075_38332082delCTCTCACA 0 2 ref NA False 44 41 PASS 1 PASS ref->het 0 NA 33,38 34,39 48,39 1 1 C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1 True hg19 CCDS41306.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA INPP5B-001 KNOWN non_canonical_conserved|basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000012966.1 PASS NA None 86 True - CTCTCACA ENST00000373024.3 THBS3 7059 __UNKNOWN__ __UNKNOWN__ 1 155177547 155177549 __UNKNOWN__ Intron DEL GAA GAA - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:155177547_155177549delGAA ENST00000368378.3 - 1 100 THBS3_ENST00000541990.1_Intron|THBS3_ENST00000457183.2_Intron|THBS3_ENST00000486260.1_Intron NM_001252607.1|NM_007112.4 NP_001239536.1|NP_009043.1 P49746 TSP3_HUMAN thrombospondin 3 NA NA NA NA bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931) extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471) calcium ion binding (GO:0005509)|heparin binding (GO:0008201) NA breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3) 48 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) GGCAAATGGGGAAGAAGCAGAGA 0.542 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 333 347.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.02 NA NA L38969 CCDS1099.1, CCDS58034.1, CCDS72937.1 1q21 2008-02-05 ENSG00000169231 ENSG00000169231 7059 11787 protein-coding gene gene with protein product 188062 NA 1601886 Standard NM_007112 NM_007112 NA Approved uc001fix.3 P49746 OTTHUMG00000035710 ENST00000368378.3:c.79+39TTC>- chr1.hg19:g.155177550_155177552delGAA 1 4 ref NA False 91 91 PASS 2 PASS ref->het 0 NA 256,260 49,50 37,32 1 1 B1AVR8|B4DQ20|Q8WV34 True hg19 CCDS1099.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA THBS3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000086856.1 PASS NA None 333 True - GAA ENST00000368378.3 TNS1 7145 __UNKNOWN__ __UNKNOWN__ 2 218669099 218669099 __UNKNOWN__ 3'UTR DEL G G - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:218669099delG ENST00000419504.1 - 0 5410 TNS1_ENST00000430930.1_3'UTR|TNS1_ENST00000171887.4_3'UTR Q9HBL0 TENS1_HUMAN tensin 1 NA NA NA NA cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925) poly(A) RNA binding (GO:0044822) NA breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1) 79 Renal(207;0.0483)|Lung NSC(271;0.213) Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013) TCCTCCTTCTGGGTTCAAGAG 0.582 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 545 521.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.41 NA NA AB209238 CCDS2407.1 2q35-q36 2014-06-13 2005-05-13 2005-05-13 ENSG00000079308 ENSG00000079308 7145 "Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs", "SH2 domain containing" 11973 protein-coding gene gene with protein product "protein phosphatase 1, regulatory subunit 155" 600076 "tensin", "matrix-remodelling associated 6" TNS, MXRA6 NA Standard NM_022648 NM_022648 NA Approved DKFZp586K0617, PPP1R155 uc002vgt.2 Q9HBL0 OTTHUMG00000133056 ENST00000419504.1:c.*83C>- chr2.hg19:g.218669099delG 2 3 ref NA False 69 69 PASS 3 PASS ref->het 0 NA 422,429 60,60 66,59 1 1 Q4ZG71|Q6IPI5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNS1-004 NOVEL basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000339207.1 PASS NA None 545 True - G ENST00000419504.1 ITIH1 3697 __UNKNOWN__ __UNKNOWN__ 3 52824827 52824849 __UNKNOWN__ Frame_Shift_Del DEL TTGAGGTTGTTTTGCACCGAGTG TTGAGGTTGTTTTGCACCGAGTG - rs144224070|rs200827836 byFrequency LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:52824827_52824849delTTGAGGTTGTTTTGCACCGAGTG ENST00000273283.2 + 20 2408_2430 c.2384_2406delTTGAGGTTGTTTTGCACCGAGTG c.(2383-2406)tttgaggttgttttgcaccgagtgfs p.FEVVLHRV795fs ITIH1_ENST00000542827.1_3'UTR|ITIH1_ENST00000540715.1_Frame_Shift_Del_p.FEVVLHRV653fs|ITIH1_ENST00000405128.3_Frame_Shift_Del_p.FEVVLHRV161fs|ITIH1_ENST00000537050.1_Frame_Shift_Del_p.FEVVLHRV507fs NM_002215.3 NP_002206.2 P19827 ITIH1_HUMAN inter-alpha-trypsin inhibitor heavy chain 1 795 Hyaluronan-binding. NA NA NA hyaluronan metabolic process (GO:0030212) blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062) calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867) NA NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1) 52 BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498) GGTGGCACCTTTGAGGTTGTTTTGCACCGAGTGTGGAAGGGGA 0.628 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 465 445.15 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.93 NA NA CCDS2864.1, CCDS54595.1 3p21.1 2011-10-26 2011-10-26 ENSG00000055957 ENSG00000055957 3697 6166 protein-coding gene gene with protein product 147270 "inter-alpha (globulin) inhibitor, H1 polypeptide" NA 1385302, 10100603 Standard NM_002215 NM_002215 NA Approved H1P, IATIH, ITIH uc003dfs.3 P19827 OTTHUMG00000150312 ENST00000273283.2:c.2384_2406delTTGAGGTTGTTTTGCACCGAGTG chr3.hg19:g.52824827_52824849delTTGAGGTTGTTTTGCACCGAGTG ENSP00000273283:p.Phe795fs 0 3 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 448,455 24,24 60,55 1 1 A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1 True hg19 CCDS2864.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ITIH1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000317522.1 PASS NA None 465 True + TTGAGGTTGTTTTGCACCGAGTG ENST00000273283.2 IL17RD 54756 __UNKNOWN__ __UNKNOWN__ 3 57128702 57128709 __UNKNOWN__ 3'UTR DEL ACCAATCT ACCAATCT - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:57128702_57128709delACCAATCT ENST00000296318.7 - 0 4020_4027 IL17RD_ENST00000320057.5_3'UTR|IL17RD_ENST00000427856.2_3'UTR NM_017563.3 NP_060033.3 Q8NFM7 I17RD_HUMAN interleukin 17 receptor D NA NA NA NA signal transduction (GO:0007165) Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886) NA breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1) 16 KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204) GTTTGGACTAACCAATCTCCTTCACAGA 0.433 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 231 228.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.15 NA NA AF494208 CCDS2880.2 3p21.1 2008-02-05 ENSG00000144730 ENSG00000144730 54756 "Interleukins and interleukin receptors" 17616 protein-coding gene gene with protein product 606807 NA 11802164, 12604616 Standard NM_017563 NM_017563 NA Approved SEF, IL17RLM, FLJ35755, IL-17RD uc003dil.3 Q8NFM7 OTTHUMG00000150171 ENST00000296318.7:c.*1719AGATTGGT>- chr3.hg19:g.57128702_57128709delACCAATCT 0 3 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 186,194 29,32 24,16 1 1 Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0 True hg19 CCDS2880.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IL17RD-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000316680.1 PASS NA None 231 True - ACCAATCT ENST00000296318.7 Unknown 0 __UNKNOWN__ __UNKNOWN__ 4 49637585 49637586 __UNKNOWN__ IGR INS - - CATCC rs374043290 LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:49637585_49637586insCATCC NA AC119751.4 (36059 upstream) : None (None downstream) NA NA NA NA NA NA tggaatggaatggaattgaatg 0.391 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 83 67.65 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 16.98 NA NA NA NA NA NA NA chr4.hg19:g.49637585_49637586insCATCC 1 2 ref NA False 33 33 PASS 0 PASS ref->het 0 NA 33,180 3,10 46,7 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 83 True CATCC SLC4A4 8671 __UNKNOWN__ __UNKNOWN__ 4 72313378 72313378 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:72313378delC ENST00000264485.5 + 9 1098 c.981delC c.(979-981)ctcfs p.L328fs SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000512686.1_Frame_Shift_Del_p.L284fs|SLC4A4_ENST00000425175.1_Frame_Shift_Del_p.L328fs|SLC4A4_ENST00000351898.6_Frame_Shift_Del_p.L328fs|SLC4A4_ENST00000340595.3_Frame_Shift_Del_p.L284fs NM_001098484.2 NP_001091954.1 Q9Y6R1 S4A4_HUMAN solute carrier family 4 (sodium bicarbonate cotransporter), member 4 328 NA NA NA bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810) basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510) NA breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1) 58 Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225) Sodium bicarbonate(DB01390) TGTTCATTCTCTTAGGTCCTA 0.408 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 369 352.2 NA NA NA 192 180 184 NA NA NA NA 4 NA NA NA NA NA NA 72313378 2203 4300 6503 SO:0001589 frameshift_variant 0.85 NA NA AF007216 CCDS3549.1, CCDS43236.1, CCDS47071.1 4q13.3 2013-07-19 2013-07-19 ENSG00000080493 ENSG00000080493 8671 "Solute carriers" 11030 protein-coding gene gene with protein product 603345 "solute carrier family 4, sodium bicarbonate cotransporter, member 4" SLC4A5 NA 9235899, 9651366 Standard NM_003759 NM_001098484 NA Approved NBC1, HNBC1, NBC2, pNBC, hhNMC uc010iic.3 Q9Y6R1 OTTHUMG00000129907 ENST00000264485.5:c.981delC chr4.hg19:g.72313378delC ENSP00000264485:p.Leu328fs 0 3 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 282,285 43,45 45,42 1 1 C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50 True hg19 CCDS43236.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC4A4-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000362090.1 PASS NA None 369 True + C ENST00000264485.5 ENOPH1 58478 __UNKNOWN__ __UNKNOWN__ 4 83376029 83376029 __UNKNOWN__ Intron DEL G G - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:83376029delG ENST00000273920.3 + 4 790 ENOPH1_ENST00000509635.1_Intron NM_021204.3 NP_067027.1 enolase-phosphatase 1 NA NA NA NA NA central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|skin(1) 13 AGTTTACTTTGTTGTTTTGAC 0.348 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 154 151.63 NA NA NA 168 153 158 NA NA NA NA 4 NA NA NA NA NA NA 83376029 2203 4300 6503 SO:0001627 intron_variant 2.13 NA NA CCDS3594.1, CCDS75154.1 4q21.3 2013-05-29 ENSG00000145293 ENSG00000145293 58478 3.1.3.77 24599 protein-coding gene gene with protein product "Enolase-phosphatase E1", "acireductone synthase" NA NA 15843022 Standard NM_021204 XM_005263168 NA Approved MASA, E1, mtnC uc003hmv.3 Q9UHY7 OTTHUMG00000130295 ENST00000273920.3:c.522+22G>- chr4.hg19:g.83376029delG 0 6 ref NA False 100 94 PASS 1 PASS ref->het 0 NA 83,84 52,52 17,17 1 1 True hg19 CCDS3594.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENOPH1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252638.2 PASS NA None 154 True + G ENST00000273920.3 CCDC69 26112 __UNKNOWN__ __UNKNOWN__ 5 150592358 150592370 __UNKNOWN__ Intron DEL ACAGCCTTGGAGG ACAGCCTTGGAGG - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:150592358_150592370delACAGCCTTGGAGG ENST00000355417.2 - 2 223 CCDC69_ENST00000521308.1_Intron NM_015621.2 NP_056436.2 A6NI79 CCD69_HUMAN coiled-coil domain containing 69 NA NA NA NA NA haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1) 9 Medulloblastoma(196;0.091)|all_hematologic(541;0.207) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) cgtgtcatctacagccttggaggacaggattgt 0.474 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 674 644.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.03 NA NA CCDS4312.1 5q33.1 2008-02-05 ENSG00000198624 ENSG00000198624 26112 24487 protein-coding gene gene with protein product NA NA 12477932 Standard NM_015621 NM_015621 NA Approved FLJ13705, DKFZP434C171 uc011dcq.3 A6NI79 OTTHUMG00000130127 ENST00000355417.2:c.49-7322CCTCCAAGGCTGT>- chr5.hg19:g.150592358_150592370delACAGCCTTGGAGG 0 4 ref NA False 47 47 PASS 1 PASS ref->het 0 NA 618,626 17,17 70,63 1 1 A8K9X6 True hg19 CCDS4312.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCDC69-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252435.1 PASS NA None 674 True - ACAGCCTTGGAGG ENST00000355417.2 BUD31 8896 __UNKNOWN__ __UNKNOWN__ 7 99014483 99014497 __UNKNOWN__ Intron DEL ACAGGTGTGCACCAC ACAGGTGTGCACCAC - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:99014483_99014497delACAGGTGTGCACCAC ENST00000431419.1 + 3 254 BUD31_ENST00000403633.2_Intron|PTCD1_ENST00000292478.4_3'UTR|BUD31_ENST00000456893.1_Intron|BUD31_ENST00000222969.5_Intron P41223 BUD31_HUMAN BUD31 homolog (S. cerevisiae) NA NA NA NA regulation of transcription from RNA polymerase II promoter (GO:0006357) nucleus (GO:0005634) sequence-specific DNA binding transcription factor activity (GO:0003700) NA autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1) 4 all_cancers(62;1.76e-08)|all_epithelial(64;1.63e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166) STAD - Stomach adenocarcinoma(171;0.215) agctgtgactacaggtgtgcaccaccacacccagc 0.521 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 66 80.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.26 NA NA BC022821 CCDS5663.1 7q22.1 2012-06-07 2007-01-12 2006-03-16 ENSG00000106245 ENSG00000106245 8896 29629 protein-coding gene gene with protein product "G10 maternal transcript homolog (Xenopus laevis)", "functional spliceosome-associated protein 17" 603477 "BUD31 homolog (yeast)" NA 7841202 Standard NM_003910 NM_003910 NA Approved YCR063W, EDG-2, EDG2, G10, fSAP17, Cwc14 uc003uqg.4 P41223 OTTHUMG00000154602 ENST00000431419.1:c.131-555ACAGGTGTGCACCAC>- chr7.hg19:g.99014483_99014497delACAGGTGTGCACCAC 0 4 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 54,55 15,15 13,12 1 1 A4D274|B7Z4S9|D6W5S6|Q6IB53|Q9UDV1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BUD31-005 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000336278.1 PASS NA None 66 True + ACAGGTGTGCACCAC ENST00000431419.1 ZCWPW1 55063 __UNKNOWN__ __UNKNOWN__ 7 100004322 100004358 __UNKNOWN__ Frame_Shift_Del DEL CTGATAGCTCCAGGGACAGCTCCTGGAAGTTCTTTAG CTGATAGCTCCAGGGACAGCTCCTGGAAGTTCTTTAG - rs527408897|rs373166304|rs369290615|rs147445817 LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:100004322_100004358delCTGATAGCTCCAGGGACAGCTCCTGGAAGTTCTTTAG ENST00000490721.1 - 9 1206_1242 c.769_805delCTAAAGAACTTCCAGGAGCTGTCCCTGGAGCTATCAG c.(769-807)ctaaagaacttccaggagctgtccctggagctatcagtcfs p.LKNFQELSLELSV257fs ZCWPW1_ENST00000360951.4_Frame_Shift_Del_p.LKNFQELSLELSV378fs|ZCWPW1_ENST00000398027.2_Frame_Shift_Del_p.LKNFQELSLELSV377fs|ZCWPW1_ENST00000324725.6_Frame_Shift_Del_p.LKNFQELSLELSV257fs Q9H0M4 ZCPW1_HUMAN zinc finger, CW type with PWWP domain 1 377 NA NA NA zinc ion binding (GO:0008270) NA breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1) 16 Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439) CTCACCATGACTGATAGCTCCAGGGACAGCTCCTGGAAGTTCTTTAGCATGTTGACT 0.443 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 506 446.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.83 NA NA AK000919 CCDS43623.1, CCDS59067.1 7q22.1 2012-02-10 2004-11-03 ENSG00000078487 ENSG00000078487 55063 23486 protein-coding gene gene with protein product NA "zinc finger, CW-type with PWWP domain 1" NA 11230166, 14607086, 20826339 Standard NM_017984 NM_017984 NA Approved FLJ10057, DKFZp434N0510, ZCW1 uc003uut.4 Q9H0M4 OTTHUMG00000159537 ENST00000490721.1:c.769_805delCTAAAGAACTTCCAGGAGCTGTCCCTGGAGCTATCAG chr7.hg19:g.100004322_100004358delCTGATAGCTCCAGGGACAGCTCCTGGAAGTTCTTTAG ENSP00000419187:p.Leu257fs 0 1 ref NA False 51 51 PASS 1 PASS ref->het 0 NA 545,551 16,17 46,42 1 1 A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZCWPW1-004 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000356086.1 PASS NA None 506 True - CTGATAGCTCCAGGGACAGCTCCTGGAAGTTCTTTAG ENST00000490721.1 ERLIN2 11160 __UNKNOWN__ __UNKNOWN__ 8 37595646 37595647 __UNKNOWN__ Intron INS - - ATA LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:37595646_37595647insATA ENST00000276461.5 + 2 174 ERLIN2_ENST00000335171.6_Intron|ERLIN2_ENST00000518586.1_Intron|ERLIN2_ENST00000397228.2_Intron|ERLIN2_ENST00000523887.1_Intron|ERLIN2_ENST00000523107.1_Intron|ERLIN2_ENST00000519638.1_Intron NM_007175.6 NP_009106.1 O94905 ERLN2_HUMAN ER lipid raft associated 2 NA NA NA NA cell death (GO:0008219)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|protein complex (GO:0043234) NA NS(1)|large_intestine(1)|lung(5) 7 Lung NSC(58;0.174) BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10) TCTCTATTTATATTTCCTTGAA 0.406 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 178 182.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.76 NA NA AY358108 CCDS6095.1, CCDS34879.1 8p11.2 2012-11-23 2007-01-26 2007-01-26 ENSG00000147475 ENSG00000147475 11160 1356 protein-coding gene gene with protein product 611605 "chromosome 8 open reading frame 2", "SPFH domain family, member 2" C8orf2, SPFH2, Erlin-2 NA 10449903, 15897872, 16835267 Standard NM_007175 NM_007175 NA Approved NET32, SPG18 uc003xke.4 O94905 OTTHUMG00000164005 ENST00000276461.5:c.107+99->ATA chr8.hg19:g.37595646_37595647insATA 1 4 ref NA False 39 39 PASS 0 PASS ref->het 0 NA 120,121 35,35 20,19 1 1 A0JLQ1|A8K5S9|B4DM38|D3DSW0|Q6NW21|Q86VS6|Q86W49 True hg19 CCDS6095.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ERLIN2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000376712.2 PASS NA None 178 True + ATA ENST00000276461.5 IFNB1 3456 __UNKNOWN__ __UNKNOWN__ 9 21077436 21077436 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:21077436delT ENST00000380232.2 - 1 507 c.433delA c.(433-435)agafs p.R145fs NM_002176.2 NP_002167.1 P01574 IFNB_HUMAN interferon, beta 1, fibroblast 145 NA NA NA adaptive immune response (GO:0002250)|B cell activation involved in immune response (GO:0002312)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of viral genome replication (GO:0045071)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337) extracellular region (GO:0005576)|extracellular space (GO:0005615) cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132) NA breast(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(1) 12 GBM - Glioblastoma multiforme(5;7.45e-142)|Lung(24;2.42e-17)|LUSC - Lung squamous cell carcinoma(38;7.17e-11) CCATAATATCTTTTCAGGTGC 0.428 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 571 541.66 NA NA NA 176 179 178 NA NA NA NA 9 NA NA NA NA NA NA 21077436 2203 4300 6503 SO:0001589 frameshift_variant 1.68 NA NA CCDS6495.1 9p22 2008-07-21 ENSG00000171855 ENSG00000171855 3456 "Interferons" 5434 protein-coding gene gene with protein product 147640 IFNB NA Standard NM_002176 NM_002176 NA Approved IFB, IFF uc003zok.3 P01574 OTTHUMG00000019652 ENST00000380232.2:c.433delA chr9.hg19:g.21077436delT ENSP00000369581:p.Arg145fs 3 5 ref NA False 82 82 PASS 4 PASS ref->het 0 NA 434,436 84,85 46,43 1 1 Q5VWC9 True hg19 CCDS6495.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IFNB1-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000051881.1 PASS NA None 571 True - T ENST00000380232.2 SECISBP2 79048 __UNKNOWN__ __UNKNOWN__ 9 91934544 91934571 __UNKNOWN__ Splice_Site DEL CAAAACCTCATATTTTTCCTCAGGGCAT CAAAACCTCATATTTTTCCTCAGGGCAT - rs41306445|rs376268692|rs575409469|rs373683691 byFrequency LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:91934544_91934571delCAAAACCTCATATTTTTCCTCAGGGCAT ENST00000375807.3 + 2 107_112 c.36_41delCAAAACCTCATATTTTTCCTCAGGGCAT c.(34-42)gacaaaacc>gac p.KT13fs SECISBP2_ENST00000534113.2_5'UTR|SECISBP2_ENST00000339901.4_5'UTR NM_001282688.1|NM_001282690.1|NM_024077.3 NP_001269617.1|NP_001269619.1|NP_076982.3 Q96T21 SEBP2_HUMAN SECIS binding protein 2 13 NA NA NA translation (GO:0006412) mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529) mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368) NA breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(3)|skin(2) 32 TGTTTGTGGCCAAAACCTCATATTTTTCCTCAGGGCATCAAGTTATCA 0.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 603 571.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 1.71 NA NA AF380995 CCDS6683.1, CCDS65076.1, CCDS65077.1 9q22 2008-02-05 ENSG00000187742 ENSG00000187742 79048 30972 protein-coding gene gene with protein product 607693 NA 11230166 Standard NM_024077 XM_005252193 NA Approved uc004aqj.1 Q96T21 OTTHUMG00000020182 ENST00000375807.3:c.37-1CAAAACCTCATATTTTTCCTCAGGGCAT>- chr9.hg19:g.91934544_91934571delCAAAACCTCATATTTTTCCTCAGGGCAT 0 4 ref NA False 158 158 PASS 1 PASS ref->het 0 NA 701,709 38,38 66,59 1 1 F8W892|Q5HYY1|Q8IYC0|Q9H0A1 True hg19 CCDS6683.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SECISBP2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000052990.3 PASS NA None 603 Frame_Shift_Del True + CAAAACCTCATATTTTTCCTCAGGGCAT ENST00000375807.3 PRRC2B 84726 __UNKNOWN__ __UNKNOWN__ 9 134349943 134349952 __UNKNOWN__ Intron DEL CAAGAAGGCC CAAGAAGGCC - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:134349943_134349952delCAAGAAGGCC ENST00000405995.1 + 15 2550 PRRC2B_ENST00000357304.4_Frame_Shift_Del_p.DKKA809fs|PRRC2B_ENST00000458550.1_Intron|PRRC2B_ENST00000372249.1_5'UTR Q5JSZ5 PRC2B_HUMAN proline-rich coiled-coil 2B NA NA NA NA poly(A) RNA binding (GO:0044822) NA cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2) 44 GTGCTTTTGACAAGAAGGCCCAAGCAGACT 0.519 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 183 188.85 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.25 NA NA AB011087 CCDS48044.1 9q34.13 2010-12-09 2010-12-09 2010-12-09 ENSG00000130723 ENSG00000130723 84726 28121 protein-coding gene gene with protein product NA "KIAA0515", "HLA-B associated transcript 2-like", "HLA-B associated transcript 2-like 1" KIAA0515, BAT2L, BAT2L1 NA 9628581 Standard NM_013318 NA Approved MGC10526, LQFBS-1 uc004can.4 Q5JSZ5 OTTHUMG00000020827 ENST00000405995.1:c.2324+832CAAGAAGGCC>- chr9.hg19:g.134349943_134349952delCAAGAAGGCC 0 3 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 154,157 28,28 22,20 1 1 O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PRRC2B-001 KNOWN basic protein_coding NA protein_coding OTTHUMT00000054751.1 PASS NA None 183 True + CAAGAAGGCC ENST00000405995.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 10 42364804 42364805 __UNKNOWN__ IGR INS - - GGAAG rs74213537 LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:42364804_42364805insGGAAG NA None (None upstream) : AL031601.1 (365545 downstream) NA NA NA NA NA NA cattccattccattccattcca 0.411 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 127 93.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 12.26 NA NA NA NA NA NA NA chr10.hg19:g.42364804_42364805insGGAAG 1 2 ref NA False 50 50 PASS 0 PASS ref->het 0 NA 59,188 3,5 63,30 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 127 True GGAAG OR5D18 219438 __UNKNOWN__ __UNKNOWN__ 11 55587075 55587086 __UNKNOWN__ 5'UTR DEL ACTAACTTTCAG ACTAACTTTCAG - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:55587075_55587086delACTAACTTTCAG ENST00000333976.4 + 0 0_1 NM_001001952.1 NP_001001952.1 Q8NGL1 OR5DI_HUMAN olfactory receptor, family 5, subfamily D, member 18 NA NA NA NA integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984) NA NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 55 all_epithelial(135;0.208) TGTTTTCAGAACTAACTTTCAGATTCGAAGAA 0.415 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 382 378.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.03 NA NA AB065781 CCDS31510.1 11q11 2012-08-09 ENSG00000186119 ENSG00000186119 219438 "GPCR / Class A : Olfactory receptors" 15285 protein-coding gene gene with protein product NA NA Standard NM_001001952 NM_001001952 NA Approved uc010rin.2 Q8NGL1 OTTHUMG00000166811 ENST00000333976.4:c.-20ACTAACTTTCAG>- chr11.hg19:g.55587075_55587086delACTAACTTTCAG 0 3 ref NA False 63 63 PASS 1 PASS ref->het 0 NA 290,296 95,95 48,44 1 1 Q6IF67|Q6IFD3|Q96RB3 True hg19 CCDS31510.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OR5D18-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000391515.1 PASS NA None 382 True + ACTAACTTTCAG ENST00000333976.4 RNF113B 140432 __UNKNOWN__ __UNKNOWN__ 13 98829111 98829121 __UNKNOWN__ Frame_Shift_Del DEL ATGGTCGGCGT ATGGTCGGCGT - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:98829111_98829121delATGGTCGGCGT ENST00000267291.6 - 1 398_408 c.370_380delACGCCGACCAT c.(370-381)acgccgaccatcfs p.TPTI124fs FARP1_ENST00000319562.6_Intron|FARP1_ENST00000376581.5_Intron|FARP1_ENST00000376586.2_Intron|FARP1_ENST00000595437.1_Intron NM_178861.4 NP_849192.1 Q8IZP6 R113B_HUMAN ring finger protein 113B 124 NA NA NA zinc ion binding (GO:0008270) p.P125L(1)|p.T124M(1) NA breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2) 18 all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) BRCA - Breast invasive adenocarcinoma(86;0.13) GCACTTGAGGATGGTCGGCGTATGGTGCTCC 0.649 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 2 Substitution - Missense(2) lung(1)|endometrium(1) NA NA NA NA NA 378 399.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 2.44 NA NA AF539427 CCDS9486.1 13q32.2 2006-08-22 2005-03-22 2005-03-22 ENSG00000139797 ENSG00000139797 140432 "RING-type (C3HC4) zinc fingers" 17267 protein-coding gene gene with protein product NA "zinc finger protein 183-like 1" ZNF183L1 NA Standard NM_178861 NM_178861 NA Approved RNF161 uc001vnk.3 Q8IZP6 OTTHUMG00000017245 ENST00000267291.6:c.370_380delACGCCGACCAT chr13.hg19:g.98829111_98829121delATGGTCGGCGT ENSP00000267291:p.Thr124fs 0 3 ref NA False 56 56 PASS 1 PASS ref->het 0 NA 336,347 28,29 73,64 1 1 Q8WWF9|Q96QY9 True hg19 CCDS9486.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RNF113B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000045536.3 PASS NA None 378 True - ATGGTCGGCGT ENST00000267291.6 DISP2 85455 __UNKNOWN__ __UNKNOWN__ 15 40660140 40660152 __UNKNOWN__ Frame_Shift_Del DEL GAGCCGCCTGCCG GAGCCGCCTGCCG - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:40660140_40660152delGAGCCGCCTGCCG ENST00000267889.3 + 8 1914_1926 c.1827_1839delGAGCCGCCTGCCG c.(1825-1839)ctgagccgcctgccgfs p.LSRLP609fs NM_033510.1 NP_277045.1 A7MBM2 DISP2_HUMAN dispatched homolog 2 (Drosophila) 609 SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}. NA NA NA smoothened signaling pathway (GO:0007224) integral component of membrane (GO:0016021) NA breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4) 30 all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247) CCAGCTACCTGAGCCGCCTGCCGGCCGTTCGCT 0.718 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 314 294.61 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.15 NA NA AB051529 CCDS10056.1 15q14 2004-01-15 ENSG00000140323 ENSG00000140323 85455 19712 protein-coding gene gene with protein product 607503 NA 11214970, 10619433 Standard NM_033510 NM_033510 NA Approved DISPB, KIAA1742, HsT16908 uc001zlk.1 A7MBM2 OTTHUMG00000129983 ENST00000267889.3:c.1827_1839delGAGCCGCCTGCCG chr15.hg19:g.40660140_40660152delGAGCCGCCTGCCG ENSP00000267889:p.Leu609fs 0 2 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 258,267 13,13 50,42 1 1 Q6AHW3|Q9C0C1 True hg19 CCDS10056.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DISP2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252249.1 PASS NA None 314 True + GAGCCGCCTGCCG ENST00000267889.3 ZNF469 84627 __UNKNOWN__ __UNKNOWN__ 16 88505676 88505702 __UNKNOWN__ In_Frame_Del DEL GCCAGCTCTTCGGGCAGAGACTAACTG GCCAGCTCTTCGGGCAGAGACTAACTG - rs370915546 LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:88505676_88505702delGCCAGCTCTTCGGGCAGAGACTAACTG ENST00000565624.1 + 1 11798_11824 c.11798_11824delGCCAGCTCTTCGGGCAGAGACTAACTG c.(11797-11826)agccagctcttcgggcagagactaactggc>agc p.QLFGQRLTG3934del ZNF469_ENST00000437464.1_In_Frame_Del_p.QLFGQRLTG3906del Q96JG9 ZN469_HUMAN zinc finger protein 469 3906 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) NA breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6) 20 GACCTCCTCAGCCAGCTCTTCGGGCAGAGACTAACTGGCTTCAAAAT 0.617 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 308 308.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 4.67 NA NA AB058761 CCDS45544.1 16q24 2010-08-04 ENSG00000225614 84627 "Zinc fingers, C2H2-type" 23216 protein-coding gene gene with protein product 612078 NA 11347906 Standard NG_012236 NM_001127464 NA Approved KIAA1858 uc002fku.2 Q96JG9 ENST00000565624.1:c.11798_11824delGCCAGCTCTTCGGGCAGAGACTAACTG chr16.hg19:g.88505676_88505702delGCCAGCTCTTCGGGCAGAGACTAACTG ENSP00000456500:p.Gln3934_Gly3942del 0 2 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 269,299 12,12 62,32 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF469-001 NOVEL basic protein_coding NA protein_coding OTTHUMT00000423023.2 PASS NA None 308 True + GCCAGCTCTTCGGGCAGAGACTAACTG ENST00000565624.1 CRNKL1 51340 __UNKNOWN__ __UNKNOWN__ 20 20029080 20029098 __UNKNOWN__ Frame_Shift_Del DEL TATTTCAGCCAGAGTGTAA TATTTCAGCCAGAGTGTAA - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:20029080_20029098delTATTTCAGCCAGAGTGTAA ENST00000536226.1 - 4 467_485 c.344_362delTTACACTCTGGCTGAAATA c.(343-363)attacactctggctgaaatacfs p.ITLWLKY115fs CRNKL1_ENST00000377327.4_Frame_Shift_Del_p.ITLWLKY264fs|CRNKL1_ENST00000377340.2_Frame_Shift_Del_p.ITLWLKY276fs Q9BZJ0 CRNL1_HUMAN crooked neck pre-mRNA splicing factor 1 276 NA NA NA mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245) catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681) poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723) NA breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6) 45 CATTTCTGCGTATTTCAGCCAGAGTGTAATATTTCGGTA 0.434 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 699 667.08 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 4.09 NA NA AF255443 CCDS33446.1, CCDS63238.1, CCDS63239.1 20p11.2 2013-10-03 2013-10-03 ENSG00000101343 ENSG00000101343 51340 15762 protein-coding gene gene with protein product "SYF3 pre-mRNA-splicing factor" 610952 "crooked neck (Drosophila Crn homolog)-like 1", "Crn, crooked neck-like 1 (Drosophila)", "crooked neck pre-mRNA splicing factor-like 1 (Drosophila)" NA Standard NM_016652 NA Approved CRN, CLF, SYF3, Clf1 uc002wrs.3 Q9BZJ0 OTTHUMG00000032000 ENST00000536226.1:c.344_362delTTACACTCTGGCTGAAATA chr20.hg19:g.20029080_20029098delTATTTCAGCCAGAGTGTAA ENSP00000440733:p.Ile115fs 0 4 ref NA False 67 67 PASS 1 PASS ref->het 0 NA 597,607 63,63 99,90 1 1 A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CRNKL1-007 PUTATIVE basic|appris_principal protein_coding NA protein_coding OTTHUMT00000378075.1 PASS NA None 699 True - TATTTCAGCCAGAGTGTAA ENST00000536226.1 ZNF182 7569 __UNKNOWN__ __UNKNOWN__ X 47861970 47861994 __UNKNOWN__ 5'UTR DEL TGAAGAAACAGACAACATACTTACC TGAAGAAACAGACAACATACTTACC - rs371032969|rs202126214|rs142706674 LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:47861970_47861994delTGAAGAAACAGACAACATACTTACC ENST00000396965.1 - 0 328_329 ZNF182_ENST00000305127.6_5'UTR|ZNF182_ENST00000376943.3_Splice_Site_p.QV5fs NM_001178099.1 NP_001171570.1 P17025 ZN182_HUMAN zinc finger protein 182 NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA endometrium(5)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1) 22 AATAGAGGAATGAAGAAACAGACAACATACTTACCTGGGGTTTGG 0.427 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 373 367.62 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.89 NA NA AK122874, R98366 CCDS35235.1, CCDS35236.1 Xp11.23 2013-01-08 2006-05-10 2006-05-10 ENSG00000147118 ENSG00000147118 7569 "Zinc fingers, C2H2-type", "-" 13001 protein-coding gene gene with protein product 314993 "zinc finger protein 182 (HHZ150)", "zinc finger protein 21 (KOX 14)" ZNF21 NA 8088786, 2014798, 8914609 Standard NM_006962 NM_001178099 NA Approved KOX14, HHZ150, Zfp182 uc004dit.3 P17025 OTTHUMG00000021460 ENST00000396965.1:c.-23GGTAAGTATGTTGTCTGTTTCTTCA>- chrX.hg19:g.47861970_47861994delTGAAGAAACAGACAACATACTTACC 0 4 ref NA False 127 126 PASS 1 PASS ref->het 0 NA 328,334 62,62 35,30 1 2 A2IDD7|Q3KP67|Q96QH7 True hg19 CCDS35236.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF182-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000277055.1 PASS NA None 373 True - TGAAGAAACAGACAACATACTTACC ENST00000396965.1 HCFC1 3054 __UNKNOWN__ __UNKNOWN__ X 153224795 153224811 __UNKNOWN__ Frame_Shift_Del DEL CTCTGTGTTGGCACAAC CTCTGTGTTGGCACAAC - LTS-026_T LTS-026_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:153224795_153224811delCTCTGTGTTGGCACAAC ENST00000369984.4 - 9 1919_1935 c.1576_1592delGTTGTGCCAACACAGAG c.(1576-1593)gttgtgccaacacagagtfs p.VVPTQS526fs HCFC1_ENST00000354233.3_Frame_Shift_Del_p.VVPTQS457fs|HCFC1_ENST00000310441.7_Frame_Shift_Del_p.VVPTQS526fs P51610 HCFC1_HUMAN host cell factor C1 526 Required for interaction with OGT. NA NA NA cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366) cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188) chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713) NA NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 47 all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) TCCCTGGGCACTCTGTGTTGGCACAACCATCCGCACT 0.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 667 609.08 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 6.18 NA NA CCDS44020.1 Xq28 2014-06-12 2014-06-09 ENSG00000172534 ENSG00000172534 3054 4839 protein-coding gene gene with protein product "VP16-accessory protein", "protein phosphatase 1, regulatory subunit 89" 300019 "mental retardation, X-linked 3", "host cell factor C1 (VP16-accessory protein)" HFC1, MRX3 NA 8392914, 23000143 Standard NM_005334 XM_005274664 NA Approved HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89 uc004fjp.3 P51610 OTTHUMG00000024222 ENST00000369984.4:c.1576_1592delGTTGTGCCAACACAGAG chrX.hg19:g.153224795_153224811delCTCTGTGTTGGCACAAC ENSP00000359001:p.Val526fs 0 2 ref NA False 79 79 PASS 1 PASS ref->het 0 NA 576,607 21,22 109,79 1 1 Q6P4G5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HCFC1-003 NOVEL not_organism_supported|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000061101.3 PASS NA None 667 True - CTCTGTGTTGGCACAAC ENST00000369984.4 FAM212B 55924 __UNKNOWN__ __UNKNOWN__ 1 112268162 112268162 __UNKNOWN__ 3'UTR DEL G G - LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:112268162delG ENST00000357260.5 - 0 2503 FAM212B_ENST00000534365.1_Intron NM_019099.4 NP_061972.1 Q9NTI7 F212B_HUMAN family with sequence similarity 212, member B NA NA NA NA NA cervix(1)|endometrium(1) 2 NA NA NA TAGGTGAGGAGGGAACAGGAG 0.597 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 110 104.21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AK055667 CCDS841.1, CCDS44195.1 1p13.2 2011-11-24 2011-11-24 2011-11-24 ENSG00000197852 ENSG00000197852 55924 28045 protein-coding gene gene with protein product NA "chromosome 1 open reading frame 183" C1orf183 NA Standard NM_019099 NM_019099 NA Approved FLJ31105 uc001ebo.2 Q9NTI7 OTTHUMG00000011953 ENST00000357260.5:c.*1428C>- chr1.hg19:g.112268162delG 2 5 ref NA False 31 31 PASS 3 PASS ref->het 0 NA 77,79 19,19 13,12 1 1 B3KP38|B4DF94|Q9NTI6 True hg19 CCDS841.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM212B-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000033060.2 PASS NA None 110 NA True - G ENST00000357260.5 INPP4A 3631 __UNKNOWN__ __UNKNOWN__ 2 99175898 99175921 __UNKNOWN__ Intron DEL ATCCATGTCGCCCTCCATTTCTGT ATCCATGTCGCCCTCCATTTCTGT - rs368119936|rs375065310 LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:99175898_99175921delATCCATGTCGCCCTCCATTTCTGT ENST00000409016.4 + 18 2117 INPP4A_ENST00000409851.3_Intron|INPP4A_ENST00000545415.1_Intron|INPP4A_ENST00000523221.1_Intron|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000074304.5_Intron|INPP4A_ENST00000409540.3_Intron Q96PE3 INP4A_HUMAN inositol polyphosphate-4-phosphatase, type I, 107kDa NA NA NA NA inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829) phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597) NA breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4) 43 NA NA NA CTCCTTAATCATCCATGTCGCCCTCCATTTCTGTGCAGATTGCA 0.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 94 88 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 U26398 CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1 2q11.2 2008-05-27 2002-08-29 ENSG00000040933 ENSG00000040933 3631 6074 protein-coding gene gene with protein product 600916 "inositol polyphosphate-4-phosphatase, type I, 107kD" INPP4 NA 7608176, 9295334 Standard NM_001566 NM_004027 NA Approved uc002syy.3 Q96PE3 OTTHUMG00000153106 ENST00000409016.4:c.1721-5ATCCATGTCGCCCTCCATTTCTGT>- chr2.hg19:g.99175898_99175921delATCCATGTCGCCCTCCATTTCTGT 0 2 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 112,113 4,5 9,9 1 1 O15326|Q13187|Q53TD8|Q8TC02 True hg19 CCDS46370.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA INPP4A-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000329566.2 PASS NA None 94 NA True + ATCCATGTCGCCCTCCATTTCTGT ENST00000409016.4 CSRNP3 80034 __UNKNOWN__ __UNKNOWN__ 2 166542475 166542477 __UNKNOWN__ 3'UTR DEL AGA AGA - LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:166542475_166542477delAGA ENST00000342316.4 + 0 8242_8244 CSRNP3_ENST00000314499.7_3'UTR NM_024969.3 NP_079245.2 Q8WYN3 CSRN3_HUMAN cysteine-serine-rich nuclear protein 3 NA NA NA NA apoptotic process (GO:0006915)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944) nucleus (GO:0005634) RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA breast(2)|cervix(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(3)|skin(2) 33 NA NA NA AGAAAGGGTTAGAAGGAGACAAA 0.305 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 67 69.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AB063300 CCDS2225.1 2q24.3 2012-04-17 2009-01-07 2009-01-07 ENSG00000178662 ENSG00000178662 80034 "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits" 30729 protein-coding gene gene with protein product "TGF beta induced apotosis protein 2", "protein phosphatase 1, regulatory subunit 73" NA "family with sequence similarity 130, member A2" FAM130A2 NA 17726538 Standard NM_024969 NM_024969 NA Approved FLJ32093, TAIP-2, PPP1R73 uc002udg.3 Q8WYN3 OTTHUMG00000132145 ENST00000342316.4:c.*6214AGA>- chr2.hg19:g.166542475_166542477delAGA 0 3 ref NA False 72 72 PASS 1 PASS ref->het 0 NA 35,35 26,26 5,5 1 1 B3KPR4|Q53SG0|Q6ZTX3|Q9HAF9 True hg19 CCDS2225.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CSRNP3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255191.2 PASS NA None 67 NA True + AGA ENST00000342316.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 5 150615244 150615247 __UNKNOWN__ IGR DEL AGGC AGGC - rs201153223 LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:150615244_150615247delAGGC NA CCDC69 (11538 upstream) : GM2A (17205 downstream) NA NA NA NA NA NA NA NA NA AAaggaaggaaggcaggcaggcag 0.564 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 25 21.65 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr5.hg19:g.150615252_150615255delAGGC 6 2 ref NA False 30 30 PASS 7 PASS ref->hom 0 NA 0,0 17,20 8,9 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 25 NA True AGGC SYNJ2 8871 __UNKNOWN__ __UNKNOWN__ 6 158499280 158499296 __UNKNOWN__ Frame_Shift_Del DEL ATGGTCGTGCGGAGCTA ATGGTCGTGCGGAGCTA - rs139533347|rs536966273 byFrequency LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:158499280_158499296delATGGTCGTGCGGAGCTA ENST00000355585.4 + 18 2609_2625 c.2534_2550delATGGTCGTGCGGAGCTA c.(2533-2550)tatggtcgtgcggagctafs p.YGRAEL845fs SYNJ2_ENST00000367121.3_Frame_Shift_Del_p.YGRAEL845fs|SYNJ2_ENST00000367122.2_Frame_Shift_Del_p.YGRAEL845fs|SYNJ2_ENST00000367112.1_5'UTR NM_001178088.1|NM_003898.3 NP_001171559.1|NP_003889.1 O15056 SYNJ2_HUMAN synaptojanin 2 845 NA NA NA phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829)|membrane (GO:0016020) nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723) NA biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 46 NA NA OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05) NA CTGCAGTATTATGGTCGTGCGGAGCTACAAGCGTCTG 0.548 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 52 48.88 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.28 AB002346 CCDS5254.1 6q25.3 2008-05-15 ENSG00000078269 ENSG00000078269 8871 11504 protein-coding gene gene with protein product 609410 NA Standard NM_003898 NA Approved INPP5H uc003qqx.2 O15056 OTTHUMG00000015904 ENST00000355585.4:c.2534_2550delATGGTCGTGCGGAGCTA chr6.hg19:g.158499280_158499296delATGGTCGTGCGGAGCTA ENSP00000347792:p.Tyr845fs 0 3 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 38,38 8,8 2,2 1 1 Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226 True hg19 CCDS5254.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SYNJ2-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000042858.2 PASS NA None 52 NA True + ATGGTCGTGCGGAGCTA ENST00000355585.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 7 57509848 57509857 __UNKNOWN__ IGR DEL GGAGAGAACA GGAGAGAACA - LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:57509848_57509857delGGAGAGAACA NA MIR3147 (37052 upstream) : ZNF716 (25 downstream) NA NA NA NA NA NA NA NA NA GAATGCAGCGGGAGAGAACAGGACGCTTCC 0.538 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 84 82.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr7.hg19:g.57509848_57509857delGGAGAGAACA 0 4 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 71,71 16,16 7,7 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 84 NA True GGAGAGAACA NAMPT 10135 __UNKNOWN__ __UNKNOWN__ 7 105891507 105891508 __UNKNOWN__ 3'UTR INS - - CACAC LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:105891507_105891508insCACAC ENST00000222553.3 - 0 1804_1805 NM_005746.2 NP_005737.1 P43490 NAMPT_HUMAN nicotinamide phosphoribosyltransferase NA NA NA NA cell-cell signaling (GO:0007267)|circadian regulation of gene expression (GO:0032922)|NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|nicotinamide metabolic process (GO:0006769)|positive regulation of cell proliferation (GO:0008284)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767) cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634) cytokine activity (GO:0005125)|nicotinamide phosphoribosyltransferase activity (GO:0047280)|nicotinate-nucleotide diphosphorylase (carboxylating) activity (GO:0004514) NA endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1) 14 NA NA NA ACATACACACAACACACACCCA 0.347 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 92 90.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.26 U02020 CCDS5737.1 7q22.3 2012-10-02 2008-03-27 2008-03-27 ENSG00000105835 ENSG00000105835 10135 30092 protein-coding gene gene with protein product "visfatin" 608764 "pre-B-cell colony enhancing factor 1" PBEF1 NA 8289818 Standard NM_182790 NM_005746 NA Approved PBEF uc003vdq.3 P43490 OTTHUMG00000140388 ENST00000222553.3:c.*22->GTGTG chr7.hg19:g.105891507_105891508insCACAC 1 3 ref NA False 88 88 PASS 0 PASS ref->het 0 NA 76,86 9,9 5,5 1 1 A4D0Q9|A4D0R0|Q3KQV0|Q8WW95 True hg19 CCDS5737.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NAMPT-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000277146.1 PASS NA None 92 NA True - CACAC ENST00000222553.3 KAT6A 7994 __UNKNOWN__ __UNKNOWN__ 8 41908851 41908868 __UNKNOWN__ Intron DEL TCAGCCCCGCTCGCCGCC TCAGCCCCGCTCGCCGCC - LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:41908851_41908868delTCAGCCCCGCTCGCCGCC ENST00000396930.3 - 1 87 KAT6A_ENST00000485568.1_Intron|KAT6A_ENST00000406337.1_Intron|KAT6A_ENST00000265713.2_Intron NM_001099412.1 NP_001092882.1 Q92794 KAT6A_HUMAN K(lysine) acetyltransferase 6A NA NA NA NA aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351) Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605) acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270) NA NA NA NA NA CGCCGGCCTGTCAGCCCCGCTCGCCGCCTCAGCCCCGC 0.766 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 24 28.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.02 U47742 CCDS6124.1 8p11 2013-01-28 2011-07-21 2011-07-21 ENSG00000083168 ENSG00000083168 7994 "Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type" 13013 protein-coding gene gene with protein product "Monocytic leukemia zinc finger protein" 601408 "runt-related transcription factor binding protein 2", "MYST histone acetyltransferase (monocytic leukemia) 3" ZNF220, RUNXBP2, MYST3 NA 8849440, 8782817 Standard NM_006766 NM_001099412 NA Approved MOZ, ZC2HC6A uc003xon.4 Q92794 OTTHUMG00000150453 ENST00000396930.3:c.456+550GGCGGCGAGCGGGGCTGA>- chr8.hg19:g.41908851_41908868delTCAGCCCCGCTCGCCGCC 0 4 ref NA False 37 37 PASS 1 PASS ref->hom 0 NA 0,0 16,19 8,5 1 1 Q76L81 True hg19 CCDS6124.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KAT6A-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000318163.1 PASS NA None 24 NA True - TCAGCCCCGCTCGCCGCC ENST00000396930.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 8 120493006 120493006 __UNKNOWN__ IGR DEL T T - rs560667281|rs112757122 byFrequency LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:120493006delT NA RP11-775B15.2 (18416 upstream) : ENPP2 (76319 downstream) NA NA NA NA NA NA NA NA NA GGGACCTTGGTTGTCTTCTTT 0.478 NA NA NA NA NA NA NA NA NA T|TT|T|insertion 314 0.0626997 0.2095 0.0202 5008 , , NA 19980 0 NA 0.0099 False NA ,,, NA NA NA 2504 0.0133 NA NA NA NA PASS NA NA NA NA NA 0 NA 25 22.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr8.hg19:g.120493006delT 1 3 ref NA False 38 38 PASS 2 PASS ref->hom 0 NA 0,0 24,26 1,1 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 25 NA True T Unknown 0 __UNKNOWN__ __UNKNOWN__ 8 129864476 129864476 __UNKNOWN__ IGR DEL C C - rs34032753 byFrequency LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:129864476delC NA AC068570.1 (32352 upstream) : LINC00977 (364236 downstream) NA NA NA NA NA NA NA NA NA cccacctcggcccccccaaag 0.512 NA NA NA NA NA NA NA NA NA cccccc|CCCCCCC|CCCCCC|insertion 3893 0.777356 0.8691 0.7781 5008 , , NA 16625 0.9256 NA 0.6223 False NA ,,, NA NA NA 2504 0.6595 NA NA NA NA PASS NA NA NA NA NA 0 NA 29 30.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.89 NA NA NA NA NA chr8.hg19:g.129864476delC 6 7 ref NA False 35 34 PASS 7 PASS ref->het 0 NA 0,1 25,30 5,4 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 29 NA True C SMARCA2 6595 __UNKNOWN__ __UNKNOWN__ 9 2056758 2056759 __UNKNOWN__ Frame_Shift_Del DEL CC CC - LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:2056758_2056759delCC ENST00000382194.1 + 6 1264_1265 c.1260_1261delCC c.(1258-1263)cgccagfs p.Q421fs SMARCA2_ENST00000349721.2_Frame_Shift_Del_p.Q421fs|SMARCA2_ENST00000382203.1_Frame_Shift_Del_p.Q421fs|SMARCA2_ENST00000357248.2_Frame_Shift_Del_p.Q421fs P51531 SMCA2_HUMAN SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 421 NA NA NA aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355) intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514) ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212) NA breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 56 NA all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09) NA GBM - Glioblastoma multiforme(50;0.0475) NA GGAGCAAGCGCCAGACTCTGAG 0.559 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 78 71.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.09 D26155 CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1 9p24.3 2008-11-11 2006-11-09 ENSG00000080503 ENSG00000080503 6595 11098 protein-coding gene gene with protein product 600014 SNF2L2 NA 8012116 Standard NM_003070 NM_003070 NA Approved BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2 uc003zhc.3 P51531 OTTHUMG00000019445 ENST00000382194.1:c.1260_1261delCC chr9.hg19:g.2056758_2056759delCC ENSP00000371629:p.Gln421fs 0 3 ref NA False 50 50 PASS 2 PASS ref->het 0 NA 62,62 11,12 5,5 1 1 B1ALG3|B1ALG4|D3DRH4|D3DRH5 True hg19 CCDS34978.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SMARCA2-004 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000051506.1 PASS NA None 78 NA True + C ENST00000382194.1 MLLT3 4300 __UNKNOWN__ __UNKNOWN__ 9 20621904 20621905 __UNKNOWN__ Intron INS - - TGTTT LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:20621904_20621905insTGTTT ENST00000380338.4 - 1 299 MLLT3_ENST00000355930.6_Intron|MLLT3_ENST00000475957.1_Intron NM_004529.2 NP_004520.2 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 NA NA NA NA anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351) extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023) NA central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7) 66 NA NA GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) NA CTTCCACCgtgtgtgtgtgtgt 0.663 NA NA TRUE MLL ALL NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Dom yes NA 9 9p22 4300 "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)" NA L 0 NA 124 119.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.35 L13744 CCDS6494.1 9p22 2008-02-05 2001-11-28 ENSG00000171843 ENSG00000171843 4300 7136 protein-coding gene gene with protein product 159558 "myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3" NA 8506309, 8414510 Standard NM_004529 NM_001286691 NA Approved AF-9, AF9, YEATS3 uc003zoe.2 P42568 OTTHUMG00000019650 ENST00000380338.4:c.12+338->AAACA chr9.hg19:g.20621904_20621905insTGTTT 1 2 ref NA False 45 45 PASS 0 PASS ref->het 0 NA 103,111 6,6 13,9 1 1 B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0 True hg19 CCDS6494.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MLLT3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000051872.1 PASS NA None 124 NA True - TGTTT ENST00000380338.4 PITRM1 10531 __UNKNOWN__ __UNKNOWN__ 10 3193380 3193386 __UNKNOWN__ Intron DEL TGACATT TGACATT - LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:3193380_3193386delTGACATT ENST00000224949.4 - 15 1773 PITRM1_ENST00000380989.2_Intron|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000451104.2_Intron|PITRM1_ENST00000380994.1_Intron|PITRM1-AS1_ENST00000601046.1_RNA Q5JRX3 PREP_HUMAN pitrilysin metallopeptidase 1 NA NA NA NA positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508) mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739) enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222) NA breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3) 33 NA NA NA CTGTGAGGAGTGACATTTAATTCCCCC 0.507 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 151 149.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.01 AB029027 CCDS55699.1, CCDS55700.1, CCDS59208.1 10p15.2 2008-07-30 2005-08-17 ENSG00000107959 ENSG00000107959 10531 17663 protein-coding gene gene with protein product "PreP peptidasome" NA "pitrilysin metalloproteinase 1" NA 1036083, 10470851, 16849325 Standard NM_014889 NA Approved MP1, KIAA1104, hMP1, PreP uc009xhv.2 Q5JRX3 OTTHUMG00000017557 ENST00000224949.4:c.1738+52AATGTCA>- chr10.hg19:g.3193380_3193386delTGACATT 0 3 ref NA False 62 62 PASS 1 PASS ref->het 0 NA 122,123 21,22 9,9 1 1 B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8 True hg19 CCDS59208.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PITRM1-007 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000046469.2 PASS NA None 151 NA True - TGACATT ENST00000224949.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 11 119006759 119006759 __UNKNOWN__ IGR DEL G G - rs67471292|rs115058854|rs137951934|rs376876934|rs386758019|rs201169628 byFrequency LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:119006759delG NA HINFP (7 upstream) : ABCG4 (12962 downstream) NA NA NA NA NA NA NA NA NA aataaagaaagaaaagaAAAA 0.438 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 33 30.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 5.25 NA NA NA NA NA chr11.hg19:g.119006759delG 0 9 ref NA False 52 52 PASS 1 PASS ref->het 0 NA 18,20 10,12 5,4 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 33 NA True G NUBP1 4682 __UNKNOWN__ __UNKNOWN__ 16 10855534 10855538 __UNKNOWN__ Intron DEL TTAAG TTAAG - rs565336258 byFrequency LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:10855534_10855538delTTAAG ENST00000283027.5 + 9 736 NUBP1_ENST00000571790.1_Intron|NUBP1_ENST00000433392.2_Intron|TVP23A_ENST00000572980.1_Intron NM_002484.2 NP_002475.2 nucleotide binding protein 1 NA NA NA NA NA large_intestine(2)|lung(3)|ovary(1)|skin(4) 10 NA NA NA TTTTTTTTTTTTAAGTTTCTTTAAA 0.351 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 72 81.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.77 U01833 CCDS10543.1, CCDS61839.1 16p13.13 2014-01-13 2011-05-19 ENSG00000103274 ENSG00000103274 4682 8041 protein-coding gene gene with protein product 600280 "nucleotide binding protein 1 (E.coli MinD like)", "nucleotide binding protein 1 (MinD homolog, E. coli)" NBP1 NA 7926816 Standard NM_002484 NM_002484 NA Approved NBP35 uc002daa.1 P53384 OTTHUMG00000129751 ENST00000283027.5:c.718-76TTAAG>- chr16.hg19:g.10855534_10855538delTTAAG 0 14 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 63,67 3,3 14,10 1 1 True hg19 CCDS10543.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NUBP1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251964.2 PASS NA None 72 NA True + TTAAG ENST00000283027.5 PLCG1 5335 __UNKNOWN__ __UNKNOWN__ 20 39793964 39793965 __UNKNOWN__ Frame_Shift_Ins INS - - T LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:39793964_39793965insT ENST00000244007.3 + 15 1663_1664 c.1466_1467insT c.(1465-1470)tctatcfs p.I490fs PLCG1_ENST00000373271.1_Frame_Shift_Ins_p.I490fs|PLCG1_ENST00000373272.2_Frame_Shift_Ins_p.I490fs P19174 PLCG1_HUMAN phospholipase C, gamma 1 490 PH 2; first part. {ECO:0000255|PROSITE- ProRule:PRU00145}. NA NA NA activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032) cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726) calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057) p.S489C(1) NA breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2) 46 NA Myeloproliferative disorder(115;0.00878) NA NA ATCAGCAACTCTATCAAGAATG 0.579 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 1 Substitution - Missense(1) lung(1) NA 148 142.72 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.95 M34667 CCDS13313.1, CCDS13314.1 20q12-q13.1 2013-02-14 2004-01-29 ENSG00000124181 ENSG00000124181 5335 3.1.4.11 "Pleckstrin homology (PH) domain containing", "EF-hand domain containing", "SH2 domain containing" 9065 protein-coding gene gene with protein product 172420 "phospholipase C, gamma 1 (formerly subtype 148)" PLC1 NA 2167438, 3254788 Standard NM_182811 NM_182811 NA Approved PLC148, PLC-II, PLCgamma1, NCKAP3 uc002xjo.1 P19174 OTTHUMG00000033082 ENST00000244007.3:c.1467dupT chr20.hg19:g.39793965_39793965dupT ENSP00000244007:p.Ile490fs 2 2 ref NA False 46 46 PASS 1 PASS ref->het 0 NA 107,110 26,26 13,11 1 1 B7ZLY7|B9EGH4|E1P5W4|Q2V575 True hg19 CCDS13313.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PLCG1-013 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000276885.1 PASS NA None 148 NA True + T ENST00000244007.3 FAM210B 116151 __UNKNOWN__ __UNKNOWN__ 20 54942707 54942717 __UNKNOWN__ 3'UTR DEL CCAGCGTAGAT CCAGCGTAGAT - rs550012955 byFrequency LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:54942707_54942717delCCAGCGTAGAT ENST00000371384.3 + 0 2034_2044 NM_080821.2 NP_543011.2 Q96KR6 F210B_HUMAN family with sequence similarity 210, member B NA NA NA NA integral component of membrane (GO:0016021) NA NA NA NA NA gaaagaaaTCCCAGCGTAGATCCAAACTGAG 0.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA 211 192.62 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.74 AL121914 CCDS13450.1 20q13.2 2011-11-24 2011-11-24 2011-11-24 ENSG00000124098 ENSG00000124098 116151 16102 protein-coding gene gene with protein product "hypothetical protein LOC116151" NA "chromosome 20 open reading frame 108" C20orf108 NA 11780052 Standard NM_080821 NM_080821 NA Approved dJ1167H4.1, DKFZP434A1114 uc002xxc.3 Q96KR6 OTTHUMG00000032793 ENST00000371384.3:c.*1374CCAGCGTAGAT>- chr20.hg19:g.54942707_54942717delCCAGCGTAGAT 0 3 ref NA False 52 52 PASS 1 PASS ref->het 0 NA 184,211 17,18 21,18 1 1 B2RBQ9|E1P5Y7|Q8WVN2|Q9BYL6|Q9H418 True hg19 CCDS13450.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM210B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000079800.2 PASS NA None 211 NA True + CCAGCGTAGAT ENST00000371384.3 HPS4 89781 __UNKNOWN__ __UNKNOWN__ 22 26875306 26875306 __UNKNOWN__ Frame_Shift_Del DEL A A - LTS-027_T LTS-027_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:26875306delA ENST00000398145.2 - 3 673 c.57delT c.(55-57)tttfs p.F19fs HPS4_ENST00000402105.3_Frame_Shift_Del_p.F14fs|HPS4_ENST00000336873.5_Frame_Shift_Del_p.F19fs|HPS4_ENST00000398141.1_Frame_Shift_Del_p.F14fs NM_022081.5 NP_071364.4 Q9NQG7 HPS4_HUMAN Hermansky-Pudlak syndrome 4 19 NA NA NA blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605) BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827) protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803) NA breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 32 NA NA NA CATCATAAAGAAAAAAATAAT 0.423 NA NA NA NA NA NA Hermansky-Pudlak syndrome NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 GRCh37 CD020569 HPS4 D NA 113 110.08 NA NA NA NA NA 76 70 72 NA NA NA NA 22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 26875306 NA 2203 4300 6503 SO:0001589 frameshift_variant 0.22 Familial Cancer Database HPS, HPS1-8 CCDS13835.1, CCDS46677.1 22q12.1 2014-09-17 ENSG00000100099 ENSG00000100099 89781 15844 protein-coding gene gene with protein product 606682 NA 11836498, 12663659 Standard NM_022081 NM_022081 NA Approved KIAA1667, LE uc003aci.4 Q9NQG7 OTTHUMG00000030459 ENST00000398145.2:c.57delT chr22.hg19:g.26875306delA ENSP00000381213:p.Phe19fs 6 10 ref NA False 91 91 PASS 7 PASS ref->het 0 NA 70,71 29,29 14,14 1 1 B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38 True hg19 CCDS13835.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HPS4-005 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000320778.1 PASS NA None 113 NA True - A ENST00000398145.2 RUFY3 22902 __UNKNOWN__ __UNKNOWN__ 4 71656834 71656835 __UNKNOWN__ Intron INS - - AAA rs375201210 LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:71656834_71656835insAAA ENST00000381006.3 + 12 1916 RUFY3_ENST00000226328.4_Intron|RUFY3_ENST00000502653.1_Intron|RUFY3_ENST00000536664.1_Intron NM_001037442.2 NP_001032519.1 Q7L099 RUFY3_HUMAN RUN and FYVE domain containing 3 NA NA NA NA NA negative regulation of axonogenesis (GO:0050771) filopodium (GO:0030175)|growth cone (GO:0030426) NA NA endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1) 16 all_hematologic(202;0.248) Lung(101;0.235) NA GAATAATGACTTATCTCTTTGA 0.272 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 16 45.05 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 4.01 NA NA AF112221 CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1 4q13.3 2009-05-29 ENSG00000018189 ENSG00000018189 22902 NA "Zinc fingers, FYVE domain containing" 30285 protein-coding gene gene with protein product "single axon-related 1" 611194 NA 17439943 Standard NM_014961 NM_001130709 NA Approved RIPx, KIAA0871, Singar1 uc003hfr.3 Q7L099 OTTHUMG00000129910 ENST00000381006.3:c.1337+1525->AAA chr4.hg19:g.71656834_71656835insAAA 3 3 ref NA False 30 30 PASS 0 PASS ref->hom 0 NA 0,0 15,16 1,1 1 1 B3KM25|B4DYW7|D9N163|O94948|Q9UI00 True hg19 CCDS34001.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RUFY3-002 NOVEL basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000252162.1 PASS NA None 16 NA True + A ENST00000381006.3 RUFY3 22902 __UNKNOWN__ __UNKNOWN__ 4 71656837 71656837 __UNKNOWN__ Intron DEL T T - rs201456019 LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:71656837delT ENST00000381006.3 + 12 1916 RUFY3_ENST00000226328.4_Intron|RUFY3_ENST00000502653.1_Intron|RUFY3_ENST00000536664.1_Intron NM_001037442.2 NP_001032519.1 Q7L099 RUFY3_HUMAN RUN and FYVE domain containing 3 NA NA NA NA NA negative regulation of axonogenesis (GO:0050771) filopodium (GO:0030175)|growth cone (GO:0030426) NA NA endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1) 16 all_hematologic(202;0.248) Lung(101;0.235) NA TAATGACTTATCTCTTTGAGT 0.274 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 20 46.71 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 4.03 NA NA AF112221 CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1 4q13.3 2009-05-29 ENSG00000018189 ENSG00000018189 22902 NA "Zinc fingers, FYVE domain containing" 30285 protein-coding gene gene with protein product "single axon-related 1" 611194 NA 17439943 Standard NM_014961 NM_001130709 NA Approved RIPx, KIAA0871, Singar1 uc003hfr.3 Q7L099 OTTHUMG00000129910 ENST00000381006.3:c.1337+1528T>- chr4.hg19:g.71656837delT 0 3 ref NA False 31 31 PASS 1 PASS ref->hom 0 NA 0,0 15,16 4,4 1 1 B3KM25|B4DYW7|D9N163|O94948|Q9UI00 True hg19 CCDS34001.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RUFY3-002 NOVEL basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000252162.1 PASS NA None 20 NA True + T ENST00000381006.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 4 190640454 190640457 __UNKNOWN__ IGR DEL AAAG AAAG - rs543471680|rs375163942|rs558255252 byFrequency LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:190640454_190640457delAAAG NA NA RNU1-51P (9586 upstream) : AF250324.1 (99365 downstream) NA NA NA NA NA NA NA NA NA agaaaaagataaagggagggaagg 0.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 21 20.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.01 NA NA NA NA NA NA NA NA chr4.hg19:g.190640454_190640457delAAAG 0 6 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 9,12 8,8 4,1 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 21 NA True AAAG RNF14 9604 __UNKNOWN__ __UNKNOWN__ 5 141364714 141364715 __UNKNOWN__ Intron DEL AC AC - rs34181518|rs398065268|rs72303922 byFrequency LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:141364714_141364715delAC ENST00000394520.2 + 8 1676 RNF14_ENST00000394519.1_Intron|RNF14_ENST00000394514.2_Intron|RNF14_ENST00000540015.1_Intron|RNF14_ENST00000356143.1_Intron|RNF14_ENST00000394515.3_Intron|RNF14_ENST00000347642.3_Intron NM_001201365.1|NM_004290.4 NP_001188294.1|NP_004281.1 Q9UBS8 RNF14_HUMAN ring finger protein 14 NA NA NA NA NA androgen receptor signaling pathway (GO:0030521)|positive regulation of transcription, DNA-templated (GO:0045893)|protein ubiquitination (GO:0016567)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleus (GO:0005634) androgen receptor binding (GO:0050681)|small conjugating protein ligase activity (GO:0019787)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270) NA NA cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 15 all_hematologic(541;0.0536)|Ovarian(839;0.118) KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GBM - Glioblastoma multiforme(465;0.0407) NA aagttttcaaacacagaaaatt 0.287 NA NA NA NA NA NA NA NA NA 4573 0.913139 0.9342 0.915 5008 , , NA 16769 0.9831 NA 0.831 False NA ,,, NA NA NA 2504 0.8957 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 37 47.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF060544 CCDS4270.1, CCDS4271.1 5q23.3-q31.1 2008-02-05 ENSG00000013561 ENSG00000013561 9604 NA "RING-type (C3HC4) zinc fingers" 10058 protein-coding gene gene with protein product 605675 NA 10085091, 10320776 Standard NM_004290 NM_183399 NA Approved ARA54, HFB30, TRIAD2 uc003lmc.3 Q9UBS8 OTTHUMG00000129660 ENST00000394520.2:c.1367+216AC>- chr5.hg19:g.141364716_141364717delAC 1 4 ref NA False 36 35 PASS 2 PASS ref->het 0 NA 1,1 29,30 7,7 1 1 A0AV26|A6NMR2|A8MTW5|B3KN72|B7ZLV2|D3DQE4|O94793|Q6IBV0 True hg19 CCDS4270.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RNF14-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251860.2 PASS NA None 37 NA True + AC ENST00000394520.2 Unknown 0 __UNKNOWN__ __UNKNOWN__ 5 170813951 170813952 __UNKNOWN__ IGR INS - - T rs199988838|rs28411383 byFrequency LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:170813951_170813952insT NA NA MIR3912 (187 upstream) : NPM1 (167 downstream) NA NA NA NA NA NA NA NA NA GCTGGGGTGCCTCGGAGTTTGT 0.436 NA NA NA NA NA NA NA NA NA T|T|TT|insertion 1506 0.300719 0.1399 0.2219 5008 , , NA 16708 0.4157 NA 0.3539 False NA ,,, NA NA NA 2504 0.4008 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 35 35.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.02 NA NA NA NA NA NA NA NA chr5.hg19:g.170813952_170813952dupT 2 3 ref NA False 38 38 PASS 1 PASS ref->hom 0 NA 0,0 24,28 10,6 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 35 NA True T BTNL3 10917 __UNKNOWN__ __UNKNOWN__ 5 180432321 180432325 __UNKNOWN__ Intron DEL CACCG CACCG - rs530298698 byFrequency LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:180432321_180432325delCACCG ENST00000342868.6 + 8 1046 NM_197975.2 NP_932079.1 Q6UXE8 BTNL3_HUMAN butyrophilin-like 3 NA NA NA NA NA integral component of membrane (GO:0016021) NA NA NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1) 25 all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114) all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248) Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272) NA CTCTCTCCCCCACCGCACCCCAGTG 0.58 NA NA NA NA NA NA NA NA NA 3 0.000599042 0 0 5008 , , NA 19899 0 NA 0.003 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 20 21.83 NA NA 4,4156 NA 0,4,2076 NA NA NA NA NA -4.8 0 NA 26 6,8120 NA 0,6,4057 no intron BTNL3 NM_197975.2 NA 0,10,6133 A1A1,A1R,RR NA 0.0738,0.0962,0.0814 NA NA NA 10,12276 NA NA NA SO:0001627 intron_variant 0 NA NA AB020625 CCDS47358.1 5q35 2014-01-14 ENSG00000168903 ENSG00000168903 10917 NA "Immunoglobulin superfamily / V-set domain containing", "Butyrophilins" 1143 protein-coding gene gene with protein product "butyrophilin-like receptor" 606192 NA 10429365 Standard NM_197975 NM_197975 NA Approved BTNLR, BTN9.1 uc003mmr.3 Q6UXE8 OTTHUMG00000162091 ENST00000342868.6:c.863-9CACCG>- chr5.hg19:g.180432321_180432325delCACCG 0 7 ref NA False 35 35 PASS 1 PASS ref->hom 0 NA 0,0 20,20 0,0 1 1 Q496L7|Q9Y2C7 True hg19 CCDS47358.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BTNL3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000367176.2 PASS NA None 20 NA True + CACCG ENST00000342868.6 Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 58777055 58777059 __UNKNOWN__ IGR DEL TGGAG TGGAG - rs9654654|rs28787309|rs56861732|rs60788840|rs4928570 LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:58777055_58777059delTGGAG NA NA RP11-143A22.1 (263195 upstream) : None (None downstream) NA NA NA NA NA NA NA NA NA ttggacctattggaggccttctttg 0.415 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 177 179.82 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.32 NA NA NA NA NA NA NA NA chr6.hg19:g.58777055_58777059delTGGAG 0 4 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 163,168 7,7 19,18 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 177 NA True TGGAG ZNF804B 219578 __UNKNOWN__ __UNKNOWN__ 7 88847451 88847451 __UNKNOWN__ Intron DEL A A - rs4140973|rs199973381|rs386715602 byFrequency LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:88847451delA ENST00000333190.4 + 2 717 NM_181646.2 NP_857597.1 A4D1E1 Z804B_HUMAN zinc finger protein 804B NA NA NA NA NA metal ion binding (GO:0046872) NA NA NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9) 144 all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151) STAD - Stomach adenocarcinoma(171;0.0513) NA ACCAACATTTATGTATTTTTT 0.348 NA NA NA NA NA NA NA NA NA HNSCC(36;0.09) ?|A|-|unsure 1374 0.274361 0.3495 0.2147 5008 , , NA 19582 0.122 NA 0.2972 False NA ,,, NA NA NA 2504 0.3487 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 119 119.61 NA NA 2474,1790 NA 934,606,592 32 35 34 NA NA 2.9 0 7 dbSNP_129 44 4430,3824 NA 1610,1210,1307 no intron ZNF804B NM_181646.2 NA 2544,1816,1899 A1A1,A1R,RR NA 46.3291,41.9794,44.8474 NA NA 88847451 6904,5614 2170 4207 6377 SO:0001627 intron_variant 0.08 NA NA AK056672 CCDS5613.1 7q21.13 2012-10-05 2006-12-18 ENSG00000182348 ENSG00000182348 219578 NA 21958 protein-coding gene gene with protein product NA "zinc finger 804B" NA Standard NM_181646 NM_181646 NA Approved FLJ32110 uc011khi.2 A4D1E1 OTTHUMG00000131037 ENST00000333190.4:c.109-18A>- chr7.hg19:g.88847451delA 0 4 ref NA False 48 48 PASS 1 PASS ref->het 0 NA 39,39 71,71 6,6 1 1 B2RTV2|Q7Z714|Q96MN7 True hg19 CCDS5613.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF804B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253683.2 PASS NA None 119 NA True + A ENST00000333190.4 ZC3HC1 51530 __UNKNOWN__ __UNKNOWN__ 7 129680929 129680929 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:129680929delC ENST00000481503.1 - 3 293 c.271delG c.(271-273)gcafs p.A91fs ZC3HC1_ENST00000311873.5_Frame_Shift_Del_p.A70fs|ZC3HC1_ENST00000358303.4_Frame_Shift_Del_p.A91fs|ZC3HC1_ENST00000360708.5_Frame_Shift_Del_p.A91fs Q86WB0 NIPA_HUMAN zinc finger, C3HC-type containing 1 91 NA NA NA NA mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567) nuclear membrane (GO:0031965)|nucleus (GO:0005634) protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270) NA NA endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1) 22 Melanoma(18;0.0435) NA GGCTTACCTGCCCATTTCAAA 0.408 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Melanoma(115;540 1606 16325 28853 48167) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 274 284.29 NA NA NA 161 158 159 NA NA NA NA 7 NA NA NA NA NA NA 129680929 2203 4300 6503 SO:0001589 frameshift_variant 4.03 NA NA AF151050 CCDS34753.1, CCDS64767.1, CCDS75659.1 7q32.2 2013-01-17 ENSG00000091732 ENSG00000091732 51530 NA "Zinc fingers, C3HC-type" 29913 protein-coding gene gene with protein product "nuclear interaction partner of ALK" NA NA 11042152 Standard NM_016478 XM_005250403 NA Approved NIPA uc003vpi.3 Q86WB0 OTTHUMG00000157648 ENST00000481503.1:c.271delG chr7.hg19:g.129680929delC ENSP00000418533:p.Ala91fs 2 3 ref NA False 51 51 PASS 3 PASS ref->het 0 NA 183,187 55,63 35,24 1 1 A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZC3HC1-004 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000349319.1 PASS NA None 274 NA True - C ENST00000481503.1 TNFSF8 944 __UNKNOWN__ __UNKNOWN__ 9 117656633 117656634 __UNKNOWN__ Intron INS - - CTG rs72468323|rs3833492|rs538529661 byFrequency LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:117656633_117656634insCTG ENST00000474301.1 - 2 82 P32971 TNFL8_HUMAN tumor necrosis factor (ligand) superfamily, member 8 NA NA NA NA NA apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165) extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887) receptor binding (GO:0005102) NA NA endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1) 12 NA tctaatttagcggaatggttct 0.381 NA NA NA NA NA NA NA NA NA 2787 0.55651 0.8404 0.7003 5008 , , NA 21788 0.3185 NA 0.4433 False NA ,,, NA NA NA 2504 0.4325 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 34 39.33 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA L09753 CCDS6810.1, CCDS75884.1 9q33 2008-02-05 ENSG00000106952 ENSG00000106952 944 NA "Tumor necrosis factor (ligand) superfamily", "CD molecules" 11938 protein-coding gene gene with protein product 603875 CD30LG NA 8391931, 9349718 Standard NM_001244 NA Approved CD153 uc004bji.2 P32971 OTTHUMG00000021025 ENST00000474301.1:c.443-189->CAG chr9.hg19:g.117656633_117656634insCTG 1 3 ref NA False 60 54 PASS 0 PASS ref->hom 0 NA 0,0 30,31 1,1 1 1 O43404 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNFSF8-002 KNOWN basic processed_transcript NA protein_coding OTTHUMT00000055465.1 PASS NA None 34 NA True - CTG ENST00000474301.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 10 42396110 42396119 __UNKNOWN__ IGR DEL GAATGGAATC GAATGGAATC - rs147826699|rs145444277|rs140021037|rs141297851|rs151017719|rs140653688|rs560616985|rs143615422 LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:42396110_42396119delGAATGGAATC NA NA None (None upstream) : AL031601.1 (334231 downstream) NA NA NA NA NA NA NA NA NA aatcatcattgaatggaatcgaatggaatc 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 830 792.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 19.64 NA NA NA NA NA NA NA NA chr10.hg19:g.42396120_42396129delGAATGGAATC 1 2 ref NA False 80 80 PASS 2 PASS ref->het 0 NA 679,935 12,25 215,166 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 830 NA True GAATGGAATC SPI1 6688 __UNKNOWN__ __UNKNOWN__ 11 47379987 47379988 __UNKNOWN__ Intron DEL AC AC - rs367603511 LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:47379987_47379988delAC ENST00000533030.1 - 2 215 SPI1_ENST00000227163.4_Intron|SPI1_ENST00000378538.3_Intron|SPI1_ENST00000533968.1_3'UTR P17947 SPI1_HUMAN Spi-1 proto-oncogene NA NA NA NA NA anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|histone H3 acetylation (GO:0043966)|hypermethylation of CpG island (GO:0044027)|lymphocyte differentiation (GO:0030098)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of erythrocyte differentiation (GO:0045646)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somatic stem cell maintenance (GO:0035019) nuclear chromatin (GO:0000790) core promoter binding (GO:0001047)|NFAT protein binding (GO:0051525)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA NA central_nervous_system(1)|large_intestine(2)|lung(4)|ovary(1) 8 Lung(87;0.0967) NA tcatgtgttgacagacacacaa 0.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 187 198.72 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.76 NA NA X52056 CCDS7933.2, CCDS44591.1 11p12-p11.22 2014-06-25 2014-06-25 ENSG00000066336 ENSG00000066336 6688 NA 11241 protein-coding gene gene with protein product "hematopoietic transcription factor PU.1", "31 kDa transforming protein" 165170 "spleen focus forming virus (SFFV) proviral integration oncogene" NA 1693183 Standard NM_003120 NM_003120 NA Approved PU.1, SPI-A, OF, SFPI1, SPI-1 uc001nfb.1 P17947 OTTHUMG00000150150 ENST00000533030.1:c.46-2890GT>- chr11.hg19:g.47379987_47379988delAC 0 2 ref NA False 70 70 PASS 1 PASS ref->het 0 NA 130,132 33,35 28,26 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SPI1-003 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000395644.2 PASS NA None 187 NA True - AC ENST00000533030.1 RP11-566K19.3 0 __UNKNOWN__ __UNKNOWN__ 15 22780686 22780693 __UNKNOWN__ RNA DEL GGTGTAGG GGTGTAGG - rs367783971|rs78920187 byFrequency LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:22780686_22780693delGGTGTAGG ENST00000560026.1 - 0 256 NA NA NA NA NA NA NA NA NA AAGGGAGGGAGGTGTAGGGGTGTAGGGT 0.476 NA NA NA NA NA NA NA NA NA 1978 0.394968 0.5106 0.2752 5008 , , NA 21505 0.4891 NA 0.328 False NA ,,, NA NA NA 2504 0.2955 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 59 62.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.15 NA NA NA NA NA NA NA NA ENST00000560026.1: chr15.hg19:g.22780694_22780701delGGTGTAGG 1 5 ref NA False 63 60 PASS 2 PASS ref->het 0 NA 4,4 43,43 11,11 2 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-566K19.3-001 KNOWN non_canonical_polymorphism|basic|readthrough_transcript processed_transcript NA processed_transcript OTTHUMT00000415617.1 PASS NA None 59 NA True - GGTGTAGG ENST00000560026.1 CSNK1A1P1 161635 __UNKNOWN__ __UNKNOWN__ 15 37109686 37109693 __UNKNOWN__ RNA DEL GGCTGGTT GGCTGGTT - rs143558048 byFrequency LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:37109686_37109693delGGCTGGTT ENST00000430593.3 - 0 733 NR_027320.1 casein kinase 1, alpha 1 pseudogene 1 NA NA NA NA NA NA NA NA NA TGCCATGGCAGGCTGGTTGGCTGGTTCT 0.428 NA NA NA NA NA NA NA NA NA 518 0.103435 0.1815 0.0418 5008 , , NA 21727 0.0446 NA 0.0795 False NA ,,, NA NA NA 2504 0.1268 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 57 55.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.01 NA NA BC028192 15q13.3 2010-09-21 2010-07-20 2010-07-20 ENSG00000223518 161635 NA 30446 pseudogene pseudogene NA "casein kinase 1, alpha 1 pseudogene" CSNK1A1P NA Standard NR_027320 NR_027320 NA Approved uc001zjg.4 ENST00000430593.3: chr15.hg19:g.37109694_37109701delGGCTGGTT 1 2 ref NA False 90 59 PASS 2 PASS ref->hom 0 NA 0,0 48,48 9,9 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CSNK1A1P1-002 KNOWN basic processed_transcript NA pseudogene OTTHUMT00000419759.1 PASS NA None 57 NA True - GGCTGGTT ENST00000430593.3 DENND4A 10260 __UNKNOWN__ __UNKNOWN__ 15 65982629 65982629 __UNKNOWN__ Intron DEL C C - rs34408949|rs148700861 byFrequency LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:65982629delC ENST00000567323.1 - 1 124 DENND4A_ENST00000431932.2_Intron|DENND4A_ENST00000443035.3_Intron Q7Z401 MYCPP_HUMAN DENN/MADD domain containing 4A NA NA NA NA NA positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112) NA NA breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 51 NA ACAAAACTTACATACCCAATG 0.308 NA NA NA NA NA NA NA NA NA C|C|-|deletion 1560 0.311502 0.146 0.1945 5008 , , NA 20890 0.7202 NA 0.164 False NA ,,, NA NA NA 2504 0.3487 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 38 39.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF534403 CCDS45285.1, CCDS53949.1 15q22.31 2012-10-03 2006-01-27 2006-01-27 10260 NA "DENN/MADD domain containing" 24321 protein-coding gene gene with protein product 600382 "c-myc promoter binding protein" MYCPBP NA 8056341, 12906859 Standard NM_005848 NM_005848 NA Approved IRLB uc002api.3 Q7Z401 ENST00000567323.1:c.482+123G>- chr15.hg19:g.65982629delC 0 2 ref NA False 34 34 PASS 1 PASS ref->hom 0 NA 0,0 34,35 4,4 1 1 E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DENND4A-007 PUTATIVE basic|exp_conf processed_transcript NA protein_coding OTTHUMT00000419613.1 PASS NA None 38 NA True - C ENST00000567323.1 RAB37 326624 __UNKNOWN__ __UNKNOWN__ 17 72740744 72740748 __UNKNOWN__ Intron DEL AGAGC AGAGC - LTS-028_T LTS-028_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:72740744_72740748delAGAGC ENST00000392613.5 + 6 488 RAB37_ENST00000528438.1_Intron|RAB37_ENST00000392614.4_Intron|RAB37_ENST00000402449.4_Intron|RAB37_ENST00000392615.5_Intron|RAB37_ENST00000392610.1_Intron|RAB37_ENST00000340415.3_Intron|RAB37_ENST00000392612.3_Intron NM_001006638.2 NP_001006639.1 Q96AX2 RAB37_HUMAN RAB37, member RAS oncogene family NA NA NA NA NA protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264) endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|secretory granule (GO:0030141) GTP binding (GO:0005525) NA NA breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1) 12 NA AGCCCCCATTAGAGCAGAGTGAACA 0.546 NA NA NA NA NA NA NA NA NA OREG0024716 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 156 176.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.44 NA NA BC040547 CCDS11703.1, CCDS32722.1, CCDS54161.1, CCDS54162.1 17q25.2 2008-02-05 ENSG00000172794 ENSG00000172794 326624 NA "RAB, member RAS oncogene" 30268 protein-coding gene gene with protein product 609956 NA 10722846 Standard NM_175738 NM_175738 NA Approved uc002jlk.3 Q96AX2 OTTHUMG00000134282 ENST00000392613.5:c.432+232AGAGC>- chr17.hg19:g.72740744_72740748delAGAGC 0 2 ref 1139 False 88 85 PASS 1 PASS ref->het 0 NA 75,77 58,60 29,26 1 1 A8MXF5|A8MYT0|Q8IWA7 True hg19 CCDS32722.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RAB37-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000258872.2 PASS NA None 156 NA True + AGAGC ENST00000392613.5 ZFP69B 65243 __UNKNOWN__ __UNKNOWN__ 1 40929109 40929152 __UNKNOWN__ Frame_Shift_Del DEL AGGCATGATTCATCCTTTGCTAAACATCAGAGAATTCATACTGG AGGCATGATTCATCCTTTGCTAAACATCAGAGAATTCATACTGG - LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:40929109_40929152delAGGCATGATTCATCCTTTGCTAAACATCAGAGAATTCATACTGG ENST00000411995.2 + 6 1828_1871 c.1453_1496delAGGCATGATTCATCCTTTGCTAAACATCAGAGAATTCATACTGG c.(1453-1497)aggcatgattcatcctttgctaaacatcagagaattcatactggafs p.RHDSSFAKHQRIHTG485fs ZFP69B_ENST00000361584.3_Frame_Shift_Del_p.RHDSSFAKHQRIHTG383fs|ZFP69B_ENST00000484445.1_3'UTR NM_023070.2 NP_075558.2 Q9UJL9 ZF69B_HUMAN ZFP69 zinc finger protein B 485 NA NA NA NA transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) p.R393I(1) NA NA NA GAAAGCCTTTAGGCATGATTCATCCTTTGCTAAACATCAGAGAATTCATACTGGAGAAAAACCT 0.381 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 1 Substitution - Missense(1) large_intestine(1) NA NA NA NA NA 1280 1257.93 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 2.29 NA NA BC017498 CCDS452.1, CCDS452.2 1p34.2 2013-01-09 2012-11-27 2012-11-27 ENSG00000187801 ENSG00000187801 65243 "Zinc fingers, C2H2-type", "-", "-", "-" 28053 protein-coding gene gene with protein product NA NA "zinc finger protein 643" ZNF643 NA Standard NM_023070 NM_023070 NA Approved ZKSCAN23B, FLJ34293, ZSCAN54B uc001cfn.2 Q9UJL9 OTTHUMG00000007302 ENST00000411995.2:c.1453_1496delAGGCATGATTCATCCTTTGCTAAACATCAGAGAATTCATACTGG chr1.hg19:g.40929109_40929152delAGGCATGATTCATCCTTTGCTAAACATCAGAGAATTCATACTGG ENSP00000399664:p.Arg485fs 0 6 ref NA False 36 36 PASS 1 PASS ref->het 0 NA 1503,1520 32,32 379,369 1 1 Q5QPL4 True hg19 CCDS452.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZFP69B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000019078.2 PASS NA None 1280 NA True + AGGCATGATTCATCCTTTGCTAAACATCAGAGAATTCATACTGG ENST00000411995.2 NHLH2 4808 __UNKNOWN__ __UNKNOWN__ 1 116381616 116381617 __UNKNOWN__ 5'UTR INS - - A LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:116381616_116381617insA ENST00000369506.1 - 0 4921_4922 NHLH2_ENST00000320238.3_Intron Q02577 HEN2_HUMAN nescient helix loop helix 2 NA NA NA NA NA cell differentiation (GO:0030154)|central nervous system development (GO:0007417)|mating behavior (GO:0007617)|ovulation cycle (GO:0042698)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634)|transcription factor complex (GO:0005667) DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102) NA prostate(1) 1 Lung SC(450;0.184) all_cancers(81;1.75e-06)|all_epithelial(167;1.16e-06)|all_lung(203;9.55e-06)|Lung NSC(69;5.83e-05) Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12) NA AGCCAGTGGCTGGGGGCGGGAA 0.624 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 441 422.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 4.8 NA NA CCDS885.1 1p12-p11 2013-05-21 ENSG00000177551 ENSG00000177551 4808 "Basic helix-loop-helix proteins" 7818 protein-coding gene gene with protein product NA 162361 HEN2 NA 1528853 Standard NM_005599 NM_005599 NA Approved NSCL2, bHLHa34 uc001efy.3 Q02577 OTTHUMG00000011969 ENST00000369506.1:c.-624->T chr1.hg19:g.116381616_116381617insA 1 8 ref NA False 105 99 PASS 0 PASS ref->het 0 NA 247,264 120,128 72,47 1 1 Q5T1P6 True hg19 CCDS885.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NHLH2-001 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000033090.1 PASS NA None 441 NA True - A ENST00000369506.1 PPP4R2 151987 __UNKNOWN__ __UNKNOWN__ 3 73108418 73108419 __UNKNOWN__ Intron INS - - T LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:73108418_73108419insT ENST00000356692.5 + 4 634 PPP4R2_ENST00000394284.3_Intron|PPP4R2_ENST00000295862.9_Intron Q9NY27 PP4R2_HUMAN protein phosphatase 4, regulatory subunit 2 NA NA NA NA NA cellular protein modification process (GO:0006464)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA processing (GO:0006397)|regulation of catalytic activity (GO:0050790)|regulation of double-strand break repair via homologous recombination (GO:0010569)|RNA splicing (GO:0008380) centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289) protein binding, bridging (GO:0030674)|protein phosphatase type 4 regulator activity (GO:0030362) NA breast(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|stomach(1)|urinary_tract(2) 12 Prostate(10;0.0187)|Lung SC(41;0.236) Epithelial(33;1.76e-07)|BRCA - Breast invasive adenocarcinoma(55;9.42e-05)|LUSC - Lung squamous cell carcinoma(21;0.00211)|Lung(16;0.00643)|KIRC - Kidney renal clear cell carcinoma(39;0.0164)|Kidney(39;0.0193)|OV - Ovarian serous cystadenocarcinoma(275;0.031) NA TTCCCAAATTGTTTTCCAAATT 0.356 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 130 138.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.21 NA NA AJ271448 CCDS2917.1 3q29 2010-06-18 ENSG00000163605 ENSG00000163605 151987 "Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits" 18296 protein-coding gene gene with protein product NA 613822 NA 10769191 Standard NM_174907 NM_174907 NA Approved uc003dph.1 Q9NY27 OTTHUMG00000158816 ENST00000356692.5:c.381+137->T chr3.hg19:g.73108422_73108422dupT 5 6 ref NA False 30 30 PASS 4 PASS ref->het 0 NA 84,88 28,29 17,14 1 1 A8K1I6|Q2TAJ9|Q498B8|Q8WXX6 True hg19 CCDS2917.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPP4R2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000352321.1 PASS NA None 130 NA True + T ENST00000356692.5 SLC9A3 6550 __UNKNOWN__ __UNKNOWN__ 5 474941 474942 __UNKNOWN__ Intron DEL CT CT - rs199785534 LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:474941_474942delCT ENST00000264938.3 - 16 2511 CTD-2228K2.7_ENST00000607286.1_RNA|SLC9A3_ENST00000514375.1_Intron NM_004174.2 NP_004165.2 P48764 SL9A3_HUMAN solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 NA NA NA NA NA ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085) apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385) NA NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1) 37 Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863) NA aggcggagacctggagggagag 0.733 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 48 56.75 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA CCDS3855.1, CCDS64116.1 5p15.3 2013-05-22 2012-03-22 ENSG00000066230 ENSG00000066230 6550 "Solute carriers" 11073 protein-coding gene gene with protein product NA 182307 "solute carrier family 9 (sodium/hydrogen exchanger), isoform 3", "solute carrier family 9 (sodium/hydrogen exchanger), member 3" NHE3 NA 8096830 Standard NM_004174 NM_004174 NA Approved uc003jbe.2 P48764 OTTHUMG00000090315 ENST00000264938.3:c.2501+55AG>- chr5.hg19:g.474941_474942delCT 0 5 ref NA False 44 44 PASS 1 PASS ref->het 0 NA 3,3 41,44 5,2 1 1 B7ZKR2|E9PF67|Q3MIW3 True hg19 CCDS3855.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC9A3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000206677.2 PASS NA None 48 NA True - CT ENST00000264938.3 RNF14 9604 __UNKNOWN__ __UNKNOWN__ 5 141353088 141353095 __UNKNOWN__ Intron DEL CCACCACA CCACCACA - LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:141353088_141353095delCCACCACA ENST00000394520.2 + 3 303 RNF14_ENST00000347642.3_Intron|RNF14_ENST00000394515.3_Intron|RNF14_ENST00000394519.1_Intron|RNF14_ENST00000356143.1_Intron|AC005740.5_ENST00000520882.1_RNA|RNF14_ENST00000502341.1_Intron|RNF14_ENST00000394514.2_Intron|RNF14_ENST00000540015.1_Intron NM_001201365.1|NM_004290.4 NP_001188294.1|NP_004281.1 Q9UBS8 RNF14_HUMAN ring finger protein 14 NA NA NA NA NA androgen receptor signaling pathway (GO:0030521)|positive regulation of transcription, DNA-templated (GO:0045893)|protein ubiquitination (GO:0016567)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleus (GO:0005634) androgen receptor binding (GO:0050681)|small conjugating protein ligase activity (GO:0019787)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270) NA cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 15 all_hematologic(541;0.0536)|Ovarian(839;0.118) KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GBM - Glioblastoma multiforme(465;0.0407) NA caggtgtgagccaccacacccggccAGC 0.514 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 236 274.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.49 NA NA AF060544 CCDS4270.1, CCDS4271.1 5q23.3-q31.1 2008-02-05 ENSG00000013561 ENSG00000013561 9604 "RING-type (C3HC4) zinc fingers" 10058 protein-coding gene gene with protein product NA 605675 NA 10085091, 10320776 Standard NM_004290 NM_183399 NA Approved ARA54, HFB30, TRIAD2 uc003lmc.3 Q9UBS8 OTTHUMG00000129660 ENST00000394520.2:c.-6-53CCACCACA>- chr5.hg19:g.141353088_141353095delCCACCACA 0 4 ref NA False 218 109 PASS 1 PASS ref->het 0 NA 112,113 111,114 32,28 1 1 A0AV26|A6NMR2|A8MTW5|B3KN72|B7ZLV2|D3DQE4|O94793|Q6IBV0 True hg19 CCDS4270.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RNF14-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251860.2 PASS NA None 236 NA True + CCACCACA ENST00000394520.2 RNF145 153830 __UNKNOWN__ __UNKNOWN__ 5 158585769 158585770 __UNKNOWN__ Frame_Shift_Del DEL GC GC - LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:158585769_158585770delGC ENST00000518802.1 - 11 2139_2140 c.1990_1991delGC c.(1990-1992)gccfs p.A664fs RNF145_ENST00000521606.2_Frame_Shift_Del_p.A651fs|RNF145_ENST00000519865.1_Frame_Shift_Del_p.A634fs|RNF145_ENST00000424310.2_Frame_Shift_Del_p.A634fs|RNF145_ENST00000518284.1_5'UTR|RNF145_ENST00000274542.2_Frame_Shift_Del_p.A662fs|RNF145_ENST00000520638.1_Frame_Shift_Del_p.A648fs NM_001199380.1 NP_001186309.1 Q96MT1 RN145_HUMAN ring finger protein 145 634 NA NA NA NA integral component of membrane (GO:0016021) zinc ion binding (GO:0008270) NA endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 30 Renal(175;0.00196) Medulloblastoma(196;0.0523) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) NA TGGTCGTCTGGCAATGTACTCA 0.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 388 391.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.84 NA NA BC042684 CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1 5q33.3 2013-01-09 ENSG00000145860 ENSG00000145860 153830 "RING-type (C3HC4) zinc fingers" 20853 protein-coding gene gene with protein product NA NA NA Standard NM_144726 NM_001199380 NA Approved FLJ31951 uc003lxo.2 Q96MT1 OTTHUMG00000130306 ENST00000518802.1:c.1990_1991delGC chr5.hg19:g.158585769_158585770delGC ENSP00000430955:p.Ala664fs 0 2 ref NA False 95 95 PASS 1 PASS ref->het 0 NA 220,224 81,82 35,31 1 1 B7Z903|B7Z949|E7EVI7|Q8IVP7 True hg19 CCDS56393.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RNF145-003 KNOWN basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000374049.1 PASS NA None 388 NA True - GC ENST00000518802.1 RNF145 153830 __UNKNOWN__ __UNKNOWN__ 5 158585773 158585786 __UNKNOWN__ Frame_Shift_Del DEL TGTACTCATTATTG TGTACTCATTATTG - rs377143245 LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:158585773_158585786delTGTACTCATTATTG ENST00000518802.1 - 11 2123_2136 c.1974_1987delCAATAATGAGTACA c.(1972-1989)gacaataatgagtacattfs p.NNEYI659fs RNF145_ENST00000521606.2_Frame_Shift_Del_p.NNEYI646fs|RNF145_ENST00000519865.1_Frame_Shift_Del_p.NNEYI629fs|RNF145_ENST00000424310.2_Frame_Shift_Del_p.NNEYI629fs|RNF145_ENST00000518284.1_5'UTR|RNF145_ENST00000274542.2_Frame_Shift_Del_p.NNEYI657fs|RNF145_ENST00000520638.1_Frame_Shift_Del_p.NNEYI643fs NM_001199380.1 NP_001186309.1 Q96MT1 RN145_HUMAN ring finger protein 145 629 NA NA NA NA integral component of membrane (GO:0016021) zinc ion binding (GO:0008270) NA endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 30 Renal(175;0.00196) Medulloblastoma(196;0.0523) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) NA CGTCTGGCAATGTACTCATTATTGTCCCTGGAAC 0.505 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 327 380.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.82 NA NA BC042684 CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1 5q33.3 2013-01-09 ENSG00000145860 ENSG00000145860 153830 "RING-type (C3HC4) zinc fingers" 20853 protein-coding gene gene with protein product NA NA NA Standard NM_144726 NM_001199380 NA Approved FLJ31951 uc003lxo.2 Q96MT1 OTTHUMG00000130306 ENST00000518802.1:c.1974_1987delCAATAATGAGTACA chr5.hg19:g.158585773_158585786delTGTACTCATTATTG ENSP00000430955:p.Asn659fs 0 3 ref NA False 103 101 PASS 1 PASS ref->het 0 NA 226,231 81,82 34,30 1 1 B7Z903|B7Z949|E7EVI7|Q8IVP7 True hg19 CCDS56393.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RNF145-003 KNOWN basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000374049.1 PASS NA None 327 NA True - TGTACTCATTATTG ENST00000518802.1 VWDE 221806 __UNKNOWN__ __UNKNOWN__ 7 12375667 12375668 __UNKNOWN__ Intron INS - - A rs367551600|rs78493184|rs74626405|rs35608044 byFrequency LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:12375667_12375668insA ENST00000275358.3 - 27 4843 NM_001135924.1 NP_001129396.1 Q8N2E2 VWDE_HUMAN von Willebrand factor D and EGF domains NA NA NA NA NA extracellular region (GO:0005576) NA breast(4)|endometrium(2)|kidney(1)|skin(1) 8 NA GCATGCTGGAGTTTTTTCCCCC 0.277 NA NA NA NA NA NA NA NA NA NA NA NA NA 1651 0.329673 0.1036 0.513 5008 , , NA 13186 0.4454 NA 0.3887 False NA ,,, NA NA NA 2504 0.3252 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 61 60.75 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.57 NA NA CCDS47544.1 7p21.3 2008-09-23 ENSG00000146530 ENSG00000146530 221806 21897 protein-coding gene gene with protein product NA NA NA 14702039, 16303743 Standard XM_371878 NM_001135924 NA Approved FLJ14712 uc003ssj.2 Q8N2E2 OTTHUMG00000152315 ENST00000275358.3:c.4654+98->T chr7.hg19:g.12375667_12375668insA 1 6 ref NA False 42 42 PASS 0 PASS ref->het 0 NA 2,2 54,55 8,7 1 1 B7ZM77|Q96SQ3 True hg19 CCDS47544.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA VWDE-001 NOVEL basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000325870.3 PASS NA None 61 NA True - A ENST00000275358.3 AVL9 23080 __UNKNOWN__ __UNKNOWN__ 7 32620325 32620326 __UNKNOWN__ Intron INS - - TG rs59720213|rs35499747|rs3217607|rs397722003 byFrequency LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:32620325_32620326insTG ENST00000318709.4 + 15 1963 AVL9_ENST00000404479.1_Intron|AVL9_ENST00000409301.1_Intron NM_015060.1 NP_055875.1 Q8NBF6 AVL9_HUMAN AVL9 homolog (S. cerevisiase) NA NA NA NA NA cell migration (GO:0016477) integral component of membrane (GO:0016021)|recycling endosome (GO:0055037) NA endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 18 NA AGAGTGACTATtgtgtgtgtgt 0.292 NA NA NA NA NA NA NA NA NA NA NA NA NA 2812 0.561502 0.3744 0.7089 5008 , , NA 18584 0.6657 NA 0.6551 False NA ,,, NA NA NA 2504 0.5061 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 38 45.11 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.08 NA NA D87682 CCDS34613.1 7p14.3 2013-05-01 2008-10-03 2008-10-03 ENSG00000105778 ENSG00000105778 23080 28994 protein-coding gene gene with protein product NA 612927 "KIAA0241" KIAA0241 NA 17229886, 22595670 Standard NM_015060 XM_005249668 NA Approved uc003tcv.1 Q8NBF6 OTTHUMG00000152929 ENST00000318709.4:c.1743-88->TG chr7.hg19:g.32620334_32620335dupTG 6 3 ref NA False 34 34 PASS 5 PASS ref->het 0 NA 2,2 34,35 2,2 1 1 Q92573 True hg19 CCDS34613.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AVL9-003 NOVEL basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000328643.1 PASS NA None 38 NA True + TG ENST00000318709.4 MOGAT3 346606 __UNKNOWN__ __UNKNOWN__ 7 100844093 100844093 __UNKNOWN__ Frame_Shift_Del DEL T T - LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:100844093delT ENST00000223114.4 - 1 209 c.43delA c.(43-45)accfs p.T15fs MOGAT3_ENST00000379423.3_Frame_Shift_Del_p.T15fs|MOGAT3_ENST00000440203.2_Frame_Shift_Del_p.T15fs NM_178176.2 NP_835470.1 Q86VF5 MOGT3_HUMAN monoacylglycerol O-acyltransferase 3 15 NA NA NA NA glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021) 2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144) NA breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(3) 22 Lung NSC(181;0.168)|all_lung(186;0.215) NA TTCTGCAAGGTTTTGGAAGTG 0.577 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 423 416.02 NA NA NA NA NA 92 74 80 NA NA NA NA 7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 100844093 NA 2203 4300 6503 SO:0001589 frameshift_variant 3.29 NA NA AY229854 CCDS5714.1, CCDS75643.1 7q22 2012-09-06 ENSG00000106384 ENSG00000106384 346606 2.3.1.20, 2.3.1.22 23249 protein-coding gene gene with protein product NA 610184 NA 12618427, 14970677 Standard NM_178176 XM_005250309 NA Approved DC7, MGAT3 uc003uyc.3 Q86VF5 OTTHUMG00000023328 ENST00000223114.4:c.43delA chr7.hg19:g.100844093delT ENSP00000223114:p.Thr15fs 3 4 ref NA False 61 61 PASS 4 PASS ref->het 0 NA 258,263 102,109 67,56 1 1 Q496A6|Q496A7|Q496A8|Q9UDW7 True hg19 CCDS5714.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MOGAT3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000059649.3 PASS NA None 423 NA True - T ENST00000223114.4 DENND2A 27147 __UNKNOWN__ __UNKNOWN__ 7 140266990 140267009 __UNKNOWN__ Frame_Shift_Del DEL ACTCGATGAGTTCCCGGGCA ACTCGATGAGTTCCCGGGCA - rs368995985|rs200776468|rs73165431|rs371604238 LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:140266990_140267009delACTCGATGAGTTCCCGGGCA ENST00000275884.6 - 8 2073_2092 c.1656_1675delTGCCCGGGAACTCATCGAGT c.(1654-1677)cttgcccgggaactcatcgagtacfs p.ARELIEY553fs DENND2A_ENST00000492720.1_Frame_Shift_Del_p.ARELIEY553fs|DENND2A_ENST00000496613.1_Frame_Shift_Del_p.ARELIEY553fs|DENND2A_ENST00000537639.1_Frame_Shift_Del_p.ARELIEY553fs Q9ULE3 DEN2A_HUMAN DENN/MADD domain containing 2A 553 NA NA NA NA positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147) actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737) Rab guanyl-nucleotide exchange factor activity (GO:0017112) NA breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 49 Melanoma(164;0.00956) NA CTCTCCTGGTACTCGATGAGTTCCCGGGCAAGTGATGGGT 0.582 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 340 344.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.3 NA NA AB033103 CCDS43659.1 7q34 2012-10-03 2005-08-17 2005-08-17 ENSG00000146966 ENSG00000146966 27147 "DENN/MADD domain containing" 22212 protein-coding gene gene with protein product NA NA "KIAA1277" KIAA1277 NA Standard NM_015689 NM_015689 NA Approved FAM31D uc010lnj.3 Q9ULE3 OTTHUMG00000157411 ENST00000275884.6:c.1656_1675delTGCCCGGGAACTCATCGAGT chr7.hg19:g.140266990_140267009delACTCGATGAGTTCCCGGGCA ENSP00000275884:p.Ala553fs 0 2 ref NA False 37 37 PASS 1 PASS ref->het 0 NA 263,267 34,35 58,53 1 1 C9JUI3|Q1RMD5|Q86XY0 True hg19 CCDS43659.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DENND2A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000348742.1 PASS NA None 340 NA True - ACTCGATGAGTTCCCGGGCA ENST00000275884.6 SGPL1 8879 __UNKNOWN__ __UNKNOWN__ 10 72635144 72635145 __UNKNOWN__ Intron DEL TT TT - rs398054497|rs3998628 byFrequency LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:72635144_72635145delTT ENST00000373202.3 + 13 1498 NM_003901.3 NP_003892.2 O95470 SGPL1_HUMAN sphingosine-1-phosphate lyase 1 NA NA NA NA NA androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|ceramide metabolic process (GO:0006672)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|fatty acid metabolic process (GO:0006631)|fibroblast migration (GO:0010761)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|regulation of multicellular organism growth (GO:0040014)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid catabolic process (GO:0030149)|sphingolipid metabolic process (GO:0006665)|vasculogenesis (GO:0001570) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176) carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)|sphinganine-1-phosphate aldolase activity (GO:0008117) NA large_intestine(4) 4 NA CCTTCATTTATTTTTTTGTTTT 0.356 NA NA NA NA NA NA NA NA NA NA NA NA NA 1555 0.310503 0.3026 0.3084 5008 , , NA 20125 0.2986 NA 0.341 False NA ,,, NA NA NA 2504 0.3037 NA NA NA Colon(151;1054 2458 6676 40971) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 104 105.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.89 NA NA AI128825 CCDS31216.1 10q21 2008-08-01 ENSG00000166224 ENSG00000166224 8879 10817 protein-coding gene gene with protein product NA 603729 NA 9464245, 17090686 Standard NM_003901 NM_003901 NA Approved SPL uc001jrm.3 O95470 OTTHUMG00000018421 ENST00000373202.3:c.1299-14TT>- chr10.hg19:g.72635148_72635149delTT 5 11 ref NA False 54 40 PASS 7 PASS ref->het 0 NA 10,10 88,89 7,6 1 1 B2RBD4|Q7Z732|Q9ULG8|Q9UN89 True hg19 CCDS31216.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SGPL1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000048533.1 PASS NA None 104 NA True + T ENST00000373202.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 14 67853631 67853634 __UNKNOWN__ IGR DEL TGTA TGTA - rs34187862|rs377639942 byFrequency LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:67853631_67853634delTGTA NA EIF2S1 (398 upstream) : PLEK2 (65 downstream) NA NA NA NA NA NA NA NA CTATAAACTTTGTATGGGATTCTA 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA 319 0.0636981 0.1505 0.0893 5008 , , NA 20682 0.0129 NA 0.0149 False NA ,,, NA NA NA 2504 0.0307 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 26 30.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA NA chr14.hg19:g.67853631_67853634delTGTA 0 4 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 1,2 23,23 2,1 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 26 NA True TGTA POLR3E 55718 __UNKNOWN__ __UNKNOWN__ 16 22345896 22345922 __UNKNOWN__ 3'UTR DEL ACATAATTTTGAAAGTTTCTAGCAACC ACATAATTTTGAAAGTTTCTAGCAACC - rs145375611 LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:22345896_22345922delACATAATTTTGAAAGTTTCTAGCAACC ENST00000299853.5 + 0 3169_3195 NM_001258033.1|NM_001258035.1|NM_018119.3 NP_001244962.1|NP_001244964.1|NP_060589.1 Q9NVU0 RPC5_HUMAN polymerase (RNA) III (DNA directed) polypeptide E (80kD) NA NA NA NA NA defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383) centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) DNA-directed RNA polymerase activity (GO:0003899) NA central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 27 GBM - Glioblastoma multiforme(48;0.012) NA cgagtcacgtacataattttgaaagtttctagcaaccacattagttt 0.383 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 171 158.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.73 NA NA AY092085 CCDS10605.1, CCDS58432.1, CCDS58433.1, CCDS58434.1, CCDS73845.1 16p12 2013-01-21 ENSG00000058600 ENSG00000058600 55718 "RNA polymerase subunits" 30347 protein-coding gene gene with protein product NA NA NA 10819331, 10521666 Standard NM_018119 NM_018119 NA Approved RPC5, SIN, FLJ10509 uc002dkk.4 Q9NVU0 OTTHUMG00000094779 ENST00000299853.5:c.*901ACATAATTTTGAAAGTTTCTAGCAACC>- chr16.hg19:g.22345896_22345922delACATAATTTTGAAAGTTTCTAGCAACC 0 3 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 100,102 39,40 42,40 1 1 B4DL24|B4DUP6|H3BT11|Q9BWF7|Q9H8W8|Q9H907|Q9P276 True hg19 CCDS10605.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA POLR3E-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000211590.1 PASS NA None 171 NA True + ACATAATTTTGAAAGTTTCTAGCAACC ENST00000299853.5 ROCK1P1 727758 __UNKNOWN__ __UNKNOWN__ 18 122168 122169 __UNKNOWN__ RNA INS - - TT rs566884677 LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:122168_122169insTT ENST00000608049.1 + 0 2406_2407 NR_033770.1 Rho-associated, coiled-coil containing protein kinase 1 pseudogene 1 NA NA NA NA NA NA NA NA TATAGTAATGACTGTGCTCATT 0.307 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 101 142.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.39 NA NA 18p11.32 2012-10-04 ENSG00000263006 ENSG00000263006 727758 37832 pseudogene pseudogene NA NA NA Standard NR_033770 NA Approved uc002kke.3 OTTHUMG00000177913 ENST00000608049.1: chr18.hg19:g.122168_122169insTT 2 1 ref NA False 59 56 PASS 0 PASS ref->het 0 NA 26,26 73,80 5,5 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ROCK1P1-003 KNOWN basic processed_transcript NA pseudogene OTTHUMT00000472417.1 PASS NA None 101 NA True + T ENST00000608049.1 RAX 30062 __UNKNOWN__ __UNKNOWN__ 18 56935259 56935287 __UNKNOWN__ 3'UTR DEL GTTCTTGTACCGCTGGTGATCAACCTTGG GTTCTTGTACCGCTGGTGATCAACCTTGG - rs574697900 LTS-029_T LTS-029_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:56935259_56935287delGTTCTTGTACCGCTGGTGATCAACCTTGG ENST00000334889.3 - 0 2176_2204 RAX_ENST00000256852.7_3'UTR NM_013435.2 NP_038463.2 Q9Y2V3 RX_HUMAN retina and anterior neural fold homeobox NA NA NA NA NA camera-type eye development (GO:0043010)|hypothalamus development (GO:0021854)|limb development (GO:0060173)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601) nucleus (GO:0005634) RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077) NA central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1) 6 Lung NSC(161;0.0804)|Colorectal(73;0.0946) STAD - Stomach adenocarcinoma(84;0.18) NA CTTTGCCTCAGTTCTTGTACCGCTGGTGATCAACCTTGGGTGTTAGGGA 0.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GBM(150;770 1898 17679 24325 37807) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA 207 204.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.5 NA NA AF115392 CCDS11972.1 18q21.31 2011-06-20 ENSG00000134438 ENSG00000134438 30062 "Homeoboxes / PRD class" 18662 protein-coding gene gene with protein product NA 601881 NA 10625658, 10766016, 14662654 Standard NM_013435 NA Approved RX uc002lhx.3 Q9Y2V3 OTTHUMG00000132757 ENST00000334889.3:c.*977CCAAGGTTGATCACCAGCGGTACAAGAAC>- chr18.hg19:g.56935259_56935287delGTTCTTGTACCGCTGGTGATCAACCTTGG 0 4 ref NA False 53 53 PASS 1 PASS ref->het 0 NA 144,150 37,37 53,48 1 1 Q86V11 True hg19 CCDS11972.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RAX-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256128.2 PASS NA None 207 NA True - GTTCTTGTACCGCTGGTGATCAACCTTGG ENST00000334889.3 RCAN3 11123 __UNKNOWN__ __UNKNOWN__ 1 24862308 24862339 __UNKNOWN__ 3'UTR DEL ATCATGGTTCTCAAGTATTTGTTCAATTAGCT ATCATGGTTCTCAAGTATTTGTTCAATTAGCT - rs149949714 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:24862308_24862339delATCATGGTTCTCAAGTATTTGTTCAATTAGCT ENST00000374395.4 + 0 1580_1611 RCAN3_ENST00000436717.2_3'UTR NM_001251978.1|NM_001251979.1|NM_001251984.1 NP_001238907.1|NP_001238908.1|NP_001238913.1 Q9UKA8 RCAN3_HUMAN RCAN family member 3 NA NA NA NA anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722) RNA binding (GO:0003723)|troponin I binding (GO:0031013) NA central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2) 7 Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19) UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14) ATTCATAGAAATCATGGTTCTCAAGTATTTGTTCAATTAGCTTTGGGGAAGA 0.349 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 69 58.63 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1 1p35.3-p33 2008-02-05 2007-06-26 2007-06-26 ENSG00000117602 ENSG00000117602 11123 3042 protein-coding gene gene with protein product 605860 "Down syndrome critical region gene 1-like 2" DSCR1L2 NA 10756093 Standard NM_001251984 NA Approved uc001bjj.3 Q9UKA8 OTTHUMG00000003298 ENST00000374395.4:c.*572ATCATGGTTCTCAAGTATTTGTTCAATTAGCT>- chr1.hg19:g.24862308_24862339delATCATGGTTCTCAAGTATTTGTTCAATTAGCT 0 4 ref NA False 64 64 PASS 1 PASS ref->het 0 NA 37,38 16,16 6,6 2 2 A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7 True hg19 CCDS254.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RCAN3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000009176.2 PASS NA None 69 True + ATCATGGTTCTCAAGTATTTGTTCAATTAGCT ENST00000374395.4 ZMPSTE24 10269 __UNKNOWN__ __UNKNOWN__ 1 40759396 40759397 __UNKNOWN__ 3'UTR INS - - T LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:40759396_40759397insT ENST00000372759.3 + 0 2648_2649 NM_005857.4 NP_005848.2 O75844 FACE1_HUMAN zinc metallopeptidase STE24 NA NA NA NA CAAX-box protein processing (GO:0071586)|nuclear envelope organization (GO:0006998)|prenylated protein catabolic process (GO:0030327)|proteolysis (GO:0006508) endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634) metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metalloexopeptidase activity (GO:0008235) NA endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1) 16 Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;6.3e-18) AATTACAGTTCTTGAAATGCAG 0.287 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 93 91.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA Y13834 CCDS449.1 1p34 2014-09-17 2012-12-10 ENSG00000084073 ENSG00000084073 10269 3.4.24.84 12877 protein-coding gene gene with protein product "Hutchinson-Gilford progeria syndrome", "CAAX prenyl protease 1 homolog" 606480 "zinc metalloproteinase (STE24 homolog, yeast)", "zinc metallopeptidase (STE24 homolog, yeast)", "zinc metallopeptidase STE24 homolog (S. cerevisiae)" NA 10373325, 9700155, 16671095 Standard NM_005857 NA Approved FACE-1, Ste24p, STE24, HGPS, PRO1 uc001cfg.4 O75844 OTTHUMG00000005762 ENST00000372759.3:c.*1056->T chr1.hg19:g.40759398_40759398dupT 3 4 ref NA False 87 86 PASS 2 PASS ref->het 0 NA 54,56 31,31 8,8 2 2 B3KQI7|D3DPU7|Q8NDZ8|Q9UBQ2 True hg19 CCDS449.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZMPSTE24-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000015766.1 PASS NA None 93 True + T ENST00000372759.3 NFASC 23114 __UNKNOWN__ __UNKNOWN__ 1 204917709 204917713 __UNKNOWN__ Intron DEL AAAAC AAAAC - rs374990603|rs147883938 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:204917709_204917713delAAAAC ENST00000401399.1 + 3 290 NFASC_ENST00000367169.4_Intron|NFASC_ENST00000338586.6_Intron|NFASC_ENST00000367172.4_Intron|NFASC_ENST00000367170.4_Intron|NFASC_ENST00000367171.4_Intron|NFASC_ENST00000338515.6_Intron|NFASC_ENST00000403080.1_Intron|NFASC_ENST00000539706.1_Intron|NFASC_ENST00000404907.1_Intron|NFASC_ENST00000360049.4_Intron|NFASC_ENST00000404076.1_Intron|NFASC_ENST00000339876.6_Intron|NFASC_ENST00000513543.1_Intron O94856 NFASC_HUMAN neurofascin NA NA NA NA axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226) axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886) NA NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1) 81 all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19) KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158) GGATTTGTTAaaaacaaaacaaaac 0.507 NA NA NA NA NA NA NA 396 0.0790735 0.115 0.0836 5008 , , NA 20833 0.001 NA 0.1004 False NA ,,, NA NA NA 2504 0.0859 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 105 99.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA AK027553 CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1 1q32.1 2013-02-11 2010-06-24 ENSG00000163531 ENSG00000163531 23114 "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing" 29866 protein-coding gene gene with protein product 609145 "neurofascin homolog (chicken)" NA 1377696, 8672144 Standard NM_001005388 NM_015090 NA Approved NRCAML, KIAA0756, FLJ46866, NF uc001hbj.3 O94856 OTTHUMG00000151697 ENST00000401399.1:c.92-1972AAAAC>- chr1.hg19:g.204917719_204917723delAAAAC 3 9 ref NA False 30 30 PASS 4 PASS ref->het 0 NA 97,100 4,4 17,17 1 1 B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50 True hg19 CCDS53460.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NFASC-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000131237.1 PASS NA None 105 True + AAAAC ENST00000401399.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 2 7386183 7386187 __UNKNOWN__ IGR DEL GCGCA GCGCA - rs541893463|rs527953067 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:7386183_7386187delGCGCA NA RN7SKP112 (104508 upstream) : RP11-557L19.1 (14814 downstream) NA NA NA NA NA NA gcatgtgtgtgcgcatgtgtgtgtg 0.546 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 115 116.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA chr2.hg19:g.7386183_7386187delGCGCA 0 2 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 107,118 4,4 10,8 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 115 True GCGCA Unknown 0 __UNKNOWN__ __UNKNOWN__ 2 7386197 7386201 __UNKNOWN__ IGR DEL GCGTG GCGTG - rs536236115 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:7386197_7386201delGCGTG NA RN7SKP112 (104522 upstream) : RP11-557L19.1 (14800 downstream) NA NA NA NA NA NA atgtgtgtgtgcgtgtgtgtatgtA 0.522 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 154 141.91 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA chr2.hg19:g.7386197_7386201delGCGTG 0 2 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 144,169 4,4 15,16 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 154 True GCGTG ICA1L 130026 __UNKNOWN__ __UNKNOWN__ 2 203684377 203684383 __UNKNOWN__ Intron DEL TTTCATA TTTCATA - rs183526646|rs191191927 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:203684377_203684383delTTTCATA ENST00000392237.2 - 6 716 ICA1L_ENST00000358299.2_Intron|ICA1L_ENST00000425178.1_3'UTR NM_138468.4 NP_612477.3 Q8NDH6 ICA1L_HUMAN islet cell autoantigen 1,69kDa-like NA NA NA NA NA breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 22 TCTGTGGCAGTTTCATATTTCATACAC 0.324 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 142 138.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.44 NA AB053317 CCDS2354.1, CCDS74632.1 2q33 2008-02-05 2006-05-26 2006-05-26 ENSG00000163596 ENSG00000163596 130026 14442 protein-coding gene gene with protein product NA "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14" ALS2CR15, ALS2CR14 NA 11586298 Standard NM_138468 NM_138468 NA Approved uc002uzh.1 Q8NDH6 OTTHUMG00000132856 ENST00000392237.2:c.558+40TATGAAA>- chr2.hg19:g.203684384_203684390delTTTCATA 1 4 ref NA False 51 51 PASS 2 PASS ref->het 0 NA 136,138 4,4 9,8 2 2 B3KRW6|Q53P45|Q53QZ4|Q53T97|Q96N47|Q96Q32|Q9BVQ2 True hg19 CCDS2354.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ICA1L-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256330.1 PASS NA None 142 True - TTTCATA ENST00000392237.2 COL6A3 1293 __UNKNOWN__ __UNKNOWN__ 2 238245105 238245119 __UNKNOWN__ In_Frame_Del DEL TCGTAGTCACCGGCT TCGTAGTCACCGGCT - rs150907698|rs367635298|rs139883752|rs143006225 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:238245105_238245119delTCGTAGTCACCGGCT ENST00000295550.4 - 40 9076_9090 c.8624_8638delAGCCGGTGACTACGA c.(8623-8640)aagccggtgactacgacg>acg p.KPVTT2875del COL6A3_ENST00000353578.4_In_Frame_Del_p.KPVTT2669del|COL6A3_ENST00000346358.4_In_Frame_Del_p.KPVTT2675del|COL6A3_ENST00000347401.3_In_Frame_Del_p.KPVTT2674del|COL6A3_ENST00000409809.1_In_Frame_Del_p.KPVTT2669del|COL6A3_ENST00000472056.1_In_Frame_Del_p.KPVTT2268del NM_004369.3 NP_004360.2 P12111 CO6A3_HUMAN collagen, type VI, alpha 3 2875 Nonhelical region.|Thr-rich. NA NA NA axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749) collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982) serine-type endopeptidase inhibitor activity (GO:0004867) NA breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4) 217 Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203) Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034) ACCGGCTTCGTCGTAGTCACCGGCTTCGTTGTCGT 0.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 221 214.82 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.01 NA X52022 CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1 2q37 2014-09-17 ENSG00000163359 ENSG00000163359 1293 "Collagens" 2213 protein-coding gene gene with protein product 120250 NA 1339440, 11992252 Standard NM_004369 NM_004369 NA Approved uc002vwl.2 P12111 OTTHUMG00000150020 ENST00000295550.4:c.8624_8638delAGCCGGTGACTACGA chr2.hg19:g.238245105_238245119delTCGTAGTCACCGGCT ENSP00000295550:p.Lys2875_Thr2879del 0 2 ref NA False 153 153 PASS 1 PASS ref->het 0 NA 201,205 21,21 22,22 1 1 A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6 True hg19 CCDS33412.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COL6A3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000315790.2 PASS NA None 221 True - TCGTAGTCACCGGCT ENST00000295550.4 RBMS3 27303 __UNKNOWN__ __UNKNOWN__ 3 29628589 29628611 __UNKNOWN__ Splice_Site DEL TTTTGTGTTTTCACAGGTTATGG TTTTGTGTTTTCACAGGTTATGG - rs199565759|rs13079497 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:29628589_29628611delTTTTGTGTTTTCACAGGTTATGG ENST00000452462.1 + 4 437_444 c.307_314delTTTTGTGTTTTCACAGGTTATGG c.(307-315)ttttgtgtt>t p.FCV103fs RBMS3_ENST00000383766.2_Splice_Site_p.FCV102fs|RBMS3_ENST00000456853.1_Splice_Site_p.FCV103fs|RBMS3_ENST00000396583.3_Splice_Site_p.FCV103fs|RBMS3_ENST00000445033.1_Splice_Site_p.FCV103fs|RBMS3_ENST00000273139.9_Splice_Site_p.FCV103fs|RBMS3_ENST00000383767.2_Splice_Site_p.FCV103fs|RBMS3_ENST00000434693.2_Splice_Site_p.FCV102fs Q6XE24 RBMS3_HUMAN RNA binding motif, single stranded interacting protein 3 103 RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}. NA NA NA positive regulation of translation (GO:0045727) cytoplasm (GO:0005737) mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166) NA breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1) 11 Ovarian(412;0.0956) AACAAGGGGATTTTGTGTTTTCACAGGTTATGGTTTTGTAGAT 0.399 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 152 132.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0 NA AF023259 CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1 3p24-p23 2013-02-12 2010-04-20 ENSG00000144642 ENSG00000144642 27303 "RNA binding motif (RRM) containing" 13427 protein-coding gene gene with protein product "RNA-binding protein" 605786 "RNA binding motif, single stranded interacting protein" NA 10675610 Standard NM_001003792 NM_001003793 NA Approved uc003cel.3 Q6XE24 OTTHUMG00000155699 ENST00000452462.1:c.308-1TTTTGTGTTTTCACAGGTTATGG>- chr3.hg19:g.29628589_29628611delTTTTGTGTTTTCACAGGTTATGG 0 5 ref NA False 39 39 PASS 1 PASS ref->het 0 NA 174,184 4,4 9,8 2 2 A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23 True hg19 CCDS54558.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RBMS3-008 NOVEL basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000341303.1 PASS NA None 152 Frame_Shift_Del True + TTTTGTGTTTTCACAGGTTATGG ENST00000452462.1 MBD4 8930 __UNKNOWN__ __UNKNOWN__ 3 129150057 129150076 __UNKNOWN__ 3'UTR DEL TTTAGAACTATTTTTCATCT TTTAGAACTATTTTTCATCT - rs534921751 LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:129150057_129150076delTTTAGAACTATTTTTCATCT ENST00000249910.1 - 0 2186_2205 MBD4_ENST00000429544.2_3'UTR NM_003925.1 NP_003916.1 O95243 MBD4_HUMAN methyl-CpG binding domain protein 4 NA NA NA NA base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314) chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696) NA NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1) 22 ttattgatagtttagaactatttttcatcttctgattata 0.314 NA NA NA NA Base excision repair (BER), DNA glycosylases NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 54 58.08 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA AF072250 CCDS3058.1, CCDS63766.1, CCDS63767.1, CCDS63768.1, CCDS63769.1 3q21.3 2004-03-02 ENSG00000129071 ENSG00000129071 8930 6919 protein-coding gene gene with protein product 603574 NA 9774669, 10097147 Standard NM_003925 NM_003925 NA Approved MED1 uc003emh.2 O95243 OTTHUMG00000159463 ENST00000249910.1:c.*287AGATGAAAAATAGTTCTAAA>- chr3.hg19:g.129150057_129150076delTTTAGAACTATTTTTCATCT 0 3 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 27,28 16,17 13,13 1 1 B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09 True hg19 CCDS3058.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MBD4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000355529.1 PASS NA None 54 True - TTTAGAACTATTTTTCATCT ENST00000249910.1 RASA1 5921 __UNKNOWN__ __UNKNOWN__ 5 86686716 86686735 __UNKNOWN__ 3'UTR DEL TGTTCTGCATGGATTCAGCA TGTTCTGCATGGATTCAGCA - rs571819598 LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:86686716_86686735delTGTTCTGCATGGATTCAGCA ENST00000274376.6 + 0 3724_3743 RASA1_ENST00000512763.1_3'UTR|RASA1_ENST00000456692.2_3'UTR|RASA1_ENST00000506290.1_3'UTR NM_002890.2 NP_002881.1 P20936 RASA1_HUMAN RAS p21 protein activator (GTPase activating protein) 1 NA NA NA NA blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570) cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726) glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102) NA NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1) 48 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) TTCGCCCCAGTGTTCTGCATGGATTCAGCATGTCCAACAT 0.409 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 115 100.76 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA CCDS34200.1, CCDS47243.1 5q13 2013-02-14 ENSG00000145715 ENSG00000145715 5921 "Pleckstrin homology (PH) domain containing", "SH2 domain containing" 9871 protein-coding gene gene with protein product "capillary malformation-arteriovenous malformation" 139150 RASA NA 15917201 Standard NM_002890 NM_022650 NA Approved GAP, CM-AVM, p120GAP, p120RASGAP uc003kiw.3 P20936 OTTHUMG00000162605 ENST00000274376.6:c.*35TGTTCTGCATGGATTCAGCA>- chr5.hg19:g.86686716_86686735delTGTTCTGCATGGATTCAGCA 0 3 ref NA False 59 59 PASS 1 PASS ref->het 0 NA 110,114 5,5 9,6 1 1 B2R6W3|Q9UDI1 True hg19 CCDS34200.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RASA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000369729.1 PASS NA None 115 True + TGTTCTGCATGGATTCAGCA ENST00000274376.6 PDE6A 5145 __UNKNOWN__ __UNKNOWN__ 5 149324157 149324175 __UNKNOWN__ Frame_Shift_Del DEL TGGAGGTTGTAGTACTGTT TGGAGGTTGTAGTACTGTT - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:149324157_149324175delTGGAGGTTGTAGTACTGTT ENST00000255266.5 - 1 181_199 c.62_80delAACAGTACTACAACCTCCA c.(61-81)aaacagtactacaacctccacfs p.KQYYNLH21fs NM_000440.2 NP_000431.2 P16499 PDE6A_HUMAN phosphodiesterase 6A, cGMP-specific, rod, alpha 21 NA NA NA cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601) photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886) 3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872) NA breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2) 44 KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147) Caffeine(DB00201) GGCCCGGTAGTGGAGGTTGTAGTACTGTTTGGCAAAGCC 0.575 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 122 111.26 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.26 NA CCDS4299.1 5q31.2-q34 2013-02-14 ENSG00000132915 ENSG00000132915 5145 3.1.4.17 "Phosphodiesterases" 8785 protein-coding gene gene with protein product 180071 PDEA NA 2155175 Standard NM_000440 NA Approved RP43 uc003lrg.4 P16499 OTTHUMG00000130047 ENST00000255266.5:c.62_80delAACAGTACTACAACCTCCA chr5.hg19:g.149324157_149324175delTGGAGGTTGTAGTACTGTT ENSP00000255266:p.Lys21fs 0 4 ref NA False 61 61 PASS 1 PASS ref->het 0 NA 69,72 28,28 32,29 2 2 Q0P638 True hg19 CCDS4299.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PDE6A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252326.2 PASS NA None 122 True - TGGAGGTTGTAGTACTGTT ENST00000255266.5 NPM1 4869 __UNKNOWN__ __UNKNOWN__ 5 170827994 170828000 __UNKNOWN__ Intron DEL AGAATCT AGAATCT - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:170827994_170828000delAGAATCT ENST00000296930.5 + 8 970 NPM1_ENST00000517671.1_Intron|NPM1_ENST00000351986.6_Intron|NPM1_ENST00000393820.2_Intron NM_002520.6 NP_002511.1 P06748 NPM_HUMAN nucleophosmin (nucleolar phosphoprotein B23, numatrin) NA NA NA NA cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032) centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616) histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082) NA NPM1/ALK(632) central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1) 4269 Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963) Medulloblastoma(196;0.0208)|all_neural(177;0.0416) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) CTACTGTGGAAGAATCTAGTGTGTCTG 0.406 NA NA "T, F " "ALK, RARA, MLF1" "NHL, APL, AML" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA Dom yes NA 5 5q35 4869 "nucleophosmin (nucleolar phosphoprotein B23, numatrin)" NA L 0 NA NA NA NA NA NA NA 202 191.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.02 NA M26697 CCDS4376.1, CCDS4377.1, CCDS43399.1 5q35.1 2014-09-17 ENSG00000181163 ENSG00000181163 4869 7910 protein-coding gene gene with protein product "nucleolar phosphoprotein B23", "numatrin", "nucleophosmin/nucleoplasmin family, member 1" 164040 NA 8471164, 8122112 Standard NM_002520 NM_002520 NA Approved B23, NPM uc003mbi.3 P06748 OTTHUMG00000130465 ENST00000296930.5:c.669+65AGAATCT>- chr5.hg19:g.170827994_170828000delAGAATCT 0 4 ref NA False 90 90 PASS 1 PASS ref->het 0 NA 182,198 10,10 17,16 1 1 A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7 True hg19 CCDS4376.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NPM1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252858.2 PASS NA None 202 True + AGAATCT ENST00000296930.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ 7 23872403 23872420 __UNKNOWN__ IGR DEL TTCACCTTCCACCACAAT TTCACCTTCCACCACAAT - rs139132494|rs2214236 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:23872403_23872420delTTCACCTTCCACCACAAT NA STK31 (271 upstream) : AC009508.1 (58902 downstream) NA NA NA NA NA NA ttactcttccttcaccttccaccacaattgtgaggcct 0.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 78 71.89 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.32 NA NA NA NA NA NA chr7.hg19:g.23872403_23872420delTTCACCTTCCACCACAAT 0 3 ref NA False 151 97 PASS 1 PASS ref->het 0 NA 30,34 36,39 14,18 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 78 True TTCACCTTCCACCACAAT KMT2E 55904 __UNKNOWN__ __UNKNOWN__ 7 104748379 104748386 __UNKNOWN__ Intron DEL AATTTAAC AATTTAAC - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:104748379_104748386delAATTTAAC ENST00000311117.3 + 22 4013 KMT2E_ENST00000257745.4_Intron|KMT2E_ENST00000334914.7_Intron|KMT2E_ENST00000334877.4_Intron NM_182931.2 NP_891847.1 Q8IZD2 KMT2E_HUMAN lysine (K)-specific methyltransferase 2E NA NA NA NA cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886) enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270) NA NA AAAGGTTACAAATTTAACAATTTATAGT 0.322 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 99 91.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.34 NA AF067804 CCDS34723.1 7q22.1 2013-05-09 2013-05-09 2013-05-09 ENSG00000005483 ENSG00000005483 55904 "Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type" 18541 protein-coding gene gene with protein product 608444 "myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)" MLL5 NA 9218106, 7672722 Standard XM_005250493 NA Approved HDCMC04P Q8IZD2 OTTHUMG00000157403 ENST00000311117.3:c.3468+7AATTTAAC>- chr7.hg19:g.104748379_104748386delAATTTAAC 0 4 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 71,74 4,4 24,21 1 1 B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7 True hg19 CCDS34723.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KMT2E-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000348697.1 PASS NA None 99 True + AATTTAAC ENST00000311117.3 DNAJB9 4189 __UNKNOWN__ __UNKNOWN__ 7 108214567 108214572 __UNKNOWN__ Intron DEL TGTGTG TGTGTG - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:108214567_108214572delTGTGTG ENST00000465725.1 + 2 229 DNAJB9_ENST00000249356.3_3'UTR Q9UBS3 DNJB9_HUMAN DnaJ (Hsp40) homolog, subfamily B, member 9 NA NA NA NA activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433) cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730) misfolded protein binding (GO:0051787) NA central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1) 13 TTTATGTGTTTGTGTGTGTGTAGTTT 0.34 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 131 115.6 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.02 NA AB026908 CCDS5752.1 7q31 2011-09-02 ENSG00000128590 ENSG00000128590 4189 "Heat shock proteins / DNAJ (HSP40)" 6968 protein-coding gene gene with protein product 602634 MDG1 NA 9533036, 11147971 Standard NM_012328 NA Approved uc003vfn.3 Q9UBS3 OTTHUMG00000154866 ENST00000465725.1:c.230-519TGTGTG>- chr7.hg19:g.108214567_108214572delTGTGTG 2 4 ref NA False 38 38 PASS 5 PASS ref->het 0 NA 112,116 4,4 20,20 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DNAJB9-004 PUTATIVE basic|exp_conf processed_transcript NA protein_coding OTTHUMT00000337417.1 PASS NA None 131 True + TG ENST00000465725.1 JAK2 3717 __UNKNOWN__ __UNKNOWN__ 9 5111225 5111225 __UNKNOWN__ Intron DEL C C - rs113238356|rs112178036 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:5111225delC ENST00000381652.3 + 23 3553 JAK2_ENST00000544510.1_Intron|JAK2_ENST00000539801.1_Intron NM_004972.3 NP_004963.1 O60674 JAK2_HUMAN Janus kinase 2 NA NA NA NA actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506) caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634) ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169) NA BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18) breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1) 32998 all_hematologic(13;0.137) Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147) GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133) Ruxolitinib(DB08877)|Tofacitinib(DB08895) GCAGCTAGCGCGGGCCTATTC 0.652 NA 1 "T, Mis, O" "ETV6, PCM1, BCR" "ALL, AML, MPD, CML" NA NA Polycythemia Vera, Familial NA NA NA -|C|-|insertion 1544 0.308307 0.4047 0.3631 5008 , , NA 17296 0.2639 NA 0.2336 False NA ,,, NA NA NA 2504 0.2618 NA NA NA PASS NA Dom yes NA 9 9p24 3717 Janus kinase 2 NA L 0 NA NA NA NA NA NA NA 46 44.41 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.33 Familial Cancer Database NA CCDS6457.1 9p24 2014-09-17 2009-04-23 ENSG00000096968 ENSG00000096968 3717 2.7.10.1 "SH2 domain containing" 6192 protein-coding gene gene with protein product 147796 NA 1848670 Standard NM_004972 NA Approved JTK10 uc003ziw.3 O60674 OTTHUMG00000019490 ENST00000381652.3:c.3060-11779C>- chr9.hg19:g.5111225delC 0 4 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 3,3 36,37 5,4 1 1 O14636|O75297 True hg19 CCDS6457.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA JAK2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000051609.1 PASS NA None 46 True + C ENST00000381652.3 UBAP2 55833 __UNKNOWN__ __UNKNOWN__ 9 34016243 34016244 __UNKNOWN__ Intron INS - - GGG rs141358835|rs371760116 LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:34016243_34016244insGGG ENST00000379238.1 - 2 217 UBAP2_ENST00000480885.1_Intron|UBAP2_ENST00000360802.1_Intron|UBAP2_ENST00000539807.1_Intron|UBAP2_ENST00000379239.4_Intron|UBAP2_ENST00000418786.2_Intron|UBAP2_ENST00000449054.1_Intron ubiquitin associated protein 2 NA NA NA NA NA endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1) 32 LUSC - Lung squamous cell carcinoma(29;0.00575) GBM - Glioblastoma multiforme(74;0.168) aaggggaggaagaggaggagga 0.554 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 36 33.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.67 NA AB040924 CCDS6547.1, CCDS75828.1 9p11.2 2008-02-05 ENSG00000137073 ENSG00000137073 55833 14185 protein-coding gene gene with protein product NA NA 8871400 Standard NM_018449 NM_018449 NA Approved KIAA1491, bA176F3.5, FLJ22435 uc003ztq.1 Q5T6F2 OTTHUMG00000000427 ENST00000379238.1:c.99+803->CCC chr9.hg19:g.34016243_34016244insGGG 4 3 ref NA False 60 59 PASS 1 PASS ref->het 0 NA 3,4 26,27 7,7 1 1 True hg19 CCDS6547.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UBAP2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000001071.1 PASS NA None 36 True - G ENST00000379238.1 EXOSC3 51010 __UNKNOWN__ __UNKNOWN__ 9 37782084 37782086 __UNKNOWN__ In_Frame_Del DEL TTC TTC - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:37782084_37782086delTTC ENST00000327304.5 - 3 535_537 c.523_525delGAA c.(523-525)gaadel p.E175del EXOSC3_ENST00000490516.1_Intron|EXOSC3_ENST00000396521.3_Intron|RP11-613M10.9_ENST00000540557.1_Intron NM_016042.3 NP_057126.2 Q9NQT5 EXOS3_HUMAN exosome component 3 175 NA NA NA CUT catabolic process (GO:0071034)|DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|isotype switching (GO:0045190)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of isotype switching (GO:0045830)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364) cytoplasm (GO:0005737)|cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327) 3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723) NA breast(2)|endometrium(1)|kidney(1) 4 GBM - Glioblastoma multiforme(29;0.00771)|Lung(182;0.221) CCATCTCTGGTTCCATGTCTTTA 0.424 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 45 45.61 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.54 NA BC002437 CCDS35016.1, CCDS43805.1 9p11 2009-01-20 ENSG00000107371 ENSG00000107371 51010 17944 protein-coding gene gene with protein product "exosome component Rrp40", "CGI-102 protein" 606489 NA 10810093, 11110791 Standard NM_016042 NM_016042 NA Approved hRrp40p, Rrp40p, RRP40, CGI-102, p10, hRrp-40 uc004aal.3 Q9NQT5 OTTHUMG00000019932 ENST00000327304.5:c.523_525delGAA chr9.hg19:g.37782084_37782086delTTC ENSP00000323046:p.Glu175del 0 2 ref NA False 116 87 PASS 1 PASS ref->het 0 NA 11,11 33,34 2,1 1 1 A8K0K6|Q5QP85|Q9Y3A8 True hg19 CCDS35016.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EXOSC3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000052478.3 PASS NA None 45 True - TTC ENST00000327304.5 NFIL3 4783 __UNKNOWN__ __UNKNOWN__ 9 94171931 94171946 __UNKNOWN__ Frame_Shift_Del DEL ATGTCTTTTAGATGTC ATGTCTTTTAGATGTC - rs147892473 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:94171931_94171946delATGTCTTTTAGATGTC ENST00000297689.3 - 2 1465_1480 c.1071_1086delGACATCTAAAAGACAT c.(1069-1086)atgacatctaaaagacatfs p.MTSKRH357fs NM_005384.2 NP_005375.2 Q16649 NFIL3_HUMAN nuclear factor, interleukin 3 regulated 357 Necessary for transcriptional repression and sufficient for interaction with DR1. NA NA NA cellular response to interleukin-4 (GO:0071353)|circadian rhythm (GO:0007623)|immune response (GO:0006955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366) nucleus (GO:0005634) DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714) NA endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1) 16 CGAGTTCGAAATGTCTTTTAGATGTCATGTCAATAG 0.417 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(152;732 1832 10053 26981 51762) PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 81 84.31 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.24 NA X64318 CCDS6690.1 9q22 2013-01-10 ENSG00000165030 ENSG00000165030 4783 "basic leucine zipper proteins" 7787 protein-coding gene gene with protein product 605327 IL3BP1 NA 7565758, 1620116 Standard NM_005384 NM_005384 NA Approved E4BP4, NFIL3A, NF-IL3A uc004arh.3 Q16649 OTTHUMG00000020209 ENST00000297689.3:c.1071_1086delGACATCTAAAAGACAT chr9.hg19:g.94171931_94171946delATGTCTTTTAGATGTC ENSP00000297689:p.Met357fs 0 3 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 78,80 3,3 9,9 1 1 B2R9Y8|Q14211|Q6FGQ8|Q96HS0 True hg19 CCDS6690.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NFIL3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000053038.2 PASS NA None 81 True - ATGTCTTTTAGATGTC ENST00000297689.3 ARID5B 84159 __UNKNOWN__ __UNKNOWN__ 10 63816865 63816865 __UNKNOWN__ Intron DEL C C - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:63816865delC ENST00000279873.7 + 6 1256 ARID5B_ENST00000309334.5_Intron NM_032199.2 NP_115575.1 Q14865 ARI5B_HUMAN AT rich interactive domain 5B (MRF1-like) NA NA NA NA adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212) NA NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 44 Prostate(12;0.016)|all_hematologic(501;0.215) GGTATATTTTCCCTTTTCCAG 0.458 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 86 78.66 NA NA NA NA NA 35 35 35 NA NA NA NA 10 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 63816865 NA 2203 4300 6503 SO:0001627 intron_variant 0.63 NA M73837 CCDS31208.1, CCDS58082.1 10q11.22 2013-02-07 ENSG00000150347 ENSG00000150347 84159 "-" 17362 protein-coding gene gene with protein product 608538 NA 11483573, 11478881 Standard XM_084482 NM_032199 NA Approved FLJ21150, MRF2 uc001jlt.2 Q14865 OTTHUMG00000018298 ENST00000279873.7:c.847-11C>- chr10.hg19:g.63816865delC 2 5 ref NA False 95 90 PASS 3 PASS ref->het 0 NA 42,42 36,37 7,6 1 1 B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786 True hg19 CCDS31208.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARID5B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000048233.1 PASS NA None 86 True + C ENST00000279873.7 DNTT 1791 __UNKNOWN__ __UNKNOWN__ 10 98079172 98079191 __UNKNOWN__ Intron DEL CAGGGCAAACGAAGGGCTTG CAGGGCAAACGAAGGGCTTG - rs565368944 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:98079172_98079191delCAGGGCAAACGAAGGGCTTG ENST00000371174.2 + 3 609 DNTT_ENST00000419175.1_Intron P04053 TDT_HUMAN DNA nucleotidylexotransferase NA NA NA NA DNA modification (GO:0006304) cytoplasm (GO:0005737)|nucleus (GO:0005634) DNA binding (GO:0003677)|DNA nucleotidylexotransferase activity (GO:0003912)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872) NA NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1) 27 Colorectal(252;0.0815)|all_hematologic(284;0.224) Epithelial(162;7.97e-08)|all cancers(201;1.89e-06) CATCAACACCCAGGGCAAACGAAGGGCTTGCAGCTTCTTT 0.436 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 78 76.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA AB046378 CCDS7447.1 10q23-q24 2013-05-21 2013-05-21 ENSG00000107447 ENSG00000107447 1791 2.7.7.31 "DNA polymerases" 2983 protein-coding gene gene with protein product "Terminal deoxynucleotidyltransferase" 187410 "deoxynucleotidyltransferase, terminal" NA Standard NM_004088 NM_004088 NA Approved TDT uc001kmf.3 P04053 OTTHUMG00000018832 ENST00000371174.2:c.507+25CAGGGCAAACGAAGGGCTTG>- chr10.hg19:g.98079172_98079191delCAGGGCAAACGAAGGGCTTG 0 4 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 58,58 11,11 10,10 1 1 Q53FH1|Q5W103|Q96E50 True hg19 CCDS7447.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DNTT-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000049607.1 PASS NA None 78 True + CAGGGCAAACGAAGGGCTTG ENST00000371174.2 DNMBP 23268 __UNKNOWN__ __UNKNOWN__ 10 101714994 101715001 __UNKNOWN__ Frame_Shift_Del DEL TTCAAACT TTCAAACT - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:101714994_101715001delTTCAAACT ENST00000324109.4 - 4 2321_2328 c.2230_2237delAGTTTGAA c.(2230-2238)agtttgaatfs p.SLN744fs DNMBP_ENST00000342239.3_Frame_Shift_Del_p.SLN744fs|DNMBP-AS1_ENST00000434409.1_RNA NM_015221.2 NP_056036.1 Q6XZF7 DNMBP_HUMAN dynamin binding protein 744 NA NA NA intracellular signal transduction (GO:0035556) cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202) Rho guanyl-nucleotide exchange factor activity (GO:0005089) NA central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1) 61 Colorectal(252;0.234) Epithelial(162;2.94e-10)|all cancers(201;3.15e-08) GAGTTCCATATTCAAACTTTCAATGTTA 0.423 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 75 77.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 NA AL833283 CCDS7485.1 10q24.31 2012-07-24 ENSG00000107554 ENSG00000107554 23268 "Rho guanine nucleotide exchange factors" 30373 protein-coding gene gene with protein product "scaffold protein TUBA" 611282 NA 10231032, 14506234 Standard NM_015221 NM_015221 NA Approved KIAA1010, Tuba, ARHGEF36 uc001kqj.2 Q6XZF7 OTTHUMG00000018897 ENST00000324109.4:c.2230_2237delAGTTTGAA chr10.hg19:g.101714994_101715001delTTCAAACT ENSP00000315659:p.Ser744fs 0 3 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 78,79 3,3 10,10 1 1 Q8IVY3|Q9Y2L3 True hg19 CCDS7485.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DNMBP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000049832.2 PASS NA None 75 True - TTCAAACT ENST00000324109.4 SLC4A8 9498 __UNKNOWN__ __UNKNOWN__ 12 51845871 51845893 __UNKNOWN__ Intron DEL GGCTAGAGCAGACCTTTCTCTTT GGCTAGAGCAGACCTTTCTCTTT - rs202005995 LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:51845871_51845893delGGCTAGAGCAGACCTTTCTCTTT ENST00000453097.2 + 4 494 SLC4A8_ENST00000514353.3_Intron|SLC4A8_ENST00000358657.3_Intron|SLC4A8_ENST00000394856.1_Intron|SLC4A8_ENST00000535225.2_Intron NM_001039960.2|NM_001258401.2 NP_001035049.1|NP_001245330.1 solute carrier family 4, sodium bicarbonate cotransporter, member 8 NA NA NA NA NA NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5) 55 BRCA - Breast invasive adenocarcinoma(357;0.15) CTAAGTGTGAGGCTAGAGCAGACCTTTCTCTTTGGTTGATTTC 0.404 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 132 122.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA AB018282 CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1 12q13.13 2013-05-22 ENSG00000050438 ENSG00000050438 9498 "Solute carriers" 11034 protein-coding gene gene with protein product 605024 NA 11133997 Standard NM_004858 NM_001039960 NA Approved NBC3 uc001rys.2 Q2Y0W8 OTTHUMG00000169489 ENST00000453097.2:c.278-15GGCTAGAGCAGACCTTTCTCTTT>- chr12.hg19:g.51845871_51845893delGGCTAGAGCAGACCTTTCTCTTT 0 4 ref NA False 62 62 PASS 1 PASS ref->het 0 NA 119,121 29,30 13,13 1 1 True hg19 CCDS44890.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC4A8-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000404356.1 PASS NA None 132 True + GGCTAGAGCAGACCTTTCTCTTT ENST00000453097.2 RAB5B 5869 __UNKNOWN__ __UNKNOWN__ 12 56374516 56374539 __UNKNOWN__ Intron DEL TTCTGAATATTCTCGAAAGATTTC TTCTGAATATTCTCGAAAGATTTC - rs185622977 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:56374516_56374539delTTCTGAATATTCTCGAAAGATTTC ENST00000448789.2 + 2 39 RAB5B_ENST00000360299.5_Intron|RAB5B_ENST00000553116.1_Intron NM_001252037.1 NP_001238966.1 P61020 RAB5B_HUMAN RAB5B, member RAS oncogene family NA NA NA NA antigen processing and presentation (GO:0019882)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|plasma membrane to endosome transport (GO:0048227)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264) endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886) GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924) NA endometrium(1)|large_intestine(1)|liver(2)|lung(4)|upper_aerodigestive_tract(1) 9 UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.235) TTTCATCCAGTTCTGAATATTCTCGAAAGATTTCTCATCCGTGA 0.496 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 157 156.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA CCDS8900.1, CCDS58244.1 12q13 2008-07-30 5869 "RAB, member RAS oncogene" 9784 protein-coding gene gene with protein product 179514 NA 1541686, 10403367 Standard NM_001252037 NA Approved uc001siw.3 P61020 ENST00000448789.2:c.-92-6114TTCTGAATATTCTCGAAAGATTTC>- chr12.hg19:g.56374516_56374539delTTCTGAATATTCTCGAAAGATTTC 0 4 ref NA False 79 79 PASS 1 PASS ref->het 0 NA 128,130 25,25 30,30 1 1 A8K982|B4DKD7|P35239|P35277|Q6PIK9|Q86TH0|Q8IXL2 True hg19 CCDS58244.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RAB5B-003 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000405402.1 PASS NA None 157 True + TTCTGAATATTCTCGAAAGATTTC ENST00000448789.2 TEP1 7011 __UNKNOWN__ __UNKNOWN__ 14 20852855 20852865 __UNKNOWN__ Frame_Shift_Del DEL CAGGCATCTGG CAGGCATCTGG - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:20852855_20852865delCAGGCATCTGG ENST00000556935.1 - 20 2830_2840 c.2791_2801delCCAGATGCCTG c.(2791-2802)ccagatgcctggfs p.PDAW931fs TEP1_ENST00000262715.5_Frame_Shift_Del_p.PDAW1039fs Q99973 TEP1_HUMAN telomerase-associated protein 1 1039 NA NA NA RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722) chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697) ATP binding (GO:0005524)|RNA binding (GO:0003723) NA NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1) 96 all_cancers(95;0.00123) all_lung(585;0.235) Epithelial(56;7.42e-08)|all cancers(55;6.46e-07) GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233) GTCAGATTTCCAGGCATCTGGCACAGAGCTG 0.526 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 87 88.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.29 NA CCDS9548.1 14q11.2 2013-01-10 ENSG00000129566 ENSG00000129566 7011 "WD repeat domain containing" 11726 protein-coding gene gene with protein product "TROVE domain family, member 1" 601686 NA 9403057 Standard NM_007110 NM_007110 NA Approved TP1, TLP1, VAULT2, p240, TROVE1 uc001vxe.3 Q99973 OTTHUMG00000029515 ENST00000556935.1:c.2791_2801delCCAGATGCCTG chr14.hg19:g.20852855_20852865delCAGGCATCTGG ENSP00000452574:p.Pro931fs 0 3 ref NA False 91 90 PASS 1 PASS ref->het 0 NA 46,47 29,29 15,15 2 2 A0AUV9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TEP1-003 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000410689.1 PASS NA None 87 True - CAGGCATCTGG ENST00000556935.1 LRRC16B 90668 __UNKNOWN__ __UNKNOWN__ 14 24538688 24538715 __UNKNOWN__ 3'UTR DEL CCAGGGCCCCCTGCCAGCCCCTGTCCTA CCAGGGCCCCCTGCCAGCCCCTGTCCTA - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:24538688_24538715delCCAGGGCCCCCTGCCAGCCCCTGTCCTA ENST00000342740.5 + 0 4348_4375 LRRC16B_ENST00000334420.7_3'UTR NM_138360.3 NP_612369.3 Q8ND23 LR16B_HUMAN leucine rich repeat containing 16B NA NA NA NA cytoplasm (GO:0005737) NA breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4) 52 GBM - Glioblastoma multiforme(265;0.019) CCCCCAGTCCCCAGGGCCCCCTGCCAGCCCCTGTCCTACAGGGGCAAG 0.645 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 242 232.11 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.78 NA AI017934 CCDS32054.1 14q11.2-q12 2010-09-10 2008-02-12 2008-02-12 90668 20272 protein-coding gene gene with protein product 614716 "chromosome 14 open reading frame 121" C14orf121 NA 19846667 Standard NM_138360 NM_138360 NA Approved BC008134, crml-1, CARMIL3 uc001wlj.2 Q8ND23 ENST00000342740.5:c.*102CCAGGGCCCCCTGCCAGCCCCTGTCCTA>- chr14.hg19:g.24538688_24538715delCCAGGGCCCCCTGCCAGCCCCTGTCCTA 0 4 ref NA False 50 50 PASS 1 PASS ref->het 0 NA 210,213 15,15 41,39 1 1 Q8TEF7|Q96HS9 True hg19 CCDS32054.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LRRC16B-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000416527.1 PASS NA None 242 True + CCAGGGCCCCCTGCCAGCCCCTGTCCTA ENST00000342740.5 MLH3 27030 __UNKNOWN__ __UNKNOWN__ 14 75503494 75503498 __UNKNOWN__ Intron DEL ATCCA ATCCA - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:75503494_75503498delATCCA ENST00000556740.1 - 5 3679 MLH3_ENST00000355774.2_Intron|MLH3_ENST00000238662.7_Intron|MLH3_ENST00000556257.1_Intron|MLH3_ENST00000544985.1_Intron|MLH3_ENST00000380968.2_Intron Q9UHC1 MLH3_HUMAN mutL homolog 3 NA NA NA NA ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130) chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795) ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697) NA breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 44 BRCA - Breast invasive adenocarcinoma(234;0.00688) ctttccccatatccaatccatcacc 0.468 NA NA NA NA Mismatch excision repair (MMR) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 134 151.01 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA AF195657 CCDS9837.1, CCDS32123.1 14q24.3 2014-09-17 2013-09-12 ENSG00000119684 27030 7128 protein-coding gene gene with protein product 604395 "mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)" NA 10615123 Standard NM_014381 XR_245681 NA Approved uc001xrd.1 Q9UHC1 ENST00000556740.1:c.3643+1544TGGAT>- chr14.hg19:g.75503499_75503503delATCCA 1 2 ref NA False 54 54 PASS 2 PASS ref->het 0 NA 114,117 4,4 18,16 1 1 P49751|Q56DK9|Q9P292|Q9UHC0 True hg19 CCDS32123.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MLH3-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000415006.1 PASS NA None 134 True - ATCCA ENST00000556740.1 ZFAND6 54469 __UNKNOWN__ __UNKNOWN__ 15 80365497 80365514 __UNKNOWN__ Intron DEL ATTTTTAATATGCTTATA ATTTTTAATATGCTTATA - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:80365497_80365514delATTTTTAATATGCTTATA ENST00000261749.6 + 1 242 ZFAND6_ENST00000558688.1_Intron|ZFAND6_ENST00000558494.1_Intron|ZFAND6_ENST00000559775.1_Intron|ZFAND6_ENST00000561060.1_Intron|ZFAND6_ENST00000559835.1_Intron|ZFAND6_ENST00000559157.1_Intron NM_001242913.1|NM_001242914.1|NM_019006.3 NP_001229842.1|NP_001229843.1|NP_061879.2 Q6FIF0 ZFAN6_HUMAN zinc finger, AN1-type domain 6 NA NA NA NA apoptotic process (GO:0006915)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|protein targeting to peroxisome (GO:0006625)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122) cytoplasm (GO:0005737) DNA binding (GO:0003677)|polyubiquitin binding (GO:0031593)|zinc ion binding (GO:0008270) NA cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1) 11 ATATGTTGACATTTTTAATATGCTTATAATTTTTAATA 0.275 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 99 107.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.01 NA BC005283 CCDS10313.1, CCDS58395.1 15q24.3 2013-01-09 2006-07-07 2006-07-07 ENSG00000086666 ENSG00000086666 54469 "Zinc fingers, AN1-type domain containing" 30164 protein-coding gene gene with protein product "protein associated with PRK1" 610183 "zinc finger, A20 domain containing 3" ZA20D3 NA 11054541 Standard NM_019006 NM_019006 NA Approved ZFAND5B, AWP1 uc002bff.2 Q6FIF0 OTTHUMG00000144169 ENST00000261749.6:c.-181+13346ATTTTTAATATGCTTATA>- chr15.hg19:g.80365497_80365514delATTTTTAATATGCTTATA 0 5 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 125,130 4,4 16,16 2 2 D3DW92|D3DW94|O95792|Q9BQF7|Q9GZY3 True hg19 CCDS10313.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZFAND6-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000291368.1 PASS NA None 99 True + ATTTTTAATATGCTTATA ENST00000261749.6 TICRR 90381 __UNKNOWN__ __UNKNOWN__ 15 90127065 90127066 __UNKNOWN__ Intron INS - - A rs397964351|rs60855382 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:90127065_90127066insA ENST00000268138.7 + 3 1039 RP11-429B14.1_ENST00000559041.1_RNA|TICRR_ENST00000560985.1_Intron Q7Z2Z1 TICRR_HUMAN TOPBP1-interacting checkpoint and replication regulator NA NA NA NA cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212) nucleus (GO:0005634) chromatin binding (GO:0003682) NA NA ctaaaggcatgagccaccacac 0.525 NA NA NA NA NA NA NA |||unknown(NO_COVERAGE) 1402 0.279952 0.084 0.2867 5008 , , NA 18209 0.3968 NA 0.332 False NA ,,, NA NA NA 2504 0.3661 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 32 27.91 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.89 NA AK123612 CCDS10352.2 15q26.1 2012-07-11 2012-07-11 2012-07-11 ENSG00000140534 ENSG00000140534 90381 28704 protein-coding gene gene with protein product "TOPBP1-interacting replication-stimulating protein", "SLD3 homolog (S. cerevisiae)" 613298 "chromosome 15 open reading frame 42" C15orf42 NA 20116089, 20080954 Standard NM_152259 NM_152259 NA Approved MGC45866, FLJ41618, Treslin, SLD3 uc002boe.3 Q7Z2Z1 OTTHUMG00000149648 ENST00000268138.7:c.935-451->A chr15.hg19:g.90127066_90127066dupA 2 2 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 2,2 26,32 4,3 1 1 B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55 True hg19 CCDS10352.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TICRR-001 KNOWN NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000312856.1 PASS NA None 32 True + A ENST00000268138.7 ABCA17P 650655 __UNKNOWN__ __UNKNOWN__ 16 2475032 2475045 __UNKNOWN__ RNA DEL GCGACCTCAGCTGG GCGACCTCAGCTGG - rs562655144 LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:2475032_2475045delGCGACCTCAGCTGG ENST00000469908.1 + 0 2992_3005 NR_003574.1 ATP-binding cassette, sub-family A (ABC1), member 17, pseudogene NA NA NA NA NA NA CTGCTGGGCCGCGACCTCAGCTGGGCGAAGTTGA 0.565 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 70 64.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.41 NA DQ266102 16p13.3 2012-03-14 2010-03-12 ENSG00000238098 ENSG00000238098 650655 "ATP binding cassette transporters / subfamily A" 32972 pseudogene pseudogene NA NA 16968533 Standard NR_003574 NR_003574 NA Approved uc002cqc.1 OTTHUMG00000154348 ENST00000469908.1: chr16.hg19:g.2475032_2475045delGCGACCTCAGCTGG 0 4 ref NA False 64 64 PASS 1 PASS ref->het 0 NA 40,41 24,25 9,7 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ABCA17P-002 KNOWN basic processed_transcript NA pseudogene OTTHUMT00000334904.1 PASS NA None 70 True + GCGACCTCAGCTGG ENST00000469908.1 ZFHX3 463 __UNKNOWN__ __UNKNOWN__ 16 72821020 72821039 __UNKNOWN__ 3'UTR DEL TTTGTATTTAAATTCATTTG TTTGTATTTAAATTCATTTG - rs367868112 LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:72821020_72821039delTTTGTATTTAAATTCATTTG ENST00000268489.5 - 0 11808_11827 RP5-991G20.1_ENST00000563328.2_RNA|ZFHX3_ENST00000397992.5_3'UTR NM_006885.3 NP_008816.3 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 NA NA NA NA brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366) mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667) enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270) NA NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11) 153 Ovarian(137;0.13) GTTATTAATTTTTGTATTTAAATTCATTTGTTTGTATTGT 0.341 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 120 139.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 4.48 NA D10250 CCDS10908.1, CCDS54035.1 16q22.3 2012-03-09 2007-08-09 2007-08-09 ENSG00000140836 ENSG00000140836 463 "Zinc fingers, C2H2-type", "Homeoboxes / ZF class" 777 protein-coding gene gene with protein product 104155 "AT-binding transcription factor 1" ATBF1 NA 1719379, 7592926 Standard NM_006885 NM_006885 NA Approved ZNF927 uc002fck.3 Q15911 OTTHUMG00000137599 ENST00000268489.5:c.*43CAAATGAATTTAAATACAAA>- chr16.hg19:g.72821020_72821039delTTTGTATTTAAATTCATTTG 0 6 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 160,165 4,4 27,28 2 2 D3DWS8|O15101|Q13719 True hg19 CCDS10908.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZFHX3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000269008.1 PASS NA None 120 True - TTTGTATTTAAATTCATTTG ENST00000268489.5 RP11-281J9.2 0 __UNKNOWN__ __UNKNOWN__ 16 78083418 78083420 __UNKNOWN__ RNA DEL GCA GCA - rs12924914|rs57738729|rs78500520|rs75368265 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:78083418_78083420delGCA ENST00000563114.1 - 0 41 NA NA NA NA NA NA TGCTGCTGCTGCAGGAGGCTCCA 0.517 NA NA NA NA NA NA NA 2289 0.457069 0.236 0.5216 5008 , , NA 21657 0.506 NA 0.5596 False NA ,,, NA NA NA 2504 0.5542 NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 18 16.27 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA ENST00000563114.1: chr16.hg19:g.78083418_78083420delGCA 0 4 ref NA False 41 40 PASS 1 PASS ref->hom 0 NA 0,0 17,18 1,1 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-281J9.2-001 KNOWN basic antisense NA antisense OTTHUMT00000434014.1 PASS NA None 18 True - GCA ENST00000563114.1 ZNF433 163059 __UNKNOWN__ __UNKNOWN__ 19 12125551 12125558 __UNKNOWN__ 3'UTR DEL TTTATTTA TTTATTTA - rs373160125 LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:12125551_12125558delTTTATTTA ENST00000419886.2 - 0 2310_2317 CTD-2006C1.2_ENST00000406892.2_RNA|CTD-2006C1.2_ENST00000476474.1_RNA|CTD-2006C1.2_ENST00000495324.1_RNA Q8N7K0 ZN433_HUMAN zinc finger protein 433 NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) NA breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1) 14 TGGAAGtctttttatttatttatttaat 0.486 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 143 127.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.72 NA AK098300 CCDS45983.1 19p13.13 2013-01-08 ENSG00000197647 ENSG00000197647 163059 "Zinc fingers, C2H2-type", "-" 20811 protein-coding gene gene with protein product NA NA Standard NM_152602 NM_001080411 NA Approved FLJ40981 uc002msy.1 Q8N7K0 OTTHUMG00000156427 ENST00000419886.2:c.*109TAAATAAA>- chr19.hg19:g.12125559_12125566delTTTATTTA 2 8 ref NA False 31 31 PASS 4 PASS ref->het 0 NA 118,128 3,5 26,27 1 1 Q86VX3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF433-001 KNOWN basic protein_coding NA protein_coding OTTHUMT00000344143.2 PASS NA None 143 True - TTTA ENST00000419886.2 TNPO2 30000 __UNKNOWN__ __UNKNOWN__ 19 12825729 12825735 __UNKNOWN__ Frame_Shift_Del DEL GGTCCTG GGTCCTG - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:12825729_12825735delGGTCCTG ENST00000450764.2 - 8 1527_1533 c.790_796delCAGGACC c.(790-798)caggaccatfs p.QDH264fs TNPO2_ENST00000588216.1_Frame_Shift_Del_p.QDH264fs|TNPO2_ENST00000356861.5_Frame_Shift_Del_p.QDH264fs|TNPO2_ENST00000589956.1_Intron|TNPO2_ENST00000441499.1_Frame_Shift_Del_p.QDH264fs|TNPO2_ENST00000425528.1_Frame_Shift_Del_p.QDH264fs|TNPO2_ENST00000592287.1_Frame_Shift_Del_p.QDH264fs O14787 TNPO2_HUMAN transportin 2 264 NA NA NA intracellular protein transport (GO:0006886) cytoplasm (GO:0005737)|nucleus (GO:0005634) nuclear localization sequence binding (GO:0008139) NA autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 28 TTCTCATCATGGTCCTGGGTCCTCTGC 0.657 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 184 185.93 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.24 NA AF019039 CCDS45991.1, CCDS45992.1 19p13.13 2009-01-12 2009-01-12 ENSG00000105576 30000 "Importins" 19998 protein-coding gene gene with protein product "importin 3", "karyopherin beta 2b" 603002 NA 9298975, 12384575 Standard NM_013433 NM_013433 NA Approved IPO3, KPNB2B, FLJ12155, TRN2 uc002muo.3 O14787 ENST00000450764.2:c.790_796delCAGGACC chr19.hg19:g.12825729_12825735delGGTCCTG ENSP00000397379:p.Gln264fs 0 3 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 175,178 4,4 29,28 2 2 O14655|Q6IN77 True hg19 CCDS45992.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNPO2-005 KNOWN alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000450783.1 PASS NA None 184 True - GGTCCTG ENST00000450764.2 PDE4C 5143 __UNKNOWN__ __UNKNOWN__ 19 18358986 18358995 __UNKNOWN__ 5'UTR DEL CTGCGGAGTC CTGCGGAGTC - LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:18358986_18358995delCTGCGGAGTC ENST00000594617.3 - 0 15_24 PDE4C_ENST00000355502.3_Intron NM_000923.4 NP_000914.2 Q08493 PDE4C_HUMAN phosphodiesterase 4C, cAMP-specific NA NA NA NA cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165) cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372) 3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872) NA breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 33 Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656) CTTACCACCACTGCGGAGTCCTGCCTGGGT 0.614 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 90 82.84 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 NA CCDS12373.1, CCDS42523.1, CCDS46016.1 19p13.11 2010-06-24 2010-06-24 ENSG00000105650 5143 3.1.4.17 "Phosphodiesterases" 8782 protein-coding gene gene with protein product "phosphodiesterase E1 dunce homolog (Drosophila)" 600128 "phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)" DPDE1 NA Standard NM_001098818 NA Approved uc002nik.4 Q08493 ENST00000594617.3:c.-224GACTCCGCAG>- chr19.hg19:g.18358986_18358995delCTGCGGAGTC 0 3 ref NA False 39 39 PASS 1 PASS ref->het 0 NA 71,71 15,15 9,9 1 1 B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6 True hg19 CCDS12373.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PDE4C-002 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000466298.3 PASS NA None 90 True - CTGCGGAGTC ENST00000594617.3 ZNF428 126299 __UNKNOWN__ __UNKNOWN__ 19 44111589 44111597 __UNKNOWN__ 3'UTR DEL TCTGAACCA TCTGAACCA - rs370373478|rs576765471 LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:44111589_44111597delTCTGAACCA ENST00000300811.3 - 0 1185_1193 SRRM5_ENST00000607544.1_Intron|SRRM5_ENST00000526798.1_Intron NM_182498.3 NP_872304.2 Q96B54 ZN428_HUMAN zinc finger protein 428 NA NA NA NA metal ion binding (GO:0046872) NA endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1) 5 Prostate(69;0.0153) acacacacacTCTGAACCAACACACACAG 0.507 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 181 174 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.2 NA AY257197 CCDS12626.1 19q13.31 2008-05-02 2006-07-04 2006-07-04 126299 "Zinc fingers, C2H2-type" 20804 protein-coding gene gene with protein product NA "chromosome 19 open reading frame 37" C19orf37 NA Standard NM_182498 NM_182498 NA Approved MGC51082, Zfp428 uc002oxa.3 Q96B54 ENST00000300811.3:c.*180TGGTTCAGA>- chr19.hg19:g.44111589_44111597delTCTGAACCA 0 3 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 174,204 5,5 32,29 1 1 O95054|Q6X3Y3 True hg19 CCDS12626.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF428-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000463349.1 PASS NA None 181 True - TCTGAACCA ENST00000300811.3 SNAP25 6616 __UNKNOWN__ __UNKNOWN__ 20 10273887 10273927 __UNKNOWN__ Splice_Site DEL TAGGAAAATTCTGCGGGCTTTGTGTGTGTCCCTGTAACAAG TAGGAAAATTCTGCGGGCTTTGTGTGTGTCCCTGTAACAAG - rs1051281|rs1051280|rs1051284|rs1131602|rs11547871|rs1131606|rs1131604|rs1131605 LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:10273887_10273927delTAGGAAAATTCTGCGGGCTTTGTGTGTGTCCCTGTAACAAG ENST00000254976.2 + 5 453_492 c.242_281delTAGGAAAATTCTGCGGGCTTTGTGTGTGTCCCTGTAACAAG c.(241-282)ctaggaaaattctgcgggctttgtgtgtgtccctgtaacaag>cg p.LGKFCGLCVCPCNK81fs SNAP25-AS1_ENST00000453544.1_RNA|SNAP25_ENST00000304886.2_Intron|SNAP25-AS1_ENST00000421143.2_RNA NM_130811.2 NP_570824.1 P60880 SNP25_HUMAN synaptosomal-associated protein, 25kDa 81 t-SNARE coiled-coil homology 1. {ECO:0000255|PROSITE-ProRule:PRU00202}. NA NA NA energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long-term synaptic potentiation (GO:0060291)|neurotransmitter secretion (GO:0007269)|neurotransmitter uptake (GO:0001504)|regulation of establishment of protein localization (GO:0070201)|regulation of insulin secretion (GO:0050796)|regulation of neuron projection development (GO:0010975)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle exocytosis (GO:0016079) cell junction (GO:0030054)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|SNARE complex (GO:0031201)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|trans-Golgi network (GO:0005802) calcium-dependent protein binding (GO:0048306) NA endometrium(1)|large_intestine(2)|lung(8)|prostate(2)|skin(4)|upper_aerodigestive_tract(1) 18 Botulinum Toxin Type A(DB00083) TTGACGGACCTAGGAAAATTCTGCGGGCTTTGTGTGTGTCCCTGTAACAAGTAGGTGCTGC 0.461 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 117 116.85 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0.58 NA CCDS13109.1, CCDS13110.1 20p12-p11.2 2008-08-01 2002-08-29 ENSG00000132639 ENSG00000132639 6616 11132 protein-coding gene gene with protein product "resistance to inhibitors of cholinesterase 4 homolog" 600322 "synaptosomal-associated protein, 25kD" SNAP NA 8661740, 10692432 Standard NM_130811 NM_003081 NA Approved SNAP-25, RIC-4, RIC4, SEC9, bA416N4.2, dJ1068F16.2 uc002wnr.2 P60880 OTTHUMG00000031863 ENST00000254976.2:c.281+1TAGGAAAATTCTGCGGGCTTTGTGTGTGTCCCTGTAACAAG>- chr20.hg19:g.10273887_10273927delTAGGAAAATTCTGCGGGCTTTGTGTGTGTCCCTGTAACAAG 0 2 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 91,91 3,3 29,30 1 1 B2RAU4|D3DW16|D3DW17|P13795|P36974|P70557|P70558|Q53EM2|Q5U0B5|Q8IXK3|Q96FM2|Q9BR45 True hg19 CCDS13110.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SNAP25-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000077976.3 PASS NA None 117 Frame_Shift_Del True + TAGGAAAATTCTGCGGGCTTTGTGTGTGTCCCTGTAACAAG ENST00000254976.2 Unknown 0 __UNKNOWN__ __UNKNOWN__ 20 55101248 55101267 __UNKNOWN__ IGR DEL TAGAAGAAAAAGTGAATGGG TAGAAGAAAAAGTGAATGGG - rs562677546|rs146673688 byFrequency LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:55101248_55101267delTAGAAGAAAAAGTGAATGGG NA FAM209A (50 upstream) : FAM209B (7034 downstream) NA NA NA NA NA NA TTTTTTTCACTAGAAGAAAAAGTGAATGGGAGACCAGTAG 0.382 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 78 64.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA chr20.hg19:g.55101248_55101267delTAGAAGAAAAAGTGAATGGG 0 4 ref NA False 104 91 PASS 1 PASS ref->het 0 NA 27,28 26,28 5,5 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 78 True TAGAAGAAAAAGTGAATGGG Unknown 0 __UNKNOWN__ __UNKNOWN__ Y 13842751 13842752 __UNKNOWN__ IGR INS - - CTTCC LTS-030_T LTS-030_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrY:13842751_13842752insCTTCC NA SLC9B1P1 (318034 upstream) : AC011293.1 (104690 downstream) NA NA NA NA NA NA tggaatggaatggaatggaatg 0.416 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA 0 NA NA NA NA NA NA NA 410 327.83 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 45.37 NA NA NA NA NA NA chrY.hg19:g.13842751_13842752insCTTCC 1 2 ref NA False 56 56 PASS 0 PASS ref->het 0 NA 115,278 5,10 280,282 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 410 True CTTCC FAM49A 81553 __UNKNOWN__ __UNKNOWN__ 2 16731532 16731536 __UNKNOWN__ 3'UTR DEL TGCAG TGCAG - rs545713034|rs139386835 LTS-031_T LTS-031_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:16731532_16731536delTGCAG ENST00000381323.3 - 0 3860_3864 NM_030797.3 NP_110424.1 Q9H0Q0 FA49A_HUMAN family with sequence similarity 49, member A NA NA NA NA NA intracellular (GO:0005622) NA NA breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|skin(3)|upper_aerodigestive_tract(1) 23 Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088) GBM - Glioblastoma multiforme(3;0.00969) NA NA CGCATGTGCATGCAGCACACACACA 0.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 200 173.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.77 NA NA AK001942 CCDS1688.1 2p24.3 2008-02-05 ENSG00000197872 ENSG00000197872 81553 NA 25373 protein-coding gene gene with protein product NA NA Standard NM_030797 NM_030797 NA Approved DKFZP566A1524, FLJ11080 uc002rck.2 Q9H0Q0 OTTHUMG00000090615 ENST00000381323.3:c.*2672CTGCA>- chr2.hg19:g.16731532_16731536delTGCAG 0 2 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 159,206 4,8 35,20 1 1 B3KNZ1|Q53QW2 True hg19 CCDS1688.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM49A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000207203.2 PASS NA None 200 True - TGCAG ENST00000381323.3 CIR1 9541 __UNKNOWN__ __UNKNOWN__ 2 175260394 175260422 __UNKNOWN__ 5'UTR DEL AACGTAAACAAACTCAGCCGCCTAACCGG AACGTAAACAAACTCAGCCGCCTAACCGG - rs111342617 LTS-031_T LTS-031_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:175260394_175260422delAACGTAAACAAACTCAGCCGCCTAACCGG ENST00000342016.3 - 0 21_49 CIR1_ENST00000362053.5_5'UTR NM_004882.3 NP_004873.3 Q86X95 CIR1_HUMAN corepressor interacting with RBPJ, 1 NA NA NA NA NA mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634) RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714) NA NA central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(5)|skin(1) 15 NA NA ATCTGTTAGCAACGTAAACAAACTCAGCCGCCTAACCGGAACTGCGTTT 0.533 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 246 237.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.06 NA NA AF098297 CCDS2256.1 2q31.1 2009-07-14 ENSG00000138433 ENSG00000138433 9541 NA 24217 protein-coding gene gene with protein product "recepin", "CBF1 interacting corepressor" 605228 NA 15652350, 11222720, 9874765 Standard NM_004882 NM_004882 NA Approved CIR uc002uim.3 Q86X95 OTTHUMG00000132338 ENST00000342016.3:c.-72CCGGTTAGGCGGCTGAGTTTGTTTACGTT>- chr2.hg19:g.175260394_175260422delAACGTAAACAAACTCAGCCGCCTAACCGG 0 2 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 296,301 5,5 21,20 2 2 A6NFI6|A8K8M4|O95367|Q12804|Q4G1B9|Q6PJI4|Q8IWI2 True hg19 CCDS2256.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CIR1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255460.1 PASS NA None 246 True - AACGTAAACAAACTCAGCCGCCTAACCGG ENST00000342016.3 GADL1 339896 __UNKNOWN__ __UNKNOWN__ 3 30842343 30842344 __UNKNOWN__ Intron INS - - TTAACT rs112790847 LTS-031_T LTS-031_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:30842343_30842344insTTAACT ENST00000282538.5 - 12 1401 GADL1_ENST00000454381.3_3'UTR NM_207359.2 NP_997242.2 Q6ZQY3 GADL1_HUMAN glutamate decarboxylase-like 1 NA NA NA NA NA carboxylic acid metabolic process (GO:0019752) aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782) NA NA breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1) 25 NA NA acacacacacagaaagagagag 0.446 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 196 174.91 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 2.82 NA NA AK128643 CCDS2649.2 3p23-p22 2009-01-14 ENSG00000144644 ENSG00000144644 339896 NA 27949 protein-coding gene gene with protein product 615601 NA Standard NM_207359 NM_207359 NA Approved uc003cep.2 Q6ZQY3 OTTHUMG00000130621 ENST00000282538.5:c.1250+36->AGTTAA chr3.hg19:g.30842343_30842344insTTAACT 1 4 ref NA False 35 35 PASS 0 PASS ref->het 0 NA 154,201 6,6 47,40 1 1 True hg19 CCDS2649.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GADL1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253106.2 PASS NA None 196 True - TTAACT ENST00000282538.5 DNAH12 201625 __UNKNOWN__ __UNKNOWN__ 3 57335757 57335762 __UNKNOWN__ Splice_Site DEL TTTTAC TTTTAC - LTS-031_T LTS-031_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:57335757_57335762delTTTTAC ENST00000351747.2 - 55 8971 c.e55+1 DNAH12_ENST00000344804.4_Splice_Site NM_178504.4 NP_848599.3 Q6ZR08 DYH12_HUMAN dynein, axonemal, heavy chain 12 NA NA NA NA NA microtubule-based movement (GO:0007018) cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874) ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777) NA NA breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1) 25 NA NA cacacacacaTTTTACCTGTAAAAAG 0.388 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 152 126.27 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 2.6 NA NA U53532, AK126276 CCDS33771.1 3p21.1 2009-02-04 2006-09-04 ENSG00000174844 ENSG00000174844 201625 NA "Axonemal dyneins" 2943 protein-coding gene gene with protein product 603340 "dynein, axonemal, heavy polypeptide 12", "dynein heavy chain domain 2", "dynein heavy domain 2", "dynein, axonemal, heavy chain 12-like", "dynein, axonemal, heavy chain 7-like" DNHD2, DNAH12L, DNAH7L NA 8812413, 8666668 Standard NM_178504 NM_198564 NA Approved DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290 uc003dit.2 Q6ZR08 OTTHUMG00000158598 ENST00000351747.2:c.8790+1GTAAAA>- chr3.hg19:g.57335757_57335762delTTTTAC 0 4 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 134,171 4,4 26,21 1 1 A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DNAH12-202 KNOWN basic|appris_principal protein_coding NA protein_coding PASS NA None 152 Intron True - TTTTAC ENST00000351747.2 KDM2A 22992 __UNKNOWN__ __UNKNOWN__ 11 67023013 67023045 __UNKNOWN__ 3'UTR DEL GGCCAGCAGCCCCAGGAGTCCCAGACCCGTGCC GGCCAGCAGCCCCAGGAGTCCCAGACCCGTGCC - rs111685640|rs546704728 LTS-031_T LTS-031_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:67023013_67023045delGGCCAGCAGCCCCAGGAGTCCCAGACCCGTGCC ENST00000529006.2 + 0 4422_4454 KDM2A_ENST00000526258.1_3'UTR|KDM2A_ENST00000398645.2_3'UTR|KDM2A_ENST00000308783.5_3'UTR|KDM2A_ENST00000530342.1_3'UTR NM_012308.2 NP_036440.1 Q9Y2K7 KDM2A_HUMAN lysine (K)-specific demethylase 2A NA NA NA NA NA histone H3-K36 demethylation (GO:0070544)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleus (GO:0005634) histone demethylase activity (H3-K36 specific) (GO:0051864)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270) NA NA NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|urinary_tract(2) 36 NA NA GCGCAGGAGGGGCCAGCAGCCCCAGGAGTCCCAGACCCGTGCCGATCACACTG 0.605 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 463 418.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.76 NA NA BC047486 CCDS44657.1, CCDS58148.1 11q13.1 2014-02-18 2009-04-06 2009-04-06 ENSG00000173120 ENSG00000173120 22992 NA "F-boxes / Leucine-rich repeats", "Chromatin-modifying enzymes / K-demethylases" 13606 protein-coding gene gene with protein product "F-box protein FBL11", "jumonji C domain-containing histone demethylase 1A" 605657 "F-box and leucine-rich repeat protein 11" FBXL11 NA 10231032, 10531037 Standard NM_012308 NM_012308 NA Approved KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7, FLJ00115, CXXC8, JHDM1A uc001ojw.3 Q9Y2K7 OTTHUMG00000167103 ENST00000529006.2:c.*519GGCCAGCAGCCCCAGGAGTCCCAGACCCGTGCC>- chr11.hg19:g.67023013_67023045delGGCCAGCAGCCCCAGGAGTCCCAGACCCGTGCC 0 6 ref NA False 58 58 PASS 1 PASS ref->het 0 NA 478,488 12,12 53,47 1 1 D4QA03|E9PIL6|I3VM55|Q49A21|Q4G0M3|Q69YY8|Q9BVH5|Q9H7H5|Q9UK66 True hg19 CCDS44657.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KDM2A-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000393140.2 PASS NA None 463 True + GGCCAGCAGCCCCAGGAGTCCCAGACCCGTGCC ENST00000529006.2 LAMA1 284217 __UNKNOWN__ __UNKNOWN__ 18 6956505 6956516 __UNKNOWN__ Intron DEL CAGCTCCAGCTC CAGCTCCAGCTC - rs562360802|rs11270496|rs72100822|rs374998825 byFrequency LTS-031_T LTS-031_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:6956505_6956516delCAGCTCCAGCTC ENST00000389658.3 - 56 8188 RP11-781P6.1_ENST00000584722.1_RNA NM_005559.3 NP_005550.2 P25391 LAMA1_HUMAN laminin, alpha 1 NA NA NA NA NA axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304) basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578) extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208) NA NA NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3) 205 Colorectal(10;0.172) NA NA ATTTTTAGCAcagctccagctccagctccagc 0.566 NA NA NA NA NA NA NA NA NA NA NA NA NA 1178 0.235224 0.3911 0.2147 5008 , , NA 17775 0.1716 NA 0.2326 False NA ,,, NA NA NA 2504 0.1074 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 179 169.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.21 NA NA X58531 CCDS32787.1 18p11.3 2013-03-01 ENSG00000101680 ENSG00000101680 284217 NA "Laminins" 6481 protein-coding gene gene with protein product 150320 LAMA NA 2591971 Standard NM_005559 NM_005559 NA Approved uc002knm.3 P25391 OTTHUMG00000133478 ENST00000389658.3:c.8094+118GAGCTGGAGCTG>- chr18.hg19:g.6956505_6956516delCAGCTCCAGCTC 2 3 ref NA False 36 36 PASS 4 PASS ref->het 0 NA 164,171 6,6 29,29 1 1 True hg19 CCDS32787.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LAMA1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257369.1 PASS NA None 179 True - CAGCTC ENST00000389658.3 ZNF133 7692 __UNKNOWN__ __UNKNOWN__ 20 18297112 18297123 __UNKNOWN__ In_Frame_Del DEL GCACAAGCGGAA GCACAAGCGGAA - rs140669678 LTS-031_T LTS-031_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:18297112_18297123delGCACAAGCGGAA ENST00000377671.3 + 7 2173_2184 c.1614_1625delGCACAAGCGGAA c.(1612-1626)aggcacaagcggaag>agg p.HKRK539del ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000401790.1_In_Frame_Del_p.HKRK540del|ZNF133_ENST00000402618.2_In_Frame_Del_p.HKRK477del|ZNF133_ENST00000538547.1_In_Frame_Del_p.HKRK445del|ZNF133_ENST00000316358.4_In_Frame_Del_p.HKRK540del|ZNF133_ENST00000535822.1_In_Frame_Del_p.HKRK445del|ZNF133_ENST00000396026.3_In_Frame_Del_p.HKRK543del NM_001083330.2|NM_003434.4 NP_001076799.1|NP_003425 P52736 ZN133_HUMAN zinc finger protein 133 540 NA NA NA NA transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA NA autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1) 26 NA NA GTCTCATCAGGCACAAGCGGAAGCACTCGAGG 0.575 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 293 287.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.01 NA NA AK123005 CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1 20p11.23 2013-01-08 2006-06-13 ENSG00000125846 ENSG00000125846 7692 NA "Zinc fingers, C2H2-type", "-" 12917 protein-coding gene gene with protein product 604075 "zinc finger protein 150 (pHZ-66)", "zinc finger protein 133 (clone pHZ-13)" ZNF150 NA 7557990, 7649249 Standard NM_003434 XM_005260819 NA Approved pHZ-13, pHZ-66 uc010gcs.3 P52736 OTTHUMG00000031965 ENST00000377671.3:c.1614_1625delGCACAAGCGGAA chr20.hg19:g.18297112_18297123delGCACAAGCGGAA ENSP00000366899:p.His539_Lys542del 0 2 ref NA False 85 85 PASS 1 PASS ref->het 0 NA 276,279 6,6 25,25 1 1 A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443 True hg19 CCDS13134.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF133-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000078158.2 PASS NA None 293 True + GCACAAGCGGAA ENST00000377671.3 CARD10 29775 __UNKNOWN__ __UNKNOWN__ 22 37906309 37906314 __UNKNOWN__ In_Frame_Del DEL CTCCTT CTCCTT - rs113275238|rs60611523 byFrequency LTS-031_T LTS-031_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:37906309_37906314delCTCCTT ENST00000403299.1 - 5 1030_1035 c.814_819delAAGGAG c.(814-819)aaggagdel p.KE272del CARD10_ENST00000251973.5_In_Frame_Del_p.KE272del|CARD10_ENST00000494166.1_5'UTR Q9BWT7 CAR10_HUMAN caspase recruitment domain family, member 10 272 NA NA NA NA activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981) CBM complex (GO:0032449)|cytoplasm (GO:0005737) receptor signaling complex scaffold activity (GO:0030159) NA NA NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 17 Melanoma(58;0.0574) NA NA CATTGTCTGGctccttctccttctcc 0.631 NA NA NA NA NA NA NA NA NA NA NA NA NA 1551 0.309704 0.4743 0.2536 5008 , , NA 16347 0.3036 NA 0.2535 False NA ,,, NA NA NA 2504 0.1912 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 138 142.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 1 NA NA AF086324 CCDS13948.1 22q13.1 2008-05-22 ENSG00000100065 ENSG00000100065 29775 NA 16422 protein-coding gene gene with protein product 607209 NA 11259443, 11356195 Standard NM_014550 NM_014550 NA Approved CARMA3, BIMP1 uc003asu.1 Q9BWT7 OTTHUMG00000150592 ENST00000403299.1:c.814_819delAAGGAG chr22.hg19:g.37906315_37906320delCTCCTT ENSP00000384570:p.Lys272_Glu273del 4 3 ref NA False 46 46 PASS 5 PASS ref->het 0 NA 118,121 4,4 30,29 1 1 Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0 True hg19 CCDS13948.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CARD10-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000318997.1 PASS NA None 138 True - CTCCTT ENST00000403299.1 PYGO2 90780 __UNKNOWN__ __UNKNOWN__ 1 154933607 154933610 __UNKNOWN__ Intron DEL CTTG CTTG - LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:154933607_154933610delCTTG ENST00000368457.2 - 2 275 PYGO2_ENST00000483463.1_Intron|PYGO2_ENST00000368456.1_Intron NM_138300.3 NP_612157.1 Q9BRQ0 PYGO2_HUMAN pygopus family PHD finger 2 NA NA NA NA brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|developmental growth (GO:0048589)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mammary gland development (GO:0030879)|palate development (GO:0060021)|positive regulation of chromatin binding (GO:0035563)|post-embryonic development (GO:0009791)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|spermatid nucleus differentiation (GO:0007289) nucleus (GO:0005634) chromatin binding (GO:0003682)|histone acetyltransferase regulator activity (GO:0035034)|zinc ion binding (GO:0008270) NA NA endometrium(2)|large_intestine(2)|lung(3)|skin(2)|urinary_tract(1) 10 all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245) BRCA - Breast invasive adenocarcinoma(34;0.00034) TCAATACATACTTGCTTATTTATT 0.397 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSCLC(87;357 1460 1955 21029 23522) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 474 493.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA BC006132 CCDS1075.1 1q22 2013-10-09 2013-10-09 ENSG00000163348 ENSG00000163348 90780 "Zinc fingers, PHD-type" 30257 protein-coding gene gene with protein product 606903 "pygopus homolog 2 (Drosophila)" NA 11988739 Standard NM_138300 NM_138300 NA Approved uc001fft.3 Q9BRQ0 OTTHUMG00000037370 ENST00000368457.2:c.104-105CAAG>- chr1.hg19:g.154933607_154933610delCTTG 0 2 ref NA False 117 117 PASS 1 PASS ref->het 0 NA 355,358 75,75 43,42 2 2 Q8WYZ4|Q96CY2 True hg19 CCDS1075.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PYGO2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000090949.1 PASS NA None 474 NA True - CTTG ENST00000368457.2 POU2F1 5451 __UNKNOWN__ __UNKNOWN__ 1 167370785 167370786 __UNKNOWN__ Frame_Shift_Del DEL CA CA - LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:167370785_167370786delCA ENST00000367862.5 + 13 1749_1750 c.1514_1515delCA c.(1513-1515)tcafs p.S505fs POU2F1_ENST00000429375.2_Frame_Shift_Del_p.S453fs|POU2F1_ENST00000367865.1_3'UTR|POU2F1_ENST00000367866.2_Frame_Shift_Del_p.S516fs|POU2F1_ENST00000541643.3_Frame_Shift_Del_p.S493fs|POU2F1_ENST00000420254.3_Frame_Shift_Del_p.S493fs NM_001198783.1 NP_001185712.1 P14859 PO2F1_HUMAN POU class 2 homeobox 1 493 NA NA NA gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383) cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA NA breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1) 30 ACGAATCTTTCAGTTACAGGTA 0.52 NA NA NA NA NA NA NA NA NA NA OREG0013970 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 75 84.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 NA NA BC001664 CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1 1q24.2 2011-06-20 2007-07-13 ENSG00000143190 ENSG00000143190 5451 "Homeoboxes / POU class" 9212 protein-coding gene gene with protein product 164175 "POU domain class 2, transcription factor 1" OTF1 NA 1887216 Standard NM_002697 NM_002697 NA Approved OCT1 uc001gee.3 P14859 OTTHUMG00000034436 ENST00000367862.5:c.1514_1515delCA chr1.hg19:g.167370785_167370786delCA ENSP00000356836:p.Ser505fs 0 4 ref 1861 False 32 32 PASS 1 PASS ref->het 0 NA 49,49 20,20 6,6 1 1 B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1 True hg19 CCDS55656.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA POU2F1-003 KNOWN basic|appris_candidate|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000083248.2 PASS NA None 75 NA True + CA ENST00000367862.5 WBSCR27 155368 __UNKNOWN__ __UNKNOWN__ 7 73255493 73255493 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:73255493delG ENST00000297873.4 - 3 208 c.159delC c.(157-159)ctcfs p.L53fs NM_152559.2 NP_689772.2 Q8N6F8 WBS27_HUMAN Williams Beuren syndrome chromosome region 27 53 NA NA NA NA NA NS(1)|central_nervous_system(1)|lung(2)|prostate(1) 5 Lung NSC(55;0.159) AGTCCACTGCGAGGCGGGGCG 0.672 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 345 331.64 NA NA NA NA NA 26 27 26 NA NA NA NA 7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 73255493 NA 2201 4299 6500 SO:0001589 frameshift_variant 1.1 NA NA AF534110 CCDS5561.1 7q11.23 2004-07-05 ENSG00000165171 ENSG00000165171 155368 19068 protein-coding gene gene with protein product 612546 NA Standard NM_152559 NM_152559 NA Approved uc003tzj.2 Q8N6F8 OTTHUMG00000130033 ENST00000297873.4:c.159delC chr7.hg19:g.73255493delG ENSP00000297873:p.Leu53fs 0 3 ref NA False 48 48 PASS 1 PASS ref->het 0 NA 260,269 30,30 53,44 1 1 True hg19 CCDS5561.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA WBSCR27-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252312.1 PASS NA None 345 NA True - G ENST00000297873.4 PHYHIP 9796 __UNKNOWN__ __UNKNOWN__ 8 22085736 22085738 __UNKNOWN__ In_Frame_Del DEL CTC CTC - LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:22085736_22085738delCTC ENST00000321613.3 - 3 589_591 c.133_135delGAG c.(133-135)gagdel p.E45del PHYHIP_ENST00000454243.2_In_Frame_Del_p.E45del NM_001099335.1 NP_001092805.1 Q92561 PHYIP_HUMAN phytanoyl-CoA 2-hydroxylase interacting protein 45 Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}. NA NA NA NA NA endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1) 10 Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629) AATTCTTATTCTCCTTCTTGTTA 0.532 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 36 33.46 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.54 NA NA D87463 CCDS43723.1 8p21.2 2010-02-17 2006-01-09 ENSG00000168490 ENSG00000168490 9796 16865 protein-coding gene gene with protein product 608511 "phytanoyl-CoA hydroxylase interacting protein", "DYRK1A interacting protein 3" DYRK1AP3 NA 9039502, 10686344 Standard NM_014759 NM_014759 NA Approved KIAA0273, PAHX-AP uc003xbj.4 Q92561 OTTHUMG00000163776 ENST00000321613.3:c.133_135delGAG chr8.hg19:g.22085736_22085738delCTC ENSP00000320017:p.Glu45del 0 4 ref NA False 124 89 PASS 1 PASS ref->het 0 NA 7,7 23,24 5,4 1 1 D3DSR1|Q8N4I9 True hg19 CCDS43723.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PHYHIP-002 PUTATIVE alternative_5_UTR|basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000375388.1 PASS NA None 36 NA True - CTC ENST00000321613.3 SLCO5A1 81796 __UNKNOWN__ __UNKNOWN__ 8 70602288 70602288 __UNKNOWN__ Intron DEL G G - rs368075578 byFrequency LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:70602288delG ENST00000524945.1 - 6 2339 SLCO5A1_ENST00000260126.4_Intron|SLCO5A1_ENST00000530307.1_Intron NM_001146008.1 NP_001139480.1 Q9H2Y9 SO5A1_HUMAN solute carrier organic anion transporter family, member 5A1 NA NA NA NA integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) transporter activity (GO:0005215) NA NA NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1) 53 Breast(64;0.0654) Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594) ttgcgggtacgggggggcgcc 0.537 NA NA NA NA NA NA NA NA NA NA 1263 0.252196 0.0401 0.2363 5008 , , NA 14633 0.3839 NA 0.3032 False NA ,,, NA NA NA 2504 0.362 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 16 22.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF205075 CCDS6205.1, CCDS55242.1, CCDS55243.1 8q13.1 2013-05-22 2003-11-25 2003-11-26 ENSG00000137571 ENSG00000137571 81796 "Solute carriers" 19046 protein-coding gene gene with protein product 613543 "solute carrier family 21 (organic anion transporter), member 15" SLC21A15 NA 12507753 Standard NM_030958 NM_030958 NA Approved OATPRP4, OATP-J, OATP5A1 uc003xyl.3 Q9H2Y9 OTTHUMG00000165121 ENST00000524945.1:c.1623-7710C>- chr8.hg19:g.70602288delG 6 8 ref NA False 34 34 PASS 7 PASS ref->hom 0 NA 0,0 3,3 15,17 1 1 A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0 True hg19 CCDS55243.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLCO5A1-004 PUTATIVE basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000381991.1 PASS NA None 16 NA True - G ENST00000524945.1 TERF1 7013 __UNKNOWN__ __UNKNOWN__ 8 73946675 73946676 __UNKNOWN__ Intron INS - - T rs34598357|rs397687875 byFrequency LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:73946675_73946676insT ENST00000276603.5 + 8 1062 TERF1_ENST00000520783.1_Intron|TERF1_ENST00000276602.6_Intron NM_017489.2 NP_059523.2 P54274 TERF1_HUMAN telomeric repeat binding factor (NIMA-interacting) 1 NA NA NA NA age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834) chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162) NA NA central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1) 9 Breast(64;0.218) Epithelial(68;0.0984) gcctttttgtgttttttgtaga 0.54 NA NA NA NA NA NA NA NA NA NA TTTTTT|TTTTTT|TTTTTTT|insertion 1822 0.363818 0.3245 0.3256 5008 , , NA 14109 0.1895 NA 0.5388 False NA ,,, NA NA NA 2504 0.4438 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 35 36.59 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.39 NA NA U74382 CCDS6210.1, CCDS6211.1 8q21.11 2011-05-24 ENSG00000147601 ENSG00000147601 7013 11728 protein-coding gene gene with protein product 600951 TRBF1 NA 9391075 Standard NM_017489 NM_003218 NA Approved PIN2, TRF1, TRF uc003xzd.2 P54274 OTTHUMG00000164522 ENST00000276603.5:c.1039+2307->T chr8.hg19:g.73946681_73946681dupT 7 7 ref NA False 37 37 PASS 6 PASS ref->het 0 NA 1,1 31,31 3,3 1 1 A7XP29|Q15553|Q8NHT6|Q93029 True hg19 CCDS6211.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TERF1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000379093.1 PASS NA None 35 NA True + T ENST00000276603.5 SKIDA1 387640 __UNKNOWN__ __UNKNOWN__ 10 21807307 21807307 __UNKNOWN__ 5'UTR DEL C C - LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:21807307delC ENST00000449193.2 - 0 1697 NM_207371.3 NP_997254.3 Q1XH10 SKDA1_HUMAN SKI/DACH domain containing 1 NA NA NA NA nucleus (GO:0005634) NA NA NA TCCACCCCTTCCCCCCAAAAT 0.433 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 167 159.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.48 NA NA AK131456 CCDS44363.1 10p12.31 2012-06-13 2012-06-13 2012-06-13 ENSG00000180592 ENSG00000180592 387640 32697 protein-coding gene gene with protein product NA "chromosome 10 open reading frame 140" C10orf140 NA Standard NM_207371 NM_207371 NA Approved FLJ45187 uc021pnx.1 Q1XH10 OTTHUMG00000017797 ENST00000449193.2:c.-556G>- chr10.hg19:g.21807307delC 5 6 ref NA False 226 135 PASS 6 PASS ref->het 0 NA 85,86 63,63 19,19 1 1 B1ANA5|Q6ZMX4|Q8N3C3 True hg19 CCDS44363.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SKIDA1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000286950.2 PASS NA None 167 NA True - C ENST00000449193.2 ERLIN1 10613 __UNKNOWN__ __UNKNOWN__ 10 101947777 101947778 __UNKNOWN__ 5'UTR INS - - TAT LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:101947777_101947778insTAT ENST00000421367.2 - 0 313_314 NM_001100626.1|NM_006459.3 NP_001094096.1|NP_006450.2 O75477 ERLN1_HUMAN ER lipid raft associated 1 NA NA NA NA ER-associated ubiquitin-dependent protein catabolic process (GO:0030433) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|protein complex (GO:0043234) NA NA NA Colorectal(252;0.234) Epithelial(162;3.85e-10)|all cancers(201;3.25e-08) GAGAGACTGCCTATTATAATAG 0.376 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 142 135.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 NA NA AF064093 CCDS7487.2 10q24.31 2014-03-03 2007-01-26 2007-01-26 ENSG00000107566 ENSG00000107566 10613 16947 protein-coding gene gene with protein product "Band_7 23-211 Keo4 (Interim) similar to C.elegans protein C42C1.9" 611604 "chromosome 10 open reading frame 69", "SPFH domain family, member 1" C10orf69, SPFH1 NA 11118313, 16835267, 24482476 Standard NM_006459 NM_006459 NA Approved KE04, Erlin-1, SPG62 uc001kqo.4 O75477 OTTHUMG00000018900 ENST00000421367.2:c.-2395->ATA chr10.hg19:g.101947781_101947783dupTAT 3 3 ref NA False 105 104 PASS 2 PASS ref->het 0 NA 87,88 39,39 15,14 1 1 B0QZ42|Q53HV0 True hg19 CCDS7487.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ERLIN1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000049840.2 PASS NA None 142 NA True - TAT ENST00000421367.2 CASP16 197350 __UNKNOWN__ __UNKNOWN__ 16 3197266 3197268 __UNKNOWN__ 5'UTR DEL AGG AGG - LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:3197266_3197268delAGG ENST00000428155.1 + 0 653_655 P0CB46 CASPG_HUMAN caspase 16, apoptosis-related cysteine peptidase (putative) NA NA NA NA extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630) cytoplasm (GO:0005737) cysteine-type endopeptidase activity (GO:0004197) NA NA NA CAGGCTTTCCAGGAGGAGCTGGC 0.66 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 165 160.41 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 NA NA 16p13.3 2014-04-01 ENSG00000228146 ENSG00000228146 197350 27290 protein-coding gene gene with protein product NA NA 18281271 Standard XM_003403459 XM_003403459 NA Approved uc002cuf.1 P0CB46 OTTHUMG00000177520 ENST00000428155.1:c.-72AGG>- chr16.hg19:g.3197269_3197271delAGG 1 4 ref NA False 60 60 PASS 2 PASS ref->het 0 NA 113,116 43,44 12,9 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CASP16-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000437342.1 PASS NA None 165 NA True + AGG ENST00000428155.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 16 33958582 33958585 __UNKNOWN__ IGR DEL TCTC TCTC - rs534468241|rs144904177|rs373437503|rs144804598 byFrequency LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:33958582_33958585delTCTC NA AC136932.2 (12561 upstream) : LINC00273 (2466 downstream) NA NA NA NA NA NA NA tatctgtctgtctctctctctctt 0.451 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 69 71.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.2 NA NA NA NA NA NA NA chr16.hg19:g.33958590_33958593delTCTC 4 2 ref NA False 57 57 PASS 6 PASS ref->het 0 NA 44,69 25,27 15,23 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 69 NA True TC ABCC3 8714 __UNKNOWN__ __UNKNOWN__ 17 48720944 48720944 __UNKNOWN__ Intron DEL A A - LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:48720944delA ENST00000285238.8 + 1 125 ABCC3_ENST00000427699.1_Intron NM_003786.3 NP_003777.2 O15438 MRP3_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 3 NA NA NA NA bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810) integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886) ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514) NA NA breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2) 33 BRCA - Breast invasive adenocarcinoma(22;3.05e-09) Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541) caaggccctcaccaaacattG 0.567 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 105 97.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA Y17151 CCDS32681.1, CCDS45739.1 17q21 2012-03-14 ENSG00000108846 ENSG00000108846 8714 "ATP binding cassette transporters / subfamily C" 54 protein-coding gene gene with protein product "canalicular multispecific organic anion transporter 2" 604323 NA 8894702, 9827529 Standard NM_020038 NM_003786 NA Approved MRP3, cMOAT2, EST90757, MLP2, MOAT-D uc002isl.3 O15438 OTTHUMG00000162245 ENST00000285238.8:c.45+8602A>- chr17.hg19:g.48720944delA 0 4 ref NA False 107 90 PASS 1 PASS ref->het 0 NA 44,45 48,48 13,13 1 1 B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52 True hg19 CCDS32681.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ABCC3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000368083.2 PASS NA None 105 NA True + A ENST00000285238.8 Unknown 0 __UNKNOWN__ __UNKNOWN__ 18 77543358 77543358 __UNKNOWN__ IGR DEL T T - rs200854326|rs57968059 byFrequency LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:77543358delT NA CTDP1 (28848 upstream) : RP11-154H12.2 (3762 downstream) NA NA NA NA NA NA NA CTCTGTTGGGTggccgggcgc 0.602 NA NA NA NA NA NA NA NA NA NA T|T|-|deletion 1403 0.280152 0.1581 0.4769 5008 , , NA 16032 0.4236 NA 0.2594 False NA ,,, NA NA NA 2504 0.1789 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 12 10.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA chr18.hg19:g.77543358delT 0 5 ref NA False 32 32 PASS 1 PASS ref->hom 0 NA 0,0 11,11 1,1 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 12 NA True T EFNA2 1943 __UNKNOWN__ __UNKNOWN__ 19 1298419 1298420 __UNKNOWN__ Intron DEL TA TA - rs34685801|rs397820313 byFrequency LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:1298419_1298420delTA ENST00000215368.2 + 3 469 MUM1_ENST00000344663.3_Intron NM_001405.3 NP_001396.2 O43921 EFNA2_HUMAN ephrin-A2 NA NA NA NA axon guidance (GO:0007411)|bone remodeling (GO:0046849)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|olfactory bulb development (GO:0021772)|osteoclast differentiation (GO:0030316) anchored component of membrane (GO:0031225)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|plasma membrane (GO:0005886) ephrin receptor binding (GO:0046875) NA NA lung(2) 2 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) GATGTACGATTAGGAGTTTTAA 0.569 NA NA NA NA NA NA NA NA NA NA 391 0.0780751 0.1271 0.1023 5008 , , NA 18018 0.0099 NA 0.1014 False NA ,,, NA NA NA 2504 0.0409 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 59 68.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.46 NA NA CCDS12061.1 19p13 2011-03-09 ENSG00000099617 ENSG00000099617 1943 "Ephrins" 3222 protein-coding gene gene with protein product 602756 EPLG6 NA Standard NM_001405 NM_001405 NA Approved ELF-1, LERK6 uc002lry.2 O43921 ENST00000215368.2:c.455-130TA>- chr19.hg19:g.1298419_1298420delTA 0 3 ref NA False 66 59 PASS 1 PASS ref->het 0 NA 2,2 53,55 3,3 1 1 O76020 True hg19 CCDS12061.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EFNA2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000450016.1 PASS NA None 59 NA True + TA ENST00000215368.2 Unknown 0 __UNKNOWN__ __UNKNOWN__ 21 9826929 9826950 __UNKNOWN__ IGR DEL GGCGCCGGGCCCGTCCTCGCGA GGCGCCGGGCCCGTCCTCGCGA - rs545692653|rs562929423 byFrequency LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:9826929_9826950delGGCGCCGGGCCCGTCCTCGCGA NA MIR3687 (666 upstream) : TEKT4P2 (80243 downstream) NA NA NA NA NA NA NA TCGCTTgcggggcgccgggcccgtcctcgcgaggccccccgg 0.752 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 180 175.98 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 2.73 NA NA NA NA NA NA NA chr21.hg19:g.9826929_9826950delGGCGCCGGGCCCGTCCTCGCGA 0 5 ref NA False 82 82 PASS 1 PASS ref->het 0 NA 169,182 5,5 45,33 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 180 NA True GGCGCCGGGCCCGTCCTCGCGA ATP5O 539 __UNKNOWN__ __UNKNOWN__ 21 35279058 35279066 __UNKNOWN__ Intron DEL AAGGCAGGT AAGGCAGGT - LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:35279058_35279066delAAGGCAGGT ENST00000290299.2 - 5 658 AP000304.12_ENST00000429238.1_Intron NM_001697.2 NP_001688.1 P48047 ATPO_HUMAN ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit NA NA NA NA ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281) extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886) drug binding (GO:0008144)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|transmembrane transporter activity (GO:0022857)|transporter activity (GO:0005215) NA NA large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1) 5 ttaggaggccaaggcaggtgggtcacttg 0.488 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 150 146.89 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.27 NA NA AF088071 CCDS13634.1 21q22 2012-10-12 2008-07-31 ENSG00000241837 ENSG00000241837 539 3.6.3.14 "Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type" 850 protein-coding gene gene with protein product "oligomycin sensitivity conferring protein" 600828 NA 7490082 Standard NM_001697 NM_001697 NA Approved OSCP, ATPO P48047 OTTHUMG00000065186 ENST00000290299.2:c.441+578ACCTGCCTT>- chr21.hg19:g.35279058_35279066delAAGGCAGGT 0 5 ref NA False 83 83 PASS 1 PASS ref->het 0 NA 100,103 37,37 13,13 1 1 B2R4E2|Q5U042|Q6IBI2 True hg19 CCDS13634.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ATP5O-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000139907.1 PASS NA None 150 NA True - AAGGCAGGT ENST00000290299.2 MBNL3 55796 __UNKNOWN__ __UNKNOWN__ X 131513196 131513196 __UNKNOWN__ 3'UTR DEL A A - LTS-032_T LTS-032_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:131513196delA ENST00000370853.3 - 0 1641 MBNL3_ENST00000370857.3_3'UTR|RAP2C-AS1_ENST00000421483.2_RNA|RAP2C-AS1_ENST00000441399.2_RNA|MBNL3_ENST00000394311.2_3'UTR|MBNL3_ENST00000538204.1_3'UTR NM_018388.3 NP_060858.2 Q9NUK0 MBNL3_HUMAN muscleblind-like splicing regulator 3 NA NA NA NA mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|negative regulation of myoblast differentiation (GO:0045662)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380) cytoplasm (GO:0005737)|nucleus (GO:0005634) metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822) NA NA NS(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|prostate(2) 16 Acute lymphoblastic leukemia(192;0.000127) TACAGTATGTAAAAACCTaac 0.328 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 406 399.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.76 NA NA AF491305 CCDS14633.1, CCDS14634.1, CCDS55492.1, CCDS55493.1, CCDS55494.1 Xq26.2 2013-01-18 2012-02-23 ENSG00000076770 ENSG00000076770 55796 "Zinc fingers, CCCH-type domain containing" 20564 protein-coding gene gene with protein product 300413 "muscleblind-like 3 (Drosophila)" NA 12297108, 10970838 Standard NM_018388 NM_018388 NA Approved CHCR, FLJ11316, MBLX39, MBXL uc004ewv.4 Q9NUK0 OTTHUMG00000022426 ENST00000370853.3:c.*498T>- chrX.hg19:g.131513196delA 4 5 ref NA False 80 80 PASS 5 PASS ref->het 0 NA 296,300 79,80 29,29 1 1 Q5JXN8|Q5JXN9|Q5JXP4|Q6UDQ1|Q8IUR4|Q8TAD9|Q8TAF4|Q9H0Z7|Q9UF37 True hg19 CCDS14633.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MBNL3-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000058319.1 PASS NA None 406 NA True - A ENST00000370853.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ M 569 570 __UNKNOWN__ IGR INS - - C NA NA LTS-033_T LTS-033_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrM:569_570insC NA None (None upstream) : MT-TF (6 downstream) NA NA NA NA NA NA NA NA NA NA NA CCCCAAAGACACCCCCCACAGT 0.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 315 321.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.76 NA NA NA NA NA NA NA NA NA chrM.hg19:g.575_575dupC 7 7 ref NA False 607 221 PASS 6 PASS ref->het 0 NA 142,147 130,133 42,43 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 315 NA True C NEXN 91624 __UNKNOWN__ __UNKNOWN__ 1 78407806 78407808 __UNKNOWN__ In_Frame_Del DEL AGA AGA - NA NA LTS-033_T LTS-033_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:78407806_78407808delAGA ENST00000334785.7 + 12 1756_1758 c.1572_1574delAGA c.(1570-1575)agagaa>aga p.E528del NEXN_ENST00000480732.2_3'UTR|NEXN_ENST00000457030.1_In_Frame_Del_p.E514del|NEXN_ENST00000330010.8_In_Frame_Del_p.E464del NM_144573.3 NP_653174.3 nexilin (F actin binding protein) NA NA NA NA NA NA breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1) 30 NA NA NA Colorectal(170;0.114) NA CTAAGGCAAGAGAAGAAGAAGAA 0.384 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 196 180.05 NA , 24,3528 NA 10,4,1762 NA NA NA NA , 5.7 1 NA NA 68 55,7803 NA 25,5,3899 no coding,coding NEXN NM_144573.3,NM_001172309.1 , 35,9,5661 A1A1,A1R,RR NA 0.6999,0.6757,0.6924 , , NA 79,11331 NA NA NA SO:0001651 inframe_deletion 0.72 NA NA AK057954 CCDS41351.1, CCDS53335.1 1p31.1 2014-09-17 ENSG00000162614 ENSG00000162614 91624 NA "Immunoglobulin superfamily / I-set domain containing" 29557 protein-coding gene gene with protein product NA 613121 NA 12053183, 8227983 Standard NM_144573 NM_144573 NA Approved nexilin, NELIN uc001dic.4 Q0ZGT2 OTTHUMG00000040533 ENST00000334785.7:c.1572_1574delAGA chr1.hg19:g.78407815_78407817delAGA ENSP00000333938:p.Glu528del 3 4 ref NA False 56 56 PASS 4 PASS ref->het 0 NA 126,127 42,44 37,36 1 1 True hg19 CCDS41351.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NEXN-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000097549.1 PASS NA None 196 NA True + AGA ENST00000334785.7 NSMF 26012 __UNKNOWN__ __UNKNOWN__ 9 140349177 140349177 __UNKNOWN__ Intron DEL C C - NA NA LTS-033_T LTS-033_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:140349177delC ENST00000371472.2 - 6 973 NSMF_ENST00000437259.1_Intron|NSMF_ENST00000265663.7_Intron|NSMF_ENST00000371474.3_Intron|NSMF_ENST00000339554.3_Intron|NSMF_ENST00000371473.3_Intron|NSMF_ENST00000392812.4_Intron|NSMF_ENST00000371475.3_Intron Q6X4W1 NSMF_HUMAN NMDA receptor synaptonuclear signaling and neuronal migration factor NA NA NA NA cellular response to amino acid stimulus (GO:0071230)|cellular response to electrical stimulus (GO:0071257)|cellular response to gonadotropin stimulus (GO:0071371)|positive regulation of neuron migration (GO:2001224)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of dendrite morphogenesis (GO:0048814)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuronal synaptic plasticity (GO:0048168) apical dendrite (GO:0097440)|cell junction (GO:0030054)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuron projection (GO:0043005)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202) calcium-dependent protein binding (GO:0048306) NA NA NA NA NA NA NA CTCTGACCTTCCGTCCTCGCC 0.647 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 370 363.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.6 NA NA CCDS7044.1, CCDS48067.1, CCDS48068.1, CCDS48069.1, CCDS55357.1 9q34.3 2013-01-14 2013-01-14 2013-01-14 ENSG00000165802 ENSG00000165802 26012 NA 29843 protein-coding gene gene with protein product NA 608137 "nasal embryonic LHRH factor" NELF NA 11230166, 10898796 Standard NM_015537 NM_015537 NA Approved uc004cna.3 Q6X4W1 OTTHUMG00000020989 ENST00000371472.2:c.774-282G>- chr9.hg19:g.140349177delC 1 2 ref NA False 84 84 PASS 2 PASS ref->het 0 NA 269,275 55,56 40,34 1 1 Q2TB96|Q6X4V7|Q6X4V8|Q6X4V9|Q8N2M2|Q96SY1|Q9NPM4|Q9NPP3|Q9NPS3 True hg19 CCDS7044.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSMF-002 PUTATIVE non_canonical_TEC|basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000055331.2 PASS NA None 370 NA True - C ENST00000371472.2 ATF7IP 55729 __UNKNOWN__ __UNKNOWN__ 12 14578302 14578303 __UNKNOWN__ Frame_Shift_Del DEL GA GA - NA NA LTS-033_T LTS-033_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:14578302_14578303delGA ENST00000540793.1 + 1 1608_1609 c.1453_1454delGA c.(1453-1455)gagfs p.E485fs ATF7IP_ENST00000543189.1_Frame_Shift_Del_p.E485fs|ATF7IP_ENST00000544627.1_Frame_Shift_Del_p.E493fs|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000536444.1_Frame_Shift_Del_p.E485fs|ATF7IP_ENST00000261168.4_Frame_Shift_Del_p.E485fs Q6VMQ6 MCAF1_HUMAN activating transcription factor 7 interacting protein 485 Glu-rich. NA NA NA DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032) nucleus (GO:0005634) NA NA cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1) 54 NA NA NA NA AGAAAGTAGTGAGAGTTTGCCA 0.381 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 348 336.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 NA NA AJ242978 CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1 12p13.1 2005-11-18 ENSG00000171681 55729 NA 20092 protein-coding gene gene with protein product NA 613644 NA 10976766, 10777215 Standard NM_018179 XM_005253424 NA Approved FLJ10688, p621 uc001rbw.3 Q6VMQ6 ENST00000540793.1:c.1453_1454delGA chr12.hg19:g.14578304_14578305delGA ENSP00000444589:p.Glu485fs 1 2 ref NA False 64 64 PASS 2 PASS ref->het 0 NA 242,243 70,70 39,38 1 1 F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8 True hg19 CCDS8663.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ATF7IP-024 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000401400.1 PASS NA None 348 NA True + GA ENST00000540793.1 ZNF783 100289678 __UNKNOWN__ __UNKNOWN__ 7 148979381 148979403 __UNKNOWN__ Frame_Shift_Del DEL GCCCGCCACGGGAGCCTGCCCCT GCCCGCCACGGGAGCCTGCCCCT - rs3735314|rs112363552|rs539045489 byFrequency LTS-034_T LTS-034_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:148979381_148979403delGCCCGCCACGGGAGCCTGCCCCT ENST00000434415.1 + 6 1751_1773 c.1588_1610delGCCCGCCACGGGAGCCTGCCCCT c.(1588-1611)gcccgccacgggagcctgcccctgfs p.ARHGSLPL530fs ZNF783_ENST00000489518.1_Intron NM_001195220.1 NP_001182149.1 Q6ZMS7 ZN783_HUMAN zinc finger family member 783 0 NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677) NA NA cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1) 22 Melanoma(164;0.15) NA OV - Ovarian serous cystadenocarcinoma(82;0.0014) NA NA TGCCGCCCCCGCCCGCCACGGGAGCCTGCCCCTGCCCTGGCCC 0.713 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 294 299.91 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 9.39 NA NA AK131504 CCDS56519.1 7q36.1 2013-01-08 2008-05-28 ENSG00000204946 ENSG00000204946 100289678 NA "Zinc fingers, C2H2-type", "-" 27222 protein-coding gene gene with protein product NA NA NA 8619474, 9110174 Standard NM_001195220 NM_001195220 NA Approved DKFZp667J212 uc011kuo.2 Q6ZMS7 OTTHUMG00000158969 ENST00000434415.1:c.1588_1610delGCCCGCCACGGGAGCCTGCCCCT chr7.hg19:g.148979381_148979403delGCCCGCCACGGGAGCCTGCCCCT ENSP00000410890:p.Ala530fs 0 8 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 242,270 8,8 58,31 1 1 C9J9J2 True hg19 CCDS56519.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF783-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000352715.1 PASS NA None 294 NA True + GCCCGCCACGGGAGCCTGCCCCT ENST00000434415.1 GXYLT1 283464 __UNKNOWN__ __UNKNOWN__ 12 42479304 42479305 __UNKNOWN__ 3'UTR INS - - TAATG LTS-034_T LTS-034_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:42479304_42479305insTAATG ENST00000398675.3 - 0 3838_3839 NM_001099650.1|NM_173601.1 NP_001093120.1|NP_775872.1 Q4G148 GXLT1_HUMAN glucoside xylosyltransferase 1 NA NA NA NA NA carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281) Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021) UDP-xylosyltransferase activity (GO:0035252) NA NA kidney(2)|large_intestine(4)|liver(3)|lung(8) 17 NA NA NA AATGCTTCCTCTAATATTTCAA 0.356 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 218 216.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 3.49 NA NA BC015597 CCDS41771.1, CCDS41772.1 12q12 2013-10-11 2009-11-17 2009-11-17 ENSG00000151233 ENSG00000151233 283464 NA "Glycosyltransferase family 8 domain containing" 27482 protein-coding gene gene with protein product NA 613321 "glycosyltransferase 8 domain containing 3" GLT8D3 NA 19940119 Standard XM_290597 NM_001099650 NA Approved FLJ43151 uc001rms.4 Q4G148 OTTHUMG00000169379 ENST00000398675.3:c.*2284->CATTA chr12.hg19:g.42479304_42479305insTAATG 1 3 ref NA False 43 43 PASS 0 PASS ref->het 0 NA 195,196 5,10 17,13 1 1 B3KWJ2|Q8IXV1|Q96BH4 True hg19 CCDS41772.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GXYLT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000403778.1 PASS NA None 218 NA True - TAATG ENST00000398675.3 FRG1B 284802 __UNKNOWN__ __UNKNOWN__ 20 29614292 29614296 __UNKNOWN__ 5'UTR DEL AAAAG AAAAG - rs376619640|rs373374584 LTS-034_T LTS-034_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:29614292_29614296delAAAAG ENST00000278882.3 + 0 285_289 FRG1B_ENST00000439954.2_5'UTR|FRG1B_ENST00000358464.4_5'UTR Q9BZ01 FRG1B_HUMAN FSHD region gene 1 family, member B NA NA NA NA NA NA NA endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9) 53 NA NA NA taagaagagaaaaagagaagatgaa 0.288 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 250 236.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 2.93 NA NA 20q11.1 2013-03-18 2007-10-11 2007-10-11 ENSG00000149531 ENSG00000149531 284802 NA 15792 other unknown NA NA "chromosome 20 open reading frame 80" C20orf80 NA Standard NR_003579 NR_003579 NA Approved bA348I14.2 uc010ztl.1 Q9BZ01 OTTHUMG00000032157 ENST00000278882.3:c.-92AAAAG>- chr20.hg19:g.29614292_29614296delAAAAG 0 6 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 219,237 6,23 47,31 1 1 C4AME5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FRG1B-001 KNOWN not_best_in_genome_evidence|basic|appris_principal protein_coding NA protein_coding OTTHUMT00000078494.2 PASS NA None 250 NA True + AAAAG ENST00000278882.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ Y 13842751 13842752 __UNKNOWN__ IGR INS - - CATCC LTS-034_T LTS-034_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrY:13842751_13842752insCATCC NA SLC9B1P1 (318034 upstream) : AC011293.1 (104690 downstream) NA NA NA NA NA NA NA NA NA NA NA tggaatggaatggaatggaatg 0.416 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 275 227.09 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 44.59 NA NA NA NA NA NA NA NA NA chrY.hg19:g.13842751_13842752insCATCC 1 2 ref NA False 34 34 PASS 0 PASS ref->het 0 NA 43,221 4,9 220,239 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 275 NA True CATCC GXYLT1 283464 __UNKNOWN__ __UNKNOWN__ 12 42479304 42479305 __UNKNOWN__ 3'UTR INS - - TAATG LTS-035_T LTS-035_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:42479304_42479305insTAATG ENST00000398675.3 - 0 3838_3839 NA NA NA NM_001099650.1|NM_173601.1 NP_001093120.1|NP_775872.1 Q4G148 GXLT1_HUMAN glucoside xylosyltransferase 1 NA NA NA NA NA carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281) Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021) UDP-xylosyltransferase activity (GO:0035252) NA NA kidney(2)|large_intestine(4)|liver(3)|lung(8) 17 NA NA NA NA NA AATGCTTCCTCTAATATTTCAA 0.356 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 249 242.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 3.31 NA NA BC015597 CCDS41771.1, CCDS41772.1 12q12 2013-10-11 2009-11-17 2009-11-17 ENSG00000151233 ENSG00000151233 283464 NA "Glycosyltransferase family 8 domain containing" 27482 protein-coding gene gene with protein product NA 613321 "glycosyltransferase 8 domain containing 3" GLT8D3 NA 19940119 Standard XM_290597 NM_001099650 NA Approved FLJ43151 uc001rms.4 Q4G148 OTTHUMG00000169379 ENST00000398675.3:c.*2284->CATTA chr12.hg19:g.42479304_42479305insTAATG NA 1 3 ref NA False 35 35 PASS 0 PASS ref->het 0 NA 216,218 4,7 28,24 1 1 B3KWJ2|Q8IXV1|Q96BH4 True hg19 CCDS41772.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GXYLT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000403778.1 PASS NA None 249 NA True - TAATG ENST00000398675.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 19 35019460 35019460 __UNKNOWN__ IGR DEL G G - rs144459636 byFrequency LTS-035_T LTS-035_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:35019460delG NA NA NA NA WTIP (22202 upstream) : AC008747.1 (32230 downstream) NA NA NA NA NA NA NA NA NA NA NA NA NA ccagcactttgggaggccaag 0.473 NA NA NA NA NA NA NA NA NA NA NA NA ggg|GGG|GG|deletion 1400 0.279553 0.1339 0.2637 5008 , , NA 18352 0.2708 NA 0.3459 False NA ,,, NA NA NA 2504 0.4284 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 22 22.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA NA NA NA chr19.hg19:g.35019460delG NA 2 5 ref NA False 34 34 PASS 3 PASS ref->hom 0 NA 0,0 20,20 2,2 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 22 NA True G Unknown 0 __UNKNOWN__ __UNKNOWN__ 1 1444851 1444852 __UNKNOWN__ IGR DEL TG TG - LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:1444851_1444852delTG NA ATAD3B (13269 upstream) : ATAD3A (2678 downstream) NA NA NA NA NA NA GCCGCACCGCTGTGTCTATTGG 0.624 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 90 97.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.62 NA NA NA NA NA NA NA chr1.hg19:g.1444853_1444854delTG 1 3 ref NA False 37 37 PASS 2 PASS ref->het 0 NA 63,67 21,23 7,3 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 90 NA True TG C1orf158 93190 __UNKNOWN__ __UNKNOWN__ 1 12822498 12822499 __UNKNOWN__ 3'UTR INS - - A rs373672762|rs587660673 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:12822498_12822499insA ENST00000288048.5 + 0 2415_2416 NM_152290.2 NP_689503.2 Q8N1D5 CA158_HUMAN chromosome 1 open reading frame 158 NA NA NA NA NA central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|ovary(1)|skin(2)|urinary_tract(3) 10 Ovarian(185;0.249) Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00575)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649) GAGGAGGAGCCGGGGGTGCAGA 0.475 NA NA NA NA NA NA NA NA |||unknown(ALL_OTHER_Ns) 2069 0.413139 0.1808 0.5375 5008 , , NA 11472 0.6091 NA 0.4324 False NA ,,, NA NA NA 2504 0.4172 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 13 22.62 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.17 NA NA BX647383 CCDS147.1 1p36.21 2008-02-05 ENSG00000157330 ENSG00000157330 93190 28567 protein-coding gene gene with protein product NA NA 12477932 Standard NM_152290 NM_152290 NA Approved MGC35194 uc001auh.3 Q8N1D5 OTTHUMG00000001888 ENST00000288048.5:c.*1615->A chr1.hg19:g.12822498_12822499insA 1 6 ref NA False 53 53 PASS 0 PASS ref->hom 0 NA 0,1 11,15 4,8 1 1 Q5VUY4 True hg19 CCDS147.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C1orf158-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000005325.1 PASS NA None 13 NA True + A ENST00000288048.5 STIL 6491 __UNKNOWN__ __UNKNOWN__ 1 47728720 47728721 __UNKNOWN__ Frame_Shift_Del DEL TC TC - LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:47728720_47728721delTC ENST00000371877.3 - 15 2830_2831 c.2683_2684delGA c.(2683-2685)gaafs p.E895fs STIL_ENST00000243182.6_Frame_Shift_Del_p.E894fs|STIL_ENST00000396221.2_Frame_Shift_Del_p.E877fs|STIL_ENST00000337817.5_Frame_Shift_Del_p.E894fs|STIL_ENST00000360380.3_Frame_Shift_Del_p.E894fs Q15468 STIL_HUMAN SCL/TAL1 interrupting locus 894 NA NA NA cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224) centrosome (GO:0005813)|cytoplasm (GO:0005737) NA central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3) 36 Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444) GCTTACACTTTCTGCCAGCTGG 0.436 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 256 248.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.04 NA NA M74558 CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1 1p32 2010-02-09 2005-11-29 2005-11-29 ENSG00000123473 ENSG00000123473 6491 10879 protein-coding gene gene with protein product 181590 "TAL1 (SCL) interrupting locus" SIL NA 2209547 Standard NM_003035 NM_003035 NA Approved MCPH7 uc001crd.1 Q15468 OTTHUMG00000007851 ENST00000371877.3:c.2683_2684delGA chr1.hg19:g.47728720_47728721delTC ENSP00000360944:p.Glu895fs 0 4 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 199,202 28,28 27,26 1 1 Q5T0C5|Q68CN9 True hg19 CCDS41329.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA STIL-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000021652.2 PASS NA None 256 NA True - TC ENST00000371877.3 TBCE 6905 __UNKNOWN__ __UNKNOWN__ 1 235600053 235600054 __UNKNOWN__ Intron INS - - C rs368118144|rs60243825 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:235600053_235600054insC ENST00000366601.3 + 11 1139 TBCE_ENST00000406207.1_Intron|TBCE_ENST00000543662.1_Intron|TBCE_ENST00000472011.1_Intron Q15813 TBCE_HUMAN tubulin folding cofactor E NA NA NA NA 'de novo' posttranslational protein folding (GO:0051084)|adult locomotory behavior (GO:0008344)|cellular protein metabolic process (GO:0044267)|developmental growth (GO:0048589)|microtubule cytoskeleton organization (GO:0000226)|muscle atrophy (GO:0014889)|peripheral nervous system neuron axonogenesis (GO:0048936)|post-chaperonin tubulin folding pathway (GO:0007023)|post-embryonic development (GO:0009791)|protein folding (GO:0006457) cytoplasm (GO:0005737)|microtubule (GO:0005874) chaperone binding (GO:0051087) NA NS(1)|endometrium(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1) 14 Ovarian(103;0.0634)|Breast(184;0.23) all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238) OV - Ovarian serous cystadenocarcinoma(106;2.56e-05) CCTCAGAGTGAAACTCCTCATA 0.361 NA NA NA NA NA NA NA NA -|-|C|insertion 1052 0.210064 0.0023 0.2997 5008 , , NA 18680 0.494 NA 0.0557 False NA ,,, NA NA NA 2504 0.2935 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 72 84.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.01 NA NA U61232 CCDS1605.1, CCDS73052.1 1q42.3 2014-02-04 2006-11-21 ENSG00000116957 ENSG00000116957 6905 11582 protein-coding gene gene with protein product 604934 "tubulin-specific chaperone e", "Kenny-Caffey syndrome", "hypoparathyroidism, growth and mental retardation, and dysmorphism" KCS, HRD NA 8706133, 9806825, 12389028 Standard NM_003193 NM_001079515 NA Approved KCS1, pac2 uc001hxa.1 Q15813 OTTHUMG00000039987 ENST00000366601.3:c.963+130->C chr1.hg19:g.235600053_235600054insC 1 3 ref NA False 30 30 PASS 0 PASS ref->het 0 NA 17,18 50,51 3,3 2 2 A8K8C2|B7Z3P1 True hg19 CCDS1605.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TBCE-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000096458.3 PASS NA None 72 NA True + C ENST00000366601.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 2 114424753 114424754 __UNKNOWN__ IGR INS - - A rs34317322 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:114424753_114424754insA NA RABL2A (23780 upstream) : AC017074.1 (1988 downstream) NA NA NA NA NA NA ATCCCTGGTCTACAGCCCCAGG 0.416 NA NA NA NA NA NA NA NA A|A|AA|insertion 1722 0.34385 0.6369 0.196 5008 , , NA 18498 0.4137 NA 0.1143 False NA ,,, NA NA NA 2504 0.2168 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 29 29.11 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA chr2.hg19:g.114424754_114424754dupA 2 2 ref NA False 40 40 PASS 1 PASS ref->hom 0 NA 0,0 27,27 4,4 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 29 NA True A RP11-644C3.1 0 __UNKNOWN__ __UNKNOWN__ 3 176561826 176561827 __UNKNOWN__ lincRNA INS - - AAA rs147464549|rs141856584 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:176561826_176561827insAAA ENST00000428516.1 - 0 198 NA NA NA NA NA NA aagaagaaaagaaggaggagga 0.421 NA NA NA NA NA NA NA NA 213 0.0425319 0.056 0.0634 5008 , , NA 15927 0 NA 0.0726 False NA ,,, NA NA NA 2504 0.0225 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 35 37.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.79 NA NA NA NA NA NA NA ENST00000428516.1: chr3.hg19:g.176561826_176561827insAAA 5 6 ref NA False 30 30 PASS 2 PASS ref->het 0 NA 5,5 28,28 4,4 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-644C3.1-001 KNOWN basic lincRNA NA lincRNA OTTHUMT00000348372.1 PASS NA None 35 NA True - A ENST00000428516.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 5 32354296 32354297 __UNKNOWN__ IGR INS - - T rs11372359|rs397819521|rs200205036 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:32354296_32354297insT NA MTMR12 (41181 upstream) : ZFR (158 downstream) NA NA NA NA NA NA TCCTGGCCCTCTAAGACTTTGG 0.396 NA NA NA NA NA NA NA NA T|T|TT|insertion 4562 0.910942 0.9811 0.8631 5008 , , NA 16762 0.8581 NA 0.9334 False NA ,,, NA NA NA 2504 0.8814 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 18 21.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA chr5.hg19:g.32354297_32354297dupT 2 4 ref NA False 30 30 PASS 1 PASS ref->hom 0 NA 0,0 16,16 3,3 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 18 NA True T RNF130 55819 __UNKNOWN__ __UNKNOWN__ 5 179442525 179442525 __UNKNOWN__ Intron DEL G G - rs66797381 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:179442525delG ENST00000261947.4 - 3 841 RNF130_ENST00000521389.1_Intron|RNF130_ENST00000522208.2_Intron NM_001280801.1 NP_001267730.1 ring finger protein 130 NA NA NA NA NA breast(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(2) 17 all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212) all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) gaaaggagtagggaaaggagt 0.493 NA NA NA NA NA NA NA NA |||unknown(ALL_OTHER_Ns) 3081 0.615216 0.5938 0.6427 5008 , , NA 20829 0.5446 NA 0.6213 False NA ,,, NA NA NA 2504 0.6912 NA NA NA GBM(24;432 554 38471 39699 51728) PASS NA NA 0 NA NA NA NA NA NA NA 25 23.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF155650 CCDS4451.1, CCDS64340.1 5q35.3 2013-01-09 ENSG00000113269 ENSG00000113269 55819 "RING-type (C3HC4) zinc fingers" 18280 protein-coding gene gene with protein product NA NA 10806348 Standard NM_018434 NM_018434 NA Approved GP, G1RZFP, GOLIATH uc003mll.1 Q86XS8 OTTHUMG00000130909 ENST00000261947.4:c.443-2214C>- chr5.hg19:g.179442525delG 2 3 ref NA False 33 32 PASS 3 PASS ref->hom 0 NA 0,0 21,21 3,3 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RNF130-003 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000374205.1 PASS NA None 25 NA True - G ENST00000261947.4 TRIM10 10107 __UNKNOWN__ __UNKNOWN__ 6 30123292 30123293 __UNKNOWN__ Intron INS - - AC rs150364915|rs370425521 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:30123292_30123293insAC ENST00000449742.2 - 6 1004 TRIM10_ENST00000376704.3_Intron NM_006778.3 NP_006769.2 Q9UDY6 TRI10_HUMAN tripartite motif containing 10 NA NA NA NA erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597) cytoplasm (GO:0005737) zinc ion binding (GO:0008270) NA ovary(1) 1 CAAACAATGTGACACACACACA 0.366 NA NA NA NA NA NA NA NA 338 0.067492 0.1112 0.1023 5008 , , NA 22934 0.0437 NA 0.0328 False NA ,,, NA NA NA 2504 0.044 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 43 50.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.25 NA NA Y07829 CCDS4676.1, CCDS34375.1 6p21.3 2013-01-09 2011-01-25 2001-11-23 ENSG00000204613 ENSG00000204613 10107 "Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers" 10072 protein-coding gene gene with protein product 605701 "tripartite motif-containing 10" RNF9 NA 9271628, 10207104 Standard NM_052828 NA Approved RFB30, HERF1 uc003npo.3 Q9UDY6 OTTHUMG00000031295 ENST00000449742.2:c.928+210->GT chr6.hg19:g.30123301_30123302dupAC 9 2 ref NA False 34 34 PASS 8 PASS ref->het 0 NA 6,6 31,31 6,6 1 1 A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024 True hg19 CCDS34375.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRIM10-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076634.1 PASS NA None 43 NA True - AC ENST00000449742.2 TNXB 7148 __UNKNOWN__ __UNKNOWN__ 6 32052090 32052101 __UNKNOWN__ Intron DEL TCCAGGAAGCCT TCCAGGAAGCCT - rs562578830|rs555588266|rs530294635 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:32052090_32052101delTCCAGGAAGCCT ENST00000375244.3 - 8 3647 TNXB_ENST00000375247.2_Intron P22105 TENX_HUMAN tenascin XB NA NA NA NA actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641) extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578) heparin binding (GO:0008201)|integrin binding (GO:0005178) NA endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1) 8 caccactgcctccaggaagccttcccggagct 0.542 NA NA NA NA NA NA NA NA 494 0.0986422 0.112 0.0389 5008 , , NA 22041 0.0347 NA 0.0994 False NA ,,, NA NA NA 2504 0.1881 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 83 87.44 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.38 NA NA X71923 CCDS4736.1 6p21.3 2013-02-11 ENSG00000168477 ENSG00000168477 7148 "Fibrinogen C domain containing", "Fibronectin type III domain containing" 11976 protein-coding gene gene with protein product 600985 TNXB1, TNXB2 NA 8530023 Standard NM_019105 NM_019105 NA Approved TNXBS, XBS, XB uc021yvf.2 P22105 OTTHUMG00000031088 ENST00000375244.3:c.3445+88AGGCTTCCTGGA>- chr6.hg19:g.32052090_32052101delTCCAGGAAGCCT 0 4 ref NA False 41 31 PASS 1 PASS ref->het 0 NA 13,13 53,53 21,21 1 1 P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNXB-001 PUTATIVE not_organism_supported|basic|appris_candidate_longest protein_coding NA protein_coding OTTHUMT00000268927.2 PASS NA None 83 NA True - TCCAGGAAGCCT ENST00000375244.3 CAPN11 11131 __UNKNOWN__ __UNKNOWN__ 6 44143930 44143931 __UNKNOWN__ Intron INS - - GGAGGAGAACGTCTCCCTGACC rs142573641|rs557654692 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:44143930_44143931insGGAGGAGAACGTCTCCCTGACC ENST00000398776.1 + 8 953 CAPN11_ENST00000542245.1_Intron NM_007058.3 NP_008989.2 Q9UMQ6 CAN11_HUMAN calpain 11 NA NA NA NA proteolysis (GO:0006508) acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737) calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233) NA breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1) 36 all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273) Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536) GACCCTGAGAAGGAGGAGAACG 0.564 NA NA NA NA NA NA NA NA 681 0.135982 0.2042 0.0692 5008 , , NA 17687 0.1052 NA 0.1203 False NA ,,, NA NA NA 2504 0.1391 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 261 289.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.15 NA NA AJ242832 CCDS47436.1 6p12 2013-01-10 ENSG00000137225 ENSG00000137225 11131 "EF-hand domain containing" 1478 protein-coding gene gene with protein product 604822 NA 10409436 Standard NM_007058 NA Approved uc003owt.1 Q9UMQ6 OTTHUMG00000014758 ENST00000398776.1:c.915+42->GGAGGAGAACGTCTCCCTGACC chr6.hg19:g.44143930_44143931insGGAGGAGAACGTCTCCCTGACC 2 4 ref NA False 50 35 PASS 1 PASS ref->het 0 NA 36,36 31,32 197,196 1 1 B2RA64|Q5T3G1|Q8N4R5 True hg19 CCDS47436.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CAPN11-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000040714.3 PASS NA None 261 NA True + GGAGGAGAACGTCTCCCTGACC ENST00000398776.1 PTPRN2 5799 __UNKNOWN__ __UNKNOWN__ 7 157800766 157800767 __UNKNOWN__ Intron DEL TG TG - rs146985842 LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:157800766_157800767delTG ENST00000389418.4 - 11 1733 PTPRN2_ENST00000404321.2_Intron|PTPRN2_ENST00000409483.1_Intron|PTPRN2_ENST00000389416.4_Intron|PTPRN2_ENST00000389413.3_Intron NM_002847.3 NP_002838.2 Q92932 PTPR2_HUMAN protein tyrosine phosphatase, receptor type, N polypeptide 2 NA NA NA NA negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470) endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195) transmembrane receptor protein tyrosine phosphatase activity (GO:0005001) NA NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1) 86 all_neural(206;0.181) all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132) OV - Ovarian serous cystadenocarcinoma(82;0.00463) STAD - Stomach adenocarcinoma(7;0.0875) gtgggtgtgctgtgtgtgggtg 0.559 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 32 38.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.96 NA NA AB002385 CCDS5947.1, CCDS5948.1, CCDS5949.1 7q36 2011-06-09 ENSG00000155093 ENSG00000155093 5799 "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like" 9677 protein-coding gene gene with protein product "IAR PTPRP" 601698 NA 8954911, 9220540 Standard NM_130842 NA Approved KIAA0387, phogrin, ICAAR, IA-2beta uc003wno.3 Q92932 OTTHUMG00000152646 ENST00000389418.4:c.1723+73222CA>- chr7.hg19:g.157800772_157800773delTG 3 2 ref NA False 53 53 PASS 4 PASS ref->het 0 NA 0,1 25,26 7,6 2 2 E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6 True hg19 CCDS5947.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PTPRN2-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000353214.1 PASS NA None 32 NA True - TG ENST00000389418.4 GDAP1 54332 __UNKNOWN__ __UNKNOWN__ 8 75274332 75274333 __UNKNOWN__ Intron DEL AT AT - rs3832592 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:75274332_75274333delAT ENST00000220822.7 + 4 659 GDAP1_ENST00000521096.1_Intron|GDAP1_ENST00000434412.2_Intron NM_001040875.2|NM_018972.2 NP_001035808.1|NP_061845.2 Q8TB36 GDAP1_HUMAN ganglioside induced differentiation associated protein 1 NA NA NA NA cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526) integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634) NA endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 10 Breast(64;0.00769) Myeloproliferative disorder(644;0.0122) BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234) ACCAGTACACATGTTACCTTTG 0.327 NA NA NA NA NA NA NA NA 1395 0.278554 0.3011 0.4207 5008 , , NA 19531 0.2778 NA 0.1889 False NA ,,, NA NA NA 2504 0.2403 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 93 109.09 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.01 NA NA CCDS34911.1, CCDS47877.1 8q13.3 2014-09-17 2012-02-09 54332 15968 protein-coding gene gene with protein product 606598 "Charcot-Marie-Tooth neuropathy 4A" CMT4A NA 8268915, 11743579 Standard NM_018972 NM_018972 NA Approved CMT4 uc003yah.3 Q8TB36 ENST00000220822.7:c.579+119AT>- chr8.hg19:g.75274332_75274333delAT 0 3 ref NA False 105 60 PASS 1 PASS ref->hom 0 NA 0,0 79,80 4,3 1 1 A8K957|E7FJF3|E7FJF4 True hg19 CCDS34911.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GDAP1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000379061.1 PASS NA None 93 NA True + AT ENST00000220822.7 Unknown 0 __UNKNOWN__ __UNKNOWN__ 8 87581724 87581725 __UNKNOWN__ IGR DEL AT AT - rs71275866|rs113989657|rs201429131 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:87581724_87581725delAT NA CPNE3 (7998 upstream) : CNGB3 (4437 downstream) NA NA NA NA NA NA acacacacacatacccacacac 0.525 NA NA NA NA NA NA NA NA 1178 0.235224 0.0764 0.4683 5008 , , NA 15266 0.3651 NA 0.168 False NA ,,, NA NA NA 2504 0.2198 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 140 165.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 2.94 NA NA NA NA NA NA NA chr8.hg19:g.87581724_87581725delAT 0 3 ref NA False 40 37 PASS 1 PASS ref->het 0 NA 25,26 94,97 29,26 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 140 NA True AT RGS22 26166 __UNKNOWN__ __UNKNOWN__ 8 101084648 101084648 __UNKNOWN__ Intron DEL T T - rs398086851|rs34914779 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:101084648delT ENST00000523437.1 - 5 380 RGS22_ENST00000523287.1_Intron|RGS22_ENST00000360863.6_Intron Q8NE09 RGS22_HUMAN regulator of G-protein signaling 22 NA NA NA NA positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032) cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886) GTPase activator activity (GO:0005096) NA RGS22/SYCP1(2) breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1) 68 Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169) CCCTGGTACGTTtttaattct 0.388 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 30 35.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AY009106 CCDS43758.1, CCDS69521.1, CCDS75775.1 8q22.2 2014-01-21 2007-08-14 ENSG00000132554 ENSG00000132554 26166 "Regulators of G-protein signaling" 24499 protein-coding gene gene with protein product 615650 "regulator of G-protein signalling 22" NA Standard NM_015668 XM_005250856 NA Approved DKFZP434I092, PRTD-NY2, CT145 uc003yjb.1 Q8NE09 OTTHUMG00000164802 ENST00000523437.1:c.340-190A>- chr8.hg19:g.101084648delT 4 5 ref NA False 31 31 PASS 5 PASS ref->hom 0 NA 0,0 27,27 3,3 1 1 A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RGS22-006 NOVEL basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000380369.1 PASS NA None 30 NA True - T ENST00000523437.1 CCDC88B 283234 __UNKNOWN__ __UNKNOWN__ 11 64116571 64116571 __UNKNOWN__ Intron DEL G G - LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:64116571delG ENST00000356786.5 + 15 2660 CCDC88B_ENST00000359902.2_Intron|CCDC88B_ENST00000463837.1_Intron|CCDC88B_ENST00000301897.4_Intron NM_032251.5 NP_115627.6 A6NC98 CC88B_HUMAN coiled-coil domain containing 88B NA NA NA NA membrane (GO:0016020) NA endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 27 tcccagcccaggggccttcct 0.577 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 294 300.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.93 NA NA AK090436 CCDS8072.2 11q13.1 2013-03-13 2007-05-31 2007-05-31 ENSG00000168071 ENSG00000168071 283234 26757 protein-coding gene gene with protein product "brain leucine zipper protein", "GRP78-interacting protein induced by ER stress" 611205 "coiled-coil domain containing 88" CCDC88 NA 15882442, 21289099 Standard NM_032251 NM_032251 NA Approved FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE uc001nzy.3 A6NC98 OTTHUMG00000045419 ENST00000356786.5:c.2617-232G>- chr11.hg19:g.64116571delG 3 4 ref NA False 52 52 PASS 4 PASS ref->het 0 NA 217,219 41,42 34,32 1 1 A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1 True hg19 CCDS8072.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCDC88B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000104845.1 PASS NA None 294 NA True + G ENST00000356786.5 GPHA2 170589 __UNKNOWN__ __UNKNOWN__ 11 64702765 64702766 __UNKNOWN__ Intron INS - - TCTG rs2307669|rs56339918|rs68036531 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:64702765_64702766insTCTG ENST00000279168.2 - 2 158 GPHA2_ENST00000532246.1_Intron|GPHA2_ENST00000533257.1_Intron NM_130769.3 NP_570125.1 Q96T91 GPHA2_HUMAN glycoprotein hormone alpha 2 NA NA NA NA extracellular region (GO:0005576) NA central_nervous_system(1)|endometrium(1)|prostate(1) 3 CCACCGTCCACTCAGCTCTTTG 0.653 NA NA NA NA NA NA NA NA 2344 0.468051 0.4402 0.4078 5008 , , NA 18601 0.251 NA 0.674 False NA ,,, NA NA NA 2504 0.5603 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 60 69.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AF260739 CCDS8086.1 11q13.1 2008-07-18 ENSG00000149735 170589 18054 protein-coding gene gene with protein product "glycoprotein alpha 2", "cysteine knot protein" 609651 NA 11809971 Standard NM_130769 NM_130769 NA Approved GPA2, ZSIG51, A2, MGC126572 uc001oca.3 Q96T91 ENST00000279168.2:c.103+63->CAGA chr11.hg19:g.64702765_64702766insTCTG 1 3 ref NA False 62 52 PASS 0 PASS ref->hom 0 NA 0,0 51,53 10,9 1 1 Q52LE2 True hg19 CCDS8086.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GPHA2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000385470.1 PASS NA None 60 NA True - TCTG ENST00000279168.2 NOVA1-AS1 387977 __UNKNOWN__ __UNKNOWN__ 14 27231124 27231125 __UNKNOWN__ RNA INS - - C rs374348524|rs148102823 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:27231124_27231125insC ENST00000548328.1 + 0 19 NOVA1-AS1_ENST00000552826.1_RNA NOVA1 antisense RNA 1 (head to head) NA NA NA NA NA NA atgtgagagattaggttgtgtg 0.49 NA NA NA NA NA NA NA NA C|-|C|deletion 990 0.197684 0.3548 0.1311 5008 , , NA 18775 0.0694 NA 0.2078 False NA ,,, NA NA NA 2504 0.1544 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 71 73.76 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 NA NA AI278049 14q12 2012-10-15 2012-10-15 2011-11-25 ENSG00000257842 ENSG00000257842 387977 "Long non-coding RNAs" 19827 non-coding RNA RNA, long non-coding NA "chromosome 14 open reading frame 22", "NOVA1 antisense RNA 1 (non-protein coding)", "NOVA1 antisense RNA 1" C14orf22 NA Standard NA Approved OTTHUMG00000170389 ENST00000548328.1: chr14.hg19:g.27231124_27231125insC 1 2 ref NA False 58 57 PASS 0 PASS ref->het 0 NA 9,9 56,58 9,7 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NOVA1-AS1-004 KNOWN basic antisense NA antisense OTTHUMT00000409031.1 PASS NA None 71 NA True + C ENST00000548328.1 ZBTB42 100128927 __UNKNOWN__ __UNKNOWN__ 14 105269239 105269239 __UNKNOWN__ 3'UTR DEL C C - LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:105269239delC ENST00000342537.7 + 0 1990 NM_001137601.1 NP_001131073.1 B2RXF5 ZBT42_HUMAN zinc finger and BTB domain containing 42 NA NA NA NA negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) NA NA CCTGGCCCCACGCTAGGTGAA 0.602 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 275 266.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.01 NA NA AX721091 CCDS45174.1 14q32.33 2013-01-09 ENSG00000179627 100128927 "-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type" 32550 protein-coding gene gene with protein product 613915 NA Standard NM_001137601 NA Approved ZNF925 uc001ypp.3 B2RXF5 ENST00000342537.7:c.*436C>- chr14.hg19:g.105269239delC 0 5 ref NA False 46 46 PASS 1 PASS ref->het 0 NA 211,214 38,38 24,23 1 1 B7ZW21 True hg19 CCDS45174.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZBTB42-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000410372.1 PASS NA None 275 NA True + C ENST00000342537.7 Unknown 0 __UNKNOWN__ __UNKNOWN__ 17 15670734 15670734 __UNKNOWN__ IGR DEL A A - rs150402750|rs112823963 LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:15670734delA NA AC005324.7 (3651 upstream) : RNA5SP436 (14920 downstream) NA NA NA NA NA NA GGGAACAAACATTTAACTAGT 0.458 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 30 30.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA chr17.hg19:g.15670734delA 0 4 ref NA False 50 48 PASS 1 PASS ref->hom 0 NA 0,0 28,28 2,2 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 30 NA True A SCN4A 6329 __UNKNOWN__ __UNKNOWN__ 17 62020564 62020576 __UNKNOWN__ Intron DEL AGAGATGACAGAG AGAGATGACAGAG - rs78341328|rs111745569|rs150461653|rs531252158|rs113825196|rs117323879 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:62020564_62020576delAGAGATGACAGAG ENST00000578147.1 - 23 4094 SCN4A_ENST00000435607.1_Intron P35499 SCN4A_HUMAN sodium channel, voltage-gated, type IV, alpha subunit NA NA NA NA membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814) integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518) voltage-gated sodium channel activity (GO:0005248) NA breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 101 Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909) cagagatgacagagatgacagagagagagagag 0.587 NA NA NA NA NA NA NA NA 1867 0.372804 0.5015 0.3228 5008 , , NA 21183 0.4216 NA 0.3569 False NA ,,, NA NA NA 2504 0.2004 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 83 88 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.62 NA NA U24693 17q23.3 2012-02-26 2007-01-23 6329 "Sodium channels", "Voltage-gated ion channels / Sodium channels" 10591 protein-coding gene gene with protein product 603967 HYKPP NA 1654742, 1659948, 16382098 Standard NM_000334 XM_005257566 NA Approved Nav1.4, HYPP, SkM1 uc002jds.1 P35499 ENST00000578147.1:c.4018-108CTCTGTCATCTCT>- chr17.hg19:g.62020564_62020576delAGAGATGACAGAG 0 2 ref NA False 61 60 PASS 1 PASS ref->het 0 NA 13,13 55,60 16,12 1 1 Q15478|Q16447|Q7Z6B1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SCN4A-001 KNOWN non_canonical_U12|basic|appris_candidate_longest protein_coding NA protein_coding OTTHUMT00000444562.1 PASS NA None 83 NA True - AGAGATGACAGAG ENST00000578147.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 17 64881643 64881644 __UNKNOWN__ IGR INS - - C rs397977799|rs57544567 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:64881643_64881644insC NA CACNG5 (40 upstream) : RNA5SP446 (9963 downstream) NA NA NA NA NA NA AGCCAGCAGCTCCCCCCAAGCC 0.599 NA NA NA NA NA NA NA NA CCCCCC|CCCCCC|CCCCCCC|insertion 1201 0.239816 0.4039 0.1297 5008 , , NA 18553 0.1597 NA 0.2207 False NA ,,, NA NA NA 2504 0.1984 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 73 78.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.19 NA NA NA NA NA NA NA chr17.hg19:g.64881649_64881649dupC 7 7 ref NA False 62 58 PASS 6 PASS ref->het 0 NA 5,5 57,57 10,10 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 73 NA True C KANK2 25959 __UNKNOWN__ __UNKNOWN__ 19 11303699 11303718 __UNKNOWN__ Frame_Shift_Del DEL GCTGTGCGGGGGCGCCAGCG GCTGTGCGGGGGCGCCAGCG - rs542262538|rs118109949|rs537320085|rs147307664|rs143966820 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:11303699_11303718delGCTGTGCGGGGGCGCCAGCG ENST00000432929.2 - 4 1398_1417 c.1038_1057delCGCTGGCGCCCCCGCACAGC c.(1036-1059)gccgctggcgcccccgcacagcggfs p.AGAPAQR347fs KANK2_ENST00000355150.5_Frame_Shift_Del_p.AGAPAQR347fs|KANK2_ENST00000589359.1_Frame_Shift_Del_p.AGAPAQR347fs|KANK2_ENST00000586659.1_Frame_Shift_Del_p.AGAPAQR347fs|KANK2_ENST00000589894.1_Frame_Shift_Del_p.AGAPAQR347fs NM_001136191.2 NP_001129663.1 Q63ZY3 KANK2_HUMAN KN motif and ankyrin repeat domains 2 347 NA NA NA apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|mitochondrion (GO:0005739) NA endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 14 CTCTGGGCCCGCTGTGCGGGGGCGCCAGCGGCTGTGCTGG 0.718 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 310 293.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.5 NA NA AK000011 CCDS12255.1, CCDS54219.1 19p13.2 2013-01-10 2008-01-29 2008-01-29 ENSG00000197256 25959 "KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing" 29300 protein-coding gene gene with protein product 614610 "matrix-remodelling associated 3", "ankyrin repeat domain 25" MXRA3, ANKRD25 NA 10819331, 17996375, 19554261 Standard NM_015493 NM_015493 NA Approved KIAA1518 uc002mqm.3 Q63ZY3 ENST00000432929.2:c.1038_1057delCGCTGGCGCCCCCGCACAGC chr19.hg19:g.11303699_11303718delGCTGTGCGGGGGCGCCAGCG ENSP00000395650:p.Ala347fs 0 4 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 278,284 9,11 56,52 1 1 B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210 True hg19 CCDS54219.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KANK2-202 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000453143.1 PASS NA None 310 NA True - GCTGTGCGGGGGCGCCAGCG ENST00000432929.2 UNC13A 23025 __UNKNOWN__ __UNKNOWN__ 19 17715670 17715671 __UNKNOWN__ 3'UTR INS - - TC rs138757763 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:17715670_17715671insTC ENST00000519716.2 - 0 6303_6304 UNC13A_ENST00000252773.7_3'UTR|UNC13A_ENST00000428389.2_3'UTR NM_001080421.2 NP_001073890.2 Q9UPW8 UN13A_HUMAN unc-13 homolog A (C. elegans) NA NA NA NA beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188) axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734) diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075) NA breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2) 61 GTGTTTGTGTTtctctctctct 0.446 NA NA NA NA NA NA NA NA 219 0.04373 0.0688 0.0677 5008 , , NA 20330 0.001 NA 0.0716 False NA ,,, NA NA NA 2504 0.0082 NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 113 117.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA AB028955 CCDS46013.1, CCDS46013.2 19p13.12 2008-02-05 ENSG00000130477 23025 23150 protein-coding gene gene with protein product 609894 NA Standard XM_038604 NM_001080421 NA Approved KIAA1032, Munc13-1 uc031rjv.1 Q9UPW8 ENST00000519716.2:c.*1193->GA chr19.hg19:g.17715679_17715680dupTC 7 4 ref NA False 38 38 PASS 6 PASS ref->het 0 NA 52,55 30,30 30,31 2 2 E5RHY9 True hg19 CCDS46013.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UNC13A-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000376169.2 PASS NA None 113 NA True - TC ENST00000519716.2 TPRX1 284355 __UNKNOWN__ __UNKNOWN__ 19 48321645 48321646 __UNKNOWN__ Intron INS - - TCCA rs371553571|rs201507309|rs113740908 LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:48321645_48321646insTCCA ENST00000535759.1 - 2 151 Q8N7U7 TPRX1_HUMAN tetra-peptide repeat homeobox 1 NA NA NA NA nucleus (GO:0005634) DNA binding (GO:0003677) NA endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1) 18 all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133) OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048) ccatccatccctccatccatcc 0.495 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(123;175 2281 3051 32395) PASS NA NA 0 NA NA NA NA NA NA NA 47 55.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.43 NA NA CCDS33066.1 19q13.33 2011-07-08 ENSG00000178928 ENSG00000178928 284355 "Homeoboxes / PRD class" 32174 protein-coding gene gene with protein product 611166 NA Standard NM_198479 XM_005258788 NA Approved FLJ40321 uc002php.2 Q8N7U7 ENST00000535759.1:c.151+78->TGGA chr19.hg19:g.48321650_48321653dupTCCA 7 5 ref NA False 32 32 PASS 6 PASS ref->het 0 NA 3,3 31,34 20,20 1 1 A5D8Y3|B2RPL5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TPRX1-201 KNOWN basic|appris_principal protein_coding NA protein_coding PASS NA None 47 NA True - TCCA ENST00000535759.1 RFPL4A 342931 __UNKNOWN__ __UNKNOWN__ 19 56273143 56273144 __UNKNOWN__ Intron INS - - T rs376429665 LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:56273143_56273144insT ENST00000434937.2 + 2 162 NM_001145014.1 NP_001138486.1 A6NLU0 RFPLA_HUMAN ret finger protein-like 4A NA NA NA NA zinc ion binding (GO:0008270) NA haematopoietic_and_lymphoid_tissue(1)|stomach(1) 2 TTCTGTGTTCATTTTTTTTCTA 0.381 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 26 36.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA CCDS46201.1 19q13.42 2013-02-22 2007-01-19 2007-01-19 ENSG00000223638 ENSG00000223638 342931 "RING-type (C3HC4) zinc fingers" 16449 protein-coding gene gene with protein product 612601 "ret finger protein-like 4" RFPL4 NA 11850190 Standard XM_292796 NM_001145014 NA Approved RNF210 uc010yge.2 A6NLU0 OTTHUMG00000165449 ENST00000434937.2:c.-9-14->T chr19.hg19:g.56273151_56273151dupT 9 9 ref NA False 68 66 PASS 8 PASS ref->het 0 NA 0,2 5,9 20,23 2 2 True hg19 CCDS46201.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RFPL4A-001 NOVEL upstream_ATG|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000384184.1 PASS NA None 26 NA True + T ENST00000434937.2 RFPL4A 342931 __UNKNOWN__ __UNKNOWN__ 19 56274503 56274508 __UNKNOWN__ In_Frame_Del DEL TCCGCT TCCGCT - rs140087406|rs147984855|rs149792632 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:56274503_56274508delTCCGCT ENST00000434937.2 + 3 997_1002 c.826_831delTCCGCT c.(826-831)tccgctdel p.SA276del NM_001145014.1 NP_001138486.1 A6NLU0 RFPLA_HUMAN ret finger protein-like 4A 276 B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}. NA NA NA zinc ion binding (GO:0008270) NA haematopoietic_and_lymphoid_tissue(1)|stomach(1) 2 GATCAATCCATCCGCTGCCAGTGCCC 0.432 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 215 266.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.85 NA NA CCDS46201.1 19q13.42 2013-02-22 2007-01-19 2007-01-19 ENSG00000223638 ENSG00000223638 342931 "RING-type (C3HC4) zinc fingers" 16449 protein-coding gene gene with protein product 612601 "ret finger protein-like 4" RFPL4 NA 11850190 Standard XM_292796 NM_001145014 NA Approved RNF210 uc010yge.2 A6NLU0 OTTHUMG00000165449 ENST00000434937.2:c.826_831delTCCGCT chr19.hg19:g.56274503_56274508delTCCGCT ENSP00000392936:p.Ser276_Ala277del 0 2 ref NA False 60 60 PASS 1 PASS ref->het 0 NA 169,195 8,10 40,54 1 1 True hg19 CCDS46201.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RFPL4A-001 NOVEL upstream_ATG|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000384184.1 PASS NA None 215 NA True + TCCGCT ENST00000434937.2 SMARCB1 6598 __UNKNOWN__ __UNKNOWN__ 22 24158827 24158827 __UNKNOWN__ Intron DEL C C - rs34737764 byFrequency LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:24158827delC ENST00000407082.3 + 5 649 SMARCB1_ENST00000477836.1_3'UTR|SMARCB1_ENST00000263121.7_Intron|SMARCB1_ENST00000407422.3_Intron|SMARCB1_ENST00000344921.6_Intron Q12824 SNF5_HUMAN SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 NA NA NA NA ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351) nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741) p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713) NA bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194) 458 Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05) AGGAAGGCCACCCCCAGTGCC 0.612 NA NA "D, N, F, S" malignant rhabdoid malignant rhabdoid NA NA NA NA NA NA CCCTC|CCCCC|CCCC|complex_deletion 735 0.146765 0.1354 0.0778 5008 , , NA 20399 0.0923 NA 0.1223 False NA ,,, NA NA NA 2504 0.2924 NA NA NA PASS yes Rec yes Rhabdoid predisposition syndrome 22 22q11 6598 "SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1" NA M 0 NA NA NA NA NA NA NA 51 57.33 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA U04847 CCDS13817.1, CCDS46671.1 22q11.23 2014-09-17 ENSG00000099956 ENSG00000099956 6598 11103 protein-coding gene gene with protein product "sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144" 601607 SNF5L1 NA 7801128, 10319872, 10365963 Standard NM_003073 NM_003073 NA Approved BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144 uc002zyb.3 Q12824 OTTHUMG00000150737 ENST00000407082.3:c.491-130C>- chr22.hg19:g.24158827delC 4 7 ref NA False 72 66 PASS 5 PASS ref->het 0 NA 4,4 40,41 7,6 1 1 O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SMARCB1-003 NOVEL not_organism_supported|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000319874.1 PASS NA None 51 NA True + C ENST00000407082.3 PCYT1B 9468 __UNKNOWN__ __UNKNOWN__ X 24579215 24579215 __UNKNOWN__ 3'UTR DEL A A - LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:24579215delA ENST00000379145.1 - 0 2295 NM_001163264.1 NP_001156736.1 Q9Y5K3 PCY1B_HUMAN phosphate cytidylyltransferase 1, choline, beta NA NA NA NA CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283) cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789) choline-phosphate cytidylyltransferase activity (GO:0004105) NA breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1) 17 Choline(DB00122) CCACGAGAACAAAATACTAAT 0.413 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA 0 NA NA NA NA NA NA NA 119 133.75 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA AF052510 CCDS14213.1, CCDS55391.1, CCDS55392.1 Xp22 2008-02-05 2005-09-05 ENSG00000102230 ENSG00000102230 9468 2.7.7.15 8755 protein-coding gene gene with protein product 604926 "phosphate cytidylyltransferase 1, choline, beta isoform" NA 9593753 Standard NM_004845 NM_004845 NA Approved CCT-beta, CTB uc004dbi.3 Q9Y5K3 OTTHUMG00000021270 ENST00000379145.1:c.*1195T>- chrX.hg19:g.24579215delA 3 6 ref NA False 32 32 PASS 4 PASS ref->het 0 NA 84,86 19,19 15,13 1 1 A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9 True hg19 CCDS55392.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PCYT1B-003 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000056102.2 PASS NA None 119 NA True - A ENST00000379145.1 SSX1 6756 __UNKNOWN__ __UNKNOWN__ X 48118245 48118246 __UNKNOWN__ Intron INS - - AC rs35066850|rs5902415 LTS-036_T LTS-036_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:48118245_48118246insAC ENST00000376919.3 + 4 416 NM_001278691.1|NM_005635.2 NP_001265620.1|NP_005626.1 Q16384 SSX1_HUMAN synovial sarcoma, X breakpoint 1 NA NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714) NA SS18/SSX1(1169)|SS18L1/SSX1(2) endometrium(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1) 9 aaacatgcaaaagtaatatgta 0.327 NA NA T SS18 synovial sarcoma NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(175;994 1982 2214 6527 18857) PASS Dom yes X Xp11.23-p11.22 6756 "synovial sarcoma, X breakpoint 1" NA M 0 NA NA NA NA NA NA NA 19 20.05 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA BC001003 CCDS14290.1 Xp11.23 2009-03-12 ENSG00000126752 ENSG00000126752 6756 11335 protein-coding gene gene with protein product "cancer/testis antigen family 5, member 1" 312820 NA 7655467 Standard NM_005635 NM_005635 NA Approved CT5.1 uc004djb.1 Q16384 OTTHUMG00000021488 ENST00000376919.3:c.280+179->AC chrX.hg19:g.48118245_48118246insAC 1 4 ref NA False 52 51 PASS 0 PASS ref->hom 0 NA 0,0 17,18 2,2 1 1 A3KN76|Q08AJ2|Q5JQ64 True hg19 CCDS14290.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SSX1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000056485.1 PASS NA None 19 NA True + AC ENST00000376919.3 FCN3 8547 __UNKNOWN__ __UNKNOWN__ 1 27699964 27699964 __UNKNOWN__ Intron DEL C C - LTS-037_T LTS-037_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:27699964delC ENST00000270879.4 - 4 271 FCN3_ENST00000354982.2_Intron NM_003665.2 NP_003656.2 O75636 FCN3_HUMAN ficolin (collagen/fibrinogen domain containing) 3 NA NA NA complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087) blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576) carbohydrate binding (GO:0030246) NA endometrium(2)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1) 7 all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419) CTGGCTCCTGCAAGGGCTGCC 0.602 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 208 208.2 NA NA NA NA NA 76 66 70 NA NA NA NA 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 27699964 NA 2203 4300 6503 SO:0001627 intron_variant 0.98 D88587 CCDS300.1, CCDS301.1 1p36.11 2014-09-17 2013-09-12 ENSG00000142748 ENSG00000142748 8547 "Fibrinogen C domain containing" 3625 protein-coding gene gene with protein product "Hakata antigen" 604973 "ficolin (collagen/fibrinogen domain-containing) 3 (Hakata antigen)" NA 9694814, 10330454 Standard NM_003665 NA Approved FCNH, HAKA1 uc001boa.3 O75636 OTTHUMG00000005722 ENST00000270879.4:c.265+14G>- chr1.hg19:g.27699964delC 0 2 ref NA False 80 80 PASS 1 PASS ref->het 0 NA 129,131 55,55 29,27 1 1 Q6IBJ5|Q8WW86 True hg19 CCDS300.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FCN3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000015667.1 PASS NA None 208 NA True - C ENST00000270879.4 SERINC2 347735 __UNKNOWN__ __UNKNOWN__ 1 31896574 31896575 __UNKNOWN__ Frame_Shift_Del DEL TG TG - LTS-037_T LTS-037_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:31896574_31896575delTG ENST00000373709.3 + 2 224_225 c.74_75delTG c.(73-75)ctgfs p.L25fs SERINC2_ENST00000536859.1_Frame_Shift_Del_p.L29fs|SERINC2_ENST00000373710.1_Frame_Shift_Del_p.L34fs|SERINC2_ENST00000536384.1_Frame_Shift_Del_p.L29fs|SERINC2_ENST00000491976.1_3'UTR NM_178865.4 NP_849196.2 Q96SA4 SERC2_HUMAN serine incorporator 2 25 NA NA phosphatidylserine metabolic process (GO:0006658)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665) extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021) L-serine transmembrane transporter activity (GO:0015194) NA cervix(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2) 12 Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123) STAD - Stomach adenocarcinoma(196;0.0541)|READ - Rectum adenocarcinoma(331;0.151) CCCTGCATCCTGTGCAGCTGCT 0.653 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 116 120.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.18 AY094595 CCDS30662.1, CCDS55583.1, CCDS55584.1, CCDS55585.1 1p35.1 2008-02-05 2005-11-01 2005-11-01 ENSG00000168528 ENSG00000168528 347735 23231 protein-coding gene gene with protein product 614549 "tumor differentially expressed 2-like" TDE2L NA 12949800 Standard NM_018565 NM_178865 NA Approved FKSG84, PRO0899, TDE2 uc010ogh.2 Q96SA4 OTTHUMG00000003796 ENST00000373709.3:c.74_75delTG chr1.hg19:g.31896576_31896577delTG ENSP00000362813:p.Leu25fs 1 2 ref NA False 111 111 PASS 2 PASS ref->het 0 NA 71,75 23,24 23,18 1 1 A0AVB4|B4DJK5|B7Z567|B7ZAP2|E7EUZ9|Q86Y23 True hg19 CCDS30662.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SERINC2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000010680.1 PASS NA None 116 NA True + TG ENST00000373709.3 PABPC4 8761 __UNKNOWN__ __UNKNOWN__ 1 40026829 40026829 __UNKNOWN__ Intron DEL A A - LTS-037_T LTS-037_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:40026829delA ENST00000372862.3 - 15 2163 PABPC4_ENST00000372857.3_Intron|PABPC4_ENST00000372856.3_Intron|PABPC4_ENST00000372858.3_Intron Q13310 PABP4_HUMAN poly(A) binding protein, cytoplasmic 4 (inducible form) NA NA NA blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412) cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529) nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266) NA NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3) 21 Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457) ATAAATGCATAATCAAATAAT 0.343 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 290 297.33 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.55 U33818 CCDS438.1, CCDS44114.1, CCDS44115.1 1p34.2 2013-02-12 2001-11-28 ENSG00000090621 ENSG00000090621 8761 "RNA binding motif (RRM) containing" 8557 protein-coding gene gene with protein product 603407 "poly(A)-binding protein, cytoplasmic 4 (inducible form)" NA 10543404 Standard NM_001135653 NM_001135653 NA Approved iPABP, APP-1 uc001cdl.2 Q13310 OTTHUMG00000009097 ENST00000372862.3:c.1846-35T>- chr1.hg19:g.40026829delA 1 3 ref NA False 90 90 PASS 2 PASS ref->het 0 NA 178,181 69,71 40,37 1 1 B1ANQ8|Q4VC03|Q6P0N3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PABPC4-003 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000025222.1 PASS NA None 290 NA True - A ENST00000372862.3 PLCG2 5336 __UNKNOWN__ __UNKNOWN__ 16 81902730 81902730 __UNKNOWN__ Intron DEL C C - rs201053730|rs77062887 byFrequency LTS-037_T LTS-037_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:81902730delC ENST00000359376.3 + 6 693 PLCG2_ENST00000565400.1_Intron NM_002661.3 NP_002652.2 P16885 PLCG2_HUMAN phospholipase C, gamma 2 (phosphatidylinositol-specific) NA NA NA B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886) phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871) NA NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1) 58 TCATAGAGGGCTGCCTGAGGT 0.498 NA NA NA NA NA NA C|C|-|deletion 1111 0.221845 0.093 0.2334 5008 , , NA 23481 0.4831 NA 0.1173 False NA ,,, NA NA NA 2504 0.226 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 50 59.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS42204.1 16q24.1 2014-09-17 ENSG00000197943 5336 3.1.4.11 "SH2 domain containing" 9066 protein-coding gene gene with protein product 600220 NA 7835906 Standard XR_248240 NA Approved uc002fgt.3 P16885 ENST00000359376.3:c.480-89C>- chr16.hg19:g.81902730delC 0 4 ref NA False 81 69 PASS 1 PASS ref->het 0 NA 4,4 43,43 3,4 1 1 D3DUL3|Q3ZTS2|Q59H45|Q969T5 True hg19 CCDS42204.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PLCG2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000432429.1 PASS NA None 50 NA True + C ENST00000359376.3 TP53 7157 __UNKNOWN__ __UNKNOWN__ 17 7579427 7579427 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-037_T LTS-037_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:7579427delG ENST00000269305.4 - 4 449 c.260delC c.(259-261)ccafs p.P87fs TP53_ENST00000359597.4_Frame_Shift_Del_p.P87fs|TP53_ENST00000445888.2_Frame_Shift_Del_p.P87fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.P87fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.P87fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.P87fs NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 87 Interaction with WWOX. NA P -> Q (in sporadic cancers; somatic mutation). NA apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032) chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657) ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270) p.0?(8)|p.A76_S90del15(3)|p.P87Q(3)|p.G59fs*23(3)|p.V73fs*9(1)|p.A86fs*59(1)|p.D48fs*55(1)|p.P85fs*58(1)|p.A86fs*34(1)|p.S33fs*23(1)|p.A86fs*33(1)|p.A86fs*32(1)|p.P85fs*59(1)|p.A79_A88del10(1)|p.P13fs*18(1)|p.P87fs*54(1)|p.A83fs*35(1) NA NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) Acetylsalicylic acid(DB00945) GGAGGGGGCTGGTGCAGGGGC 0.627 NA 111 "Mis, N, F" NA "breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types" "breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types" NA Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(47;798 1329 9957 10801) PASS yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 NA "L, E, M, O" 30 Deletion - Frameshift(15)|Whole gene deletion(8)|Deletion - In frame(4)|Substitution - Missense(3) upper_aerodigestive_tract(5)|haematopoietic_and_lymphoid_tissue(5)|lung(4)|bone(4)|central_nervous_system(3)|ovary(3)|urinary_tract(2)|stomach(1)|soft_tissue(1)|breast(1)|prostate(1) NA NA NA NA NA 37 35.94 NA NA NA NA NA 47 54 51 NA NA NA NA 17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7579427 NA 2202 4298 6500 SO:0001589 frameshift_variant 0 Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; AF307851 CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1 17p13.1 2014-09-17 2008-01-16 ENSG00000141510 ENSG00000141510 7157 11998 protein-coding gene gene with protein product "Li-Fraumeni syndrome" 191170 NA 6396087, 3456488, 2047879 Standard NM_000546 NM_001126115 NA Approved p53, LFS1 uc002gij.3 P04637 OTTHUMG00000162125 ENST00000269305.4:c.260delC chr17.hg19:g.7579427delG ENSP00000269305:p.Pro87fs 1 3 ref NA False 72 71 PASS 2 PASS ref->het 0 NA 7,7 22,22 8,8 1 1 Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61 True hg19 CCDS11118.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TP53-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000367397.1 PASS NA None 37 NA True - G ENST00000269305.4 GABRE 2564 __UNKNOWN__ __UNKNOWN__ X 151122554 151122555 __UNKNOWN__ 3'UTR INS - - C LTS-037_T LTS-037_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:151122554_151122555insC ENST00000370328.3 - 0 2192_2193 GABRE_ENST00000370325.1_3'UTR|GABRE_ENST00000483564.1_5'UTR NM_004961.3 NP_004952.2 P78334 GBRE_HUMAN gamma-aminobutyric acid (GABA) A receptor, epsilon NA NA NA gamma-aminobutyric acid signaling pathway (GO:0007214)|transport (GO:0006810) cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211) chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890) NA breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|skin(1) 27 Acute lymphoblastic leukemia(192;6.56e-05) Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897) CTCTCTTGCTGCCCCCCCCTCT 0.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 57 57.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 Y09765 CCDS14703.1 Xq28 2012-06-22 ENSG00000102287 ENSG00000102287 2564 "GABA receptors", "Ligand-gated ion channels / GABA(A) receptors" 4085 protein-coding gene gene with protein product "GABA(A) receptor, epsilon" 300093 NA 9039914, 9084408 Standard NM_004961, NM_021990, NM_021984 NM_004961 NA Approved uc004ffi.3 P78334 OTTHUMG00000024176 ENST00000370328.3:c.*619->G chrX.hg19:g.151122562_151122562dupC 9 9 ref NA False 38 38 PASS 8 PASS ref->het 0 NA 11,11 36,37 12,11 1 1 E7ET93|O15345|O15346|Q6PCD2|Q99520 True hg19 CCDS14703.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GABRE-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000060903.1 PASS NA None 57 NA True - C ENST00000370328.3 THEM5 284486 __UNKNOWN__ __UNKNOWN__ 1 151825981 151825981 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:151825981delC ENST00000368817.5 - 1 192 c.61delG c.(61-63)gccfs p.A21fs NM_182578.3 NP_872384 Q8N1Q8 ACO15_HUMAN thioesterase superfamily member 5 21 NA NA NA cardiolipin acyl-chain remodeling (GO:0035965)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA metabolic process (GO:0035336) mitochondrial matrix (GO:0005759) palmitoyl-CoA hydrolase activity (GO:0016290) NA NA breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2) 15 Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14) LUSC - Lung squamous cell carcinoma(543;0.181) ATACGGGGGGCCTCAAGAAGG 0.582 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 246 239.9 NA NA NA 101 101 101 NA NA NA NA 1 NA NA NA NA NA NA 151825981 2203 4300 6503 SO:0001589 frameshift_variant 1.13 NA NA AK095283 CCDS1005.1 1q21.3 2008-02-05 ENSG00000196407 ENSG00000196407 284486 26755 protein-coding gene gene with protein product 615653 NA Standard NM_182578 NM_182578 NA Approved FLJ37964 uc021oyw.1 Q8N1Q8 OTTHUMG00000013070 ENST00000368817.5:c.61delG chr1.hg19:g.151825981delC ENSP00000357807:p.Ala21fs 1 6 ref NA False 38 38 PASS 2 PASS ref->het 0 NA 169,170 45,46 32,31 1 1 Q5T1C3 True hg19 CCDS1005.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA THEM5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000036678.2 PASS NA None 246 True - C ENST00000368817.5 NID1 4811 __UNKNOWN__ __UNKNOWN__ 1 236140339 236140357 __UNKNOWN__ 3'UTR DEL ATAATTAGTAATCTTTGGT ATAATTAGTAATCTTTGGT - LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:236140339_236140357delATAATTAGTAATCTTTGGT ENST00000264187.6 - 0 4636_4654 NID1_ENST00000366595.3_3'UTR NM_002508.2 NP_002499.2 P14543 NID1_HUMAN nidogen 1 NA NA NA NA basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811) basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062) calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394) NA NA breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1) 66 Ovarian(103;0.0544)|Breast(184;0.23) all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229) OV - Ovarian serous cystadenocarcinoma(106;0.00162) Urokinase(DB00013) GCAAAGAGGAATAATTAGTAATCTTTGGTATAATTTAAG 0.393 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 291 268.21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.31 NA NA BC045606 CCDS1608.1 1q43 2011-05-08 2005-06-02 2005-06-02 ENSG00000116962 ENSG00000116962 4811 7821 protein-coding gene gene with protein product 131390 "nidogen (enactin)" NID NA 2471408, 7557988 Standard NM_002508 NM_002508 NA Approved entactin uc001hxo.3 P14543 OTTHUMG00000040071 ENST00000264187.6:c.*828ACCAAAGATTACTAATTAT>- chr1.hg19:g.236140339_236140357delATAATTAGTAATCTTTGGT 0 4 ref NA False 50 50 PASS 1 PASS ref->het 0 NA 239,241 37,37 48,47 2 2 Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7 True hg19 CCDS1608.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NID1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000096647.2 PASS NA None 291 True - ATAATTAGTAATCTTTGGT ENST00000264187.6 SUPT7L 9913 __UNKNOWN__ __UNKNOWN__ 2 27875017 27875020 __UNKNOWN__ 3'UTR DEL AAAT AAAT - rs140128093 LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:27875017_27875020delAAAT ENST00000337768.5 - 0 3146_3149 NM_001282729.1|NM_014860.1 NP_001269658.1|NP_055675.1 O94864 ST65G_HUMAN suppressor of Ty 7 (S. cerevisiae)-like NA NA NA NA chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|maintenance of protein location in nucleus (GO:0051457)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634)|STAGA complex (GO:0030914) transcription coactivator activity (GO:0003713) NA NA endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(2)|urinary_tract(1) 16 Acute lymphoblastic leukemia(172;0.155) tccatctcaaaaataaataaataa 0.368 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 36 44.82 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA AF197954 CCDS42667.1, CCDS62885.1, CCDS62886.1 2p23.3 2008-02-05 ENSG00000119760 ENSG00000119760 9913 30632 protein-coding gene gene with protein product 612762 NA 9872452, 11564863 Standard NM_014860 NM_001282732 NA Approved STAF65, gamma, KIAA0764, SPT7L uc002rli.1 O94864 OTTHUMG00000151947 ENST00000337768.5:c.*1335ATTT>- chr2.hg19:g.27875025_27875028delAAAT 5 8 ref NA False 54 54 PASS 6 PASS ref->het 0 NA 1,1 27,29 8,8 1 1 B4E3W3|Q6IB21|Q9H2T6 True hg19 CCDS42667.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SUPT7L-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000324568.1 PASS NA None 36 True - AAAT ENST00000337768.5 CCT4 10575 __UNKNOWN__ __UNKNOWN__ 2 62095772 62095773 __UNKNOWN__ 3'UTR INS - - TTCCA LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:62095772_62095773insTTCCA ENST00000394440.3 - 0 1970_1971 CCT4_ENST00000544185.1_3'UTR|CCT4_ENST00000461540.2_5'UTR|CCT4_ENST00000544079.1_3'UTR|AC107081.5_ENST00000425779.1_RNA|CCT4_ENST00000538252.1_3'UTR NM_006430.3 NP_006421.2 P50991 TCPD_HUMAN chaperonin containing TCP1, subunit 4 (delta) NA NA NA NA 'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457) cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199) ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082) NA NA breast(1)|large_intestine(2)|lung(6)|ovary(2) 11 Lung NSC(7;0.035)|all_lung(7;0.0691) LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221) AGGTGATCTTCTTCCATTCCAG 0.381 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 317 303.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.23 NA NA CCDS33206.1, CCDS58711.1 2p15 2011-09-02 ENSG00000115484 ENSG00000115484 10575 "Heat Shock Proteins / Chaperonins" 1617 protein-coding gene gene with protein product 605142 NA 9819444 Standard NM_001256721 NA Approved Cctd uc002sbo.4 P50991 OTTHUMG00000152166 ENST00000394440.3:c.*55->TGGAA chr2.hg19:g.62095778_62095782dupTTCCA 3 4 ref NA False 37 37 PASS 2 PASS ref->het 0 NA 245,248 23,23 44,42 1 1 B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51 True hg19 CCDS33206.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCT4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000325548.2 PASS NA None 317 True - TTCCA ENST00000394440.3 DPH3 285381 __UNKNOWN__ __UNKNOWN__ 3 16302227 16302227 __UNKNOWN__ 3'UTR DEL G G - LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:16302227delG ENST00000488423.1 - 0 388 DPH3_ENST00000285082.4_5'UTR|DPH3_ENST00000383775.4_3'UTR NM_206831.2 NP_996662.1 Q96FX2 DPH3_HUMAN diphthamide biosynthesis 3 NA NA NA NA negative regulation of protein secretion (GO:0050709)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|positive regulation of binding (GO:0051099) cytoplasm (GO:0005737)|nucleus (GO:0005634) metal ion binding (GO:0046872) NA NA large_intestine(2) 2 ATTTCTATCTGGGCTCATTCC 0.413 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 531 486.6 NA NA NA 74 71 72 NA NA NA NA 3 NA NA NA NA NA NA 16302227 2203 4300 6503 SO:0001624 3_prime_UTR_variant 0.26 NA NA BC010181 CCDS2629.1, CCDS43058.1 3p25.1 2013-06-19 2013-06-19 2006-10-25 ENSG00000154813 ENSG00000154813 285381 27717 protein-coding gene gene with protein product "DPH3A, KTI11 homolog A (S. cerevisiae)" 608959 "zinc finger, CSL-type containing 2", "DPH3 homolog (KTI11, S. cerevisiae)", "DPH3, KTI11 homolog (S. cerevisiae)" ZCSL2 NA 14527407, 14980502, 15485916, 16648478 Standard NM_206831 NM_001047434 NA Approved DESR1, DELGIP1, MGC20197, KTI11, DELGIP, DPH3A uc003cau.3 Q96FX2 OTTHUMG00000129866 ENST00000488423.1:c.*44C>- chr3.hg19:g.16302227delG 2 3 ref NA False 55 55 PASS 3 PASS ref->het 0 NA 413,415 67,68 52,51 1 1 True hg19 CCDS2629.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DPH3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252108.2 PASS NA None 531 True - G ENST00000488423.1 SOX30 11063 __UNKNOWN__ __UNKNOWN__ 5 157075944 157075945 __UNKNOWN__ Intron DEL AC AC - rs10548995|rs199736160|rs72284585|rs3217237 byFrequency LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:157075944_157075945delAC ENST00000265007.6 - 2 1309 SOX30_ENST00000311371.5_Intron|SOX30_ENST00000519442.1_Intron NM_178424.1 NP_848511.1 O94993 SOX30_HUMAN SRY (sex determining region Y)-box 30 NA NA NA NA regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981) NA NA central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1) 23 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.138) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) AATGTGCCATACACACACACAC 0.366 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Esophageal Squamous(31;525 799 19355 21125 41744) PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 82 82.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AB022083 CCDS4339.1, CCDS4340.1 5q33 2010-10-21 ENSG00000039600 ENSG00000039600 11063 "SRY (sex determining region Y)-boxes" 30635 protein-coding gene gene with protein product 606698 NA 15019997, 11678506 Standard NM_007017 NM_178424 NA Approved uc003lxb.1 O94993 OTTHUMG00000130247 ENST00000265007.6:c.968-40GT>- chr5.hg19:g.157075954_157075955delAC 7 2 ref NA False 36 36 PASS 8 PASS ref->het 0 NA 7,8 45,47 28,28 2 2 O94995|Q8IYX6 True hg19 CCDS4339.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SOX30-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000252571.2 PASS NA None 82 True - AC ENST00000265007.6 SCIN 85477 __UNKNOWN__ __UNKNOWN__ 7 12668822 12668841 __UNKNOWN__ Frame_Shift_Del DEL CCCAGAGGACAGATTATCTA CCCAGAGGACAGATTATCTA - LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:12668822_12668841delCCCAGAGGACAGATTATCTA ENST00000297029.5 + 9 1395_1414 c.1294_1313delCCCAGAGGACAGATTATCTA c.(1294-1314)cccagaggacagattatctacfs p.PRGQIIY432fs SCIN_ENST00000445618.2_Frame_Shift_Del_p.PRGQIIY185fs|SCIN_ENST00000519209.1_Frame_Shift_Del_p.PRGQIIY185fs NM_001112706.2 NP_001106177.1 Q9Y6U3 ADSV_HUMAN scinderin 432 Ca(2+)-dependent actin binding. NA NA NA actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330) cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234) 1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786) NA NA endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2) 17 UCEC - Uterine corpus endometrioid carcinoma (126;0.195) CTACACCTATCCCAGAGGACAGATTATCTACACGTGGTGA 0.409 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 268 257.23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 NA NA AF276507 CCDS47545.1, CCDS47546.1 7p21.3 2006-04-25 ENSG00000006747 ENSG00000006747 85477 21695 protein-coding gene gene with protein product 613416 NA Standard NM_033128 NM_033128 NA Approved adseverin, KIAA1905 uc003ssn.4 Q9Y6U3 OTTHUMG00000152385 ENST00000297029.5:c.1294_1313delCCCAGAGGACAGATTATCTA chr7.hg19:g.12668822_12668841delCCCAGAGGACAGATTATCTA ENSP00000297029:p.Pro432fs 0 3 ref NA False 61 61 PASS 1 PASS ref->het 0 NA 196,199 44,44 46,45 1 1 A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2 True hg19 CCDS47545.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SCIN-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000326041.1 PASS NA None 268 True + CCCAGAGGACAGATTATCTA ENST00000297029.5 MYOM2 9172 __UNKNOWN__ __UNKNOWN__ 8 2040340 2040341 __UNKNOWN__ In_Frame_Ins INS - - AATAACAGG LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:2040340_2040341insAATAACAGG ENST00000262113.4 + 16 2136_2137 c.1995_1996insAATAACAGG c.(1996-1998)tac>AATAACAGGtac p.665_666insNNR MYOM2_ENST00000523438.1_In_Frame_Ins_p.90_91insNNR NM_003970.2 NP_003961.2 P54296 MYOM2_HUMAN myomesin 2 665 Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}. NA NA NA muscle contraction (GO:0006936) M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982) structural constituent of muscle (GO:0008307) NA NA autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3) 104 Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217) BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179) AGCCCATTGGATACAACAGGTG 0.629 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 58 73.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001652 inframe_insertion 0.81 NA NA CCDS5957.1 8p23.3 2014-06-06 2012-10-17 ENSG00000036448 ENSG00000036448 9172 "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing" 7614 protein-coding gene gene with protein product 603509 "myomesin (M-protein) 2 (165kD)", "myomesin (M-protein) 2, 165kDa" NA Standard NM_003970 XM_006716237 NA Approved uc003wpx.4 P54296 OTTHUMG00000129175 ENST00000262113.4:c.1995_1996insAATAACAGG chr8.hg19:g.2040340_2040341insAATAACAGG ENSP00000262113:p.Gly665_Tyr666insAsnAsnArg 1 2 ref NA False 86 82 PASS 0 PASS ref->het 0 NA 14,15 37,37 5,5 2 1 Q7Z3Y2 True hg19 CCDS5957.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MYOM2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251249.1 PASS NA None 58 True + AATAACAGG ENST00000262113.4 GLI4 2738 __UNKNOWN__ __UNKNOWN__ 8 144358562 144358570 __UNKNOWN__ In_Frame_Del DEL AGTGCGGCC AGTGCGGCC - LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:144358562_144358570delAGTGCGGCC ENST00000523522.1 + 3 758_766 c.719_727delAGTGCGGCC c.(718-729)gagtgcggccag>gag p.CGQ241del ZFP41_ENST00000522452.1_3'UTR|GLI4_ENST00000523812.1_3'UTR|GLI4_ENST00000340042.1_In_Frame_Del_p.CGQ241del P10075 GLI4_HUMAN GLI family zinc finger 4 241 NA NA NA regulation of transcription, DNA-templated (GO:0006355) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA NA endometrium(3)|large_intestine(1)|lung(5) 9 all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173) AAGCCCTACGAGTGCGGCCAGTGCGGCCG 0.684 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 317 314.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 1.5 NA NA CCDS6398.1 8q24.3 2013-01-08 2009-03-05 ENSG00000250571 ENSG00000250571 2738 "Zinc fingers, C2H2-type" 4320 protein-coding gene gene with protein product 165280 "GLI-Kruppel family member GLI4", "glioma-associated oncogene family zinc finger 4" NA 2850480 Standard NM_138465 NA Approved HKR4, ZNF928 uc003yxx.3 P10075 OTTHUMG00000164952 ENST00000523522.1:c.719_727delAGTGCGGCC chr8.hg19:g.144358571_144358579delAGTGCGGCC ENSP00000430987:p.Cys241_Gln243del 1 2 ref NA False 50 50 PASS 2 PASS ref->het 0 NA 269,283 6,7 66,53 1 1 Q96CK9 True hg19 CCDS6398.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GLI4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000381128.2 PASS NA None 317 True + AGTGCGGCC ENST00000523522.1 ALAD 210 __UNKNOWN__ __UNKNOWN__ 9 116155669 116155670 __UNKNOWN__ Intron INS - - CCCCAA rs8177793|rs79604432 byFrequency LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:116155669_116155670insCCCCAA ENST00000409155.3 - 2 310 ALAD_ENST00000277315.5_Intron NM_000031.5 NP_000022.3 P13716 HEM2_HUMAN aminolevulinate dehydratase NA NA NA NA cellular response to interleukin-4 (GO:0071353)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protein homooligomerization (GO:0051260)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634) catalytic activity (GO:0003824)|identical protein binding (GO:0042802)|lead ion binding (GO:0032791)|porphobilinogen synthase activity (GO:0004655)|zinc ion binding (GO:0008270) NA NA endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|stomach(1) 9 Aminolevulinic acid(DB00855) CAACACTCCCTccccaacccca 0.559 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 26 38.46 NA NA 282,3982 NA 8,266,1858 NA NA NA NA NA -6.9 0 NA dbSNP_117 38 1570,6684 NA 161,1248,2718 no intron ALAD NM_000031.5 NA 169,1514,4576 A1A1,A1R,RR NA 19.0211,6.6135,14.7947 NA NA NA 1852,10666 NA NA NA SO:0001627 intron_variant 0 NA NA M13928 CCDS6794.2 9q32 2010-04-29 2010-04-29 ENSG00000148218 ENSG00000148218 210 4.2.1.24 395 protein-coding gene gene with protein product "porphobilinogen synthase" 125270 "aminolevulinate, delta-, dehydratase" NA 6839527, 6378062 Standard NM_001003945 NM_000031 NA Approved ALADH, PBGS uc011lxf.2 P13716 OTTHUMG00000020522 ENST00000409155.3:c.113+56->TTGGGG chr9.hg19:g.116155670_116155675dupCCCCAA 4 7 ref NA False 31 31 PASS 3 PASS ref->het 0 NA 13,13 8,8 8,8 1 1 A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9 True hg19 CCDS6794.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ALAD-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000053724.3 PASS NA None 26 True - CCCCAA ENST00000409155.3 NR5A1 2516 __UNKNOWN__ __UNKNOWN__ 9 127262865 127262865 __UNKNOWN__ Frame_Shift_Del DEL G G - LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:127262865delG ENST00000373588.4 - 4 570 c.374delC c.(373-375)ccgfs p.P125fs NM_004959.4 NP_004950.2 Q13285 STF1_HUMAN nuclear receptor subfamily 5, group A, member 1 125 NA NA NA adrenal gland development (GO:0030325)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|hormone metabolic process (GO:0042445)|intracellular receptor signaling pathway (GO:0030522)|luteinization (GO:0001553)|maintenance of protein location in nucleus (GO:0051457)|male gonad development (GO:0008584)|multicellular organismal aging (GO:0010259)|negative regulation of female gonad development (GO:2000195)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|primary sex determination (GO:0007538)|regulation of steroid biosynthetic process (GO:0050810)|tissue development (GO:0009888)|transcription initiation from RNA polymerase II promoter (GO:0006367) nucleoplasm (GO:0005654)|nucleus (GO:0005634) chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270) NA NA lung(1)|upper_aerodigestive_tract(1) 2 CACCCCCATCGGGGGCCCTGT 0.682 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 126 131.7 NA NA NA 21 24 23 NA NA NA NA 9 NA NA NA NA NA NA 127262865 2132 4125 6257 SO:0001589 frameshift_variant 1.84 NA NA D88155 CCDS6856.1 9q33 2013-01-16 ENSG00000136931 ENSG00000136931 2516 "Nuclear hormone receptors" 7983 protein-coding gene gene with protein product 184757 FTZF1 NA 7789992 Standard NM_004959 NM_004959 NA Approved FTZ1, SF-1, ELP, AD4BP uc004boo.1 Q13285 OTTHUMG00000020655 ENST00000373588.4:c.374delC chr9.hg19:g.127262865delG ENSP00000362690:p.Pro125fs 4 5 ref NA False 53 53 PASS 5 PASS ref->het 0 NA 38,39 68,77 21,13 1 1 O15196|Q5T6F5 True hg19 CCDS6856.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NR5A1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000054029.1 PASS NA None 126 True - G ENST00000373588.4 CUL2 8453 __UNKNOWN__ __UNKNOWN__ 10 35320460 35320491 __UNKNOWN__ Frame_Shift_Del DEL TGATGAAGCTCGTGAGCCTGTCTTCCACTTCA TGATGAAGCTCGTGAGCCTGTCTTCCACTTCA - LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:35320460_35320491delTGATGAAGCTCGTGAGCCTGTCTTCCACTTCA ENST00000374748.1 - 14 1540_1571 c.1227_1258delTGAAGTGGAAGACAGGCTCACGAGCTTCATCA c.(1225-1260)aatgaagtggaagacaggctcacgagcttcatcacafs p.EVEDRLTSFIT410fs CUL2_ENST00000602371.1_Frame_Shift_Del_p.EVEDRLTSFIT353fs|CUL2_ENST00000374749.3_Frame_Shift_Del_p.EVEDRLTSFIT410fs|CUL2_ENST00000374746.1_Frame_Shift_Del_p.EVEDRLTSFIT410fs|CUL2_ENST00000374751.3_Frame_Shift_Del_p.EVEDRLTSFIT410fs|CUL2_ENST00000374742.1_Frame_Shift_Del_p.EVEDRLTSFIT410fs|CUL2_ENST00000537177.1_Frame_Shift_Del_p.EVEDRLTSFIT429fs Q13617 CUL2_HUMAN cullin 2 410 NA NA NA cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032) Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891) ubiquitin protein ligase binding (GO:0031625) NA NA breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2) 31 TTGAACACTGTGATGAAGCTCGTGAGCCTGTCTTCCACTTCATTCTCTGTCA 0.371 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 425 381.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.21 NA NA U83410 CCDS7179.1, CCDS73086.1 10p11.2 2011-05-24 ENSG00000108094 ENSG00000108094 8453 2552 protein-coding gene gene with protein product 603135 NA 8681378 Standard NM_003591 NM_003591 NA Approved uc021ppa.1 Q13617 OTTHUMG00000017950 ENST00000374748.1:c.1227_1258delTGAAGTGGAAGACAGGCTCACGAGCTTCATCA chr10.hg19:g.35320460_35320491delTGATGAAGCTCGTGAGCCTGTCTTCCACTTCA ENSP00000363880:p.Glu410fs 0 3 ref NA False 40 40 PASS 1 PASS ref->het 0 NA 458,465 18,18 44,40 1 1 B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9 True hg19 CCDS7179.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CUL2-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000047538.1 PASS NA None 425 True - TGATGAAGCTCGTGAGCCTGTCTTCCACTTCA ENST00000374748.1 ARL1 400 __UNKNOWN__ __UNKNOWN__ 12 101797010 101797012 __UNKNOWN__ Intron DEL GAT GAT - LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:101797010_101797012delGAT ENST00000551828.1 - 3 324 ARL1_ENST00000539055.1_Intron|ARL1_ENST00000551688.1_Intron|ARL1_ENST00000536227.1_Intron|ARL1_ENST00000261636.8_Intron|ARL1_ENST00000551671.1_Intron P40616 ARL1_HUMAN ADP-ribosylation factor-like 1 NA NA NA NA activation of phospholipase D activity (GO:0031584)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)|toxin metabolic process (GO:0009404) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802) enzyme activator activity (GO:0008047)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904) NA NA central_nervous_system(1)|upper_aerodigestive_tract(1) 2 Lung NSC(355;2.1e-05)|Breast(359;0.00015)|Myeloproliferative disorder(1001;0.163) GBM - Glioblastoma multiforme(134;1.67e-09)|BRCA - Breast invasive adenocarcinoma(302;0.0125) CCATCTTCAGGATATTTTTTAAA 0.291 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 176 161.58 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 11.94 NA NA BX537387 CCDS44958.1, CCDS73510.1 12q23.3 2014-05-09 400 "ADP-ribosylation factors-like", "ADP-ribosylation factors" 692 protein-coding gene gene with protein product 603425 NA Standard NM_001177 XM_005268869 NA Approved ARFL1 uc001tib.3 P40616 OTTHUMG00000170271 ENST00000551828.1:c.92-286ATC>- chr12.hg19:g.101797010_101797012delGAT 0 7 ref NA False 56 56 PASS 1 PASS ref->het 0 NA 106,106 28,28 20,20 1 1 B4DWW1|P80417|Q53XB1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARL1-011 PUTATIVE alternative_5_UTR|upstream_uORF|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000408253.1 PASS NA None 176 True - GAT ENST00000551828.1 ARL1 400 __UNKNOWN__ __UNKNOWN__ 12 101797018 101797022 __UNKNOWN__ Intron DEL TTAAA TTAAA - LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:101797018_101797022delTTAAA ENST00000551828.1 - 3 324 ARL1_ENST00000539055.1_Intron|ARL1_ENST00000551688.1_Intron|ARL1_ENST00000536227.1_Intron|ARL1_ENST00000261636.8_Intron|ARL1_ENST00000551671.1_Intron P40616 ARL1_HUMAN ADP-ribosylation factor-like 1 NA NA NA NA activation of phospholipase D activity (GO:0031584)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)|toxin metabolic process (GO:0009404) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802) enzyme activator activity (GO:0008047)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904) NA NA central_nervous_system(1)|upper_aerodigestive_tract(1) 2 Lung NSC(355;2.1e-05)|Breast(359;0.00015)|Myeloproliferative disorder(1001;0.163) GBM - Glioblastoma multiforme(134;1.67e-09)|BRCA - Breast invasive adenocarcinoma(302;0.0125) AGGATATTTTTTAAAAGCCAGCAGT 0.298 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 138 150.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 11.94 NA NA BX537387 CCDS44958.1, CCDS73510.1 12q23.3 2014-05-09 400 "ADP-ribosylation factors-like", "ADP-ribosylation factors" 692 protein-coding gene gene with protein product 603425 NA Standard NM_001177 XM_005268869 NA Approved ARFL1 uc001tib.3 P40616 OTTHUMG00000170271 ENST00000551828.1:c.92-294TTTAA>- chr12.hg19:g.101797018_101797022delTTAAA 0 7 ref NA False 53 53 PASS 1 PASS ref->het 0 NA 103,103 28,28 5,5 1 1 B4DWW1|P80417|Q53XB1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARL1-011 PUTATIVE alternative_5_UTR|upstream_uORF|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000408253.1 PASS NA None 138 True - TTAAA ENST00000551828.1 PCK2 5106 __UNKNOWN__ __UNKNOWN__ 14 24569128 24569137 __UNKNOWN__ Intron DEL GGAGCAGGAC GGAGCAGGAC - rs2857584 LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:24569128_24569137delGGAGCAGGAC ENST00000561286.1 + 7 944 PCK2_ENST00000559250.1_Intron|NRL_ENST00000561028.1_Intron|PCK2_ENST00000216780.4_Intron|PCK2_ENST00000558096.1_Intron|PCK2_ENST00000545054.2_Intron|PCK2_ENST00000396973.4_Intron Q16822 PCKGM_HUMAN phosphoenolpyruvate carboxykinase 2 (mitochondrial) NA NA NA NA carbohydrate metabolic process (GO:0005975)|cellular response to glucose stimulus (GO:0071333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|NADH oxidation (GO:0006116)|oxaloacetate metabolic process (GO:0006107)|positive regulation of insulin secretion (GO:0032024)|pyruvate metabolic process (GO:0006090)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281) extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739) GTP binding (GO:0005525)|metal ion binding (GO:0046872)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)|phosphoenolpyruvate carboxykinase activity (GO:0004611) NA NA breast(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1) 18 GBM - Glioblastoma multiforme(265;0.0184) AGGGGTGGGTGGAGCAGGACCTTCTTTGGT 0.543 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 145 168.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.18 NA NA AK129934 CCDS9609.1, CCDS41928.1 14q12 2006-06-09 ENSG00000100889 ENSG00000100889 5106 4.1.1.32 8725 protein-coding gene gene with protein product 614095 NA 8645161, 9657976 Standard NM_001018073 XM_005267726 NA Approved PEPCK, PEPCK2 uc001wlt.3 Q16822 OTTHUMG00000028791 ENST00000561286.1:c.614-67GGAGCAGGAC>- chr14.hg19:g.24569128_24569137delGGAGCAGGAC 0 5 ref NA False 62 62 PASS 1 PASS ref->het 0 NA 98,98 36,36 20,20 1 1 O43253|Q86U01|Q9BV62 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PCK2-005 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000416426.1 PASS NA None 145 True + GGAGCAGGAC ENST00000561286.1 WDR90 197335 __UNKNOWN__ __UNKNOWN__ 16 710589 710631 __UNKNOWN__ Splice_Site DEL CATCCGGGTCTCCTTCCTCGCAGGGCACTTGCCCGCCTCCCGC CATCCGGGTCTCCTTCCTCGCAGGGCACTTGCCCGCCTCCCGC - rs375330337|rs563570587|rs564250498|rs181743607|rs545936270 LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:710589_710631delCATCCGGGTCTCCTTCCTCGCAGGGCACTTGCCCGCCTCCCGC ENST00000293879.4 + 28 3288_3308 c.3288_3308delCATCCGGGTCTCCTTCCTCGCAGGGCACTTGCCCGCCTCCCGC c.(3286-3309)aacatccgggtctccttcctcgca>aaa p.NIRVSFLA1096fs WDR90_ENST00000549091.1_Splice_Site_p.NIRVSFLA1096fs Q96KV7 WDR90_HUMAN WD repeat domain 90 1096 NA NA NA NA NA endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2) 37 Hepatocellular(780;0.0218) GCCCCAGCAGCATCCGGGTCTCCTTCCTCGCAGGGCACTTGCCCGCCTCCCGCCAGCGGTGGG 0.683 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 182 173.57 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0 NA NA AB067511 CCDS42092.1 16p13.3 2013-01-09 ENSG00000161996 ENSG00000161996 197335 "WD repeat domain containing" 26960 protein-coding gene gene with protein product NA "chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18" C16orf17, C16orf15, C16orf16, C16orf19, C16orf18 NA 11572484, 11157797 Standard NM_145294 XM_005255160 NA Approved FLJ36483, KIAA1924 uc002cii.1 Q96KV7 OTTHUMG00000048040 ENST00000293879.4:c.3289-1CATCCGGGTCTCCTTCCTCGCAGGGCACTTGCCCGCCTCCCGC>- chr16.hg19:g.710589_710631delCATCCGGGTCTCCTTCCTCGCAGGGCACTTGCCCGCCTCCCGC 0 5 ref NA False 58 58 PASS 1 PASS ref->het 0 NA 215,221 11,11 53,47 1 1 Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18 True hg19 CCDS42092.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA WDR90-002 NOVEL basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000404335.1 PASS NA None 182 Frame_Shift_Del True + CATCCGGGTCTCCTTCCTCGCAGGGCACTTGCCCGCCTCCCGC ENST00000293879.4 ENGASE 64772 __UNKNOWN__ __UNKNOWN__ 17 77075625 77075642 __UNKNOWN__ In_Frame_Del DEL CATCGACGTCTTTGTGTA CATCGACGTCTTTGTGTA - rs538416262|rs201376470|rs3744182|rs201681138 byFrequency LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:77075625_77075642delCATCGACGTCTTTGTGTA ENST00000579016.1 + 4 471_488 c.471_488delCATCGACGTCTTTGTGTA c.(469-489)tgcatcgacgtctttgtgtac>tgc p.IDVFVY158del ENGASE_ENST00000539857.2_Intron NM_001042573.2 NP_001036038.1 Q8NFI3 ENASE_HUMAN endo-beta-N-acetylglucosaminidase 158 NA NA NA cytoplasm (GO:0005737) mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925) NA NA breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1) 25 ACTGGCAGTGCATCGACGTCTTTGTGTACTTCAGCCAC 0.583 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 395 351.44 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.41 NA NA AF512564 CCDS42394.1 17q25.3 2009-03-03 ENSG00000167280 ENSG00000167280 64772 3.2.1.96 24622 protein-coding gene gene with protein product "Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase", "Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase" 611898 NA 12114544, 18586680 Standard NM_022759 NM_001042573 NA Approved FLJ21865 uc002jwv.4 Q8NFI3 OTTHUMG00000167714 ENST00000579016.1:c.471_488delCATCGACGTCTTTGTGTA chr17.hg19:g.77075625_77075642delCATCGACGTCTTTGTGTA ENSP00000462333:p.Ile158_Tyr163del 0 2 ref NA False 379 125 PASS 1 PASS ref->het 0 NA 156,156 195,198 68,66 1 1 Q659F0|Q8TB86|Q9H6U4 True hg19 CCDS42394.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENGASE-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000395807.1 PASS NA None 395 True + CATCGACGTCTTTGTGTA ENST00000579016.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 19 1725171 1725172 __UNKNOWN__ IGR INS - - T rs575182565|rs11372358 byFrequency LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:1725171_1725172insT NA TCF3 (72567 upstream) : AC005256.1 (22986 downstream) NA NA NA NA NA NA NA taatttttgtatttttttgtag 0.515 NA NA NA NA NA NA NA NA NA NA NA NA tttttt|TTTTTTT|TTTTTTTT|cryptic_indel 2316 0.46246 0.3737 0.4524 5008 , , NA 16057 0.4623 NA 0.508 False NA ,,, NA NA NA 2504 0.5429 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 13 13.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA chr19.hg19:g.1725178_1725178dupT 8 8 ref NA False 40 40 PASS 7 PASS ref->hom 0 NA 0,0 12,13 1,0 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 13 True T ZNF470 388566 __UNKNOWN__ __UNKNOWN__ 19 57088774 57088783 __UNKNOWN__ Frame_Shift_Del DEL ACCTTGCTCA ACCTTGCTCA - LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:57088774_57088783delACCTTGCTCA ENST00000330619.8 + 6 1663_1672 c.977_986delACCTTGCTCA c.(976-987)caccttgctcaafs p.HLAQ326fs ZNF470_ENST00000391709.3_Frame_Shift_Del_p.HLAQ326fs|ZNF470_ENST00000601902.1_Intron NM_001001668.3 NP_001001668.3 Q6ECI4 ZN470_HUMAN zinc finger protein 470 326 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA NA endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 41 Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157) GBM - Glioblastoma multiforme(193;0.0294) CAGCTTGCACACCTTGCTCAACATCAGAGG 0.443 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 151 155.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.3 NA NA AK129686 CCDS33122.1 19q13.43 2013-01-08 ENSG00000197016 388566 "Zinc fingers, C2H2-type", "-" 22220 protein-coding gene gene with protein product NA NA 15302581 Standard NM_001001668 NM_001001668 NA Approved CZF-1, FLJ26175 uc002qnl.4 Q6ECI4 ENST00000330619.8:c.977_986delACCTTGCTCA chr19.hg19:g.57088774_57088783delACCTTGCTCA ENSP00000333223:p.His326fs 0 3 ref NA False 61 61 PASS 1 PASS ref->het 0 NA 109,113 31,31 18,15 1 1 A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9 True hg19 CCDS33122.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF470-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000459707.2 PASS NA None 151 True + ACCTTGCTCA ENST00000330619.8 TUBA8 51807 __UNKNOWN__ __UNKNOWN__ 22 18614398 18614436 __UNKNOWN__ 3'UTR DEL CACCCTGTCCTAGGCACTGAGAGCTGGAGAGTTGGTGAT CACCCTGTCCTAGGCACTGAGAGCTGGAGAGTTGGTGAT - rs362189|rs139145930 byFrequency LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:18614398_18614436delCACCCTGTCCTAGGCACTGAGAGCTGGAGAGTTGGTGAT ENST00000330423.3 + 0 1918_1956 NM_018943.2 NP_061816.1 Q9NY65 TBA8_HUMAN tubulin, alpha 8 NA NA NA NA microtubule-based process (GO:0007017)|protein polymerization (GO:0051258) cytoplasm (GO:0005737)|microtubule (GO:0005874) GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200) NA NA breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1) 14 ttccaatacacaccctgtcctaggcactgagagctggagagttggtgataagcgagacg 0.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 242 208.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.04 NA NA AJ245922 CCDS13751.1, CCDS54495.1 22q11 2005-06-11 ENSG00000183785 ENSG00000183785 51807 "Tubulins" 12410 protein-coding gene gene with protein product 605742 TUBAL2 NA 10772959, 10591208 Standard NM_018943 NM_001193414 NA Approved uc002znv.2 Q9NY65 OTTHUMG00000150097 ENST00000330423.3:c.*533CACCCTGTCCTAGGCACTGAGAGCTGGAGAGTTGGTGAT>- chr22.hg19:g.18614398_18614436delCACCCTGTCCTAGGCACTGAGAGCTGGAGAGTTGGTGAT 0 4 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 201,202 24,25 18,18 1 1 B2RCX2|B3KPW9|B4DWG3|Q2M3N4 True hg19 CCDS13751.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TUBA8-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000316232.3 PASS NA None 242 True + CACCCTGTCCTAGGCACTGAGAGCTGGAGAGTTGGTGAT ENST00000330423.3 NHP2L1 4809 __UNKNOWN__ __UNKNOWN__ 22 42084639 42084639 __UNKNOWN__ Intron DEL C C - rs550117749 LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:42084639delC ENST00000401959.1 - 1 88 NHP2L1_ENST00000355257.3_Intron|NHP2L1_ENST00000402458.1_Intron|NHP2L1_ENST00000463675.1_Intron NM_005008.3 NP_004999.1 P55769 NH2L1_HUMAN NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae) NA NA NA NA gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ribosome biogenesis (GO:0042254)|RNA splicing (GO:0008380) box C/D snoRNP complex (GO:0031428)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681) poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723) NA NA endometrium(1)|kidney(1)|lung(1)|prostate(1) 4 GCTGCTGGGACCCCGCCGCTG 0.617 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 138 149.72 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.6 NA NA CCDS14022.1, CCDS33653.1 22q13 2009-01-06 2001-11-28 ENSG00000100138 ENSG00000100138 4809 7819 protein-coding gene gene with protein product "small nuclear ribonucleoprotein 15.5kDa (U4/U6.U5)" 601304 "non-histone chromosome protein 2 (S. cerevisiae)-like 1", "sperm specific antigen 1" SSFA1 NA 8978773 Standard NM_001003796 NM_005008 NA Approved SNU13, FA-1, SPAG12, SNRNP15-5, 15.5K uc003bav.3 P55769 OTTHUMG00000151189 ENST00000401959.1:c.228+158G>- chr22.hg19:g.42084639delC 3 6 ref NA False 130 93 PASS 4 PASS ref->het 0 NA 58,61 64,66 18,14 1 1 True hg19 CCDS14022.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NHP2L1-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000321682.1 PASS NA None 138 True - C ENST00000401959.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ X 43138957 43138958 __UNKNOWN__ IGR INS - - GCCGCC LTS-038_T LTS-038_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:43138957_43138958insGCCGCC NA RP3-326I13.1 (53110 upstream) : MAOA (376508 downstream) NA NA NA NA NA NA NA cagccgctgcagccgccgccgc 0.738 NA NA NA NA NA NA NA NA NA NA NA NA 884 0.234172 0.146 0.0663 3775 , , NA 3801 0.1756 NA 0.171 False NA ,,, NA NA NA 2504 0.3027 NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 61 59.15 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 3.1 NA NA NA NA NA NA NA chrX.hg19:g.43138958_43138963dupGCCGCC 7 2 ref NA False 35 35 PASS 5 PASS ref->het 0 NA 5,9 16,24 39,27 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 61 True GCC TOMM20 9804 __UNKNOWN__ __UNKNOWN__ 1 235275426 235275429 __UNKNOWN__ Intron DEL GAAA GAAA - LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:235275426_235275429delGAAA ENST00000366607.4 - 5 614 TOMM20_ENST00000467767.1_Intron NM_014765.2 NP_055580.1 Q15388 TOM20_HUMAN translocase of outer mitochondrial membrane 20 homolog (yeast) NA NA NA NA cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806) ER-mitochondrion membrane contact site (GO:0044233)|integral component of membrane (GO:0016021)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739) P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)|unfolded protein binding (GO:0051082) NA NA lung(2)|prostate(1) 3 Ovarian(103;0.0398) all_cancers(173;0.177)|Prostate(94;0.0166) OV - Ovarian serous cystadenocarcinoma(106;6.33e-05)|Epithelial(3;8.26e-05) NA NA ACAATTCTCTGAAAGaaaaaaaaa 0.245 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 1618 1431.92 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 4.37 NA NA CCDS1603.1 1q42 2008-07-18 ENSG00000173726 ENSG00000173726 9804 20947 protein-coding gene gene with protein product "translocase of outer mitochondrial membrane 20 homolog type II" 601848 NA 7498524, 7589431, 15733919 Standard NM_014765 NM_014765 NA Approved KIAA0016, TOM20, MOM19, MAS20 uc001hwl.3 Q15388 OTTHUMG00000039619 ENST00000366607.4:c.394-3TTTC>- chr1.hg19:g.235275430_235275433delGAAA 1 13 ref NA False 119 118 PASS 2 PASS ref->het 0 NA 1157,1189 281,288 185,160 1 1 A8K195|Q498B3|Q6IBT4 True hg19 CCDS1603.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TOMM20-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000095551.1 PASS NA None 1618 True - GAAA ENST00000366607.4 TNIP3 79931 __UNKNOWN__ __UNKNOWN__ 4 122068299 122068299 __UNKNOWN__ Frame_Shift_Del DEL C C - LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:122068299delC ENST00000509841.1 - 10 949 c.871delG c.(871-873)gaafs p.E291fs TNIP3_ENST00000454328.1_Frame_Shift_Del_p.E214fs|TNIP3_ENST00000511909.1_5'UTR|TNIP3_ENST00000507879.1_Frame_Shift_Del_p.E284fs|TNIP3_ENST00000057513.3_Frame_Shift_Del_p.E214fs NM_001244764.1 NP_001231693.1 TNFAIP3 interacting protein 3 NA NA NA NA NA NA NS(1)|endometrium(4)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(2) 24 NA NA TCCGATCGTTCCTTTTTGAAG 0.368 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 132 128.77 NA NA NA 191 185 187 NA NA NA NA 4 NA NA NA NA NA NA 122068299 2203 4300 6503 SO:0001589 frameshift_variant 0 NA NA AJ320534 CCDS3718.1, CCDS58925.1, CCDS58926.1 4q27 2008-02-05 ENSG00000050730 ENSG00000050730 79931 19315 protein-coding gene gene with protein product 608019 NA 11345586 Standard NM_024873 NM_024873 NA Approved LIND, FLJ21162, ABIN-3 uc021xrj.1 Q96KP6 OTTHUMG00000132969 ENST00000509841.1:c.871delG chr4.hg19:g.122068299delC ENSP00000426613:p.Glu291fs 1 5 ref NA False 79 79 PASS 2 PASS ref->het 0 NA 94,94 25,26 14,13 1 1 True hg19 CCDS58926.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TNIP3-003 PUTATIVE basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000364000.4 PASS NA None 132 True - C ENST00000509841.1 LYRM7 90624 __UNKNOWN__ __UNKNOWN__ 5 130540241 130540247 __UNKNOWN__ 3'UTR DEL TCCAAAG TCCAAAG - LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:130540241_130540247delTCCAAAG ENST00000379380.4 + 0 5473_5479 NM_181705.2 NP_859056.2 Q5U5X0 LYRM7_HUMAN LYR motif containing 7 NA NA NA NA mitochondrion (GO:0005739) NA NA upper_aerodigestive_tract(1) 1 all_cancers(142;0.0377)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) NA NA attcaaatgctccaaagtccaaaactt 0.425 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 98 88.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.33 NA NA BC047079 CCDS4148.1 5q31.1 2013-05-24 2012-10-23 2006-10-17 ENSG00000186687 ENSG00000186687 90624 "LYR motif containing" 28072 protein-coding gene gene with protein product 615831 "chromosome 5 open reading frame 31", "Lyrm7 homolog (mouse)" C5orf31 NA 23168492 Standard NM_181705 NM_181705 NA Approved FLJ20796, MZM1L uc003kvg.1 Q5U5X0 OTTHUMG00000128994 ENST00000379380.4:c.*4953TCCAAAG>- chr5.hg19:g.130540241_130540247delTCCAAAG 0 3 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 82,86 4,4 16,14 1 1 A8MPQ9|Q86Y68 True hg19 CCDS4148.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LYRM7-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250983.1 PASS NA None 98 True + TCCAAAG ENST00000379380.4 SYNPO 11346 __UNKNOWN__ __UNKNOWN__ 5 150030063 150030063 __UNKNOWN__ Intron DEL C C - LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:150030063delC ENST00000307662.4 + 2 2557 SYNPO_ENST00000519664.1_3'UTR|SYNPO_ENST00000522122.1_3'UTR|SYNPO_ENST00000394243.1_3'UTR NM_007286.5 NP_009217.3 Q8N3V7 SYNPO_HUMAN synaptopodin NA NA NA NA positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492) actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923) actin binding (GO:0003779) NA NA NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2) 18 Medulloblastoma(196;0.134)|all_hematologic(541;0.224) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) NA NA cgagtcgcctcccctctctga 0.612 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 173 155.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.25 NA NA AF499137 CCDS4308.1, CCDS54937.1, CCDS54938.1 5q33.1 2008-02-05 ENSG00000171992 ENSG00000171992 11346 30672 protein-coding gene gene with protein product 608155 NA 9314539, 10470851 Standard NM_007286 NM_007286 NA Approved KIAA1029 uc003lsn.3 Q8N3V7 OTTHUMG00000130078 ENST00000307662.4:c.2028+198C>- chr5.hg19:g.150030063delC 3 6 ref NA False 153 92 PASS 4 PASS ref->het 0 NA 56,57 101,103 15,12 1 1 A5PKZ8|D3DQG8|O15271|Q9UPX1 True hg19 CCDS4308.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SYNPO-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000252370.1 PASS NA None 173 True + C ENST00000307662.4 BPHL 670 __UNKNOWN__ __UNKNOWN__ 6 3138419 3138419 __UNKNOWN__ Intron DEL T T - rs11307799|rs57842152 byFrequency LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:3138419delT ENST00000434640.1 + 6 974 BPHL_ENST00000380375.3_Intron|BPHL_ENST00000380379.5_Intron|BPHL_ENST00000380368.2_Intron Q86WA6 BPHL_HUMAN biphenyl hydrolase-like (serine hydrolase) NA NA NA NA cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636) extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739) hydrolase activity (GO:0016787) NA NA endometrium(4)|kidney(1)|large_intestine(2)|lung(6) 13 Ovarian(93;0.0386) all_hematologic(90;0.108) NA NA cacaggcacattttttttgta 0.542 NA NA NA NA NA NA NA NA NA NA TTTTTTT|TTTTTTTT|TTTTTTT|insertion 2251 0.449481 0.2587 0.4625 5008 , , NA 16842 0.504 NA 0.6809 False NA ,,, NA NA NA 2504 0.4039 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 20 18.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA X81372 CCDS4483.2 6p25 2008-08-29 2008-08-29 ENSG00000137274 ENSG00000137274 670 1094 protein-coding gene gene with protein product "breast epithelial mucin-associated antigen" 603156 MCNAA NA 7759552, 9721218, 15832508 Standard NM_004332 NA Approved Bph-rp uc003mva.3 Q86WA6 OTTHUMG00000014140 ENST00000434640.1:c.613+692T>- chr6.hg19:g.3138419delT 7 9 ref NA False 31 31 PASS 8 PASS ref->hom 0 NA 0,0 18,20 2,2 1 1 Q00306|Q13855|Q3KP51 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BPHL-007 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000346932.2 PASS NA None 20 True + T ENST00000434640.1 MAPK13 5603 __UNKNOWN__ __UNKNOWN__ 6 36098497 36098498 __UNKNOWN__ Intron INS - - GGGGGGC rs70975134|rs146539855 byFrequency LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:36098497_36098498insGGGGGGC ENST00000211287.4 + 1 381 MAPK13_ENST00000373759.1_Intron|MAPK13_ENST00000373761.6_Intron|MAPK13_ENST00000373766.5_Intron NM_002754.4 NP_002745.1 O15264 MK13_HUMAN mitogen-activated protein kinase 13 NA NA NA NA cell cycle (GO:0007049)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 production (GO:0032755)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351) cytosol (GO:0005829) ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674) NA NA breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|prostate(2)|skin(1) 12 NA NA CCTgggccgctggggggcgggg 0.738 NA NA NA NA NA NA NA NA NA NA 3314 0.661741 0.7231 0.634 5008 , , NA 5726 0.8492 NA 0.5606 False NA ,,, NA NA NA 2504 0.5092 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 62 65.25 NA NA 771,1323 NA 335,101,611 NA NA NA NA NA -5.2 0 NA dbSNP_134 6 1638,3514 NA 643,352,1581 no intron MAPK13 NM_002754.3 NA 978,453,2192 A1A1,A1R,RR NA 31.7935,36.8195,33.2459 NA NA NA 2409,4837 NA NA NA SO:0001627 intron_variant 0.26 NA NA Y10488 CCDS4818.1 6p21 2011-06-09 ENSG00000156711 ENSG00000156711 5603 2.7.11.1 "Mitogen-activated protein kinase cascade / Kinases" 6875 protein-coding gene gene with protein product 602899 PRKM13 NA 9295308, 9218798 Standard NM_002754 NA Approved SAPK4, p38delta uc003ols.4 O15264 OTTHUMG00000014587 ENST00000211287.4:c.119+19->GGGGGGC chr6.hg19:g.36098498_36098504dupGGGGGGC 3 12 ref NA False 42 42 PASS 2 PASS ref->het 0 NA 7,7 7,7 48,48 1 1 O14739|O15124|Q5U4A5|Q6FI46|Q9UNU0 True hg19 CCDS4818.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAPK13-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000040328.1 PASS NA None 62 True + GGGGGGC ENST00000211287.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 7 53934394 53934394 __UNKNOWN__ IGR DEL A A - LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:53934394delA NA GS1-179L18.1 (54770 upstream) : RP11-806J6.1 (59974 downstream) NA NA NA NA NA NA NA NA NA TCCTCAATGTAAAAGTATTGA 0.333 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 164 169.76 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.04 NA NA NA NA NA NA NA chr7.hg19:g.53934394delA 3 4 ref NA False 41 41 PASS 4 PASS ref->het 0 NA 121,123 27,27 16,17 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 164 True A BAZ2A 11176 __UNKNOWN__ __UNKNOWN__ 12 56990824 56990829 __UNKNOWN__ 3'UTR DEL GTACCC GTACCC - LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:56990824_56990829delGTACCC ENST00000551812.1 - 0 7484_7489 BAZ2A_ENST00000379441.3_3'UTR|BAZ2A_ENST00000179765.5_3'UTR NM_013449.3 NP_038477.2 Q9UIF9 BAZ2A_HUMAN bromodomain adjacent to zinc finger domain, 2A NA NA NA NA chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553) DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270) NA NA breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1) 31 NA NA CCCAGTGCAAGTACCCGTAATCTCTG 0.602 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 168 171.88 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.61 NA NA AB032254 CCDS44924.1, CCDS73483.1 12q13.3 2013-01-28 ENSG00000076108 11176 "Zinc fingers, PHD-type" 962 protein-coding gene gene with protein product "TTF-I interacting peptide 5" 605682 NA 10662543, 11532953 Standard NM_013449 XM_005268596 NA Approved KIAA0314, TIP5, WALp3 uc001slq.1 Q9UIF9 OTTHUMG00000170332 ENST00000551812.1:c.*1578GGGTAC>- chr12.hg19:g.56990824_56990829delGTACCC 0 3 ref NA False 47 47 PASS 1 PASS ref->het 0 NA 119,121 25,26 28,26 1 1 B3KN66|O00536|O15030|Q68DI8|Q96H26 True hg19 CCDS44924.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BAZ2A-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000408561.1 PASS NA None 168 True - GTACCC ENST00000551812.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 13 103394292 103394292 __UNKNOWN__ IGR DEL C C - LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:103394292delC NA CCDC168 (5133 upstream) : LINC00283 (1047 downstream) NA NA NA NA NA NA NA NA NA TGTTTTTGTTCCTTTTCTCTA 0.363 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 72 78.87 NA NA NA 103 81 87 NA NA NA NA 13 NA NA NA NA NA NA 103394292 692 1591 2283 SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA chr13.hg19:g.103394292delC 1 7 ref NA False 39 39 PASS 2 PASS ref->het 0 NA 40,41 22,22 9,9 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 72 True C RPGRIP1L 23322 __UNKNOWN__ __UNKNOWN__ 16 53730063 53730064 __UNKNOWN__ Splice_Site INS - - T LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:53730063_53730064insT ENST00000568653.3 - 3 280_281 c.229_230insA c.(229-231)agg>aAgg p.R77fs RPGRIP1L_ENST00000564374.1_Splice_Site_p.R77fs|RPGRIP1L_ENST00000262135.4_Splice_Site_p.R77fs|RPGRIP1L_ENST00000379925.3_Splice_Site_p.R77fs|RPGRIP1L_ENST00000566096.1_Frame_Shift_Ins_p.R77fs|RPGRIP1L_ENST00000563746.1_Splice_Site_p.R77fs Q68CZ1 FTM_HUMAN RPGRIP1-like 77 NA NA NA camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589) axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923) thromboxane A2 receptor binding (GO:0031870) NA NA endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2) 46 all_cancers(37;0.0973) NA NA TTATCATAACCTTTTAATTTTA 0.351 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 99 96.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001630 splice_region_variant 0 NA NA CCDS32447.1, CCDS45486.1 16q12.2 2014-09-17 ENSG00000103494 23322 29168 protein-coding gene gene with protein product "fantom homolog", "Meckel syndrome, type 5", "protein phosphatase 1, regulatory subunit 134" 610937 NA 10231032 Standard NM_015272 NM_015272 NA Approved KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134 uc002ehp.3 Q68CZ1 ENST00000568653.3:c.230+1->A chr16.hg19:g.53730067_53730067dupT 5 4 ref NA False 39 39 PASS 4 PASS ref->het 0 NA 69,69 19,19 12,12 1 1 A0PJ88|Q9Y2K8 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPGRIP1L-002 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000422194.3 PASS NA None 99 Frame_Shift_Ins True - T ENST00000568653.3 CPNE2 221184 __UNKNOWN__ __UNKNOWN__ 16 57180127 57180138 __UNKNOWN__ In_Frame_Del DEL CTGCCATGGAGT CTGCCATGGAGT - rs374277054 LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:57180127_57180138delCTGCCATGGAGT ENST00000535318.2 + 16 1794_1805 c.1433_1444delCTGCCATGGAGT c.(1432-1446)gctgccatggagttc>gtc p.478_482AAMEF>V CPNE2_ENST00000537605.1_In_Frame_Del_p.376_380AAMEF>V|CPNE2_ENST00000565951.1_3'UTR|CPNE2_ENST00000565874.1_In_Frame_Del_p.478_482AAMEF>V|CPNE2_ENST00000290776.8_In_Frame_Del_p.478_482AAMEF>V Q96FN4 CPNE2_HUMAN copine II 478 VWFA. NA NA NA extracellular vesicular exosome (GO:0070062) NA NA central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(5) 21 all_neural(199;0.224) NA NA GCGGACTTCGCTGCCATGGAGTTCCTGGATGG 0.618 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 353 351.13 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.36 NA NA CCDS10774.1 16q13 2008-02-05 ENSG00000140848 ENSG00000140848 221184 2315 protein-coding gene gene with protein product 604206 NA 9430674 Standard NM_152727 NM_152727 NA Approved CPN2 uc002eks.2 Q96FN4 OTTHUMG00000133471 ENST00000535318.2:c.1433_1444delCTGCCATGGAGT chr16.hg19:g.57180127_57180138delCTGCCATGGAGT ENSP00000439018:p.Ala478_Phe482delinsVal 0 2 ref NA False 58 58 PASS 1 PASS ref->het 0 NA 342,350 23,23 34,28 1 1 Q68D19|Q719H8|Q86XP9 True hg19 CCDS10774.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CPNE2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000432986.2 PASS NA None 353 True + CTGCCATGGAGT ENST00000535318.2 Unknown 0 __UNKNOWN__ __UNKNOWN__ 17 1930206 1930207 __UNKNOWN__ IGR INS - - GCTGA rs368191332|rs67432030|rs143602528 byFrequency LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:1930206_1930207insGCTGA NA RTN4RL1 (1567 upstream) : DPH1 (3196 downstream) NA NA NA NA NA NA NA NA NA cactttgggaggctgagcagat 0.51 NA NA NA NA NA NA NA NA NA NA 1928 0.384984 0.4244 0.304 5008 , , NA 13558 0.2153 NA 0.4642 False NA ,,, NA NA NA 2504 0.4826 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 34 35.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.09 NA NA NA NA NA NA NA chr17.hg19:g.1930207_1930211dupGCTGA 2 5 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 1,1 24,27 9,10 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 34 True GCTGA Unknown 0 __UNKNOWN__ __UNKNOWN__ 17 48622244 48622247 __UNKNOWN__ IGR DEL TCTT TCTT - rs72372795|rs146009878|rs562354242|rs370409573|rs539223938|rs35609032|rs531471269 byFrequency LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:48622244_48622247delTCTT NA EPN3 (1133 upstream) : SPATA20 (2202 downstream) NA NA NA NA NA NA NA NA NA cccttctgtgtctttctttctttc 0.534 NA NA NA NA NA NA NA NA NA NA 2103 0.419928 0.7126 0.3847 5008 , , NA 25535 0.0724 NA 0.5348 False NA ,,, NA NA NA 2504 0.2894 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 28 28.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA chr17.hg19:g.48622252_48622255delTCTT 5 6 ref NA False 31 31 PASS 6 PASS ref->het 0 NA 2,3 23,26 7,7 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 28 True TCTT Unknown 0 __UNKNOWN__ __UNKNOWN__ 19 5805951 5805952 __UNKNOWN__ IGR INS - - CGC rs71172773|rs141700858 byFrequency LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:5805951_5805952insCGC NA DUS3L (14702 upstream) : AC011499.1 (16983 downstream) NA NA NA NA NA NA NA NA NA CGTTCCCTGCTCGCCGCCGCCG 0.713 NA NA NA NA NA NA NA NA NA NA OREG0025186 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 175 0.0349441 0.0023 0.0432 5008 , , NA 13564 0.001 NA 0.1203 False NA ,,, NA NA NA 2504 0.0204 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 22 20.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA NA NA chr19.hg19:g.5805958_5805960dupCGC 6 3 ref 629 False 42 41 PASS 5 PASS ref->hom 0 NA 0,0 21,21 1,1 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 22 True CGC PHLDB3 653583 __UNKNOWN__ __UNKNOWN__ 19 43979658 43979670 __UNKNOWN__ Frame_Shift_Del DEL GTAGGTTTTGACG GTAGGTTTTGACG - rs375901143 LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:43979658_43979670delGTAGGTTTTGACG ENST00000292140.5 - 16 2175_2187 c.1815_1827delCGTCAAAACCTAC c.(1813-1827)tgcgtcaaaacctacfs p.CVKTY605fs NM_198850.3 NP_942147.3 Q6NSJ2 PHLB3_HUMAN pleckstrin homology-like domain, family B, member 3 605 PH. {ECO:0000255|PROSITE- ProRule:PRU00145}. NA NA NA enzyme binding (GO:0019899) NA NA breast(1)|central_nervous_system(1)|lung(5) 7 Prostate(69;0.0153) NA NA AAAGGCGTTCGTAGGTTTTGACGCAGAAGGTCA 0.582 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 398 394.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.57 NA NA CCDS12621.2 19q13.31 2013-01-10 ENSG00000176531 ENSG00000176531 653583 "Pleckstrin homology (PH) domain containing" 30499 protein-coding gene gene with protein product NA NA Standard NM_198850 NA Approved FLJ40193 uc002own.4 Q6NSJ2 OTTHUMG00000150693 ENST00000292140.5:c.1815_1827delCGTCAAAACCTAC chr19.hg19:g.43979658_43979670delGTAGGTTTTGACG ENSP00000292140:p.Cys605fs 0 2 ref NA False 88 88 PASS 1 PASS ref->het 0 NA 363,375 8,8 55,46 1 1 Q8N7Z4 True hg19 CCDS12621.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PHLDB3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000319643.2 PASS NA None 398 True - GTAGGTTTTGACG ENST00000292140.5 ELMO2 63916 __UNKNOWN__ __UNKNOWN__ 20 44995048 44995057 __UNKNOWN__ 3'UTR DEL GGCCTCAGCC GGCCTCAGCC - rs57636673|rs375353248 LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:44995048_44995057delGGCCTCAGCC ENST00000290246.6 - 0 3299_3308 ELMO2_ENST00000396391.1_3'UTR|ELMO2_ENST00000372176.1_3'UTR NM_133171.3 NP_573403.1 Q96JJ3 ELMO2_HUMAN engulfment and cell motility 2 NA NA NA NA apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087) cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020) receptor tyrosine kinase binding (GO:0030971) NA NA breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1) 16 Myeloproliferative disorder(115;0.0122) NA NA GCACAGGTGTGGCCTCAGCCGGCCTCAGCC 0.552 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 334 325.71 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.32 NA NA AF398886 CCDS13398.1 20q13 2010-03-18 2006-01-20 ENSG00000062598 ENSG00000062598 63916 "Engulfment and cell motility proteins" 17233 protein-coding gene gene with protein product 606421 "engulfment and cell motility 2 (ced-12 homolog, C. elegans)" NA 11595183 Standard NM_022086 NM_133171 NA Approved CED12, ELMO-2, CED-12, KIAA1834, FLJ11656 uc002xru.1 Q96JJ3 OTTHUMG00000033070 ENST00000290246.6:c.*951GGCTGAGGCC>- chr20.hg19:g.44995058_44995067delGGCCTCAGCC 1 3 ref NA False 35 35 PASS 2 PASS ref->het 0 NA 265,270 27,27 62,60 1 1 E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6 True hg19 CCDS13398.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ELMO2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000080466.1 PASS NA None 334 True - GGCCTCAGCC ENST00000290246.6 TMSB4X 7114 __UNKNOWN__ __UNKNOWN__ X 12994519 12994547 __UNKNOWN__ Intron DEL TGGGAGCGGCCGGTGGGAGGGCGGGAGGC TGGGAGCGGCCGGTGGGAGGGCGGGAGGC - rs375118619|rs1817509|rs368084887 LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:12994519_12994547delTGGGAGCGGCCGGTGGGAGGGCGGGAGGC ENST00000380635.1 + 2 316 TMSB4X_ENST00000380633.1_Intron|TMSB4X_ENST00000380636.1_Intron|TMSB4X_ENST00000451311.2_Intron P62328 TYB4_HUMAN thymosin beta 4, X-linked NA NA NA NA actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sequestering of actin monomers (GO:0042989) cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093) poly(A) RNA binding (GO:0044822) NA NA upper_aerodigestive_tract(1) 1 NA NA AAAGGCTGGGTGGGAGCGGCCGGTGGGAGGGCGGGAGGCTGGGAGCGGC 0.555 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 279 252.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.38 NA NA CCDS35202.1 Xp22.2 2013-05-14 2008-02-25 ENSG00000205542 ENSG00000205542 7114 11881 protein-coding gene gene with protein product 300159 "thymosin, beta 4, X chromosome" TMSB4 NA 2677145, 9381176 Standard NM_021109 NM_021109 NA Approved TB4X uc004cvf.3 P62328 OTTHUMG00000021144 ENST00000380635.1:c.100+39TGGGAGCGGCCGGTGGGAGGGCGGGAGGC>- chrX.hg19:g.12994519_12994547delTGGGAGCGGCCGGTGGGAGGGCGGGAGGC 0 6 ref NA False 111 111 PASS 1 PASS ref->het 0 NA 172,178 22,23 109,104 1 1 P01253|P01254|Q546P5|Q63576|Q9UE55 True hg19 CCDS35202.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMSB4X-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000055779.1 PASS NA None 279 True + TGGGAGCGGCCGGTGGGAGGGCGGGAGGC ENST00000380635.1 HCFC1 3054 __UNKNOWN__ __UNKNOWN__ X 153217234 153217234 __UNKNOWN__ Intron DEL C C - LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:153217234delC ENST00000369984.4 - 20 5739 HCFC1_ENST00000310441.7_Intron|HCFC1_ENST00000354233.3_Intron P51610 HCFC1_HUMAN host cell factor C1 NA NA NA NA cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366) cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188) chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713) NA NA NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 47 all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) NA NA TCCCGTCCTGCCCTCACCTCC 0.622 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 146 145.08 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.23 NA NA CCDS44020.1 Xq28 2014-06-12 2014-06-09 ENSG00000172534 ENSG00000172534 3054 4839 protein-coding gene gene with protein product "VP16-accessory protein", "protein phosphatase 1, regulatory subunit 89" 300019 "mental retardation, X-linked 3", "host cell factor C1 (VP16-accessory protein)" HFC1, MRX3 NA 8392914, 23000143 Standard NM_005334 XM_005274664 NA Approved HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89 uc004fjp.3 P51610 OTTHUMG00000024222 ENST00000369984.4:c.5395+57G>- chrX.hg19:g.153217234delC 2 4 ref NA False 139 115 PASS 3 PASS ref->het 0 NA 83,87 49,49 15,12 2 1 Q6P4G5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HCFC1-003 NOVEL not_organism_supported|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000061101.3 PASS NA None 146 True - C ENST00000369984.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ Y 13300088 13300089 __UNKNOWN__ IGR DEL AG AG - LTS-039_T LTS-039_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrY:13300088_13300089delAG NA None (None upstream) : AC134878.2 (40269 downstream) NA NA NA NA NA NA NA NA NA GTCCCTGGACAGAGATACATAA 0.361 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 84 76.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 12.47 NA NA NA NA NA NA NA chrY.hg19:g.13300090_13300091delAG 1 2 ref NA False 32 32 PASS 2 PASS ref->het 0 NA 42,74 15,17 30,7 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 84 True AG PSMB4 5692 __UNKNOWN__ __UNKNOWN__ 1 151373604 151373606 __UNKNOWN__ Intron DEL AAG AAG - rs572371530 LTS-040_T LTS-040_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:151373604_151373606delAAG ENST00000290541.6 + 5 630 NM_002796.2 NP_002787.2 P28070 PSB4_HUMAN proteasome (prosome, macropain) subunit, beta type, 4 NA NA NA NA anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839) lipopolysaccharide binding (GO:0001530)|threonine-type endopeptidase activity (GO:0004298) NA NA endometrium(1)|lung(9)|ovary(2)|prostate(1)|skin(1) 14 Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181) CTGGTGAGGCAAGAAGTAGAATG 0.424 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 307 325.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA D26600 CCDS996.1 1q21 2008-02-05 ENSG00000159377 ENSG00000159377 5692 "Proteasome (prosome, macropain) subunits" 9541 protein-coding gene gene with protein product 602177 NA 7918633 Standard NM_002796 NM_002796 NA Approved HN3, PROS26 uc001eyc.1 P28070 OTTHUMG00000012494 ENST00000290541.6:c.577-109AAG>- chr1.hg19:g.151373607_151373609delAAG 1 4 ref NA False 64 64 PASS 2 PASS ref->het 0 NA 221,221 73,73 26,26 1 1 B2R9L3|P31148|Q5SZS5|Q6IBI4|Q969L6 True hg19 CCDS996.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PSMB4-001 KNOWN mRNA_start_NF|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000034885.1 PASS NA None 307 NA True + AAG ENST00000290541.6 ANKRD36C 400986 __UNKNOWN__ __UNKNOWN__ 2 96601300 96601301 __UNKNOWN__ Intron INS - - TAATTGAG LTS-040_T LTS-040_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:96601300_96601301insTAATTGAG ENST00000456556.1 - 24 1747 Q5JPF3 AN36C_HUMAN ankyrin repeat domain 36C NA NA NA NA ion channel inhibitor activity (GO:0008200) NA NA breast(1)|endometrium(8)|kidney(5)|lung(4) 18 AACATAATGATTAATATATCAT 0.356 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 359 358.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.05 NA NA AL832836 2q11.1 2013-01-10 ENSG00000174501 ENSG00000174501 400986 "Ankyrin repeat domain containing" 32946 protein-coding gene gene with protein product "protein immuno-reactive with anti-PTH polyclonal antibodies" NA NA Standard NM_001010914 XR_251121 NA Approved DKFZp667P0924 uc002suz.1 Q5JPF3 OTTHUMG00000155211 ENST00000456556.1:c.1663-26->CTCAATTA chr2.hg19:g.96601300_96601301insTAATTGAG 1 2 ref NA False 33 33 PASS 0 PASS ref->het 0 NA 294,318 16,20 50,57 1 1 C9JZ08|Q15694|Q53S06|Q658V2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ANKRD36C-001 KNOWN not_best_in_genome_evidence|basic|appris_principal protein_coding NA protein_coding OTTHUMT00000338799.2 PASS NA None 359 NA True - TAATTGAG ENST00000456556.1 BHLHE40 8553 __UNKNOWN__ __UNKNOWN__ 3 5026281 5026306 __UNKNOWN__ 3'UTR DEL CAATTCCATCCTAAAACTCCTTTTAA CAATTCCATCCTAAAACTCCTTTTAA - LTS-040_T LTS-040_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:5026281_5026306delCAATTCCATCCTAAAACTCCTTTTAA ENST00000256495.3 + 0 2746_2771 NM_003670.2 NP_003661.1 O14503 BHE40_HUMAN basic helix-loop-helix family, member e40 NA NA NA NA circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366) Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634) bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|MRF binding (GO:0043426)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714) NA NA breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2) 12 ACTCAGTTTTCAATTCCATCCTAAAACTCCTTTTAACCAAGCTTAG 0.478 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 168 167.31 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.42 NA NA AB004066 CCDS2565.1 3p26 2009-01-12 2009-01-12 2009-01-12 ENSG00000134107 ENSG00000134107 8553 "Basic helix-loop-helix proteins" 1046 protein-coding gene gene with protein product "differentially expressed in chondrocytes 1", " differentiated embryo chondrocyte expressed gene 1" 604256 "basic helix-loop-helix domain containing, class B, 2" STRA13, BHLHB2 NA 9240428, 10449910, 18557763 Standard NM_003670 NM_003670 NA Approved DEC1, bHLHe40 uc003bqf.3 O14503 OTTHUMG00000119035 ENST00000256495.3:c.*929CAATTCCATCCTAAAACTCCTTTTAA>- chr3.hg19:g.5026281_5026306delCAATTCCATCCTAAAACTCCTTTTAA 0 4 ref NA False 54 54 PASS 1 PASS ref->het 0 NA 114,115 34,35 44,43 1 1 Q96TD3 True hg19 CCDS2565.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BHLHE40-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000239244.2 PASS NA None 168 NA True + CAATTCCATCCTAAAACTCCTTTTAA ENST00000256495.3 AP3S1 1176 __UNKNOWN__ __UNKNOWN__ 5 115249647 115249647 __UNKNOWN__ 3'UTR DEL G G - rs145060439 byFrequency LTS-040_T LTS-040_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:115249647delG ENST00000316788.7 + 0 1599 NM_001284.2 NP_001275.1 Q92572 AP3S1_HUMAN adaptor-related protein complex 3, sigma 1 subunit NA NA NA NA anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transport (GO:0006886) AP-3 adaptor complex (GO:0030123)|AP-type membrane coat adaptor complex (GO:0030119)|Golgi apparatus (GO:0005794)|transport vesicle (GO:0030133) protein transporter activity (GO:0008565)|transporter activity (GO:0005215) NA NA cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1) 12 all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245) OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05) TTTTCTCTTAGTTTAAATAAA 0.333 NA NA NA NA NA NA NA NA NA NA NA NA G|G|-|deletion 1219 0.243411 0.2685 0.2089 5008 , , NA 21725 0.2063 NA 0.2604 False NA ,,, NA NA NA 2504 0.2546 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 296 318.11 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.27 NA NA D63643 CCDS4123.1 5q22 2010-06-29 ENSG00000177879 ENSG00000177879 1176 2013 protein-coding gene gene with protein product 601507 CLAPS3 NA 8697810, 9118953 Standard NM_001284 NA Approved uc003krl.3 Q92572 OTTHUMG00000128887 ENST00000316788.7:c.*460G>- chr5.hg19:g.115249647delG 0 3 ref NA False 36 36 PASS 1 PASS ref->het 0 NA 202,203 50,61 38,39 1 1 O00647|O00676|O00721|O00727|Q53XL4|Q6ICQ2 True hg19 CCDS4123.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AP3S1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250847.2 PASS NA None 296 NA True + G ENST00000316788.7 HIST1H2BL 8340 __UNKNOWN__ __UNKNOWN__ 6 27775683 27775690 __UNKNOWN__ Start_Codon_Del DEL ATAATGAA ATAATGAA - rs145663173 LTS-040_T LTS-040_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:27775683_27775690delATAATGAA ENST00000377401.2 - 0 19_26 NM_003519.3 NP_003510.1 Q99880 H2B1L_HUMAN histone cluster 1, H2bl NA NA NA NA chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334) extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634) DNA binding (GO:0003677) NA NA cervix(1)|endometrium(1)|large_intestine(2)|lung(7)|urinary_tract(1) 12 CAGCTCGGGCATAATGAAACAATAGTGG 0.514 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 487 469.36 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001582 initiator_codon_variant 0.43 NA NA Z83740 CCDS4625.1 6p22.1 2011-01-27 2006-10-11 2003-02-28 ENSG00000185130 ENSG00000185130 8340 "Histones / Replication-dependent" 4748 protein-coding gene gene with protein product 602800 "H2B histone family, member C", "histone 1, H2bl" H2BFC NA 9439656, 12408966 Standard NM_003519 NM_003519 NA Approved H2B/c, dJ97D16.4 uc003njl.3 Q99880 OTTHUMG00000014485 ENST00000377401.2: chr6.hg19:g.27775683_27775690delATAATGAA 0 5 ref NA False 117 117 PASS 1 PASS ref->het 0 NA 419,427 38,39 54,50 1 1 B2R5A3|Q52LW9 True hg19 CCDS4625.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HIST1H2BL-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000040153.1 PASS NA None 487 NA True - ATAATGAA ENST00000377401.2 ASCC3 10973 __UNKNOWN__ __UNKNOWN__ 6 101306006 101306010 __UNKNOWN__ Intron DEL TAAAT TAAAT - rs537604315|rs71028040|rs67936868 byFrequency LTS-040_T LTS-040_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:101306006_101306010delTAAAT ENST00000369162.2 - 3 586 ASCC3_ENST00000522650.1_Intron|ASCC3_ENST00000369143.2_3'UTR NM_006828.2 NP_006819.2 Q8N3C0 ASCC3_HUMAN activating signal cointegrator 1 complex subunit 3 NA NA NA NA cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634) ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822) NA NA breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 92 all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13) BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199) aaacgtaaaataaattaaaatttta 0.205 NA NA NA NA NA NA NA NA NA NA NA NA 802 0.160144 0.0628 0.3242 5008 , , NA 15540 0.0764 NA 0.2903 False NA ,,, NA NA NA 2504 0.1278 NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 42 41.31 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 NA NA AJ223948 CCDS5046.1, CCDS5047.1, CCDS75497.1 6q16 2008-02-05 2004-07-28 ENSG00000112249 ENSG00000112249 10973 18697 protein-coding gene gene with protein product "RNA helicase family" 614217 "helicase, ATP binding 1" HELIC1 NA 10218103 Standard NM_006828 NM_006828 NA Approved RNAH, ASC1p200, dJ121G13.4, dJ467N11.1 uc003pqk.3 Q8N3C0 OTTHUMG00000015279 ENST00000369162.2:c.241+5929ATTTA>- chr6.hg19:g.101306006_101306010delTAAAT 0 7 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 4,4 32,32 9,9 1 1 E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0 True hg19 CCDS5046.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ASCC3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041632.2 PASS NA None 42 NA True - TAAAT ENST00000369162.2 HSF1 3297 __UNKNOWN__ __UNKNOWN__ 8 145535250 145535264 __UNKNOWN__ In_Frame_Del DEL TCTCCCTGGAGCACG TCTCCCTGGAGCACG - rs541862486 LTS-040_T LTS-040_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:145535250_145535264delTCTCCCTGGAGCACG ENST00000400780.4 + 6 570_584 c.491_505delTCTCCCTGGAGCACG c.(490-507)ttctccctggagcacgtc>ttc p.SLEHV165del HSF1_ENST00000528838.1_In_Frame_Del_p.SLEHV230del Q00613 HSF1_HUMAN heat shock transcription factor 1 230 Hydrophobic repeat HR-A/B. NA NA NA cellular response to heat (GO:0034605)|defense response (GO:0006952)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|female meiotic division (GO:0007143)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)|response to lipopolysaccharide (GO:0032496)|spermatogenesis (GO:0007283) cytoplasm (GO:0005737)|nucleus (GO:0005634)|pronucleus (GO:0045120)|protein complex (GO:0043234) chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)|sequence-specific DNA binding transcription factor activity (GO:0003700) NA NA endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)|urinary_tract(2) 11 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055) AGCCGGCAGTTCTCCCTGGAGCACGTCCACGGCTC 0.679 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 293 285.65 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0.32 NA NA M64673 CCDS6419.1 8q24.3 2014-04-10 ENSG00000185122 ENSG00000185122 3297 5224 protein-coding gene gene with protein product 140580 NA 1871105 Standard NM_005526 NM_005526 NA Approved HSTF1 uc003zbt.4 Q00613 OTTHUMG00000174604 ENST00000400780.4:c.491_505delTCTCCCTGGAGCACG chr8.hg19:g.145535250_145535264delTCTCCCTGGAGCACG ENSP00000383590:p.Ser165_Val169del 0 3 ref NA False 37 37 PASS 1 PASS ref->het 0 NA 256,263 34,34 34,27 1 1 A8K4L0|A8MW26|Q53XT4 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HSF1-006 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000382056.1 PASS NA None 293 NA True + TCTCCCTGGAGCACG ENST00000400780.4 LTA4H 4048 __UNKNOWN__ __UNKNOWN__ 12 96412935 96412935 __UNKNOWN__ Intron DEL A A - LTS-040_T LTS-040_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:96412935delA ENST00000228740.2 - 7 853 LTA4H_ENST00000413268.2_Intron|LTA4H_ENST00000552789.1_Intron NM_000895.2 NP_000886.1 P09960 LKHA4_HUMAN leukotriene A4 hydrolase NA NA NA NA arachidonic acid metabolic process (GO:0019369)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|peptide catabolic process (GO:0043171)|small molecule metabolic process (GO:0044281) cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634) aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|leukotriene-A4 hydrolase activity (GO:0004463)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270) NA NA haematopoietic_and_lymphoid_tissue(2)|kidney(3)|lung(4)|skin(2)|stomach(1) 12 Captopril(DB01197) AAGGATAACTAAATGACCAAC 0.383 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 295 272.75 NA NA NA NA NA 96 92 93 NA NA NA NA 12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 96412935 NA 2203 4300 6503 SO:0001627 intron_variant 0 NA NA BC032528 CCDS9059.1, CCDS58266.1, CCDS58267.1 12q22 2005-10-06 ENSG00000111144 4048 3.3.2.6 6710 protein-coding gene gene with protein product 151570 NA 7628486 Standard NM_000895 NM_000895 NA Approved uc001ten.2 P09960 OTTHUMG00000170355 ENST00000228740.2:c.711+10T>- chr12.hg19:g.96412935delA 2 3 ref NA False 50 50 PASS 3 PASS ref->het 0 NA 212,213 42,42 41,41 1 1 B4DNQ9|F8VV40|Q6IAT6|Q9UCT7 True hg19 CCDS9059.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LTA4H-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000408655.1 PASS NA None 295 NA True - A ENST00000228740.2 Unknown 0 __UNKNOWN__ __UNKNOWN__ 16 33957978 33957979 __UNKNOWN__ IGR DEL CT CT - rs373442834 LTS-040_T LTS-040_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:33957978_33957979delCT NA AC136932.2 (11957 upstream) : LINC00273 (3072 downstream) NA NA NA NA NA NA NA ttctgtcttactctctttctct 0.48 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 61 44.58 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 8.74 NA NA NA NA NA NA NA chr16.hg19:g.33957982_33957983delCT 2 2 ref NA False 32 32 PASS 3 PASS ref->het 0 NA 40,68 11,12 10,11 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 61 NA True CT EPB41L1 2036 __UNKNOWN__ __UNKNOWN__ 20 34797450 34797451 __UNKNOWN__ Frame_Shift_Ins INS - - ACCAAGTCAA LTS-040_T LTS-040_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:34797450_34797451insACCAAGTCAA ENST00000338074.2 + 15 1870_1871 c.1709_1710insACCAAGTCAA c.(1708-1713)ccaccafs p.-571fs EPB41L1_ENST00000373950.2_Frame_Shift_Ins_p.-462fs|EPB41L1_ENST00000479336.1_3'UTR|EPB41L1_ENST00000441639.1_Frame_Shift_Ins_p.-497fs|EPB41L1_ENST00000202028.5_Frame_Shift_Ins_p.-497fs|EPB41L1_ENST00000373941.1_Frame_Shift_Ins_p.-571fs|EPB41L1_ENST00000373946.3_Intron NM_001258329.1|NM_012156.2 NP_001245258.1|NP_036288.2 Q9H4G0 E41L1_HUMAN erythrocyte membrane protein band 4.1-like 1 NA NA NA NA cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268) cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886) structural molecule activity (GO:0005198) NA NA breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 37 Breast(12;0.0239) AAAGTCAAACCACCACGTCCCC 0.579 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA NA NA 286 289.04 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.43 NA NA AB002336 CCDS13271.1, CCDS13272.1, CCDS58771.1 20q11.2-q12 2003-03-17 ENSG00000088367 ENSG00000088367 2036 3378 protein-coding gene gene with protein product 602879 NA 9570967, 9828140 Standard NM_012156 NM_012156 NA Approved KIAA0338 uc002xfb.3 Q9H4G0 OTTHUMG00000032378 ENST00000338074.2:c.1709_1710insACCAAGTCAA chr20.hg19:g.34797450_34797451insACCAAGTCAA ENSP00000337168:p.Pro571fs 1 4 ref NA False 43 43 PASS 0 PASS ref->het 0 NA 240,240 19,19 27,27 1 1 O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65 True hg19 CCDS13271.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EPB41L1-008 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000078978.3 PASS NA None 286 NA True + ACCAAGTCAA ENST00000338074.2 TP73 7161 __UNKNOWN__ __UNKNOWN__ 1 3650311 3650312 __UNKNOWN__ 3'UTR INS - - C LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:3650311_3650312insC ENST00000378295.4 + 0 2734_2735 TP73_ENST00000357733.3_3'UTR|TP73_ENST00000346387.4_3'UTR|TP73_ENST00000378288.4_3'UTR|TP73_ENST00000604074.1_3'UTR NM_001204185.1|NM_005427.3 NP_001191114.1|NP_005418.1 O15350 P73_HUMAN tumor protein p73 NA NA NA activation of MAPK activity (GO:0000187)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|cerebrospinal fluid secretion (GO:0033326)|digestive tract morphogenesis (GO:0048546)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|hippocampus development (GO:0021766)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|kidney development (GO:0001822)|mismatch repair (GO:0006298)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron development (GO:0048666)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell size (GO:0045793)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein tetramerization (GO:0051262)|release of cytochrome c from mitochondria (GO:0001836)|response to gamma radiation (GO:0010332)|response to organonitrogen compound (GO:0010243)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351) chromatin (GO:0000785)|cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667) chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212) breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|lung(8)|ovary(1)|prostate(1) 20 all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198) all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127) Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226) GGAGGGCGCAACCCCCCCCAGG 0.639 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 191 177.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.27 AB055065 CCDS49.1, CCDS44049.1, CCDS44050.1, CCDS44051.1, CCDS55566.1, CCDS55567.1, CCDS55568.1, CCDS55569.1, CCDS59965.1 1p36.3 2010-06-15 ENSG00000078900 ENSG00000078900 7161 12003 protein-coding gene gene with protein product 601990 NA 9296498, 9288759 Standard NM_005427 NM_001204186 NA Approved P73 uc001akp.3 O15350 OTTHUMG00000000610 ENST00000378295.4:c.*669->C chr1.hg19:g.3650319_3650319dupC 9 8 ref NA False 35 35 PASS 8 PASS ref->het 0 NA 138,143 28,30 24,18 1 1 B7Z7J4|B7Z8Z1|B7Z9C1|C9J521|O15351|Q17RN8|Q5TBV5|Q5TBV6|Q8NHW9|Q8TDY5|Q8TDY6|Q9NTK8 True hg19 CCDS49.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TP73-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000001468.4 PASS NA None 191 NA True + C ENST00000378295.4 H6PD 9563 __UNKNOWN__ __UNKNOWN__ 1 9304979 9304986 __UNKNOWN__ 5'UTR DEL CCCAGGCA CCCAGGCA - rs139855605 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:9304979_9304986delCCCAGGCA ENST00000377403.2 + 0 292_295 H6PD_ENST00000602477.1_Splice_Site_p.SQ8fs NM_001282587.1|NM_004285.3 NP_001269516.1|NP_004276.2 O95479 G6PE_HUMAN hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase) NA NA NA pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305) endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739) 6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661) breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1) 23 all_lung(157;0.23) all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419) CTCTTTGCACCCCAGGCACCCAGGCATG 0.553 NA NA NA 542 0.108227 0.0106 0.2291 5008 , , NA 22511 0.0724 NA 0.1471 False NA ,,, NA NA NA 2504 0.1513 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 594 567.88 NA 126,4140 NA 1,124,2008 NA NA NA -2.7 0 NA dbSNP_134 67 1102,7150 NA 77,948,3101 no splice-3 H6PD NM_004285.3 78,1072,5109 A1A1,A1R,RR NA 13.3543,2.9536,9.8099 NA 1228,11290 NA NA NA SO:0001623 5_prime_UTR_variant 0.89 AJ012590 CCDS101.1, CCDS72697.1 1p36 2008-02-05 2003-10-10 ENSG00000049239 ENSG00000049239 9563 1.1.1.47 4795 protein-coding gene gene with protein product 138090 "glucose dehyrogenase" GDH NA 10349511 Standard NM_004285 NM_001282587 NA Approved uc001apt.3 O95479 OTTHUMG00000001768 ENST00000377403.2:c.-8CCCAGGCA>- chr1.hg19:g.9304987_9304994delCCCAGGCA 1 5 ref NA False 82 82 PASS 2 PASS ref->het 0 NA 491,495 43,43 79,78 1 1 Q4TT33|Q66I35|Q68DT3 True hg19 CCDS101.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA H6PD-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000004928.2 PASS NA None 594 NA True + CCCAGGCA ENST00000377403.2 HSPB7 27129 __UNKNOWN__ __UNKNOWN__ 1 16346009 16346010 __UNKNOWN__ 5'UTR INS - - C rs397758991|rs3841842|rs570886659 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:16346009_16346010insC ENST00000375718.4 - 0 79_80 CLCNKA_ENST00000464764.1_Intron Q9UBY9 HSPB7_HUMAN heat shock 27kDa protein family, member 7 (cardiovascular) NA NA NA regulation of heart contraction (GO:0008016)|response to unfolded protein (GO:0006986) actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634) protein C-terminus binding (GO:0008022) breast(1)|large_intestine(1)|liver(1)|lung(6)|skin(1) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.21e-08)|COAD - Colon adenocarcinoma(227;5.5e-06)|BRCA - Breast invasive adenocarcinoma(304;9.08e-05)|Kidney(64;0.000162)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649) TTTTGTCTGAGCCCCCTACAAC 0.554 NA NA NA CCCCC|CCCCC|CCCCCC|insertion 2165 0.432308 0.3343 0.3112 5008 , , NA 18046 0.6696 NA 0.4195 False NA ,,, NA NA NA 2504 0.4192 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 498 477.83 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.01 AF155908 CCDS30611.1 1p36.23-p34.3 2011-09-02 2002-08-29 ENSG00000173641 ENSG00000173641 27129 "Heat shock proteins / HSPB" 5249 protein-coding gene gene with protein product 610692 "heat shock 27kD protein family, member 7 (cardiovascular)" NA 10593960 Standard NM_014424 NM_014424 NA Approved cvHSP uc001axo.2 Q9UBY9 OTTHUMG00000009531 ENST00000375718.4:c.-46->G chr1.hg19:g.16346014_16346014dupC 6 5 ref NA False 160 160 PASS 5 PASS ref->het 0 NA 380,385 74,75 37,35 2 2 B3KQ37|C9K0Y0|Q9NU17 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HSPB7-001 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000026333.1 PASS NA None 498 NA True - C ENST00000375718.4 CAPZB 832 __UNKNOWN__ __UNKNOWN__ 1 19810810 19810811 __UNKNOWN__ 5'UTR INS - - C rs11450129|rs397727565|rs397965964 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:19810810_19810811insC ENST00000433834.1 - 0 347_348 CAPZB_ENST00000264202.6_Intron|CAPZB_ENST00000375142.1_Intron|CAPZB_ENST00000482808.1_Intron|CAPZB_ENST00000401084.2_Intron|CAPZB_ENST00000264203.3_Intron P47756 CAPZB_HUMAN capping protein (actin filament) muscle Z-line, beta NA NA NA actin cytoskeleton organization (GO:0030036)|barbed-end actin filament capping (GO:0051016)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|muscle fiber development (GO:0048747)|negative regulation of microtubule polymerization (GO:0031115)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)|regulation of protein kinase C signaling (GO:0090036) acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|membrane (GO:0016020)|WASH complex (GO:0071203)|Z disc (GO:0030018) actin binding (GO:0003779) endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1) 7 Colorectal(325;3.93e-05)|Renal(390;0.000147)|all_lung(284;0.000169)|Lung NSC(340;0.000202)|Breast(348;0.000496)|Ovarian(437;0.00428)|Myeloproliferative disorder(586;0.0262) UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Kidney(64;8.63e-06)|BRCA - Breast invasive adenocarcinoma(304;4.06e-05)|KIRC - Kidney renal clear cell carcinoma(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000525)|STAD - Stomach adenocarcinoma(196;0.00779)|READ - Rectum adenocarcinoma(331;0.103)|Lung(427;0.173) GGGCCTGGTGGCCCCCCAAGGC 0.658 NA NA NA CCCCCC|CCCCCC|CCCCCCC|insertion 773 0.154353 0.1256 0.1225 5008 , , NA 17875 0.2232 NA 0.1064 False NA ,,, NA NA NA 2504 0.1943 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 337 345.41 NA ,, 330,2344 NA 58,214,1065 NA NA NA ,, 0.5 0 NA dbSNP_120 13 694,4556 NA 120,454,2051 no intron,intron,intron CAPZB NM_004930.3,NM_001206541.1,NM_001206540.1 ,, 178,668,3116 A1A1,A1R,RR NA 13.219,12.3411,12.9228 ,, ,, NA 1024,6900 NA NA NA SO:0001623 5_prime_UTR_variant 0.41 U03271 CCDS41277.1, CCDS55579.1, CCDS72717.1, CCDS72718.1 1p36.1 2014-05-09 ENSG00000077549 ENSG00000077549 832 1491 protein-coding gene gene with protein product 601572 NA Standard NM_004930 NA Approved uc021ohr.1 P47756 OTTHUMG00000002556 ENST00000433834.1:c.-38->G chr1.hg19:g.19810816_19810816dupC 7 6 ref NA False 131 131 PASS 6 PASS ref->het 0 NA 228,228 56,58 45,44 1 1 Q32Q68|Q5U0L4|Q8TB49|Q9NUC4 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CAPZB-008 KNOWN basic protein_coding NA protein_coding OTTHUMT00000007265.1 PASS NA None 337 NA True - C ENST00000433834.1 BSDC1 55108 __UNKNOWN__ __UNKNOWN__ 1 32843538 32843539 __UNKNOWN__ Intron DEL GA GA - rs142016597|rs200234101 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:32843538_32843539delGA ENST00000455895.2 - 8 710 BSDC1_ENST00000526031.1_Intron|BSDC1_ENST00000446293.2_Intron|BSDC1_ENST00000449308.1_Intron|BSDC1_ENST00000419121.2_Intron|BSDC1_ENST00000413080.1_Intron|BSDC1_ENST00000341071.7_Intron NM_001143888.1|NM_018045.6 NP_001137360.1|NP_060515.3 Q9NW68 BSDC1_HUMAN BSD domain containing 1 NA NA NA breast(1)|central_nervous_system(2)|kidney(1)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1) 17 Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186) GCACAGATGTGACACTTGCCCC 0.599 NA NA NA 28 0.00559105 0 0.0014 5008 , , NA 19093 0 NA 0.0089 False NA ,,, NA NA NA 2504 0.0184 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 395 368.07 NA ,,, 3,4263 NA 0,3,2130 NA NA NA ,,, 2.2 0 NA 100 62,8192 NA 2,58,4067 no intron,intron,intron,intron BSDC1 NM_018045.6,NM_001143890.1,NM_001143889.1,NM_001143888.1 ,,, 2,61,6197 A1A1,A1R,RR NA 0.7512,0.0703,0.5192 ,,, ,,, NA 65,12455 NA NA NA SO:0001627 intron_variant 1.16 BX641056 CCDS363.2, CCDS44101.1, CCDS44102.1, CCDS44103.1, CCDS72752.1 1p35.1 2008-02-05 ENSG00000160058 ENSG00000160058 55108 25501 protein-coding gene gene with protein product NA NA 12477932 Standard NM_018045 XM_005270985 NA Approved FLJ10276, RP4-811H24.7 uc010ohg.2 Q9NW68 OTTHUMG00000007588 ENST00000455895.2:c.676+31TC>- chr1.hg19:g.32843538_32843539delGA 0 2 ref NA False 48 48 PASS 1 PASS ref->het 0 NA 318,320 43,43 41,40 1 1 B4DMS7|B4DTI7|B4DTP7|B4E2X8|Q49AT8|Q68DY6|Q6IAA3|Q6MZK1|Q6UXS1|Q9HAL9 True hg19 CCDS363.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BSDC1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000020056.3 PASS NA None 395 NA True - GA ENST00000455895.2 NASP 4678 __UNKNOWN__ __UNKNOWN__ 1 46049922 46049945 __UNKNOWN__ Intron DEL GGAGGGCTAATGGACGGGGGCTCC GGAGGGCTAATGGACGGGGGCTCC - rs377682344|rs186337763 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:46049922_46049945delGGAGGGCTAATGGACGGGGGCTCC ENST00000350030.3 + 1 146 NASP_ENST00000351223.3_Intron|NASP_ENST00000372052.4_Intron|NASP_ENST00000402363.3_Intron|NASP_ENST00000537798.1_Intron NM_002482.3 NP_002473.2 P49321 NASP_HUMAN nuclear autoantigenic sperm protein (histone-binding) NA NA NA blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031) cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234) Hsp90 protein binding (GO:0051879) breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1) 17 Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211) CAGTCCGCGGGGAGGGCTAATGGACGGGGGCTCCGGAGAAGGGG 0.638 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 265 254.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.11 M97856 CCDS524.1, CCDS525.1, CCDS55597.1 1p34.1 2013-01-10 ENSG00000132780 ENSG00000132780 4678 "Tetratricopeptide (TTC) repeat domain containing" 7644 protein-coding gene gene with protein product 603185 NA 1426632 Standard NM_002482 NM_002482 NA Approved FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999 uc001coi.2 P49321 OTTHUMG00000007826 ENST00000350030.3:c.59+45GGAGGGCTAATGGACGGGGGCTCC>- chr1.hg19:g.46049922_46049945delGGAGGGCTAATGGACGGGGGCTCC 0 7 ref NA False 69 69 PASS 1 PASS ref->het 0 NA 222,230 14,14 45,40 1 1 A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2 True hg19 CCDS524.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NASP-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000021533.2 PASS NA None 265 NA True + GGAGGGCTAATGGACGGGGGCTCC ENST00000350030.3 NSUN4 387338 __UNKNOWN__ __UNKNOWN__ 1 46806275 46806276 __UNKNOWN__ 5'UTR DEL AG AG - rs112712935 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:46806275_46806276delAG ENST00000474844.1 + 0 427_428 NM_199044.3 NP_950245.2 Q96CB9 NSUN4_HUMAN NOP2/Sun domain family, member 4 NA NA NA rRNA methylation (GO:0031167) mitochondrial large ribosomal subunit (GO:0005762) methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843) endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1) 8 Acute lymphoblastic leukemia(166;0.155) gcatccaggcagagtcattatt 0.599 NA NA NA OREG0013456 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 671 0.133986 0.1384 0.147 5008 , , NA 17462 0.0188 NA 0.2783 False NA ,,, NA NA NA 2504 0.089 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 245 259.85 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.01 AK021577 CCDS534.1, CCDS57996.1 1p34 2012-02-24 2009-11-23 ENSG00000117481 ENSG00000117481 387338 "NOP2/Sun domain containing" 31802 protein-coding gene gene with protein product "sperm head and tail associated protein" 615394 "NOL1/NOP2/Sun domain family 4", "NOL1/NOP2/Sun domain family, member 4" NA Standard NM_199044 NM_199044 NA Approved MGC22960, SHTAP uc001cpr.2 Q96CB9 OTTHUMG00000007808 ENST00000474844.1:c.-223AG>- chr1.hg19:g.46806277_46806278delAG 1 2 ref 942 False 152 138 PASS 2 PASS ref->het 0 NA 158,158 55,55 28,28 1 1 A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8 True hg19 CCDS534.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSUN4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000021427.1 PASS NA None 245 NA True + AG ENST00000474844.1 ANGPTL3 27329 __UNKNOWN__ __UNKNOWN__ 1 63070538 63070546 __UNKNOWN__ 3'UTR DEL GTTAATGTG GTTAATGTG - rs67461605|rs34483103 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:63070538_63070546delGTTAATGTG ENST00000371129.3 + 0 1513_1521 DOCK7_ENST00000404627.2_Intron|DOCK7_ENST00000340370.5_Intron|DOCK7_ENST00000251157.5_Intron NM_014495.2 NP_055310.1 Q9Y5C1 ANGL3_HUMAN angiopoietin-like 3 NA NA NA acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328) cell surface (GO:0009986)|extracellular space (GO:0005615) enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859) breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1) 13 CTCATTCCAAGTTAATGTGGTCTAATAAT 0.282 NA NA NA 1745 0.348442 0.4539 0.3501 5008 , , NA 16580 0.1776 NA 0.3022 False NA ,,, NA NA NA 2504 0.4284 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 186 197.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF152562 CCDS622.1 1p31.3 2013-02-06 ENSG00000132855 ENSG00000132855 27329 "Fibrinogen C domain containing" 491 protein-coding gene gene with protein product "angiopoietin 5" 604774 ANGPT5 NA 10644446 Standard NM_014495 NM_014495 NA Approved uc001das.2 Q9Y5C1 OTTHUMG00000009146 ENST00000371129.3:c.*58GTTAATGTG>- chr1.hg19:g.63070538_63070546delGTTAATGTG 0 3 ref NA False 59 59 PASS 1 PASS ref->het 0 NA 116,117 43,43 26,25 1 1 A0JLS0|B1ALJ0|B2RCW1 True hg19 CCDS622.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ANGPTL3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000025344.1 PASS NA None 186 NA True + GTTAATGTG ENST00000371129.3 C1orf52 148423 __UNKNOWN__ __UNKNOWN__ 1 85725354 85725360 __UNKNOWN__ 5'UTR DEL CCGGAAA CCGGAAA - rs113622579|rs533388228|rs112918702 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:85725354_85725360delCCGGAAA ENST00000294661.4 - 0 0_1 NR_024113.1 Q8N6N3 CA052_HUMAN chromosome 1 open reading frame 52 NA NA NA poly(A) RNA binding (GO:0044822) endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1) 10 all cancers(265;0.0105)|Epithelial(280;0.0293) CCGCCGGAAGCCGGAAACCGGAAACCG 0.671 NA NA NA OREG0013580 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 2026 0.404553 0.4682 0.317 5008 , , NA 10373 0.3363 NA 0.4006 False NA ,,, NA NA NA 2504 0.455 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 179 173.18 NA 1247,1967 NA 444,359,804 NA NA NA 0.6 1 NA dbSNP_129 3 2245,4109 NA 803,639,1735 no utr-5 C1orf52 NM_198077.3 1247,998,2539 A1A1,A1R,RR NA 35.3321,38.799,36.4967 NA 3492,6076 NA NA NA SO:0001623 5_prime_UTR_variant 1.49 BC029538 CCDS703.1 1p22.3 2008-02-05 ENSG00000162642 ENSG00000162642 148423 24871 protein-coding gene gene with protein product NA NA 11891061 Standard NM_198077 NM_198077 NA Approved gm117, FLJ44982 uc001dkv.3 Q8N6N3 OTTHUMG00000009966 ENST00000294661.4:c.-3388TTTCCGG>- chr1.hg19:g.85725361_85725367delCCGGAAA 1 3 ref 1239 False 67 67 PASS 2 PASS ref->het 0 NA 113,117 24,26 45,39 1 1 B3KX89|Q8TDK5|Q8TDK6 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C1orf52-003 KNOWN basic processed_transcript NA protein_coding OTTHUMT00000027614.2 PASS NA None 179 NA True - CCGGAAA ENST00000294661.4 CDC7 8317 __UNKNOWN__ __UNKNOWN__ 1 91990988 91990989 __UNKNOWN__ 3'UTR INS - - GT rs72510777|rs13447561|rs397808242 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:91990988_91990989insGT ENST00000428239.1 + 0 2980_2981 CDC7_ENST00000234626.6_3'UTR NM_001134420.1 NP_001127892.1 O00311 CDC7_HUMAN cell division cycle 7 NA NA NA cell cycle phase transition (GO:0044770)|cell division (GO:0051301)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571) cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674) breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|stomach(2) 23 all_lung(203;0.0165)|Lung NSC(277;0.0562) all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124) CAGATAATGAAGTAGGCAAAGA 0.396 NA NA NA 469 0.0936502 0.0371 0.1888 5008 , , NA 17653 0.1964 NA 0.0179 False NA ,,, NA NA NA 2504 0.0746 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 135 139.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.26 AF015592 CCDS734.1 1p22 2013-01-17 2013-01-17 2003-07-23 ENSG00000097046 ENSG00000097046 8317 1745 protein-coding gene gene with protein product 603311 "CDC7 (cell division cycle 7, S. cerevisiae, homolog)-like 1", "CDC7 cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 (S. cerevisiae)", "cell division cycle 7 homolog (S. cerevisiae)" CDC7L1 NA 9405610, 9250678 Standard NM_003503 NM_003503 NA Approved Hsk1, huCdc7, HsCdc7 uc001dof.3 O00311 OTTHUMG00000047810 ENST00000428239.1:c.*997->GT chr1.hg19:g.91990989_91990990dupGT 2 2 ref NA False 44 44 PASS 1 PASS ref->het 0 NA 102,104 18,18 15,13 1 1 D3DT31|O00558|Q5T5U5 True hg19 CCDS734.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDC7-201 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000027928.1 PASS NA None 135 NA True + GT ENST00000428239.1 CLCC1 23155 __UNKNOWN__ __UNKNOWN__ 1 109486241 109486241 __UNKNOWN__ Intron DEL A A - rs200578118|rs3215062|rs397840046 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:109486241delA ENST00000369971.2 - 6 691 CLCC1_ENST00000482889.1_Intron|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000348264.2_Intron|CLCC1_ENST00000369970.3_Intron|CLCC1_ENST00000415331.1_Intron|CLCC1_ENST00000369969.2_Intron|CLCC1_ENST00000356970.2_Intron|CLCC1_ENST00000369976.1_Intron|CLCC1_ENST00000302500.4_Intron|CLCC1_ENST00000369968.2_Intron NM_001048210.1 NP_001041675.1 Q96S66 CLCC1_HUMAN chloride channel CLIC-like 1 NA NA NA chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634) chloride channel activity (GO:0005254) autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1) 14 all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626) Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231) GAAGTACCTTAAAACAGAGAG 0.393 NA NA NA AAAA|AAAA|AAA|deletion 2422 0.483626 0.6263 0.4726 5008 , , NA 20144 0.3948 NA 0.4632 False NA ,,, NA NA NA 2504 0.411 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 332 293.07 NA , 2592,1674 NA 783,1026,324 46 58 54 , -10.3 0 1 dbSNP_126 97 3768,4486 NA 844,2080,1203 no intron,intron CLCC1 NM_015127.3,NM_001048210.1 , 1627,3106,1527 A1A1,A1R,RR NA 45.6506,39.2405,49.2013 , , 109486241 6360,6160 2198 4290 6488 SO:0001627 intron_variant 1.24 AB018304 CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1 1p13.3 2008-02-05 ENSG00000121940 ENSG00000121940 23155 29675 protein-coding gene gene with protein product "Mid1-related chloride channel (yeast)" NA NA 9872452, 11279057 Standard NM_015127 NM_001048210 NA Approved MCLC uc001dwf.2 Q96S66 OTTHUMG00000011732 ENST00000369971.2:c.562-4T>- chr1.hg19:g.109486241delA 3 5 ref NA False 149 119 PASS 4 PASS ref->het 0 NA 207,209 92,93 28,26 1 1 O94861|Q8WYP8|Q8WYP9|Q9BU25 True hg19 CCDS41362.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CLCC1-203 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000032405.1 PASS NA None 332 NA True - A ENST00000369971.2 TSPAN2 10100 __UNKNOWN__ __UNKNOWN__ 1 115592611 115592612 __UNKNOWN__ 3'UTR DEL AC AC - rs5777209|rs61428640 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:115592611_115592612delAC ENST00000369516.2 - 0 1196_1197 NM_005725.4 NP_005716.2 O60636 TSN2_HUMAN tetraspanin 2 NA NA NA astrocyte development (GO:0014002)|axon development (GO:0061564)|brain development (GO:0007420)|inflammatory response (GO:0006954)|microglia development (GO:0014005)|myelination (GO:0042552)|oligodendrocyte differentiation (GO:0048709) integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886) central_nervous_system(1)|large_intestine(4)|lung(3)|pancreas(1)|prostate(1) 10 Lung SC(450;0.211) all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191) Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179) CCCAACTTAGACACAGTCAGTT 0.347 NA NA NA 727 0.145168 0.0885 0.1542 5008 , , NA 16665 0.0456 NA 0.2495 False NA ,,, NA NA NA 2504 0.2106 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 133 126.64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF054839 CCDS881.1 1p13.1 2013-02-14 ENSG00000134198 ENSG00000134198 10100 "Tetraspanins" 20659 protein-coding gene gene with protein product 613133 NA 9714763, 11739647 Standard NM_005725 NM_005725 NA Approved TSPAN-2, TSN2, FLJ12082 uc001eft.3 O60636 OTTHUMG00000011878 ENST00000369516.2:c.*500GT>- chr1.hg19:g.115592613_115592614delAC 1 2 ref NA False 35 35 PASS 2 PASS ref->het 0 NA 102,103 20,20 10,10 2 2 D6PTH4|Q5TET2|Q8WU05 True hg19 CCDS881.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TSPAN2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000032828.1 PASS NA None 133 NA True - AC ENST00000369516.2 PDE4DIP 9659 __UNKNOWN__ __UNKNOWN__ 1 144932197 144932207 __UNKNOWN__ Intron DEL TCCGGCTCTGC TCCGGCTCTGC - rs33943525|rs386635176 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:144932197_144932207delTCCGGCTCTGC ENST00000530740.1 - 9 1086 PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000369354.3_Intron|PDE4DIP_ENST00000313431.9_5'UTR|PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000479408.2_Intron Q5VU43 MYOME_HUMAN phosphodiesterase 4D interacting protein NA NA NA cellular protein complex assembly (GO:0043623) centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634) enzyme binding (GO:0019899) NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2) 176 Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126) TCAGCGGGCTTCCGGCTCTGCGCATGCGAGG 0.664 NA NA T PDGFRB MPD NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS Dom yes 1 1q12 9659 phosphodiesterase 4D interacting protein (myomegalin) NA L 0 NA NA NA NA NA 480 508.42 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.46 AB007923, AB007946 CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1 1q21.1 2008-07-31 2008-07-31 ENSG00000178104 ENSG00000178104 9659 15580 protein-coding gene gene with protein product "myomegalin" 608117 "cardiomyopathy associated 2" CMYA2 NA 9455484, 11134006 Standard NM_022359 NM_022359 NA Approved KIAA0477, KIAA0454, MMGL uc021ouh.1 Q5VU43 OTTHUMG00000013846 ENST00000530740.1:c.1048-8376GCAGAGCCGGA>- chr1.hg19:g.144932197_144932207delTCCGGCTCTGC 0 2 ref NA False 175 175 PASS 1 PASS ref->het 0 NA 444,450 22,22 60,58 1 1 A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PDE4DIP-036 NOVEL not_organism_supported|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000384663.2 PASS NA None 480 NA True - TCCGGCTCTGC ENST00000530740.1 EFNA1 1942 __UNKNOWN__ __UNKNOWN__ 1 155107153 155107154 __UNKNOWN__ 3'UTR INS - - A LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:155107153_155107154insA ENST00000368407.3 + 0 1746_1747 EFNA1_ENST00000368406.2_3'UTR NM_004428.2 NP_004419.2 P20827 EFNA1_HUMAN ephrin-A1 NA NA NA activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|ephrin receptor signaling pathway (GO:0048013)|mitral valve morphogenesis (GO:0003183)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|notochord formation (GO:0014028)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of angiogenesis (GO:0045765)|regulation of axonogenesis (GO:0050770)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|substrate adhesion-dependent cell spreading (GO:0034446) anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887) ephrin receptor binding (GO:0046875)|receptor binding (GO:0005102) breast(1)|endometrium(1)|kidney(1)|lung(1)|skin(1) 5 all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193) AACCTGTTCTTAGAGTGTAGCT 0.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 203 193.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.01 CCDS1091.1, CCDS1092.1 1q21-q22 2011-03-09 ENSG00000169242 ENSG00000169242 1942 "Ephrins" 3221 protein-coding gene gene with protein product 191164 TNFAIP4, EPLG1 NA 2233719, 8660976 Standard NM_004428 NM_182685 NA Approved LERK1, ECKLG uc001fhh.3 P20827 OTTHUMG00000035312 ENST00000368407.3:c.*611->A chr1.hg19:g.155107154_155107154dupA 2 4 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 151,152 23,23 28,27 1 1 D3DV86|Q5SR60|Q5SR61|Q6I9T9|Q8N578 True hg19 CCDS1091.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EFNA1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000085428.1 PASS NA None 203 NA True + A ENST00000368407.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 1 161110982 161110982 __UNKNOWN__ IGR DEL G G - rs35769518|rs397718040 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:161110982delG NA DEDD (8504 upstream) : ACA64 (15 downstream) NA NA NA NA AGCCACACCCGGGGGGAGGCC 0.687 NA NA NA GGGGGG|GGGGGG|GGGGG|deletion 1317 0.262979 0.1286 0.3084 5008 , , NA 7779 0.3839 NA 0.325 False NA ,,, NA NA NA 2504 0.2239 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 151 139.36 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr1.hg19:g.161110982delG 5 8 ref NA False 87 87 PASS 6 PASS ref->het 0 NA 101,102 35,35 15,14 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 151 NA True G DPT 1805 __UNKNOWN__ __UNKNOWN__ 1 168665747 168665748 __UNKNOWN__ 3'UTR INS - - T rs71685037|rs201706806|rs78760104|rs1433 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:168665747_168665748insT ENST00000367817.3 - 0 734_735 NM_001937.4 NP_001928.2 Q07507 DERM_HUMAN dermatopontin NA NA NA cell adhesion (GO:0007155)|collagen fibril organization (GO:0030199)|negative regulation of cell proliferation (GO:0008285) extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578) kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2) 12 all_hematologic(923;0.208) CTCCTGTCCCCGGCCCCTTTCC 0.465 NA NA NA T|-|T|deletion 3238 0.646565 0.8313 0.5821 5008 , , NA 21475 0.5804 NA 0.5417 False NA ,,, NA NA NA 2504 0.6186 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 514 487.69 NA 3381,885 NA 1341,699,93 NA NA NA 2.3 0 NA dbSNP_36 58 4400,3854 NA 1198,2004,925 no utr-3 DPT NM_001937.4 2539,2703,1018 A1A1,A1R,RR NA 46.6925,20.7454,37.8514 NA 7781,4739 NA NA NA SO:0001624 3_prime_UTR_variant 0.4 BC033736 CCDS1275.1 1q12-q23 2008-02-05 ENSG00000143196 ENSG00000143196 1805 3011 protein-coding gene gene with protein product 125597 NA 8104875 Standard NM_001937 NM_001937 NA Approved uc001gfp.3 Q07507 OTTHUMG00000034554 ENST00000367817.3:c.*40->A chr1.hg19:g.168665747_168665748insT 1 4 ref NA False 81 81 PASS 0 PASS ref->het 0 NA 385,389 81,81 45,44 1 1 A8K981|Q8N4R2|Q9UIX8 True hg19 CCDS1275.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DPT-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000083618.1 PASS NA None 514 NA True - T ENST00000367817.3 KIFAP3 22920 __UNKNOWN__ __UNKNOWN__ 1 170043482 170043483 __UNKNOWN__ Intron INS - - AACTAGCG rs3841721|rs555991600 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:170043482_170043483insAACTAGCG ENST00000361580.2 - 1 260 KIFAP3_ENST00000367767.1_Intron|KIFAP3_ENST00000538366.1_Intron|KIFAP3_ENST00000490550.1_Intron NM_014970.3 NP_055785.2 Q92845 KIFA3_HUMAN kinesin-associated protein 3 NA NA NA antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|membrane organization (GO:0061024)|microtubule-based movement (GO:0007018)|microtubule-based process (GO:0007017)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of calcium-dependent cell-cell adhesion (GO:0046587)|protein complex assembly (GO:0006461)|protein localization (GO:0008104)|signal transduction (GO:0007165) centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule cytoskeleton (GO:0015630) kinesin binding (GO:0019894) endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|prostate(2)|skin(3)|urinary_tract(2) 35 all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181) CCCGTCTGCTAAACTAGCGTTG 0.535 NA NA NA 710 0.141773 0.0673 0.2363 5008 , , NA 18334 0.1905 NA 0.1064 False NA ,,, NA NA NA 2504 0.1616 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 203 199.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 U59919 CCDS1288.1, CCDS55659.1, CCDS55660.1, CCDS55661.1 1q24.2 2012-09-20 ENSG00000075945 ENSG00000075945 22920 17060 protein-coding gene gene with protein product "Smg GDS" 601836 NA 8900189 Standard NM_014970 NM_014970 NA Approved SMAP, KAP3, FLA3, KAP-1 uc001ggv.3 Q92845 OTTHUMG00000035947 ENST00000361580.2:c.32+93->CGCTAGTT chr1.hg19:g.170043483_170043490dupAACTAGCG 2 3 ref NA False 76 76 PASS 1 PASS ref->het 0 NA 152,152 29,29 22,22 1 1 B1AKU4|B1AKU5|B2RDL1|B7Z8A3|F5H591|Q8NHU7|Q9H416 True hg19 CCDS1288.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KIFAP3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000087568.1 PASS NA None 203 NA True - AACTAGCG ENST00000361580.2 EDEM3 80267 __UNKNOWN__ __UNKNOWN__ 1 184660111 184660111 __UNKNOWN__ 3'UTR DEL A A - rs11358304 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:184660111delA ENST00000318130.8 - 0 6151 NM_025191.3 NP_079467.3 Q9BZQ6 EDEM3_HUMAN ER degradation enhancer, mannosidase alpha-like 3 NA NA NA cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986) endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789) calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571) breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 30 GCTTTACTATAAAAAAGGTTG 0.294 NA NA NA AAAAA|AAAAAA|AAAAA|insertion 2174 0.434105 0.1906 0.3977 5008 , , NA 15421 0.631 NA 0.4344 False NA ,,, NA NA NA 2504 0.5859 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 227 227.57 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.56 AF288393 CCDS1363.2 1q25 2008-02-05 2006-03-31 2006-03-31 ENSG00000116406 ENSG00000116406 80267 16787 protein-coding gene gene with protein product 610214 "chromosome 1 open reading frame 22" C1orf22 NA 15537790, 15579471 Standard NM_025191 NM_025191 NA Approved uc010pok.2 Q9BZQ6 OTTHUMG00000035387 ENST00000318130.8:c.*3086T>- chr1.hg19:g.184660111delA 5 7 ref NA False 100 100 PASS 6 PASS ref->het 0 NA 156,156 46,47 24,23 1 1 B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7 True hg19 CCDS1363.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EDEM3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000085785.3 PASS NA None 227 NA True - A ENST00000318130.8 EDEM3 80267 __UNKNOWN__ __UNKNOWN__ 1 184706213 184706213 __UNKNOWN__ Intron DEL T T - rs10711907|rs397692142 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:184706213delT ENST00000318130.8 - 4 572 EDEM3_ENST00000367512.3_Intron NM_025191.3 NP_079467.3 Q9BZQ6 EDEM3_HUMAN ER degradation enhancer, mannosidase alpha-like 3 NA NA NA cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986) endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789) calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571) breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 30 GAAACAAGCGTTAACAAGATA 0.308 NA NA NA T|TT|T|insertion 3220 0.642971 0.8177 0.5072 5008 , , NA 18775 0.7004 NA 0.4751 False NA ,,, NA NA NA 2504 0.6166 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 129 124.47 NA 3262,1004 NA 1258,746,129 24 47 40 1.8 0.1 1 dbSNP_119 81 3938,4302 NA 960,2018,1142 no intron EDEM3 NM_025191.3 2218,2764,1271 A1A1,A1R,RR NA 47.7913,23.5349,42.4276 184706213 7200,5306 1996 4144 6140 SO:0001627 intron_variant 0 AF288393 CCDS1363.2 1q25 2008-02-05 2006-03-31 2006-03-31 ENSG00000116406 ENSG00000116406 80267 16787 protein-coding gene gene with protein product 610214 "chromosome 1 open reading frame 22" C1orf22 NA 15537790, 15579471 Standard NM_025191 NM_025191 NA Approved uc010pok.2 Q9BZQ6 OTTHUMG00000035387 ENST00000318130.8:c.306-15A>- chr1.hg19:g.184706213delT 1 2 ref NA False 49 49 PASS 2 PASS ref->het 0 NA 97,97 24,24 10,10 1 1 B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7 True hg19 CCDS1363.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EDEM3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000085785.3 PASS NA None 129 NA True - T ENST00000318130.8 PLA2G4A 5321 __UNKNOWN__ __UNKNOWN__ 1 186839880 186839881 __UNKNOWN__ Intron DEL AG AG - rs12720508|rs200627651|rs397843969 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:186839880_186839881delAG ENST00000367466.3 + 3 267 PLA2G4A_ENST00000466600.1_Intron|PLA2G4A_ENST00000442353.2_Intron NM_024420.2 NP_077734 P47712 PA24A_HUMAN phospholipase A2, group IVA (cytosolic, calcium-dependent) NA NA NA arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281) cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743) calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623) breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1) 53 Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786) GACATGCGTAAGAGTGCCCTTA 0.391 NA NA NA 1430 0.285543 0.3033 0.1859 5008 , , NA 20124 0.4375 NA 0.1998 False NA ,,, NA NA NA 2504 0.2638 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 191 178.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 M72393 CCDS1372.1 1q25 2014-09-17 ENSG00000116711 ENSG00000116711 5321 3.1.1.4, 3.1.1.5 9035 protein-coding gene gene with protein product 600522 PLA2G4 NA 8175726 Standard NM_024420 NM_024420 NA Approved cPLA2-alpha uc001gsc.3 P47712 OTTHUMG00000035512 ENST00000367466.3:c.115+232AG>- chr1.hg19:g.186839882_186839883delAG 1 3 ref NA False 30 30 PASS 2 PASS ref->het 0 NA 150,151 25,25 19,19 1 1 B1AKG4|Q29R80 True hg19 CCDS1372.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PLA2G4A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000086236.1 PASS NA None 191 NA True + AG ENST00000367466.3 CAMSAP2 23271 __UNKNOWN__ __UNKNOWN__ 1 200818180 200818181 __UNKNOWN__ Frame_Shift_Del DEL GC GC - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:200818180_200818181delGC ENST00000358823.2 + 11 2553_2554 c.2283_2284delGC c.(2281-2286)aggcgtfs p.RR761fs CAMSAP2_ENST00000236925.4_Frame_Shift_Del_p.RR772fs|CAMSAP2_ENST00000413307.2_Frame_Shift_Del_p.RR745fs NM_203459.1 NP_982284.1 Q08AD1 CAMP2_HUMAN calmodulin regulated spectrin-associated protein family, member 2 772 NA NA microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043) cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449) microtubule minus-end binding (GO:0051011) NA AAGAAAAGAGGCGTGCTATAGA 0.446 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 195 203.01 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.09 AB029001 CCDS1404.1, CCDS72998.1, CCDS72999.1 1q32 2011-08-18 2011-08-18 2011-08-18 ENSG00000118200 ENSG00000118200 23271 29188 protein-coding gene gene with protein product 613775 "calmodulin regulated spectrin-associated protein 1-like 1" CAMSAP1L1 NA 15897902, 19508979 Standard NM_203459 XM_005245040 NA Approved KIAA1078 uc001gvk.3 Q08AD1 OTTHUMG00000035740 ENST00000358823.2:c.2283_2284delGC chr1.hg19:g.200818180_200818181delGC ENSP00000351684:p.Arg761fs 0 3 ref NA False 96 90 PASS 1 PASS ref->het 0 NA 102,102 73,74 24,24 1 1 B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4 True hg19 CCDS1404.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CAMSAP2-002 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000087034.2 PASS NA None 195 NA True + GC ENST00000358823.2 FLVCR1 28982 __UNKNOWN__ __UNKNOWN__ 1 213031639 213031639 __UNKNOWN__ 5'UTR DEL T T - rs17676799|rs373452417 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:213031639delT ENST00000366971.4 + 0 43 NM_014053.3 NP_054772.1 Q9Y5Y0 FLVC1_HUMAN feline leukemia virus subgroup C cellular receptor 1 NA NA NA blood vessel development (GO:0001568)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|head morphogenesis (GO:0060323)|heme export (GO:0097037)|heme transport (GO:0015886)|in utero embryonic development (GO:0001701)|mitochondrial transport (GO:0006839)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|regulation of organ growth (GO:0046620)|spleen development (GO:0048536)|transmembrane transport (GO:0055085)|transport (GO:0006810) integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886) heme transporter activity (GO:0015232)|transporter activity (GO:0005215) cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(2) 12 OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11) GTTCACGCGGTAGCGCGGATT 0.726 NA NA NA T|T|-|deletion 51 0.0101837 0 0.0072 5008 , , NA 11768 0 NA 0.0268 False NA ,,, NA NA NA 2504 0.0194 NA NA NA Esophageal Squamous(199;2235 2952 19233 26256) PASS NA NA NA 0 NA NA NA NA NA 49 45.05 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 AF118637 CCDS1510.1 1q32.3 2014-05-30 ENSG00000162769 ENSG00000162769 28982 "Solute carriers" 24682 protein-coding gene gene with protein product 609144 "ataxia, posterior column 1, with retinitis pigmentosa" AXPC1 NA 10400745, 10648427, 21070897 Standard NM_014053 NM_014053 NA Approved FLVCR, MFSD7B, PCA uc001hjt.3 Q9Y5Y0 OTTHUMG00000036924 ENST00000366971.4:c.-156T>- chr1.hg19:g.213031639delT 0 3 ref NA False 57 57 PASS 1 PASS ref->het 0 NA 31,31 13,13 4,4 1 1 Q1HE16|Q86XY9|Q9NVR9 True hg19 CCDS1510.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FLVCR1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000089678.2 PASS NA None 49 NA True + T ENST00000366971.4 LYPLAL1 127018 __UNKNOWN__ __UNKNOWN__ 1 219366404 219366405 __UNKNOWN__ Intron INS - - A LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:219366404_219366405insA ENST00000366928.5 + 3 238 LYPLAL1_ENST00000366927.3_Intron|LYPLAL1_ENST00000483635.1_Intron NM_138794.3 NP_620149 Q5VWZ2 LYPL1_HUMAN lysophospholipase-like 1 NA NA NA negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|protein depalmitoylation (GO:0002084) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062) lysophospholipase activity (GO:0004622) large_intestine(1)|lung(5) 6 GBM - Glioblastoma multiforme(131;0.055)|all cancers(67;0.105)|OV - Ovarian serous cystadenocarcinoma(81;0.116) TTTTTTTGGGGGGGGGCGGTTG 0.327 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 41 42.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 BC016711 CCDS1522.1, CCDS73032.1 1q41 2008-02-05 ENSG00000143353 ENSG00000143353 127018 20440 protein-coding gene gene with protein product NA NA Standard NM_138794 XM_005273046 NA Approved Q96AV0 uc001hlq.4 Q5VWZ2 OTTHUMG00000037141 ENST00000366928.5:c.192-19->A chr1.hg19:g.219366404_219366405insA 1 11 ref NA False 34 34 PASS 0 PASS ref->het 0 NA 16,17 17,17 9,9 1 1 A8K677|Q5VWZ3|Q7Z4A3|Q96AV0 True hg19 CCDS1522.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LYPLAL1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000090208.1 PASS NA None 41 NA True + A ENST00000366928.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ 1 226313676 226313677 __UNKNOWN__ IGR INS - - G rs1877157|rs569900804|rs564627812 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:226313676_226313677insG NA RP11-396C23.2 (36479 upstream) : ACBD3 (18702 downstream) NA NA NA NA gcagcagcggcggcggcggcgg 0.574 NA NA NA |||unknown(STR2?) 14 0.00279553 0 0.0043 5008 , , NA 14814 0.001 NA 0.001 False NA ,,, NA NA NA 2504 0.0092 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 53 47.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.01 NA NA NA NA NA chr1.hg19:g.226313678_226313678dupG 3 4 ref NA False 41 41 PASS 2 PASS ref->het 0 NA 35,37 11,12 7,4 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 53 NA True G ACBD3 64746 __UNKNOWN__ __UNKNOWN__ 1 226333536 226333540 __UNKNOWN__ 3'UTR DEL CAAAA CAAAA - rs71574561|rs575000281|rs72264515 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:226333536_226333540delCAAAA ENST00000366812.5 - 0 2412_2416 NM_022735.3 NP_073572.2 Q9H3P7 GCP60_HUMAN acyl-CoA binding domain containing 3 NA NA NA steroid biosynthetic process (GO:0006694)|transport (GO:0006810) Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739) fatty-acyl-CoA binding (GO:0000062) breast(2)|endometrium(3)|large_intestine(5)|lung(7)|skin(1)|urinary_tract(2) 20 Breast(184;0.158) GBM - Glioblastoma multiforme(131;0.121) TCTATGAAGCcaaaacaaaacaaaa 0.273 NA NA NA 1568 0.313099 0.2579 0.4035 5008 , , NA 20180 0.2956 NA 0.3738 False NA ,,, NA NA NA 2504 0.2791 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 228 225.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.04 AB043587 CCDS1551.1 1q41 2013-10-16 2010-04-30 2003-11-12 ENSG00000182827 ENSG00000182827 64746 "A-kinase anchor proteins" 15453 protein-coding gene gene with protein product "PBR- and PKA-associated protein 7" 606809 "golgi complex associated protein 1, 60kDa", "acyl-Coenzyme A binding domain containing 3" GOLPH1, GOCAP1 NA 12692076, 20150326 Standard NM_022735 NM_022735 NA Approved GCP60, PAP7 uc001hpy.3 Q9H3P7 OTTHUMG00000037560 ENST00000366812.5:c.*775TTTTG>- chr1.hg19:g.226333546_226333550delCAAAA 4 8 ref NA False 69 69 PASS 5 PASS ref->het 0 NA 151,152 36,36 52,52 1 1 B2RB29|Q5VTJ0|Q6P9F1|Q8IZC5|Q8N4D6|Q9H6U3 True hg19 CCDS1551.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACBD3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000091528.1 PASS NA None 228 NA True - CAAAA ENST00000366812.5 ITPKB 3707 __UNKNOWN__ __UNKNOWN__ 1 226923147 226923147 __UNKNOWN__ Intron DEL T T - rs11337528 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:226923147delT ENST00000272117.3 - 1 1932 ITPKB_ENST00000366784.1_Intron|ITPKB_ENST00000429204.1_Intron P27987 IP3KB_HUMAN inositol-trisphosphate 3-kinase B NA NA NA cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829) ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440) central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1) 30 Prostate(94;0.0773) GTGTAGAAAGTTAAGAAAAAG 0.468 NA NA NA T|TT|T|insertion 1737 0.346845 0.3041 0.451 5008 , , NA 19887 0.3373 NA 0.3141 False NA ,,, NA NA NA 2504 0.3742 NA NA NA Colon(84;110 1851 5306 33547) PASS NA NA NA 0 NA NA NA NA NA 75 75.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AJ242780 CCDS1555.1 1q42.12 2011-04-28 2011-04-28 ENSG00000143772 ENSG00000143772 3707 2.7.1.127 6179 protein-coding gene gene with protein product 147522 "inositol 1,4,5-trisphosphate 3-kinase B" NA 1654894, 1330886 Standard NM_002221 NM_002221 NA Approved IP3KB, IP3-3KB uc010pvo.2 P27987 OTTHUMG00000037582 ENST00000272117.3:c.1932+80A>- chr1.hg19:g.226923147delT 1 3 ref NA False 52 52 PASS 2 PASS ref->het 0 NA 49,50 20,20 7,6 1 1 Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47 True hg19 CCDS1555.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ITPKB-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000091632.1 PASS NA None 75 NA True - T ENST00000272117.3 ITPKB 3707 __UNKNOWN__ __UNKNOWN__ 1 226924876 226924884 __UNKNOWN__ In_Frame_Del DEL CTGCCGCTG CTGCCGCTG - rs147889095 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:226924876_226924884delCTGCCGCTG ENST00000272117.3 - 1 275_283 c.276_284delCAGCGGCAG c.(274-285)agcagcggcagt>agt p.92_95SSGS>S ITPKB_ENST00000366784.1_In_Frame_Del_p.92_95SSGS>S|ITPKB_ENST00000429204.1_In_Frame_Del_p.92_95SSGS>S P27987 IP3KB_HUMAN inositol-trisphosphate 3-kinase B 92 NA NA cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829) ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440) central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1) 30 Prostate(94;0.0773) GCTCACgctactgccgctgctgccgctgc 0.746 NA NA NA 1412 0.281949 0.2428 0.317 5008 , , NA 9854 0.2659 NA 0.3141 False NA ,,, NA NA NA 2504 0.2935 NA NA NA Colon(84;110 1851 5306 33547) PASS NA NA NA 0 NA NA NA NA NA 110 115.69 NA 530,2426 NA 156,218,1104 NA NA NA 0.6 1 NA dbSNP_120 7 1381,4925 NA 379,623,2151 no coding ITPKB NM_002221.3 535,841,3255 A1A1,A1R,RR NA 21.8998,17.9296,20.6327 NA 1911,7351 NA NA NA SO:0001651 inframe_deletion 0 AJ242780 CCDS1555.1 1q42.12 2011-04-28 2011-04-28 ENSG00000143772 ENSG00000143772 3707 2.7.1.127 6179 protein-coding gene gene with protein product 147522 "inositol 1,4,5-trisphosphate 3-kinase B" NA 1654894, 1330886 Standard NM_002221 NM_002221 NA Approved IP3KB, IP3-3KB uc010pvo.2 P27987 OTTHUMG00000037582 ENST00000272117.3:c.276_284delCAGCGGCAG chr1.hg19:g.226924885_226924893delCTGCCGCTG ENSP00000272117:p.Ser92_Gly94del 1 1 ref NA False 60 60 PASS 2 PASS ref->het 0 NA 64,65 16,17 35,34 1 1 Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47 True hg19 CCDS1555.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ITPKB-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000091632.1 PASS NA None 110 NA True - CTGCCGCTG ENST00000272117.3 CDC42BPA 8476 __UNKNOWN__ __UNKNOWN__ 1 227505361 227505362 __UNKNOWN__ 5'UTR INS - - A rs34452846|rs528011996|rs200717391 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:227505361_227505362insA ENST00000366769.3 - 0 813_814 CDC42BPA_ENST00000366764.2_5'UTR|CDC42BPA_ENST00000366766.2_5'UTR|CDC42BPA_ENST00000334218.5_5'UTR|CDC42BPA_ENST00000366765.3_5'UTR NM_003607.3 NP_003598.2 CDC42 binding protein kinase alpha (DMPK-like) NA NA NA NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2) 77 all_cancers(173;0.156)|Prostate(94;0.0792) GAAAAGGGAGGAAAAAAACAGA 0.431 NA NA NA aaaaaaa|AAAAAAA|AAAAAAAA|insertion 488 0.0974441 0.0325 0.0562 5008 , , NA 13565 0.0853 NA 0.1332 False NA ,,, NA NA NA 2504 0.1902 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 106 105.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 U59305 CCDS1558.1, CCDS1559.1 1q42.11 2011-11-23 2001-11-28 ENSG00000143776 ENSG00000143776 8476 1737 protein-coding gene gene with protein product "myotonic dystrophy kinase-related Cdc42-binding kinase" 603412 "CDC42-binding protein kinase alpha (DMPK-like)" NA Standard NM_014826 NM_003607 NA Approved MRCKA, PK428, FLJ23347, KIAA0451, MRCK uc001hqr.3 Q5VT25 OTTHUMG00000037618 ENST00000366769.3:c.-479->T chr1.hg19:g.227505368_227505368dupA 8 8 ref NA False 61 61 PASS 7 PASS ref->het 0 NA 69,69 21,21 15,15 1 1 True hg19 CCDS1558.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDC42BPA-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000091696.1 PASS NA None 106 NA True - A ENST00000366769.3 COG2 22796 __UNKNOWN__ __UNKNOWN__ 1 230819296 230819298 __UNKNOWN__ Intron DEL TTC TTC - rs35405940|rs6143664|rs5781596|rs34594064 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:230819296_230819298delTTC ENST00000366669.4 + 11 1281 COG2_ENST00000366668.3_Intron|COG2_ENST00000534989.1_Intron|COG2_ENST00000546013.1_Intron|COG2_ENST00000535166.1_Intron NM_001145036.1|NM_007357.2 NP_001138508.1|NP_031383.1 Q14746 COG2_HUMAN component of oligomeric golgi complex 2 NA NA NA Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486) cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119) protein transporter activity (GO:0008565) NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3) 27 Breast(184;0.0871)|Ovarian(103;0.183) Prostate(94;0.178) TAAACATTAATTCTTCTTCTTGT 0.424 NA NA NA 1758 0.351038 0.2466 0.438 5008 , , NA 17286 0.5982 NA 0.2107 False NA ,,, NA NA NA 2504 0.32 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 135 138.55 NA , 935,3331 NA 102,731,1300 NA NA NA , 2.4 0 NA dbSNP_114 142 1827,6427 NA 212,1403,2512 no intron,intron COG2 NM_007357.2,NM_001145036.1 , 314,2134,3812 A1A1,A1R,RR NA 22.1347,21.9175,22.0607 , , NA 2762,9758 NA NA NA SO:0001627 intron_variant 0.57 Z34975 CCDS1584.1, CCDS44329.1 1q42.2 2008-02-05 2002-05-28 2002-05-31 ENSG00000135775 ENSG00000135775 22796 "Components of oligomeric golgi complex" 6546 protein-coding gene gene with protein product 606974 "low density lipoprotein receptor defect C complementing" LDLC NA 7962052 Standard NM_007357 NM_007357 NA Approved uc001htw.3 Q14746 OTTHUMG00000037753 ENST00000366669.4:c.1167-22TTC>- chr1.hg19:g.230819302_230819304delTTC 2 4 ref NA False 33 33 PASS 3 PASS ref->het 0 NA 102,103 21,21 19,18 1 1 Q86U99 True hg19 CCDS1584.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COG2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000092087.1 PASS NA None 135 NA True + TTC ENST00000366669.4 KCNK1 3775 __UNKNOWN__ __UNKNOWN__ 1 233807886 233807887 __UNKNOWN__ 3'UTR DEL TA TA - rs398053909|rs16360 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:233807886_233807887delTA ENST00000366621.3 + 0 1789_1790 KCNK1_ENST00000366620.1_3'UTR NM_002245.3 NP_002236.1 O00180 KCNK1_HUMAN potassium channel, subfamily K, member 1 NA NA NA potassium ion transport (GO:0006813)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268) apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076) inward rectifier potassium channel activity (GO:0005242) NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1) 11 all_cancers(173;0.00217)|all_epithelial(177;0.121)|Prostate(94;0.122)|Acute lymphoblastic leukemia(190;0.175) Ibutilide(DB00308)|Quinidine barbiturate(DB01346)|Quinidine(DB00908) AAACTAAGACTATAGATATTTT 0.282 NA NA NA 781 0.15595 0.1188 0.1873 5008 , , NA 16375 0.0496 NA 0.2932 False NA ,,, NA NA NA 2504 0.1524 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 87 95.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 U33632 CCDS1599.1 1q42-q43 2012-03-07 ENSG00000135750 ENSG00000135750 3775 "Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P" 6272 protein-coding gene gene with protein product 601745 NA 8661042, 16382106 Standard NM_002245 NM_002245 NA Approved K2p1.1, DPK, TWIK-1 uc010pxo.1 O00180 OTTHUMG00000037923 ENST00000366621.3:c.*611TA>- chr1.hg19:g.233807888_233807889delTA 1 2 ref NA False 30 30 PASS 2 PASS ref->het 0 NA 68,69 13,14 6,6 1 1 Q13307|Q5T5E8 True hg19 CCDS1599.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KCNK1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000092565.1 PASS NA None 87 NA True + TA ENST00000366621.3 COX20 116228 __UNKNOWN__ __UNKNOWN__ 1 245006492 245006493 __UNKNOWN__ 3'UTR INS - - AGAAA rs373567823|rs59190751|rs199795132 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:245006492_245006493insAGAAA ENST00000411948.2 + 0 764_765 COX20_ENST00000366528.3_3'UTR|COX20_ENST00000498262.1_3'UTR NM_198076.4 NP_932342.1 Q5RI15 COX20_HUMAN COX20 cytochrome C oxidase assembly factor NA NA NA integral component of membrane (GO:0016021)|mitochondrion (GO:0005739) NA ATCTTGAGCATAGAAGTCAATG 0.337 NA NA NA 426 0.0850639 0.2126 0.049 5008 , , NA 18464 0.003 NA 0.0835 False NA ,,, NA NA NA 2504 0.0245 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 512 477.54 NA 350,3646 NA 149,52,1797 NA NA NA -6.8 0 NA dbSNP_129 56 178,7968 NA 66,46,3961 no utr-3 FAM36A NM_198076.4 215,98,5758 A1A1,A1R,RR NA 2.1851,8.7588,4.3485 NA 528,11614 NA NA NA SO:0001624 3_prime_UTR_variant 0.2 BC062419 CCDS31080.1 1q44 2013-05-24 2013-05-23 2012-02-24 ENSG00000203667 ENSG00000203667 116228 "Mitochondrial respiratory chain complex assembly factors" 26970 protein-coding gene gene with protein product 614698 "family with sequence similarity 36, member A", "COX20 Cox2 chaperone homolog (S. cerevisiae)" FAM36A NA 22356826, 23125284 Standard NM_198076 NM_198076 NA Approved FLJ43269 uc001iar.3 Q5RI15 OTTHUMG00000040401 ENST00000411948.2:c.*15->AGAAA chr1.hg19:g.245006492_245006493insAGAAA 1 3 ref NA False 86 86 PASS 0 PASS ref->het 0 NA 453,454 12,13 47,46 1 1 Q8WV86 True hg19 CCDS31080.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COX20-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000097174.1 PASS NA None 512 NA True + AGAAA ENST00000411948.2 OR2B11 127623 __UNKNOWN__ __UNKNOWN__ 1 247615262 247615262 __UNKNOWN__ Frame_Shift_Del DEL A A - rs35305980|rs397733455 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr1:247615262delA ENST00000318749.6 - 1 46 c.23delT c.(22-24)ttcfs p.F8fs NM_001004492.1 NP_001004492.1 Q5JQS5 OR2BB_HUMAN olfactory receptor, family 2, subfamily B, member 11 8 NA NA integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984) endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1) 60 all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.241) OV - Ovarian serous cystadenocarcinoma(106;0.0188) GTCCCCTAAGAAGCTATGGTT 0.473 NA NA NA AA|AA|A|deletion 2249 0.449081 0.2852 0.5274 5008 , , NA 21865 0.4762 NA 0.4563 False NA ,,, NA NA NA 2504 0.5798 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 448 432.18 NA 1318,2948 NA 196,926,1011 74 72 73 0 0 1 dbSNP_131 112 3624,4628 NA 809,2006,1311 no frameshift OR2B11 NM_001004492.1 1005,2932,2322 A1A1,A1R,RR NA 43.9166,30.8955,39.4792 247615262 4942,7576 2167 4183 6350 SO:0001589 frameshift_variant 0 CCDS31090.1 1q44 2012-08-09 ENSG00000177535 ENSG00000177535 127623 "GPCR / Class A : Olfactory receptors" 31249 protein-coding gene gene with protein product NA NA Standard NM_001004492 NM_001004492 NA Approved uc010pyx.2 Q5JQS5 OTTHUMG00000040572 ENST00000318749.6:c.23delT chr1.hg19:g.247615262delA ENSP00000325682:p.Phe8fs 1 4 ref NA False 40 40 PASS 2 PASS ref->het 0 NA 305,305 98,99 42,41 1 1 B2RP03 True hg19 CCDS31090.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OR2B11-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000097620.1 PASS NA None 448 NA True - A ENST00000318749.6 GEN1 348654 __UNKNOWN__ __UNKNOWN__ 2 17962994 17962998 __UNKNOWN__ Frame_Shift_Del DEL AAGTT AAGTT - rs113873109|rs149936944 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:17962994_17962998delAAGTT ENST00000381254.2 + 14 2729_2733 c.2515_2519delAAGTT c.(2515-2520)aagttgfs p.KL839fs GEN1_ENST00000317402.7_Frame_Shift_Del_p.KL839fs|SMC6_ENST00000402989.1_Intron NM_001130009.1 NP_001123481.1 Q17RS7 GEN_HUMAN GEN1 Holliday junction 5' flap endonuclease 839 NA NA DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139) centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634) crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872) breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 16 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158) TGGCCATAACAAGTTGAGTAGCCCT 0.371 NA NA NA Homologous recombination 297 0.0593051 0.0076 0.0548 5008 , , NA 20614 0.1081 NA 0.0905 False NA ,,, NA NA NA 2504 0.0501 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 184 185.27 NA , 107,4159 NA 0,107,2026 NA NA NA , 3.6 0 NA dbSNP_131 57 906,7340 NA 48,810,3265 no frameshift,frameshift GEN1 NM_182625.3,NM_001130009.1 , 48,917,5291 A1A1,A1R,RR NA 10.9871,2.5082,8.0962 , , NA 1013,11499 NA NA NA SO:0001589 frameshift_variant 0.28 AK098188 CCDS1691.1 2p24.2 2013-06-04 2013-06-04 ENSG00000178295 ENSG00000178295 348654 26881 protein-coding gene gene with protein product "Holliday junction resolvase" 612449 "Gen endonuclease homolog 1 (Drosophila)" NA 15576351 Standard NM_182625 NM_182625 NA Approved FLJ40869, Gen uc002rct.2 Q17RS7 OTTHUMG00000121173 ENST00000381254.2:c.2515_2519delAAGTT chr2.hg19:g.17962994_17962998delAAGTT ENSP00000370653:p.Lys839fs 0 4 ref NA False 74 74 PASS 1 PASS ref->het 0 NA 113,115 55,55 10,9 1 1 Q17RS9|Q6ZN37 True hg19 CCDS1691.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GEN1-201 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000241661.2 PASS NA None 184 NA True + AAGTT ENST00000381254.2 LTBP1 4052 __UNKNOWN__ __UNKNOWN__ 2 33407406 33407406 __UNKNOWN__ Intron DEL G G - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:33407406delG ENST00000402934.1 + 2 336 LTBP1_ENST00000354476.3_Intron|LTBP1_ENST00000390003.4_Intron|LTBP1_ENST00000407925.1_Intron|LTBP1_ENST00000404816.2_Intron|LTBP1_ENST00000418533.2_Intron|LTBP1_ENST00000404525.1_Intron Q14766 LTBP1_HUMAN latent transforming growth factor beta binding protein 1 NA NA NA extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178) extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578) calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024) breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3) 108 all_hematologic(175;0.115) Medulloblastoma(90;0.215) CCTTGTAAAAGTCAATTGGTT 0.448 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 143 155.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1 2p22-p21 2008-05-23 ENSG00000049323 ENSG00000049323 4052 "Latent transforming growth factor, beta binding proteins" 6714 protein-coding gene gene with protein product "TGF-beta1-BP-1" 150390 NA 2350783, 11104663 Standard NM_206943 NM_206943 NA Approved uc021vft.1 Q14766 OTTHUMG00000152118 ENST00000402934.1:c.224-4517G>- chr2.hg19:g.33407406delG 0 4 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 97,97 31,31 10,10 1 1 A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LTBP1-008 NOVEL not_organism_supported|basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000325421.3 PASS NA None 143 NA True + G ENST00000402934.1 FEZ2 9637 __UNKNOWN__ __UNKNOWN__ 2 36779655 36779656 __UNKNOWN__ 3'UTR INS - - ACTT rs397774857|rs35775049|rs5830428|rs3076528 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:36779655_36779656insACTT ENST00000379245.4 - 0 1841_1842 FEZ2_ENST00000305852.7_3'UTR|FEZ2_ENST00000405912.3_3'UTR NM_001042548.1 NP_001036013.1 Q9UHY8 FEZ2_HUMAN fasciculation and elongation protein zeta 2 (zygin II) NA NA NA axon guidance (GO:0007411)|nervous system development (GO:0007399)|signal transduction (GO:0007165) breast(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1) 7 all_hematologic(82;0.21) TGAAAATCAAAACTTAAATACA 0.376 NA NA NA 1280 0.255591 0.2595 0.2594 5008 , , NA 18483 0.1577 NA 0.3618 False NA ,,, NA NA NA 2504 0.2393 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 113 118.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 U60061 CCDS46257.1, CCDS46258.1 2p21 2008-05-15 ENSG00000171055 ENSG00000171055 9637 3660 protein-coding gene gene with protein product 604826 NA 9096408 Standard NM_005102 NA Approved uc002rpg.2 Q9UHY8 OTTHUMG00000152148 ENST00000379245.4:c.*651->AAGT chr2.hg19:g.36779656_36779659dupACTT 2 4 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 80,82 21,21 12,11 2 2 Q5EBN3|Q76LN0|Q99690 True hg19 CCDS46258.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FEZ2-001 NOVEL basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000325431.2 PASS NA None 113 NA True - ACTT ENST00000379245.4 CYP1B1 1545 __UNKNOWN__ __UNKNOWN__ 2 38297654 38297655 __UNKNOWN__ 3'UTR INS - - A rs4646431 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:38297654_38297655insA ENST00000260630.3 - 0 2243_2244 CYP1B1_ENST00000494864.1_5'UTR|CYP1B1_ENST00000407341.1_3'UTR NM_000104.3 NP_000095 Q16678 CP1B1_HUMAN cytochrome P450, family 1, subfamily B, polypeptide 1 NA NA NA angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805) endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739) aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825) breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1) 13 all_hematologic(82;0.21) Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277) GTCTTTGACTCAAAAAAATCTC 0.406 NA NA NA ?|AAAAAAA|AAAAAAAA|unsure 2629 0.52496 0.0507 0.6628 5008 , , NA 17605 0.8333 NA 0.5398 False NA ,,, NA NA NA 2504 0.7352 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 74 76.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 U56438 CCDS1793.1 2p22.2 2008-02-05 2003-01-14 ENSG00000138061 ENSG00000138061 1545 "Cytochrome P450s" 2597 protein-coding gene gene with protein product 601771 "cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)" GLC3A NA 8175734, 15128046 Standard NM_000104 NM_000104 NA Approved CP1B uc002rqo.2 Q16678 OTTHUMG00000100970 ENST00000260630.3:c.*211->T chr2.hg19:g.38297661_38297661dupA 8 7 ref NA False 94 93 PASS 7 PASS ref->het 0 NA 42,42 25,25 7,7 1 1 Q5TZW8|Q93089|Q9H316 True hg19 CCDS1793.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CYP1B1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000218580.3 PASS NA None 74 NA True - A ENST00000260630.3 USP34 9736 __UNKNOWN__ __UNKNOWN__ 2 61528299 61528300 __UNKNOWN__ Intron INS - - A rs11428092|rs386390303|rs386390304 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:61528299_61528300insA ENST00000398571.2 - 29 3995 NM_014709.3 NP_055524.3 Q70CQ2 UBP34_HUMAN ubiquitin specific peptidase 34 NA NA NA positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055) cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843) autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2) 138 Epithelial(17;0.229) ATACCATCTATAAAAAACAGGA 0.366 NA NA NA AAAAAA|AAAAAA|AAAAAAA|insertion 1586 0.316693 0.2345 0.3401 5008 , , NA 17875 0.3224 NA 0.3429 False NA ,,, NA NA NA 2504 0.3783 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 143 134.76 NA 866,2646 NA 118,630,1008 NA NA NA -10 0 NA dbSNP_120 71 2878,4936 NA 537,1804,1566 no intron USP34 NM_014709.3 655,2434,2574 A1A1,A1R,RR NA 36.8313,24.6583,33.0567 NA 3744,7582 NA NA NA SO:0001627 intron_variant 0.04 AB011142 CCDS42686.1 2p16.1-p15 2005-08-08 2005-08-08 ENSG00000115464 ENSG00000115464 9736 "Ubiquitin-specific peptidases" 20066 protein-coding gene gene with protein product 615295 "ubiquitin specific protease 34" NA 12838346 Standard NM_014709 NA Approved KIAA0570, KIAA0729 uc002sbe.3 Q70CQ2 OTTHUMG00000152265 ENST00000398571.2:c.3919-4->T chr2.hg19:g.61528305_61528305dupA 7 7 ref NA False 49 49 PASS 6 PASS ref->het 0 NA 90,90 32,32 17,17 1 1 A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1 True hg19 CCDS42686.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA USP34-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000325650.4 PASS NA None 143 NA True - A ENST00000398571.2 CEP68 23177 __UNKNOWN__ __UNKNOWN__ 2 65298647 65298649 __UNKNOWN__ In_Frame_Del DEL AAC AAC - rs199636840|rs147392467 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:65298647_65298649delAAC ENST00000260569.4 + 3 527_529 c.417_419delAAC c.(415-420)agaaca>aga p.T142del RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000546106.1_In_Frame_Del_p.T142del|CEP68_ENST00000497039.1_3'UTR|CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000377990.2_In_Frame_Del_p.T142del Q76N32 CEP68_HUMAN centrosomal protein 68kDa 142 NA NA centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365) centrosome (GO:0005813)|cytoplasm (GO:0005737) protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901) breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 32 GCCTTCCCAGAACAACAACTATT 0.502 NA NA NA 371 0.0740815 0.0681 0.0749 5008 , , NA 23192 0 NA 0.1233 False NA ,,, NA NA NA 2504 0.1074 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 253 264.07 NA 372,3894 NA 14,344,1775 NA NA NA 1.5 0 NA dbSNP_132 95 1019,7235 NA 59,901,3167 no coding CEP68 NM_015147.2 73,1245,4942 A1A1,A1R,RR NA 12.3455,8.7201,11.1102 NA 1391,11129 NA NA NA SO:0001651 inframe_deletion 0 BC004873 CCDS1880.2 2p14 2014-02-20 2005-12-01 2005-12-01 ENSG00000011523 ENSG00000011523 23177 29076 protein-coding gene gene with protein product NA "KIAA0582" KIAA0582 NA 9628581, 9847074, 14654843 Standard NM_015147 NM_015147 NA Approved uc002sdl.4 Q76N32 OTTHUMG00000129538 ENST00000260569.4:c.417_419delAAC chr2.hg19:g.65298653_65298655delAAC ENSP00000260569:p.Thr142del 2 4 ref NA False 58 58 PASS 3 PASS ref->het 0 NA 175,179 56,56 37,36 1 1 B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CEP68-002 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000251728.2 PASS NA None 253 NA True + AAC ENST00000260569.4 RP11-474G23.1 0 __UNKNOWN__ __UNKNOWN__ 2 68389482 68389483 __UNKNOWN__ Intron DEL TT TT - rs200587964|rs202169380|rs3217588 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:68389482_68389483delTT ENST00000406334.3 - 7 654 PNO1_ENST00000263657.2_Intron NA NA NA NA GTCTGCGCTCTTGTGTCGCTGA 0.366 NA NA NA 1523 0.304113 0.0575 0.2695 5008 , , NA 17484 0.4772 NA 0.2863 False NA ,,, NA NA NA 2504 0.502 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 212 199.61 NA 399,3867 NA 17,365,1751 NA NA NA -0.2 0 NA dbSNP_106 141 2067,6187 NA 263,1541,2323 no intron PNO1 NM_020143.2 280,1906,4074 A1A1,A1R,RR NA 25.0424,9.353,19.6965 NA 2466,10054 NA NA NA SO:0001627 intron_variant 0.25 NA NA NA NA NA ENST00000406334.3:c.436-4228AA>- chr2.hg19:g.68389482_68389483delTT 0 3 ref NA False 73 73 PASS 2 PASS ref->het 0 NA 149,151 34,34 27,26 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-474G23.1-001 KNOWN basic|appris_principal|readthrough_transcript nonsense_mediated_decay NA protein_coding OTTHUMT00000471754.1 PASS NA None 212 NA True - T ENST00000406334.3 PPP3R1 5534 __UNKNOWN__ __UNKNOWN__ 2 68444171 68444172 __UNKNOWN__ Intron INS - - ACGCAG rs374427852|rs35225743|rs11126181 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:68444171_68444172insACGCAG ENST00000234310.3 - 2 447 PPP3R1_ENST00000409377.1_Intron|PPP3R1_ENST00000409752.1_Intron|RP11-474G23.1_ENST00000406334.3_Intron NM_000945.3 NP_000936.1 P63098 CANB1_HUMAN protein phosphatase 3, regulatory subunit B, alpha NA NA NA apoptotic process (GO:0006915)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lung epithelial cell differentiation (GO:0060487)|NFAT protein import into nucleus (GO:0051531)|patterning of blood vessels (GO:0001569)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein dephosphorylation (GO:0006470) calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|sarcolemma (GO:0042383) calcium ion binding (GO:0005509)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|protein domain specific binding (GO:0019904) large_intestine(1) 1 cacacacacacaGAGAGAGATG 0.391 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 234 247.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.9 M30773 CCDS46310.1 2p14 2013-01-10 2010-04-14 ENSG00000221823 ENSG00000221823 5534 3.1.3.16 "Serine/threonine phosphatases / Protein phosphatase 3, regulatory subunits", "EF-hand domain containing" 9317 protein-coding gene gene with protein product "calcineurin B, type I (19kDa)", "protein phosphatase 2B regulatory subunit B alpha" 601302 "protein phosphatase 3 (formerly 2B), regulatory subunit B (19kD), alpha isoform (calcineurin B, type I)", "protein phosphatase 3 (formerly 2B), regulatory subunit B, 19kDa, alpha isoform (calcineurin B, type I)", "protein phosphatase 3 (formerly 2B), regulatory subunit B, alpha isoform" NA 8978785, 2558868 Standard NM_000945 NM_000945 NA Approved CALNB1, CNB, CNB1 uc002sei.1 P63098 OTTHUMG00000129561 ENST00000234310.3:c.43+51->CTGCGT chr2.hg19:g.68444171_68444172insACGCAG 1 2 ref NA False 61 61 PASS 0 PASS ref->het 0 NA 165,170 32,35 45,43 1 1 B2RC10|B5MDU4|P06705|P15117|Q08044|Q53SL0 True hg19 CCDS46310.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPP3R1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000326765.4 PASS NA None 234 NA True - ACGCAG ENST00000234310.3 PCYOX1 51449 __UNKNOWN__ __UNKNOWN__ 2 70506332 70506334 __UNKNOWN__ 3'UTR DEL CTT CTT - rs397770441|rs71692679|rs55789088 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:70506332_70506334delCTT ENST00000433351.2 + 0 3354_3356 NM_016297.3 NP_057381.3 Q9UHG3 PCYOX_HUMAN prenylcysteine oxidase 1 NA NA NA prenylated protein catabolic process (GO:0030327)|prenylcysteine catabolic process (GO:0030328)|prenylcysteine metabolic process (GO:0030329) extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361) chloride-transporting ATPase activity (GO:0008555)|prenylcysteine oxidase activity (GO:0001735) breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6) 15 GTAAAAATGACTTCTTCCCTACC 0.335 NA NA NA 1809 0.361222 0.0431 0.4179 5008 , , NA 19803 0.3194 NA 0.6113 False NA ,,, NA NA NA 2504 0.5368 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 147 146.79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.3 AB020715 CCDS1902.1 2p13.3 2008-02-05 ENSG00000116005 ENSG00000116005 51449 1.8.3.5 20588 protein-coding gene gene with protein product 610995 NA 10585463, 12186880 Standard NM_016297 NM_016297 NA Approved KIAA0908, PCL1 uc002sgn.4 Q9UHG3 OTTHUMG00000129671 ENST00000433351.2:c.*1810CTT>- chr2.hg19:g.70506335_70506337delCTT 1 4 ref NA False 32 32 PASS 2 PASS ref->het 0 NA 102,102 27,27 18,18 1 1 B2RB14|B7Z9P8|O94982|Q8N4N5|Q96QM8 True hg19 CCDS1902.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PCYOX1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000251872.3 PASS NA None 147 NA True + CTT ENST00000433351.2 ZNF638 27332 __UNKNOWN__ __UNKNOWN__ 2 71626680 71626680 __UNKNOWN__ Intron DEL T T - rs34538815|rs397783069 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:71626680delT ENST00000409544.1 + 13 3130 ZNF638_ENST00000264447.4_Intron|ZNF638_ENST00000355812.3_Intron NM_001252612.1 NP_001239541.1 Q14966 ZN638_HUMAN zinc finger protein 638 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270) breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1) 63 CTGACTGTACTTTTACAAGCA 0.338 NA NA NA TTTT|TTTT|TTT|deletion 812 0.162141 0.3268 0.0937 5008 , , NA 17841 0.004 NA 0.1899 False NA ,,, NA NA NA 2504 0.1227 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 174 178.15 NA NA 81 103 95 NA NA 2 NA NA NA 71626680 2196 4293 6489 SO:0001627 intron_variant 0.21 D83032 CCDS1917.1 2p13.1 2013-02-12 2004-07-29 2004-07-30 ENSG00000075292 ENSG00000075292 27332 "RNA binding motif (RRM) containing" 17894 protein-coding gene gene with protein product 614349 "zinc finger, matrin-like" ZFML NA 8647861 Standard NM_014497 NM_014497 NA Approved NP220, MGC26130, Zfp638 uc002shy.3 Q14966 OTTHUMG00000129735 ENST00000409544.1:c.2501-9T>- chr2.hg19:g.71626680delT 3 4 ref NA False 35 35 PASS 4 PASS ref->het 0 NA 134,135 22,23 21,21 1 1 B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37 True hg19 CCDS1917.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF638-002 NOVEL alternative_5_UTR|basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000327431.1 PASS NA None 174 NA True + T ENST00000409544.1 KDM3A 55818 __UNKNOWN__ __UNKNOWN__ 2 86709231 86709234 __UNKNOWN__ Intron DEL TGTT TGTT - rs200787123|rs193921056 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:86709231_86709234delTGTT ENST00000409556.1 + 18 3050 KDM3A_ENST00000542128.1_Intron|KDM3A_ENST00000312912.5_Intron|KDM3A_ENST00000409064.1_Intron Q9Y4C1 KDM3A_HUMAN lysine (K)-specific demethylase 3A NA NA NA androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634) androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976) NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2) 47 GAAAGGTATGTGTTTGTTTGTTGG 0.392 NA NA NA 293 0.0585064 0.0749 0.0576 5008 , , NA 20593 0.006 NA 0.1044 False NA ,,, NA NA NA 2504 0.044 NA NA NA NSCLC(96;1150 1523 6936 46253 49736) PASS NA NA NA 0 NA NA NA NA NA 358 372.8 NA , 304,3958 NA 14,276,1841 NA NA NA , 4.4 0.7 NA dbSNP_134 81 620,7634 NA 26,568,3533 no intron,intron KDM3A NM_018433.5,NM_001146688.1 , 40,844,5374 A1A1,A1R,RR NA 7.5115,7.1328,7.3826 , , NA 924,11592 NA NA NA SO:0001627 intron_variant 0.11 AB018285 CCDS1990.1 2p11.2 2011-07-01 2009-04-06 2009-04-06 ENSG00000115548 ENSG00000115548 55818 "Chromatin-modifying enzymes / K-demethylases" 20815 protein-coding gene gene with protein product "jumonji C domain-containing histone demethylase 2A" 611512 "jumonji domain containing 1", "jumonji domain containing 1A" JMJD1, JMJD1A NA 9872452 Standard NM_018433 NM_018433 NA Approved TSGA, KIAA0742, JHMD2A uc010ytj.2 Q9Y4C1 OTTHUMG00000130204 ENST00000409556.1:c.2685+6TGTT>- chr2.hg19:g.86709239_86709242delTGTT 2 6 ref NA False 58 58 PASS 3 PASS ref->het 0 NA 239,243 48,48 70,70 1 1 D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08 True hg19 CCDS1990.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KDM3A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252522.2 PASS NA None 358 NA True + TGTT ENST00000409556.1 POLR1B 84172 __UNKNOWN__ __UNKNOWN__ 2 113300060 113300066 __UNKNOWN__ 5'UTR DEL GCAGGTG GCAGGTG - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:113300060_113300066delGCAGGTG ENST00000417433.2 + 0 19_25 POLR1B_ENST00000263331.5_5'UTR|POLR1B_ENST00000537335.1_5'UTR|POLR1B_ENST00000541869.1_Frame_Shift_Del_p.AGG35fs|POLR1B_ENST00000409894.3_5'UTR NM_001137604.1 NP_001131076.1 Q9H9Y6 RPA2_HUMAN polymerase (RNA) I polypeptide B, 128kDa NA NA NA gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361) cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654) DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549) breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 42 CGTCCGGTGTGCAGGTGGCCACATGGA 0.633 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Ovarian(16;256 576 9537 23969 41147) PASS NA NA NA 0 NA NA NA NA NA 1228 1215.05 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.06 AK001678 CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1 2q13 2013-01-21 ENSG00000125630 ENSG00000125630 84172 "RNA polymerase subunits" 20454 protein-coding gene gene with protein product 602000 NA Standard NM_019014 NM_001137604 NA Approved Rpo1-2, FLJ21921, FLJ10816, RPA2 uc002thw.2 Q9H9Y6 OTTHUMG00000131314 ENST00000417433.2:c.-6GCAGGTG>- chr2.hg19:g.113300060_113300066delGCAGGTG 0 4 ref NA False 218 218 PASS 1 PASS ref->het 0 NA 1073,1087 92,92 140,134 1 1 B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3 True hg19 CCDS46395.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA POLR1B-005 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000330626.1 PASS NA None 1228 NA True + GCAGGTG ENST00000417433.2 ORC4 5000 __UNKNOWN__ __UNKNOWN__ 2 148733548 148733549 __UNKNOWN__ Intron INS - - A rs397833095|rs2307399|rs397719519 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:148733548_148733549insA ENST00000392857.5 - 2 91 ORC4_ENST00000535373.1_Intron|ORC4_ENST00000264169.2_Intron|ORC4_ENST00000536575.1_Intron|ORC4_ENST00000392858.1_Intron|ORC4_ENST00000540442.1_Intron|ORC4_ENST00000542387.1_Intron NM_001190879.2|NM_001190882.2|NM_002552.4|NM_181741.3 NP_001177808.1|NP_001177811.1|NP_002543.2|NP_859525.1 O43929 ORC4_HUMAN origin recognition complex, subunit 4 NA NA NA DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278) nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808) ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166) cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1) 14 TCAAATCCTTTAAAAAAATTGG 0.257 NA NA NA AAAAAAA|AAAAAAA|AAAAAAAA|insertion 3236 0.646166 0.8646 0.6527 5008 , , NA 17400 0.5942 NA 0.5915 False NA ,,, NA NA NA 2504 0.456 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 523 487.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.28 AF022108 CCDS2187.1, CCDS54404.1, CCDS54405.1 2q22-q23 2010-10-12 2010-10-12 2010-10-12 ENSG00000115947 ENSG00000115947 5000 "ATPases / AAA-type" 8490 protein-coding gene gene with protein product 603056 "origin recognition complex, subunit 4 (yeast homolog)-like", "origin recognition complex, subunit 4-like (yeast)", "origin recognition complex, subunit 4-like (S. cerevisiae)", "origin recognition complex, subunit 4 homolog (S. cerevisiae)" ORC4L NA 9353276, 9691185 Standard NM_181742 NM_181742 NA Approved HsORC4, Orc4p uc002twk.3 O43929 OTTHUMG00000131849 ENST00000392857.5:c.17-4->T chr2.hg19:g.148733555_148733555dupA 8 7 ref NA False 94 94 PASS 7 PASS ref->het 0 NA 374,374 86,86 54,54 1 1 B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42 True hg19 CCDS2187.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ORC4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254797.3 PASS NA None 523 NA True - A ENST00000392857.5 HOXD-AS2 100506783 __UNKNOWN__ __UNKNOWN__ 2 176994155 176994167 __UNKNOWN__ RNA DEL GCAAAAGCCACGG GCAAAAGCCACGG - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:176994155_176994167delGCAAAAGCCACGG ENST00000440016.2 - 0 497 HOXD cluster antisense RNA 2 NA NA NA NA GTCCAGAGCTGCAAAAGCCACGGGCAACCTCTG 0.601 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 361 338.27 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.26 BC034000 2q31.1 2012-10-12 2012-08-15 ENSG00000237380 ENSG00000237380 100506783 "Long non-coding RNAs" 43756 non-coding RNA RNA, long non-coding NA "HOXD cluster antisense RNA 2 (non-protein coding)" NA Standard NR_038435 NR_038435 NA Approved uc002ukq.3 OTTHUMG00000154174 ENST00000440016.2: chr2.hg19:g.176994155_176994167delGCAAAAGCCACGG 0 3 ref NA False 299 179 PASS 1 PASS ref->het 0 NA 213,218 96,97 60,57 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HOXD-AS2-001 KNOWN basic antisense NA antisense OTTHUMT00000334239.2 PASS NA None 361 NA True - GCAAAAGCCACGG ENST00000440016.2 HOXD3 3232 __UNKNOWN__ __UNKNOWN__ 2 177037183 177037184 __UNKNOWN__ 3'UTR INS - - TCT rs112414246|rs60794848|rs34952493|rs148548656 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:177037183_177037184insTCT ENST00000468418.3 + 0 3570_3571 HOXD3_ENST00000410016.1_3'UTR|HOXD3_ENST00000249440.3_3'UTR P31249 HXD3_HUMAN homeobox D3 NA NA NA anterior/posterior pattern specification (GO:0009952)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|embryonic skeletal system morphogenesis (GO:0048704)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron differentiation (GO:0045666)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700) breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(11)|prostate(1)|upper_aerodigestive_tract(2) 23 OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226) Colorectal(32;0.247) CTCCATGGGCGTCCTTTGGGTG 0.639 NA NA NA 907 0.18111 0.205 0.183 5008 , , NA 13198 0.0218 NA 0.3052 False NA ,,, NA NA NA 2504 0.184 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 257 247.63 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 CCDS2270.1 2q31.1 2011-06-20 2005-12-22 ENSG00000128652 ENSG00000128652 3232 "Homeoboxes / ANTP class : HOXL subclass" 5137 protein-coding gene gene with protein product 142980 "homeo box D3" HOX4A, HOX4, HOX1D NA 1973146, 1358459 Standard NM_006898 NA Approved uc002ukt.1 P31249 OTTHUMG00000132517 ENST00000468418.3:c.*182->TCT chr2.hg19:g.177037183_177037184insTCT 1 4 ref NA False 36 36 PASS 0 PASS ref->het 0 NA 200,202 32,32 23,23 1 1 Q99955|Q9BSC5 True hg19 CCDS2270.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HOXD3-005 KNOWN alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000334246.4 PASS NA None 257 NA True + TCT ENST00000468418.3 CLK1 1195 __UNKNOWN__ __UNKNOWN__ 2 201729212 201729213 __UNKNOWN__ Intron DEL AG AG - rs575277010|rs34085624 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:201729212_201729213delAG ENST00000321356.4 - 1 136 CLK1_ENST00000492793.1_Intron|CLK1_ENST00000434813.2_5'UTR NM_004071.3 NP_004062.2 P49759 CLK1_HUMAN CDC-like kinase 1 NA NA NA cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484) cytoplasm (GO:0005737)|nucleus (GO:0005634) ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712) NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 33 AAGCAGGAAAAGGGGGCATCGC 0.673 NA NA NA 13 0.00259585 8e-04 0 5008 , , NA 15649 0 NA 0.0119 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 213 213.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 L29219 CCDS2331.1, CCDS54427.1 2q33 2008-05-02 ENSG00000013441 ENSG00000013441 1195 "CDC-like kinases" 2068 protein-coding gene gene with protein product 601951 NA 9856501 Standard NM_004071 NA Approved uc002uwe.2 P49759 OTTHUMG00000132784 ENST00000321356.4:c.0+73CT>- chr2.hg19:g.201729212_201729213delAG 0 5 ref NA False 141 141 PASS 1 PASS ref->het 0 NA 161,162 25,26 28,27 1 1 B4DFW7|Q0P694|Q8N5V8 True hg19 CCDS2331.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CLK1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256192.2 PASS NA None 213 NA True - AG ENST00000321356.4 FZD7 8324 __UNKNOWN__ __UNKNOWN__ 2 202902871 202902876 __UNKNOWN__ 3'UTR DEL TTAAAG TTAAAG - rs34875167|rs199703495|rs141053316 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:202902871_202902876delTTAAAG ENST00000286201.1 + 0 3562_3567 NM_003507.1 NP_003498.1 O75084 FZD7_HUMAN frizzled class receptor 7 NA NA NA axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|mesenchymal to epithelial transition (GO:0060231)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of ectodermal cell fate specification (GO:0042666)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of catenin import into nucleus (GO:0035412)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|stem cell maintenance (GO:0019827)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223) apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886) frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147) breast(1)|endometrium(6)|large_intestine(6)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2) 31 GCTTTTTACATTAAAGTTAAAATCGA 0.32 NA NA NA 887 0.177117 0.2421 0.2709 5008 , , NA 16477 0.004 NA 0.2913 False NA ,,, NA NA NA 2504 0.0838 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 116 122.55 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AB010881 CCDS2351.1 2q33 2014-01-29 2014-01-29 ENSG00000155760 ENSG00000155760 8324 "GPCR / Class F : Frizzled receptors" 4045 protein-coding gene gene with protein product 603410 "frizzled (Drosophila) homolog 7", "frizzled homolog 7 (Drosophila)", "frizzled 7, seven transmembrane spanning receptor", "frizzled family receptor 7" NA 9707618, 9813155 Standard NM_003507 NM_003507 NA Approved FzE3 uc002uyw.1 O75084 OTTHUMG00000132841 ENST00000286201.1:c.*1781TTAAAG>- chr2.hg19:g.202902871_202902876delTTAAAG 0 3 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 94,95 15,15 11,11 1 1 O94816|Q53S59|Q96B74 True hg19 CCDS2351.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FZD7-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256314.1 PASS NA None 116 NA True + TTAAAG ENST00000286201.1 PIKFYVE 200576 __UNKNOWN__ __UNKNOWN__ 2 209182678 209182690 __UNKNOWN__ Intron DEL AGTTCAGCAGTGA AGTTCAGCAGTGA - rs553140058|rs112715599|rs72402005 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:209182678_209182690delAGTTCAGCAGTGA ENST00000264380.4 + 16 2240 NM_015040.3 NP_055855.2 Q9Y2I7 FYV1_HUMAN phosphoinositide kinase, FYVE finger containing NA NA NA cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281) cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506) 1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270) NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2) 107 AATGTGATTCAGTTCAGCAGTGAAGTTCAGCAA 0.418 NA NA NA 577 0.115216 0.2088 0.1138 5008 , , NA 22678 0.0089 NA 0.1282 False NA ,,, NA NA NA 2504 0.0859 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 340 329.76 NA 791,3473 NA 75,641,1416 NA NA NA -0.5 0 NA dbSNP_132 136 1070,7182 NA 68,934,3124 no intron PIKFYVE NM_015040.3 143,1575,4540 A1A1,A1R,RR NA 12.9666,18.5507,14.869 NA 1861,10655 NA NA NA SO:0001627 intron_variant 0 AB023198 CCDS2382.1, CCDS33368.1, CCDS54431.1 2q34 2014-01-15 2009-04-17 2009-04-17 ENSG00000115020 ENSG00000115020 200576 "Zinc fingers, FYVE domain containing" 23785 protein-coding gene gene with protein product "zinc finger, FYVE domain containing 29" 609414 "phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III" PIP5K3 NA 9858586, 12270933 Standard NM_015040 NM_015040 NA Approved MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1 uc002vcz.3 Q9Y2I7 OTTHUMG00000132945 ENST00000264380.4:c.2082+13AGTTCAGCAGTGA>- chr2.hg19:g.209182678_209182690delAGTTCAGCAGTGA 0 2 ref NA False 50 50 PASS 1 PASS ref->het 0 NA 323,327 28,28 43,43 1 1 Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67 True hg19 CCDS2382.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PIKFYVE-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256477.2 PASS NA None 340 NA True + AGTTCAGCAGTGA ENST00000264380.4 ATG9A 79065 __UNKNOWN__ __UNKNOWN__ 2 220089590 220089591 __UNKNOWN__ Intron INS - - G rs3216709|rs74441929|rs397840291|rs67100330 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:220089590_220089591insG ENST00000409618.1 - 8 956 ATG9A_ENST00000361242.4_Intron|ATG9A_ENST00000396761.2_Intron|ATG9A_ENST00000409422.1_Intron Q7Z3C6 ATG9A_HUMAN autophagy related 9A NA NA NA autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031) autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802) endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1) 13 Renal(207;0.0474) Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942) CGGGGTGGGGTGGGGAAGAGAC 0.559 NA NA NA 3651 0.729034 0.4024 0.8343 5008 , , NA 18400 0.8621 NA 0.8887 False NA ,,, NA NA NA 2504 0.7945 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 101 108.98 NA , 1735,5,2014 NA 464,2,805,1,1,604 NA NA NA , -8.8 0 NA dbSNP_130 41 6922,93,815 NA 3085,79,673,1,12,65 no intron,intron ATG9A NM_024085.3,NM_001077198.1 , 3549,81,1478,2,13,669 A1A1,A1A2,A1R,A2A2,A2R,RR NA 11.5964,46.3506,25.2676 , , NA 8657,98,2829 NA NA NA SO:0001627 intron_variant 0 AK021732 CCDS42820.1 2q35 2014-02-12 2012-06-06 2005-09-11 ENSG00000198925 ENSG00000198925 79065 22408 protein-coding gene gene with protein product 612204 "APG9 autophagy 9-like 1 (S. cerevisiae)", "ATG9 autophagy related 9 homolog A (S. cerevisiae)" APG9L1 NA Standard NM_024085 NM_024085 NA Approved FLJ22169 uc002vkf.1 Q7Z3C6 OTTHUMG00000154557 ENST00000409618.1:c.517-14->C chr2.hg19:g.220089594_220089594dupG 5 8 ref NA False 43 43 PASS 4 PASS ref->het 0 NA 66,68 26,26 7,6 2 2 Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7 True hg19 CCDS42820.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ATG9A-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000335930.1 PASS NA None 101 NA True - G ENST00000409618.1 CUL3 8452 __UNKNOWN__ __UNKNOWN__ 2 225449973 225449974 __UNKNOWN__ 5'UTR INS - - G rs543866738|rs376959002 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:225449973_225449974insG ENST00000264414.4 - 0 91_92 CUL3_ENST00000344951.4_5'UTR NM_003590.4 NP_003581.1 Q13618 CUL3_HUMAN cullin 3 NA NA NA cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055) Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827) POZ domain binding (GO:0031208) endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3) 46 all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138) Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902) GGCGGCTCCGCGGGGTCCCCCT 0.792 NA NA NA GGGG|GGGG|GGGGG|insertion 91 0.0181709 0.0038 0.0144 5008 , , NA 4376 0.006 NA 0.0258 False NA ,,, NA NA NA 2504 0.045 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 78 83.76 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.71 U58089 CCDS2462.1, CCDS58751.1 2q36.2 2011-05-24 ENSG00000036257 ENSG00000036257 8452 2553 protein-coding gene gene with protein product 603136 NA 8681378, 17192413 Standard NM_003590 NA Approved uc002vny.3 Q13618 OTTHUMG00000133167 ENST00000264414.4:c.-248->C chr2.hg19:g.225449977_225449977dupG 5 5 ref NA False 52 52 PASS 4 PASS ref->het 0 NA 49,52 13,14 16,12 1 1 A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7 True hg19 CCDS2462.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CUL3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256871.2 PASS NA None 78 NA True - G ENST00000264414.4 NDUFA10 4705 __UNKNOWN__ __UNKNOWN__ 2 240900608 240900608 __UNKNOWN__ Intron DEL G G - rs201255198|rs138479490 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr2:240900608delG ENST00000252711.2 - 10 1100 NDUFA10_ENST00000404554.1_Intron|NDUFA10_ENST00000471378.1_Intron NM_004544.3 NP_004535.1 O95299 NDUAA_HUMAN NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10, 42kDa NA NA NA cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281) mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747) ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|nucleoside kinase activity (GO:0019206) central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8) 16 all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244) Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202) CGGCAGCTGTGGGGGAAAAAG 0.542 NA NA NA GGGGG|GGGGG|GGGG|deletion 1239 0.247404 0.093 0.2767 5008 , , NA 20026 0.4038 NA 0.3539 False NA ,,, NA NA NA 2504 0.1646 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 357 346.61 NA 572,3694 NA 38,496,1599 96 60 72 -9.7 0 2 dbSNP_134 95 2740,5514 NA 456,1828,1843 no intron NDUFA10 NM_004544.3 494,2324,3442 A1A1,A1R,RR NA 33.196,13.4083,26.4537 240900608 3312,9208 2203 4296 6499 SO:0001627 intron_variant 0.72 AF087661 CCDS2531.1 2q37.3 2011-07-04 2002-08-29 ENSG00000130414 ENSG00000130414 4705 "Mitochondrial respiratory chain complex / Complex I" 7684 protein-coding gene gene with protein product "complex I 42kDa subunit" 603835 "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10 (42kD)" NA 9878551 Standard NM_004544 NM_004544 NA Approved CI-42k uc002vyn.3 O95299 OTTHUMG00000133350 ENST00000252711.2:c.1000-5C>- chr2.hg19:g.240900608delG 4 6 ref NA False 105 105 PASS 5 PASS ref->het 0 NA 253,255 55,56 48,47 1 1 Q8WXC9 True hg19 CCDS2531.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NDUFA10-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257180.2 PASS NA None 357 NA True - G ENST00000252711.2 CRBN 51185 __UNKNOWN__ __UNKNOWN__ 3 3191961 3191962 __UNKNOWN__ 3'UTR INS - - A rs200243789 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:3191961_3191962insA ENST00000231948.4 - 0 1938_1939 CRBN_ENST00000432408.2_3'UTR NM_016302.3 NP_057386.2 Q96SW2 CRBN_HUMAN cereblon NA NA NA negative regulation of ion transmembrane transport (GO:0034766)|negative regulation of protein homooligomerization (GO:0032463)|positive regulation of protein homodimerization activity (GO:0090073)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567) Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634) ATP-dependent peptidase activity (GO:0004176) endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2) 11 Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079) Lenalidomide(DB00480)|Pomalidomide(DB08910)|Thalidomide(DB01041) TTCGTGGGCTCAAAAAACTGCA 0.302 NA NA NA AAAAAA|AAAAAA|AAAAAAA|insertion 22 0.00439297 0 0.0072 5008 , , NA 17356 0 NA 0.0149 False NA ,,, NA NA NA 2504 0.002 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 109 108.09 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 BC017419 CCDS2562.1, CCDS54547.1 3p26.3 2014-05-27 ENSG00000113851 ENSG00000113851 51185 30185 protein-coding gene gene with protein product 609262 "mental retardation, non-syndromic, autosomal recessive, 2A" MRT2A NA 15557513 Standard NM_016302 NM_016302 NA Approved MRT2 uc003bpq.3 Q96SW2 OTTHUMG00000090261 ENST00000231948.4:c.*588->T chr3.hg19:g.3191967_3191967dupA 7 6 ref NA False 35 35 PASS 6 PASS ref->het 0 NA 77,77 14,14 17,17 1 1 B2R6H4|C9IZA9|C9JAH6|Q6AI62|Q6NVZ0|Q9UHW4 True hg19 CCDS2562.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CRBN-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000206579.3 PASS NA None 109 NA True - A ENST00000231948.4 STT3B 201595 __UNKNOWN__ __UNKNOWN__ 3 31574393 31574394 __UNKNOWN__ 5'UTR INS - - TCCTCC rs529181821|rs375544928 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:31574393_31574394insTCCTCC ENST00000295770.2 + 0 112_113 STT3B_ENST00000453168.1_3'UTR NM_178862.1 NP_849193.1 Q8TCJ2 STT3B_HUMAN STT3B, subunit of the oligosaccharyltransferase complex (catalytic) NA NA NA co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986) integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250) dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579) autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1) 19 ctcctttttcttcctcctcctc 0.738 NA NA NA 441 0.0880591 0.0015 0.0274 5008 , , NA 11704 0.3095 NA 0.0586 False NA ,,, NA NA NA 2504 0.0501 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 283 290.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.29 AK027789 CCDS2650.1 3p24.1 2013-03-06 2013-03-06 ENSG00000163527 ENSG00000163527 201595 2.4.99.18 30611 protein-coding gene gene with protein product "source of immunodominant MHC associated peptides", "dolichyl-diphosphooligosaccharide protein glycotransferase" 608605 "STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)" NA 12887896, 12439619 Standard NM_178862 XM_006713017 NA Approved SIMP, FLJ90106, STT3-B uc011axe.2 Q8TCJ2 OTTHUMG00000130673 ENST00000295770.2:c.-97->TCCTCC chr3.hg19:g.31574394_31574399dupTCCTCC 9 7 ref NA False 65 65 PASS 7 PASS ref->het 0 NA 155,156 28,28 101,100 1 1 Q96JZ4|Q96KY7 True hg19 CCDS2650.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA STT3B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253166.2 PASS NA None 283 NA True + TCC ENST00000295770.2 EIF1B 10289 __UNKNOWN__ __UNKNOWN__ 3 40353426 40353427 __UNKNOWN__ Intron DEL AG AG - rs34544743 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:40353426_40353427delAG ENST00000232905.3 + 4 555 NM_005875.2 NP_005866.1 O60739 EIF1B_HUMAN eukaryotic translation initiation factor 1B NA NA NA regulation of translational initiation (GO:0006446) poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743) central_nervous_system(1)|lung(3) 4 KIRC - Kidney renal clear cell carcinoma(284;0.0509)|Kidney(284;0.064) TATATTTCTCAGAGTTATTTTG 0.332 NA NA NA 2420 0.483227 0.4433 0.379 5008 , , NA 17946 0.6716 NA 0.3628 False NA ,,, NA NA NA 2504 0.5409 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 332 340.6 NA 1873,2379 NA 415,1043,668 NA NA NA -2.3 0 NA dbSNP_130 40 3094,5150 NA 590,1914,1618 no intron EIF1B NM_005875.2 1005,2957,2286 A1A1,A1R,RR NA 37.5303,44.0499,39.7487 NA 4967,7529 NA NA NA SO:0001627 intron_variant 0.03 BC006996 CCDS2690.1 3p22.1 2006-02-03 ENSG00000114784 ENSG00000114784 10289 30792 protein-coding gene gene with protein product NA NA 7904817 Standard NM_005875 NM_005875 NA Approved GC20 uc003ckc.3 O60739 OTTHUMG00000131388 ENST00000232905.3:c.298-34AG>- chr3.hg19:g.40353428_40353429delAG 1 2 ref NA False 53 53 PASS 2 PASS ref->het 0 NA 269,270 39,39 32,32 1 1 Q9UQF8 True hg19 CCDS2690.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EIF1B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254177.1 PASS NA None 332 NA True + AG ENST00000232905.3 NKTR 4820 __UNKNOWN__ __UNKNOWN__ 3 42642634 42642635 __UNKNOWN__ Intron INS - - C rs397826227|rs57577390 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:42642634_42642635insC ENST00000232978.8 + 2 246 NKTR_ENST00000442970.1_Intron|NKTR_ENST00000460910.1_Intron NM_005385.3 NP_005376.2 P30414 NKTR_HUMAN natural killer cell triggering receptor NA NA NA protein folding (GO:0006457) membrane (GO:0016020) cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755) breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4) 41 KIRC - Kidney renal clear cell carcinoma(284;0.24) TCAGCAACCCTCCCCCGGCCTT 0.629 NA NA NA CCCCCC|CCCCC|CCCCCC|deletion 955 0.190695 0.3079 0.0706 5008 , , NA 13790 0.1101 NA 0.1402 False NA ,,, NA NA NA 2504 0.2526 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 26 26.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS2702.1 3p22.1 2014-01-20 2014-01-20 ENSG00000114857 ENSG00000114857 4820 7833 protein-coding gene gene with protein product "NK-tumor recognition protein", "natural-killer cells cyclophilin-related protein", "NK-TR protein" 161565 "natural killer-tumor recognition sequence" NA 8314596, 8144875 Standard NM_005385 XM_005265173 NA Approved p104 uc003clo.3 P30414 OTTHUMG00000133037 ENST00000232978.8:c.58+78->C chr3.hg19:g.42642639_42642639dupC 6 8 ref NA False 33 33 PASS 5 PASS ref->het 0 NA 14,14 7,7 5,5 1 1 True hg19 CCDS2702.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NKTR-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256642.2 PASS NA None 26 NA True + C ENST00000232978.8 Unknown 0 __UNKNOWN__ __UNKNOWN__ 3 49711430 49711431 __UNKNOWN__ IGR INS - - C rs140606103|rs567500737 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:49711430_49711431insC NA BSN (2452 upstream) : APEH (3 downstream) NA NA NA NA GCCTTGCAGCACCCCCTCAACC 0.678 NA NA NA ?|CCCCC|CCCCCC|unsure 167 0.0333466 0.1036 0.0115 5008 , , NA 10655 0 NA 0.0089 False NA ,,, NA NA NA 2504 0.0133 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 241 256.08 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.98 NA NA NA NA NA chr3.hg19:g.49711435_49711435dupC 6 6 ref NA False 81 81 PASS 5 PASS ref->het 0 NA 172,179 41,41 28,21 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 241 NA True C PXK 54899 __UNKNOWN__ __UNKNOWN__ 3 58409300 58409301 __UNKNOWN__ Intron INS - - TT rs35853090|rs386396762|rs397700395 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:58409300_58409301insTT ENST00000356151.2 + 18 1637 PXK_ENST00000536660.1_Intron|PXK_ENST00000463280.1_Intron|PXK_ENST00000383716.3_Intron|PXK_ENST00000302779.5_Intron|PXK_ENST00000479241.1_Intron NM_017771.3 NP_060241.2 PX domain containing serine/threonine kinase NA NA NA cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22) TGAGTATTGTGTTGGTGATTCT 0.401 NA NA NA 1029 0.205471 0.2141 0.2839 5008 , , NA 22138 0.001 NA 0.3777 False NA ,,, NA NA NA 2504 0.1718 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 402 376.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.16 AY274811 CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1 3p21.2 2008-02-05 ENSG00000168297 ENSG00000168297 54899 23326 protein-coding gene gene with protein product 611450 NA Standard NM_017771 XM_005265255 NA Approved FLJ20335 uc003djz.1 Q7Z7A4 OTTHUMG00000159149 ENST00000356151.2:c.1529-1178->TT chr3.hg19:g.58409301_58409302dupTT 4 3 ref NA False 40 40 PASS 2 PASS ref->het 0 NA 318,320 48,48 34,34 1 1 True hg19 CCDS2889.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PXK-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000353499.1 PASS NA None 402 NA True + T ENST00000356151.2 DHFRL1 200895 __UNKNOWN__ __UNKNOWN__ 3 93776830 93776835 __UNKNOWN__ 3'UTR DEL TAAAAT TAAAAT - rs145016958|rs201902000|rs533331137 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:93776830_93776835delTAAAAT ENST00000394221.2 - 0 3970_3975 DHFRL1_ENST00000314636.2_3'UTR|DHFRL1_ENST00000481631.1_Intron NM_001195643.1 NP_001182572.1 Q86XF0 DYRL1_HUMAN dihydrofolate reductase-like 1 NA NA NA glycine biosynthetic process (GO:0006545)|nucleotide biosynthetic process (GO:0009165)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate biosynthetic process (GO:0046654)|tetrahydrofolate metabolic process (GO:0046653)|thymidine biosynthetic process (GO:0046105) mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739) dihydrofolate reductase activity (GO:0004146)|mRNA binding (GO:0003729)|NADP binding (GO:0050661) kidney(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1) 8 AAAAATGTGATAAAATTAATATGACC 0.262 NA NA NA 114 0.0227636 0.0045 0.0389 5008 , , NA 14248 0.002 NA 0.0547 False NA ,,, NA NA NA 2504 0.0245 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 315 288.55 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.36 AL832912 CCDS2926.1 3q11.2 2005-08-16 2005-02-07 ENSG00000178700 ENSG00000178700 200895 27309 protein-coding gene gene with protein product NA "dihydrofolate reductase pseudogene 4" DHFRP4 NA 12477932 Standard NM_176815 NM_001195643 NA Approved FLJ16119 uc003drj.3 Q86XF0 OTTHUMG00000159014 ENST00000394221.2:c.*2962ATTTTA>- chr3.hg19:g.93776830_93776835delTAAAAT 0 5 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 274,274 29,29 31,31 1 1 D3DN30|Q6P4I9 True hg19 CCDS2926.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DHFRL1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000352910.1 PASS NA None 315 NA True - TAAAAT ENST00000394221.2 CEP97 79598 __UNKNOWN__ __UNKNOWN__ 3 101443146 101443146 __UNKNOWN__ 5'UTR DEL T T - rs397875404|rs35159419 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:101443146delT ENST00000341893.3 + 0 378 Q8IW35 CEP97_HUMAN centrosomal protein 97kDa NA NA NA cell projection organization (GO:0030030) centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234) cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1) 29 TTATTCACAATTATCAAAAGA 0.353 NA NA NA TT|TT|T|deletion 1380 0.275559 0.1551 0.2392 5008 , , NA 17544 0.4772 NA 0.1948 False NA ,,, NA NA NA 2504 0.3395 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 140 130.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 AL833269 CCDS2944.1 3q12.3 2014-02-20 2008-01-08 2008-01-08 ENSG00000182504 ENSG00000182504 79598 26244 protein-coding gene gene with protein product 615864 "leucine-rich repeats and IQ motif containing 2" LRRIQ2 NA 17719545, 18068367 Standard NM_024548 NM_024548 NA Approved FLJ23047 uc003dvk.1 Q8IW35 OTTHUMG00000159162 ENST00000341893.3:c.-375T>- chr3.hg19:g.101443146delT 1 3 ref NA False 74 74 PASS 2 PASS ref->het 0 NA 94,94 28,28 19,20 1 1 B5MDY8|Q8NA71|Q9H5T9 True hg19 CCDS2944.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CEP97-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000353597.2 PASS NA None 140 NA True + T ENST00000341893.3 GSK3B 2932 __UNKNOWN__ __UNKNOWN__ 3 119812809 119812809 __UNKNOWN__ 5'UTR DEL A A - rs58853520 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:119812809delA ENST00000264235.8 - 0 455 NM_001146156.1|NM_002093.3 NP_001139628.1|NP_002084.2 P49841 GSK3B_HUMAN glycogen synthase kinase 3 beta NA NA NA axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109) beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529) ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625) endometrium(1)|large_intestine(8)|lung(7)|prostate(2) 18 GBM - Glioblastoma multiforme(114;0.24) Lithium(DB01356) CAGCTCCGGCAAGCCGCGGGA 0.711 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 90 100.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.08 BC012760 CCDS2996.1, CCDS54628.1 3q13.3 2008-02-15 ENSG00000082701 ENSG00000082701 2932 4617 protein-coding gene gene with protein product 605004 NA 10486203 Standard NM_002093 NA Approved uc003edm.3 P49841 OTTHUMG00000133765 ENST00000264235.8:c.-528T>- chr3.hg19:g.119812809delA 1 2 ref NA False 35 35 PASS 2 PASS ref->het 0 NA 56,65 13,15 23,12 1 1 D3DN89|Q9BWH3|Q9UL47 True hg19 CCDS54628.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GSK3B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000258240.2 PASS NA None 90 NA True - A ENST00000264235.8 ROPN1B 152015 __UNKNOWN__ __UNKNOWN__ 3 125691021 125691022 __UNKNOWN__ Intron DEL CT CT - rs530628677 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:125691021_125691022delCT ENST00000514116.1 + 3 431 ROPN1B_ENST00000251776.4_Intron|ROPN1B_ENST00000504401.1_Frame_Shift_Del_p.L43fs|ROPN1B_ENST00000511862.1_Intron Q9BZX4 ROP1B_HUMAN rhophilin associated tail protein 1B NA NA NA acrosome reaction (GO:0007340)|cytokinesis (GO:0000910)|fusion of sperm to egg plasma membrane (GO:0007342)|Rho protein signal transduction (GO:0007266)|single organismal cell-cell adhesion (GO:0016337)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283) cytoplasm (GO:0005737)|motile cilium (GO:0031514) protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor signaling complex scaffold activity (GO:0030159) endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|stomach(1) 8 GBM - Glioblastoma multiforme(114;0.151) CGAGTACGTGCTCCTTTCTCGC 0.629 NA NA NA 11 0.00219649 0 0.0115 5008 , , NA 16526 0 NA 0.003 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 664 648.35 NA 2,4264 NA 0,2,2131 NA NA NA -2.1 0.3 NA 38 22,8232 NA 0,22,4105 no intron ROPN1B NM_001012337.1 0,24,6236 A1A1,A1R,RR NA 0.2665,0.0469,0.1917 NA 24,12496 NA NA NA SO:0001627 intron_variant 1.05 AF231410 CCDS33841.1 3q21.2 2011-01-20 2011-01-20 ENSG00000114547 ENSG00000114547 152015 31927 protein-coding gene gene with protein product NA "ropporin, rhophilin associated protein 1B" NA Standard NM_001012337 XM_005247137 NA Approved uc003eih.3 Q9BZX4 OTTHUMG00000162651 ENST00000514116.1:c.116+8CT>- chr3.hg19:g.125691021_125691022delCT 0 3 ref NA False 72 72 PASS 1 PASS ref->het 0 NA 524,535 87,87 56,47 2 2 D3DNA6|Q96BM7 True hg19 CCDS33841.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ROPN1B-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000369931.1 PASS NA None 664 NA True + CT ENST00000514116.1 FAM194A 0 __UNKNOWN__ __UNKNOWN__ 3 150420588 150420589 __UNKNOWN__ Intron INS - - TTAAA rs397721438|rs10663389|rs62756861 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:150420588_150420589insTTAAA ENST00000295910.6 - 2 456 FAM194A_ENST00000491361.1_Intron NM_152394.3 NP_689607.2 NA NA NA NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1) 38 AGCACAGGATGTTAAACACAAA 0.411 NA NA NA 4099 0.81849 0.7156 0.902 5008 , , NA 12761 0.9554 NA 0.8161 False NA ,,, NA NA NA 2504 0.7597 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 275 245.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 5.22 NA NA NA NA NA ENST00000295910.6:c.404-623->TTTAA chr3.hg19:g.150420589_150420593dupTTAAA 2 3 ref NA False 55 55 PASS 1 PASS ref->het 0 NA 219,233 16,20 42,28 1 1 True hg19 CCDS3151.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM194A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257666.1 PASS NA None 275 NA True - TTAAA ENST00000295910.6 GOLIM4 27333 __UNKNOWN__ __UNKNOWN__ 3 167727381 167727381 __UNKNOWN__ 3'UTR DEL G G - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:167727381delG ENST00000470487.1 - 0 3456 NM_014498.3 NP_055313.1 O00461 GOLI4_HUMAN golgi integral membrane protein 4 NA NA NA transport (GO:0006810) cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634) breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 47 CCAGGATACTGCCACATGAGT 0.323 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 282 268.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 U55853 CCDS3204.1 3q26 2007-07-30 2007-07-30 2007-07-30 ENSG00000173905 ENSG00000173905 27333 15448 protein-coding gene gene with protein product 606805 "golgi phosphoprotein 4" GOLPH4 NA 9201717, 15004235 Standard NM_014498 NA Approved GPP130, GIMPC, P138 uc003ffe.2 O00461 OTTHUMG00000158554 ENST00000470487.1:c.*676C>- chr3.hg19:g.167727381delG 0 3 ref NA False 120 80 PASS 1 PASS ref->het 0 NA 76,77 175,181 26,27 1 1 True hg19 CCDS3204.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GOLIM4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000351278.2 PASS NA None 282 NA True - G ENST00000470487.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 3 170668995 170668995 __UNKNOWN__ IGR DEL C C - rs202054689 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:170668995delC NA EIF5A2 (42513 upstream) : RNU1-70P (43663 downstream) NA NA NA NA ATTTGATGGTCCTAAAGGCAG 0.418 NA NA NA |||unknown(NO_COVERAGE) 46 0.0091853 0.0023 0.0159 5008 , , NA 19202 0 NA 0.0288 False NA ,,, NA NA NA 2504 0.0031 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 144 137.82 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr3.hg19:g.170668995delC 1 2 ref NA False 38 38 PASS 2 PASS ref->het 0 NA 28,28 103,103 13,13 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 144 NA True C EPHB3 2049 __UNKNOWN__ __UNKNOWN__ 3 184279675 184279675 __UNKNOWN__ 5'UTR DEL C C - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:184279675delC ENST00000330394.2 + 0 104 EIF2B5_ENST00000444495.1_Intron NM_004443.3 NP_004434.2 P54753 EPHB3_HUMAN EPH receptor B3 NA NA NA angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655) cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887) ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003) breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 51 all_cancers(143;1.89e-10)|Ovarian(172;0.0339) Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22) CAGCTGACCGCCAGATTACTG 0.716 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 531 517.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.67 X75208 CCDS3268.1 3q27.1 2013-09-19 2004-10-28 ENSG00000182580 ENSG00000182580 2049 "EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing" 3394 protein-coding gene gene with protein product 601839 "EphB3" ETK2 NA 8397371 Standard NM_004443 NM_004443 NA Approved Hek2, Tyro6 uc003foz.3 P54753 OTTHUMG00000156710 ENST00000330394.2:c.-349C>- chr3.hg19:g.184279675delC 1 4 ref NA False 171 171 PASS 2 PASS ref->het 0 NA 419,425 56,59 54,45 1 1 Q7Z740 True hg19 CCDS3268.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EPHB3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000345413.1 PASS NA None 531 NA True + C ENST00000330394.2 VPS8 23355 __UNKNOWN__ __UNKNOWN__ 3 184561140 184561141 __UNKNOWN__ Intron INS - - A rs397774481|rs567218429|rs11384502 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr3:184561140_184561141insA ENST00000436792.2 + 7 678 VPS8_ENST00000437079.3_Intron|VPS8_ENST00000287546.4_Intron|VPS8_ENST00000446204.2_Intron Q8N3P4 VPS8_HUMAN vacuolar protein sorting 8 homolog (S. cerevisiae) NA NA NA zinc ion binding (GO:0008270) NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 54 all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247) Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22) AATGCTTATTGAAAAAAACCCA 0.257 NA NA NA AAAAAAAA|AAAAAAA|AAAAAAAA|deletion 2866 0.572284 0.7133 0.4726 5008 , , NA 15383 0.6657 NA 0.3757 False NA ,,, NA NA NA 2504 0.5583 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 78 71.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.34 AK056661 CCDS46972.1 3q27.2 2006-07-07 2006-07-07 2006-07-07 ENSG00000156931 ENSG00000156931 23355 29122 protein-coding gene gene with protein product NA "KIAA0804" KIAA0804 NA 9872452 Standard NM_015303 NM_001009921 NA Approved FLJ32099 uc003fpb.1 Q8N3P4 OTTHUMG00000156707 ENST00000436792.2:c.535+3600->A chr3.hg19:g.184561147_184561147dupA 8 7 ref NA False 30 30 PASS 7 PASS ref->het 0 NA 55,55 19,19 3,3 1 1 A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0 True hg19 CCDS46972.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA VPS8-002 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000345396.2 PASS NA None 78 NA True + A ENST00000436792.2 ZFYVE28 57732 __UNKNOWN__ __UNKNOWN__ 4 2322039 2322040 __UNKNOWN__ Intron INS - - C rs113929105 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:2322039_2322040insC ENST00000290974.2 - 7 1041 ZFYVE28_ENST00000515312.1_Intron|ZFYVE28_ENST00000511071.1_Intron NM_020972.2 NP_066023.2 Q9HCC9 LST2_HUMAN zinc finger, FYVE domain containing 28 NA NA NA negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175) cytosol (GO:0005829)|early endosome membrane (GO:0031901) metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266) NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4) 31 AGGCCCTGTGGCCCCCTGGGTG 0.634 NA NA NA CCCCC|CCCCC|CCCCCC|insertion 1098 0.219249 0.1157 0.3012 5008 , , NA 13829 0.1429 NA 0.331 False NA ,,, NA NA NA 2504 0.2648 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 152 162.12 NA ,, 616,3650 NA 48,520,1565 NA NA NA ,, 2.8 0 NA dbSNP_132 39 2766,5486 NA 438,1890,1798 no intron,intron,intron ZFYVE28 NM_020972.2,NM_001172659.1,NM_001172656.1 ,, 486,2410,3363 A1A1,A1R,RR NA 33.5191,14.4398,27.0171 ,, ,, NA 3382,9136 NA NA NA SO:0001627 intron_variant 0.4 AK126692 CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1 4p16.3 2008-05-02 ENSG00000159733 ENSG00000159733 57732 "Zinc fingers, FYVE domain containing" 29334 protein-coding gene gene with protein product 614176 NA 10997877 Standard XM_035371 NM_020972 NA Approved KIAA1643 uc003gex.2 Q9HCC9 OTTHUMG00000160292 ENST00000290974.2:c.702-41->G chr4.hg19:g.2322044_2322044dupC 6 5 ref NA False 35 35 PASS 5 PASS ref->het 0 NA 87,87 39,39 23,24 1 1 B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3 True hg19 CCDS33942.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZFYVE28-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000360078.1 PASS NA None 152 NA True - C ENST00000290974.2 MFSD10 10227 __UNKNOWN__ __UNKNOWN__ 4 2936009 2936014 __UNKNOWN__ 5'UTR DEL GATCCC GATCCC - rs7675980 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:2936009_2936014delGATCCC ENST00000329687.4 - 0 171_176 MFSD10_ENST00000508221.1_Intron|MFSD10_ENST00000355443.4_Intron|MFSD10_ENST00000507555.1_Intron NM_001120.4 NP_001111.3 Q14728 MFS10_HUMAN major facilitator superfamily domain containing 10 NA NA NA apoptotic process (GO:0006915)|tetracycline transport (GO:0015904)|transmembrane transport (GO:0055085)|transport (GO:0006810) integral component of membrane (GO:0016021) tetracycline transporter activity (GO:0008493) breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|skin(1) 7 UCEC - Uterine corpus endometrioid carcinoma (64;0.163) GGGGaacccggatcccgatcccgatc 0.733 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 111 109.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 L11669 CCDS3365.1 4p16.3 2008-03-03 ENSG00000109736 ENSG00000109736 10227 16894 protein-coding gene gene with protein product "tetracycline transporter like protein" 610977 NA 8353488, 17362938 Standard NM_001120 NM_001120 NA Approved TETRAN, IT10C3 uc003gfz.3 Q14728 OTTHUMG00000122081 ENST00000329687.4:c.-364GGGATC>- chr4.hg19:g.2936015_2936020delGATCCC 4 3 ref NA False 44 44 PASS 5 PASS ref->het 0 NA 50,52 15,15 47,46 1 1 Q07706 True hg19 CCDS3365.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MFSD10-010 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000358072.2 PASS NA None 111 NA True - GATCCC ENST00000329687.4 PPP2R2C 5522 __UNKNOWN__ __UNKNOWN__ 4 6374230 6374231 __UNKNOWN__ Intron INS - - A rs35520578|rs201247014|rs397962598 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:6374230_6374231insA ENST00000382599.4 - 5 842 PPP2R2C_ENST00000515571.1_Intron|PPP2R2C_ENST00000506140.1_Intron|PPP2R2C_ENST00000314348.8_Intron|PPP2R2C_ENST00000335585.5_Intron|PPP2R2C_ENST00000507294.1_Intron Q9Y2T4 2ABG_HUMAN protein phosphatase 2, regulatory subunit B, gamma NA NA NA regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165) protein phosphatase type 2A complex (GO:0000159) protein phosphatase type 2A regulator activity (GO:0008601) central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1) 28 AGGCACTGGCCAGGCCACAGTG 0.564 NA NA NA A|A|AA|insertion 1061 0.211861 0.0287 0.2406 5008 , , NA 20505 0.4048 NA 0.2167 False NA ,,, NA NA NA 2504 0.2352 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 115 118.25 NA ,,, 1308,2958 NA 202,904,1027 NA NA NA ,,, -2.8 0 NA dbSNP_126 82 6045,2209 NA 2224,1597,306 no intron,intron,intron,intron PPP2R2C NM_181876.2,NM_001206996.1,NM_001206995.1,NM_001206994.1 ,,, 2426,2501,1333 A1A1,A1R,RR NA 26.7628,30.661,41.27 ,,, ,,, NA 7353,5167 NA NA NA SO:0001627 intron_variant 0.04 AF086924 CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1 4p16.1 2013-01-10 2010-04-14 ENSG00000074211 ENSG00000074211 5522 3.1.3.16 "Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing" 9306 protein-coding gene gene with protein product "PP2A subunit B isoform gamma" 605997 "protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform" NA 10574460, 10945473 Standard NM_181876 NM_020416 NA Approved PR52, IMYPNO, MGC33570, PR55G uc003gja.3 Q9Y2T4 OTTHUMG00000090445 ENST00000382599.4:c.625+18->T chr4.hg19:g.6374231_6374231dupA 2 2 ref NA False 37 37 PASS 1 PASS ref->het 0 NA 69,70 29,29 16,15 1 1 A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPP2R2C-001 NOVEL overlapping_uORF|basic|appris_principal protein_coding NA protein_coding OTTHUMT00000206889.2 PASS NA None 115 NA True - A ENST00000382599.4 SORCS2 57537 __UNKNOWN__ __UNKNOWN__ 4 7649916 7649918 __UNKNOWN__ Intron DEL GAG GAG - rs56241745|rs398063236|rs72347309 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:7649916_7649918delGAG ENST00000507866.2 + 5 922 SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000511199.1_Intron NM_020777.2 NP_065828.2 Q96PQ0 SORC2_HUMAN sortilin-related VPS10 domain containing receptor 2 NA NA NA neuropeptide signaling pathway (GO:0007218) integral component of membrane (GO:0016021)|membrane (GO:0016020) neuropeptide receptor activity (GO:0008188) autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2) 42 TGAGACCGCAgaggaggaggagg 0.631 NA NA NA 4618 0.922125 0.7549 0.9568 5008 , , NA 15734 1 NA 0.9712 False NA ,,, NA NA NA 2504 0.9928 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 24 21.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AB037750 CCDS47008.1 4p16.1 2008-02-05 ENSG00000184985 ENSG00000184985 57537 16698 protein-coding gene gene with protein product 606284 NA 11499680 Standard NM_020777 NM_020777 NA Approved KIAA1329 uc003gkb.4 Q96PQ0 OTTHUMG00000159981 ENST00000507866.2:c.814-5943GAG>- chr4.hg19:g.7649925_7649927delGAG 7 4 ref NA True 50 49 PASS 8 PASS ref->hom 0 NA 0,0 22,22 2,2 1 1 Q9P2L7 True hg19 CCDS47008.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SORCS2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000358685.4 PASS NA None 24 NA True + GAG ENST00000507866.2 ATP10D 57205 __UNKNOWN__ __UNKNOWN__ 4 47493308 47493309 __UNKNOWN__ Intron INS - - TAACAC rs137930666|rs397974993|rs59041603 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:47493308_47493309insTAACAC ENST00000273859.3 + 1 232 ATP10D_ENST00000504445.1_Intron NM_020453.3 NP_065186.3 Q9P241 AT10D_HUMAN ATPase, class V, type 10D NA NA NA cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886) ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012) NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1) 66 TTTTGCCATGGTAACACTGGTG 0.431 NA NA NA 1700 0.339457 0.2133 0.3487 5008 , , NA 18871 0.5982 NA 0.2028 False NA ,,, NA NA NA 2504 0.3773 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 88 87.57 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AB040920 CCDS3476.1 4p12 2010-04-20 2007-09-19 ENSG00000145246 ENSG00000145246 57205 "ATPases / P-type" 13549 protein-coding gene gene with protein product NA "ATPase, Class V, type 10D" NA 12532265 Standard NM_020453 NM_020453 NA Approved ATPVD, KIAA1487 uc003gxk.1 Q9P241 OTTHUMG00000160784 ENST00000273859.3:c.-38+5772->TAACAC chr4.hg19:g.47493309_47493314dupTAACAC 2 2 ref NA False 39 39 PASS 1 PASS ref->het 0 NA 60,60 18,18 9,10 1 1 A2RRC8|D6REN2|Q8NC70|Q96SR3 True hg19 CCDS3476.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ATP10D-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000216900.1 PASS NA None 88 NA True + TAACAC ENST00000273859.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 4 71554129 71554129 __UNKNOWN__ IGR DEL A A - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:71554129delA NA ENAM (1596 upstream) : UTP3 (66 downstream) NA NA NA NA GACTGGCGTTAAAGGGCACAG 0.517 NA NA NA OREG0016219 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 121 118.41 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.11 NA NA NA NA NA chr4.hg19:g.71554129delA 2 3 ref 1130 False 61 61 PASS 3 PASS ref->het 0 NA 85,86 19,19 18,17 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 121 NA True A ADAMTS3 9508 __UNKNOWN__ __UNKNOWN__ 4 73433123 73433123 __UNKNOWN__ Intron DEL A A - rs33925079|rs398092497|rs76734627 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:73433123delA ENST00000286657.4 - 2 106 ADAMTS3_ENST00000505193.1_Intron NM_014243.2 NP_055058.2 O15072 ATS3_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 3 NA NA NA collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573) extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578) endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270) NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 76 Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154) ACCAGCCTGGAAAGGAGGGGG 0.373 NA NA NA AAA|AAA|AA|deletion 2113 0.421925 0.2761 0.6095 5008 , , NA 7003 0.3909 NA 0.5865 False NA ,,, NA NA NA 2504 0.3487 NA NA NA NSCLC(168;1941 2048 2918 13048 43078) PASS NA NA NA 0 NA NA NA NA NA 109 115.06 NA 1358,2908 NA 215,928,990 51 37 42 3.8 1 4 dbSNP_126 71 4590,3664 NA 1251,2088,788 no intron ADAMTS3 NM_014243.2 1466,3016,1778 A1A1,A1R,RR NA 44.3906,31.8331,47.508 73433123 5948,6572 2155 4073 6228 SO:0001627 intron_variant 0 AB002364 CCDS3553.1 4q21 2008-07-29 2005-08-19 ENSG00000156140 ENSG00000156140 9508 3.4.24.- "ADAM metallopeptidases with thrombospondin type 1 motif" 219 protein-coding gene gene with protein product 605011 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3" NA 10094461 Standard NM_014243 NA Approved KIAA0366, ADAMTS-4 uc003hgk.2 O15072 OTTHUMG00000129912 ENST00000286657.4:c.70-5T>- chr4.hg19:g.73433123delA 2 3 ref NA False 36 36 PASS 3 PASS ref->het 0 NA 83,84 13,13 13,13 1 1 A1L3U9|Q9BXZ8 True hg19 CCDS3553.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ADAMTS3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252164.2 PASS NA None 109 NA True - A ENST00000286657.4 NUP54 53371 __UNKNOWN__ __UNKNOWN__ 4 77065318 77065319 __UNKNOWN__ Intron INS - - TGT rs76406406|rs57577548|rs36024409|rs67608403 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:77065318_77065319insTGT ENST00000514987.1 - 2 174 NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000458189.2_5'UTR|NUP54_ENST00000515460.1_5'UTR|NUP54_ENST00000264883.3_In_Frame_Ins_p.93_93Q>QQ Q7Z3B4 NUP54_HUMAN nucleoporin 54kDa NA NA NA carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032) cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654) nucleocytoplasmic transporter activity (GO:0005487) p.Q93>HK(1) cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1) 19 GCTGCTGCTGCTGTGTATTAAA 0.411 NA NA NA 776 0.154952 0.0567 0.1282 5008 , , NA 16499 0.3512 NA 0.1312 False NA ,,, NA NA NA 2504 0.1288 NA NA NA PASS NA NA NA 1 Complex - insertion inframe(1) kidney(1) NA NA NA NA NA 366 369.21 NA 300,3966 NA 14,272,1847 NA NA NA 5.2 1 NA dbSNP_126 211 1244,7010 NA 96,1052,2979 no coding NUP54 NM_017426.2 110,1324,4826 A1A1,A1R,RR NA 15.0715,7.0323,12.3323 NA 1544,10976 NA NA NA SO:0001627 intron_variant 0.62 AF157322 CCDS3576.1, CCDS63998.1 4q21.1 2008-07-03 2002-08-29 ENSG00000138750 ENSG00000138750 53371 17359 protein-coding gene gene with protein product 607607 "nucleoporin 54kD" NA 8707840 Standard NM_017426 NA Approved uc003hjs.3 Q7Z3B4 OTTHUMG00000130098 ENST00000514987.1:c.151+223->ACA chr4.hg19:g.77065319_77065321dupTGT 2 2 ref NA False 49 49 PASS 1 PASS ref->het 0 NA 292,295 47,47 29,28 1 1 B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NUP54-004 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000362699.1 PASS NA None 366 NA True - TGT ENST00000514987.1 CCNI 10983 __UNKNOWN__ __UNKNOWN__ 4 77996796 77996801 __UNKNOWN__ 5'UTR DEL GGGCGC GGGCGC - rs147494324 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:77996796_77996801delGGGCGC ENST00000237654.4 - 0 357_362 CCNI_ENST00000537948.1_5'UTR NM_006835.2 NP_006826.1 Q14094 CCNI_HUMAN cyclin I NA NA NA regulation of cell cycle (GO:0051726)|spermatogenesis (GO:0007283) NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1) 9 GCGGATcggggggcgcgggcgcgggc 0.733 NA NA NA 723 0.144369 0.2186 0.147 5008 , , NA 6386 0.1181 NA 0.0507 False NA ,,, NA NA NA 2504 0.1656 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 222 249.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.38 D50310 CCDS3580.1 4q21.1 2014-07-03 ENSG00000118816 ENSG00000118816 10983 1595 protein-coding gene gene with protein product NA NA 7493655 Standard NM_006835 NM_006835 NA Approved CCNI1 uc003hkm.3 Q14094 OTTHUMG00000130106 ENST00000237654.4:c.-220GCGCCC>- chr4.hg19:g.77996802_77996807delGGGCGC 2 7 ref NA False 190 179 PASS 3 PASS ref->het 0 NA 131,134 45,45 51,48 2 1 B2R6M0|B7Z6X4 True hg19 CCDS3580.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CCNI-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252412.2 PASS NA None 222 NA True - GGGCGC ENST00000237654.4 COPS4 51138 __UNKNOWN__ __UNKNOWN__ 4 83955801 83955802 __UNKNOWN__ 5'UTR INS - - G rs34006389 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:83955801_83955802insG ENST00000509093.1 + 0 202_203 NM_001258006.1 NP_001244935.1 Q9BT78 CSN4_HUMAN COP9 signalosome subunit 4 NA NA NA cullin deneddylation (GO:0010388)|protein deneddylation (GO:0000338) cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021) endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(2) 13 Hepatocellular(203;0.114) cccggccgaaaggggggatatt 0.554 NA NA NA GGGGGG|GGGGGG|GGGGGGG|insertion 1038 0.207268 0.1218 0.1383 5008 , , NA 15344 0.2679 NA 0.1829 False NA ,,, NA NA NA 2504 0.3344 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 160 157.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 AF100757 CCDS3600.1, CCDS58909.1 4q21.22 2013-03-14 2013-03-14 ENSG00000138663 ENSG00000138663 51138 16702 protein-coding gene gene with protein product NA "COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 4", "COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)" NA 9707402 Standard NM_016129 NA Approved CSN4 uc003hoa.3 Q9BT78 OTTHUMG00000130298 ENST00000509093.1:c.-576->G chr4.hg19:g.83955807_83955807dupG 7 6 ref NA False 95 95 PASS 6 PASS ref->het 0 NA 108,109 29,29 23,23 1 1 B3KN88|B3KST5|Q561W7|Q9NW31|Q9Y677 True hg19 CCDS58909.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COPS4-002 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000363091.1 PASS NA None 160 NA True + G ENST00000509093.1 AFF1 4299 __UNKNOWN__ __UNKNOWN__ 4 88056720 88056720 __UNKNOWN__ Intron DEL T T - rs398083273|rs56703224 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:88056720delT ENST00000307808.6 + 20 3931 AFF1_ENST00000395146.4_Intron|AFF1_ENST00000544085.1_Intron NM_005935.2 NP_005926.1 P51825 AFF1_HUMAN AF4/FMR2 family, member 1 NA NA NA positive regulation of transcription, DNA-templated (GO:0045893) transcription elongation factor complex (GO:0008023) sequence-specific DNA binding transcription factor activity (GO:0003700) breast(1)|large_intestine(2) 3 Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;0.000233) ttttgttttgttttttttGCA 0.403 NA NA NA TTTTGTTTTT|TTTTTTTT|TTTTTTT|cryptic_indel 2856 0.570288 0.5492 0.6715 5008 , , NA 21370 0.6002 NA 0.6083 False NA ,,, NA NA NA 2504 0.4571 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 142 152.47 NA NA 13 12 12 NA NA 4 NA NA NA 88056720 2099 4052 6151 SO:0001627 intron_variant 0 L22179 CCDS3616.1, CCDS54775.1 4q21.3 2009-08-04 2005-06-27 2005-06-27 ENSG00000172493 ENSG00000172493 4299 7135 protein-coding gene gene with protein product 159557 "myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1" PBM1, MLLT2 NA 7689231, 1423625, 8353274 Standard NM_005935 NM_005935 NA Approved AF-4, AF4 uc011ccz.2 P51825 OTTHUMG00000130603 ENST00000307808.6:c.3512-12T>- chr4.hg19:g.88056720delT 7 12 ref NA False 65 65 PASS 8 PASS ref->het 0 NA 89,91 38,40 18,18 1 1 B4DTU1|E9PBM3 True hg19 CCDS3616.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFF1-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000253053.3 PASS NA None 142 NA True + T ENST00000307808.6 AFF1 4299 __UNKNOWN__ __UNKNOWN__ 4 88058643 88058644 __UNKNOWN__ 3'UTR INS - - T rs397744403|rs3841986 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:88058643_88058644insT ENST00000307808.6 + 0 5843_5844 AFF1_ENST00000395146.4_3'UTR NM_005935.2 NP_005926.1 P51825 AFF1_HUMAN AF4/FMR2 family, member 1 NA NA NA positive regulation of transcription, DNA-templated (GO:0045893) transcription elongation factor complex (GO:0008023) sequence-specific DNA binding transcription factor activity (GO:0003700) breast(1)|large_intestine(2) 3 Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;0.000233) TTGGTTGTCACTAAGTCAGAGG 0.475 NA NA NA T|T|TT|insertion 1205 0.240615 0.2564 0.2363 5008 , , NA 20041 0.3978 NA 0.2058 False NA ,,, NA NA NA 2504 0.0961 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 106 112.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 L22179 CCDS3616.1, CCDS54775.1 4q21.3 2009-08-04 2005-06-27 2005-06-27 ENSG00000172493 ENSG00000172493 4299 7135 protein-coding gene gene with protein product 159557 "myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1" PBM1, MLLT2 NA 7689231, 1423625, 8353274 Standard NM_005935 NM_005935 NA Approved AF-4, AF4 uc011ccz.2 P51825 OTTHUMG00000130603 ENST00000307808.6:c.*1791->T chr4.hg19:g.88058644_88058644dupT 2 2 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 78,79 17,17 10,10 1 1 B4DTU1|E9PBM3 True hg19 CCDS3616.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AFF1-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000253053.3 PASS NA None 106 NA True + T ENST00000307808.6 HSD17B13 345275 __UNKNOWN__ __UNKNOWN__ 4 88231392 88231393 __UNKNOWN__ Intron INS - - A rs72613567 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:88231392_88231393insA ENST00000328546.4 - 6 877 HSD17B13_ENST00000302219.6_Intron NM_178135.3 NP_835236.2 Q7Z5P4 DHB13_HUMAN hydroxysteroid (17-beta) dehydrogenase 13 NA NA NA extracellular region (GO:0005576) oxidoreductase activity (GO:0016491) endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1) 8 Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248) OV - Ovarian serous cystadenocarcinoma(123;0.000308) GTGCTGTACTTACTTCTGTAGT 0.347 NA NA NA A|A|AA|insertion 920 0.183706 0.0469 0.1643 5008 , , NA 14297 0.3373 NA 0.2435 False NA ,,, NA NA NA 2504 0.1626 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 73 69.89 NA , 318,3948 NA 12,294,1827 NA NA NA , 4.9 1 NA dbSNP_126 118 2274,5980 NA 319,1636,2172 no splice-5,splice-5 HSD17B13 NM_178135.3,NM_001136230.1 , 331,1930,3999 A1A1,A1R,RR NA 27.5503,7.4543,20.7029 , , NA 2592,9928 NA NA NA SO:0001627 intron_variant 1.68 CCDS3618.1, CCDS47097.1 4q22.1 2011-09-20 ENSG00000170509 ENSG00000170509 345275 1.1.-.- "Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3" 18685 protein-coding gene gene with protein product "short chain dehydrogenase/reductase family 16C, member 3" 612127 NA 19027726 Standard NM_178135 NM_178135 NA Approved SCDR9, SDR16C3 uc003hqo.2 Q7Z5P4 OTTHUMG00000130602 ENST00000328546.4:c.812+1->T chr4.hg19:g.88231393_88231393dupA 2 2 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 43,44 20,21 10,9 1 1 A8K9R9|Q2M1L5|Q86W22|Q86W23 True hg19 CCDS3618.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HSD17B13-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253052.1 PASS NA None 73 NA True - A ENST00000328546.4 PRSS12 8492 __UNKNOWN__ __UNKNOWN__ 4 119256617 119256618 __UNKNOWN__ Intron INS - - T rs3215324|rs397746205 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:119256617_119256618insT ENST00000296498.3 - 3 1103 NM_003619.3 NP_003610.2 P56730 NETR_HUMAN protease, serine, 12 (neurotrypsin, motopsin) NA NA NA exocytosis (GO:0006887)|zymogen activation (GO:0031638) axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195) scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236) endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1) 29 GAACTTTTTTCTTTTTTTTACC 0.356 NA NA NA ?|TTTTTTTT|TTTTTTTTT|unsure 499 0.0996406 0.0318 0.1066 5008 , , NA 14876 0.0446 NA 0.1511 False NA ,,, NA NA NA 2504 0.1902 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 230 224.44 NA 233,4033 NA 5,223,1905 NA NA NA -0.3 0 NA dbSNP_120 67 1280,6974 NA 98,1084,2945 no intron PRSS12 NM_003619.3 103,1307,4850 A1A1,A1R,RR NA 15.5076,5.4618,12.0847 NA 1513,11007 NA NA NA SO:0001627 intron_variant 0.09 AJ001531 CCDS3709.1 4q25-q26 2010-05-07 ENSG00000164099 ENSG00000164099 8492 "Serine peptidases / Serine peptidases" 9477 protein-coding gene gene with protein product 606709 NA 9540828, 9245503 Standard NM_003619 NA Approved BSSP-3, MRT1 uc003ica.2 P56730 OTTHUMG00000161166 ENST00000296498.3:c.820+9->A chr4.hg19:g.119256625_119256625dupT 9 14 ref NA False 66 66 PASS 8 PASS ref->het 0 NA 155,156 53,54 23,22 1 1 Q9UP16 True hg19 CCDS3709.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PRSS12-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256516.2 PASS NA None 230 NA True - T ENST00000296498.3 SYNPO2 171024 __UNKNOWN__ __UNKNOWN__ 4 119979129 119979129 __UNKNOWN__ 3'UTR DEL A A - rs61064985 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:119979129delA ENST00000307142.4 + 0 4022 SYNPO2_ENST00000448416.2_3'UTR NM_133477.2 NP_597734.2 Q9UMS6 SYNP2_HUMAN synaptopodin 2 NA NA NA actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018) 14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371) breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1) 64 GTAGTTTTTTAAAAAAAACGC 0.368 NA NA NA 1146 0.228834 0.4183 0.17 5008 , , NA 19027 0.1438 NA 0.1332 False NA ,,, NA NA NA 2504 0.2004 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 349 346.3 NA 9,1523,2674 NA 1,0,7,337,849,909 NA NA NA 0.6 0 NA dbSNP_134 21 21,1041,7134 NA 2,0,17,99,843,3137 no utr-3 SYNPO2 NM_133477.2 3,0,24,436,1692,4046 A1A1,A1A2,A1R,A2A2,A2R,RR NA 12.9575,36.4242,20.916 NA 30,2564,9808 NA NA NA SO:0001624 3_prime_UTR_variant 0.48 AJ010482 CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1 4q26 2008-08-29 ENSG00000172403 ENSG00000172403 171024 17732 protein-coding gene gene with protein product NA NA 11673475, 17828378 Standard NM_133477 NA Approved MYOPODIN uc010inb.3 Q9UMS6 OTTHUMG00000161165 ENST00000307142.4:c.*40A>- chr4.hg19:g.119979129delA 7 8 ref NA False 60 60 PASS 8 PASS ref->het 0 NA 248,251 43,43 52,50 1 1 B2RWP6|B2Y8J9|Q9UK89|S5XAM4 True hg19 CCDS34054.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SYNPO2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000364018.1 PASS NA None 349 NA True + A ENST00000307142.4 BBS7 55212 __UNKNOWN__ __UNKNOWN__ 4 122746286 122746286 __UNKNOWN__ 3'UTR DEL C C - rs397995200|rs202086156|rs3217754|rs398083460 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:122746286delC ENST00000264499.4 - 0 3060 NM_176824.2 NP_789794.1 Q8IWZ6 BBS7_HUMAN Bardet-Biedl syndrome 7 NA NA NA brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601) axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886) RNA polymerase II repressing transcription factor binding (GO:0001103) central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2) 30 TAATTAAGATCCCCCGACTCT 0.418 NA NA NA Bardet-Biedl syndrome CCCCC|CCCCC|CCCC|deletion 1386 0.276757 0.0234 0.428 5008 , , NA 15491 0.4276 NA 0.3579 False NA ,,, NA NA NA 2504 0.273 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 107 101.01 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 Familial Cancer Database BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome AF521644 CCDS3724.1, CCDS54799.1 4q27 2013-01-08 ENSG00000138686 ENSG00000138686 55212 18758 protein-coding gene gene with protein product 607590 NA Standard NM_176824 NA Approved FLJ10715, BBS2L1 uc003ied.3 Q8IWZ6 OTTHUMG00000133076 ENST00000264499.4:c.*729G>- chr4.hg19:g.122746286delC 4 5 ref NA False 54 54 PASS 5 PASS ref->het 0 NA 72,72 22,22 11,11 1 1 Q4W5P8|Q8N581|Q9NVI4 True hg19 CCDS3724.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BBS7-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256716.1 PASS NA None 107 NA True - C ENST00000264499.4 PHF17 0 __UNKNOWN__ __UNKNOWN__ 4 129795663 129795664 __UNKNOWN__ 3'UTR INS - - A rs530620862|rs397753505|rs56384527|rs3836574 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:129795663_129795664insA ENST00000226319.6 + 0 5055_5056 PHF17_ENST00000452328.2_3'UTR NM_199320.2 NP_955352.1 NA NA NA NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 29 caaaaaatattaaaaaaaaccc 0.327 NA NA NA ?|AAAAAAAA|AAAAAAAAA|unsure 2659 0.53095 0.9334 0.4669 5008 , , NA 15822 0.381 NA 0.3966 False NA ,,, NA NA NA 2504 0.3252 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 191 193.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 NA NA NA NA NA ENST00000226319.6:c.*2247->A chr4.hg19:g.129795671_129795671dupA 9 8 ref NA False 76 76 PASS 8 PASS ref->het 0 NA 116,117 41,41 33,33 1 1 True hg19 CCDS34062.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PHF17-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000364280.1 PASS NA None 191 NA True + A ENST00000226319.6 RNF150 57484 __UNKNOWN__ __UNKNOWN__ 4 141927449 141927450 __UNKNOWN__ Intron INS - - AC rs146785909|rs397936199|rs539763916|rs55837616 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:141927449_141927450insAC ENST00000515673.2 - 2 518 RNF150_ENST00000420921.2_Intron|RNF150_ENST00000306799.3_Intron|RNF150_ENST00000507500.1_Intron|RNF150_ENST00000379512.2_Intron Q9ULK6 RN150_HUMAN ring finger protein 150 NA NA NA integral component of membrane (GO:0016021) zinc ion binding (GO:0008270) breast(1)|large_intestine(10)|lung(7)|ovary(1) 19 all_hematologic(180;0.162) cgtatatatatacaCACACACA 0.257 NA NA NA 97 0.019369 0.0212 0.0014 5008 , , NA 12600 0.0417 NA 0.007 False NA ,,, NA NA NA 2504 0.0194 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 125 115.15 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AB033040 CCDS34065.1 4q31.1 2013-01-09 ENSG00000170153 ENSG00000170153 57484 "RING-type (C3HC4) zinc fingers" 23138 protein-coding gene gene with protein product NA NA 10574462 Standard XM_291090 XM_005263150 NA Approved KIAA1214 uc003iio.1 Q9ULK6 OTTHUMG00000161380 ENST00000515673.2:c.485-38422->GT chr4.hg19:g.141927458_141927459dupAC 8 2 ref NA False 36 36 PASS 7 PASS ref->het 0 NA 90,90 20,20 16,16 1 1 Q3T1D0|Q6ZNW6 True hg19 CCDS34065.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RNF150-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000364739.2 PASS NA None 125 NA True - AC ENST00000515673.2 MAP9 79884 __UNKNOWN__ __UNKNOWN__ 4 156294624 156294625 __UNKNOWN__ Intron INS - - A rs5863149|rs34053877 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:156294624_156294625insA ENST00000311277.4 - 4 424 AC097467.2_ENST00000596165.1_RNA|MAP9_ENST00000379248.2_Intron|MAP9_ENST00000515654.1_Intron NM_001039580.1 NP_001034669.1 Q49MG5 MAP9_HUMAN microtubule-associated protein 9 NA NA NA cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307) astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023) NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2) 26 all_hematologic(180;0.24) Renal(120;0.0458) COAD - Colon adenocarcinoma(41;0.143) AAATGGAAAAGAAAAATGTTTT 0.262 NA NA NA AAAAAA|AAAAA|AAAAAA|deletion 2652 0.529553 0.916 0.3458 5008 , , NA 17809 0.7183 NA 0.2247 False NA ,,, NA NA NA 2504 0.2566 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 156 150.59 NA 3037,739 NA 1291,455,142 NA NA NA -1.9 0 NA dbSNP_114 11 1773,6169 NA 264,1245,2462 no intron MAP9 NM_001039580.1 1555,1700,2604 A1A1,A1R,RR NA 22.3244,19.571,41.048 NA 4810,6908 NA NA NA SO:0001627 intron_variant 0.86 AK024812 CCDS35493.1 4q32.1 2008-02-05 ENSG00000164114 ENSG00000164114 79884 26118 protein-coding gene gene with protein product "aster-associated protein" 610070 NA 16049101 Standard NM_001039580 XM_006714306 NA Approved ASAP, FLJ21159 uc003ios.3 Q49MG5 OTTHUMG00000133628 ENST00000311277.4:c.161-16->T chr4.hg19:g.156294629_156294629dupA 6 9 ref NA False 30 30 PASS 5 PASS ref->het 0 NA 121,121 20,20 12,12 1 1 Q4W5I7|Q68DU1|Q9H781|Q9H7B6 True hg19 CCDS35493.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAP9-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257771.3 PASS NA None 156 NA True - A ENST00000311277.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 4 160025021 160025022 __UNKNOWN__ IGR INS - - GAG rs139404823 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:160025021_160025022insGAG NA Y_RNA (39471 upstream) : AC095064.1 (19762 downstream) NA NA NA NA GCGGCgaggaagaggaggagga 0.767 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 23 21.88 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr4.hg19:g.160025028_160025030dupGAG 6 3 ref NA False 32 32 PASS 5 PASS ref->het 0 NA 13,14 8,8 2,1 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 23 NA True GAG MARCH1 55016 __UNKNOWN__ __UNKNOWN__ 4 164446785 164446786 __UNKNOWN__ 3'UTR INS - - TATGGTATTGA rs58604262|rs11271036|rs35609422 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:164446785_164446786insTATGGTATTGA ENST00000503008.1 - 0 4960_4961 MARCH1_ENST00000274056.7_3'UTR NM_001166373.1 NP_001159845.1 Q8TCQ1 MARH1_HUMAN membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase NA NA NA antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209) cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588) ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270) endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 36 all_hematologic(180;0.166) Prostate(90;0.0959)|all_neural(102;0.223) AATGTCTGGTTTAATACTGAAG 0.248 NA NA NA 2023 0.403954 0.3321 0.6066 5008 , , NA 16743 0.3423 NA 0.4761 False NA ,,, NA NA NA 2504 0.3466 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 168 157.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AK000675 CCDS3806.1, CCDS54814.1 4q32.2 2013-01-09 2012-02-23 ENSG00000145416 55016 "MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers" 26077 protein-coding gene gene with protein product 613331 "membrane-associated ring finger (C3HC4) 1" NA 14722266 Standard NM_017923 NM_017923 NA Approved FLJ20668, MARCH-I, RNF171 uc003iqs.2 Q8TCQ1 ENST00000503008.1:c.*3115->TCAATACCATA chr4.hg19:g.164446785_164446786insTATGGTATTGA 1 3 ref NA False 48 48 PASS 0 PASS ref->het 0 NA 106,107 37,37 23,23 1 1 D3DP29|Q9NWR0 True hg19 CCDS54814.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MARCH1-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000364493.2 PASS NA None 168 NA True - TATGGTATTGA ENST00000503008.1 KIAA1430 0 __UNKNOWN__ __UNKNOWN__ 4 186081578 186081579 __UNKNOWN__ 3'UTR INS - - A rs34442501|rs397778634 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr4:186081578_186081579insA ENST00000458385.2 - 0 4091_4092 NM_020827.1 NP_065878.1 Q9P2B7 K1430_HUMAN NA NA NA endometrium(3)|kidney(2)|large_intestine(5)|upper_aerodigestive_tract(1) 11 all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243) all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165) TCATGTCCTTGAAATGAGAAGA 0.282 NA NA NA ?|AAA|AAAA|unsure 2527 0.504593 0.6566 0.4625 5008 , , NA 15127 0.3988 NA 0.504 False NA ,,, NA NA NA 2504 0.4387 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 211 204.04 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.25 NA NA NA NA NA ENST00000458385.2:c.*2374->T chr4.hg19:g.186081581_186081581dupA 4 3 ref NA False 39 39 PASS 3 PASS ref->het 0 NA 152,154 29,29 28,28 1 1 B3KRP7|D3DP60|Q05CU1|Q4W5M4|Q8N6E7|Q9UF45 True hg19 CCDS47168.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KIAA1430-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000360717.2 PASS NA None 211 NA True - A ENST00000458385.2 ADAMTS12 81792 __UNKNOWN__ __UNKNOWN__ 5 33561164 33561171 __UNKNOWN__ Frame_Shift_Del DEL AGGGACGG AGGGACGG - rs137953508|rs371245056 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:33561164_33561171delAGGGACGG ENST00000504830.1 - 20 4421_4428 c.4086_4093delCCGTCCCT c.(4084-4095)ctccgtccctgtfs p.RPC1363fs ADAMTS12_ENST00000352040.3_Frame_Shift_Del_p.RPC1278fs NM_030955.2 NP_112217.2 P58397 ATS12_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 12 1363 TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}. NA NA cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727) extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578) metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270) p.R1363C(1)|p.P1364S(1) NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5) 216 CAGCCAGCACAGGGACGGAGGTGGCATC 0.562 NA NA NA HNSCC(64;0.19) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 2 Substitution - Missense(2) upper_aerodigestive_tract(1)|lung(1) NA NA NA NA NA 381 366.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.65 AJ250725 CCDS34140.1 5q35 2008-07-18 2005-08-19 ENSG00000151388 ENSG00000151388 81792 "ADAM metallopeptidases with thrombospondin type 1 motif" 14605 protein-coding gene gene with protein product 606184 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12" NA 11279086 Standard NM_030955 NM_030955 NA Approved uc003jia.1 P58397 OTTHUMG00000162088 ENST00000504830.1:c.4086_4093delCCGTCCCT chr5.hg19:g.33561164_33561171delAGGGACGG ENSP00000422554:p.Arg1363fs 0 4 ref NA False 67 67 PASS 1 PASS ref->het 0 NA 276,277 69,69 55,56 1 1 A2RRN9|A5D6V6|Q6UWL3 True hg19 CCDS34140.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ADAMTS12-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000367164.2 PASS NA None 381 NA True - AGGGACGG ENST00000504830.1 RAD1 5810 __UNKNOWN__ __UNKNOWN__ 5 34915571 34915572 __UNKNOWN__ 5'UTR INS - - AGAGG LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:34915571_34915572insAGAGG ENST00000382038.2 - 0 1299_1300 BRIX1_ENST00000336767.5_5'UTR|RAD1_ENST00000341754.4_5'UTR NM_002853.3 NP_002844.1 O60671 RAD1_HUMAN RAD1 checkpoint DNA exonuclease NA NA NA cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|meiotic recombination checkpoint (GO:0051598)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|substantia nigra development (GO:0021762) chromosome (GO:0005694)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) 3'-5' exonuclease activity (GO:0008408)|damaged DNA binding (GO:0003684)|exodeoxyribonuclease III activity (GO:0008853) endometrium(3)|large_intestine(1)|lung(5)|urinary_tract(1) 10 all_lung(31;0.000107) Lung NSC(810;5.19e-05)|Ovarian(839;0.0448)|Breast(839;0.198) COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229) AAAGTCCCTGAAGAGGAGCGAG 0.649 NA NA NA Other conserved DNA damage response genes NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 338 319.32 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 19.79 AF074717 CCDS3905.1 5p13 2014-08-08 2014-08-08 ENSG00000113456 ENSG00000113456 5810 3.1.11.2 9806 protein-coding gene gene with protein product "exonuclease homolog RAD1", "checkpoint control protein HRAD1", "cell cycle checkpoint protein Hrad1", "Rad1-like DNA damage checkpoint", "DNA repair exonuclease REC1" 603153 "RAD1 (S. pombe) homolog", "RAD1 homolog (S. pombe)" NA 9716408, 9828137 Standard NM_002853 NR_026591 NA Approved HRAD1, REC1 uc003jix.3 O60671 OTTHUMG00000090783 ENST00000382038.2:c.-121->CCTCT chr5.hg19:g.34915572_34915576dupAGAGG 2 3 ref NA False 106 106 PASS 1 PASS ref->het 0 NA 221,237 42,46 75,55 1 1 O75572|O95304|Q1W161|Q5KSM0|Q5KSM1|Q9UEP1 True hg19 CCDS3905.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RAD1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000207567.1 PASS NA None 338 NA True - AGAGG ENST00000382038.2 DNAJC21 134218 __UNKNOWN__ __UNKNOWN__ 5 34929761 34929762 __UNKNOWN__ 5'UTR INS - - CCGCCGCCG rs574306683 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:34929761_34929762insCCGCCGCCG ENST00000342382.4 + 0 64_65 DNAJC21_ENST00000303525.7_5'UTR|DNAJC21_ENST00000382021.2_5'UTR Q5F1R6 DJC21_HUMAN DnaJ (Hsp40) homolog, subfamily C, member 21 NA NA NA protein folding (GO:0006457) ribosome (GO:0005840) poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270) breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(2)|upper_aerodigestive_tract(1) 21 all_lung(31;7.08e-05) COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229) GACCTACAccaccgccgccgcc 0.822 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 72 64 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.21 CCDS3907.2, CCDS34144.1 5p13-p12 2012-10-05 ENSG00000168724 ENSG00000168724 134218 "Heat shock proteins / DNAJ (HSP40)" 27030 protein-coding gene gene with protein product "JJJ1 DnaJ domain protein homolog (S. cerevisiae)" NA NA 15067379 Standard NM_194283 XM_005248250 NA Approved GS3, DNAJA5, JJJ1 uc003jjc.3 Q5F1R6 OTTHUMG00000074103 ENST00000342382.4:c.-163->CCGCCGCCG chr5.hg19:g.34929762_34929770dupCCGCCGCCG 11 4 ref NA False 30 30 PASS 8 PASS ref->het 0 NA 22,22 6,7 42,41 1 1 Q3B7J9|Q6P086|Q6ZS43|Q86VC6 True hg19 CCDS34144.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DNAJC21-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000157337.1 PASS NA None 72 NA True + CCG ENST00000342382.4 NLN 57486 __UNKNOWN__ __UNKNOWN__ 5 65120266 65120266 __UNKNOWN__ 3'UTR DEL A A - rs149227729 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:65120266delA ENST00000380985.5 + 0 3816 NLN_ENST00000502464.1_3'UTR NM_020726.4 NP_065777.1 Q9BYT8 NEUL_HUMAN neurolysin (metallopeptidase M3 family) NA NA NA mitochondrion (GO:0005739)|plasma membrane (GO:0005886) metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277) central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1) 26 Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186) UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616) TTCTCTTCCCACACACTCACT 0.428 NA NA NA -|A|-|insertion 547 0.109225 0.2587 0.062 5008 , , NA 14979 0.002 NA 0.0557 False NA ,,, NA NA NA 2504 0.1063 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 306 285.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AJ300837 CCDS3989.1 5q12.3 2008-02-05 2005-03-31 ENSG00000123213 ENSG00000123213 57486 3.4.24.16 16058 protein-coding gene gene with protein product 611530 "angiotensin binding protein" AGTBP NA 10574462 Standard NM_020726 NA Approved KIAA1226 uc003juf.3 Q9BYT8 OTTHUMG00000097803 ENST00000380985.5:c.*1523A>- chr5.hg19:g.65120266delA 0 4 ref NA False 50 50 PASS 1 PASS ref->het 0 NA 234,235 41,41 30,30 1 1 Q9ULJ4 True hg19 CCDS3989.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NLN-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000215060.1 PASS NA None 306 NA True + A ENST00000380985.5 NLN 57486 __UNKNOWN__ __UNKNOWN__ 5 65124780 65124781 __UNKNOWN__ 3'UTR INS - - C rs199653320 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:65124780_65124781insC ENST00000380985.5 + 0 8330_8331 NLN_ENST00000502464.1_3'UTR NM_020726.4 NP_065777.1 Q9BYT8 NEUL_HUMAN neurolysin (metallopeptidase M3 family) NA NA NA mitochondrion (GO:0005739)|plasma membrane (GO:0005886) metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277) central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1) 26 Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186) UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616) GAGGTTAATTACCGGTTTTCTG 0.416 NA NA NA CC|CC|CCC|insertion 153 0.0305511 0.084 0.013 5008 , , NA 20447 0.002 NA 0.0099 False NA ,,, NA NA NA 2504 0.0215 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 117 107.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AJ300837 CCDS3989.1 5q12.3 2008-02-05 2005-03-31 ENSG00000123213 ENSG00000123213 57486 3.4.24.16 16058 protein-coding gene gene with protein product 611530 "angiotensin binding protein" AGTBP NA 10574462 Standard NM_020726 NA Approved KIAA1226 uc003juf.3 Q9BYT8 OTTHUMG00000097803 ENST00000380985.5:c.*6038->C chr5.hg19:g.65124782_65124782dupC 3 2 ref NA False 42 42 PASS 2 PASS ref->het 0 NA 77,79 18,18 19,17 1 1 Q9ULJ4 True hg19 CCDS3989.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NLN-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000215060.1 PASS NA None 117 NA True + C ENST00000380985.5 MSH3 4437 __UNKNOWN__ __UNKNOWN__ 5 79950709 79950717 __UNKNOWN__ In_Frame_Del DEL GCAGCGGCC GCAGCGGCC - rs144776112|rs201874762|rs2431220|rs201906899 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:79950709_79950717delGCAGCGGCC ENST00000265081.6 + 1 243_251 c.163_171delGCAGCGGCC c.(163-171)gcagcggccdel p.AAA58del DHFR_ENST00000439211.2_5'UTR NM_002439.4 NP_002430.3 P20585 MSH3_HUMAN mutS homolog 3 58 Poly-Ala. NA Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8942985}. NA ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447) membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634) ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403) NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 29 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) Tgcagcggctgcagcggccgcagcggccg 0.694 NA NA NA Mismatch excision repair (MMR) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Melanoma(88;1010 1399 13793 26548 36275) PASS NA NA NA 0 NA NA NA NA NA 354 353.17 NA , 841,2699 NA 233,375,1162 NA NA NA , NA 0.1 NA dbSNP_100 9 1241,5749 NA 368,505,2622 no coding,utr-5 DHFR,MSH3 NM_002439.3,NM_000791.3 , 601,880,3784 A1A1,A1R,RR NA 17.7539,23.7571,19.7721 , , NA 2082,8448 NA NA NA SO:0001651 inframe_deletion 0 U61981 CCDS34195.1 5q11-q12 2013-09-12 2013-09-12 ENSG00000113318 ENSG00000113318 4437 7326 protein-coding gene gene with protein product "Divergent upstream protein", "Mismatch repair protein 1" 600887 "mutS (E. coli) homolog 3", "mutS homolog 3 (E. coli)" NA Standard NM_002439 NM_002439 NA Approved DUP, MRP1 uc003kgz.4 P20585 OTTHUMG00000162540 ENST00000265081.6:c.163_171delGCAGCGGCC chr5.hg19:g.79950718_79950726delGCAGCGGCC ENSP00000265081:p.Ala58_Ala60del 1 3 ref NA False 256 169 PASS 2 PASS ref->het 0 NA 166,167 75,75 110,109 1 1 A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867 True hg19 CCDS34195.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MSH3-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000369471.1 PASS NA None 354 NA True + GCAGCGGCC ENST00000265081.6 RASA1 5921 __UNKNOWN__ __UNKNOWN__ 5 86563775 86563776 __UNKNOWN__ 5'UTR INS - - A rs397841595|rs3840522|rs199648902 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:86563775_86563776insA ENST00000274376.6 + 0 71_72 NM_002890.2 NP_002881.1 P20936 RASA1_HUMAN RAS p21 protein activator (GTPase activating protein) 1 NA NA NA blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570) cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726) glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102) NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1) 48 all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423) OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31) CTTGCCCCCCCACCCCTCTCAT 0.639 NA NA NA 1210 0.241613 0.149 0.147 5008 , , NA 8415 0.4097 NA 0.1779 False NA ,,, NA NA NA 2504 0.3262 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 53 58.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.31 CCDS34200.1, CCDS47243.1 5q13 2013-02-14 ENSG00000145715 ENSG00000145715 5921 "Pleckstrin homology (PH) domain containing", "SH2 domain containing" 9871 protein-coding gene gene with protein product "capillary malformation-arteriovenous malformation" 139150 RASA NA 15917201 Standard NM_002890 NM_022650 NA Approved GAP, CM-AVM, p120GAP, p120RASGAP uc003kiw.3 P20936 OTTHUMG00000162605 ENST00000274376.6:c.-493->A chr5.hg19:g.86563776_86563776dupA 2 11 ref NA False 61 61 PASS 1 PASS ref->het 0 NA 26,27 12,14 17,14 1 1 B2R6W3|Q9UDI1 True hg19 CCDS34200.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RASA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000369729.1 PASS NA None 53 NA True + A ENST00000274376.6 ARRDC3 57561 __UNKNOWN__ __UNKNOWN__ 5 90665573 90665574 __UNKNOWN__ 3'UTR INS - - ACA rs201912294|rs200438683 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:90665573_90665574insACA ENST00000265138.3 - 0 3154_3155 NM_020801.2 NP_065852.1 Q96B67 ARRD3_HUMAN arrestin domain containing 3 NA NA NA fat pad development (GO:0060613)|negative regulation of heat generation (GO:0031651)|negative regulation of locomotion involved in locomotory behavior (GO:0090327)|negative regulation of multicellular organismal metabolic process (GO:0044252)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|skin development (GO:0043588)|temperature homeostasis (GO:0001659) endosome (GO:0005768)|plasma membrane (GO:0005886) beta-3 adrenergic receptor binding (GO:0031699) breast(2)|endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1) 18 all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207) OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22) CCTTCTAAAATacaacaacaac 0.342 NA NA NA 40 0.00798722 8e-04 0.0173 5008 , , NA 18871 0.0198 NA 0.004 False NA ,,, NA NA NA 2504 0.0031 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 142 136.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AB037797 CCDS34202.1 5q14.3 2013-10-11 ENSG00000113369 ENSG00000113369 57561 29263 protein-coding gene gene with protein product "alpha-arrestin 3" 612464 NA 10718198, 19605364 Standard NM_020801 NM_020801 NA Approved KIAA1376 uc003kjz.2 Q96B67 OTTHUMG00000162616 ENST00000265138.3:c.*1644->TGT chr5.hg19:g.90665580_90665582dupACA 8 5 ref NA False 63 63 PASS 7 PASS ref->het 0 NA 79,80 26,26 37,37 2 2 A8K6T8|Q9P2H1 True hg19 CCDS34202.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARRDC3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000369763.2 PASS NA None 142 NA True - ACA ENST00000265138.3 LNPEP 4012 __UNKNOWN__ __UNKNOWN__ 5 96332086 96332086 __UNKNOWN__ Intron DEL C C - rs398050568|rs3836862 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:96332086delC ENST00000231368.5 + 7 2099 LNPEP_ENST00000395770.3_Intron NM_005575.2 NP_005566.2 Q9UIQ6 LCAP_HUMAN leucyl/cystinyl aminopeptidase NA NA NA antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508) cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886) aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270) breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1) 34 all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244) COAD - Colon adenocarcinoma(37;0.072) TGTTTTCTCTCCCCCCAGTGG 0.358 NA NA NA CCCCC|CCCCCC|CCCCC|insertion 3045 0.608027 0.6006 0.6801 5008 , , NA 14117 0.6071 NA 0.5865 False NA ,,, NA NA NA 2504 0.59 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 389 347.17 NA NA 45 45 45 NA NA 5 NA NA NA 96332086 2163 4192 6355 SO:0001627 intron_variant 0.02 D50810 CCDS4087.1, CCDS43346.1 5q15 2011-07-25 ENSG00000113441 ENSG00000113441 4012 3.4.11.3 6656 protein-coding gene gene with protein product "cystinyl aminopeptidase", "placental leucine aminopeptidase" 151300 NA 8550619 Standard NM_005575 NM_175920 NA Approved CAP, PLAP, P-LAP uc003kmw.1 Q9UIQ6 OTTHUMG00000128719 ENST00000231368.5:c.1408-8C>- chr5.hg19:g.96332086delC 5 7 ref NA False 77 77 PASS 6 PASS ref->het 0 NA 293,294 62,63 37,36 1 1 O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7 True hg19 CCDS4087.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LNPEP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250624.1 PASS NA None 389 NA True + C ENST00000231368.5 NREP 9315 __UNKNOWN__ __UNKNOWN__ 5 111065696 111065697 __UNKNOWN__ 3'UTR INS - - AAAG rs397760057|rs60068753|rs112695340 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:111065696_111065697insAAAG ENST00000379671.3 - 0 1392_1393 NREP_ENST00000257435.7_3'UTR|NREP_ENST00000509025.1_Intron|NREP_ENST00000395634.3_3'UTR|STARD4-AS1_ENST00000500779.2_RNA|NREP_ENST00000446294.2_3'UTR|NREP_ENST00000447165.2_3'UTR NM_001142478.1 NP_001135950.1 Q16612 NREP_HUMAN neuronal regeneration related protein NA NA NA axon regeneration (GO:0031103)|regulation of neuron differentiation (GO:0045664)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015) cytoplasm (GO:0005737)|nucleus (GO:0005634) NA AGAAAGAACCCAAAGAGACACC 0.386 NA NA NA 1849 0.369209 0.7103 0.3213 5008 , , NA 18527 0.3393 NA 0.1918 False NA ,,, NA NA NA 2504 0.1554 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 388 396.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF119859 CCDS4105.1, CCDS47255.1 5q22.1 2012-12-07 2012-12-07 2012-01-23 ENSG00000134986 ENSG00000134986 9315 16834 protein-coding gene gene with protein product "neuronal protein 3.1" 607332 "chromosome 5 open reading frame 13", "neuronal regeneration related protein homolog (rat)" C5orf13 NA 8261136, 10981724, 15485502 Standard NM_004772 NM_004772 NA Approved P311, D4S114, PRO1873, PTZ17, SEZ17 uc011cvr.2 Q16612 OTTHUMG00000128795 ENST00000379671.3:c.*922->CTTT chr5.hg19:g.111065697_111065700dupAAAG 2 4 ref NA False 73 73 PASS 1 PASS ref->het 0 NA 295,297 46,46 40,40 1 1 B2RDN8|B7Z5D2|D3DSZ8 True hg19 CCDS4105.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NREP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250722.1 PASS NA None 388 NA True - AAAG ENST00000379671.3 NREP 9315 __UNKNOWN__ __UNKNOWN__ 5 111066240 111066241 __UNKNOWN__ 3'UTR INS - - GT rs138896342 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:111066240_111066241insGT ENST00000379671.3 - 0 848_849 NREP_ENST00000257435.7_3'UTR|NREP_ENST00000509025.1_Intron|NREP_ENST00000395634.3_3'UTR|STARD4-AS1_ENST00000500779.2_RNA|NREP_ENST00000515855.1_3'UTR|NREP_ENST00000446294.2_3'UTR|NREP_ENST00000447165.2_3'UTR|STARD4-AS1_ENST00000513221.1_RNA NM_001142478.1 NP_001135950.1 Q16612 NREP_HUMAN neuronal regeneration related protein NA NA NA axon regeneration (GO:0031103)|regulation of neuron differentiation (GO:0045664)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015) cytoplasm (GO:0005737)|nucleus (GO:0005634) NA AAAAGGTGGGGGGGGGACTCTC 0.436 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 157 190.95 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 8.39 AF119859 CCDS4105.1, CCDS47255.1 5q22.1 2012-12-07 2012-12-07 2012-01-23 ENSG00000134986 ENSG00000134986 9315 16834 protein-coding gene gene with protein product "neuronal protein 3.1" 607332 "chromosome 5 open reading frame 13", "neuronal regeneration related protein homolog (rat)" C5orf13 NA 8261136, 10981724, 15485502 Standard NM_004772 NM_004772 NA Approved P311, D4S114, PRO1873, PTZ17, SEZ17 uc011cvr.2 Q16612 OTTHUMG00000128795 ENST00000379671.3:c.*378->AC chr5.hg19:g.111066240_111066241insGT 1 11 ref NA False 58 58 PASS 0 PASS ref->het 0 NA 82,102 23,23 85,69 1 1 B2RDN8|B7Z5D2|D3DSZ8 True hg19 CCDS4105.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NREP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000250722.1 PASS NA None 157 NA True - GT ENST00000379671.3 SEMA6A 57556 __UNKNOWN__ __UNKNOWN__ 5 115780204 115780205 __UNKNOWN__ 3'UTR INS - - AAC rs3832329|rs531926313|rs149831771|rs397840724|rs572418224 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:115780204_115780205insAAC ENST00000343348.6 - 0 5984_5985 NM_020796.3 NP_065847 Q9H2E6 SEM6A_HUMAN sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A NA NA NA apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526) axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887) transmembrane signaling receptor activity (GO:0004888) central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 31 all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203) OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151) CTGTTTAAAAAAACAACAACAA 0.337 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 153 148.71 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AB037789 CCDS47256.1, CCDS75288.1 5q23.1 2014-07-29 ENSG00000092421 57556 "Semaphorins" 10738 protein-coding gene gene with protein product "sema VIa" 605885 SEMAQ NA 9204478, 10993894 Standard NM_020796 XM_006714663 NA Approved KIAA1368, SEMA6A1, SEMA, HT018 uc010jck.3 Q9H2E6 OTTHUMG00000162987 ENST00000343348.6:c.*2105->GTT chr5.hg19:g.115780211_115780213dupAAC 5 9 ref NA False 34 34 PASS 4 PASS ref->het 0 NA 102,105 23,23 27,28 2 2 Q9P2H9 True hg19 CCDS47256.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SEMA6A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000371270.1 PASS NA None 153 NA True - AAC ENST00000343348.6 Unknown 0 __UNKNOWN__ __UNKNOWN__ 5 134363154 134363154 __UNKNOWN__ IGR DEL G G - rs33940950|rs540173459 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:134363154delG NA CATSPER3 (15762 upstream) : PITX1 (270 downstream) NA NA NA NA CGCGGAGGGAGGGGGTTCTCG 0.701 NA NA NA GGGGG|GGGGG|GGGG|deletion 899 0.179513 0.4554 0.2061 5008 , , NA 16531 0.001 NA 0.1064 False NA ,,, NA NA NA 2504 0.047 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 520 486.92 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.5 NA NA NA NA NA chr5.hg19:g.134363154delG 4 8 ref NA False 40 40 PASS 5 PASS ref->het 0 NA 398,410 49,51 68,55 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 520 NA True G ARAP3 64411 __UNKNOWN__ __UNKNOWN__ 5 141052542 141052543 __UNKNOWN__ Intron INS - - T rs5871781|rs397881551 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:141052542_141052543insT ENST00000508305.1 - 7 1109 ARAP3_ENST00000239440.4_Intron|ARAP3_ENST00000513878.1_Intron Q8WWN8 ARAP3_HUMAN ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3 NA NA NA cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192) cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726) ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270) NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1) 53 CACAGCCTCCCTCCCTCCTGCC 0.624 NA NA NA T|T|TT|insertion 219 0.04373 0.0454 0.0346 5008 , , NA 13571 0.0526 NA 0.0447 False NA ,,, NA NA NA 2504 0.0378 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 261 253.54 NA 172,4092 NA 2,168,1962 NA NA NA -1.2 0 NA dbSNP_114 59 342,7912 NA 7,328,3792 no intron ARAP3 NM_022481.5 9,496,5754 A1A1,A1R,RR NA 4.1434,4.0338,4.1061 NA 514,12004 NA NA NA SO:0001627 intron_variant 0 AJ310567 CCDS4266.1 5q31.3 2013-01-11 2008-09-22 2008-09-22 ENSG00000120318 ENSG00000120318 64411 "ADP-ribosylation factor GTPase activating proteins", "Sterile alpha motif (SAM) domain containing", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing" 24097 protein-coding gene gene with protein product 606647 "centaurin, delta 3" CENTD3 NA 11804589, 12015138 Standard NM_022481 XM_005268497 NA Approved FLJ21065, DRAG1 uc003llm.3 Q8WWN8 OTTHUMG00000129610 ENST00000508305.1:c.859+36->A chr5.hg19:g.141052543_141052543dupT 2 6 ref NA False 56 56 PASS 1 PASS ref->het 0 NA 178,179 43,43 39,38 1 1 B4DIT1|D3DQE3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARAP3-002 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000373653.2 PASS NA None 261 NA True - T ENST00000508305.1 ERGIC1 57222 __UNKNOWN__ __UNKNOWN__ 5 172342029 172342030 __UNKNOWN__ Intron INS - - T rs397950731|rs35941893 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:172342029_172342030insT ENST00000523291.1 + 5 378 ERGIC1_ENST00000393784.3_Intron|ERGIC1_ENST00000326654.2_Frame_Shift_Ins_p.GF143fs Q969X5 ERGI1_HUMAN endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1 NA NA NA ER to Golgi vesicle-mediated transport (GO:0006888) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020) endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2) 9 Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594) Medulloblastoma(196;0.0399)|all_neural(177;0.0966) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) GCTCCCTGGGGTTTTAAGCCCC 0.609 NA NA NA TTTT|TTTT|TTTTT|insertion 782 0.15615 0.0817 0.1571 5008 , , NA 17386 0.1339 NA 0.2247 False NA ,,, NA NA NA 2504 0.2086 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 340 332.22 NA 377,3401 NA 37,303,1549 NA NA NA -3.6 0 NA dbSNP_126 34 1634,5632 NA 327,980,2326 no intron ERGIC1 NM_001031711.2 364,1283,3875 A1A1,A1R,RR NA 22.4883,9.9788,18.209 NA 2011,9033 NA NA NA SO:0001627 intron_variant 0.4 AF267855 CCDS34292.1 5q35.1 2009-11-06 ENSG00000113719 ENSG00000113719 57222 29205 protein-coding gene gene with protein product NA NA 10574461, 15308636 Standard NM_020462 NM_001031711 NA Approved ERGIC32, ERGIC-32, KIAA1181, NET24 uc003mbw.4 Q969X5 OTTHUMG00000130520 ENST00000523291.1:c.375+188->T chr5.hg19:g.172342033_172342033dupT 5 4 ref NA False 64 64 PASS 4 PASS ref->het 0 NA 255,259 43,43 40,38 1 1 Q9H0L0|Q9H2J2|Q9ULN9 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ERGIC1-013 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000329263.1 PASS NA None 340 NA True + T ENST00000523291.1 HNRNPH1 3187 __UNKNOWN__ __UNKNOWN__ 5 179043993 179043994 __UNKNOWN__ Intron INS - - A rs71591434 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:179043993_179043994insA ENST00000356731.5 - 10 2653 HNRNPH1_ENST00000511300.2_Intron|HNRNPH1_ENST00000510411.1_Intron|HNRNPH1_ENST00000329433.6_Intron|HNRNPH1_ENST00000393432.4_Intron|HNRNPH1_ENST00000442819.2_Intron P31943 HNRH1_HUMAN heterogeneous nuclear ribonucleoprotein H1 (H) NA NA NA gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380) catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723) breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|skin(1) 14 AAGGTTAGCTTAAAAAAAAGAC 0.426 NA NA NA AAAAAAAA|AAAAAAAA|AAAAAAAAA|insertion 287 0.0573083 0.0091 0.0432 5008 , , NA 18168 0.0417 NA 0.0934 False NA ,,, NA NA NA 2504 0.1115 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 248 263.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 BC001348 CCDS4446.1 5q35.3 2013-02-12 2008-04-18 ENSG00000169045 ENSG00000169045 3187 "RNA binding motif (RRM) containing" 5041 protein-coding gene gene with protein product 601035 HNRPH1 NA 7499401 Standard NM_005520 NM_005520 NA Approved hnRNPH uc003mkf.5 P31943 OTTHUMG00000130908 ENST00000356731.5:c.1118-34->T chr5.hg19:g.179044001_179044001dupA 9 9 ref NA False 46 46 PASS 8 PASS ref->het 0 NA 193,195 26,26 28,27 1 1 B3KW86|D3DWQ2|Q6IBM4 True hg19 CCDS4446.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HNRNPH1-001 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000253497.3 PASS NA None 248 NA True - A ENST00000356731.5 GFPT2 9945 __UNKNOWN__ __UNKNOWN__ 5 179780293 179780301 __UNKNOWN__ 5'UTR DEL CTCCGTGGG CTCCGTGGG - rs373706173|rs202171607|rs199818683 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr5:179780293_179780301delCTCCGTGGG ENST00000253778.8 - 0 86_94 NM_005110.2 NP_005101.1 O94808 GFPT2_HUMAN glutamine-fructose-6-phosphate transaminase 2 NA NA NA carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048) cytosol (GO:0005829) carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360) breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2) 34 all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137) Medulloblastoma(196;0.0392)|all_neural(177;0.0529) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) L-Glutamine(DB00130) ccgtgggctcctccgtgggctccgtgggc 0.751 NA NA NA 1538 0.307109 0.3767 0.3401 5008 , , NA 6807 0.1944 NA 0.3678 False NA ,,, NA NA NA 2504 0.2434 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 106 99.49 NA 550,662 NA 241,68,297 NA NA NA NA 0 NA dbSNP_114 6 1363,2331 NA 501,361,985 no utr-5 GFPT2 NM_005110.2 742,429,1282 A1A1,A1R,RR NA 36.8977,45.3795,38.9931 NA 1913,2993 NA NA NA SO:0001623 5_prime_UTR_variant 0.8 AB016789 CCDS43411.1 5q 2008-07-18 ENSG00000131459 ENSG00000131459 9945 4242 protein-coding gene gene with protein product "glutamine: fructose-6-phosphate aminotransferase 2" 603865 NA 10198162 Standard NM_005110 NM_005110 NA Approved GFAT2 uc003mlw.1 O94808 OTTHUMG00000163442 ENST00000253778.8:c.-84CCCACGGAG>- chr5.hg19:g.179780302_179780310delCTCCGTGGG 2 4 ref NA False 61 61 PASS 3 PASS ref->het 0 NA 54,57 21,21 38,36 1 1 Q53XM2|Q9BWS4 True hg19 CCDS43411.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GFPT2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000373444.4 PASS NA None 106 NA True - CTCCGTGGG ENST00000253778.8 SSR1 6745 __UNKNOWN__ __UNKNOWN__ 6 7295301 7295301 __UNKNOWN__ Intron DEL A A - rs35998405 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:7295301delA ENST00000244763.4 - 7 880 SSR1_ENST00000474597.1_Intron|SSR1_ENST00000479365.1_Intron|RP11-69L16.4_ENST00000379928.4_RNA|SSR1_ENST00000489567.1_Intron|SSR1_ENST00000534851.1_Intron|SSR1_ENST00000397511.2_Intron NM_003144.3 NP_003135.2 P43307 SSRA_HUMAN signal sequence receptor, alpha NA NA NA activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|positive regulation of cell proliferation (GO:0008284)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021) NS(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(1) 9 Ovarian(93;0.0398) AAAAACCATTAAAAAAATTAA 0.323 NA NA NA ?|AAAAAAA|AAAAAA|unsure 1230 0.245607 0.2973 0.1844 5008 , , NA 14536 0.1617 NA 0.2266 False NA ,,, NA NA NA 2504 0.3252 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 629 581.48 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS4499.1 6p24.3 2010-11-24 2008-08-26 ENSG00000124783 ENSG00000124783 6745 11323 protein-coding gene gene with protein product "translocon-associated protein alpha" 600868 NA Standard NM_001292008 NA Approved TRAPA uc003mxf.4 P43307 OTTHUMG00000014202 ENST00000244763.4:c.793+323T>- chr6.hg19:g.7295301delA 6 7 ref NA False 121 120 PASS 7 PASS ref->het 0 NA 462,463 105,105 62,62 1 1 A8K685|Q53GX2|Q53H19|Q5TAM3|Q6IB43|Q8NBH9|Q96IA2|Q9TNQ8|Q9UN49 True hg19 CCDS4499.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SSR1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000039775.2 PASS NA None 629 NA True - A ENST00000244763.4 ACOT13 55856 __UNKNOWN__ __UNKNOWN__ 6 24667405 24667407 __UNKNOWN__ 5'UTR DEL TCC TCC - rs17243150|rs202090405|rs28364821 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:24667405_24667407delTCC ENST00000230048.4 + 0 107_109 ACOT13_ENST00000537591.1_5'UTR NM_018473.3 NP_060943.1 Q9NPJ3 ACO13_HUMAN acyl-CoA thioesterase 13 NA NA NA metabolic process (GO:0008152)|protein homotetramerization (GO:0051289) cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634) acyl-CoA hydrolase activity (GO:0047617) large_intestine(1) 1 GCCCTTTGTGTCCTCCTTCTTTC 0.591 NA NA NA OREG0017230 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 314 0.0626997 0.1218 0.0288 5008 , , NA 16327 0.0655 NA 0.0427 False NA ,,, NA NA NA 2504 0.0245 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 476 511.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.83 AF220186 CCDS4558.1, CCDS54972.1 6p22.1 2009-11-20 2009-05-05 2009-05-05 ENSG00000112304 ENSG00000112304 55856 "Acyl CoA thioesterases" 20999 protein-coding gene gene with protein product 615652 "thioesterase superfamily member 2" THEM2 NA 16934754, 19405909 Standard NM_018473 NM_018473 NA Approved HT012 uc003nek.3 Q9NPJ3 OTTHUMG00000014359 ENST00000230048.4:c.-85TCC>- chr6.hg19:g.24667408_24667410delTCC 1 4 ref 773 False 101 101 PASS 2 PASS ref->het 0 NA 361,368 58,58 56,53 1 1 F5H2L4|O95549 True hg19 CCDS4558.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACOT13-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000040010.2 PASS NA None 476 NA True + TCC ENST00000230048.4 ZSCAN12 9753 __UNKNOWN__ __UNKNOWN__ 6 28349845 28349864 __UNKNOWN__ 3'UTR DEL CAAGCTATAAGTGATCCTCC CAAGCTATAAGTGATCCTCC - rs70983940|rs373360241|rs3832424|rs369210512 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:28349845_28349864delCAAGCTATAAGTGATCCTCC ENST00000361028.1 - 0 2362_2381 ZSCAN12_ENST00000396827.3_Intron O43309 ZSC12_HUMAN zinc finger and SCAN domain containing 12 NA NA NA transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) breast(2)|endometrium(3)|urinary_tract(1) 6 TTTTGCTAGTCAAGCTATAAGTGATCCTCCCAAGCTTTCC 0.427 NA NA NA 1418 0.283147 0.4811 0.2478 5008 , , NA 22029 0.1607 NA 0.2406 False NA ,,, NA NA NA 2504 0.2106 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 270 254.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.18 AB007886 6p21 2013-01-08 2007-02-20 2007-02-20 ENSG00000158691 ENSG00000158691 9753 "-", "Zinc fingers, C2H2-type" 13172 protein-coding gene gene with protein product 603978 "zinc finger protein 305", "zinc finger protein 96" ZNF305, ZNF96 NA 9244436 Standard NM_014724 NM_001163391 NA Approved KIAA0426, ZNF29K1, ZFP96, dJ29K1.2 uc011dlh.2 O43309 OTTHUMG00000014522 ENST00000361028.1:c.*421GGAGGATCACTTATAGCTTG>- chr6.hg19:g.28349845_28349864delCAAGCTATAAGTGATCCTCC 0 5 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 270,274 13,13 31,29 1 1 O43724 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZSCAN12-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000040190.1 PASS NA None 270 NA True - CAAGCTATAAGTGATCCTCC ENST00000361028.1 OR2H2 7932 __UNKNOWN__ __UNKNOWN__ 6 29556681 29556686 __UNKNOWN__ 3'UTR DEL TTTAAA TTTAAA - rs188661866 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:29556681_29556686delTTTAAA ENST00000383640.2 + 0 999_1004 GABBR1_ENST00000355973.3_Intron NM_007160.3 NP_009091.3 O95918 OR2H2_HUMAN olfactory receptor, family 2, subfamily H, member 2 NA NA NA defense response (GO:0006952)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|mating (GO:0007618) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984) central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1) 14 CTTAATGTGCTTTAAAAGAGAGGAGA 0.471 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 348 339.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.68 CCDS34365.1 6p22.2-p21.31 2012-08-09 ENSG00000204657 7932 "GPCR / Class A : Olfactory receptors" 8253 protein-coding gene gene with protein product 600578 NA Standard XM_005249407 NA Approved hs6M1-12 uc003nmr.1 O95918 ENST00000383640.2:c.*26TTTAAA>- chr6.hg19:g.29556681_29556686delTTTAAA 0 5 ref NA False 46 46 PASS 1 PASS ref->het 0 NA 280,283 51,51 26,26 1 1 Q15062|Q2M1Y3|Q5STL8|Q5SUK1|Q6IFN7|Q6NTB7|Q96R14 True hg19 CCDS34365.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OR2H2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076057.2 PASS NA None 348 NA True + TTTAAA ENST00000383640.2 Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 29893292 29893293 __UNKNOWN__ IGR DEL CG CG - rs544866553|rs199548039|rs75006454 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:29893292_29893293delCG NA HLA-G (94390 upstream) : HLA-A (15743 downstream) NA NA NA NA CATATAGTAACGCAGTGTGCTA 0.455 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 218 190.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr6.hg19:g.29893292_29893293delCG 0 2 ref NA False 77 77 PASS 1 PASS ref->het 0 NA 152,153 40,40 25,24 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 218 NA True CG Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 29896126 29896127 __UNKNOWN__ IGR INS - - G rs571568833 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:29896126_29896127insG NA HLA-G (97224 upstream) : HLA-A (12909 downstream) NA NA NA NA AGATGAGTGGAGGGGGGGTCAT 0.599 NA NA NA g???gggggg|GGGGGGG|GGGGGGGG|cryptic_indel 118 0.0235623 0.0144 0.0187 5008 , , NA 14266 0.005 NA 0.0417 False NA ,,, NA NA NA 2504 0.0399 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 115 107.58 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 4.58 NA NA NA NA NA chr6.hg19:g.29896133_29896133dupG 8 9 ref NA False 54 54 PASS 7 PASS ref->het 0 NA 69,76 19,24 29,19 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 115 NA True G HLA-A 3105 __UNKNOWN__ __UNKNOWN__ 6 29910421 29910421 __UNKNOWN__ Intron DEL A A - rs9278464|rs386698548 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:29910421delA ENST00000396634.1 + 3 414 HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Intron|HLA-A_ENST00000376806.5_Intron P16189 1A31_HUMAN major histocompatibility complex, class I, A NA NA NA antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032) cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886) beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977) central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2) 30 CGGGGTCGGGAGGGAAACCGC 0.746 NA NA NA Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of Multiple Myeloma(9;0.094) a|A|-|deletion 738 0.147364 0.1831 0.1412 5008 , , NA 11673 0.1349 NA 0.1123 False NA ,,, NA NA NA 2504 0.1524 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 102 114.42 NA 689,3539 NA 47,595,1472 12 15 14 1 0 6 dbSNP_118 16 857,7331 NA 44,769,3281 no intron HLA-A NM_002116.7 91,1364,4753 A1A1,A1R,RR NA 10.4665,16.2961,12.4517 29910421 1546,10870 2145 4249 6394 SO:0001627 intron_variant 10.92 Familial Cancer Database Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial D32129 CCDS34373.1 6p21.3 2013-01-11 ENSG00000206503 ENSG00000206503 3105 "Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing" 4931 protein-coding gene gene with protein product 142800 NA 8838351 Standard NM_002116 NM_001242758 NA Approved uc003nol.3 P01891 OTTHUMG00000130501 ENST00000396634.1:c.73+18A>- chr6.hg19:g.29910421delA 0 6 ref NA False 91 90 PASS 1 PASS ref->het 0 NA 37,63 22,36 42,5 1 1 O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7 True hg19 CCDS34373.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HLA-A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252909.1 PASS NA None 102 NA True + A ENST00000396634.1 HCG17 414778 __UNKNOWN__ __UNKNOWN__ 6 30228399 30228399 __UNKNOWN__ lincRNA DEL G G - rs573355170|rs371252667 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:30228399delG ENST00000453558.1 - 0 126 HLA-L_ENST00000463348.1_RNA HLA complex group 17 (non-protein coding) NA NA NA NA CAGGGGCCACGGGGGCGCCTC 0.627 NA NA NA GGGG|GGGGG|GGGG|insertion 1991 0.397564 0.3003 0.4496 5008 , , NA 15675 0.5308 NA 0.2465 False NA ,,, NA NA NA 2504 0.5102 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 203 196.88 NA 1052,2672 NA 201,650,1011 29 29 29 1.6 0 6 dbSNP_126 14 1746,5536 NA 325,1096,2220 no intergenic 526,1746,3231 A1A1,A1R,RR NA 23.9769,28.2492,25.4225 30228399 2798,8208 1506 2702 4208 0 AB023055 6p21 2012-11-02 2008-08-13 ENSG00000241701 ENSG00000270604 414778 "Long non-coding RNAs" 31339 non-coding RNA RNA, long non-coding "non-protein coding RNA 46", "long intergenic non-protein coding RNA 46" NA NA Standard NR_052012 NR_052012 NA Approved NCRNA00046, LINC00046 uc031snc.1 OTTHUMG00000031114 ENST00000453558.1: chr6.hg19:g.30228399delG 4 6 ref NA False 35 35 PASS 5 PASS ref->het 0 NA 156,157 26,26 23,22 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HCG17-002 KNOWN basic|exp_conf lincRNA NA lincRNA OTTHUMT00000256054.1 PASS NA None 203 NA True - G ENST00000453558.1 HLA-C 3107 __UNKNOWN__ __UNKNOWN__ 6 31239151 31239151 __UNKNOWN__ Intron DEL A A - rs67420880|rs373379283 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:31239151delA ENST00000376228.5 - 3 358 HLA-C_ENST00000383329.3_Intron NM_002117.5 NP_002108.4 Q95604 1C17_HUMAN major histocompatibility complex, class I, C NA NA NA antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032) cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886) peptide antigen binding (GO:0042605) central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1) 17 CGGTCAGCCCAGTCCCCCGAG 0.701 NA NA NA ?|A|-|unsure 179 0.0357428 0.0817 0.0274 5008 , , NA 7582 0.001 NA 0.0447 False NA ,,, NA NA NA 2504 0.0061 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 96 142.76 NA NA 4 5 5 NA NA 6 NA NA NA 31239151 1833 3750 5583 SO:0001627 intron_variant 3.31 M11886 CCDS34393.1 6p21.3 2014-01-30 ENSG00000204525 ENSG00000204525 3107 "Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing" 4933 protein-coding gene gene with protein product 142840 "psoriasis susceptibility 1" HLA-JY3, D6S204, PSORS1 NA 3863816, 16642438 Standard NM_002117 NM_001243042 NA Approved uc003nsy.3 P04222 OTTHUMG00000031154 ENST00000376228.5:c.344-26T>- chr6.hg19:g.31239151delA 0 3 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 43,56 14,14 33,20 1 1 O02864|O02958|Q29643|Q9MY30 True hg19 CCDS34393.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HLA-C-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076281.3 PASS NA None 96 NA True - A ENST00000376228.5 HLA-B 3106 __UNKNOWN__ __UNKNOWN__ 6 31323525 31323527 __UNKNOWN__ Intron DEL CTC CTC - rs145440646|rs41552017|rs34032483 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:31323525_31323527delCTC ENST00000412585.2 - 4 648 NM_005514.6 NP_005505.2 P30486 1B48_HUMAN major histocompatibility complex, class I, B NA NA NA antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032) cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612) peptide antigen binding (GO:0042605) endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2) 27 CTGGGATAATCTCCTATTCATTG 0.567 NA NA NA Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of 452 0.0902556 0.0605 0.1585 5008 , , NA 19002 0.0804 NA 0.1143 False NA ,,, NA NA NA 2504 0.0675 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 223 223.63 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.01 Familial Cancer Database ;Lichen Sclerosis, Familial M15470 CCDS34394.1 6p21.3 2013-01-11 ENSG00000234745 ENSG00000234745 3106 "Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing" 4932 protein-coding gene gene with protein product 142830 "ankylosing spondylitis" AS NA 3459708 Standard NM_005514 NM_005514 NA Approved uc011imz.2 P01889 OTTHUMG00000031153 ENST00000412585.2:c.620-156GAG>- chr6.hg19:g.31323525_31323527delCTC 0 3 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 182,187 23,23 26,24 1 1 Q29764 True hg19 CCDS34394.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HLA-B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076280.4 PASS NA None 223 NA True - CTC ENST00000412585.2 HLA-B 3106 __UNKNOWN__ __UNKNOWN__ 6 31324247 31324248 __UNKNOWN__ Intron INS - - C rs374975243 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:31324247_31324248insC ENST00000412585.2 - 3 372 NM_005514.6 NP_005505.2 P30486 1B48_HUMAN major histocompatibility complex, class I, B NA NA NA antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032) cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612) peptide antigen binding (GO:0042605) endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2) 27 GTCAGCCCAGTCCCCCGAGCCC 0.718 NA NA NA Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 97 140.36 NA 582,1944 NA 212,158,893 NA NA NA http://www.ncbi.nlm.nih.gov/sites/varvu?gene 0.1 0 NA dbSNP_114 4 1409,4223 NA 447,515,1854 no intron HLA-B NM_005514.6 659,673,2747 A1A1,A1R,RR NA 25.0178,23.0404,24.4055 NA 1991,6167 NA NA NA SO:0001627 intron_variant 15.12 Familial Cancer Database ;Lichen Sclerosis, Familial M15470 CCDS34394.1 6p21.3 2013-01-11 ENSG00000234745 ENSG00000234745 3106 "Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing" 4932 protein-coding gene gene with protein product 142830 "ankylosing spondylitis" AS NA 3459708 Standard NM_005514 NM_005514 NA Approved uc011imz.2 P01889 OTTHUMG00000031153 ENST00000412585.2:c.344-28->G chr6.hg19:g.31324252_31324252dupC 6 5 ref NA False 83 83 PASS 5 PASS ref->het 0 NA 39,54 24,27 37,20 1 1 Q29764 True hg19 CCDS34394.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HLA-B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076280.4 PASS NA None 97 NA True - C ENST00000412585.2 HSPA1B 3304 __UNKNOWN__ __UNKNOWN__ 6 31797769 31797770 __UNKNOWN__ 3'UTR INS - - AAGTT rs548786990|rs9281590|rs77674559 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:31797769_31797770insAAGTT ENST00000375650.3 + 0 2258_2259 NM_005346.4 NP_005337.2 P08107 HSP71_HUMAN heat shock 70kDa protein 1B NA NA NA ATP catabolic process (GO:0006200)|cellular heat acclimation (GO:0070370)|cellular response to heat (GO:0034605)|gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of inclusion body assembly (GO:0090084)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of erythrocyte differentiation (GO:0045648)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070) aggresome (GO:0016235)|blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|inclusion body (GO:0016234)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982) ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|protein N-terminus binding (GO:0047485)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|virus receptor activity (GO:0001618) breast(1)|large_intestine(1)|prostate(1) 3 ACTTCTTTGTAAAGTTGTAACC 0.376 NA NA NA 2253 0.44988 0.7095 0.428 5008 , , NA 17933 0.2619 NA 0.3658 False NA ,,, NA NA NA 2504 0.3947 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 349 341.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.89 CCDS34415.1 6p21.3 2011-09-02 2002-08-29 ENSG00000204388 ENSG00000204388 3304 "Heat shock proteins / HSP70" 5233 protein-coding gene gene with protein product 603012 "heat shock 70kD protein 1B" NA 1700760 Standard NM_005346 NA Approved HSP70-2 uc003nxk.2 P08107 OTTHUMG00000031202 ENST00000375650.3:c.*117->AAGTT chr6.hg19:g.31797770_31797774dupAAGTT 2 3 ref NA False 65 65 PASS 1 PASS ref->het 0 NA 256,258 37,37 52,52 1 1 B4E3B6|P19790|Q5JQI4|Q5SP17|Q9UQL9|Q9UQM0 True hg19 CCDS34415.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HSPA1B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000076402.2 PASS NA None 349 NA True + AAGTT ENST00000375650.3 CPNE5 57699 __UNKNOWN__ __UNKNOWN__ 6 36789940 36789941 __UNKNOWN__ Intron INS - - G rs72550148|rs3842097 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:36789940_36789941insG ENST00000244751.2 - 3 761 NM_020939.1 NP_065990.1 Q9HCH3 CPNE5_HUMAN copine V NA NA NA extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025) central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(4)|liver(1)|lung(9)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 25 ACGCACACTGCGGGGGGAGGAG 0.589 NA NA NA GGGGGG|GGGGGG|GGGGGGG|insertion 901 0.179912 0.0136 0.2305 5008 , , NA 20862 0.3204 NA 0.2505 False NA ,,, NA NA NA 2504 0.1513 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 267 250.2 NA 234,3996 NA 17,200,1898 NA NA NA -9.8 0 NA dbSNP_107 61 2121,6039 NA 319,1483,2278 no intron CPNE5 NM_020939.1 336,1683,4176 A1A1,A1R,RR NA 25.9926,5.5319,19.0073 NA 2355,10035 NA NA NA SO:0001627 intron_variant 0.15 H09181 CCDS4825.1 6p21.2 2010-05-28 ENSG00000124772 ENSG00000124772 57699 2318 protein-coding gene gene with protein product 604209 NA 9430674 Standard NM_020939 NM_020939 NA Approved CPN5, COPN5, KIAA1599 uc003omr.1 Q9HCH3 OTTHUMG00000014602 ENST00000244751.2:c.137-4->C chr6.hg19:g.36789946_36789946dupG 7 8 ref NA False 30 30 PASS 6 PASS ref->het 0 NA 211,214 29,29 25,23 1 1 Q7Z6C8 True hg19 CCDS4825.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CPNE5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000040351.1 PASS NA None 267 NA True - G ENST00000244751.2 CNPY3 10695 __UNKNOWN__ __UNKNOWN__ 6 42896948 42896949 __UNKNOWN__ 5'UTR INS - - CTC rs562972889|rs76992623 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:42896948_42896949insCTC ENST00000372836.4 + 0 11_12 NM_006586.3 NP_006577.2 Q9BT09 CNPY3_HUMAN canopy FGF signaling regulator 3 NA NA NA innate immune response (GO:0045087)|toll-like receptor signaling pathway (GO:0002224) endoplasmic reticulum lumen (GO:0005788) central_nervous_system(1)|endometrium(1)|lung(3)|ovary(1) 6 Colorectal(47;0.196) all cancers(41;0.000954)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388) GCAGGCTTCTTCTCGGGTCTTG 0.619 NA NA NA 3123 0.623602 0.9644 0.4741 5008 , , NA 14690 0.3988 NA 0.492 False NA ,,, NA NA NA 2504 0.636 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 122 134.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 U80744 CCDS4875.1 6p21.1 2013-09-19 2013-07-23 2007-10-22 ENSG00000137161 ENSG00000137161 10695 "Trinucleotide (CAG) repeat containing" 11968 protein-coding gene gene with protein product 610774 "trinucleotide repeat containing 5", "canopy 3 homolog (zebrafish)" TNRC5 NA 9225980 Standard NM_006586 NM_006586 NA Approved CAG4A uc003ota.4 Q9BT09 OTTHUMG00000014708 ENST00000372836.4:c.-360->CTC chr6.hg19:g.42896949_42896951dupCTC 2 4 ref NA False 47 47 PASS 1 PASS ref->het 0 NA 84,86 22,22 17,16 2 2 O15412|Q0P6I2|Q8NF54|Q8WTU8|Q9P0F2 True hg19 CCDS4875.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CNPY3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000040564.1 PASS NA None 122 NA True + CTC ENST00000372836.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 80580068 80580079 __UNKNOWN__ IGR DEL TTAGTTCCTCTG TTAGTTCCTCTG - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:80580068_80580079delTTAGTTCCTCTG NA AL132875.1 (43466 upstream) : RP1-92C4.2 (1510 downstream) NA NA NA NA TCTTGGAATTTTAGTTCCTCTGTTAAACTTAG 0.443 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 309 312.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.86 NA NA NA NA NA chr6.hg19:g.80580068_80580079delTTAGTTCCTCTG 0 4 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 283,286 18,18 35,32 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 309 NA True TTAGTTCCTCTG UBE2J1 51465 __UNKNOWN__ __UNKNOWN__ 6 90062329 90062330 __UNKNOWN__ 5'UTR INS - - A rs578129743 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:90062329_90062330insA ENST00000435041.2 - 0 237_238 NM_016021.2 NP_057105.2 Q9Y385 UB2J1_HUMAN ubiquitin-conjugating enzyme E2, J1 NA NA NA ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021) acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524) NS(1)|breast(2)|kidney(1)|large_intestine(2)|lung(11)|stomach(1) 18 all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238) BRCA - Breast invasive adenocarcinoma(108;0.0139) GGGCCGCTGCCACCTCCTCTCC 0.743 NA NA NA A|A|AA|insertion 17 0.00339457 8e-04 0.0014 5008 , , NA 10448 0 NA 0.0129 False NA ,,, NA NA NA 2504 0.002 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 292 272.29 NA 15,4113 NA 0,15,2049 NA NA NA 3 0.3 NA 9 170,7812 NA 15,140,3836 no utr-5 UBE2J1 NM_016021.2 15,155,5885 A1A1,A1R,RR NA 2.1298,0.3634,1.5277 NA 185,11925 NA NA NA SO:0001623 5_prime_UTR_variant 0.15 AJ245898 CCDS5021.1 6q15 2014-01-28 2012-06-08 ENSG00000198833 ENSG00000198833 51465 "Ubiquitin-conjugating enzymes E2" 17598 protein-coding gene gene with protein product NA "ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)" NA 10708578 Standard NM_016021 NM_016021 NA Approved HSPC153, CGI-76, NCUBE1, UBC6 uc003pnc.3 Q9Y385 OTTHUMG00000016337 ENST00000435041.2:c.-42->T chr6.hg19:g.90062330_90062330dupA 2 4 ref NA False 103 103 PASS 1 PASS ref->het 0 NA 222,222 45,45 22,22 1 1 A8K3F9|Q53F25|Q5W0N4|Q9BZ32|Q9NQL3|Q9NY66|Q9P011|Q9P0S0|Q9UF10 True hg19 CCDS5021.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA UBE2J1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000043742.2 PASS NA None 292 NA True - A ENST00000435041.2 Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 90348480 90348481 __UNKNOWN__ IGR INS - - G rs397822836|rs57174507 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:90348480_90348481insG NA LYRM2 (8 upstream) : MDN1 (3736 downstream) NA NA NA NA GGAGCGGAAGTGGGGTTCGACC 0.668 NA NA NA GGGG|GGGG|GGGGG|insertion 825 0.164736 0.1286 0.1138 5008 , , NA 15859 0.0407 NA 0.2078 False NA ,,, NA NA NA 2504 0.3333 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 273 268.63 NA 539,3725 NA 39,461,1632 NA NA NA 3.6 0.9 NA dbSNP_129 50 1705,6549 NA 164,1377,2586 no near-gene-5 203,1838,4218 A1A1,A1R,RR NA 20.6567,12.6407,17.9262 NA 2244,10274 NA NA NA SO:0001628 intergenic_variant 0.29 NA NA NA NA NA chr6.hg19:g.90348484_90348484dupG 5 5 ref NA False 228 140 PASS 4 PASS ref->het 0 NA 139,140 85,86 44,42 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 273 NA True G CD164 8763 __UNKNOWN__ __UNKNOWN__ 6 109691554 109691555 __UNKNOWN__ Intron INS - - TA rs368060819|rs3831331 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:109691554_109691555insTA ENST00000310786.4 - 5 493 CD164_ENST00000324953.5_Intron|CD164_ENST00000506649.1_Intron|CD164_ENST00000413644.2_Intron|CD164_ENST00000504373.1_Intron|CD164_ENST00000275080.7_Intron|CD164_ENST00000368961.5_Intron|CD164_ENST00000512821.1_Intron NM_001142404.1|NM_006016.4 NP_001135876.1|NP_006007.2 Q04900 MUC24_HUMAN CD164 molecule, sialomucin NA NA NA cell adhesion (GO:0007155)|hemopoiesis (GO:0030097)|heterophilic cell-cell adhesion (GO:0007157)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|muscle organ development (GO:0007517)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165) endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886) breast(1)|lung(2) 3 all_cancers(87;4.65e-22)|all_epithelial(87;2.54e-20)|all_lung(197;1.6e-05)|Lung NSC(302;2.92e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.0175) Epithelial(106;7.83e-46)|all cancers(137;1.15e-45)|OV - Ovarian serous cystadenocarcinoma(136;2.89e-26)|BRCA - Breast invasive adenocarcinoma(108;0.00128)|GBM - Glioblastoma multiforme(226;0.16) GGCAGAAATTGTAAAGGGCAAC 0.411 NA NA NA 252 0.0503195 0.0129 0.0893 5008 , , NA 18663 0.0278 NA 0.0527 False NA ,,, NA NA NA 2504 0.0941 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 141 133.55 NA ,,,, 79,4185 NA 0,79,2053 NA NA NA ,,,, -0.5 0 NA dbSNP_107 108 462,7792 NA 18,426,3683 no intron,intron,intron,intron,intron CD164 NM_006016.4,NM_001142404.1,NM_001142403.1,NM_001142402.1,NM_001142401.1 ,,,, 18,505,5736 A1A1,A1R,RR NA 5.5973,1.8527,4.3218 ,,,, ,,,, NA 541,11977 NA NA NA SO:0001627 intron_variant 0 AF106518 CCDS5073.1, CCDS47462.1, CCDS47463.1, CCDS47464.1, CCDS47465.1 6q21 2014-09-05 2006-03-28 ENSG00000135535 ENSG00000135535 8763 "CD molecules" 1632 protein-coding gene gene with protein product 603356 "CD164 antigen, sialomucin" NA 9680353, 9763543 Standard NM_006016 NM_006016 NA Approved MUC-24, MGC-24 uc003pte.3 Q04900 OTTHUMG00000015339 ENST00000310786.4:c.427+58->TA chr6.hg19:g.109691555_109691556dupTA 2 3 ref NA False 70 70 PASS 1 PASS ref->het 0 NA 98,98 31,32 14,14 1 1 B4DQ85|E1P5E7|E1P5E8|E1P5E9|O95413|Q5JSU6|Q9BPV0|Q9NR26 True hg19 CCDS5073.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CD164-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041742.1 PASS NA None 141 NA True - TA ENST00000310786.4 SMPD2 6610 __UNKNOWN__ __UNKNOWN__ 6 109763948 109763948 __UNKNOWN__ Intron DEL C C - rs111892331|rs35444917|rs397888578 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:109763948delC ENST00000258052.3 + 7 850 NM_003080.2 NP_003071.2 O60906 NSMA_HUMAN sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase) NA NA NA apoptotic signaling pathway (GO:0097190)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|neurotrophin TRK receptor signaling pathway (GO:0048011)|response to mechanical stimulus (GO:0009612)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin metabolic process (GO:0006684) caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767) endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2) 8 all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548) Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566) CAACCTGGTTCCCCCAGCCAC 0.587 NA NA NA CCCCC|CCCCC|CCCC|deletion 1123 0.224241 0.5015 0.1744 5008 , , NA 19802 0.1032 NA 0.0785 False NA ,,, NA NA NA 2504 0.1595 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 102 113 NA 1812,2452 NA 382,1048,702 58 76 70 1.5 0 6 dbSNP_132 83 686,7568 NA 33,620,3474 no intron SMPD2 NM_003080.2 415,1668,4176 A1A1,A1R,RR NA 8.3111,42.4953,19.9553 109763948 2498,10020 2200 4299 6499 SO:0001627 intron_variant 0.5 AJ222801 CCDS5075.1 6q21 2009-10-23 ENSG00000135587 ENSG00000135587 6610 3.1.4.12 11121 protein-coding gene gene with protein product 603498 NA 9520418 Standard XM_005267109 NA Approved nSMase, ISC1 uc003pti.3 O60906 OTTHUMG00000015348 ENST00000258052.3:c.492-7C>- chr6.hg19:g.109763948delC 4 5 ref NA False 41 41 PASS 5 PASS ref->het 0 NA 68,68 24,25 12,11 1 1 Q5TED1|Q9BWR3 True hg19 CCDS5075.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SMPD2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041755.1 PASS NA None 102 NA True + C ENST00000258052.3 AK9 221264 __UNKNOWN__ __UNKNOWN__ 6 109849810 109849811 __UNKNOWN__ 3'UTR INS - - TGCAGT rs148271752 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:109849810_109849811insTGCAGT ENST00000355283.1 - 0 1519_1520 AK9_ENST00000424296.2_Intron|AK9_ENST00000341338.6_In_Frame_Ins_p.337_338insAT Q5TCS8 KAD9_HUMAN adenylate kinase 9 NA NA NA ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569) cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634) ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145) NA TGCTTTGTGCCTGCAGTTGCAG 0.431 NA NA NA 266 0.053115 0.034 0.0893 5008 , , NA 20886 0.0129 NA 0.0547 False NA ,,, NA NA NA 2504 0.093 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 308 284.61 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.44 AK131244, BC146443, BC087860 CCDS5077.1, CCDS55048.1 6q21 2013-04-29 2013-04-29 2013-04-29 221264 2.7.4.3 33814 protein-coding gene gene with protein product 615358 "chromosome 6 open reading frame 224", "adenylate kinase domain containing 2", "chromosome 6 open reading frame 199", "adenylate kinase domain containing 1" C6orf224, AKD2, C6orf199, AKD1 NA 23416111 Standard NM_001145128 NM_145025 NA Approved FLJ42177, FLJ25791, dJ70A9.1, MGC26954 Q5TCS8 ENST00000355283.1:c.*263->ACTGCA chr6.hg19:g.109849811_109849816dupTGCAGT 4 2 ref NA False 37 37 PASS 3 PASS ref->het 0 NA 201,202 36,36 69,68 1 1 A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AK9-001 NOVEL basic protein_coding NA protein_coding OTTHUMT00000349355.1 PASS NA None 308 NA True - TGCAGT ENST00000355283.1 CDC40 51362 __UNKNOWN__ __UNKNOWN__ 6 110551409 110551411 __UNKNOWN__ 3'UTR DEL TGA TGA - rs562527067|rs143209780 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:110551409_110551411delTGA ENST00000368932.1 + 0 1916_1918 CDC40_ENST00000368930.1_Intron|CDC40_ENST00000445340.2_Intron|CDC40_ENST00000307731.1_3'UTR O60508 PRP17_HUMAN cell division cycle 40 NA NA NA gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366) catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681) poly(A) RNA binding (GO:0044822) breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1) 18 all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488) Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034) taaatGTATCTGATGATAACTTG 0.256 NA NA NA 183 0.0365415 0.0038 0.0764 5008 , , NA 16014 0.001 NA 0.1083 False NA ,,, NA NA NA 2504 0.0153 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 57 62.55 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF015044 CCDS5081.1 6q22.1 2013-01-17 2013-01-17 ENSG00000168438 ENSG00000168438 51362 "WD repeat domain containing" 17350 protein-coding gene gene with protein product 605585 "cell division cycle 40 homolog (yeast)", "cell division cycle 40 homolog (S. cerevisiae)" NA 9769104, 9830021 Standard NM_015891 NM_015891 NA Approved PRP17, EHB3, PRPF17, FLJ10564 uc003pua.3 O60508 OTTHUMG00000015358 ENST00000368932.1:c.*77TGA>- chr6.hg19:g.110551412_110551414delTGA 1 2 ref NA False 34 34 PASS 2 PASS ref->het 0 NA 37,38 15,16 12,12 1 1 B2RBC5|O75471|Q5SRN0|Q9UPG1 True hg19 CCDS5081.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDC40-005 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041791.1 PASS NA None 57 NA True + TGA ENST00000368932.1 AMD1 262 __UNKNOWN__ __UNKNOWN__ 6 111216654 111216658 __UNKNOWN__ 3'UTR DEL TTTTG TTTTG - rs147095707|rs200800942|rs74922286 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:111216654_111216658delTTTTG ENST00000368885.3 + 0 3176_3180 AMD1_ENST00000368882.3_3'UTR|AMD1_ENST00000368876.1_3'UTR NM_001634.4 NP_001625.2 P17707 DCAM_HUMAN adenosylmethionine decarboxylase 1 NA NA NA cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|S-adenosylmethioninamine biosynthetic process (GO:0006557)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)|spermine biosynthetic process (GO:0006597) cytosol (GO:0005829) adenosylmethionine decarboxylase activity (GO:0004014) breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2) 8 all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209) OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143) S-Adenosylmethionine(DB00118) ttggttttgtttttgttttgttttg 0.327 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 46 50.02 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 M88006 CCDS5086.1, CCDS75504.1, CCDS75505.1 6q21 2014-05-13 ENSG00000123505 ENSG00000123505 262 4.1.1.50 457 protein-coding gene gene with protein product 180980 "S-adenosylmethionine decarboxylase 1" NA Standard NM_001634 NA Approved SAMDC uc003puk.1 P17707 OTTHUMG00000015369 ENST00000368885.3:c.*1839TTTTG>- chr6.hg19:g.111216664_111216668delTTTTG 4 9 ref NA False 40 40 PASS 5 PASS ref->het 0 NA 27,28 13,13 11,10 1 1 E1P5F7|Q5VXN4|Q5VXN6|Q9BWK4 True hg19 CCDS5086.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AMD1-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000041816.1 PASS NA None 46 NA True + TTTTG ENST00000368885.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 111279745 111279747 __UNKNOWN__ IGR DEL GAG GAG - rs3839364|rs35732925 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:111279745_111279747delGAG NA AMD1 (62829 upstream) : GTF3C6 (15 downstream) NA NA NA NA ACCGAGAAACGAGGAGGCCCGTG 0.709 NA NA NA 1072 0.214058 0.1929 0.1153 5008 , , NA 11618 0.256 NA 0.168 False NA ,,, NA NA NA 2504 0.317 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 167 156.95 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr6.hg19:g.111279748_111279750delGAG 1 4 ref NA False 288 186 PASS 2 PASS ref->het 0 NA 97,98 56,56 16,15 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 167 NA True GAG LAMA4 3910 __UNKNOWN__ __UNKNOWN__ 6 112438913 112438913 __UNKNOWN__ Intron DEL A A - rs3216857 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:112438913delA ENST00000230538.7 - 35 5379 LAMA4_ENST00000522006.1_Intron|LAMA4_ENST00000424408.2_Intron|LAMA4_ENST00000389463.4_Intron NM_001105206.2 NP_001098676.2 Q16363 LAMA4_HUMAN laminin, alpha 4 NA NA NA blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995) basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606) extracellular matrix structural constituent (GO:0005201) NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8) 100 all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209) all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242) GCATTTCATGACTCATATTTT 0.428 NA NA NA A|A|-|deletion 1148 0.229233 0.0393 0.2709 5008 , , NA 22488 0.3919 NA 0.1869 False NA ,,, NA NA NA 2504 0.3323 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 140 142.89 NA ,, 266,3998 NA 11,244,1877 105 89 94 ,, 3.5 0 6 dbSNP_106 103 1393,6861 NA 119,1155,2853 no intron,intron,intron LAMA4 NM_002290.3,NM_001105207.1,NM_001105206.1 ,, 130,1399,4730 A1A1,A1R,RR NA 16.8767,6.2383,13.2529 ,, ,, 112438913 1659,10859 2202 4277 6479 SO:0001627 intron_variant 0 CCDS34514.1, CCDS43491.1, CCDS43492.1 6q21 2014-09-17 ENSG00000112769 ENSG00000112769 3910 "Laminins" 6484 protein-coding gene gene with protein product 600133 NA 7959779 Standard NM_001105206 NM_001105206 NA Approved LAMA3 uc003pvu.3 Q16363 OTTHUMG00000015386 ENST00000230538.7:c.4981+28T>- chr6.hg19:g.112438913delA 0 2 ref NA False 55 55 PASS 1 PASS ref->het 0 NA 96,97 33,33 12,13 1 1 Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9 True hg19 CCDS43491.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LAMA4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000041876.2 PASS NA None 140 NA True - A ENST00000230538.7 TRDN 10345 __UNKNOWN__ __UNKNOWN__ 6 123778835 123778836 __UNKNOWN__ Intron INS - - AACTG rs71021450|rs143257093|rs144693987 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:123778835_123778836insAACTG ENST00000334268.4 - 10 1249 RP11-532N4.2_ENST00000418467.2_RNA|TRDN_ENST00000398178.3_Intron|RP11-532N4.2_ENST00000427828.1_RNA|RP11-532N4.2_ENST00000434768.1_RNA|RP11-532N4.2_ENST00000587049.1_RNA|RP11-532N4.2_ENST00000589182.1_RNA|RP11-532N4.2_ENST00000587106.2_RNA Q13061 TRDN_HUMAN triadin NA NA NA cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085) calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017) ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803) NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2) 41 GBM - Glioblastoma multiforme(226;0.184) TTTAACATATTAACTGAAAGAT 0.272 NA NA NA 583 0.116414 0.0091 0.0793 5008 , , NA 14751 0.0288 NA 0.1899 False NA ,,, NA NA NA 2504 0.3027 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 126 119.89 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 U18985 CCDS59035.1, CCDS75511.1 6q22.31 2008-05-15 ENSG00000186439 ENSG00000186439 10345 12261 protein-coding gene gene with protein product 603283 NA 7588753 Standard NM_001251987 NA Approved uc003pzj.2 Q13061 OTTHUMG00000015497 ENST00000334268.4:c.931+7214->CAGTT chr6.hg19:g.123778836_123778840dupAACTG 2 3 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 80,80 33,33 12,13 1 1 A5D6W5|F5H2W7|Q6NSB8 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRDN-001 KNOWN basic protein_coding NA protein_coding OTTHUMT00000042050.1 PASS NA None 126 NA True - AACTG ENST00000334268.4 HEBP2 23593 __UNKNOWN__ __UNKNOWN__ 6 138725317 138725318 __UNKNOWN__ Intron INS - - G rs11441776|rs397790604 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:138725317_138725318insG ENST00000448741.1 + 1 168 Q9Y5Z4 HEBP2_HUMAN heme binding protein 2 NA NA NA negative regulation of mitochondrial membrane potential (GO:0010917)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of necrotic cell death (GO:0010940) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739) endometrium(1)|large_intestine(1)|lung(3) 5 Breast(32;0.0933) GBM - Glioblastoma multiforme(68;0.000732)|OV - Ovarian serous cystadenocarcinoma(155;0.00171) GGGGCGGGGGCGGAAGTGCCTC 0.688 NA NA NA GGG|GG|GGG|deletion 961 0.191893 0.4818 0.1398 5008 , , NA 10032 0.1022 NA 0.0537 False NA ,,, NA NA NA 2504 0.0716 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 88 85.75 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.08 AF117616 CCDS5191.1 6q24 2008-08-29 2002-09-23 2002-09-27 ENSG00000051620 ENSG00000051620 23593 15716 protein-coding gene gene with protein product 605825 "chromosome 6 open reading frame 34" C6orf34 NA 10640688, 17098234 Standard NM_014320 NA Approved SOUL uc003qhw.1 Q9Y5Z4 OTTHUMG00000015671 ENST00000448741.1:c.135+482->G chr6.hg19:g.138725319_138725319dupG 3 7 ref NA False 39 39 PASS 2 PASS ref->het 0 NA 59,64 15,16 12,6 1 1 Q96P57 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HEBP2-004 PUTATIVE basic protein_coding NA protein_coding OTTHUMT00000348263.1 PASS NA None 88 NA True + G ENST00000448741.1 SASH1 23328 __UNKNOWN__ __UNKNOWN__ 6 148664242 148664243 __UNKNOWN__ In_Frame_Ins INS - - GAGCCC rs76317765|rs569482367 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:148664242_148664243insGAGCCC ENST00000367467.3 + 1 514_515 c.39_40insGAGCCC c.(40-42)gag>GAGCCCgag p.14_14E>EPE SASH1_ENST00000367469.1_Intron NM_015278.3 NP_056093.3 O94885 SASH1_HUMAN SAM and SH3 domain containing 1 14 Pro-rich. NA NA positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044) membrane (GO:0016020)|protein complex (GO:0043234) mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901) breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 52 Ovarian(120;0.0169) OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701) ggccggagcctgagcccgagcc 0.792 NA NA NA 393 0.0784744 0.0159 0.0879 5008 , , NA 6564 0.1151 NA 0.1571 False NA ,,, NA NA NA 2504 0.0378 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 108 141.1 NA 105,3589 NA 18,69,1760 NA NA NA -8.8 0 NA 7 1036,6366 NA 164,708,2829 no coding SASH1 NM_015278.3 182,777,4589 A1A1,A1R,RR NA 13.9962,2.8424,10.283 NA 1141,9955 NA NA NA SO:0001652 inframe_insertion 0.3 AB018333 CCDS5212.1 6q24.3 2013-01-10 ENSG00000111961 ENSG00000111961 23328 "SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing" 19182 protein-coding gene gene with protein product 607955 NA 9872452, 12771949 Standard NM_015278 NM_015278 NA Approved KIAA0790, dJ323M4.1, SH3D6A uc003qme.1 O94885 OTTHUMG00000015773 ENST00000367467.3:c.46_51dupGAGCCC chr6.hg19:g.148664243_148664248dupGAGCCC ENSP00000356437:p.ProGlu22dup 3 2 ref NA False 62 62 PASS 2 PASS ref->het 0 NA 74,76 23,23 15,13 2 2 Q5TGN5|Q8TAI0|Q9H7R7 True hg19 CCDS5212.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SASH1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000042619.1 PASS NA None 108 NA True + GAGCCC ENST00000367467.3 SASH1 23328 __UNKNOWN__ __UNKNOWN__ 6 148835437 148835437 __UNKNOWN__ Intron DEL T T - rs145246370|rs201901289 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:148835437delT ENST00000367467.3 + 9 1204 NM_015278.3 NP_056093.3 O94885 SASH1_HUMAN SAM and SH3 domain containing 1 NA NA NA positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044) membrane (GO:0016020)|protein complex (GO:0043234) mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901) breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 52 Ovarian(120;0.0169) OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701) CCTGATTAACTTTTTCCTTTG 0.498 NA NA NA TTTT|TTTTT|TTTT|insertion 1367 0.272963 0.2216 0.2983 5008 , , NA 16426 0.1825 NA 0.4026 False NA ,,, NA NA NA 2504 0.2843 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 120 112.42 NA NA 46 38 40 NA NA 6 NA NA NA 148835437 2195 4261 6456 SO:0001627 intron_variant 0 AB018333 CCDS5212.1 6q24.3 2013-01-10 ENSG00000111961 ENSG00000111961 23328 "SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing" 19182 protein-coding gene gene with protein product 607955 NA 9872452, 12771949 Standard NM_015278 NM_015278 NA Approved KIAA0790, dJ323M4.1, SH3D6A uc003qme.1 O94885 OTTHUMG00000015773 ENST00000367467.3:c.730-23T>- chr6.hg19:g.148835437delT 4 5 ref NA False 53 53 PASS 5 PASS ref->het 0 NA 87,89 16,16 18,16 2 2 Q5TGN5|Q8TAI0|Q9H7R7 True hg19 CCDS5212.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SASH1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000042619.1 PASS NA None 120 NA True + T ENST00000367467.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 6 154831796 154831796 __UNKNOWN__ IGR DEL A A - rs146668281 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:154831796delA NA CNKSR3 (3 upstream) : SCAF8 (222662 downstream) NA NA NA NA GCAAAGTTTCAGCTCCGGTTG 0.706 NA NA NA A|A|-|deletion 659 0.131589 0.152 0.1225 5008 , , NA 12856 0.119 NA 0.175 False NA ,,, NA NA NA 2504 0.0787 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 71 66.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr6.hg19:g.154831796delA 0 3 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 56,57 9,9 7,6 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 71 NA True A MAP3K4 4216 __UNKNOWN__ __UNKNOWN__ 6 161413044 161413045 __UNKNOWN__ In_Frame_Ins INS - - CCG rs369151355|rs569609736 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:161413044_161413045insCCG ENST00000392142.4 + 1 229_230 c.81_82insCCG c.(82-84)ccg>CCGccg p.28_28P>PP RP3-428L16.2_ENST00000608721.1_RNA|MAP3K4_ENST00000366920.2_In_Frame_Ins_p.28_28P>PP|MAP3K4_ENST00000348824.7_In_Frame_Ins_p.28_28P>PP|MAP3K4_ENST00000366919.2_In_Frame_Ins_p.28_28P>PP NM_005922.2 NP_005913 Q9Y6R4 M3K4_HUMAN mitogen-activated protein kinase kinase kinase 4 28 Poly-Pro. NA NA activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225) cytoplasm (GO:0005737) ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872) breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1) 77 Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771) OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05) Agccgccgccaccgccgccgcc 0.738 NA NA NA 185 0.0369409 0.0083 0.0303 5008 , , NA 9103 0.0288 NA 0.0487 False NA ,,, NA NA NA 2504 0.0767 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 181 188.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001652 inframe_insertion 0.32 AF002715 CCDS34565.1, CCDS34566.1, CCDS75544.1 6q26 2012-10-02 ENSG00000085511 ENSG00000085511 4216 "Mitogen-activated protein kinase cascade / Kinase kinase kinases" 6856 protein-coding gene gene with protein product 602425 MEKK4 NA 9305639 Standard XM_005266988 NA Approved MTK1, MAPKKK4, KIAA0213 uc003qtn.3 Q9Y6R4 OTTHUMG00000015968 ENST00000392142.4:c.91_93dupCCG chr6.hg19:g.161413051_161413053dupCCG ENSP00000375986:p.Pro36dup 5 4 ref NA False 64 64 PASS 4 PASS ref->het 0 NA 127,127 20,21 35,34 1 1 A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408 True hg19 CCDS34565.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAP3K4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000042988.3 PASS NA None 181 NA True + CCG ENST00000392142.4 THBS2 7058 __UNKNOWN__ __UNKNOWN__ 6 169616259 169616261 __UNKNOWN__ 3'UTR DEL AAC AAC - rs35009372|rs200915200|rs148174605 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:169616259_169616261delAAC ENST00000366787.3 - 0 5424_5426 XXyac-YX65C7_A.2_ENST00000444188.1_RNA NM_003247.2 NP_003238.2 P35442 TSP2_HUMAN thrombospondin 2 NA NA NA cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965) basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091) calcium ion binding (GO:0005509)|heparin binding (GO:0008201) NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1) 111 Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247) OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379) AGTGCAGCAAAACAACAACACAA 0.384 NA NA NA 1113 0.222244 0.2867 0.2205 5008 , , NA 20044 0.1518 NA 0.2048 False NA ,,, NA NA NA 2504 0.227 NA NA NA Esophageal Squamous(91;219 1934 18562 44706) PASS NA NA NA 0 NA NA NA NA NA 166 155.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 CCDS34574.1 6q27 2008-07-28 ENSG00000186340 ENSG00000186340 7058 11786 protein-coding gene gene with protein product 188061 NA 18455130 Standard NM_003247 NM_003247 NA Approved TSP2 uc003qwt.3 P35442 OTTHUMG00000045408 ENST00000366787.3:c.*1658GTT>- chr6.hg19:g.169616265_169616267delAAC 2 6 ref NA False 58 58 PASS 3 PASS ref->het 0 NA 132,134 16,16 19,19 1 1 A6H8N1|A7E232|Q5RI52 True hg19 CCDS34574.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA THBS2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000105439.1 PASS NA None 166 NA True - AAC ENST00000366787.3 THBS2 7058 __UNKNOWN__ __UNKNOWN__ 6 169616509 169616512 __UNKNOWN__ 3'UTR DEL AAAC AAAC - rs398049010|rs55724365 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr6:169616509_169616512delAAAC ENST00000366787.3 - 0 5173_5176 XXyac-YX65C7_A.2_ENST00000444188.1_RNA NM_003247.2 NP_003238.2 P35442 TSP2_HUMAN thrombospondin 2 NA NA NA cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965) basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091) calcium ion binding (GO:0005509)|heparin binding (GO:0008201) NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1) 111 Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247) OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379) TAAAGCAAaaaaacaaaccaacca 0.363 NA NA NA 1112 0.222045 0.2859 0.2205 5008 , , NA 26119 0.1518 NA 0.2048 False NA ,,, NA NA NA 2504 0.227 NA NA NA Esophageal Squamous(91;219 1934 18562 44706) PASS NA NA NA 0 NA NA NA NA NA 75 83.49 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.04 CCDS34574.1 6q27 2008-07-28 ENSG00000186340 ENSG00000186340 7058 11786 protein-coding gene gene with protein product 188061 NA 18455130 Standard NM_003247 NM_003247 NA Approved TSP2 uc003qwt.3 P35442 OTTHUMG00000045408 ENST00000366787.3:c.*1408GTTT>- chr6.hg19:g.169616513_169616516delAAAC 1 10 ref NA False 30 30 PASS 2 PASS ref->het 0 NA 58,60 10,10 11,10 1 1 A6H8N1|A7E232|Q5RI52 True hg19 CCDS34574.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA THBS2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000105439.1 PASS NA None 75 NA True - AAAC ENST00000366787.3 INTS1 26173 __UNKNOWN__ __UNKNOWN__ 7 1543476 1543477 __UNKNOWN__ Intron INS - - CCCCAAAGAC rs145605530|rs142464192|rs11283071|rs544389785 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:1543476_1543477insCCCCAAAGAC ENST00000404767.3 - 2 144 INTS1_ENST00000389470.4_Intron NM_001080453.2 NP_001073922.2 Q8N201 INT1_HUMAN integrator complex subunit 1 NA NA NA inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474) integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020) autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 62 Ovarian(82;0.0253) UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15) GCAGCTGAGATccccaaagacc 0.668 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 132 130.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.14 AB037861 CCDS47526.1 7p22.3 2009-11-06 ENSG00000164880 ENSG00000164880 26173 24555 protein-coding gene gene with protein product 611345 NA 16239144 Standard NM_001080453 NA Approved DKFZp586J0619, KIAA1440, INT1, NET28 uc003skn.2 Q8N201 OTTHUMG00000151449 ENST00000404767.3:c.58+61->GTCTTTGGGG chr7.hg19:g.1543477_1543486dupCCCCAAAGAC 4 4 ref NA False 76 76 PASS 3 PASS ref->het 0 NA 62,63 19,19 52,51 1 1 A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8 True hg19 CCDS47526.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA INTS1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000323683.1 PASS NA None 132 NA True - CCCCAAAGAC ENST00000404767.3 OCM 654231 __UNKNOWN__ __UNKNOWN__ 7 5922100 5922101 __UNKNOWN__ Intron INS - - T rs66509786|rs35069590 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:5922100_5922101insT ENST00000242104.5 + 2 153 OCM_ENST00000416608.1_Intron NM_001097622.1 NP_001091091.1 P0CE72 ONCO_HUMAN oncomodulin NA NA NA calcium ion binding (GO:0005509) endometrium(1)|large_intestine(3)|lung(2) 6 Ovarian(82;0.0694) UCEC - Uterine corpus endometrioid carcinoma (126;0.0978)|OV - Ovarian serous cystadenocarcinoma(56;2.11e-14) CAAGCGTCAGAATAACCAATTC 0.431 NA NA NA -|-|T|insertion 1430 0.285543 0.0272 0.2723 5008 , , NA 20057 0.4921 NA 0.2972 False NA ,,, NA NA NA 2504 0.4192 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 206 194.5 NA 315,3949 NA 14,287,1831 NA NA NA -0.2 0 NA dbSNP_126 103 2466,5788 NA 378,1710,2039 no intron OCM NM_001097622.1 392,1997,3870 A1A1,A1R,RR NA 29.8764,7.3874,22.216 NA 2781,9737 NA NA NA SO:0001627 intron_variant 0 BC069468 CCDS43548.1 7p22.1 2013-01-10 654231 "EF-hand domain containing" 8105 protein-coding gene gene with protein product "oncomodulin 1" 164795 NA 1559707, 8354278 Standard NM_001097622 NM_001097622 NA Approved OCM1 uc003spe.4 P0CE72 ENST00000242104.5:c.62-23->T chr7.hg19:g.5922100_5922101insT 1 4 ref NA False 36 36 PASS 0 PASS ref->het 0 NA 149,149 34,34 23,23 1 1 B9EJH7|P32930|Q6ISI5|Q75MW0 True hg19 CCDS43548.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OCM-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000340372.1 PASS NA None 206 NA True + T ENST00000242104.5 NUPL2 11097 __UNKNOWN__ __UNKNOWN__ 7 23221797 23221798 __UNKNOWN__ In_Frame_Ins INS - - CGGCAGCAACCG rs200880793|rs371896223 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:23221797_23221798insCGGCAGCAACCG ENST00000410002.3 + 1 141_142 c.93_94insCGGCAGCAACCG c.(94-96)cgg>CGGCAGCAACCGcgg p.32_32R>RQQPR NUPL2_ENST00000258742.5_In_Frame_Ins_p.32_32R>RQQPR|AC005082.1_ENST00000366347.4_Intron|NUPL2_ENST00000487595.1_3'UTR O15504 NUPL2_HUMAN nucleoporin like 2 32 NA NA carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032) cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634) metal ion binding (GO:0046872)|nuclear export signal receptor activity (GO:0005049)|poly(A) RNA binding (GO:0044822) breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 19 CAGGAGGAGGACGGCAGCAACC 0.649 NA NA NA 62 0.0123802 0.0015 0.0303 5008 , , NA 15515 0 NA 0.0368 False NA ,,, NA NA NA 2504 0.002 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 425 429.51 NA 35,4229 NA 1,33,2098 NA NA NA 0 1 NA 54 407,7847 NA 9,389,3729 no coding NUPL2 NM_007342.2 10,422,5827 A1A1,A1R,RR NA 4.9309,0.8208,3.5309 NA 442,12076 NA NA NA SO:0001652 inframe_insertion 0.93 U97198 CCDS5379.1 7p15 2003-08-07 ENSG00000136243 ENSG00000136243 11097 17010 protein-coding gene gene with protein product "nucleoporin-like protein 1" NA NA 10358091, 9450185 Standard NM_007342 NM_007342 NA Approved NLP_1, CG1, hCG1, H_RG271G13.9 uc003svu.3 O15504 OTTHUMG00000096955 ENST00000410002.3:c.94_105dupCGGCAGCAACCG chr7.hg19:g.23221797_23221798insCGGCAGCAACCG Exception_encountered 2 2 ref NA False 69 69 PASS 1 PASS ref->het 0 NA 301,304 27,27 90,88 1 1 A4D143|B4DP42|Q49AE7|Q9BS49 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NUPL2-008 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000327180.1 PASS NA None 425 NA True + CGGCAGCAACCG ENST00000410002.3 RP11-467H10.2 0 __UNKNOWN__ __UNKNOWN__ 7 76748904 76748911 __UNKNOWN__ RNA DEL ACTTCTAC ACTTCTAC - rs532069120|rs559307267|rs529620224|rs73705179|rs139039802 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:76748904_76748911delACTTCTAC ENST00000459742.1 + 0 58 NA NA NA NA AATACTTTGAACTTCTACACAGCCAGAC 0.341 NA NA NA 1326 0.264776 0.1861 0.3674 5008 , , NA 18791 0.2917 NA 0.164 False NA ,,, NA NA NA 2504 0.3742 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 567 518.41 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.33 NA NA NA NA NA ENST00000459742.1: chr7.hg19:g.76748904_76748911delACTTCTAC 0 2 ref NA False 54 54 PASS 1 PASS ref->het 0 NA 522,524 19,21 40,38 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-467H10.2-001 KNOWN basic|readthrough_transcript processed_transcript NA processed_transcript OTTHUMT00000473089.1 PASS NA None 567 NA True + ACTTCTAC ENST00000459742.1 PDK4 5166 __UNKNOWN__ __UNKNOWN__ 7 95214609 95214609 __UNKNOWN__ 3'UTR DEL T T - rs3214118|rs201711605|rs397708336 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:95214609delT ENST00000005178.5 - 0 1777 NM_002612.3 NP_002603.1 Q16654 PDK4_HUMAN pyruvate dehydrogenase kinase, isozyme 4 NA NA NA cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281) mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739) ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740) endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1) 15 all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151) STAD - Stomach adenocarcinoma(171;0.0151) AATATCAGTCTTAGTGAAACT 0.353 NA NA NA T|TT|T|insertion 2782 0.555511 0.5923 0.3343 5008 , , NA 19149 0.8631 NA 0.4483 False NA ,,, NA NA NA 2504 0.456 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 443 414.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.84 U54617 CCDS5643.1 7q21.3-q22.1 2008-07-18 2005-11-16 ENSG00000004799 ENSG00000004799 5166 8812 protein-coding gene gene with protein product 602527 "pyruvate dehydrogenase kinase, isoenzyme 4" NA 7499431 Standard NM_002612 NM_002612 NA Approved uc003uoa.3 Q16654 OTTHUMG00000153977 ENST00000005178.5:c.*344A>- chr7.hg19:g.95214609delT 1 3 ref NA False 55 55 PASS 2 PASS ref->het 0 NA 348,350 66,66 27,27 2 2 True hg19 CCDS5643.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PDK4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000333298.1 PASS NA None 443 NA True - T ENST00000005178.5 PDK4 5166 __UNKNOWN__ __UNKNOWN__ 7 95225786 95225787 __UNKNOWN__ 5'UTR INS - - AG rs553835966|rs111789210 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:95225786_95225787insAG ENST00000005178.5 - 0 16_17 NM_002612.3 NP_002603.1 Q16654 PDK4_HUMAN pyruvate dehydrogenase kinase, isozyme 4 NA NA NA cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281) mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739) ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740) endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1) 15 all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151) STAD - Stomach adenocarcinoma(171;0.0151) AGAGTCTGGGCAGAGTCGGAGA 0.673 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 119 107.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.38 U54617 CCDS5643.1 7q21.3-q22.1 2008-07-18 2005-11-16 ENSG00000004799 ENSG00000004799 5166 8812 protein-coding gene gene with protein product 602527 "pyruvate dehydrogenase kinase, isoenzyme 4" NA 7499431 Standard NM_002612 NM_002612 NA Approved uc003uoa.3 Q16654 OTTHUMG00000153977 ENST00000005178.5:c.-182->CT chr7.hg19:g.95225789_95225790dupAG 3 3 ref NA False 35 35 PASS 2 PASS ref->het 0 NA 87,89 17,18 14,13 1 1 True hg19 CCDS5643.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PDK4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000333298.1 PASS NA None 119 NA True - AG ENST00000005178.5 Unknown 0 __UNKNOWN__ __UNKNOWN__ 7 138916202 138916202 __UNKNOWN__ IGR DEL A A - rs139437904 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:138916202delA NA TTC26 (39470 upstream) : UBN2 (28 downstream) NA NA NA NA CGCCGGCTCGAGCAAAAGCGG 0.682 NA NA NA 28 0.00559105 0 0.0043 5008 , , NA 12306 0 NA 0.0229 False NA ,,, NA NA NA 2504 0.002 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 570 525.67 NA 8,2350 NA 1,6,1172 4 5 5 3.3 0.6 7 dbSNP_134 5 80,4532 NA 13,54,2239 no near-gene-5 14,60,3411 A1A1,A1R,RR NA 1.7346,0.3393,1.2626 138916202 88,6882 619 1504 2123 SO:0001628 intergenic_variant 0.32 NA NA NA NA NA chr7.hg19:g.138916202delA 0 2 ref NA False 113 113 PASS 1 PASS ref->het 0 NA 427,436 80,81 64,55 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 570 NA True A TPK1 27010 __UNKNOWN__ __UNKNOWN__ 7 144532829 144532830 __UNKNOWN__ Intron INS - - G rs111798915 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:144532829_144532830insG ENST00000360057.3 - 2 87 TPK1_ENST00000378099.3_Intron NM_022445.3 NP_071890.2 Q9H3S4 TPK1_HUMAN thiamin pyrophosphokinase 1 NA NA NA small molecule metabolic process (GO:0044281)|thiamine diphosphate biosynthetic process (GO:0009229)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767) cytosol (GO:0005829) ATP binding (GO:0005524)|kinase activity (GO:0016301)|thiamine binding (GO:0030975)|thiamine diphosphokinase activity (GO:0004788) large_intestine(3)|lung(12)|ovary(2)|urinary_tract(2) 19 Thiamine(DB00152) TCCGGGACCCAGGAGCCAGCTG 0.703 NA NA NA GG|GG|GGG|insertion 1393 0.278155 0.4569 0.3184 5008 , , NA 8102 0.0486 NA 0.3757 False NA ,,, NA NA NA 2504 0.1442 NA NA NA Ovarian(45;88 1034 2073 5829 28455) PASS NA NA NA 0 NA NA NA NA NA 159 161.26 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 4.41 AB028138 CCDS5888.1, CCDS55178.1 7q34-q35 2008-07-18 ENSG00000196511 ENSG00000196511 27010 17358 protein-coding gene gene with protein product "placental protein 20", "thiamine pyrophosphokinase 1", "thiamine kinase", "thiamine diphosphokinase" 606370 NA 11342111 Standard NM_022445 NM_022445 NA Approved HTPK1, PP20 uc003weq.3 Q9H3S4 OTTHUMG00000152774 ENST00000360057.3:c.16-118->C chr7.hg19:g.144532831_144532831dupG 3 3 ref NA False 46 46 PASS 2 PASS ref->het 0 NA 100,109 18,20 40,29 1 1 A8K0T7|D3DWG0|I6L9B8|Q6NUR5|Q9H602 True hg19 CCDS5888.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TPK1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000327777.1 PASS NA None 159 NA True - G ENST00000360057.3 PTPRN2 5799 __UNKNOWN__ __UNKNOWN__ 7 157332394 157332396 __UNKNOWN__ 3'UTR DEL CTC CTC - rs3832496|rs397840739|rs398112077|rs3189441|rs397738945|rs199863894 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:157332394_157332396delCTC ENST00000389418.4 - 0 4069_4071 PTPRN2_ENST00000409483.1_3'UTR|PTPRN2_ENST00000389413.3_3'UTR|PTPRN2_ENST00000389416.4_3'UTR NM_002847.3 NP_002838.2 Q92932 PTPR2_HUMAN protein tyrosine phosphatase, receptor type, N polypeptide 2 NA NA NA negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470) endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195) transmembrane receptor protein tyrosine phosphatase activity (GO:0005001) NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1) 86 all_neural(206;0.181) all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132) OV - Ovarian serous cystadenocarcinoma(82;0.00463) STAD - Stomach adenocarcinoma(7;0.0875) TCGCCCTGATCTCCTCTCCCGGG 0.631 NA NA NA 1263 0.252196 0.3124 0.281 5008 , , NA 15449 0.0397 NA 0.4056 False NA ,,, NA NA NA 2504 0.2117 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 330 311.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.5 AB002385 CCDS5947.1, CCDS5948.1, CCDS5949.1 7q36 2011-06-09 ENSG00000155093 ENSG00000155093 5799 "Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like" 9677 protein-coding gene gene with protein product "IAR PTPRP" 601698 NA 8954911, 9220540 Standard NM_130842 NA Approved KIAA0387, phogrin, ICAAR, IA-2beta uc003wno.3 Q92932 OTTHUMG00000152646 ENST00000389418.4:c.*1014GAG>- chr7.hg19:g.157332397_157332399delCTC 1 3 ref NA False 31 31 PASS 2 PASS ref->het 0 NA 237,243 61,61 37,33 1 1 E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6 True hg19 CCDS5947.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PTPRN2-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000353214.1 PASS NA None 330 NA True - CTC ENST00000389418.4 ESYT2 57488 __UNKNOWN__ __UNKNOWN__ 7 158534265 158534266 __UNKNOWN__ Frame_Shift_Del DEL GA GA - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr7:158534265_158534266delGA ENST00000251527.5 - 17 2262_2263 c.2197_2198delTC c.(2197-2199)tcgfs p.S733fs ESYT2_ENST00000435514.2_Frame_Shift_Del_p.S168fs NM_020728.2 NP_065779.1 A0FGR8 ESYT2_HUMAN extended synaptotagmin-like protein 2 761 NA NA endocytosis (GO:0006897)|lipid transport (GO:0006869) extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232) calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091) breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2) 32 GATGGGCAGCGAGATGTCCGAG 0.634 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 360 356.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 AB033054 CCDS34791.1 7q36.3 2014-07-02 2009-06-23 2009-06-23 ENSG00000117868 ENSG00000117868 57488 "Synaptotagmins" 22211 protein-coding gene gene with protein product NA "family with sequence similarity 62 (C2 domain containing), member B" FAM62B NA 17672888 Standard NM_020728 NM_020728 NA Approved KIAA1228, CHR2SYT uc003wob.1 A0FGR8 OTTHUMG00000151436 ENST00000251527.5:c.2197_2198delTC chr7.hg19:g.158534267_158534268delGA ENSP00000251527:p.Ser733fs 1 2 ref NA False 69 69 PASS 2 PASS ref->het 0 NA 282,283 52,52 34,34 1 1 A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2 True hg19 CCDS34791.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ESYT2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000322647.1 PASS NA None 360 NA True - GA ENST00000251527.5 TDRP 157695 __UNKNOWN__ __UNKNOWN__ 8 494659 494664 __UNKNOWN__ In_Frame_Del DEL GGCGGC GGCGGC - rs71202629 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:494659_494664delGGCGGC ENST00000324079.6 - 1 334_339 c.94_99delGCCGCC c.(94-99)gccgccdel p.AA32del TDRP_ENST00000427263.2_In_Frame_Del_p.AA32del|TDRP_ENST00000523656.1_In_Frame_Del_p.AA32del Q86YL5 TDRP_HUMAN testis development related protein 32 Poly-Ala. NA NA spermatogenesis (GO:0007283) cytoplasm (GO:0005737)|nucleus (GO:0005634) p.A32_A33delAA(1) NA CCTGCGCCTGggcggcggcggcggcg 0.782 NA NA NA 1130 0.225639 0.056 0.4049 5008 , , NA 8817 0.1677 NA 0.3439 False NA ,,, NA NA NA 2504 0.2658 NA NA NA PASS NA NA NA 1 Deletion - In frame(1) upper_aerodigestive_tract(1) NA NA NA NA NA 40 41.4 NA 110,14,698 NA 47,1,15,6,1,341 NA NA NA 1 0 NA dbSNP_134 2 1280,14,1322 NA 556,0,168,7,0,577 no codingComplex C8orf42 NM_175075.3 603,1,183,13,1,918 A1A1,A1A2,A1R,A2A2,A2R,RR NA 49.4648,15.0852,41.2449 NA 1390,28,2020 NA NA NA SO:0001651 inframe_deletion 0.22 AY194292 CCDS47759.1, CCDS59090.1 8p23.3 2013-06-03 2013-06-03 2013-06-03 ENSG00000180190 ENSG00000180190 157695 26951 protein-coding gene gene with protein product NA "chromosome 8 open reading frame 42" C8orf42 NA 20170638 Standard NM_175075 NM_175075 NA Approved INM01, TDRP1, TDRP2 Q86YL5 OTTHUMG00000163593 ENST00000324079.6:c.94_99delGCCGCC chr8.hg19:g.494665_494670delGGCGGC ENSP00000315111:p.Ala32_Ala33del 4 5 ref NA False 42 42 PASS 6 PASS ref->het 0 NA 20,20 11,12 12,11 1 1 B6VF03|B9EG53 True hg19 CCDS47759.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TDRP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000374442.1 PASS NA None 40 NA True - GGC ENST00000324079.6 ERI1 90459 __UNKNOWN__ __UNKNOWN__ 8 8916351 8916362 __UNKNOWN__ Intron DEL ATAAATAAATAA ATAAATAAATAA - rs58770201|rs113766274|rs557053598|rs138972535 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:8916351_8916362delATAAATAAATAA ENST00000520332.1 + 5 399 Q8IV48 ERI1_HUMAN exoribonuclease 1 NA NA NA gene silencing by RNA (GO:0031047)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|rRNA 3'-end processing (GO:0031125) cytoplasm (GO:0005737)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleolus (GO:0005730)|nucleus (GO:0005634) 3'-5' exonuclease activity (GO:0008408)|histone pre-mRNA stem-loop binding (GO:0071207)|metal ion binding (GO:0046872)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843) NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1) 11 aacttcattgataaataaataaataaataaat 0.311 NA NA NA 627 0.1252 0.1936 0.1095 5008 , , NA 17537 0.004 NA 0.175 False NA ,,, NA NA NA 2504 0.1176 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 18 24.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 BC035279 CCDS5972.1 8p23.1 2008-12-16 2008-12-16 2008-12-16 ENSG00000104626 ENSG00000104626 90459 "Enhanced RNAi three prime mRNA exonucleases" 23994 protein-coding gene gene with protein product "exoribonuclease 1", "enhanced RNAi three prime mRNA exonuclease homolog 1 (C.elegans)" 608739 "three prime histone mRNA exonuclease 1" THEX1 NA 14536070 Standard NM_153332 NM_153332 NA Approved 3'HEXO uc003wsk.2 Q8IV48 OTTHUMG00000129328 ENST00000520332.1:c.400-29608ATAAATAAATAA>- chr8.hg19:g.8916351_8916362delATAAATAAATAA 4 6 ref NA False 84 81 PASS 7 PASS ref->het 0 NA 7,8 14,14 7,6 1 1 A8K4U7|Q9NSX3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ERI1-007 KNOWN basic processed_transcript NA protein_coding OTTHUMT00000374780.2 PASS NA None 18 NA True + ATAA ENST00000520332.1 BMP1 649 __UNKNOWN__ __UNKNOWN__ 8 22035248 22035249 __UNKNOWN__ Intron INS - - G rs377158841|rs75016937 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:22035248_22035249insG ENST00000306385.5 + 6 1400 BMP1_ENST00000306349.8_Intron|BMP1_ENST00000397816.3_Intron|BMP1_ENST00000397814.3_Intron|BMP1_ENST00000354870.5_Intron NM_006129.4 NP_006120.1 P13497 BMP1_HUMAN bone morphogenetic protein 1 NA NA NA cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281) extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578) calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270) breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3) 30 Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11) ACCCTCAGGTAGGGGGACTCTC 0.624 NA NA NA GGGGG|GGGGG|GGGGGG|insertion 2068 0.412939 0.1044 0.4769 5008 , , NA 15511 0.6478 NA 0.4433 False NA ,,, NA NA NA 2504 0.5112 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 279 277.44 NA , 746,3518 NA 71,604,1457 NA NA NA , 0.2 0.9 NA dbSNP_131 63 3643,4609 NA 825,1993,1308 no intron,intron BMP1 NM_006129.4,NM_001199.3 , 896,2597,2765 A1A1,A1R,RR NA 44.1469,17.4953,35.0671 , , NA 4389,8127 NA NA NA SO:0001627 intron_variant 0.59 CCDS6026.1, CCDS34856.1 8p21 2013-02-06 2004-08-09 ENSG00000168487 ENSG00000168487 649 3.4.24.19 "Bone morphogenetic proteins" 1067 protein-coding gene gene with protein product "procollagen C-endopeptidase" 112264 "procollagen C-endopeptidase" PCOLC NA 2004778 Standard NM_006132 NM_006129 NA Approved uc003xbg.3 P13497 OTTHUMG00000097761 ENST00000306385.5:c.731-116->G chr8.hg19:g.22035253_22035253dupG 6 5 ref NA False 86 86 PASS 5 PASS ref->het 0 NA 191,196 47,48 39,34 1 1 A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38 True hg19 CCDS6026.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BMP1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000214995.2 PASS NA None 279 NA True + G ENST00000306385.5 SLC39A14 23516 __UNKNOWN__ __UNKNOWN__ 8 22262229 22262234 __UNKNOWN__ In_Frame_Del DEL GCTGCT GCTGCT - rs145380823|rs111662782|rs3052256|rs150063686 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:22262229_22262234delGCTGCT ENST00000359741.5 + 2 181_186 c.6_11delGCTGCT c.(4-12)aagctgctg>aag p.LL5del SLC39A14_ENST00000289952.5_In_Frame_Del_p.LL5del|SLC39A14_ENST00000381237.1_In_Frame_Del_p.LL5del|SLC39A14_ENST00000240095.6_In_Frame_Del_p.LL5del NM_015359.4 NP_056174.2 Q15043 S39AE_HUMAN solute carrier family 39 (zinc transporter), member 14 5 NA NA cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577) cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385) NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1) 12 Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731) TCACCATGAAGCTGCTGCTGCTGCAC 0.617 NA NA NA 1591 0.317692 0.6929 0.1571 5008 , , NA 16427 0.1806 NA 0.2078 False NA ,,, NA NA NA 2504 0.1789 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 201 198.99 NA ,,, 2454,1772 NA 745,964,404 NA NA NA ,,, 3.4 1 NA dbSNP_132 80 1420,6814 NA 142,1136,2839 no coding,coding,coding,coding SLC39A14 NM_015359.4,NM_001135154.1,NM_001135153.1,NM_001128431.2 ,,, 887,2100,3243 A1A1,A1R,RR NA 17.2456,41.9309,31.0915 ,,, ,,, NA 3874,8586 NA NA NA SO:0001651 inframe_deletion 0.22 D31887 CCDS6030.1, CCDS47822.1, CCDS47823.1 8p21.2 2013-05-22 ENSG00000104635 ENSG00000104635 23516 "Solute carriers" 20858 protein-coding gene gene with protein product 608736 "solute carrier family 39 (metal ion transporter), member 14" NA 12659941 Standard XM_046677 NM_015359 NA Approved KIAA0062, NET34, ZIP14 uc011kzh.2 Q15043 OTTHUMG00000097791 ENST00000359741.5:c.6_11delGCTGCT chr8.hg19:g.22262235_22262240delGCTGCT ENSP00000352779:p.Leu5_Leu6del 2 2 ref NA False 38 38 PASS 4 PASS ref->het 0 NA 169,169 22,24 21,22 1 1 A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3 True hg19 CCDS6030.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC39A14-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000215038.2 PASS NA None 201 NA True + GCT ENST00000359741.5 SLC39A14 23516 __UNKNOWN__ __UNKNOWN__ 8 22279010 22279011 __UNKNOWN__ 3'UTR INS - - GGA rs376234210|rs3830580 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:22279010_22279011insGGA ENST00000359741.5 + 0 3453_3454 SLC39A14_ENST00000381237.1_3'UTR|SLC39A14_ENST00000240095.6_Intron NM_015359.4 NP_056174.2 Q15043 S39AE_HUMAN solute carrier family 39 (zinc transporter), member 14 NA NA NA cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577) cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385) NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1) 12 Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731) ATTTCCTGGTGGGATTATGGTC 0.337 NA NA NA 2014 0.402157 0.1589 0.4236 5008 , , NA 18196 0.5863 NA 0.3837 False NA ,,, NA NA NA 2504 0.545 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 77 73.96 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 D31887 CCDS6030.1, CCDS47822.1, CCDS47823.1 8p21.2 2013-05-22 ENSG00000104635 ENSG00000104635 23516 "Solute carriers" 20858 protein-coding gene gene with protein product 608736 "solute carrier family 39 (metal ion transporter), member 14" NA 12659941 Standard XM_046677 NM_015359 NA Approved KIAA0062, NET34, ZIP14 uc011kzh.2 Q15043 OTTHUMG00000097791 ENST00000359741.5:c.*1800->GGA chr8.hg19:g.22279011_22279013dupGGA 2 5 ref NA False 39 39 PASS 1 PASS ref->het 0 NA 39,39 26,26 11,11 1 1 A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3 True hg19 CCDS6030.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC39A14-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000215038.2 PASS NA None 77 NA True + GGA ENST00000359741.5 PPP2R2A 5520 __UNKNOWN__ __UNKNOWN__ 8 26149120 26149121 __UNKNOWN__ 5'UTR DEL AG AG - rs529323999 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:26149120_26149121delAG ENST00000380737.3 + 0 114_115 NM_002717.3 NP_002708.1 P63151 2ABA_HUMAN protein phosphatase 2, regulatory subunit B, alpha NA NA NA G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165) cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159) protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722) kidney(1)|large_intestine(2)|ovary(1) 4 all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157) UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155) tgccgGAGAAAGAGCACGAGCG 0.723 NA NA NA 104 0.0207668 0.0045 0.0562 5008 , , NA 4953 0.0188 NA 0.0308 False NA ,,, NA NA NA 2504 0.0092 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 136 112.29 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.12 M64929 CCDS34867.1, CCDS55213.1 8p21.2 2013-01-10 2010-04-14 ENSG00000221914 ENSG00000221914 5520 3.1.3.16 "Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing" 9304 protein-coding gene gene with protein product "PP2A subunit B isoform alpha" 604941 "protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform" NA 1849734 Standard NM_002717 NM_001177591 NA Approved PR52A, PR55A, B55A P63151 OTTHUMG00000163850 ENST00000380737.3:c.-215AG>- chr8.hg19:g.26149122_26149123delAG 1 4 ref NA False 162 145 PASS 2 PASS ref->het 0 NA 87,91 38,39 13,8 1 1 B2RBU8|B4E1T7|P50409|Q00007 True hg19 CCDS34867.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPP2R2A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000375954.2 PASS NA None 136 NA True + AG ENST00000380737.3 FZD3 7976 __UNKNOWN__ __UNKNOWN__ 8 28424107 28424110 __UNKNOWN__ 3'UTR DEL TTAG TTAG - rs548807182 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:28424107_28424110delTTAG ENST00000240093.3 + 0 6058_6061 NM_017412.3 NP_059108.1 Q9NPG1 FZD3_HUMAN frizzled class receptor 3 NA NA NA canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944) apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786) G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147) central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1) 41 Ovarian(32;2.06e-05) KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23) TGTACCCATCTTAGTTAGGCTATA 0.279 NA NA NA 10 0.00199681 8e-04 0.0058 5008 , , NA 16715 0 NA 0.005 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 87 81.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AJ272427 CCDS6069.1 8p21 2014-06-27 2014-01-29 ENSG00000104290 ENSG00000104290 7976 "GPCR / Class F : Frizzled receptors" 4041 protein-coding gene gene with protein product 606143 "frizzled (Drosophila) homolog 3", "frizzled homolog 3 (Drosophila)", "frizzled 3, seven transmembrane spanning receptor", "frizzled family receptor 3" NA 10777673, 10873558 Standard NM_145866 NM_145866 NA Approved uc010lvb.3 Q9NPG1 OTTHUMG00000102145 ENST00000240093.3:c.*3582TTAG>- chr8.hg19:g.28424111_28424114delTTAG 1 3 ref NA False 51 51 PASS 2 PASS ref->het 0 NA 62,62 22,22 2,3 1 1 A8K615 True hg19 CCDS6069.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FZD3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000219986.2 PASS NA None 87 NA True + TTAG ENST00000240093.3 HMBOX1 79618 __UNKNOWN__ __UNKNOWN__ 8 28908874 28908875 __UNKNOWN__ Intron INS - - AACC rs3830316|rs34984916|rs146960848|rs35389793 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:28908874_28908875insAACC ENST00000519047.1 + 10 1233 HMBOX1_ENST00000444075.1_3'UTR|HMBOX1_ENST00000524238.1_3'UTR|HMBOX1_ENST00000397358.3_3'UTR|HMBOX1_ENST00000355231.5_Intron|HMBOX1_ENST00000287701.10_3'UTR Q6NT76 HMBX1_HUMAN homeobox containing 1 NA NA NA negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleus (GO:0005634) DNA binding (GO:0003677) cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1) 11 Ovarian(32;0.0192) KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161) CAGTAAATAATAACCAACCAAC 0.455 NA NA NA 2264 0.452077 0.652 0.3069 5008 , , NA 20173 0.3383 NA 0.3748 False NA ,,, NA NA NA 2504 0.4816 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 182 170.63 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AY522342 CCDS6071.1 8p12 2013-05-23 ENSG00000147421 ENSG00000147421 79618 "Homeoboxes / HNF class" 26137 protein-coding gene gene with protein product "homeobox telomere-binding protein 1" NA NA 16825764 Standard NM_024567 NM_024567 NA Approved HNF1LA, PBHNF, FLJ21616, HOT1 uc003xhd.4 Q6NT76 OTTHUMG00000172138 ENST00000519047.1:c.1123-195->AACC chr8.hg19:g.28908879_28908882dupAACC 5 4 ref NA False 78 78 PASS 4 PASS ref->het 0 NA 97,97 54,54 31,32 1 1 A4K385|A8K3R8|B4DHY5|D3DSU0|Q3Y6P1|Q96GS5|Q9H701 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HMBOX1-005 PUTATIVE alternative_5_UTR|NAGNAG_splice_site|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000376869.1 PASS NA None 182 NA True + AACC ENST00000519047.1 MAK16 84549 __UNKNOWN__ __UNKNOWN__ 8 33342318 33342319 __UNKNOWN__ 5'UTR INS - - C rs3840687 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:33342318_33342319insC ENST00000360128.6 + 0 51_52 TTI2_ENST00000519356.1_Intron NM_032509.3 NP_115898.2 Q9BXY0 MAK16_HUMAN MAK16 homolog (S. cerevisiae) NA NA NA nucleus (GO:0005634) poly(A) RNA binding (GO:0044822) endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1) 8 CCCAGCCTCCTCCCAGCAGAGG 0.752 NA NA NA CCC|CCC|CCCC|insertion 2374 0.474042 0.4274 0.4553 5008 , , NA 13010 0.4851 NA 0.6024 False NA ,,, NA NA NA 2504 0.407 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 332 335.31 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.22 AF251062 CCDS6089.1 8p12 2011-10-13 2008-06-04 2008-06-04 ENSG00000198042 ENSG00000198042 84549 "RNA binding motif (RRM) containing" 13703 protein-coding gene gene with protein product NA "RNA binding motif protein 13" RBM13 NA Standard NM_032509 NM_032509 NA Approved MAK16L uc003xjj.3 Q9BXY0 OTTHUMG00000163957 ENST00000360128.6:c.-406->C chr8.hg19:g.33342321_33342321dupC 4 5 ref NA False 253 179 PASS 3 PASS ref->het 0 NA 217,220 85,87 28,25 1 1 B2RB44|Q5U5T1|Q86UC4|Q96SY6 True hg19 CCDS6089.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAK16-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000376559.3 PASS NA None 332 NA True + C ENST00000360128.6 TACC1 6867 __UNKNOWN__ __UNKNOWN__ 8 38709452 38709455 __UNKNOWN__ 3'UTR DEL TGAC TGAC - rs72517023|rs112953621 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:38709452_38709455delTGAC ENST00000317827.4 + 0 6708_6711 TACC1_ENST00000379931.3_3'UTR|TACC1_ENST00000348567.4_3'UTR|TACC1_ENST00000276520.8_3'UTR|TACC1_ENST00000330691.6_3'UTR NM_006283.2 NP_006274.2 O75410 TACC1_HUMAN transforming, acidic coiled-coil containing protein 1 NA NA NA cell cycle (GO:0007049)|cell division (GO:0051301)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886) cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634) breast(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(3) 17 all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065) LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235) CAAAAAGGTTTGACTGGCCTCCAG 0.377 NA NA NA 547 0.109225 0.0696 0.1412 5008 , , NA 18012 0.004 NA 0.2058 False NA ,,, NA NA NA 2504 0.1493 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 254 258.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.63 AF049910 CCDS6109.1, CCDS47845.1, CCDS55224.1 8p11 2012-12-20 ENSG00000147526 ENSG00000147526 6867 11522 protein-coding gene gene with protein product 605301 NA Standard NM_006283 NM_006283 NA Approved uc010lwp.3 O75410 OTTHUMG00000164018 ENST00000317827.4:c.*3914TGAC>- chr8.hg19:g.38709452_38709455delTGAC 0 3 ref NA False 132 132 PASS 1 PASS ref->het 0 NA 207,209 37,37 20,19 1 1 B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9 True hg19 CCDS6109.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TACC1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000376768.1 PASS NA None 254 NA True + TGAC ENST00000317827.4 HEY1 23462 __UNKNOWN__ __UNKNOWN__ 8 80676259 80676259 __UNKNOWN__ 3'UTR DEL T T - rs397840875|rs3833691 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:80676259delT ENST00000337919.5 - 0 2284 HEY1_ENST00000354724.3_3'UTR NM_001040708.1 NP_001035798.1 Q9Y5J3 HEY1_HUMAN hes-related family bHLH transcription factor with YRPW motif 1 NA NA NA angiogenesis (GO:0001525)|anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular valve formation (GO:0003190)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac septum morphogenesis (GO:0060411)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to glucocorticoid stimulus (GO:0071385)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion morphogenesis (GO:0003203)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve morphogenesis (GO:0003184)|regulation of vasculogenesis (GO:2001212)|transcription from RNA polymerase II promoter (GO:0006366)|umbilical cord morphogenesis (GO:0036304)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222) cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134) HEY1/NCOA2(10) cervix(1)|kidney(2)|large_intestine(5)|lung(14) 22 all_lung(9;5.1e-05) Epithelial(68;0.076)|all cancers(69;0.179) TTGTTCTTTCTTTTTTATTTA 0.373 NA NA T NCOA2 mesenchymal chondrosarcoma NA TTTTTT|TTTTTT|TTTTT|deletion 1275 0.254593 0.2784 0.1542 5008 , , NA 23419 0.1905 NA 0.2117 False NA ,,, NA NA NA 2504 0.4039 NA NA NA PASS Dom yes 8 8q21 23462 hairy/enhancer-of-split related with YRPW motif 1 NA M 0 NA NA NA NA NA 79 81.76 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF151522 CCDS6225.1, CCDS43749.1, CCDS64915.1 8q21 2013-10-17 2013-10-17 23462 "Basic helix-loop-helix proteins" 4880 protein-coding gene gene with protein product 602953 "hairy/enhancer-of-split related with YRPW motif 1" NA 10415358, 10403790 Standard NM_012258 NM_001040708 NA Approved HESR-1, CHF2, HESR1, HRT-1, CHF-2, HERP2, BHLHb31 uc003ybl.3 Q9Y5J3 ENST00000337919.5:c.*1164A>- chr8.hg19:g.80676259delT 5 9 ref NA False 54 54 PASS 6 PASS ref->het 0 NA 53,53 23,23 4,4 1 1 B2R883|Q5TZS3|Q8NAM2|Q9NYP4 True hg19 CCDS43749.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HEY1-009 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000380558.1 PASS NA None 79 NA True - T ENST00000337919.5 HEY1 23462 __UNKNOWN__ __UNKNOWN__ 8 80678494 80678500 __UNKNOWN__ Start_Codon_Del DEL GGCATGT GGCATGT - rs142613628 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:80678494_80678500delGGCATGT ENST00000523976.1 - 0 210_216 HEY1_ENST00000337919.5_Intron|HEY1_ENST00000354724.3_Intron|HEY1_ENST00000435063.2_Intron Q9Y5J3 HEY1_HUMAN hes-related family bHLH transcription factor with YRPW motif 1 NA NA NA angiogenesis (GO:0001525)|anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular valve formation (GO:0003190)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac septum morphogenesis (GO:0060411)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to glucocorticoid stimulus (GO:0071385)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion morphogenesis (GO:0003203)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve morphogenesis (GO:0003184)|regulation of vasculogenesis (GO:2001212)|transcription from RNA polymerase II promoter (GO:0006366)|umbilical cord morphogenesis (GO:0036304)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222) cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134) HEY1/NCOA2(10) cervix(1)|kidney(2)|large_intestine(5)|lung(14) 22 all_lung(9;5.1e-05) Epithelial(68;0.076)|all cancers(69;0.179) TTCCTCAAGAGGCATGTGGCAGCACCT 0.372 NA NA T NCOA2 mesenchymal chondrosarcoma NA 698 0.139377 0.1725 0.0951 5008 , , NA 20880 0.001 NA 0.1372 False NA ,,, NA NA NA 2504 0.271 NA NA NA PASS Dom yes 8 8q21 23462 hairy/enhancer-of-split related with YRPW motif 1 NA M 0 NA NA NA NA NA 208 198.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001582 initiator_codon_variant 0 AF151522 CCDS6225.1, CCDS43749.1, CCDS64915.1 8q21 2013-10-17 2013-10-17 23462 "Basic helix-loop-helix proteins" 4880 protein-coding gene gene with protein product 602953 "hairy/enhancer-of-split related with YRPW motif 1" NA 10415358, 10403790 Standard NM_012258 NM_001040708 NA Approved HESR-1, CHF2, HESR1, HRT-1, CHF-2, HERP2, BHLHb31 uc003ybl.3 Q9Y5J3 ENST00000523976.1: chr8.hg19:g.80678494_80678500delGGCATGT 0 3 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 179,180 12,12 20,20 1 1 B2R883|Q5TZS3|Q8NAM2|Q9NYP4 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HEY1-004 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000379520.1 PASS NA None 208 NA True - GGCATGT ENST00000523976.1 CA2 760 __UNKNOWN__ __UNKNOWN__ 8 86376376 86376382 __UNKNOWN__ Intron DEL CCCCGAT CCCCGAT - rs553482175|rs556322781 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:86376376_86376382delCCCCGAT ENST00000285379.5 + 1 264 RP11-317J10.2_ENST00000517697.1_RNA|RP11-317J10.2_ENST00000521761.1_RNA NM_000067.2 NP_000058.1 P00918 CAH2_HUMAN carbonic anhydrase II NA NA NA angiotensin-activated signaling pathway (GO:0038166)|bicarbonate transport (GO:0015701)|kidney development (GO:0001822)|morphogenesis of an epithelium (GO:0002009)|odontogenesis of dentin-containing tooth (GO:0042475)|one-carbon metabolic process (GO:0006730)|positive regulation of bone resorption (GO:0045780)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of dipeptide transmembrane transport (GO:2001150)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of anion transport (GO:0044070)|regulation of chloride transport (GO:2001225)|regulation of intracellular pH (GO:0051453)|response to estrogen (GO:0043627)|response to pH (GO:0009268)|response to zinc ion (GO:0010043)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281) apical part of cell (GO:0045177)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886) carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270) central_nervous_system(2)|cervix(1)|large_intestine(2)|lung(5)|prostate(1) 11 Acetazolamide(DB00819)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Diclofenamide(DB01144)|Dorzolamide(DB00869)|Ethinamate(DB01031)|Furosemide(DB00695)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Topiramate(DB00273)|Trichlormethiazide(DB01021)|Zonisamide(DB00909) CGCGGGGGCGccccgatccccgatccc 0.744 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 258 242.82 NA 44,2396 NA 19,6,1195 NA NA NA -7.5 0 NA dbSNP_132 6 284,4806 NA 80,124,2341 no intron CA2 NM_000067.2 99,130,3536 A1A1,A1R,RR NA 5.5796,1.8033,4.3559 NA 328,7202 NA NA NA SO:0001627 intron_variant 0 J03037 CCDS6239.1 8q21.2 2012-10-02 ENSG00000104267 ENSG00000104267 760 4.2.1.1 "Carbonic anhydrases" 1373 protein-coding gene gene with protein product 611492 NA 3107918 Standard NM_000067 NM_000067 NA Approved Car2, CA-II, CAII uc003ydk.2 P00918 OTTHUMG00000164944 ENST00000285379.5:c.34+32CCCCGAT>- chr8.hg19:g.86376383_86376389delCCCCGAT 3 6 ref NA False 53 53 PASS 4 PASS ref->het 0 NA 120,122 33,34 109,106 1 1 B2R7G8|Q6FI12|Q96ET9 True hg19 CCDS6239.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CA2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000381097.2 PASS NA None 258 NA True + CCCCGAT ENST00000285379.5 VPS13B 157680 __UNKNOWN__ __UNKNOWN__ 8 100888593 100888595 __UNKNOWN__ 3'UTR DEL TGA TGA - rs398068077|rs10542429|rs200421894|rs60078732 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:100888593_100888595delTGA ENST00000358544.2 + 0 12879_12881 VPS13B_ENST00000357162.2_3'UTR|VPS13B_ENST00000395996.1_3'UTR NM_017890.4 NP_060360.3 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13 homolog B (yeast) NA NA NA protein transport (GO:0015031) NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9) 193 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TACAACAGTCTGATGATTGATTG 0.325 NA NA NA 1034 0.20647 0.4274 0.1441 5008 , , NA 22213 0.127 NA 0.1421 False NA ,,, NA NA NA 2504 0.1002 NA NA NA Colon(161;2205 2542 7338 31318) PASS NA NA NA 0 NA NA NA NA NA 134 128.27 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AJ608772 CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1 8q22-q23 2014-09-17 2006-12-19 2005-04-08 ENSG00000132549 ENSG00000132549 157680 2183 protein-coding gene gene with protein product 607817 "Cohen syndrome 1" CHS1, COH1 NA 7920642, 15498460 Standard NM_184042 NM_181661 NA Approved uc003yiv.4 Q7Z7G8 OTTHUMG00000140383 ENST00000358544.2:c.*701TGA>- chr8.hg19:g.100888596_100888598delTGA 1 2 ref NA False 47 47 PASS 2 PASS ref->het 0 NA 99,102 23,23 11,11 2 2 C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7 True hg19 CCDS6280.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA VPS13B-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000277138.1 PASS NA None 134 NA True + TGA ENST00000358544.2 YWHAZ 7534 __UNKNOWN__ __UNKNOWN__ 8 101964226 101964227 __UNKNOWN__ Intron INS - - GCG rs111529284 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:101964226_101964227insGCG ENST00000395948.2 - 1 141 YWHAZ_ENST00000521309.1_5'UTR|YWHAZ_ENST00000492736.1_5'UTR|YWHAZ_ENST00000353245.3_Intron|YWHAZ_ENST00000457309.1_Intron|YWHAZ_ENST00000395958.2_5'UTR|YWHAZ_ENST00000395957.2_5'UTR P63104 1433Z_HUMAN tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta NA NA NA apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|gene expression (GO:0010467)|histamine secretion by mast cell (GO:0002553)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|platelet activation (GO:0030168)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting to mitochondrion (GO:0006626)|response to drug (GO:0042493)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165) blood microparticle (GO:0072562)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mast cell granule (GO:0042629)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)|protein complex (GO:0043234) identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134) large_intestine(1)|lung(2) 3 all_cancers(14;7.43e-06)|all_epithelial(15;2.77e-08)|Lung NSC(17;6.08e-05)|all_lung(17;0.000197) Epithelial(11;2.79e-11)|all cancers(13;5.45e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.75e-05) cggcggcagcagcggcgAGGCT 0.723 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 34 32.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.36 U28964 CCDS6290.1 8q22.3 2013-12-03 2013-12-03 ENSG00000164924 ENSG00000164924 7534 12855 protein-coding gene gene with protein product "14-3-3 zeta", "14-3-3 delta" 601288 "tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, delta polypeptide", "tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide" YWHAD NA 8617504, 7890696 Standard NM_145690 NM_003406 NA Approved KCIP-1, 14-3-3-zeta uc010mbr.2 P63104 OTTHUMG00000134291 ENST00000395948.2:c.73+850->CGC chr8.hg19:g.101964230_101964232dupGCG 3 3 ref NA False 40 40 PASS 2 PASS ref->het 0 NA 23,23 8,8 3,3 1 1 A8K1N0|B7Z465|P29213|P29312|Q32P43|Q5XJ08|Q6GPI2|Q6IN74|Q6NUR9|Q6P3U9|Q86V33 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA YWHAZ-008 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000259024.2 PASS NA None 34 NA True - GCG ENST00000395948.2 SLC25A32 81034 __UNKNOWN__ __UNKNOWN__ 8 104426906 104426907 __UNKNOWN__ Intron DEL AC AC - rs386728404|rs139201908|rs367610017|rs5025988 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:104426906_104426907delAC ENST00000297578.4 - 1 321 SLC25A32_ENST00000543107.1_Intron NM_030780.3 NP_110407.2 Q9H2D1 MFTC_HUMAN solute carrier family 25 (mitochondrial folate carrier), member 32 NA NA NA folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767) integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743) folic acid transporter activity (GO:0008517) central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2) 9 OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197) Folic Acid(DB00158) GCGGACAGCAACGCTCCCTTCA 0.599 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 69 85.41 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.15 AF283645 CCDS6300.1 8q22.3 2013-05-22 2013-03-15 ENSG00000164933 ENSG00000164933 81034 "Solute carriers" 29683 protein-coding gene gene with protein product 610815 "solute carrier family 25, member 32" NA 10978331 Standard NM_030780 NM_030780 NA Approved MFTC uc003yll.4 Q9H2D1 OTTHUMG00000164790 ENST00000297578.4:c.154+104GT>- chr8.hg19:g.104426906_104426907delAC 0 2 ref NA False 48 48 PASS 1 PASS ref->het 0 NA 49,50 14,15 8,7 1 1 Q96JZ6|Q96SU7 True hg19 CCDS6300.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC25A32-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000380290.2 PASS NA None 69 NA True - AC ENST00000297578.4 RP11-127H5.1 0 __UNKNOWN__ __UNKNOWN__ 8 105907787 105907787 __UNKNOWN__ 3'UTR DEL T T - rs3214884|rs397840022 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:105907787delT ENST00000521923.1 + 0 562 NA NA NA NA TGGAAAACAGTTAATTTTAAC 0.353 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 184 195.84 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.05 NA NA NA NA NA ENST00000521923.1:c.*108T>- chr8.hg19:g.105907787delT 1 2 ref NA False 32 32 PASS 2 PASS ref->het 0 NA 122,122 28,28 26,26 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-127H5.1-001 PUTATIVE basic|appris_principal|exp_conf protein_coding NA protein_coding OTTHUMT00000380421.1 PASS NA None 184 NA True + T ENST00000521923.1 OXR1 55074 __UNKNOWN__ __UNKNOWN__ 8 107670114 107670114 __UNKNOWN__ 5'UTR DEL T T - rs28921373 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:107670114delT ENST00000312046.6 + 0 33 OXR1_ENST00000442977.2_Intron|OXR1_ENST00000531443.1_Intron|OXR1_ENST00000517566.2_Intron|OXR1_ENST00000452423.2_Intron|OXR1_ENST00000497705.1_Intron|OXR1_ENST00000445937.1_Intron NM_181354.4 NP_851999.2 Q8N573 OXR1_HUMAN oxidation resistance 1 NA NA NA adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979) mitochondrion (GO:0005739)|nucleolus (GO:0005730) oxidoreductase activity (GO:0016491) NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4) 31 OV - Ovarian serous cystadenocarcinoma(57;1.81e-09) CCGCCTCCCCTGGGTCAGGTC 0.741 NA NA NA T|T|-|deletion 161 0.0321486 0.0068 0.0548 5008 , , NA 9379 0.002 NA 0.0954 False NA ,,, NA NA NA 2504 0.0164 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 162 164.93 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.29 AF309387 CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1 8q23 2013-03-14 ENSG00000164830 ENSG00000164830 55074 15822 protein-coding gene gene with protein product "TBC/LysM-associated domain containing 3" 605609 NA 11114193 Standard NM_181354 NM_181354 NA Approved TLDC3 uc011lht.2 Q8N573 OTTHUMG00000167682 ENST00000312046.6:c.-101T>- chr8.hg19:g.107670114delT 0 6 ref NA False 61 61 PASS 1 PASS ref->het 0 NA 113,114 27,27 19,18 2 2 A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7 True hg19 CCDS6304.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA OXR1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000343925.2 PASS NA None 162 NA True + T ENST00000312046.6 RSPO2 340419 __UNKNOWN__ __UNKNOWN__ 8 108970264 108970265 __UNKNOWN__ Intron INS - - CA rs3039298|rs397718609|rs374495043 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:108970264_108970265insCA ENST00000276659.5 - 5 1237 RSPO2_ENST00000517781.1_Intron|RSPO2_ENST00000517939.1_Intron|RSPO2_ENST00000378439.2_Intron NM_178565.4 NP_848660.3 Q6UXX9 RSPO2_HUMAN R-spondin 2 NA NA NA bone mineralization (GO:0030282)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|lung growth (GO:0060437)|osteoblast differentiation (GO:0001649)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055) cell surface (GO:0009986)|extracellular region (GO:0005576) heparin binding (GO:0008201)|receptor binding (GO:0005102) EIF3E/RSPO2(6) haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3) 28 OV - Ovarian serous cystadenocarcinoma(57;1.55e-09) GCGGGAGAATTCAGGAAGCACA 0.416 NA NA NA 2455 0.490216 0.0764 0.598 5008 , , NA 18741 0.6885 NA 0.6551 False NA ,,, NA NA NA 2504 0.5992 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 135 141.06 NA 747,3517 NA 60,627,1445 NA NA NA 0.7 0 NA dbSNP_126 207 5164,3090 NA 1612,1940,575 no intron RSPO2 NM_178565.4 1672,2567,2020 A1A1,A1R,RR NA 37.4364,17.5188,47.22 NA 5911,6607 NA NA NA SO:0001627 intron_variant 0 AK123023 CCDS6307.1, CCDS64953.1 8q23.1 2014-01-30 2011-06-29 ENSG00000147655 ENSG00000147655 340419 "Endogenous ligands" 28583 protein-coding gene gene with protein product 610575 "R-spondin 2 homolog (Xenopus laevis)" NA 15469841 Standard NM_178565 NM_178565 NA Approved MGC35555 uc003yms.3 Q6UXX9 OTTHUMG00000164893 ENST00000276659.5:c.616+42->TG chr8.hg19:g.108970265_108970266dupCA 2 2 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 99,100 27,27 9,9 1 1 B3KVP0|Q4G0U4|Q8N6X6 True hg19 CCDS6307.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RSPO2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000380830.1 PASS NA None 135 NA True - CA ENST00000276659.5 RNF139 11236 __UNKNOWN__ __UNKNOWN__ 8 125487136 125487137 __UNKNOWN__ 5'UTR INS - - GCC rs573765096|rs150293365|rs374789094 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:125487136_125487137insGCC ENST00000303545.3 + 0 158_159 NM_007218.3 NP_009149.2 ring finger protein 139 NA NA NA breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(1) 20 Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108) STAD - Stomach adenocarcinoma(47;0.00288) CCTCCTGGGGAgccgccgccgc 0.718 NA NA NA 1480 0.295527 0.2095 0.3444 5008 , , NA 12043 0.2877 NA 0.2545 False NA ,,, NA NA NA 2504 0.4274 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 602 579.38 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 3.58 AF064801 CCDS6350.1 8q24 2013-01-09 ENSG00000170881 ENSG00000170881 11236 "RING-type (C3HC4) zinc fingers" 17023 protein-coding gene gene with protein product 603046 NA 9689122 Standard NM_007218 NM_007218 NA Approved TRC8, RCA1, HRCA1 uc003yrc.3 Q8WU17 OTTHUMG00000165072 ENST00000303545.3:c.-214->GCC chr8.hg19:g.125487143_125487145dupGCC 6 5 ref NA False 671 259 PASS 5 PASS ref->het 0 NA 265,272 203,209 128,117 1 1 True hg19 CCDS6350.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RNF139-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000381692.1 PASS NA None 602 NA True + GCC ENST00000303545.3 LRRC14 9684 __UNKNOWN__ __UNKNOWN__ 8 145747618 145747619 __UNKNOWN__ 3'UTR INS - - C rs191944424|rs3834368 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr8:145747618_145747619insC ENST00000292524.1 + 0 2384_2385 NM_001272036.1|NM_014665.2 NP_001258965.1|NP_055480.1 Q15048 LRC14_HUMAN leucine rich repeat containing 14 NA NA NA endometrium(1)|lung(3)|prostate(1) 5 all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055) CCAGCGAGGGACCCCCCCCATG 0.663 NA NA NA CCCCCCC|CCCCCCCC|CCCCCCCCC|cryptic_indel 2081 0.415535 0.2852 0.4467 5008 , , NA 14428 0.4792 NA 0.3708 False NA ,,, NA NA NA 2504 0.5501 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 722 752.6 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 4.31 BC011377 CCDS6432.1 8q24.3 2012-08-20 ENSG00000160959 ENSG00000160959 9684 20419 protein-coding gene gene with protein product NA NA 7584026 Standard NM_014665 NM_001272036 NA Approved KIAA0014, LRRC14A uc003zdk.3 Q15048 OTTHUMG00000165179 ENST00000292524.1:c.*757->C chr8.hg19:g.145747626_145747626dupC 9 8 ref NA False 62 62 PASS 8 PASS ref->het 0 NA 527,538 77,81 111,100 2 2 A8K0A8|D3DWM8 True hg19 CCDS6432.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LRRC14-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000382494.1 PASS NA None 722 NA True + C ENST00000292524.1 ADAMTSL1 92949 __UNKNOWN__ __UNKNOWN__ 9 18684837 18684838 __UNKNOWN__ Intron DEL TG TG - rs140349388|rs3833713|rs41268981 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:18684837_18684838delTG ENST00000276935.6 + 13 1574 ADAMTSL1_ENST00000380548.4_Intron|ADAMTSL1_ENST00000327883.7_3'UTR Q8N6G6 ATL1_HUMAN ADAMTS-like 1 NA NA NA proteinaceous extracellular matrix (GO:0005578) metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270) breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 42 GBM - Glioblastoma multiforme(50;1.29e-17) TATTTGAAACTGTTTTGTTTAA 0.401 NA NA NA 742 0.148163 0.0219 0.1859 5008 , , NA 19659 0.1518 NA 0.1899 False NA ,,, NA NA NA 2504 0.2454 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 377 367.75 NA , 225,4037 NA 8,209,1914 NA NA NA , -0.7 0 NA dbSNP_107 47 1606,6640 NA 139,1328,2656 no utr-3,intron ADAMTSL1 NM_052866.4,NM_001040272.5 , 147,1537,4570 A1A1,A1R,RR NA 19.4761,5.2792,14.6386 , , NA 1831,10677 NA NA NA SO:0001627 intron_variant 0 AF176313 CCDS6485.1, CCDS47954.1 9p21.3 2013-01-11 ENSG00000178031 ENSG00000178031 92949 "Immunoglobulin superfamily / I-set domain containing" 14632 protein-coding gene gene with protein product "punctin" 609198 "chromosome 9 open reading frame 94" C9orf94 NA 9628581, 11805097 Standard NM_001040272 NA Approved ADAMTSR1, FLJ35283 uc003zne.4 Q8N6G6 OTTHUMG00000019604 ENST00000276935.6:c.1574+39TG>- chr9.hg19:g.18684837_18684838delTG 0 7 ref NA False 175 144 PASS 1 PASS ref->het 0 NA 252,254 91,93 35,34 1 1 A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ADAMTSL1-005 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000051804.5 PASS NA None 377 NA True + TG ENST00000276935.6 C9orf72 203228 __UNKNOWN__ __UNKNOWN__ 9 27547924 27547925 __UNKNOWN__ 3'UTR INS - - A rs200583482 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:27547924_27547925insA ENST00000380003.3 - 0 1818_1819 C9orf72_ENST00000488117.1_5'UTR NM_001256054.1|NM_018325.3 NP_001242983.1|NP_060795.1 Q96LT7 CI072_HUMAN chromosome 9 open reading frame 72 NA NA NA autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897) autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634) Rab GTPase binding (GO:0017137) breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1) 23 all_neural(11;7.57e-10) LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016) TCATGTATTTCAAAAAAACAGT 0.292 NA NA NA ?|AAAAAAA|AAAAAAAA|unsure 129 0.0257588 0.0484 0.0101 5008 , , NA 18508 0.003 NA 0.0179 False NA ,,, NA NA NA 2504 0.0378 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 156 155.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.62 AL832467 CCDS6522.1, CCDS6523.1 9p21.1 2014-09-17 ENSG00000147894 ENSG00000147894 203228 28337 protein-coding gene gene with protein product 614260 NA 21944778, 24549040 Standard NM_018325 NM_145005 NA Approved MGC23980 uc003zqq.3 Q96LT7 OTTHUMG00000019716 ENST00000380003.3:c.*310->T chr9.hg19:g.27547931_27547931dupA 8 8 ref NA False 35 35 PASS 7 PASS ref->het 0 NA 106,109 23,23 26,24 1 1 A8K5W0|D3DRK6|G8I0B6|Q6NUS9 True hg19 CCDS6522.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C9orf72-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000051969.1 PASS NA None 156 NA True - A ENST00000380003.3 B4GALT1 2683 __UNKNOWN__ __UNKNOWN__ 9 33166711 33166712 __UNKNOWN__ Intron INS - - G rs111399879 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:33166711_33166712insG ENST00000379731.4 - 1 599 B4GALT1_ENST00000535206.1_Intron NM_001497.3 NP_001488.2 P15291 B4GT1_HUMAN UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 NA NA NA acute inflammatory response (GO:0002526)|angiogenesis involved in wound healing (GO:0060055)|binding of sperm to zona pellucida (GO:0007339)|branching morphogenesis of an epithelial tube (GO:0048754)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|development of secondary sexual characteristics (GO:0045136)|epithelial cell development (GO:0002064)|extracellular matrix organization (GO:0030198)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|lactose biosynthetic process (GO:0005989)|leukocyte migration (GO:0050900)|mammary gland development (GO:0030879)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|oligosaccharide biosynthetic process (GO:0009312)|penetration of zona pellucida (GO:0007341)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of acrosome reaction (GO:0060046)|regulation of cellular component movement (GO:0051270)|single fertilization (GO:0007338)|small molecule metabolic process (GO:0044281) basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|desmosome (GO:0030057)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|glycocalyx (GO:0030112)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886) alpha-tubulin binding (GO:0043014)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|beta-tubulin binding (GO:0048487)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|manganese ion binding (GO:0030145)|N-acetyllactosamine synthase activity (GO:0003945)|protein homodimerization activity (GO:0042803)|UDP-galactosyltransferase activity (GO:0035250) endometrium(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1) 14 LUSC - Lung squamous cell carcinoma(29;0.0084) GBM - Glioblastoma multiforme(74;0.121) N-Acetyl-D-glucosamine(DB00141) CGGGGAAATCCGGGGGGGTCCC 0.639 NA NA NA GGGGGGG|GGGGGGG|GGGGGGGG|insertion 150 0.0299521 0.0174 0.0504 5008 , , NA 15660 0.0565 NA 0.0179 False NA ,,, NA NA NA 2504 0.0174 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 267 268.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.36 X14085 CCDS6535.1 9p13 2013-02-19 ENSG00000086062 ENSG00000086062 2683 2.4.1.22 "Beta 4-glycosyltransferases" 924 protein-coding gene gene with protein product 137060 GGTB2 NA 9597550 Standard NM_001497 NM_001497 NA Approved beta4Gal-T1 uc003zsg.2 P15291 OTTHUMG00000019764 ENST00000379731.4:c.412+43->C chr9.hg19:g.33166718_33166718dupG 8 7 ref NA False 106 106 PASS 7 PASS ref->het 0 NA 183,187 39,39 42,39 1 1 B2R710|D3DRL2|Q12909|Q12910|Q12911|Q14456|Q14509|Q14523 True hg19 CCDS6535.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA B4GALT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000052039.1 PASS NA None 267 NA True - G ENST00000379731.4 FAM166B 730112 __UNKNOWN__ __UNKNOWN__ 9 35562329 35562332 __UNKNOWN__ Intron DEL ACAA ACAA - rs60180088|rs5897609|rs74715439 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:35562329_35562332delACAA ENST00000399742.2 - 5 810 FAM166B_ENST00000492890.1_Intron NM_001099951.2|NM_001164310.1 NP_001093421.1|NP_001157782.1 A8MTA8 F166B_HUMAN family with sequence similarity 166, member B NA NA NA kidney(3)|large_intestine(1)|lung(4)|ovary(1) 9 CCATACCCATACAAACAAACATTC 0.505 NA NA NA 1937 0.386781 0.3343 0.6037 5008 , , NA 14329 0.3046 NA 0.4622 False NA ,,, NA NA NA 2504 0.3108 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 64 69.84 NA , 1095,2139 NA 275,545,797 NA NA NA , -1.4 0 NA dbSNP_114 9 3412,3784 NA 1018,1376,1204 no intron,intron FAM166B NM_001164310.1,NM_001099951.2 , 1293,1921,2001 A1A1,A1R,RR NA 47.4152,33.859,43.2119 , , NA 4507,5923 NA NA NA SO:0001627 intron_variant 0 BC129999 CCDS47963.1, CCDS56572.1 9p13.3 2008-06-10 ENSG00000215187 ENSG00000215187 730112 34242 protein-coding gene gene with protein product NA NA Standard NM_001099951 NM_001099951 NA Approved uc010mkr.3 A8MTA8 OTTHUMG00000019858 ENST00000399742.2:c.739+44TTGT>- chr9.hg19:g.35562333_35562336delACAA 1 6 ref NA False 33 33 PASS 2 PASS ref->het 0 NA 45,47 17,17 8,7 1 1 A1L3B2|B7ZBJ0 True hg19 CCDS56572.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM166B-005 NOVEL basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000336563.1 PASS NA None 64 NA True - ACAA ENST00000399742.2 TPM2 7169 __UNKNOWN__ __UNKNOWN__ 9 35682764 35682765 __UNKNOWN__ Intron INS - - G rs138163723 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:35682764_35682765insG ENST00000378292.3 - 9 1975 TPM2_ENST00000378300.5_Frame_Shift_Ins_p.W304fs|TPM2_ENST00000329305.2_Intron NM_213674.1 NP_998839.1 P07951 TPM2_HUMAN tropomyosin 2 (beta) NA NA NA muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462) cytosol (GO:0005829)|muscle thin filament tropomyosin (GO:0005862) actin binding (GO:0003779)|structural constituent of muscle (GO:0008307) NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 15 all_epithelial(49;0.121) Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194) AGCGACAGCCAGGGAGTGCCTG 0.609 NA NA NA GGG|GGG|GGGG|insertion 691 0.137979 0.2829 0.0951 5008 , , NA 18295 0.0268 NA 0.1412 False NA ,,, NA NA NA 2504 0.0838 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 89 83.87 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.26 CCDS6586.1, CCDS6587.1 9p13 2014-09-17 2003-12-02 ENSG00000198467 ENSG00000198467 7169 "Tropomyosins" 12011 protein-coding gene gene with protein product "nemaline myopathy type 4" 190990 "arthrogryposis multiplex congenital, distal, type 1" AMCD1 NA 7606936 Standard NM_003289 NM_003289 NA Approved DA1, NEM4 uc003zxq.3 P07951 OTTHUMG00000019878 ENST00000378292.3:c.773-604->C chr9.hg19:g.35682767_35682767dupG 4 4 ref NA False 44 44 PASS 3 PASS ref->het 0 NA 61,64 18,18 10,9 1 1 A6NM85|P06468|Q13894|Q53FM4|Q5TCU4|Q5TCU7|Q9UH67 True hg19 CCDS6586.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TPM2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000052375.1 PASS NA None 89 NA True - G ENST00000378292.3 TMEM252 169693 __UNKNOWN__ __UNKNOWN__ 9 71151993 71151994 __UNKNOWN__ 3'UTR INS - - T rs35122443 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:71151993_71151994insT ENST00000377311.3 - 0 746_747 NM_153237.1 NP_694969.1 Q8N6L7 TM252_HUMAN transmembrane protein 252 NA NA NA integral component of membrane (GO:0016021) NA TCCAGGGCCCCTGGCCTGCCCT 0.589 NA NA NA T|T|TT|insertion 1097 0.21905 0.2141 0.1182 5008 , , NA 19376 0.2302 NA 0.1471 False NA ,,, NA NA NA 2504 0.3599 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 126 139.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 BC029780 CCDS35040.1 9q21.13 2012-07-19 2012-07-19 2012-07-19 ENSG00000181778 ENSG00000181778 169693 28537 protein-coding gene gene with protein product NA "chromosome 9 open reading frame 71" C9orf71 NA 12477932 Standard NM_153237 NM_153237 NA Approved MGC34760 uc004agt.3 Q8N6L7 OTTHUMG00000019967 ENST00000377311.3:c.*182->A chr9.hg19:g.71151994_71151994dupT 2 4 ref NA False 36 36 PASS 1 PASS ref->het 0 NA 96,98 22,22 8,6 1 1 True hg19 CCDS35040.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM252-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000052551.1 PASS NA None 126 NA True - T ENST00000377311.3 PTAR1 375743 __UNKNOWN__ __UNKNOWN__ 9 72374702 72374703 __UNKNOWN__ Intron INS - - GGACGCTTG rs3831183 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:72374702_72374703insGGACGCTTG ENST00000472967.2 - 1 107 PTAR1_ENST00000377200.5_Intron|PTAR1_ENST00000340434.4_Intron Q7Z6K3 PTAR1_HUMAN protein prenyltransferase alpha subunit repeat containing 1 NA NA NA protein prenylation (GO:0018342) protein prenyltransferase activity (GO:0008318) central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2) 5 CGAGGTCGGGTGGACGCTTGGC 0.738 NA NA NA 1304 0.260383 0.1006 0.4597 5008 , , NA 8820 0.1151 NA 0.3459 False NA ,,, NA NA NA 2504 0.3967 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 102 119.73 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.42 BC053622 CCDS47978.1 9q21.13 2008-10-01 ENSG00000188647 ENSG00000188647 375743 "Prenyltransferase alpha subunit repeat containing" 30449 protein-coding gene gene with protein product NA NA 12477932 Standard NM_001099666 NM_001099666 NA Approved uc004ahj.4 Q7Z6K3 OTTHUMG00000019982 ENST00000472967.2:c.86+65->CAAGCGTCC chr9.hg19:g.72374703_72374711dupGGACGCTTG 2 5 ref NA False 91 91 PASS 1 PASS ref->het 0 NA 66,66 20,21 16,16 1 1 Q5T7V5|Q5T7V6 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PTAR1-004 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000052584.2 PASS NA None 102 NA True - GGACGCTTG ENST00000472967.2 S1PR3 1903 __UNKNOWN__ __UNKNOWN__ 9 91608049 91608050 __UNKNOWN__ Intron INS - - A rs397707977|rs397807482|rs11398943 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:91608049_91608050insA ENST00000358157.2 + 1 249 C9orf47_ENST00000375851.2_3'UTR|C9orf47_ENST00000334490.5_3'UTR NM_005226.3 NP_005217.2 Q99500 S1PR3_HUMAN sphingosine-1-phosphate receptor 3 NA NA NA adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651) integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886) G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036) NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1) 34 CTACCATATACAAAGGGTAGAG 0.347 NA NA NA AAA|AAA|AAAA|insertion 2341 0.467452 0.6377 0.3833 5008 , , NA 17849 0.3452 NA 0.4394 False NA ,,, NA NA NA 2504 0.4519 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 83 90.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF022139 CCDS6680.1 9q22.1-q22.2 2012-08-08 2008-04-30 2008-04-30 ENSG00000213694 ENSG00000213694 1903 "GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate" 3167 protein-coding gene gene with protein product "sphingosine-1-phosphate receptor 3" 601965 "endothelial differentiation, sphingolipid G-protein-coupled receptor, 3" EDG3 NA 8878560, 9409733 Standard NM_005226 NM_005226 NA Approved EDG-3 uc004aqe.4 Q99500 OTTHUMG00000020173 ENST00000358157.2:c.-148+1439->A chr9.hg19:g.91608052_91608052dupA 4 4 ref NA False 60 60 PASS 3 PASS ref->het 0 NA 51,51 24,24 8,8 1 1 Q5SQD8|Q7Z5I2 True hg19 CCDS6680.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA S1PR3-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000355971.1 PASS NA None 83 NA True + A ENST00000358157.2 CTNNAL1 8727 __UNKNOWN__ __UNKNOWN__ 9 111775548 111775550 __UNKNOWN__ Intron DEL AGG AGG - rs10538092 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:111775548_111775550delAGG ENST00000325551.4 - 1 228 CTNNAL1_ENST00000325580.6_Intron|CTNNAL1_ENST00000374593.4_Intron|CTNNAL1_ENST00000374595.4_Intron NM_003798.2 NP_003789.1 Q9UBT7 CTNL1_HUMAN catenin (cadherin-associated protein), alpha-like 1 NA NA NA cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266) actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886) structural molecule activity (GO:0005198) cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2) 25 STAD - Stomach adenocarcinoma(157;0.0768) CGCGGCGGGAAGGAGAAGAGGGG 0.704 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 314 314.54 NA 505,2431 NA 112,281,1075 NA NA NA -1.5 0 NA dbSNP_119 7 723,4737 NA 137,449,2144 no intron CTNNAL1 NM_003798.2 249,730,3219 A1A1,A1R,RR NA 13.2418,17.2003,14.626 NA 1228,7168 NA NA NA SO:0001627 intron_variant 1.6 AF030233 CCDS6775.1, CCDS69638.1 9q31.2 2008-07-21 ENSG00000119326 ENSG00000119326 8727 2512 protein-coding gene gene with protein product "alpha-catulin", "alpha2-catulin" 604785 NA 9806841 Standard NM_003798 XM_005252291 NA Approved CLLP, alpha-CATU uc004bdo.1 Q9UBT7 OTTHUMG00000020466 ENST00000325551.4:c.141+31CCT>- chr9.hg19:g.111775548_111775550delAGG 0 3 ref NA False 151 151 PASS 1 PASS ref->het 0 NA 214,224 48,53 66,51 1 1 B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401 True hg19 CCDS6775.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CTNNAL1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000053577.1 PASS NA None 314 NA True - AGG ENST00000325551.4 ZNF618 114991 __UNKNOWN__ __UNKNOWN__ 9 116764833 116764839 __UNKNOWN__ Intron DEL TTTGCAC TTTGCAC - rs148995274|rs79577972|rs372954408 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:116764833_116764839delTTTGCAC ENST00000374126.5 + 6 610 ZNF618_ENST00000288466.7_Intron Q5T7W0 ZN618_HUMAN zinc finger protein 618 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) breast(1)|endometrium(4)|lung(10)|urinary_tract(1) 16 CATGTTCTCTTTTGCACTTGGCACTGG 0.633 NA NA NA 856 0.170927 0.0598 0.2378 5008 , , NA 17417 0.0119 NA 0.3082 False NA ,,, NA NA NA 2504 0.2965 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 316 304.12 NA 393,3393 NA 35,323,1535 NA NA NA -2.3 0 NA dbSNP_120 13 2521,5401 NA 446,1629,1886 no intron ZNF618 NM_133374.2 481,1952,3421 A1A1,A1R,RR NA 31.8228,10.3803,24.889 NA 2914,8794 NA NA NA SO:0001627 intron_variant 0.34 BC012922 CCDS48008.1 9q33.1 2010-04-21 ENSG00000157657 ENSG00000157657 114991 "Zinc fingers, C2H2-type" 29416 protein-coding gene gene with protein product "neural precursor cell expressed, developmentally down-regulated 10" NA NA 11853319 Standard XM_054983 NM_133374 NA Approved KIAA1952, NEDD10 uc004bic.3 Q5T7W0 OTTHUMG00000020532 ENST00000374126.5:c.512-65TTTGCAC>- chr9.hg19:g.116764833_116764839delTTTGCAC 0 5 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 278,280 34,35 26,26 1 1 B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF618-004 KNOWN basic|appris_candidate_longest protein_coding NA protein_coding OTTHUMT00000053749.1 PASS NA None 316 NA True + TTTGCAC ENST00000374126.5 ZNF618 114991 __UNKNOWN__ __UNKNOWN__ 9 116764883 116764884 __UNKNOWN__ Intron INS - - CT rs367882585|rs3034072|rs547301471|rs558325879|rs544778767 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:116764883_116764884insCT ENST00000374126.5 + 6 610 ZNF618_ENST00000288466.7_Intron Q5T7W0 ZN618_HUMAN zinc finger protein 618 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) breast(1)|endometrium(4)|lung(10)|urinary_tract(1) 16 CACCCCCATCCCTCTCTCTCTC 0.624 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 401 349.26 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.51 BC012922 CCDS48008.1 9q33.1 2010-04-21 ENSG00000157657 ENSG00000157657 114991 "Zinc fingers, C2H2-type" 29416 protein-coding gene gene with protein product "neural precursor cell expressed, developmentally down-regulated 10" NA NA 11853319 Standard XM_054983 NM_133374 NA Approved KIAA1952, NEDD10 uc004bic.3 Q5T7W0 OTTHUMG00000020532 ENST00000374126.5:c.512-20->CT chr9.hg19:g.116764892_116764893dupCT 8 4 ref NA False 54 54 PASS 7 PASS ref->het 0 NA 259,266 57,57 83,79 1 1 B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF618-004 KNOWN basic|appris_candidate_longest protein_coding NA protein_coding OTTHUMT00000053749.1 PASS NA None 401 NA True + CT ENST00000374126.5 TTLL11 158135 __UNKNOWN__ __UNKNOWN__ 9 124855330 124855331 __UNKNOWN__ In_Frame_Ins INS - - TGGCCT rs3833704|rs201653732 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:124855330_124855331insTGGCCT ENST00000373776.3 - 1 554_555 c.367_368insAGGCCA c.(367-369)aca>aAGGCCAca p.122_123insKA TTLL11_ENST00000474723.1_5'UTR|TTLL11_ENST00000321582.5_In_Frame_Ins_p.122_123insKA NM_194252.2 NP_919228.2 Q8NHH1 TTL11_HUMAN tubulin tyrosine ligase-like family, member 11 122 NA NA cellular protein modification process (GO:0006464) cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856) ligase activity (GO:0016874) breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1) 18 cgtctccgctgtggcctcggcc 0.762 NA NA NA 678 0.135383 0.1044 0.1254 5008 , , NA 10384 0.0367 NA 0.2773 False NA ,,, NA NA NA 2504 0.1401 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 72 70.29 NA , 363,1875 NA 124,115,880 NA NA NA , -4.8 0 NA dbSNP_107 2 1330,3776 NA 463,404,1686 no coding,coding TTLL11 NM_194252.2,NM_001139442.1 , 587,519,2566 A1A1,A1R,RR NA 26.0478,16.2198,23.0528 , , NA 1693,5651 NA NA NA SO:0001652 inframe_insertion 0.58 AF521886 CCDS6834.2, CCDS48012.1 9q34.11 2013-02-14 2005-07-28 2005-07-28 ENSG00000175764 ENSG00000175764 158135 "Tubulin tyrosine ligase-like family" 18113 protein-coding gene gene with protein product NA "chromosome 9 open reading frame 20" C9orf20 NA 15890843 Standard XM_088486 NM_001139442 NA Approved bA244O19.1 uc011lyl.2 Q8NHH1 OTTHUMG00000020597 ENST00000373776.3:c.362_367dupAGGCCA chr9.hg19:g.124855331_124855336dupTGGCCT ENSP00000362881:p.Ala122_Thr123insLysAla 2 3 ref NA False 53 53 PASS 1 PASS ref->het 0 NA 49,50 18,18 4,4 1 1 True hg19 CCDS6834.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TTLL11-004 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000053907.1 PASS NA None 72 NA True - TGGCCT ENST00000373776.3 WDR38 401551 __UNKNOWN__ __UNKNOWN__ 9 127615910 127615911 __UNKNOWN__ Intron INS - - GGGA LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:127615910_127615911insGGGA ENST00000373574.1 + 1 125 NM_001045476.1|NM_001276374.1 NP_001038941.1|NP_001263303.1 Q5JTN6 WDR38_HUMAN WD repeat domain 38 NA NA NA hematopoietic progenitor cell differentiation (GO:0002244) breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1) 8 CCCAGACTCCCGGCTTTGGATG 0.604 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 145 138.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS43876.1, CCDS75898.1, CCDS75899.1 9q33.3 2013-01-09 ENSG00000136918 ENSG00000136918 401551 "WD repeat domain containing" 23745 protein-coding gene gene with protein product NA NA Standard NM_001045476 NM_001276375 NA Approved uc011lzo.3 Q5JTN6 OTTHUMG00000020664 ENST00000373574.1:c.69+31->GGGA chr9.hg19:g.127615910_127615911insGGGA 1 4 ref NA False 52 52 PASS 0 PASS ref->het 0 NA 102,104 26,27 17,14 1 1 A0PK24 True hg19 CCDS43876.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA WDR38-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000054048.1 PASS NA None 145 NA True + GGGA ENST00000373574.1 MVB12B 89853 __UNKNOWN__ __UNKNOWN__ 9 129265898 129265906 __UNKNOWN__ 3'UTR DEL GCTCCCTCC GCTCCCTCC - rs561869726|rs3841410|rs201530400 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:129265898_129265906delGCTCCCTCC ENST00000361171.3 + 0 1397_1405 MVB12B_ENST00000485886.1_3'UTR NM_033446.2 NP_258257.1 Q9H7P6 MB12B_HUMAN multivesicular body subunit 12B NA NA NA protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162) cytosol (GO:0005829)|early endosome (GO:0005769)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982) lipid binding (GO:0008289) NA ACGCCCACCGGCTCCCTCCGCTCCCTCCT 0.636 NA NA NA 1251 0.2498 0.4584 0.1556 5008 , , NA 16265 0.1538 NA 0.2078 False NA ,,, NA NA NA 2504 0.1769 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 580 577.33 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AK000001 CCDS35142.1 9q34.12 2012-12-03 2012-12-03 2012-12-03 ENSG00000196814 ENSG00000196814 89853 23368 protein-coding gene gene with protein product NA "chromosome 9 open reading frame 28", "family with sequence similarity 125, member B" C9orf28, FAM125B NA 18005716, 20654576, 22232651 Standard XM_088525 NM_033446 NA Approved FLJ00001 uc004bqh.2 Q9H7P6 OTTHUMG00000020687 ENST00000361171.3:c.*364GCTCCCTCC>- chr9.hg19:g.129265907_129265915delGCTCCCTCC 1 5 ref NA False 35 35 PASS 2 PASS ref->het 0 NA 456,461 53,53 99,95 1 1 Q8N6S7 True hg19 CCDS35142.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MVB12B-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000054110.1 PASS NA None 580 NA True + GCTCCCTCC ENST00000361171.3 PTGES 9536 __UNKNOWN__ __UNKNOWN__ 9 132501706 132501707 __UNKNOWN__ 3'UTR INS - - ACACAT rs1134680|rs137962222|rs35042232|rs3884098|rs367837009 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:132501706_132501707insACACAT ENST00000340607.4 - 0 676_677 PTGES_ENST00000481476.1_De_novo_Start_OutOfFrame NM_004878.4 NP_004869.1 O14684 PTGES_HUMAN prostaglandin E synthase NA NA NA acute inflammatory response (GO:0002526)|arachidonic acid metabolic process (GO:0019369)|chronic inflammatory response (GO:0002544)|cyclooxygenase pathway (GO:0019371)|negative regulation of cell proliferation (GO:0008285)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|response to calcium ion (GO:0051592)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281) endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471) glutathione binding (GO:0043295)|prostaglandin-E synthase activity (GO:0050220) lung(1)|skin(1) 2 Ovarian(14;0.00556) Aacatacacacacacatacaca 0.525 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 143 138.31 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.68 AF010316 CCDS6927.1 9q34.3 2008-07-21 ENSG00000148344 ENSG00000148344 9536 9599 protein-coding gene gene with protein product "microsomal glutathione S-transferase 1-like 1", "tumor protein p53 inducible protein 12", "p53-induced gene 12", "microsomal prostaglandin E synthase-1", "glutathione S-transferase 1-like 1", "MGST1-like 1" 605172 MGST1L1 NA 9305847, 10091672 Standard NM_004878 NM_004878 NA Approved MGST-IV, PIG12, MGST1-L1, TP53I12 uc004byi.3 O14684 OTTHUMG00000020791 ENST00000340607.4:c.*184->ATGTGT chr9.hg19:g.132501707_132501712dupACACAT 2 2 ref NA False 42 42 PASS 1 PASS ref->het 0 NA 97,97 24,24 23,25 1 1 O14900|Q5SZC0 True hg19 CCDS6927.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PTGES-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000054599.2 PASS NA None 143 NA True - ACACAT ENST00000340607.4 MAN1B1 11253 __UNKNOWN__ __UNKNOWN__ 9 139997646 139997647 __UNKNOWN__ Intron DEL TG TG - rs369265025 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr9:139997646_139997647delTG ENST00000371589.4 + 8 1327 MAN1B1_ENST00000474902.1_Intron NM_016219.4 NP_057303.2 Q9UKM7 MA1B1_HUMAN mannosidase, alpha, class 1B, member 1 NA NA NA cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982) calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571) autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2) 14 all_cancers(76;0.0926) Myeloproliferative disorder(178;0.0511) STAD - Stomach adenocarcinoma(284;0.0878) OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513) ACATTCACACTGTTGCAGGCGT 0.569 NA NA NA 369 0.0736821 0.261 0.0115 5008 , , NA 29025 0.005 NA 0.002 False NA ,,, NA NA NA 2504 0.0092 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 520 537.68 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 7.88 AF145732 CCDS7029.1 9q34.3 2014-05-27 ENSG00000177239 ENSG00000177239 11253 6823 protein-coding gene gene with protein product "endoplasmic reticulum alpha-mannosidase 1", "alpha 1,2-mannosidase", "endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1", "ER alpha 1,2-mannosidase", "Man9GlcNAc2-specific processing alpha-mannosidase" 604346 NA 10409699, 10521544 Standard NM_016219 NM_016219 NA Approved MANA-ER, MRT15 uc004cld.3 Q9UKM7 OTTHUMG00000020978 ENST00000371589.4:c.1254+1522TG>- chr9.hg19:g.139997646_139997647delTG 0 3 ref NA False 36 36 PASS 1 PASS ref->het 0 NA 410,479 55,62 58,44 1 1 Q5VSG3|Q9BRS9|Q9Y5K7 True hg19 CCDS7029.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAN1B1-004 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000055294.2 PASS NA None 520 NA True + TG ENST00000371589.4 TRDMT1 1787 __UNKNOWN__ __UNKNOWN__ 10 17243443 17243444 __UNKNOWN__ Intron INS - - CCGCCCCACAGTGT rs36094500|rs577437637 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:17243443_17243444insCCGCCCCACAGTGT ENST00000377799.3 - 1 112 TRDMT1_ENST00000377766.5_Intron|TRDMT1_ENST00000457442.2_Intron|TRDMT1_ENST00000412821.3_Intron|TRDMT1_ENST00000488990.1_Intron|TRDMT1_ENST00000358282.7_Intron|TRDMT1_ENST00000351358.4_Intron NM_004412.5 NP_004403.1 O14717 TRDMT_HUMAN tRNA aspartic acid methyltransferase 1 NA NA NA C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488) cytoplasm (GO:0005737)|nucleus (GO:0005634) DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175) breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1) 18 Pentamidine(DB00738) ACAACCGAGGGCCGCCCCACAG 0.718 NA NA NA 1062 0.212061 0.1793 0.1758 5008 , , NA 16463 0.1964 NA 0.2982 False NA ,,, NA NA NA 2504 0.2096 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 104 126.26 NA 417,2233 NA 87,243,995 NA NA NA 1 0 NA dbSNP_120 21 1076,3638 NA 250,576,1531 no intron TRDMT1 NM_004412.5 337,819,2526 A1A1,A1R,RR NA 22.8256,15.7358,20.2743 NA 1493,5871 NA NA NA SO:0001627 intron_variant 0 AJ223333 CCDS7114.1 10p15.1 2006-10-23 2006-10-23 2006-10-23 ENSG00000107614 ENSG00000107614 1787 2.1.1.37 2977 protein-coding gene gene with protein product 602478 "DNA (cytosine-5-)-methyltransferase 2" DNMT2 NA 9425235, 9763678, 16424344 Standard NM_004412 NM_004412 NA Approved RNMT1 uc001iop.3 O14717 OTTHUMG00000017745 ENST00000377799.3:c.64+125->ACACTGTGGGGCGG chr10.hg19:g.17243443_17243444insCCGCCCCACAGTGT 3 6 ref NA False 50 50 PASS 2 PASS ref->het 0 NA 69,69 7,7 30,30 1 1 B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6 True hg19 CCDS7114.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRDMT1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000047024.3 PASS NA None 104 NA True - CCGCCCCACAGTGT ENST00000377799.3 CXCL12 6387 __UNKNOWN__ __UNKNOWN__ 10 44873992 44873993 __UNKNOWN__ Intron INS - - CT rs2839694|rs200544719|rs71761625 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:44873992_44873993insCT ENST00000395794.2 - 3 310 CXCL12_ENST00000374426.2_Intron|AL137026.1_ENST00000593376.1_Intron|CXCL12_ENST00000374429.2_Intron|CXCL12_ENST00000395793.3_Intron|CXCL12_ENST00000395795.4_Intron|CXCL12_ENST00000343575.6_3'UTR NM_001178134.1 NP_001171605.1 P48061 SDF1_HUMAN chemokine (C-X-C motif) ligand 12 NA NA NA adult locomotory behavior (GO:0008344)|ameboidal cell migration (GO:0001667)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|motor neuron axon guidance (GO:0008045)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of leukocyte tethering or rolling (GO:1903237)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|patterning of blood vessels (GO:0001569)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell adhesion (GO:0045785)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of T cell migration (GO:2000406)|regulation of actin polymerization or depolymerization (GO:0008064)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to peptide hormone (GO:0043434)|response to radiation (GO:0009314)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|telencephalon cell migration (GO:0022029) external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062) chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|CXCR chemokine receptor binding (GO:0045236)|receptor binding (GO:0005102) endometrium(1)|large_intestine(1)|lung(3)|skin(1) 6 Tinzaparin(DB06822) GTTAAGGCCCCCTCCCCCACGT 0.5 NA NA NA 959 0.191494 0.0484 0.438 5008 , , NA 19550 0.129 NA 0.2594 False NA ,,, NA NA NA 2504 0.2045 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 751 786.13 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.41 L36033 CCDS7207.1, CCDS31186.1, CCDS44373.1, CCDS53527.1, CCDS60518.1 10q11.1 2013-02-28 2010-05-11 2002-08-23 ENSG00000107562 ENSG00000107562 6387 "Endogenous ligands" 10672 protein-coding gene gene with protein product 600835 "stromal cell-derived factor 1" SDF1A, SDF1B, SDF1 NA 7490086 Standard NM_000609 NM_001033886 NA Approved SCYB12, SDF-1a, SDF-1b, PBSF, TLSF-a, TLSF-b, TPAR1 uc021ppm.1 P48061 OTTHUMG00000018054 ENST00000395794.2:c.266+91->AG chr10.hg19:g.44873993_44873994dupCT 2 10 ref NA False 66 66 PASS 1 PASS ref->het 0 NA 603,611 72,72 70,67 1 1 B2R4G0|E7EVL0|H7BYN8|Q2L985|Q2L986|Q2L988|Q5IT36|Q6ICW0|Q9H554 True hg19 CCDS53527.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CXCL12-004 PUTATIVE basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000358151.1 PASS NA None 751 NA True - CT ENST00000395794.2 NRBF2 29982 __UNKNOWN__ __UNKNOWN__ 10 64914016 64914017 __UNKNOWN__ 3'UTR INS - - A rs398013793|rs35751397 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:64914016_64914017insA ENST00000277746.6 + 0 1083_1084 NRBF2_ENST00000435510.2_3'UTR NM_030759.3 NP_110386.2 Q96F24 NRBF2_HUMAN nuclear receptor binding factor 2 NA NA NA gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367) cytoplasm (GO:0005737)|nucleoplasm (GO:0005654) large_intestine(2)|lung(3)|skin(1) 6 Prostate(12;0.0119)|all_hematologic(501;0.191) GAGGAAATAATACAGTAATCGT 0.401 NA NA NA A|A|AA|insertion 1958 0.390974 0.2859 0.3112 5008 , , NA 20232 0.3591 NA 0.4891 False NA ,,, NA NA NA 2504 0.5215 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 754 694.78 NA 1118,2082 NA 315,488,797 NA NA NA 2.8 0.1 NA dbSNP_126 16 2929,3097 NA 931,1067,1015 no utr-3 NRBF2 NM_030759.3 1246,1555,1812 A1A1,A1R,RR NA 48.606,34.9375,43.8652 NA 4047,5179 NA NA NA SO:0001624 3_prime_UTR_variant 0.58 D82519 CCDS7268.1, CCDS60537.1 10q22.1 2012-11-01 ENSG00000148572 ENSG00000148572 29982 19692 protein-coding gene gene with protein product "comodulator of PPAR and RXR 1", "comodulator of PPAR and RXR 2" NA NA 10786636 Standard NM_030759 NM_001282405 NA Approved DKFZp564C1664, FLJ30395, COPR1, COPR2 uc001jmj.4 Q96F24 OTTHUMG00000018309 ENST00000277746.6:c.*39->A chr10.hg19:g.64914017_64914017dupA 2 3 ref NA False 132 132 PASS 1 PASS ref->het 0 NA 600,603 84,84 66,65 1 1 A6PW36|B4DWS0|Q86UR2|Q96NP6|Q9H0S9|Q9H2I2 True hg19 CCDS7268.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NRBF2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000048247.1 PASS NA None 754 NA True + A ENST00000277746.6 JMJD1C-AS1 84989 __UNKNOWN__ __UNKNOWN__ 10 65225899 65225900 __UNKNOWN__ RNA INS - - GGCGGC rs56314550|rs3841602 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:65225899_65225900insGGCGGC ENST00000609436.1 + 0 911_912 NR_027182.1 JMJD1C antisense RNA 1 NA NA NA NA CCAGATCCAGAggcggcggcgg 0.663 NA NA NA 1972 0.39377 0.2761 0.2997 5008 , , NA 10943 0.3978 NA 0.4831 False NA ,,, NA NA NA 2504 0.5235 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 60 54.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.51 AK314171 10q21.3 2013-02-07 ENSG00000272767 84989 "Long non-coding RNAs" 28222 non-coding RNA RNA, long non-coding NA NA 12477932 Standard NR_027182 NR_027182 NA Approved uc010qir.2 ENST00000609436.1: chr10.hg19:g.65225900_65225905dupGGCGGC 8 4 ref NA False 32 32 PASS 6 PASS ref->het 0 NA 31,35 10,10 18,16 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA JMJD1C-AS1-001 KNOWN basic antisense NA antisense OTTHUMT00000472626.1 PASS NA None 60 NA True + GGC ENST00000609436.1 PAX2 5076 __UNKNOWN__ __UNKNOWN__ 10 102588580 102588584 __UNKNOWN__ 3'UTR DEL AACAA AACAA - rs71013469 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:102588580_102588584delAACAA ENST00000355243.3 + 0 2939_2943 PAX2_ENST00000428433.1_3'UTR|PAX2_ENST00000361791.3_3'UTR|PAX2_ENST00000370296.2_3'UTR NM_000278.3|NM_003989.3 NP_000269|NP_003980.2 Q02962 PAX2_HUMAN paired box 2 NA NA NA aging (GO:0007568)|axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cell fate determination (GO:0001709)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucose stimulus (GO:0071333)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|glial cell differentiation (GO:0010001)|inner ear morphogenesis (GO:0042472)|mesenchymal to epithelial transition (GO:0060231)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|mesonephric duct development (GO:0072177)|mesonephric tubule formation (GO:0072172)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric nephron tubule formation (GO:0072289)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytolysis (GO:0045918)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of programmed cell death (GO:0043069)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|neural tube closure (GO:0001843)|optic chiasma development (GO:0061360)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|optic nerve development (GO:0021554)|optic nerve morphogenesis (GO:0021631)|optic nerve structural organization (GO:0021633)|pancreas development (GO:0031016)|paramesonephric duct development (GO:0061205)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of optic nerve formation (GO:2000597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|protein kinase B signaling (GO:0043491)|reactive oxygen species metabolic process (GO:0072593)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of metanephros size (GO:0035566)|response to nutrient levels (GO:0031667)|retinal pigment epithelium development (GO:0003406)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|ureter development (GO:0072189)|ureter maturation (GO:0035799)|ureter morphogenesis (GO:0072197)|urogenital system development (GO:0001655)|vestibulocochlear nerve formation (GO:0021650)|visual perception (GO:0007601) centriolar satellite (GO:0034451)|lysosome (GO:0005764)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993) core promoter proximal region sequence-specific DNA binding (GO:0000987)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|superoxide-generating NADPH oxidase activity (GO:0016175)|transcription regulatory region DNA binding (GO:0044212) endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1) 18 Colorectal(252;0.234) Epithelial(162;1.32e-08)|all cancers(201;7.32e-07) TGCAAAAAGGAACAAAACAACACAA 0.522 NA NA NA 394 0.0786741 0.0045 0.0922 5008 , , NA 14029 0.004 NA 0.173 False NA ,,, NA NA NA 2504 0.1493 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 92 94.41 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 CCDS7499.1, CCDS41561.1 10q24.31 2011-06-20 2007-07-12 ENSG00000075891 ENSG00000075891 5076 "Paired boxes", "Homeoboxes / PRD class" 8616 protein-coding gene gene with protein product 167409 "paired box gene 2" NA 8431641, 7981748 Standard NM_003990 NA Approved uc001krk.4 Q02962 OTTHUMG00000018913 ENST00000355243.3:c.*1208AACAA>- chr10.hg19:g.102588585_102588589delAACAA 1 6 ref NA False 34 34 PASS 2 PASS ref->het 0 NA 61,61 23,24 8,8 1 1 Q15105|Q15110|Q15837|Q5SZP2|Q5SZP3 True hg19 CCDS41561.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PAX2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000049868.2 PASS NA None 92 NA True + AACAA ENST00000355243.3 DUSP5 1847 __UNKNOWN__ __UNKNOWN__ 10 112271242 112271244 __UNKNOWN__ 3'UTR DEL GTT GTT - rs3833737 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:112271242_112271244delGTT ENST00000369583.3 + 0 2497_2499 NM_004419.3 NP_004410.3 Q16690 DUS5_HUMAN dual specificity phosphatase 5 NA NA NA endoderm formation (GO:0001706)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470) nucleus (GO:0005634) MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138) kidney(2)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2) 13 Breast(234;0.0848) Epithelial(162;0.000276)|all cancers(201;0.00465)|BRCA - Breast invasive adenocarcinoma(275;0.12) TATGTTACTGGTTGTTGTTGTTG 0.325 NA NA NA 421 0.0840655 0.0197 0.0591 5008 , , NA 25195 0.1637 NA 0.0835 False NA ,,, NA NA NA 2504 0.1074 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 245 239.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.02 U16996 CCDS7566.1 10q25 2011-06-09 ENSG00000138166 ENSG00000138166 1847 "Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases" 3071 protein-coding gene gene with protein product 603069 NA 7806236 Standard NM_004419 NM_004419 NA Approved HVH3 uc001kzd.3 Q16690 OTTHUMG00000019040 ENST00000369583.3:c.*1060GTT>- chr10.hg19:g.112271251_112271253delGTT 4 4 ref NA False 39 39 PASS 5 PASS ref->het 0 NA 170,172 35,35 48,48 2 2 Q12997|Q5T603 True hg19 CCDS7566.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DUSP5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000050333.1 PASS NA None 245 NA True + GTT ENST00000369583.3 CASP7 840 __UNKNOWN__ __UNKNOWN__ 10 115439641 115439642 __UNKNOWN__ 5'UTR DEL TT TT - rs10553596 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:115439641_115439642delTT ENST00000345633.4 + 0 214_215 CASP7_ENST00000369321.2_5'UTR|CASP7_ENST00000369318.3_5'UTR|CASP7_ENST00000369331.4_Intron NM_033339.4 NP_203125.1 P55210 CASP7_HUMAN caspase 7, apoptosis-related cysteine peptidase NA NA NA activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway (GO:0097193)|proteolysis (GO:0006508) cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234) kidney(1)|large_intestine(1)|lung(5)|ovary(1) 8 Colorectal(252;0.0946)|Breast(234;0.188) Epithelial(162;0.012)|all cancers(201;0.014) GCGCCGAGACTTTTAGTTTCGC 0.693 NA NA NA 1456 0.290735 0.4244 0.1945 5008 , , NA 14114 0.252 NA 0.2416 False NA ,,, NA NA NA 2504 0.2689 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 178 176.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 U37448 CCDS7580.1, CCDS7581.1, CCDS7582.1, CCDS58096.1, CCDS73200.1 10q25 2006-02-17 2005-08-17 ENSG00000165806 ENSG00000165806 840 "Caspases" 1508 protein-coding gene gene with protein product 601761 "caspase 7, apoptosis-related cysteine protease" NA 8521391, 8576161 Standard NM_033338 NM_033338 NA Approved MCH3, CMH-1, ICE-LAP3 uc010qsa.3 P55210 OTTHUMG00000019076 ENST00000345633.4:c.-170TT>- chr10.hg19:g.115439643_115439644delTT 2 4 ref NA False 53 53 PASS 4 PASS ref->het 0 NA 132,136 27,27 23,20 1 1 B4DQU7|B5BU45|D3DRB8|Q13364|Q53YD5|Q5SVL0|Q5SVL3|Q96BA0 True hg19 CCDS7581.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CASP7-005 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000050439.1 PASS NA None 178 NA True + T ENST00000345633.4 BUB3 9184 __UNKNOWN__ __UNKNOWN__ 10 124914414 124914415 __UNKNOWN__ Intron INS - - CTGA rs113756220|rs72053976 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr10:124914414_124914415insCTGA ENST00000368859.2 + 2 84 BUB3_ENST00000368865.4_Intron|BUB3_ENST00000538238.1_Intron|BUB3_ENST00000368858.5_Intron O43684 BUB3_HUMAN BUB3 mitotic checkpoint protein NA NA NA anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|attachment of spindle microtubules to kinetochore (GO:0008608)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|regulation of chromosome segregation (GO:0051983)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|spindle assembly checkpoint (GO:0071173) cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634) endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1) 9 all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163) CCCTGGGGACTCTGGGCGCCTG 0.668 NA NA NA 1216 0.242812 0.3419 0.1383 5008 , , NA 13491 0.375 NA 0.1153 False NA ,,, NA NA NA 2504 0.1779 NA NA NA GBM(161;1111 1985 17553 20049 26037) PASS NA NA NA 0 NA NA NA NA NA 112 115.04 NA , 1248,3014 NA 182,884,1065 NA NA NA , 0.2 0.1 NA dbSNP_130 37 1053,7201 NA 83,887,3157 no intron,intron BUB3 NM_004725.3,NM_001007793.2 , 265,1771,4222 A1A1,A1R,RR NA 12.7575,29.282,18.3845 , , NA 2301,10215 NA NA NA SO:0001627 intron_variant 0 AF053304 CCDS7635.1, CCDS31306.1 10q24 2013-01-17 2013-01-17 ENSG00000154473 ENSG00000154473 9184 "WD repeat domain containing" 1151 protein-coding gene gene with protein product 603719 "BUB3 (budding uninhibited by benzimidazoles 3, yeast) homolog", "budding uninhibited by benzimidazoles 3 homolog (yeast)" NA 9660858 Standard NM_004725 NA Approved BUB3L uc001lhe.2 O43684 OTTHUMG00000019197 ENST00000368859.2:c.0-19->CTGA chr10.hg19:g.124914414_124914415insCTGA 1 2 ref NA False 37 37 PASS 0 PASS ref->het 0 NA 79,80 20,20 14,14 1 1 A6NJ42|B2R6E7|D3DRE9|O43685 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BUB3-004 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000050838.2 PASS NA None 112 NA True + CTGA ENST00000368859.2 BET1L 51272 __UNKNOWN__ __UNKNOWN__ 11 207359 207360 __UNKNOWN__ 5'UTR INS - - GGCCACAGCCGCCTCAGACGT rs71286246|rs11274545|rs6144172|rs556691696 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:207359_207360insGGCCACAGCCGCCTCAGACGT ENST00000382762.3 - 0 68_69 BET1L_ENST00000325147.9_5'UTR|BET1L_ENST00000410108.1_5'UTR|BET1L_ENST00000529614.2_5'UTR NM_001098787.1|NM_016526.4 NP_001092257.1|NP_057610.2 Bet1 golgi vesicular membrane trafficking protein-like NA NA NA NA all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713) all cancers(45;4.2e-27)|Epithelial(43;2.8e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.7e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122) GACACCGACGCGGCCACAGCCG 0.762 NA NA NA 3056 0.610224 0.5877 0.7133 5008 , , NA 15935 0.62 NA 0.6889 False NA ,,, NA NA NA 2504 0.4765 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 65 55.56 NA , 1835,899 NA 837,161,369 NA NA NA , -2.6 0 NA dbSNP_126 4 4289,1397 NA 1969,351,523 no utr-5,utr-5 BET1L NM_016526.4,NM_001098787.1 , 2806,512,892 A1A1,A1R,RR NA 24.5691,32.8822,27.2684 , , NA 6124,2296 NA NA NA SO:0001623 5_prime_UTR_variant 0.1 AF234160 CCDS7689.1, CCDS41582.1 11p15.5 2013-03-08 2013-03-08 ENSG00000177951 ENSG00000177951 51272 19348 protein-coding gene gene with protein product "golgi integral membrane protein 3" 615417 "blocked early in transport 1 homolog (S. cerevisiae) like", "blocked early in transport 1 homolog (S. cerevisiae)-like" NA 9242691, 15004235 Standard NM_016526 NM_016526 NA Approved GS15, GOLIM3 uc001loe.2 Q9NYM9 OTTHUMG00000119071 ENST00000382762.3:c.-39->ACGTCTGAGGCGGCTGTGGCC chr11.hg19:g.207359_207360insGGCCACAGCCGCCTCAGACGT 2 3 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 6,8 8,9 54,51 1 1 True hg19 CCDS41582.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BET1L-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000239285.1 PASS NA None 65 NA True - GGCCACAGCCGCCTCAGACGT ENST00000382762.3 RPLP2 6181 __UNKNOWN__ __UNKNOWN__ 11 810010 810018 __UNKNOWN__ 5'UTR DEL CTCCGCCGC CTCCGCCGC - rs11540443|rs17155725|rs542687757 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:810010_810018delCTCCGCCGC ENST00000321153.4 + 0 364_372 RPLP2_ENST00000530797.1_5'UTR|RPLP2_ENST00000532004.1_3'UTR NM_001004.3 NP_000995.1 P05387 RLA2_HUMAN ribosomal protein, large, P2 NA NA NA cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083) cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020) RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735) lung(1) 1 all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198) all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703) CGTGAGACTTCTCCGCCGCCTCCGCCGCA 0.713 NA NA NA 1438 0.287141 0.0877 0.2017 5008 , , NA 15128 0.4018 NA 0.3161 False NA ,,, NA NA NA 2504 0.4693 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 50 43.61 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.12 M17887 CCDS7717.1 11p15.5 2011-07-29 ENSG00000177600 ENSG00000177600 6181 "L ribosomal proteins" 10377 protein-coding gene gene with protein product "60S acidic ribosomal protein P2", "acidic ribosomal phosphoprotein P2" 180530 D11S2243E NA 3323886 Standard NM_001004 NM_001004 NA Approved P2, RPP2, MGC71408, LP2 uc001lrq.1 P05387 OTTHUMG00000133317 ENST00000321153.4:c.-23CTCCGCCGC>- chr11.hg19:g.810019_810027delCTCCGCCGC 1 4 ref NA False 33 33 PASS 2 PASS ref->het 0 NA 40,41 3,3 8,9 1 1 Q6FG96 True hg19 CCDS7717.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPLP2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257115.2 PASS NA None 50 NA True + CTCCGCCGC ENST00000321153.4 CDKN1C 1028 __UNKNOWN__ __UNKNOWN__ 11 2905204 2905205 __UNKNOWN__ Intron INS - - C rs34289096 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:2905204_2905205insC ENST00000380725.1 - 3 517 CDKN1C_ENST00000414822.3_Intron|CDKN1C_ENST00000440480.2_Intron|CDKN1C_ENST00000313407.6_Intron|CDKN1C_ENST00000430149.2_Intron P49918 CDN1C_HUMAN cyclin-dependent kinase inhibitor 1C (p57, Kip2) NA NA NA adrenal gland development (GO:0030325)|aging (GO:0007568)|camera-type eye development (GO:0043010)|cell cycle arrest (GO:0007050)|digestive system development (GO:0055123)|embryonic placenta morphogenesis (GO:0060669)|genetic imprinting (GO:0071514)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|myeloid cell differentiation (GO:0030099)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of kinase activity (GO:0033673)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron maturation (GO:0042551)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|skeletal system development (GO:0001501)|uterus development (GO:0060065) cytoplasm (GO:0005737)|nucleus (GO:0005634) cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861) central_nervous_system(1)|lung(1) 2 all_epithelial(84;0.000187)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|Breast(177;0.00328)|all_neural(188;0.00681)|all_lung(207;0.157)|Lung NSC(207;0.216) BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19) GGCCCTCCGCGCCCCCCCAGGT 0.733 NA NA NA CCCCCC|CCCCCCC|CCCCCCCC|cryptic_indel 1866 0.372604 0.2156 0.3112 5008 , , NA 8397 0.6319 NA 0.3231 False NA ,,, NA NA NA 2504 0.4121 NA NA NA GBM(111;59 1151 2497 5746 16112 18241 29216) PASS NA NA NA 0 NA NA NA NA NA 245 239.94 NA ,, 55,642,2361 NA 17,2,19,188,264,1039 NA NA NA ,, -5 0 NA dbSNP_126 4 119,1919,4610 NA 30,18,41,505,891,1839 no intron,intron,intron CDKN1C NM_001122631.1,NM_001122630.1,NM_000076.2 ,, 47,20,60,693,1155,2878 A1A1,A1A2,A1R,A2A2,A2R,RR NA 30.6558,22.7927,28.1784 ,, ,, NA 174,2561,6971 NA NA NA SO:0001627 intron_variant 0.21 D64137 CCDS7738.1, CCDS44519.1 11p15.5 2014-09-17 2004-02-13 ENSG00000129757 ENSG00000129757 1028 1786 protein-coding gene gene with protein product 600856 "Beckwith-Wiedemann syndrome" BWCR, BWS NA 7729684 Standard NM_000076 NM_000076 NA Approved P57, KIP2 uc001lws.4 P49918 OTTHUMG00000010040 ENST00000380725.1:c.391+23->G chr11.hg19:g.2905211_2905211dupC 8 8 ref NA False 108 108 PASS 7 PASS ref->het 0 NA 163,163 37,39 40,38 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDKN1C-002 PUTATIVE basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000027775.1 PASS NA None 245 NA True - C ENST00000380725.1 NUP98 4928 __UNKNOWN__ __UNKNOWN__ 11 3733434 3733435 __UNKNOWN__ Intron DEL TG TG - rs200207788|rs36088476 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:3733434_3733435delTG ENST00000324932.7 - 20 3163 NUP98_ENST00000359171.4_Intron|NUP98_ENST00000397004.4_3'UTR|NUP98_ENST00000355260.3_Intron|NUP98_ENST00000397007.4_3'UTR NM_016320.4|NM_139132.3 NP_057404.2|NP_624358.2 P52948 NUP98_HUMAN nucleoporin 98kDa NA NA NA carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032) cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654) peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215) NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 66 Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227) BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199) AAGATTAAACTGCACATCAGGT 0.322 NA NA T "HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11" AML NA 855 0.170727 0.1346 0.0692 5008 , , NA 18003 0.2688 NA 0.1819 False NA ,,, NA NA NA 2504 0.1789 NA NA NA PASS Dom yes 11 11p15 4928 nucleoporin 98kDa NA L 0 NA NA NA NA NA 178 178.03 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF071076, AF231130, BC012906, BG773331 CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1 11p15 2008-02-26 2002-08-29 ENSG00000110713 ENSG00000110713 4928 8068 protein-coding gene gene with protein product 601021 "nucleoporin 98kD" NA 9166830 Standard NM_016320 NM_139131 NA Approved NUP96 uc001lyh.3 P52948 OTTHUMG00000011846 ENST00000324932.7:c.2742+358CA>- chr11.hg19:g.3733434_3733435delTG 0 3 ref NA False 44 44 PASS 1 PASS ref->het 0 NA 141,141 20,20 16,16 1 1 Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5 True hg19 CCDS7746.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NUP98-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000032766.3 PASS NA None 178 NA True - TG ENST00000324932.7 STIM1 6786 __UNKNOWN__ __UNKNOWN__ 11 3877114 3877118 __UNKNOWN__ 5'UTR DEL TCTCT TCTCT - rs147711952|rs199526280|rs3061890|rs200604943 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:3877114_3877118delTCTCT ENST00000300737.4 + 0 183_187 NM_003156.3 NP_003147.2 Q13586 STIM1_HUMAN stromal interaction molecule 1 NA NA NA activation of store-operated calcium channel activity (GO:0032237)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|regulation of calcium ion transport (GO:0051924)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115) cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)|microtubule (GO:0005874) calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|microtubule plus-end binding (GO:0051010)|store-operated calcium channel activity (GO:0015279) haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|liver(1)|lung(14)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 30 Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233) BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141) CCTTCTCGCCtctcttctcttctct 0.683 NA NA NA 1346 0.26877 0.0734 0.3746 5008 , , NA 10637 0.3542 NA 0.3807 False NA ,,, NA NA NA 2504 0.2546 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 261 228.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.02 BC021300, U52426 CCDS7749.1, CCDS60706.1, CCDS73247.1 11p15.5 2014-09-17 ENSG00000167323 ENSG00000167323 6786 "Sterile alpha motif (SAM) domain containing" 11386 protein-coding gene gene with protein product 605921 NA 8921403, 11463338, 11983428 Standard NM_003156 NM_003156 NA Approved GOK, D11S4896E uc021qco.1 Q13586 OTTHUMG00000133360 ENST00000300737.4:c.-383TCTCT>- chr11.hg19:g.3877124_3877128delTCTCT 3 3 ref NA False 259 138 PASS 4 PASS ref->het 0 NA 122,123 86,88 56,53 1 1 E9PQJ4|Q8N382 True hg19 CCDS7749.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA STIM1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000257196.1 PASS NA None 261 NA True + TCTCT ENST00000300737.4 TUB 7275 __UNKNOWN__ __UNKNOWN__ 11 8123006 8123009 __UNKNOWN__ Intron DEL TCTG TCTG - rs66906803|rs398054959|rs3841659|rs72093838 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:8123006_8123009delTCTG ENST00000299506.2 + 12 1536 TUB_ENST00000305253.4_Intron|TUB_ENST00000534099.1_Intron NM_177972.2 NP_813977.1 P50607 TUB_HUMAN tubby bipartite transcription factor NA NA NA multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605) cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886) G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403) breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1) 26 all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17) Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184) TGTCCTTTTCTCTGTCTGTGCCTG 0.534 NA NA NA 1224 0.244409 0.2383 0.2925 5008 , , NA 23000 0.2857 NA 0.174 False NA ,,, NA NA NA 2504 0.2485 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 277 265.53 NA , 983,3281 NA 102,779,1251 NA NA NA , -2.3 0 NA dbSNP_130 118 1507,6747 NA 149,1209,2769 no intron,intron TUB NM_177972.2,NM_003320.4 , 251,1988,4020 A1A1,A1R,RR NA 18.2578,23.0535,19.8914 , , NA 2490,10028 NA NA NA SO:0001627 intron_variant 0 U54644 CCDS7786.1, CCDS7787.1 11p15.5 2013-08-06 2013-08-06 ENSG00000166402 ENSG00000166402 7275 12406 protein-coding gene gene with protein product 601197 "tubby (mouse) homolog", "tubby homolog (mouse)" NA 8612280 Standard NM_003320 NM_003320 NA Approved rd5 uc001mfy.3 P50607 OTTHUMG00000165690 ENST00000299506.2:c.1388-24TCTG>- chr11.hg19:g.8123010_8123013delTCTG 1 5 ref NA False 71 71 PASS 2 PASS ref->het 0 NA 192,193 66,66 29,30 2 2 D3DQU4|O00293|Q6B007 True hg19 CCDS7787.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TUB-003 PUTATIVE basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000385823.1 PASS NA None 277 NA True + TCTG ENST00000299506.2 RPL27A 6157 __UNKNOWN__ __UNKNOWN__ 11 8715262 8715263 __UNKNOWN__ Intron INS - - CAGG rs55680964|rs397775044|rs3833781 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:8715262_8715263insCAGG ENST00000531102.1 + 1 174 ST5_ENST00000534127.1_3'UTR|RP11-152H18.3_ENST00000529883.1_RNA|ST5_ENST00000357665.1_3'UTR|ST5_ENST00000530991.1_3'UTR|ST5_ENST00000313726.6_3'UTR|ST5_ENST00000526757.1_3'UTR P46776 RL27A_HUMAN ribosomal protein L27a NA NA NA cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083) cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020) poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735) haematopoietic_and_lymphoid_tissue(1)|lung(1) 2 Epithelial(150;3.24e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189) AGCGGGGACCTCAGGCAGGCAG 0.535 NA NA NA 1715 0.342452 0.3147 0.3429 5008 , , NA 18392 0.3006 NA 0.4066 False NA ,,, NA NA NA 2504 0.3569 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 95 102.5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.18 U14968 CCDS7790.1 11p15 2011-04-06 ENSG00000166441 6157 "L ribosomal proteins" 10329 protein-coding gene gene with protein product 603637 NA 7772601, 9582194 Standard NM_000990 NM_000990 NA Approved L27A uc001mgs.4 P46776 ENST00000531102.1:c.174+4412->CAGG chr11.hg19:g.8715267_8715270dupCAGG 5 3 ref NA False 33 33 PASS 4 PASS ref->het 0 NA 68,69 15,15 12,11 1 1 B2R4B3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPL27A-012 PUTATIVE basic|exp_conf processed_transcript NA protein_coding OTTHUMT00000386600.1 PASS NA None 95 NA True + CAGG ENST00000531102.1 AMPD3 272 __UNKNOWN__ __UNKNOWN__ 11 10472493 10472493 __UNKNOWN__ 5'UTR DEL C C - rs397849293|rs35417007|rs398075717 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:10472493delC ENST00000396554.3 + 0 266 AMPD3_ENST00000444303.2_Intron NM_000480.2 NP_000471.1 Q01432 AMPD3_HUMAN adenosine monophosphate deaminase 3 NA NA NA ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281) cytosol (GO:0005829) AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872) central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1) 25 all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291) GGCCTCAGTGCCCAGCAGCCC 0.791 NA NA NA CCC|CCC|CC|deletion 2654 0.529952 0.3192 0.4798 5008 , , NA 8777 0.7609 NA 0.6362 False NA ,,, NA NA NA 2504 0.5031 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 61 69.68 NA , 1281,2121 NA 445,391,865 2 2 2 , -0.1 0 11 dbSNP_131 3 4335,2351 NA 1754,827,762 no intron,utr-5 AMPD3 NM_001172431.1,NM_000480.2 , 2199,1218,1627 A1A1,A1R,RR NA 35.163,37.6543,44.3299 , , 10472493 5616,4472 490 897 1387 SO:0001623 5_prime_UTR_variant 0.38 M84722 CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1 11p15 2010-02-10 2010-02-10 ENSG00000133805 272 3.5.4.6 470 protein-coding gene gene with protein product "erythrocyte-specific AMP deaminase" 102772 "adenosine monophosphate deaminase (isoform E)" NA 1400401 Standard NM_000480 NM_001172430 NA Approved uc001min.1 Q01432 ENST00000396554.3:c.-76C>- chr11.hg19:g.10472493delC 2 3 ref NA False 59 59 PASS 3 PASS ref->het 0 NA 35,37 19,19 9,7 1 1 A0AUX0|B7Z2S2|B7Z763|B7Z877 True hg19 CCDS7802.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AMPD3-001 PUTATIVE basic|CCDS protein_coding NA protein_coding OTTHUMT00000385783.2 PASS NA None 61 NA True + C ENST00000396554.3 MICALCL 84953 __UNKNOWN__ __UNKNOWN__ 11 12380132 12380133 __UNKNOWN__ 3'UTR INS - - AA rs3045408|rs33990468 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:12380132_12380133insAA ENST00000256186.2 + 0 2485_2486 NM_032867.2 NP_116256.2 Q6ZW33 MICLK_HUMAN MICAL C-terminal like NA NA NA cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283) cytoplasm (GO:0005737) mitogen-activated protein kinase binding (GO:0051019) breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1) 30 Epithelial(150;0.00177) CCCTGGAACTTGTTATACCTTA 0.47 NA NA NA 4516 0.901757 0.9032 0.9438 5008 , , NA 18336 0.9306 NA 0.9006 False NA ,,, NA NA NA 2504 0.8415 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 35 33.65 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 BK000463 CCDS41620.1 11p15.3 2005-11-01 ENSG00000133808 ENSG00000133808 84953 25933 protein-coding gene gene with protein product 612355 NA 12110185 Standard NM_032867 NM_032867 NA Approved FLJ14966 uc001mkg.1 Q6ZW33 OTTHUMG00000165777 ENST00000256186.2:c.*107->AA chr11.hg19:g.12380132_12380133insAA 2 4 ref NA False 35 35 PASS 0 PASS ref->het 0 NA 2,2 32,33 0,0 1 1 Q7RTP7|Q96JU6 True hg19 CCDS41620.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MICALCL-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000386164.1 PASS NA None 35 NA True + A ENST00000256186.2 Unknown 0 __UNKNOWN__ __UNKNOWN__ 11 57479732 57479732 __UNKNOWN__ IGR DEL G G - rs201700765|rs71061531|rs1424751|rs367961913|rs141274831 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:57479732delG NA MED19 (51 upstream) : TMX2 (342 downstream) NA NA NA NA GTACCCCCCCGCCCTTTCTCA 0.537 NA NA NA ?|G|-|unsure 1954 0.390176 0.2519 0.4078 5008 , , NA 14133 0.626 NA 0.328 False NA ,,, NA NA NA 2504 0.3855 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 70 86.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 1.66 NA NA NA NA NA chr11.hg19:g.57479732delG 0 10 ref NA False 48 48 PASS 1 PASS ref->het 0 NA 44,48 12,13 13,8 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 70 NA True G Unknown 0 __UNKNOWN__ __UNKNOWN__ 11 58346538 58346539 __UNKNOWN__ IGR INS - - GC rs35866007|rs368912219 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:58346538_58346539insGC NA LPXN (845 upstream) : ZFP91 (44 downstream) NA NA NA NA GAGCGTCTGTggcgcgcgcgcg 0.748 NA NA NA 1099 0.219449 0.205 0.2061 5008 , , NA 4562 0.1835 NA 0.2366 False NA ,,, NA NA NA 2504 0.2679 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 185 178.76 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 3.45 NA NA NA NA NA chr11.hg19:g.58346547_58346548dupGC 9 3 ref NA False 89 89 PASS 8 PASS ref->het 0 NA 83,95 18,22 84,70 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 185 NA True GC EML3 256364 __UNKNOWN__ __UNKNOWN__ 11 62370490 62370491 __UNKNOWN__ Intron INS - - GAGGGCCG rs371950898|rs78641800|rs71458425 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:62370490_62370491insGAGGGCCG ENST00000394773.2 - 20 2664 EML3_ENST00000529309.1_Intron|EML3_ENST00000531557.1_Intron|EML3_ENST00000278845.4_Intron|EML3_ENST00000494176.2_Intron NM_153265.2 NP_694997.2 Q32P44 EMAL3_HUMAN echinoderm microtubule associated protein like 3 NA NA NA cytoplasm (GO:0005737)|microtubule (GO:0005874) biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 26 TTCCCGGTCCCGAGGGGCCTCC 0.673 NA NA NA 973 0.194289 0.1687 0.2133 5008 , , NA 15087 0.0526 NA 0.3241 False NA ,,, NA NA NA 2504 0.228 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 388 449.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.33 AK093146 CCDS8023.2 11q12.3 2013-01-10 ENSG00000149499 ENSG00000149499 256364 "WD repeat domain containing" 26666 protein-coding gene gene with protein product NA NA 15225882, 14744259 Standard NM_153265 NM_153265 NA Approved FLJ35827, ELP95 uc001ntu.1 Q32P44 OTTHUMG00000149817 ENST00000394773.2:c.2356+129->CGGCCCTC chr11.hg19:g.62370490_62370491insGAGGGCCG 1 5 ref NA False 65 65 PASS 0 PASS ref->het 0 NA 305,309 36,36 48,46 1 1 Q6ZQW7|Q8NA55 True hg19 CCDS8023.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EML3-001 KNOWN NAGNAG_splice_site|basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000313432.1 PASS NA None 388 NA True - GAGGGCCG ENST00000394773.2 RCOR2 283248 __UNKNOWN__ __UNKNOWN__ 11 63682318 63682318 __UNKNOWN__ Intron DEL G G - rs113862705|rs11231638|rs113350066|rs386754304|rs386754305 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:63682318delG ENST00000301459.4 - 5 706 NM_173587.3 NP_775858.2 Q8IZ40 RCOR2_HUMAN REST corepressor 2 NA NA NA negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351) chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667) chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714) kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1) 17 AGCTGAGCCTGAGCTGCCCCG 0.632 NA NA NA ?|G|-|unsure 1654 0.330272 0.3268 0.2464 5008 , , NA 14913 0.0794 NA 0.4533 False NA ,,, NA NA NA 2504 0.5266 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 699 711.33 NA NA 65 50 55 NA NA 11 NA NA NA 63682318 2122 4057 6179 SO:0001627 intron_variant 35.78 BC010608 CCDS8052.1 11q13.1 2008-02-05 ENSG00000167771 ENSG00000167771 283248 27455 protein-coding gene gene with protein product NA NA 12477932 Standard NM_173587 NM_173587 NA Approved uc001nyc.3 Q8IZ40 OTTHUMG00000150472 ENST00000301459.4:c.319-30C>- chr11.hg19:g.63682318delG 0 2 ref NA False 57 57 PASS 1 PASS ref->het 0 NA 578,592 75,75 42,29 1 1 Q96FP3 True hg19 CCDS8052.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RCOR2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000318233.1 PASS NA None 699 NA True - G ENST00000301459.4 RPS6KA4 8986 __UNKNOWN__ __UNKNOWN__ 11 64135542 64135543 __UNKNOWN__ Intron DEL TC TC - rs397840377|rs3217512 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:64135542_64135543delTC ENST00000334205.4 + 10 1136 RPS6KA4_ENST00000294261.4_Intron|RPS6KA4_ENST00000528057.1_Intron NM_003942.2 NP_003933.1 O75676 KS6A4_HUMAN ribosomal protein S6 kinase, 90kDa, polypeptide 4 NA NA NA axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355) cytoplasm (GO:0005737)|nucleus (GO:0005634) ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711) breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1) 13 CCCACCAGAGTCTCCTCACCCG 0.594 NA NA NA 1231 0.245807 0.0303 0.3818 5008 , , NA 14601 0.2073 NA 0.3708 False NA ,,, NA NA NA 2504 0.3517 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 293 328.23 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.01 AJ010119 CCDS8073.1, CCDS73313.1 11q11-q13 2011-04-05 2002-08-29 ENSG00000162302 ENSG00000162302 8986 10433 protein-coding gene gene with protein product 603606 "ribosomal protein S6 kinase, 90kD, polypeptide 4" NA 9792677, 9687510 Standard NM_003942 XM_005274379 NA Approved RSK-B, MSK2 uc001oae.3 O75676 OTTHUMG00000046094 ENST00000334205.4:c.1072-61TC>- chr11.hg19:g.64135544_64135545delTC 1 3 ref NA False 41 41 PASS 2 PASS ref->het 0 NA 213,214 67,67 21,23 1 1 A8K7Z8|O75585|Q53ES8 True hg19 CCDS8073.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPS6KA4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000106246.2 PASS NA None 293 NA True + TC ENST00000334205.4 ATG16L2 89849 __UNKNOWN__ __UNKNOWN__ 11 72533625 72533631 __UNKNOWN__ Intron DEL CTGCCTC CTGCCTC - rs139902397|rs200280731|rs374500366 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:72533625_72533631delCTGCCTC ENST00000534905.1 + 3 358 ATG16L2_ENST00000321297.5_Intron Q8NAA4 A16L2_HUMAN autophagy related 16-like 2 (S. cerevisiae) NA NA NA autophagy (GO:0006914)|negative stranded viral RNA replication (GO:0039689)|protein transport (GO:0015031) cytoplasm (GO:0005737)|nucleus (GO:0005634) breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9) 14 BRCA - Breast invasive adenocarcinoma(5;2.73e-06) CCCTTGCGTTCTGCCTCCCGCCCCGCC 0.681 NA NA NA 204 0.0407348 0.0204 0.0605 5008 , , NA 14441 0.001 NA 0.1113 False NA ,,, NA NA NA 2504 0.0225 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 179 201.69 NA 177,4075 NA 3,171,1952 NA NA NA -9.1 0 NA dbSNP_134 42 823,7425 NA 49,725,3350 no intron ATG16L2 NM_033388.1 52,896,5302 A1A1,A1R,RR NA 9.9782,4.1627,8.0 NA 1000,11500 NA NA NA SO:0001627 intron_variant 0.76 AK024423 CCDS31634.1 11q13.4 2014-02-12 2012-06-06 ENSG00000168010 ENSG00000168010 89849 "WD repeat domain containing" 25464 protein-coding gene gene with protein product NA "ATG16 autophagy related 16-like 2 (S. cerevisiae)" NA 11214971 Standard NM_033388 XM_005274378 NA Approved FLJ00012, WDR80, ATG16B uc001otd.3 Q8NAA4 OTTHUMG00000167961 ENST00000534905.1:c.318+4725CTGCCTC>- chr11.hg19:g.72533625_72533631delCTGCCTC 0 7 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 141,150 12,12 26,19 1 1 A5PL30|B2RPK5|Q658V4|Q6PID3|Q8NBG0 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ATG16L2-002 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000397306.1 PASS NA None 179 NA True + CTGCCTC ENST00000534905.1 RSF1 51773 __UNKNOWN__ __UNKNOWN__ 11 77373629 77373630 __UNKNOWN__ 3'UTR INS - - A rs3216737|rs113506611 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:77373629_77373630insA ENST00000308488.6 - 0 8960_8961 Q96T23 RSF1_HUMAN remodeling and spacing factor 1 NA NA NA CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434) nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213) histone binding (GO:0042393)|zinc ion binding (GO:0008270) breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 43 all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152) Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31) GAAAACAAATTAGTGAACATAT 0.292 NA NA NA AA|A|AA|deletion 3718 0.742412 0.9871 0.6729 5008 , , NA 19997 0.7312 NA 0.7008 False NA ,,, NA NA NA 2504 0.5153 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 277 274.08 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF380176, AF227948 CCDS8253.1 11q14.1 2013-01-28 2006-05-25 2006-05-25 ENSG00000048649 ENSG00000048649 51773 "Zinc fingers, PHD-type" 18118 protein-coding gene gene with protein product 608522 "hepatitis B virus x associated protein" HBXAP NA 11788598, 12972596 Standard NM_016578 NM_016578 NA Approved XAP8, RSF-1, p325 uc001oyn.3 Q96T23 OTTHUMG00000150433 ENST00000308488.6:c.*4333->T chr11.hg19:g.77373630_77373630dupA 2 2 ref NA False 46 46 PASS 1 PASS ref->het 0 NA 199,202 44,44 32,32 1 1 Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0 True hg19 CCDS8253.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RSF1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000318075.2 PASS NA None 277 NA True - A ENST00000308488.6 CHORDC1 26973 __UNKNOWN__ __UNKNOWN__ 11 89956396 89956396 __UNKNOWN__ 5'UTR DEL C C - rs397840940|rs3834438 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:89956396delC ENST00000320585.6 - 0 136 NM_012124.2 NP_036256.2 Q9UHD1 CHRD1_HUMAN cysteine and histidine-rich domain (CHORD) containing 1 NA NA NA chaperone-mediated protein folding (GO:0061077)|negative regulation of Rho-dependent protein serine/threonine kinase activity (GO:2000299)|regulation of cellular response to heat (GO:1900034)|regulation of centrosome duplication (GO:0010824)|response to stress (GO:0006950) Hsp90 protein binding (GO:0051879)|zinc ion binding (GO:0008270) endometrium(2)|large_intestine(2)|liver(1)|lung(6) 11 Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.00915) GGAAGTGGAGCCCAGACAACA 0.587 NA NA NA CCC|CCC|CC|deletion 760 0.151757 0.0673 0.062 5008 , , NA 15863 0.2708 NA 0.1859 False NA ,,, NA NA NA 2504 0.1718 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 436 417.55 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 5.18 AF192466 CCDS8289.1, CCDS44705.1 11q14.3 2011-01-25 2011-01-25 ENSG00000110172 ENSG00000110172 26973 14525 protein-coding gene gene with protein product 604353 "cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1", "cysteine and histidine-rich domain (CHORD)-containing 1" NA 10571178 Standard NM_012124 NM_012124 NA Approved CHP1 uc001pdg.2 Q9UHD1 OTTHUMG00000167305 ENST00000320585.6:c.-274G>- chr11.hg19:g.89956396delC 2 3 ref NA False 72 72 PASS 3 PASS ref->het 0 NA 312,320 57,57 63,58 2 2 B2R6P8|Q6IN49|Q8WVL9|Q9H3D6 True hg19 CCDS8289.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CHORDC1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000394111.1 PASS NA None 436 NA True - C ENST00000320585.6 CUL5 8065 __UNKNOWN__ __UNKNOWN__ 11 107879720 107879721 __UNKNOWN__ 5'UTR INS - - A rs144520409 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:107879720_107879721insA ENST00000393094.2 + 0 262_263 NM_003478.3 NP_003469.2 Q93034 CUL5_HUMAN cullin 5 NA NA NA calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032) Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886) calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625) endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1) 23 all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217) GCGGCGGGTGCAACCACAAAGG 0.644 NA NA NA OREG0021319 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) AA|AA|AAA|insertion 550 0.109824 0.1672 0.0677 5008 , , NA 15909 0.0317 NA 0.1153 False NA ,,, NA NA NA 2504 0.137 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 834 783.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 2.07 X81882 CCDS31668.1 11q22.3 2011-05-24 ENSG00000166266 ENSG00000166266 8065 2556 protein-coding gene gene with protein product 601741 NA 8681378, 9037604 Standard XM_005271682 NA Approved VACM-1 uc001pjv.3 Q93034 OTTHUMG00000166369 ENST00000393094.2:c.-354->A chr11.hg19:g.107879722_107879722dupA 3 2 ref 1408 False 329 225 PASS 2 PASS ref->het 0 NA 561,581 178,180 93,72 1 1 A8K960|O14766|Q9BZC6 True hg19 CCDS31668.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CUL5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000389429.1 PASS NA None 834 NA True + A ENST00000393094.2 IGSF9B 22997 __UNKNOWN__ __UNKNOWN__ 11 133826723 133826733 __UNKNOWN__ 5'UTR DEL GCGCCCGCCTC GCGCCCGCCTC - rs544014217 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr11:133826723_133826733delGCGCCCGCCTC ENST00000533871.2 - 0 147_157 IGSF9B_ENST00000321016.8_5'UTR|AP000911.1_ENST00000582427.1_RNA NM_001277285.1 NP_001264214.1 Q9UPX0 TUTLB_HUMAN immunoglobulin superfamily, member 9B NA NA NA homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151) dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886) breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 44 all_hematologic(175;0.127) all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559) Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221) tcgcgcccgagcgcccgcctcgcgcccgcct 0.72 NA NA NA 9 0.00179712 0.0045 0 5008 , , NA 7017 0.001 NA 0.002 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 180 193.39 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.52 AK097578 CCDS61010.1 11q25 2013-02-11 2005-10-12 2005-11-20 22997 "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing" 32326 protein-coding gene gene with protein product 613773 NA Standard XM_290502 NM_001277285 NA Approved KIAA1030 uc031qfh.1 Q9UPX0 ENST00000533871.2:c.-84GAGGCGGGCGC>- chr11.hg19:g.133826723_133826733delGCGCCCGCCTC 1 3 ref NA False 33 33 PASS 2 PASS ref->het 0 NA 81,81 24,24 76,76 1 1 G5EA26 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IGSF9B-002 PUTATIVE not_organism_supported|basic|appris_candidate_longest protein_coding NA protein_coding OTTHUMT00000471431.1 PASS NA None 180 NA True - GCGCCCGCCTC ENST00000533871.2 LRP6 4040 __UNKNOWN__ __UNKNOWN__ 12 12317313 12317346 __UNKNOWN__ Frame_Shift_Del DEL GTTTCCAGAGAAATTCGTCTGATATCTGCTCTCC GTTTCCAGAGAAATTCGTCTGATATCTGCTCTCC - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:12317313_12317346delGTTTCCAGAGAAATTCGTCTGATATCTGCTCTCC ENST00000543091.1 - 9 1946_1979 c.1913_1946delGGAGAGCAGATATCAGACGAATTTCTCTGGAAAC c.(1912-1947)cggagagcagatatcagacgaatttctctggaaacafs p.RRADIRRISLET638fs LRP6_ENST00000261349.4_Frame_Shift_Del_p.RRADIRRISLET638fs O75581 LRP6_HUMAN low density lipoprotein receptor-related protein 6 638 Beta-propeller 3. NA NA anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244) cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202) apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147) p.S646Y(1)|p.R638Q(1)|p.R644*(1) breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1) 85 Prostate(47;0.0865) ATTATTGTTTGTTTCCAGAGAAATTCGTCTGATATCTGCTCTCCGTGAAAACAA 0.423 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 3 Substitution - Missense(2)|Substitution - Nonsense(1) large_intestine(2)|lung(1) NA NA NA NA NA 354 319.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0 AF074264 CCDS8647.1 12p13.2 2013-05-29 ENSG00000070018 ENSG00000070018 4040 "Low density lipoprotein receptors" 6698 protein-coding gene gene with protein product 603507 NA 9704021 Standard NM_002336 NA Approved ADCAD2 uc001rah.4 O75581 OTTHUMG00000168540 ENST00000543091.1:c.1913_1946delGGAGAGCAGATATCAGACGAATTTCTCTGGAAAC chr12.hg19:g.12317313_12317346delGTTTCCAGAGAAATTCGTCTGATATCTGCTCTCC ENSP00000442472:p.Arg638fs 0 6 ref NA False 52 52 PASS 1 PASS ref->het 0 NA 378,380 27,27 45,44 1 1 Q17RZ2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LRP6-004 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000400140.1 PASS NA None 354 NA True - GTTTCCAGAGAAATTCGTCTGATATCTGCTCTCC ENST00000543091.1 CASC1 55259 __UNKNOWN__ __UNKNOWN__ 12 25276352 25276359 __UNKNOWN__ Intron DEL GCTCTACC GCTCTACC - rs201964043|rs3830289 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:25276352_25276359delGCTCTACC ENST00000395987.3 - 10 1068 CASC1_ENST00000395990.2_Intron|CASC1_ENST00000320267.9_Intron|CASC1_ENST00000557684.1_Intron|CASC1_ENST00000537577.1_Intron|CASC1_ENST00000545133.1_Intron|CASC1_ENST00000354189.5_Intron NM_018272.3 NP_060742 Q6TDU7 CASC1_HUMAN cancer susceptibility candidate 1 NA NA NA breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 31 Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11) OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13) ACTGATACTTGCTCTACCATAAAACTGG 0.389 NA NA NA 798 0.159345 0.1452 0.1772 5008 , , NA 17643 0.0952 NA 0.1978 False NA ,,, NA NA NA 2504 0.1922 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 293 294.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.35 AK093102 CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1 12p12.1 2012-04-17 ENSG00000118307 ENSG00000118307 55259 "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits" 29599 protein-coding gene gene with protein product "protein phosphatase 1, regulatory subunit 54" NA NA 14583591 Standard NM_018272 NM_018272 NA Approved LAS1, FLJ10921, PPP1R54 uc001rgk.3 Q6TDU7 OTTHUMG00000150195 ENST00000395987.3:c.1003-132GGTAGAGC>- chr12.hg19:g.25276352_25276359delGCTCTACC 0 5 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 215,215 38,38 25,25 1 1 B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50 True hg19 CCDS31759.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CASC1-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000316763.1 PASS NA None 293 NA True - GCTCTACC ENST00000395987.3 PPFIBP1 8496 __UNKNOWN__ __UNKNOWN__ 12 27817409 27817409 __UNKNOWN__ Intron DEL T T - rs398018997|rs34613698 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:27817409delT ENST00000228425.6 + 12 1224 PPFIBP1_ENST00000542629.1_Intron|PPFIBP1_ENST00000318304.8_Intron|PPFIBP1_ENST00000537927.1_Intron NM_003622.3 NP_003613 Q86W92 LIPB1_HUMAN PTPRF interacting protein, binding protein 1 (liprin beta 1) NA NA NA cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165) focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786) PPFIBP1/ALK(3) central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1) 32 Lung SC(9;0.0873) GTTTTTCTACTTTGGTTGACT 0.398 NA NA NA TTT|TTT|TT|deletion 2382 0.475639 0.4342 0.5605 5008 , , NA 18714 0.5367 NA 0.4294 False NA ,,, NA NA NA 2504 0.456 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 246 236.44 NA ,,, 1728,2534 NA 351,1026,754 45 48 47 ,,, 3.5 0 12 dbSNP_126 73 3546,4704 NA 735,2076,1314 no intron,intron,intron,intron PPFIBP1 NM_177444.2,NM_003622.3,NM_001198916.1,NM_001198915.1 ,,, 1086,3102,2068 A1A1,A1R,RR NA 42.9818,40.5443,42.1515 ,,, ,,, 27817409 5274,7238 2168 4169 6337 SO:0001627 intron_variant 0.14 AF034802 CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1 12p12.1 2013-01-10 8496 "Sterile alpha motif (SAM) domain containing" 9249 protein-coding gene gene with protein product 603141 NA 9624153, 11836260 Standard NM_003622 NM_003622 NA Approved L2, hSGT2, hSgt2p, SGT2 uc001ric.2 Q86W92 ENST00000228425.6:c.991+30T>- chr12.hg19:g.27817409delT 2 3 ref NA False 54 54 PASS 3 PASS ref->het 0 NA 187,188 38,38 21,22 1 1 O75336|Q86X70|Q9NY03|Q9ULJ0 True hg19 CCDS8713.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPFIBP1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000402880.1 PASS NA None 246 NA True + T ENST00000228425.6 ALG10 84920 __UNKNOWN__ __UNKNOWN__ 12 34175313 34175314 __UNKNOWN__ 5'UTR INS - - A rs60273288|rs34004926 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:34175313_34175314insA ENST00000266483.2 + 0 98_99 RP11-847H18.2_ENST00000501954.2_RNA NM_032834.3 NP_116223.3 Q5BKT4 AG10A_HUMAN ALG10, alpha-1,2-glucosyltransferase NA NA NA cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021) transferase activity, transferring hexosyl groups (GO:0016758) NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1) 26 Lung NSC(5;3.82e-05)|Acute lymphoblastic leukemia(23;0.0142)|all_hematologic(23;0.0429) Lung NSC(34;0.204)|all_lung(34;0.235) ATGCGATTGAGAGGGTAATCAT 0.584 NA NA NA OREG0021730 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) A|A|AA|insertion 861 0.171925 0.0295 0.2161 5008 , , NA 12686 0.0407 NA 0.3877 False NA ,,, NA NA NA 2504 0.2464 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 848 754.41 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 2.63 AJ312278 CCDS41769.1 12p11.21 2013-03-04 2013-03-04 ENSG00000139133 ENSG00000139133 84920 2.4.1.256 23162 protein-coding gene gene with protein product "derepression of ITR1 expression 2 homolog (S. cerevisiae)", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase" 603313 "asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog (yeast)", "asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog (S. pombe)" NA Standard NM_032834 NM_032834 NA Approved FLJ14751, DIE2, ALG10A uc001rlm.3 Q5BKT4 OTTHUMG00000169285 ENST00000266483.2:c.-221->A chr12.hg19:g.34175314_34175314dupA 2 4 ref 845 False 188 188 PASS 1 PASS ref->het 0 NA 635,644 87,90 117,110 1 1 Q6NS98|Q96DU0|Q96SM6 True hg19 CCDS41769.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ALG10-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000403309.1 PASS NA None 848 NA True + A ENST00000266483.2 PRKAG1 5571 __UNKNOWN__ __UNKNOWN__ 12 49411146 49411147 __UNKNOWN__ Intron INS - - CAT rs68098951|rs4994587|rs4018509 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:49411146_49411147insCAT ENST00000548065.1 - 1 466 RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|PRKAG1_ENST00000547306.1_Intron|RP11-386G11.5_ENST00000552933.1_RNA|PRKAG1_ENST00000552212.1_Intron|PRKAG1_ENST00000395170.3_Intron|PRKAG1_ENST00000316299.5_Intron P54619 AAKG1_HUMAN protein kinase, AMP-activated, gamma 1 non-catalytic subunit NA NA NA cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|insulin receptor signaling pathway (GO:0008286)|membrane organization (GO:0061024)|positive regulation of gene expression (GO:0010628)|positive regulation of protein kinase activity (GO:0045860)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of glycolytic process (GO:0006110)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283) AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634) ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901) cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1) 9 Acetylsalicylic acid(DB00945) accaccaccacgcctgggtaat 0.53 NA NA NA 2130 0.425319 0.5015 0.2954 5008 , , NA 16385 0.4454 NA 0.3489 False NA ,,, NA NA NA 2504 0.4724 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 76 72.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.37 U42412 CCDS8777.1, CCDS55824.1, CCDS55825.1 12q12-q14 1998-07-16 ENSG00000181929 5571 9385 protein-coding gene gene with protein product 602742 NA 8557660, 8621499 Standard NM_002733 NM_002733 NA Approved uc001rsz.3 P54619 OTTHUMG00000170406 ENST00000548065.1:c.9+1367->ATG chr12.hg19:g.49411146_49411147insCAT 1 3 ref NA False 33 33 PASS 0 PASS ref->het 0 NA 55,56 12,12 9,9 1 1 B4DDT7|Q8N7V9 True hg19 CCDS8777.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PRKAG1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000408946.1 PASS NA None 76 NA True - CAT ENST00000548065.1 KRT2 3849 __UNKNOWN__ __UNKNOWN__ 12 53045615 53045616 __UNKNOWN__ In_Frame_Ins INS - - CCTCCAAAGCCGCTGCCG rs150409603|rs532019270|rs75253159 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:53045615_53045616insCCTCCAAAGCCGCTGCCG ENST00000309680.3 - 1 332_333 c.311_312insCGGCAGCGGCTTTGGAGG c.(310-312)ggt>ggCGGCAGCGGCTTTGGAGGt p.104_104G>GGSGFGG NM_000423.2 NP_000414.2 P35908 K22E_HUMAN keratin 2 104 Head. NA NA epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616) cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634) structural constituent of cytoskeleton (GO:0005200) endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1) 32 BRCA - Breast invasive adenocarcinoma(357;0.19) agccgctgccacctccaaagct 0.619 NA NA NA 905 0.180711 0.0151 0.1441 5008 , , NA 13575 0.3948 NA 0.168 False NA ,,, NA NA NA 2504 0.2229 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 226 280.98 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001652 inframe_insertion 0.71 CCDS8835.1 12q13.13 2013-01-16 2008-08-01 2006-07-17 ENSG00000172867 ENSG00000172867 3849 "-", "Intermediate filaments type II, keratins (basic)" 6439 protein-coding gene gene with protein product "epidermal ichthyosis bullosa of Siemens" 600194 "keratin 2A (epidermal ichthyosis bullosa of Siemens)" KRT2A NA 7524919, 16831889 Standard NM_000423 NM_000423 NA Approved KRTE uc001sat.3 P35908 OTTHUMG00000169748 ENST00000309680.3:c.311_312insCGGCAGCGGCTTTGGAGG chr12.hg19:g.53045615_53045616insCCTCCAAAGCCGCTGCCG Exception_encountered 1 4 ref NA False 57 57 PASS 0 PASS ref->het 0 NA 168,171 32,32 57,56 1 1 Q4VAQ2 True hg19 CCDS8835.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KRT2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000405704.1 PASS NA None 226 NA True - CCTCCAAAGCCGCTGCCG ENST00000309680.3 SPRYD3 84926 __UNKNOWN__ __UNKNOWN__ 12 53460341 53460341 __UNKNOWN__ Intron DEL C C - rs201218863 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:53460341delC ENST00000547837.1 - 10 1176 SPRYD3_ENST00000301463.4_Intron Q8NCJ5 SPRY3_HUMAN SPRY domain containing 3 NA NA NA central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(2) 17 TGGCTGGCCACCCCTACCCCA 0.587 NA NA NA OREG0021856 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) cccc|CCCC|CCC|deletion 50 0.00998403 0.0045 0.0259 5008 , , NA 18482 0 NA 0.0249 False NA ,,, NA NA NA 2504 0.001 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 635 621.15 NA 26,4238 NA 2,22,2108 102 85 91 -1.2 0 12 92 207,8045 NA 8,191,3927 no intron SPRYD3 NM_032840.2 10,213,6035 A1A1,A1R,RR NA 2.5085,0.6098,1.8616 53460341 233,12283 2203 4300 6503 SO:0001627 intron_variant 0.99 AK074694 CCDS8845.1 12q13.13 2006-11-29 2006-02-02 ENSG00000167778 84926 25920 protein-coding gene gene with protein product NA NA 14702039 Standard NM_032840 NM_032840 NA Approved FLJ14800 uc001sbt.2 Q8NCJ5 OTTHUMG00000170101 ENST00000547837.1:c.1132+15G>- chr12.hg19:g.53460341delC 3 6 ref 992 False 125 125 PASS 4 PASS ref->het 0 NA 510,519 64,64 57,51 1 1 B9EG99|Q96SK5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SPRYD3-003 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000407266.1 PASS NA None 635 NA True - C ENST00000547837.1 ZBTB39 9880 __UNKNOWN__ __UNKNOWN__ 12 57395499 57395502 __UNKNOWN__ 3'UTR DEL GACA GACA - rs3044224|rs5798399|rs5798400 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:57395499_57395502delGACA ENST00000300101.2 - 0 3285_3288 NM_014830.2 NP_055645.1 O15060 ZBT39_HUMAN zinc finger and BTB domain containing 39 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|prostate(1) 16 ACCCGACTAGGACAGACAGTCAGA 0.525 NA NA NA OREG0021929 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 666 0.132987 0.1225 0.1225 5008 , , NA 20527 0.1895 NA 0.1054 False NA ,,, NA NA NA 2504 0.1247 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 446 429.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.56 AB002350 CCDS31839.1 12q13.3 2013-01-09 ENSG00000166860 9880 "-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type" 29014 protein-coding gene gene with protein product NA NA 9205841 Standard NM_014830 NM_014830 NA Approved KIAA0352, ZNF922 uc001sml.2 O15060 ENST00000300101.2:c.*1064TGTC>- chr12.hg19:g.57395503_57395506delGACA 1 2 ref 1022 False 70 70 PASS 2 PASS ref->het 0 NA 366,367 55,55 30,29 1 1 A7MD38|Q9UD98 True hg19 CCDS31839.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZBTB39-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000411214.1 PASS NA None 446 NA True - GACA ENST00000300101.2 GLIPR1L2 144321 __UNKNOWN__ __UNKNOWN__ 12 75816814 75816815 __UNKNOWN__ Intron INS - - ACA rs199738162|rs397750292|rs144850646|rs59277111 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:75816814_75816815insACA ENST00000550916.1 + 4 717 GLIPR1L2_ENST00000378692.3_Intron|GLIPR1L2_ENST00000441218.1_Intron|GLIPR1L2_ENST00000320460.4_In_Frame_Ins_p.239_240insN|GLIPR1L2_ENST00000435775.1_Intron NM_001270396.1 NP_001257325.1 Q4G1C9 GRPL2_HUMAN GLI pathogenesis-related 1 like 2 NA NA NA integral component of membrane (GO:0016021) kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1) 16 TAATGGATTGGACAAGAAAAAT 0.312 NA NA NA 1714 0.342252 0.2511 0.2622 5008 , , NA 17045 0.4683 NA 0.3767 False NA ,,, NA NA NA 2504 0.3569 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 230 251.83 NA 1181,3083 NA 163,855,1114 NA NA NA 0 0 NA dbSNP_130 117 3246,5006 NA 650,1946,1530 no coding GLIPR1L2 NM_152436.1 813,2801,2644 A1A1,A1R,RR NA 39.3359,27.697,35.3707 NA 4427,8089 NA NA NA SO:0001627 intron_variant 0.42 BC029557 CCDS9010.1, CCDS58258.1 12q21.1 2014-06-03 ENSG00000180481 144321 28592 protein-coding gene gene with protein product 610394 NA 12477932 Standard NM_152436 NM_001270396 NA Approved MGC39497 uc001sxr.2 Q4G1C9 OTTHUMG00000169756 ENST00000550916.1:c.670+45->ACA chr12.hg19:g.75816815_75816817dupACA 2 3 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 166,166 35,36 28,28 1 1 Q6MZS1|Q8N6N0|Q8NA43 True hg19 CCDS58258.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GLIPR1L2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000405718.1 PASS NA None 230 NA True + ACA ENST00000550916.1 PHLDA1 22822 __UNKNOWN__ __UNKNOWN__ 12 76426111 76426112 __UNKNOWN__ 5'UTR DEL GA GA - rs372797067|rs398098314|rs77949675 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:76426111_76426112delGA ENST00000266671.5 - 0 1600_1601 Q8WV24 PHLA1_HUMAN pleckstrin homology-like domain, family A, member 1 NA NA NA apoptotic process (GO:0006915)|FasL biosynthetic process (GO:0045210)|forebrain neuron differentiation (GO:0021879)|positive regulation of apoptotic process (GO:0043065) cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)|nucleus (GO:0005634) breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1) 14 Colorectal(145;0.09) GCCACGGGTGGAGAGAGGCGGA 0.569 NA NA NA 1872 0.373802 0.1755 0.3847 5008 , , NA 16652 0.7679 NA 0.1779 False NA ,,, NA NA NA 2504 0.4294 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 406 399.15 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 Z50194 CCDS31861.1 12q15 2008-08-05 ENSG00000139289 22822 8933 protein-coding gene gene with protein product "proline-histidine rich protein" 605335 NA 12384558, 15037619 Standard NM_007350 NM_007350 NA Approved TDAG51, DT1P1B11, PHRIP uc001sxu.3 Q8WV24 ENST00000266671.5:c.-591TC>- chr12.hg19:g.76426115_76426116delGA 2 5 ref NA False 149 129 PASS 3 PASS ref->het 0 NA 284,285 77,78 44,42 1 1 A1A4G9|Q15184|Q2TAN2|Q9NZ17 True hg19 CCDS31861.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PHLDA1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000405846.2 PASS NA None 406 NA True - GA ENST00000266671.5 NAV3 89795 __UNKNOWN__ __UNKNOWN__ 12 78537138 78537139 __UNKNOWN__ Intron INS - - GGT rs67454920|rs534516769|rs10661027|rs71441911 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:78537138_78537139insGGT ENST00000536525.2 + 21 4856 NAV3_ENST00000266692.7_Intron|NAV3_ENST00000228327.6_Intron|NAV3_ENST00000397909.2_Intron NM_014903.4 NP_055718.4 Q8IVL0 NAV3_HUMAN neuron navigator 3 NA NA NA membrane (GO:0016020)|nuclear envelope (GO:0005635) NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1) 236 Aggccaagcgcggtggctcatg 0.505 NA NA NA HNSCC(70;0.22) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 82 81.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.04 AB023155 CCDS41815.1, CCDS66432.1 12q14.3 2008-08-05 ENSG00000067798 89795 15998 protein-coding gene gene with protein product "pore membrane and/or filament interacting like protein 1", "steerin 3" 611629 NA 12079279, 12062803 Standard NM_001024383 XM_005269215 NA Approved KIAA0938, POMFIL1 uc001syo.3 Q8IVL0 OTTHUMG00000170001 ENST00000536525.2:c.4684-3010->GGT chr12.hg19:g.78537139_78537141dupGGT 2 4 ref NA False 48 48 PASS 1 PASS ref->het 0 NA 47,50 23,23 10,9 2 2 Q8NFW7|Q9Y2E7 True hg19 CCDS41815.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NAV3-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000406811.1 PASS NA None 82 NA True + GGT ENST00000536525.2 NAV3 89795 __UNKNOWN__ __UNKNOWN__ 12 78605386 78605387 __UNKNOWN__ 3'UTR DEL AT AT - rs528863700 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:78605386_78605387delAT ENST00000397909.2 + 0 8420_8421 NAV3_ENST00000266692.7_3'UTR|NAV3_ENST00000228327.6_3'UTR Q8IVL0 NAV3_HUMAN neuron navigator 3 NA NA NA membrane (GO:0016020)|nuclear envelope (GO:0005635) NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1) 236 AACCTAAGACATGTGGCGAAAT 0.396 NA NA NA HNSCC(70;0.22) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 162 156.34 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.31 AB023155 CCDS41815.1, CCDS66432.1 12q14.3 2008-08-05 ENSG00000067798 89795 15998 protein-coding gene gene with protein product "pore membrane and/or filament interacting like protein 1", "steerin 3" 611629 NA 12079279, 12062803 Standard NM_001024383 XM_005269215 NA Approved KIAA0938, POMFIL1 uc001syo.3 Q8IVL0 OTTHUMG00000170001 ENST00000397909.2:c.*1090AT>- chr12.hg19:g.78605386_78605387delAT 0 3 ref NA False 51 51 PASS 1 PASS ref->het 0 NA 125,125 28,29 8,8 1 1 Q8NFW7|Q9Y2E7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NAV3-001 KNOWN basic protein_coding NA protein_coding OTTHUMT00000406812.1 PASS NA None 162 NA True + AT ENST00000397909.2 NAV3 89795 __UNKNOWN__ __UNKNOWN__ 12 78605521 78605522 __UNKNOWN__ 3'UTR INS - - TT rs139201184 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:78605521_78605522insTT ENST00000397909.2 + 0 8555_8556 NAV3_ENST00000266692.7_3'UTR|NAV3_ENST00000228327.6_3'UTR Q8IVL0 NAV3_HUMAN neuron navigator 3 NA NA NA membrane (GO:0016020)|nuclear envelope (GO:0005635) NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1) 236 TATTGTTTTTGTTTTTTTAATG 0.386 NA NA NA HNSCC(70;0.22) 226 0.0451278 0.0023 0.0663 5008 , , NA 18149 0.0298 NA 0.1233 False NA ,,, NA NA NA 2504 0.0235 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 104 108.3 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AB023155 CCDS41815.1, CCDS66432.1 12q14.3 2008-08-05 ENSG00000067798 89795 15998 protein-coding gene gene with protein product "pore membrane and/or filament interacting like protein 1", "steerin 3" 611629 NA 12079279, 12062803 Standard NM_001024383 XM_005269215 NA Approved KIAA0938, POMFIL1 uc001syo.3 Q8IVL0 OTTHUMG00000170001 ENST00000397909.2:c.*1225->TT chr12.hg19:g.78605526_78605527dupTT 9 12 ref NA False 43 43 PASS 7 PASS ref->het 0 NA 61,62 29,29 13,13 2 2 Q8NFW7|Q9Y2E7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NAV3-001 KNOWN basic protein_coding NA protein_coding OTTHUMT00000406812.1 PASS NA None 104 NA True + T ENST00000397909.2 EEA1 8411 __UNKNOWN__ __UNKNOWN__ 12 93168310 93168315 __UNKNOWN__ 3'UTR DEL AATATT AATATT - rs558162133 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:93168310_93168315delAATATT ENST00000322349.8 - 0 5972_5977 NM_003566.3 NP_003557 Q15075 EEA1_HUMAN early endosome antigen 1 NA NA NA early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906) axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969) 1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270) endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3) 36 TTAATAAACCAATATTAATAACTTCT 0.238 NA NA NA 3 0.000599042 0 0 5008 , , NA 16579 0 NA 0.001 False NA ,,, NA NA NA 2504 0.002 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 123 117.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 L40157 CCDS31874.1 12q22 2007-02-23 2007-02-23 ENSG00000102189 8411 "Zinc fingers, FYVE domain containing" 3185 protein-coding gene gene with protein product 605070 "early endosome antigen 1, 162kD" NA 7768953, 9697774 Standard NM_003566 NM_003566 NA Approved ZFYVE2 uc001tck.3 Q15075 OTTHUMG00000170110 ENST00000322349.8:c.*1477AATATT>- chr12.hg19:g.93168310_93168315delAATATT 0 4 ref NA False 32 32 PASS 1 PASS ref->het 0 NA 94,95 20,20 18,18 1 1 Q14221 True hg19 CCDS31874.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EEA1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000407304.1 PASS NA None 123 NA True - AATATT ENST00000322349.8 SLC25A3 5250 __UNKNOWN__ __UNKNOWN__ 12 98991843 98991843 __UNKNOWN__ Intron DEL C C - rs138634912 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:98991843delC ENST00000228318.3 + 4 582 SLC25A3_ENST00000547534.1_3'UTR|SLC25A3_ENST00000188376.5_Intron|SLC25A3_ENST00000551917.1_Intron|SLC25A3_ENST00000401722.3_Intron|SLC25A3_ENST00000549338.1_Intron|SLC25A3_ENST00000552981.1_Intron|SLC25A3_ENST00000548847.1_Intron NM_005888.3 NP_005879.1 Q00325 MPCP_HUMAN solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 NA NA NA generation of precursor metabolites and energy (GO:0006091)|phosphate ion transmembrane transport (GO:0035435)|transport (GO:0006810) extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739) phosphate ion carrier activity (GO:0015320)|protein complex binding (GO:0032403)|symporter activity (GO:0015293) breast(1)|endometrium(2)|large_intestine(4)|lung(8)|prostate(1) 16 Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255) GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115) ATTGAATGTTCCGAGTGTTTA 0.353 NA NA NA CC|CC|C|deletion 289 0.0577077 0.0166 0.0692 5008 , , NA 18086 0.002 NA 0.1292 False NA ,,, NA NA NA 2504 0.089 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 404 384.39 NA ,, 155,4109 NA 4,147,1981 51 48 49 ,, -9.4 0 12 dbSNP_134 54 968,7286 NA 55,858,3214 no intron,intron,intron SLC25A3 NM_213611.2,NM_005888.3,NM_002635.3 ,, 59,1005,5195 A1A1,A1R,RR NA 11.7276,3.6351,8.9711 ,, ,, 98991843 1123,11395 2203 4299 6502 SO:0001627 intron_variant 0 CCDS9065.1, CCDS9066.1 12q23.1 2013-05-22 ENSG00000075415 ENSG00000075415 5250 "Solute carriers" 10989 protein-coding gene gene with protein product 600370 PHC NA 8168843 Standard NM_005888 NM_213611 NA Approved uc001tfo.3 Q00325 OTTHUMG00000170212 ENST00000228318.3:c.462+30C>- chr12.hg19:g.98991843delC 1 3 ref NA False 37 37 PASS 2 PASS ref->het 0 NA 316,316 38,38 47,48 1 1 B3KS34|Q7Z7N7|Q96A03 True hg19 CCDS9066.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC25A3-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000407989.1 PASS NA None 404 NA True + C ENST00000228318.3 SLC5A8 160728 __UNKNOWN__ __UNKNOWN__ 12 101581318 101581319 __UNKNOWN__ Intron DEL AA AA - rs35400143|rs369347558 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:101581318_101581319delAA ENST00000536262.2 - 7 1392 NM_145913.3 NP_666018.3 solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8 NA NA NA breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 47 ACAAACCAGCAAAAGACAACTG 0.386 NA NA NA 1601 0.319688 0.3661 0.1412 5008 , , NA 20219 0.5427 NA 0.2485 False NA ,,, NA NA NA 2504 0.227 NA NA NA GBM(60;420 1056 13605 22380 47675) PASS NA NA NA 0 NA NA NA NA NA 155 149.5 NA 1342,2922 NA 216,910,1006 NA NA NA -4 0 NA dbSNP_129 60 1851,6403 NA 189,1473,2465 no intron SLC5A8 NM_145913.3 405,2383,3471 A1A1,A1R,RR NA 22.4255,31.4728,25.5073 NA 3193,9325 NA NA NA SO:0001627 intron_variant 0 AY081220 CCDS9080.1 12q23.1 2013-07-19 2013-07-19 ENSG00000256870 ENSG00000256870 160728 "Solute carriers" 19119 protein-coding gene gene with protein product 608044 "solute carrier family 5 (iodide transporter), member 8" NA 12107270, 12829793 Standard NM_145913 NM_145913 NA Approved AIT uc001thz.4 Q8N695 OTTHUMG00000170499 ENST00000536262.2:c.834-25TT>- chr12.hg19:g.101581320_101581321delAA 2 5 ref NA False 36 36 PASS 4 PASS ref->het 0 NA 105,105 34,34 15,15 1 1 True hg19 CCDS9080.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC5A8-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000409401.1 PASS NA None 155 NA True - A ENST00000536262.2 BTBD11 121551 __UNKNOWN__ __UNKNOWN__ 12 108043856 108043857 __UNKNOWN__ Intron INS - - GTCCAGGTGCCTGGCTGAC rs61940014|rs141305409|rs74362898 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:108043856_108043857insGTCCAGGTGCCTGGCTGAC ENST00000280758.5 + 15 3519 BTBD11_ENST00000357167.4_Intron|BTBD11_ENST00000494235.2_Intron|BTBD11_ENST00000420571.2_Intron|BTBD11_ENST00000490090.2_3'UTR NM_001018072.1 NP_001018082.1 A6QL63 BTBDB_HUMAN BTB (POZ) domain containing 11 NA NA NA integral component of membrane (GO:0016021) NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 53 ACCTGGCTGATGAGAGATGTCA 0.505 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 132 130.7 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AK091276 CCDS31893.1, CCDS41827.1 12q24.11 2013-10-02 ENSG00000151136 ENSG00000151136 121551 "BTB/POZ domain containing", "Ankyrin repeat domain containing" 23844 protein-coding gene gene with protein product NA NA Standard NM_152322 XM_005268645 NA Approved FLJ33957, ABTB2B uc001tmk.1 A6QL63 OTTHUMG00000150413 ENST00000280758.5:c.2991+805->GTCCAGGTGCCTGGCTGAC chr12.hg19:g.108043856_108043857insGTCCAGGTGCCTGGCTGAC 1 2 ref NA False 30 30 PASS 0 PASS ref->het 0 NA 104,104 12,12 18,18 1 1 A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245 True hg19 CCDS31893.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BTBD11-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000318003.1 PASS NA None 132 NA True + GTCCAGGTGCCTGGCTGAC ENST00000280758.5 ISCU 23479 __UNKNOWN__ __UNKNOWN__ 12 108961597 108961598 __UNKNOWN__ Intron INS - - A rs201531720 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:108961597_108961598insA ENST00000547005.1 + 5 526 ISCU_ENST00000539593.1_3'UTR|ISCU_ENST00000431221.2_Intron|ISCU_ENST00000540154.1_Intron|ISCU_ENST00000311893.9_Intron|ISCU_ENST00000535729.1_3'UTR|ISCU_ENST00000392807.4_Intron|ISCU_ENST00000338291.4_Intron Q9H1K1 ISCU_HUMAN iron-sulfur cluster assembly enzyme NA NA NA iron-sulfur cluster assembly (GO:0016226)|nitrogen fixation (GO:0009399)|small molecule metabolic process (GO:0044281) cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634) iron ion binding (GO:0005506)|iron-sulfur cluster binding (GO:0051536)|protein complex scaffold (GO:0032947) kidney(2)|large_intestine(2)|lung(4)|prostate(2)|urinary_tract(1) 11 CCTGCTATCCTAAAAAAAAGCC 0.421 NA NA NA AAAAAAAA|AAAAAAAA|AAAAAAAAA|insertion 8 0.00159744 0 0.0043 5008 , , NA 20726 0 NA 0.004 False NA ,,, NA NA NA 2504 0.001 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 1009 949.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.74 U47101 CCDS9118.1, CCDS44966.1, CCDS73518.1 12q24.1 2013-08-05 2013-08-05 2006-10-24 ENSG00000136003 ENSG00000136003 23479 29882 protein-coding gene gene with protein product 611911 "NifU-like N-terminal domain containing", "IscU iron-sulfur cluster scaffold homolog (E. coli)", "iron-sulfur cluster scaffold homolog (E. coli)" NIFUN NA 8875867, 11060020 Standard NM_014301 XM_005268760 NA Approved ISU2, hnifU, IscU uc010sxc.2 Q9H1K1 OTTHUMG00000168420 ENST00000547005.1:c.462+78->A chr12.hg19:g.108961605_108961605dupA 9 8 ref NA False 112 112 PASS 8 PASS ref->het 0 NA 770,777 111,112 126,122 1 1 Q6P713|Q99617|Q9H1K2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ISCU-012 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000404008.1 PASS NA None 1009 NA True + A ENST00000547005.1 SFSWAP 6433 __UNKNOWN__ __UNKNOWN__ 12 132209933 132209934 __UNKNOWN__ Intron DEL TG TG - rs368520549|rs200738132|rs140232729|rs138640311 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr12:132209933_132209934delTG ENST00000541286.1 + 5 699 SFSWAP_ENST00000261674.4_Intron NM_001261411.1 NP_001248340.1 Q12872 SFSWA_HUMAN splicing factor, suppressor of white-apricot family NA NA NA mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) RNA binding (GO:0003723) endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2) 25 GACGTGAATATGTGTGTTTTCC 0.475 NA NA NA 1619 0.323283 0.1649 0.3674 5008 , , NA 20420 0.4187 NA 0.4254 False NA ,,, NA NA NA 2504 0.3027 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 840 790.7 NA 939,3325 NA 113,713,1306 NA NA NA -9.8 0 NA dbSNP_134 76 3669,4585 NA 825,2019,1283 no intron SFSWAP NM_004592.2 938,2732,2589 A1A1,A1R,RR NA 44.4512,22.0216,36.811 NA 4608,7910 NA NA NA SO:0001627 intron_variant 0.68 U08377 CCDS9273.1, CCDS58290.1 12q24.33 2014-04-14 2014-04-14 2010-09-15 ENSG00000061936 ENSG00000061936 6433 10790 protein-coding gene gene with protein product 601945 "splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)", "splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)", "splicing factor, suppressor of white-apricot homolog (Drosophila)" SFRS8 NA 8940107 Standard NM_004592 NM_004592 NA Approved SWAP uc010tbn.2 Q12872 OTTHUMG00000168319 ENST00000541286.1:c.607-16TG>- chr12.hg19:g.132209937_132209938delTG 2 3 ref NA False 203 119 PASS 3 PASS ref->het 0 NA 545,548 226,226 67,66 2 2 B2RN45|B7ZM97|F5H6B8|Q6PJF7 True hg19 CCDS58290.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SFSWAP-003 NOVEL basic|appris_candidate_longest|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000399280.1 PASS NA None 840 NA True + TG ENST00000541286.1 GJA3 2700 __UNKNOWN__ __UNKNOWN__ 13 20712747 20712747 __UNKNOWN__ 3'UTR DEL A A - rs144410256 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:20712747delA ENST00000241125.3 - 0 4857 NM_021954.3 NP_068773.2 Q9Y6H8 CXA3_HUMAN gap junction protein, alpha 3, 46kDa NA NA NA cell-cell signaling (GO:0007267)|transport (GO:0006810)|visual perception (GO:0007601) connexon complex (GO:0005922)|integral component of membrane (GO:0016021) gap junction channel activity (GO:0005243) NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1) 7 all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822) all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784) TTAAATGTACAATGTCCATAT 0.383 NA NA NA AA|AA|A|deletion 1341 0.267772 0.087 0.3847 5008 , , NA 17321 0.4058 NA 0.2217 False NA ,,, NA NA NA 2504 0.3344 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 111 108.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF075290 CCDS9289.1 13q12.11 2008-02-05 2007-01-16 ENSG00000121743 ENSG00000121743 2700 "Ion channels / Gap junction proteins (connexins)" 4277 protein-coding gene gene with protein product "connexin 46" 121015 "gap junction protein, alpha 3, 46kD (connexin 46)", "gap junction protein, alpha 3, 46kDa (connexin 46)" CZP3 NA 10205266, 7342922 Standard NM_021954 NM_021954 NA Approved CX46 uc001umx.1 Q9Y6H8 OTTHUMG00000016510 ENST00000241125.3:c.*3373T>- chr13.hg19:g.20712747delA 1 3 ref NA False 43 43 PASS 2 PASS ref->het 0 NA 71,72 30,30 10,10 2 2 Q0VAB7|Q9H537 True hg19 CCDS9289.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GJA3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044059.3 PASS NA None 111 NA True - A ENST00000241125.3 GJA3 2700 __UNKNOWN__ __UNKNOWN__ 13 20715931 20715932 __UNKNOWN__ 3'UTR DEL CA CA - rs35815144 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:20715931_20715932delCA ENST00000241125.3 - 0 1672_1673 NM_021954.3 NP_068773.2 Q9Y6H8 CXA3_HUMAN gap junction protein, alpha 3, 46kDa NA NA NA cell-cell signaling (GO:0007267)|transport (GO:0006810)|visual perception (GO:0007601) connexon complex (GO:0005922)|integral component of membrane (GO:0016021) gap junction channel activity (GO:0005243) NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1) 7 all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822) all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784) CACTGTAACTCACAGTGCTAAG 0.55 NA NA NA 1213 0.242212 0.0393 0.3617 5008 , , NA 17261 0.4018 NA 0.1928 False NA ,,, NA NA NA 2504 0.318 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 163 153.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF075290 CCDS9289.1 13q12.11 2008-02-05 2007-01-16 ENSG00000121743 ENSG00000121743 2700 "Ion channels / Gap junction proteins (connexins)" 4277 protein-coding gene gene with protein product "connexin 46" 121015 "gap junction protein, alpha 3, 46kD (connexin 46)", "gap junction protein, alpha 3, 46kDa (connexin 46)" CZP3 NA 10205266, 7342922 Standard NM_021954 NM_021954 NA Approved CX46 uc001umx.1 Q9Y6H8 OTTHUMG00000016510 ENST00000241125.3:c.*189TG>- chr13.hg19:g.20715933_20715934delCA 1 2 ref NA False 39 39 PASS 2 PASS ref->het 0 NA 113,115 26,26 21,20 1 1 Q0VAB7|Q9H537 True hg19 CCDS9289.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GJA3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044059.3 PASS NA None 163 NA True - CA ENST00000241125.3 Unknown 0 __UNKNOWN__ __UNKNOWN__ 13 28194633 28194634 __UNKNOWN__ IGR INS - - CGC rs541190078|rs373438242|rs559703439|rs530368033|rs542151624 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:28194633_28194634insCGC NA LNX2 (92 upstream) : POLR1D (268 downstream) NA NA NA NA CCGCCAGGAATcgccgccgccg 0.743 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 32 28.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr13.hg19:g.28194640_28194642dupCGC 9 3 ref NA False 31 31 PASS 8 PASS ref->het 0 NA 17,18 7,8 8,6 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 32 NA True CGC DCLK1 9201 __UNKNOWN__ __UNKNOWN__ 13 36700350 36700352 __UNKNOWN__ Intron DEL ATA ATA - rs537892866|rs535178347|rs148384031|rs10604618 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:36700350_36700352delATA ENST00000255448.4 - 2 193 DCLK1_ENST00000360631.3_Intron|DCLK1_ENST00000379892.4_Intron NM_004734.4 NP_004725.1 O15075 DCLK1_HUMAN doublecortin-like kinase 1 NA NA NA axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615) integral component of plasma membrane (GO:0005887) ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057) breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1) 64 Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638) ATATATATATATATAtttttttg 0.429 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 61 111.6 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.44 AB002367 CCDS9354.1, CCDS55895.1, CCDS73561.1 13q13.3 2008-02-05 2007-04-02 2007-04-02 ENSG00000133083 ENSG00000133083 9201 2700 protein-coding gene gene with protein product 604742 "doublecortin and CaM kinase-like 1" DCAMKL1 NA 9747029, 10036192 Standard NM_004734 NM_004734 NA Approved KIAA0369, DCLK, DCDC3A uc001uvf.3 O15075 OTTHUMG00000016729 ENST00000255448.4:c.19-57TAT>- chr13.hg19:g.36700350_36700352delATA 0 8 ref NA False 47 47 PASS 1 PASS ref->het 0 NA 33,33 23,23 15,15 1 1 B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1 True hg19 CCDS9354.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DCLK1-006 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044483.1 PASS NA None 61 NA True - ATA ENST00000255448.4 DCLK1 9201 __UNKNOWN__ __UNKNOWN__ 13 36700356 36700357 __UNKNOWN__ Intron INS - - G rs113810001|rs76991389|rs148384031|rs55712539 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:36700356_36700357insG ENST00000255448.4 - 2 193 DCLK1_ENST00000360631.3_Intron|DCLK1_ENST00000379892.4_Intron NM_004734.4 NP_004725.1 O15075 DCLK1_HUMAN doublecortin-like kinase 1 NA NA NA axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615) integral component of plasma membrane (GO:0005887) ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057) breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1) 64 Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638) ATATATATAtttttttgttttt 0.426 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 56 93.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.37 AB002367 CCDS9354.1, CCDS55895.1, CCDS73561.1 13q13.3 2008-02-05 2007-04-02 2007-04-02 ENSG00000133083 ENSG00000133083 9201 2700 protein-coding gene gene with protein product 604742 "doublecortin and CaM kinase-like 1" DCAMKL1 NA 9747029, 10036192 Standard NM_004734 NM_004734 NA Approved KIAA0369, DCLK, DCDC3A uc001uvf.3 O15075 OTTHUMG00000016729 ENST00000255448.4:c.19-63->C chr13.hg19:g.36700356_36700357insG 1 12 ref NA False 36 36 PASS 0 PASS ref->het 0 NA 24,24 23,23 13,13 1 1 B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1 True hg19 CCDS9354.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DCLK1-006 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044483.1 PASS NA None 56 NA True - G ENST00000255448.4 SERP2 387923 __UNKNOWN__ __UNKNOWN__ 13 44971783 44971784 __UNKNOWN__ 3'UTR INS - - TTC rs71789975|rs138267707 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:44971783_44971784insTTC ENST00000379179.3 + 0 717_718 NM_001010897.1 NP_001010897.1 Q8N6R1 SERP2_HUMAN stress-associated endoplasmic reticulum protein family member 2 NA NA NA protein transport (GO:0015031) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021) large_intestine(1) 1 all_hematologic(4;1.49e-06)|Acute lymphoblastic leukemia(4;1.5e-06)|Lung NSC(96;0.00043)|Breast(139;0.0044)|Prostate(109;0.0137)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556) GBM - Glioblastoma multiforme(144;0.00026)|BRCA - Breast invasive adenocarcinoma(63;0.123) ACTGGTTTACTTTCTATGGATA 0.421 NA NA NA 252 0.0503195 0.0908 0.1009 5008 , , NA 20384 0.001 NA 0.0537 False NA ,,, NA NA NA 2504 0.0072 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 113 112.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 BC029067 CCDS31965.1 13q14.11 2008-02-05 2007-12-07 2007-12-07 ENSG00000151778 ENSG00000151778 387923 20607 protein-coding gene gene with protein product NA "chromosome 13 open reading frame 21" C13orf21 NA Standard NM_001010897 NM_001010897 NA Approved bA269C23.1 uc001uzj.3 Q8N6R1 OTTHUMG00000016833 ENST00000379179.3:c.*336->TTC chr13.hg19:g.44971784_44971786dupTTC 2 4 ref NA False 70 70 PASS 1 PASS ref->het 0 NA 78,80 22,22 12,12 2 2 True hg19 CCDS31965.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SERP2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044736.1 PASS NA None 113 NA True + TTC ENST00000379179.3 KPNA3 3839 __UNKNOWN__ __UNKNOWN__ 13 50366680 50366681 __UNKNOWN__ 5'UTR INS - - GCG rs377544239|rs375322361 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:50366680_50366681insGCG ENST00000261667.3 - 0 376_377 NM_002267.3 NP_002258.2 O00505 IMA4_HUMAN karyopherin alpha 3 (importin alpha 4) NA NA NA cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)|protein complex assembly (GO:0006461)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732) cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654) nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565) cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(4) 21 Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19) GBM - Glioblastoma multiforme(99;1.42e-09) CTCCTgcggctgcggcggcggc 0.703 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 158 154.6 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.08 D89618 CCDS9421.1 13q14.3 2013-02-14 ENSG00000102753 ENSG00000102753 3839 "Importins", "Armadillo repeat containing" 6396 protein-coding gene gene with protein product 601892 NA 9154134, 9435235 Standard NM_002267 NM_002267 NA Approved SRP1gamma, SRP4, hSRP1, IPOA4 uc001vdj.2 O00505 OTTHUMG00000016922 ENST00000261667.3:c.-39->CGC chr13.hg19:g.50366687_50366689dupGCG 7 3 ref NA False 88 88 PASS 6 PASS ref->het 0 NA 61,65 26,26 68,66 1 1 O00191|O43195|Q5JVM9|Q96AA7 True hg19 CCDS9421.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KPNA3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000044939.2 PASS NA None 158 NA True - GCG ENST00000261667.3 VPS36 51028 __UNKNOWN__ __UNKNOWN__ 13 52987513 52987513 __UNKNOWN__ 3'UTR DEL A A - rs367817882|rs574195816|rs149617054 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:52987513delA ENST00000378060.4 - 0 3640 NM_001282168.1|NM_001282169.1|NM_016075.2 NP_001269097.1|NP_001269098.1|NP_057159.2 Q86VN1 VPS36_HUMAN vacuolar protein sorting 36 homolog (S. cerevisiae) NA NA NA endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634) phosphatidylinositol-3-phosphate binding (GO:0032266) breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(2) 17 Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173) GBM - Glioblastoma multiforme(99;3.14e-08) GCTCAATGTCATAAGTATTTA 0.279 NA NA NA A|A|-|deletion 29 0.00579073 8e-04 0.0086 5008 , , NA 17083 0 NA 0.0169 False NA ,,, NA NA NA 2504 0.0051 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 163 160.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF151903 CCDS9434.1, CCDS73577.1 13q14.13 2008-02-05 2007-01-12 2005-08-02 ENSG00000136100 ENSG00000136100 51028 20312 protein-coding gene gene with protein product 610903 "chromosome 13 open reading frame 9", "vacuolar protein sorting 36 homolog (yeast)" C13orf9 NA 11278625, 15755741 Standard NM_016075 NA Approved CGI-145, Eap45 uc001vgs.3 Q86VN1 OTTHUMG00000016964 ENST00000378060.4:c.*2452T>- chr13.hg19:g.52987513delA 0 3 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 113,114 27,27 18,18 1 1 A8K125|Q3ZCV7|Q5H9S1|Q5VXB6|Q9H8Z5|Q9Y3E3 True hg19 CCDS9434.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA VPS36-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000045059.3 PASS NA None 163 NA True - A ENST00000378060.4 COL4A2 1284 __UNKNOWN__ __UNKNOWN__ 13 111120685 111120685 __UNKNOWN__ Intron DEL T T - rs34167123 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:111120685delT ENST00000360467.5 + 28 2401 NM_001846.2 NP_001837.2 P08572 CO4A2_HUMAN collagen, type IV, alpha 2 NA NA NA angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351) collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231) extracellular matrix structural constituent (GO:0005201) NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1) 80 all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922) Breast(118;0.212) BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151) CATCCATGGATTTCAACACCG 0.522 NA NA NA TTT|TTT|TT|deletion 906 0.180911 0.1467 0.1585 5008 , , NA 20044 0.1677 NA 0.2366 False NA ,,, NA NA NA 2504 0.1994 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 695 657.21 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.31 AK025912 CCDS41907.1 13q34 2013-09-05 ENSG00000134871 ENSG00000134871 1284 "Collagens" 2203 protein-coding gene gene with protein product "canstatin", "collagen type IV alpha 2" 120090 NA 2439508, 3025878 Standard NM_001846 NM_001846 NA Approved FLJ22259, DKFZp686I14213 uc001vqx.3 P08572 OTTHUMG00000017344 ENST00000360467.5:c.2096-879T>- chr13.hg19:g.111120685delT 2 3 ref NA False 107 107 PASS 3 PASS ref->het 0 NA 526,529 109,111 60,57 1 1 Q14052|Q548C3|Q5VZA9|Q66K23 True hg19 CCDS41907.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COL4A2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000045761.2 PASS NA None 695 NA True + T ENST00000360467.5 ATP11A 23250 __UNKNOWN__ __UNKNOWN__ 13 113473599 113473600 __UNKNOWN__ Intron DEL AT AT - rs34166778|rs201547328 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:113473599_113473600delAT ENST00000487903.1 + 7 658 ATP11A_ENST00000375645.3_Intron|ATP11A_ENST00000375630.2_Intron|ATP11A_ENST00000283558.8_Intron P98196 AT11A_HUMAN ATPase, class VI, type 11A NA NA NA phospholipid translocation (GO:0045332) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037) ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012) NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1) 51 all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163) all_lung(25;0.134)|all_epithelial(44;0.141) GTGAGCTCACATGTCTTGTGCA 0.515 NA NA NA 1212 0.242013 0.2254 0.268 5008 , , NA 18796 0.254 NA 0.2604 False NA ,,, NA NA NA 2504 0.2147 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 157 147 NA , 997,3267 NA 112,773,1247 NA NA NA , 1.6 0 NA dbSNP_126 91 2239,6015 NA 313,1613,2201 no intron,intron ATP11A NM_032189.3,NM_015205.2 , 425,2386,3448 A1A1,A1R,RR NA 27.1262,23.3818,25.8508 , , NA 3236,9282 NA NA NA SO:0001627 intron_variant 0 AB028944 CCDS32011.1 13q34 2010-04-20 2007-09-19 ENSG00000068650 ENSG00000068650 23250 3.6.3.1 "ATPases / P-type" 13552 protein-coding gene gene with protein product "potential phospholipid-transporting ATPase IH", "phospholipid-translocating ATPase" 605868 "ATPase, Class VI, type 11A" NA 11015572 Standard NM_015205 NM_032189 NA Approved ATPIH, ATPIS, KIAA1021 uc001vsj.4 P98196 OTTHUMG00000017371 ENST00000487903.1:c.571-18AT>- chr13.hg19:g.113473599_113473600delAT 0 2 ref NA False 36 36 PASS 1 PASS ref->het 0 NA 115,116 26,26 22,22 1 1 Q5VXT2 True hg19 CCDS32011.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ATP11A-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000045834.3 PASS NA None 157 NA True + AT ENST00000487903.1 DCUN1D2 55208 __UNKNOWN__ __UNKNOWN__ 13 114111788 114111788 __UNKNOWN__ 3'UTR DEL A A - rs143495578 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr13:114111788delA ENST00000478244.1 - 0 1618 DCUN1D2_ENST00000332592.3_3'UTR NM_001014283.1 NP_001014305.1 Q6PH85 DCNL2_HUMAN DCN1, defective in cullin neddylation 1, domain containing 2 NA NA NA breast(1)|endometrium(1)|large_intestine(1)|lung(3)|stomach(1) 7 Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188) all cancers(43;0.029)|GBM - Glioblastoma multiforme(44;0.234) TAGAGCTGGTAAATCTAGATA 0.353 NA NA NA AAA|AAA|AA|deletion 181 0.0361422 0.0015 0.0101 5008 , , NA 14819 0.121 NA 0.0288 False NA ,,, NA NA NA 2504 0.0215 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 192 197.56 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.3 AK001566 CCDS32013.1 13q34 2013-06-10 2013-06-10 2005-10-04 ENSG00000150401 ENSG00000150401 55208 20328 protein-coding gene gene with protein product NA "chromosome 13 open reading frame 17", "DCN1, defective in cullin neddylation 1, domain containing 2 (S. cerevisiae)" C13orf17 NA 15988528 Standard NM_018185 XM_005268320 NA Approved FLJ10704, FLJ20092 uc001vtr.1 Q6PH85 OTTHUMG00000017390 ENST00000478244.1:c.*556T>- chr13.hg19:g.114111788delA 2 3 ref NA False 30 30 PASS 3 PASS ref->het 0 NA 156,156 22,22 16,16 1 1 Q5JSA5|Q5JSA6|Q5JSA7|Q9NVJ1|Q9NXR6 True hg19 CCDS32013.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DCUN1D2-006 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000045938.4 PASS NA None 192 NA True - A ENST00000478244.1 METTL17 64745 __UNKNOWN__ __UNKNOWN__ 14 21458321 21458324 __UNKNOWN__ Intron DEL CCCG CCCG - rs550671084|rs36002749|rs147038155 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:21458321_21458324delCCCG ENST00000339374.6 + 2 308 METTL17_ENST00000555177.1_Intron|METTL17_ENST00000382985.4_Intron|METTL17_ENST00000556670.2_Intron NM_001029991.1|NM_022734.2 NP_001025162.1|NP_073571.1 Q9H7H0 MET17_HUMAN methyltransferase like 17 NA NA NA translation (GO:0006412) mitochondrion (GO:0005739)|ribosome (GO:0005840) copper ion binding (GO:0005507)|methyltransferase activity (GO:0008168) central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(2) 20 CCTGGCAGCCCCCGCCCTAGCGAT 0.623 NA NA NA 1441 0.28774 0.236 0.3429 5008 , , NA 14948 0.2391 NA 0.3131 False NA ,,, NA NA NA 2504 0.3425 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 696 734.48 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.73 AK024512 CCDS9562.1, CCDS41913.1 14q11.2 2011-03-03 2011-03-02 2011-03-02 ENSG00000165792 ENSG00000165792 64745 19280 protein-coding gene gene with protein product NA "methyltransferase 11 domain containing 1" METT11D1 NA 11278769 Standard NM_022734 XM_006720235 NA Approved FLJ20859 uc001vyn.3 Q9H7H0 OTTHUMG00000029610 ENST00000339374.6:c.76-65CCCG>- chr14.hg19:g.21458321_21458324delCCCG 0 8 ref NA False 112 112 PASS 1 PASS ref->het 0 NA 567,573 83,84 94,92 1 1 Q9BSH1|Q9BZH2|Q9BZH3 True hg19 CCDS9562.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA METTL17-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000073804.4 PASS NA None 696 NA True + CCCG ENST00000339374.6 AE000661.50 0 __UNKNOWN__ __UNKNOWN__ 14 22887460 22887460 __UNKNOWN__ lincRNA DEL G G - rs397688315|rs3216790|rs398077624 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:22887460delG ENST00000555460.1 + 0 270 AE000661.37_ENST00000537850.1_RNA|AE000661.37_ENST00000535351.1_RNA|AE000661.37_ENST00000514473.2_RNA|AE000661.37_ENST00000545670.1_RNA|AE000661.37_ENST00000541008.1_RNA NA NA NA NA TGAGGTTATCGGGGAAATGAA 0.443 NA NA NA ?|GGGG|GGG|unsure 2396 0.478435 0.2874 0.3329 5008 , , NA 22289 0.6885 NA 0.4513 False NA ,,, NA NA NA 2504 0.6513 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 150 148.72 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.59 NA NA NA NA NA ENST00000555460.1: chr14.hg19:g.22887460delG 3 4 ref NA False 33 33 PASS 4 PASS ref->het 0 NA 105,105 32,32 15,15 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AE000661.50-001 KNOWN basic|exp_conf lincRNA NA lincRNA OTTHUMT00000410668.1 PASS NA None 150 NA True + G ENST00000555460.1 ACIN1 22985 __UNKNOWN__ __UNKNOWN__ 14 23548783 23548784 __UNKNOWN__ In_Frame_Ins INS - - GAACGT rs78164858|rs148403158|rs61741621|rs5807202|rs3077646 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:23548783_23548784insGAACGT ENST00000262710.1 - 6 2261_2262 c.1934_1935insACGTTC c.(1933-1935)tct>tcACGTTCt p.645_645S>SRS ACIN1_ENST00000605057.1_In_Frame_Ins_p.587_587S>SRS|ACIN1_ENST00000555053.1_In_Frame_Ins_p.645_645S>SRS|ACIN1_ENST00000457657.1_In_Frame_Ins_p.605_605S>SRS NM_001164814.1|NM_014977.3 NP_001158286.1|NP_055792 Q9UKV3 ACINU_HUMAN apoptotic chromatin condensation inducer 1 645 Ser-rich. NA NA apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380) ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886) ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822) breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1) 37 all_cancers(95;1.36e-05) GBM - Glioblastoma multiforme(265;0.00816) ATGCTGAACGAGAACGTGAACG 0.485 NA NA NA 1942 0.38778 0.5318 0.2637 5008 , , NA 21370 0.4226 NA 0.2664 False NA ,,, NA NA NA 2504 0.3701 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 137 134.55 NA ,, 2635,143,113,3,1370 NA 775,98,106,3,878,1,1,0,42,0,0,6,0,0,222 NA NA NA ,, -4.2 0.3 NA dbSNP_126 219 3073,1,288,0,4892 NA 417,1,253,0,1985,0,0,0,0,0,0,35,0,0,1436 no codingComplex,codingComplex,codingComplex ACIN1 NM_014977.3,NM_001164815.1,NM_001164814.1 ,, 1192,99,359,3,2863,1,1,0,42,0,0,41,0,0,1658 A1A1,A1A2,A1A3,A1A4,A1R,A2A2,A2A3,A2A4,A2R,A3A3,A3A4,A3R,A4A4,A4R,RR NA 40.7318,38.2036,49.976 ,, ,, NA 5708,144,401,3,6262 NA NA NA SO:0001652 inframe_insertion 0 AB014570 CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1 14q11.2 2008-11-25 2004-03-31 2004-04-01 ENSG00000100813 ENSG00000100813 22985 17066 protein-coding gene gene with protein product "functional spliceosome-associated protein 152" 604562 "apoptotic chromatin condensation inducer in the nucleus" ACINUS NA 9734811, 10490026 Standard NM_014977 NM_014977 NA Approved KIAA0670, fSAP152 uc001wit.4 Q9UKV3 OTTHUMG00000028716 ENST00000262710.1:c.1929_1934dupACGTTC chr14.hg19:g.23548784_23548789dupGAACGT ENSP00000262710:p.ArgSer647dup 3 3 ref NA False 48 48 PASS 2 PASS ref->het 0 NA 90,91 19,19 32,32 1 1 B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2 True hg19 CCDS9587.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ACIN1-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000071707.3 PASS NA None 137 NA True - GAACGT ENST00000262710.1 EFS 10278 __UNKNOWN__ __UNKNOWN__ 14 23834175 23834177 __UNKNOWN__ Intron DEL GGA GGA - rs72127341|rs374623998 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:23834175_23834177delGGA ENST00000216733.3 - 1 626 EFS_ENST00000429593.2_Intron|EFS_ENST00000351354.3_Intron NM_005864.2 NP_005855.1 O43281 EFS_HUMAN embryonal Fyn-associated substrate NA NA NA cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556) cytoplasm (GO:0005737) protein domain specific binding (GO:0019904) endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2) 16 all_cancers(95;7.12e-06) GBM - Glioblastoma multiforme(265;0.00649) GGCAGGCCGTGGAGGTCTCTCCC 0.631 NA NA NA 581 0.116014 0.2738 0.072 5008 , , NA 12554 0.001 NA 0.0964 False NA ,,, NA NA NA 2504 0.0726 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 132 138.58 NA , 1011,12,3199 NA 152,0,707,6,0,1246 NA NA NA , 0.4 0 NA dbSNP_130 28 1054,34,7118 NA 110,0,834,16,2,3141 no intron,intron EFS NM_032459.1,NM_005864.2 , 262,0,1541,22,2,4387 A1A1,A1A2,A1R,A2A2,A2R,RR NA 13.2586,24.2302,16.9858 , , NA 2065,46,10317 NA NA NA SO:0001627 intron_variant 0 AB001466 CCDS9595.1, CCDS9596.1, CCDS61404.1 14q11.2-q12 2011-04-13 ENSG00000100842 ENSG00000100842 10278 "Cas scaffolding proteins" 16898 protein-coding gene gene with protein product "Cas scaffolding protein family member 3" 609906 NA 9349509 Standard NM_005864 NA Approved EFS2, EFS1, HEFS, SIN, CASS3 uc001wjo.4 O43281 OTTHUMG00000028741 ENST00000216733.3:c.18+39TCC>- chr14.hg19:g.23834175_23834177delGGA 0 4 ref NA False 50 50 PASS 1 PASS ref->het 0 NA 109,109 19,19 7,7 1 1 B2RAJ7|B4DJ56|E9PGU2|O43282 True hg19 CCDS9595.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EFS-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000071770.2 PASS NA None 132 NA True - GGA ENST00000216733.3 AP1G2 8906 __UNKNOWN__ __UNKNOWN__ 14 24031695 24031695 __UNKNOWN__ Intron DEL C C - rs58786222|rs398099231 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:24031695delC ENST00000308724.5 - 14 2256 AP1G2_ENST00000397120.3_Intron|RP11-66N24.3_ENST00000555968.1_RNA NM_003917.2 NP_003908.1 O75843 AP1G2_HUMAN adaptor-related protein complex 1, gamma 2 subunit NA NA NA intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032) AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133) protein transporter activity (GO:0008565) breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1) 28 all_cancers(95;0.000251) GBM - Glioblastoma multiforme(265;0.00672) CCTCAGTGTACCCCCAATGAG 0.587 NA NA NA OREG0022605 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) CCCCC|CCCCC|CCCC|deletion 741 0.147963 0.0061 0.1383 5008 , , NA 19791 0.123 NA 0.1958 False NA ,,, NA NA NA 2504 0.3231 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 310 310.16 NA 165,4099 NA 7,151,1974 83 64 71 -7.8 0 14 dbSNP_129 80 1586,6668 NA 150,1286,2691 no intron AP1G2 NM_003917.2 157,1437,4665 A1A1,A1R,RR NA 19.2149,3.8696,13.9879 24031695 1751,10767 2203 4299 6502 SO:0001627 intron_variant 0.04 AB015318 CCDS9602.1 14q11.2 2008-07-03 ENSG00000213983 ENSG00000213983 8906 556 protein-coding gene gene with protein product 603534 NA 9733768, 9762922 Standard NM_003917 XM_005268167 NA Approved G2AD uc001wkl.2 O75843 OTTHUMG00000028760 ENST00000308724.5:c.1500+17G>- chr14.hg19:g.24031695delC 4 5 ref 768 False 47 47 PASS 5 PASS ref->het 0 NA 241,243 37,38 30,29 1 1 D3DS51|O75504 True hg19 CCDS9602.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AP1G2-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000071812.4 PASS NA None 310 NA True - C ENST00000308724.5 KHNYN 23351 __UNKNOWN__ __UNKNOWN__ 14 24907039 24907039 __UNKNOWN__ 3'UTR DEL T T - rs142280100 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:24907039delT ENST00000251343.5 + 0 2724 KHNYN_ENST00000553935.1_3'UTR O15037 KHNYN_HUMAN KH and NYN domain containing NA NA NA RNA binding (GO:0003723) kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3) 24 gctatgcctgttttgtgacct 0.498 NA NA NA TTT|TTTT|TTT|insertion 842 0.168131 0.3926 0.1138 5008 , , NA 23295 0.125 NA 0.0527 False NA ,,, NA NA NA 2504 0.0665 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 123 119.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.01 AB002321 CCDS32058.1 14q11.2 2010-11-23 2009-10-14 2009-10-14 ENSG00000100441 ENSG00000100441 23351 20166 protein-coding gene gene with protein product NA "KIAA0323" KIAA0323 NA 17114934 Standard NM_015299 NA Approved uc001wph.4 O15037 ENST00000251343.5:c.*548T>- chr14.hg19:g.24907039delT 3 5 ref NA False 30 30 PASS 4 PASS ref->het 0 NA 92,93 17,17 14,14 1 1 Q86TZ6|Q8IUQ2|Q96BA9 True hg19 CCDS32058.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KHNYN-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000412928.1 PASS NA None 123 NA True + T ENST00000251343.5 KHNYN 23351 __UNKNOWN__ __UNKNOWN__ 14 24907508 24907509 __UNKNOWN__ 3'UTR INS - - A rs71815016 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:24907508_24907509insA ENST00000251343.5 + 0 3193_3194 KHNYN_ENST00000553935.1_3'UTR O15037 KHNYN_HUMAN KH and NYN domain containing NA NA NA RNA binding (GO:0003723) kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3) 24 GATTTTTCACCAATCGATGAAG 0.416 NA NA NA AAA|AA|AAA|deletion 843 0.168331 0.3926 0.1138 5008 , , NA 24326 0.126 NA 0.0527 False NA ,,, NA NA NA 2504 0.0665 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 172 171.77 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AB002321 CCDS32058.1 14q11.2 2010-11-23 2009-10-14 2009-10-14 ENSG00000100441 ENSG00000100441 23351 20166 protein-coding gene gene with protein product NA "KIAA0323" KIAA0323 NA 17114934 Standard NM_015299 NA Approved uc001wph.4 O15037 ENST00000251343.5:c.*1018->A chr14.hg19:g.24907510_24907510dupA 3 3 ref NA False 56 56 PASS 2 PASS ref->het 0 NA 130,130 28,28 14,14 1 1 Q86TZ6|Q8IUQ2|Q96BA9 True hg19 CCDS32058.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KHNYN-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000412928.1 PASS NA None 172 NA True + A ENST00000251343.5 BNIP3P1 319138 __UNKNOWN__ __UNKNOWN__ 14 28734446 28734469 __UNKNOWN__ RNA DEL GTTTATTTGTTCTGTAAATGCTGC GTTTATTTGTTCTGTAAATGCTGC - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:28734446_28734469delGTTTATTTGTTCTGTAAATGCTGC ENST00000550043.1 + 0 851_874 BCL2/adenovirus E1B 19kDa interacting protein 3 pseudogene 1 NA NA NA NA CGTCACTTGTGTTTATTTGTTCTGTAAATGCTGCGTTCCTAATT 0.379 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 261 241.09 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.36 14q12 2014-02-04 2011-03-18 2011-03-18 ENSG00000197358 ENSG00000197358 319138 19922 pseudogene pseudogene NA "BCL2/adenovirus E1B 19kDa interacting protein 3 pseudogene" BNIP3P NA Standard NG_002516 NA Approved OTTHUMG00000170378 ENST00000550043.1: chr14.hg19:g.28734446_28734469delGTTTATTTGTTCTGTAAATGCTGC 0 4 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 208,212 38,39 37,37 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BNIP3P1-002 KNOWN basic processed_transcript NA pseudogene OTTHUMT00000408770.1 PASS NA None 261 NA True + GTTTATTTGTTCTGTAAATGCTGC ENST00000550043.1 SAMD4A 23034 __UNKNOWN__ __UNKNOWN__ 14 55034377 55034378 __UNKNOWN__ 5'UTR INS - - A rs76372748|rs60147860|rs71746986 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:55034377_55034378insA ENST00000554335.1 + 0 406_407 SAMD4A_ENST00000251091.5_5'UTR|SAMD4A_ENST00000555112.1_3'UTR Q9UPU9 SMAG1_HUMAN sterile alpha motif domain containing 4A NA NA NA negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727) cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202) poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371) breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1) 29 AAAAAGTCGTTTTTTTTTTTAA 0.47 NA NA NA A|-|A|deletion 2175 0.434305 0.5484 0.3213 5008 , , NA 13982 0.5605 NA 0.17 False NA ,,, NA NA NA 2504 0.502 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 122 130.25 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.01 AB028976 CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2 14q22.2 2013-01-10 2006-01-27 2006-01-27 ENSG00000020577 ENSG00000020577 23034 "Sterile alpha motif (SAM) domain containing" 23023 protein-coding gene gene with protein product "smaug homolog (Drosophila)" 610747 "sterile alpha motif domain containing 4" SAMD4 NA 16221671 Standard NM_015589 NM_001161577 NA Approved KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1 uc001xbb.4 Q9UPU9 OTTHUMG00000170999 ENST00000554335.1:c.-257->A chr14.hg19:g.55034377_55034378insA 1 11 ref NA False 61 61 PASS 0 PASS ref->het 0 NA 74,77 28,28 17,14 1 1 A8MPZ5|Q0VA96|Q6PEW4 True hg19 CCDS32084.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SAMD4A-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000411186.1 PASS NA None 122 NA True + A ENST00000554335.1 WDHD1 11169 __UNKNOWN__ __UNKNOWN__ 14 55406315 55406317 __UNKNOWN__ 3'UTR DEL AAG AAG - rs199893292|rs111931746|rs59191914|rs202102011 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:55406315_55406317delAAG ENST00000360586.3 - 0 5346_5348 NM_007086.3 NP_009017.1 O75717 WDHD1_HUMAN WD repeat and HMG-box DNA binding protein 1 NA NA NA heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396) chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723) breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2) 42 AAAAAAAAAAAAGAACACTGGAA 0.271 NA NA NA 1282 0.25599 0.2451 0.2911 5008 , , NA 16614 0.1677 NA 0.2734 False NA ,,, NA NA NA 2504 0.319 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 85 82.54 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 2.57 AJ006266 CCDS9721.1, CCDS41955.1 14q22.2 2013-01-09 ENSG00000198554 ENSG00000198554 11169 "WD repeat domain containing" 23170 protein-coding gene gene with protein product "CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)" 608126 NA 9175701, 20028748 Standard NM_007086 NM_007086 NA Approved AND-1, CTF4, CHTF4 uc001xbm.2 O75717 OTTHUMG00000140304 ENST00000360586.3:c.*1893CTT>- chr14.hg19:g.55406315_55406317delAAG 0 14 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 54,58 25,25 15,11 2 2 C9JW18|F6W0U7 True hg19 CCDS9721.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA WDHD1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000276897.2 PASS NA None 85 NA True - AAG ENST00000360586.3 SOCS4 122809 __UNKNOWN__ __UNKNOWN__ 14 55511365 55511366 __UNKNOWN__ 3'UTR INS - - TTTC rs71748778|rs202163326 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:55511365_55511366insTTTC ENST00000395472.2 + 0 1938_1939 SOCS4_ENST00000555846.1_3'UTR|SOCS4_ENST00000339298.2_3'UTR NM_080867.2|NM_199421.1 NP_543143.1|NP_955453.1 Q8WXH5 SOCS4_HUMAN suppressor of cytokine signaling 4 NA NA NA intracellular signal transduction (GO:0035556)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008) central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1) 14 CATGATCCTTTTTCCTTAATTT 0.277 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 93 108.84 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AF424815 CCDS9722.1 14q22.1 2013-02-14 2004-02-25 2004-02-27 ENSG00000180008 ENSG00000180008 122809 "Suppressors of cytokine signaling", "SH2 domain containing" 19392 protein-coding gene gene with protein product NA "suppressor of cytokine signaling 7" SOCS7 NA 12076535, 10500304 Standard NM_080867 NA Approved uc001xbp.3 Q8WXH5 OTTHUMG00000140311 ENST00000395472.2:c.*284->TTTC chr14.hg19:g.55511365_55511366insTTTC 1 5 ref NA False 86 86 PASS 0 PASS ref->het 0 NA 55,56 33,33 21,21 1 1 True hg19 CCDS9722.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SOCS4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000276910.1 PASS NA None 93 NA True + TTTC ENST00000395472.2 KTN1 3895 __UNKNOWN__ __UNKNOWN__ 14 56139314 56139314 __UNKNOWN__ Intron DEL T T - rs397780205|rs3215766|rs202094368 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:56139314delT ENST00000395314.3 + 38 3599 KTN1_ENST00000395309.3_Intron|KTN1_ENST00000413890.2_Intron|KTN1_ENST00000395308.1_Intron|KTN1_ENST00000438792.2_Intron|KTN1_ENST00000554507.1_Intron|KTN1_ENST00000395311.1_Intron|KTN1_ENST00000416613.1_Intron|KTN1_ENST00000555573.1_Intron NM_001079521.1 NP_001072989.1 Q86UP2 KTN1_HUMAN kinectin 1 (kinesin receptor) NA NA NA microtubule-based movement (GO:0007018) endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020) poly(A) RNA binding (GO:0044822) breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1) 19 TCCTTGGTGGTTTTACTTGGC 0.333 NA NA T RET papillary thryoid NA TTT|TTTT|TTT|insertion 1753 0.35004 0.3343 0.304 5008 , , NA 19255 0.3651 NA 0.334 False NA ,,, NA NA NA 2504 0.4049 NA NA NA PASS Dom yes 14 14q22.1 3895 kinectin 1 (kinesin receptor) NA E 0 NA NA NA NA NA 311 290.78 NA NA 58 55 56 NA NA 14 NA NA NA 56139314 2181 4231 6412 SO:0001627 intron_variant 0 CCDS41957.1, CCDS41958.1, CCDS41959.1 14q22.1 2008-05-02 ENSG00000126777 ENSG00000126777 3895 6467 protein-coding gene gene with protein product 600381 NA 9605849 Standard NM_001079521 NA Approved KIAA0004, CG1 uc001xcc.3 Q86UP2 OTTHUMG00000140312 ENST00000395314.3:c.3532-34T>- chr14.hg19:g.56139314delT 3 4 ref NA False 102 91 PASS 4 PASS ref->het 0 NA 202,206 80,80 32,32 2 2 B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57 True hg19 CCDS41957.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA KTN1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000276912.2 PASS NA None 311 NA True + T ENST00000395314.3 C14orf37 145407 __UNKNOWN__ __UNKNOWN__ 14 58469756 58469762 __UNKNOWN__ 3'UTR DEL ATAACTG ATAACTG - rs59769953|rs36203267|rs199530585 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:58469756_58469762delATAACTG ENST00000267485.7 - 0 4211_4217 NM_001001872.2 NP_001001872.2 Q86TY3 CN037_HUMAN chromosome 14 open reading frame 37 NA NA NA integral component of membrane (GO:0016021) breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1) 33 TGTAAAGGAAATAACTGATAACTGAGA 0.348 NA NA NA 1907 0.380791 0.2784 0.3357 5008 , , NA 21347 0.5863 NA 0.3658 False NA ,,, NA NA NA 2504 0.3548 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 90 89.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 CCDS32089.1 14q23.1 2012-09-03 ENSG00000139971 ENSG00000139971 145407 19846 protein-coding gene gene with protein product NA NA Standard NM_001001872 NM_001001872 NA Approved uc001xdc.3 Q86TY3 OTTHUMG00000171173 ENST00000267485.7:c.*1698CAGTTAT>- chr14.hg19:g.58469763_58469769delATAACTG 1 5 ref NA False 30 30 PASS 2 PASS ref->het 0 NA 64,65 20,20 11,11 1 1 A8K8Z8|Q6P5Q1|Q86TY1 True hg19 CCDS32089.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C14orf37-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000412059.1 PASS NA None 90 NA True - ATAACTG ENST00000267485.7 L3HYPDH 112849 __UNKNOWN__ __UNKNOWN__ 14 59939812 59939814 __UNKNOWN__ Intron DEL AAA AAA - rs369803867|rs142508867 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:59939812_59939814delAAA ENST00000543619.1 - 3 569 L3HYPDH_ENST00000247194.4_Intron Q96EM0 T3HPD_HUMAN L-3-hydroxyproline dehydratase (trans-) NA NA NA metabolic process (GO:0008152) hydro-lyase activity (GO:0016836)|trans-L-3-hydroxyproline dehydratase activity (GO:0050346) NA L-Proline(DB00172) TCGCTTCCTGAAAAAAGATGAAG 0.384 NA NA NA 28 0.00559105 0 0.0101 5008 , , NA 21292 0 NA 0.0169 False NA ,,, NA NA NA 2504 0.0041 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 255 260.04 NA 14,4248 NA 0,14,2117 NA NA NA 2 0.9 NA dbSNP_134 125 131,8119 NA 2,127,3996 no intron C14orf149 NM_144581.1 2,141,6113 A1A1,A1R,RR NA 1.5879,0.3285,1.1589 NA 145,12367 NA NA NA SO:0001627 intron_variant 0 AI762327 CCDS9739.1 14q23.1 2012-08-15 2012-08-15 2012-08-15 ENSG00000126790 ENSG00000126790 112849 4.2.1.77 20488 protein-coding gene gene with protein product "trans-L-3-hydroxyproline dehydratase" 614811 "chromosome 14 open reading frame 149" C14orf149 NA 22528483 Standard NM_144581 NM_144581 NA Approved FLJ25436 uc001xee.1 Q96EM0 OTTHUMG00000028941 ENST00000543619.1:c.121-4TTT>- chr14.hg19:g.59939815_59939817delAAA 3 7 ref NA False 49 49 PASS 6 PASS ref->het 0 NA 184,184 38,38 32,33 1 1 Q96LJ5 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA L3HYPDH-011 PUTATIVE basic|exp_conf processed_transcript NA protein_coding OTTHUMT00000400574.1 PASS NA None 255 NA True - A ENST00000543619.1 JKAMP 51528 __UNKNOWN__ __UNKNOWN__ 14 59961972 59961972 __UNKNOWN__ Intron DEL G G - rs200511858|rs35919683|rs76512452 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:59961972delG ENST00000261247.9 + 4 605 RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000556985.1_3'UTR|JKAMP_ENST00000356057.5_Intron|JKAMP_ENST00000425728.2_Intron|JKAMP_ENST00000554271.1_Intron NM_001098625.1|NM_001284203.1|NM_016475.3 NP_001092095.1|NP_001271132.1|NP_057559.2 Q9P055 JKAMP_HUMAN JNK1/MAPK8-associated membrane protein NA NA NA ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|response to unfolded protein (GO:0006986) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021) ubiquitin protein ligase binding (GO:0031625) breast(1)|endometrium(1)|kidney(1)|lung(3) 6 TAAGATCATTGTTTTTTTTTA 0.398 NA NA NA -|G|-|insertion 1794 0.358227 0.4584 0.4352 5008 , , NA 18453 0.1895 NA 0.2992 False NA ,,, NA NA NA 2504 0.4029 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 102 109.13 NA NA 30 37 35 NA NA 14 NA NA NA 59961972 1682 3958 5640 SO:0001627 intron_variant 0.84 AF212245 CCDS45116.1, CCDS45117.1, CCDS61462.1, CCDS61463.1 14q22.3 2014-02-14 2009-08-13 2009-08-13 ENSG00000050130 ENSG00000050130 51528 20184 protein-coding gene gene with protein product "Jun N-terminal kinase 1-associated membrane protein" 611176 "chromosome 14 open reading frame 100" C14orf100 NA 16166642, 19269966 Standard NM_001098625 NM_001284202 NA Approved HSPC213, JAMP, HSPC327, CDA06 uc001xef.4 Q9P055 OTTHUMG00000171054 ENST00000261247.9:c.458+30G>- chr14.hg19:g.59961972delG 0 11 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 67,67 17,19 19,17 1 1 B4DP67|Q6FIB6|Q6IAJ2|Q7Z5D4|Q86SY6|Q9H0Q6|Q9H2W0|Q9HAH5|Q9P0R3 True hg19 CCDS45116.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA JKAMP-001 NOVEL basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000411430.1 PASS NA None 102 NA True + G ENST00000261247.9 PPP2R5E 5529 __UNKNOWN__ __UNKNOWN__ 14 63840221 63840226 __UNKNOWN__ 3'UTR DEL AAAAAA AAAAAA - rs201881490|rs3081717 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:63840221_63840226delAAAAAA ENST00000337537.3 - 0 4507_4512 NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2 NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1 Q16537 2A5E_HUMAN protein phosphatase 2, regulatory subunit B', epsilon isoform NA NA NA regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165) cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159) protein phosphatase type 2A regulator activity (GO:0008601) endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1) 15 OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128) ACTTTCCATTAAAAAAGAAAAAGACG 0.354 NA NA NA 895 0.178714 0.1657 0.121 5008 , , NA 20620 0.3651 NA 0.0815 False NA ,,, NA NA NA 2504 0.1452 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 206 203.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.07 L76703 CCDS9758.1, CCDS61467.1, CCDS61468.1 14q23.2 2010-06-18 2007-01-22 ENSG00000154001 ENSG00000154001 5529 "Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits" 9313 protein-coding gene gene with protein product 601647 "protein phosphatase 2, regulatory subunit B (B56), epsilon isoform" NA 7592815 Standard NM_006246 NM_006246 NA Approved uc001xgd.1 Q16537 OTTHUMG00000140341 ENST00000337537.3:c.*2506TTTTTT>- chr14.hg19:g.63840221_63840226delAAAAAA 0 11 ref NA False 35 35 PASS 6 PASS ref->het 0 NA 168,168 27,27 24,24 1 1 A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4 True hg19 CCDS9758.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PPP2R5E-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000276973.1 PASS NA None 206 NA True - A ENST00000337537.3 SYNE2 23224 __UNKNOWN__ __UNKNOWN__ 14 64682283 64682284 __UNKNOWN__ Intron INS - - C rs397746112|rs138806575|rs56402661 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:64682283_64682284insC ENST00000554584.1 + 108 19210 SYNE2_ENST00000458046.2_Intron|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555022.1_Intron|SYNE2_ENST00000555002.1_Intron|SYNE2_ENST00000358025.3_Intron|SYNE2_ENST00000394768.2_Intron|SYNE2_ENST00000554805.1_Intron|SYNE2_ENST00000441438.2_5'UTR|SYNE2_ENST00000357395.3_Intron|SYNE2_ENST00000344113.4_Intron Q8WXH0 SYNE2_HUMAN spectrin repeat containing, nuclear envelope 2 NA NA NA centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504) aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018) actin binding (GO:0003779) NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4) 224 all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681) CTCGATGCCAACCCCCTCTCCT 0.505 NA NA NA CCCCC|CCCCC|CCCCCC|insertion 270 0.0539137 0.0552 0.1037 5008 , , NA 19831 0.006 NA 0.0944 False NA ,,, NA NA NA 2504 0.0245 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 159 153.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.09 AB023228 CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1 14q22.1-q22.3 2014-09-17 ENSG00000054654 ENSG00000054654 23224 17084 protein-coding gene gene with protein product "nuclear envelope spectrin repeat-2", "nucleus and actin connecting element" 608442 NA 10231032, 10878022 Standard NM_182914 NM_182910 NA Approved SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2 uc001xgl.3 Q8WXH0 OTTHUMG00000140349 ENST00000554584.1:c.19160-682->C chr14.hg19:g.64682288_64682288dupC 6 6 ref NA False 42 42 PASS 5 PASS ref->het 0 NA 114,115 25,25 17,17 1 1 Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SYNE2-002 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000411905.1 PASS NA None 159 NA True + C ENST00000554584.1 ZNF410 57862 __UNKNOWN__ __UNKNOWN__ 14 74358704 74358705 __UNKNOWN__ Intron DEL CT CT - rs140665239 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:74358704_74358705delCT ENST00000540593.1 + 2 299 RP5-1021I20.4_ENST00000556551.2_Intron|ZNF410_ENST00000442160.3_Intron|ZNF410_ENST00000412490.3_Intron|ZNF410_ENST00000324593.6_Intron|ZNF410_ENST00000555044.1_Intron NM_001242927.1 NP_001229856.1 Q86VK4 ZN410_HUMAN zinc finger protein 410 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) breast(1)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1) 13 BRCA - Breast invasive adenocarcinoma(234;0.00369) TTAATGCCCCCTCTCTCTTTTT 0.361 NA NA NA 966 0.192891 0.034 0.3242 5008 , , NA 18483 0.0486 NA 0.4105 False NA ,,, NA NA NA 2504 0.2393 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 178 189.82 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.4 U90919 CCDS9821.1, CCDS55929.1, CCDS55930.1, CCDS55931.1 14q24.3 2013-01-08 ENSG00000119725 57862 "Zinc fingers, C2H2-type" 20144 protein-coding gene gene with protein product NA NA 12370286 Standard NM_021188 NM_001242924 NA Approved APA1, APA-1 uc010arz.2 Q86VK4 ENST00000540593.1:c.-149-25CT>- chr14.hg19:g.74358710_74358711delCT 3 6 ref NA False 63 63 PASS 4 PASS ref->het 0 NA 125,127 34,34 23,23 1 1 B4DDV5|B4DR78|O00153|Q9BQ19 True hg19 CCDS55931.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF410-002 NOVEL basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000412583.1 PASS NA None 178 NA True + CT ENST00000540593.1 DLST 1743 __UNKNOWN__ __UNKNOWN__ 14 75359758 75359759 __UNKNOWN__ Intron DEL CT CT - rs58288168 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:75359758_75359759delCT ENST00000334220.4 + 8 656 DLST_ENST00000334212.6_Intron|DLST_ENST00000555190.1_Intron NM_001933.4 NP_001924.2 P36957 ODO2_HUMAN dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex) NA NA NA cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|generation of precursor metabolites and energy (GO:0006091)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099) extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|oxoglutarate dehydrogenase complex (GO:0045252) dihydrolipoyllysine-residue succinyltransferase activity (GO:0004149) breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 18 BRCA - Breast invasive adenocarcinoma(234;0.00698) AAAGGGTAAACTCTAGACTGAT 0.47 NA NA NA 722 0.144169 0.3654 0.0994 5008 , , NA 20834 0.0069 NA 0.0746 False NA ,,, NA NA NA 2504 0.09 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 108 118.22 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.74 CCDS9833.1 14q23.1 2008-08-11 ENSG00000119689 ENSG00000119689 1743 2.3.1.61 2911 protein-coding gene gene with protein product 126063 DLTS NA 8009371 Standard NM_001933 NA Approved uc001xqv.2 P36957 ENST00000334220.4:c.595+69CT>- chr14.hg19:g.75359760_75359761delCT 1 3 ref NA False 37 37 PASS 2 PASS ref->het 0 NA 73,75 20,20 13,12 1 1 B7Z5W8|E7ESY5|Q7LDY7|Q9BQ32 True hg19 CCDS9833.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DLST-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000413637.1 PASS NA None 108 NA True + CT ENST00000334220.4 TTLL5 23093 __UNKNOWN__ __UNKNOWN__ 14 76211404 76211405 __UNKNOWN__ Intron INS - - T rs151227507|rs553892320 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:76211404_76211405insT ENST00000557636.1 + 17 1538 TTLL5_ENST00000555422.1_Intron|TTLL5_ENST00000298832.9_Intron Q6EMB2 TTLL5_HUMAN tubulin tyrosine ligase-like family, member 5 NA NA NA fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351) centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634) ligase activity (GO:0016874) NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2) 50 BRCA - Breast invasive adenocarcinoma(234;0.029) AACTTAAAAAATTTTTTTTACT 0.386 NA NA NA ?|TTTTTTTT|TTTTTTTTT|unsure 12 0.00239617 0 0.0029 5008 , , NA 17924 0 NA 0.004 False NA ,,, NA NA NA 2504 0.0061 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 213 233.32 NA 13,4247 NA 0,13,2117 NA NA NA -7.5 0 NA 3 98,8146 NA 4,90,4028 no intron TTLL5 NM_015072.4 4,103,6145 A1A1,A1R,RR NA 1.1887,0.3052,0.8877 NA 111,12393 NA NA NA SO:0001627 intron_variant 0.09 AF107885 CCDS32124.1 14q24.3 2014-09-09 2005-07-29 2005-07-29 ENSG00000119685 ENSG00000119685 23093 "Tubulin tyrosine ligase-like family" 19963 protein-coding gene gene with protein product 612268 "KIAA0998" KIAA0998 NA 15890843 Standard NM_015072 NM_015072 NA Approved uc001xrx.3 Q6EMB2 OTTHUMG00000171611 ENST00000557636.1:c.1324-33->T chr14.hg19:g.76211412_76211412dupT 9 8 ref NA False 79 79 PASS 8 PASS ref->het 0 NA 149,150 38,38 26,26 1 1 B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TTLL5-016 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000414451.1 PASS NA None 213 NA True + T ENST00000557636.1 SLC24A4 123041 __UNKNOWN__ __UNKNOWN__ 14 92949111 92949111 __UNKNOWN__ Frame_Shift_Del DEL G G - rs149298860 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:92949111delG ENST00000531433.1 + 14 1382 c.1286delG c.(1285-1287)cgcfs p.R429fs SLC24A4_ENST00000393265.2_Frame_Shift_Del_p.R384fs|SLC24A4_ENST00000298877.1_Frame_Shift_Del_p.R431fs|SLC24A4_ENST00000532405.1_Frame_Shift_Del_p.R448fs|SLC24A4_ENST00000351924.5_Frame_Shift_Del_p.R412fs NM_153647.3 NP_705933.2 Q8NFF2 NCKX4_HUMAN solute carrier family 24 (sodium/potassium/calcium exchanger), member 4 448 NA NA amelogenesis (GO:0097186)|cellular calcium ion homeostasis (GO:0006874)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|sensory perception of smell (GO:0007608)|transmembrane transport (GO:0055085) cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886) calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293) breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(20)|ovary(2)|skin(1) 36 all_cancers(154;0.0347)|all_epithelial(191;0.163) Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182) AGCAAGCCCCGCTGGGAGAAG 0.602 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NSCLC(10;315 435 10383 28450 38798) PASS NA NA NA 0 NA NA NA NA NA 383 362.16 NA NA 118 99 105 NA NA 14 NA NA NA 92949111 2203 4300 6503 SO:0001589 frameshift_variant 0.95 AF520704 CCDS9903.1, CCDS45155.1, CCDS45156.1, CCDS9903.2, CCDS45155.2 14q32.12 2013-05-22 ENSG00000140090 ENSG00000140090 123041 "Solute carriers" 10978 protein-coding gene gene with protein product 609840 NA Standard NM_153646 NM_153646 NA Approved NCKX4 uc001yak.3 Q8NFF2 OTTHUMG00000167589 ENST00000531433.1:c.1286delG chr14.hg19:g.92949111delG ENSP00000433302:p.Arg429fs 0 5 ref NA False 31 31 PASS 1 PASS ref->het 0 NA 289,294 43,43 44,39 1 1 B4DHE7|B9ZVY2|Q8N8U6|Q8NCX1|Q8NFF0|Q8NFF1 True hg19 CCDS45155.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLC24A4-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000395239.1 PASS NA None 383 NA True + G ENST00000531433.1 PRIMA1 145270 __UNKNOWN__ __UNKNOWN__ 14 94253884 94253884 __UNKNOWN__ Intron DEL G G - rs144186506 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr14:94253884delG ENST00000393140.1 - 2 196 PRIMA1_ENST00000393143.1_Intron|PRIMA1_ENST00000316227.3_Intron NM_178013.3 NP_821092.1 Q86XR5 PRIMA_HUMAN proline rich membrane anchor 1 NA NA NA establishment of localization in cell (GO:0051649)|neurotransmitter catabolic process (GO:0042135) cell junction (GO:0030054)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|synapse (GO:0045202) endometrium(1)|large_intestine(2)|lung(3)|skin(1) 7 all_cancers(154;0.127) Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229) TGGGGTGGCTGCAAGAGGCCA 0.597 NA NA NA G|G|-|deletion 346 0.0690895 0.0416 0.0677 5008 , , NA 15869 0.004 NA 0.0855 False NA ,,, NA NA NA 2504 0.1575 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 161 154.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS9912.1 14q32.13 2008-08-29 ENSG00000175785 ENSG00000175785 145270 18319 protein-coding gene gene with protein product "membrane anchor of acetylcholinesterase" 613851 NA 11804574 Standard NM_178013 NM_178013 NA Approved PRIMA uc001ybw.1 Q86XR5 OTTHUMG00000141313 ENST00000393140.1:c.93+87C>- chr14.hg19:g.94253884delG 0 2 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 121,126 18,18 24,21 1 1 Q86XR6 True hg19 CCDS9912.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PRIMA1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000280658.1 PASS NA None 161 NA True - G ENST00000393140.1 RPUSD2 27079 __UNKNOWN__ __UNKNOWN__ 15 40862191 40862192 __UNKNOWN__ Intron INS - - GTTTTGTTTTGTTTTGTTTT rs71307498|rs141235042 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:40862191_40862192insGTTTTGTTTTGTTTTGTTTT ENST00000559271.1 + 1 429 RPUSD2_ENST00000315616.7_Intron Q8IZ73 RUSD2_HUMAN RNA pseudouridylate synthase domain containing 2 NA NA NA pseudouridine synthesis (GO:0001522) poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982) kidney(4)|lung(4)|skin(3) 11 all_cancers(109;2.74e-14)|all_epithelial(112;1.64e-11)|Lung NSC(122;6.69e-09)|all_lung(180;1.22e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243) GBM - Glioblastoma multiforme(113;3.1e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0786) AAAGGGGCCGGgttttgttttg 0.48 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 198 169.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AK055971 CCDS10061.1, CCDS66737.1 15q13.3 2013-02-11 2005-01-31 2005-02-07 ENSG00000166133 ENSG00000166133 27079 "RNA pseudouridylate synthase domain containing" 24180 protein-coding gene gene with protein product NA "chromosome 15 open reading frame 19" C15orf19 NA 12477932 Standard NM_152260 NM_001286407 NA Approved C18B11, FLJ31409 uc001zmd.1 Q8IZ73 OTTHUMG00000130031 ENST00000559271.1:c.423+232->GTTTTGTTTTGTTTTGTTTT chr15.hg19:g.40862191_40862192insGTTTTGTTTTGTTTTGTTTT 9 4 ref NA False 30 30 PASS 5 PASS ref->het 0 NA 78,78 5,5 112,113 1 1 B4DDD1|Q7L989|Q92939|Q96IA7|Q96N50 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RPUSD2-004 NOVEL basic|appris_candidate|exp_conf protein_coding NA protein_coding OTTHUMT00000418791.2 PASS NA None 198 NA True + GTTTT ENST00000559271.1 FBN1 2200 __UNKNOWN__ __UNKNOWN__ 15 48780505 48780510 __UNKNOWN__ Intron DEL TAAAGA TAAAGA - rs143836403 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:48780505_48780510delTAAAGA ENST00000316623.5 - 26 3664 NM_000138.4 NP_000129 P35555 FBN1_HUMAN fibrillin 1 NA NA NA extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501) basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578) calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201) NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2) 139 all_lung(180;0.00279) all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05) GACAATATGTTAAAGATAAAGAGTTT 0.456 NA NA NA 244 0.048722 0.0469 0.0576 5008 , , NA 22704 0 NA 0.1014 False NA ,,, NA NA NA 2504 0.0409 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 544 512.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.05 X63556 CCDS32232.1 15q21.1 2014-09-17 2006-04-25 ENSG00000166147 2200 3603 protein-coding gene gene with protein product "Marfan syndrome" 134797 "fibrillin 1 (Marfan syndrome)" FBN, MFS1, WMS NA 10036187, 12525539 Standard NM_000138 NA Approved MASS, OCTD, SGS uc001zwx.2 P35555 ENST00000316623.5:c.3208+54TCTTTA>- chr15.hg19:g.48780511_48780516delTAAAGA 1 4 ref NA False 58 58 PASS 2 PASS ref->het 0 NA 472,474 33,33 45,43 1 1 B2RUU0|D2JYH6|Q15972|Q75N87 True hg19 CCDS32232.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FBN1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000417355.1 PASS NA None 544 NA True - TAAAGA ENST00000316623.5 USP3 9960 __UNKNOWN__ __UNKNOWN__ 15 63804547 63804555 __UNKNOWN__ Intron DEL TCTTCCTCT TCTTCCTCT - rs375403713|rs60592263|rs12915297|rs150788178 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:63804547_63804555delTCTTCCTCT ENST00000380324.3 + 1 220 USP3_ENST00000540797.1_Intron|USP3_ENST00000539772.1_Intron|USP3_ENST00000536001.1_Intron|USP3_ENST00000268049.7_Intron NM_006537.3 NP_006528.2 Q9Y6I4 UBP3_HUMAN ubiquitin specific peptidase 3 NA NA NA DNA repair (GO:0006281)|histone deubiquitination (GO:0016578)|mitotic cell cycle (GO:0000278)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511) nuclear chromatin (GO:0000790) histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270) endometrium(3)|large_intestine(7)|lung(4) 14 GBM - Glioblastoma multiforme(80;0.0187) ctcttcctcctcttcctcttcttcttctt 0.368 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 18 16.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF073344 CCDS32265.1, CCDS58370.1 15q22.3 2008-04-11 2005-08-08 ENSG00000140455 9960 "Ubiquitin-specific peptidases" 12626 protein-coding gene gene with protein product 604728 "ubiquitin specific protease 3" NA 12838346 Standard NM_006537 NA Approved uc002amf.4 Q9Y6I4 ENST00000380324.3:c.91+7518TCTTCCTCT>- chr15.hg19:g.63804547_63804555delTCTTCCTCT 0 4 ref NA False 33 33 PASS 1 PASS ref->het 0 NA 10,10 8,8 2,2 1 1 B4DVU5|F5H1A6|Q8WVD0 True hg19 CCDS32265.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA USP3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000417773.1 PASS NA None 18 NA True + TCTTCCTCT ENST00000380324.3 FAM96A 84191 __UNKNOWN__ __UNKNOWN__ 15 64367353 64367358 __UNKNOWN__ Intron DEL TTCAAT TTCAAT - rs145913637|rs2307519 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:64367353_64367358delTTCAAT ENST00000300030.3 - 4 635 FAM96A_ENST00000380290.3_Intron|FAM96A_ENST00000557835.1_3'UTR NM_032231.4 NP_115607.1 Q9H5X1 FA96A_HUMAN family with sequence similarity 96, member A NA NA NA chromosome segregation (GO:0007059) cytoplasm (GO:0005737)|nucleus (GO:0005634) metal ion binding (GO:0046872) kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1) 9 TTGCTAGACCTTCAATTTCAAGTACA 0.422 NA NA NA 1695 0.338458 0.3941 0.3444 5008 , , NA 17352 0.1696 NA 0.1889 False NA ,,, NA NA NA 2504 0.5869 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 242 234.45 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.41 CCDS10189.1, CCDS45278.1 15q22.31 2014-01-16 ENSG00000166797 ENSG00000166797 84191 26235 protein-coding gene gene with protein product NA NA 23891004 Standard NM_032231 NM_032231 NA Approved FLJ22875 uc002amt.1 Q9H5X1 OTTHUMG00000132961 ENST00000300030.3:c.385+332ATTGAA>- chr15.hg19:g.64367353_64367358delTTCAAT 0 3 ref NA False 36 36 PASS 1 PASS ref->het 0 NA 205,209 23,23 21,21 1 1 A6NKS1|B2R5F8|B7Z8Z5 True hg19 CCDS10189.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAM96A-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256520.1 PASS NA None 242 NA True - TTCAAT ENST00000300030.3 MAP2K1 5604 __UNKNOWN__ __UNKNOWN__ 15 66679851 66679851 __UNKNOWN__ Intron DEL G G - rs71447901 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:66679851delG ENST00000307102.5 + 1 611 NM_002755.3 NP_002746.1 Q02750 MP2K1_HUMAN mitogen-activated protein kinase kinase 1 NA NA NA activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi inheritance (GO:0048313)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte differentiation (GO:0030216)|labyrinthine layer development (GO:0060711)|MAPK cascade (GO:0000165)|melanosome transport (GO:0032402)|mitotic nuclear division (GO:0007067)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell proliferation (GO:0008285)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|neurotrophin TRK receptor signaling pathway (GO:0048011)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|regulation of vascular smooth muscle contraction (GO:0003056)|response to axon injury (GO:0048678)|response to glucocorticoid (GO:0051384)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vesicle transport along microtubule (GO:0047496) cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886) ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine phosphatase activity (GO:0004728) endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(8)|urinary_tract(1) 20 Bosutinib(DB06616)|Trametinib(DB08911) GCTCCGATCTGGTTTGTCACG 0.662 NA NA NA GG|GG|G|deletion 181 0.0361422 0.0106 0.0346 5008 , , NA 11380 0.001 NA 0.1064 False NA ,,, NA NA NA 2504 0.0358 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 117 134.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 L11284 CCDS10216.1 15q22.1-q22.33 2014-09-17 ENSG00000169032 ENSG00000169032 5604 2.7.12.2 "Mitogen-activated protein kinase cascade / Kinase kinases" 6840 protein-coding gene gene with protein product 176872 PRKMK1 NA 9465908, 8388392 Standard NM_002755 NA Approved MEK1, MAPKK1 uc010bhq.3 Q02750 OTTHUMG00000133196 ENST00000307102.5:c.80+86G>- chr15.hg19:g.66679851delG 1 3 ref NA False 65 65 PASS 2 PASS ref->het 0 NA 84,84 18,18 13,14 1 1 True hg19 CCDS10216.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAP2K1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256906.4 PASS NA None 117 NA True + G ENST00000307102.5 PSMA4 5685 __UNKNOWN__ __UNKNOWN__ 15 78836632 78836634 __UNKNOWN__ Intron DEL TGA TGA - rs56827168|rs67437837|rs398057850 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:78836632_78836634delTGA ENST00000558341.1 + 5 332 PSMA4_ENST00000560217.1_Intron|PSMA4_ENST00000044462.7_Intron|PSMA4_ENST00000559082.1_Intron|PSMA4_ENST00000413382.2_Intron|PSMA4_ENST00000557929.1_Intron|PSMA4_ENST00000558281.1_Intron P25789 PSA4_HUMAN proteasome (prosome, macropain) subunit, alpha type, 4 NA NA NA anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032) cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773) threonine-type endopeptidase activity (GO:0004298) kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1) 9 ATAGCATAACTGATGATACAGAA 0.414 NA NA NA 3775 0.753794 0.8495 0.7781 5008 , , NA 16604 0.8522 NA 0.6282 False NA ,,, NA NA NA 2504 0.635 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 223 234.48 NA ,, 3266,998 NA 1265,736,131 NA NA NA ,, -1.4 0 NA dbSNP_130 68 4796,3458 NA 1407,1982,738 no intron,intron,intron PSMA4 NM_002789.4,NM_001102668.1,NM_001102667.1 ,, 2672,2718,869 A1A1,A1R,RR NA 41.8948,23.4053,35.5967 ,, ,, NA 8062,4456 NA NA NA SO:0001627 intron_variant 1.96 BC005361 CCDS10303.1, CCDS45319.1 15q24.1 2004-01-19 ENSG00000041357 ENSG00000041357 5685 "Proteasome (prosome, macropain) subunits" 9533 protein-coding gene gene with protein product 176846 NA 2025653 Standard NM_002789 NM_002789 NA Approved HC9, HsT17706 uc010blf.3 P25789 OTTHUMG00000143859 ENST00000558341.1:c.287+23TGA>- chr15.hg19:g.78836635_78836637delTGA 1 2 ref NA False 42 42 PASS 2 PASS ref->het 0 NA 147,158 35,38 38,26 1 1 D3DW86|Q53XP2|Q567Q5|Q8TBD1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PSMA4-017 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000418909.1 PASS NA None 223 NA True + TGA ENST00000558341.1 FAH 2184 __UNKNOWN__ __UNKNOWN__ 15 80445512 80445513 __UNKNOWN__ Intron INS - - G rs534453827|rs376322780|rs71699670|rs57837512 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:80445512_80445513insG ENST00000407106.1 + 2 236 FAH_ENST00000561421.1_Intron|FAH_ENST00000261755.5_Intron P16930 FAAA_HUMAN fumarylacetoacetate hydrolase (fumarylacetoacetase) NA NA NA arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572) cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062) fumarylacetoacetase activity (GO:0004334)|metal ion binding (GO:0046872) endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 19 GGGCGCGGggagggagtggagt 0.609 NA NA NA Tyrosinemia, type 1 ?|GGG|GGGG|unsure 1763 0.352037 0.4357 0.2406 5008 , , NA 12058 0.5258 NA 0.1551 False NA ,,, NA NA NA 2504 0.3415 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 299 297.63 NA 116,1697,2451 NA 1,87,27,297,1016,704 NA NA NA -2.9 0 NA dbSNP_130 36 39,1057,7158 NA 0,2,37,68,919,3101 no intron FAH NM_000137.2 1,89,64,365,1935,3805 A1A1,A1A2,A1R,A2A2,A2R,RR NA 13.2784,42.5188,23.2385 NA 155,2754,9609 NA NA NA SO:0001627 intron_variant 0.07 Familial Cancer Database Fumarylacetoacetase Deficiency, Hepatorenal Tyrosinemia, Hereditary Tyrosinemia 1, HT1 M55150 CCDS10314.1 15q25.1 2012-08-30 ENSG00000103876 ENSG00000103876 2184 3.7.1.2 3579 protein-coding gene gene with protein product 613871 NA 1998338, 2336361 Standard NM_000137 NA Approved uc002bfm.2 P16930 OTTHUMG00000144187 ENST00000407106.1:c.81+35->G chr15.hg19:g.80445515_80445515dupG 4 7 ref NA False 98 98 PASS 3 PASS ref->het 0 NA 198,206 51,52 47,46 1 1 B2R9X1|D3DW95|Q53XA7 True hg19 CCDS10314.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FAH-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000291392.2 PASS NA None 299 NA True + G ENST00000407106.1 STARD5 80765 __UNKNOWN__ __UNKNOWN__ 15 81616177 81616178 __UNKNOWN__ Intron INS - - T rs148236522 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:81616177_81616178insT ENST00000302824.6 - 1 125 STARD5_ENST00000559913.1_5'UTR NM_181900.2 NP_871629.1 Q9NSY2 STAR5_HUMAN StAR-related lipid transfer (START) domain containing 5 NA NA NA C21-steroid hormone biosynthetic process (GO:0006700)|lipid transport (GO:0006869)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202) cytosol (GO:0005829) lipid binding (GO:0008289) large_intestine(3)|ovary(1)|skin(1)|stomach(1) 6 CAGGCCCAATCTTTTTTTTAAA 0.49 NA NA NA ?|TTTTTTTT|TTTTTTTTT|unsure 384 0.0766773 0.0983 0.0476 5008 , , NA 20100 0.0694 NA 0.0616 False NA ,,, NA NA NA 2504 0.091 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 335 293.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.03 AF480304 CCDS10318.1 15q26 2011-09-12 2007-08-16 ENSG00000172345 ENSG00000172345 80765 "StAR-related lipid transfer (START) domain containing" 18065 protein-coding gene gene with protein product 607050 "START domain containing 5" NA 12011452 Standard NM_181900 NA Approved MGC10327 uc002bgm.3 Q9NSY2 OTTHUMG00000147342 ENST00000302824.6:c.99+163->A chr15.hg19:g.81616185_81616185dupT 9 9 ref NA False 74 74 PASS 8 PASS ref->het 0 NA 248,253 35,35 52,49 1 1 P59094 True hg19 CCDS10318.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA STARD5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000303950.2 PASS NA None 335 NA True - T ENST00000302824.6 Unknown 0 __UNKNOWN__ __UNKNOWN__ 15 82422556 82422557 __UNKNOWN__ IGR DEL AT AT - rs2903621|rs71826728 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:82422556_82422557delAT NA RP11-597K23.2 (34508 upstream) : EFTUD1 (13 downstream) NA NA NA NA CTTGGAAAACATGTTCTCTAAC 0.317 NA NA NA 1119 0.223442 0.0197 0.2608 5008 , , NA 20424 0.1905 NA 0.3419 False NA ,,, NA NA NA 2504 0.3845 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 215 199.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.5 NA NA NA NA NA chr15.hg19:g.82422556_82422557delAT 0 5 ref NA False 72 72 PASS 1 PASS ref->het 0 NA 162,162 31,31 17,17 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 215 NA True AT CIB1 10519 __UNKNOWN__ __UNKNOWN__ 15 90774448 90774451 __UNKNOWN__ Intron DEL AGAG AGAG - rs199557034|rs71715019|rs201909717|rs34604050 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:90774448_90774451delAGAG ENST00000328649.6 - 5 508 NM_006384.3 NP_006375.2 Q99828 CIB1_HUMAN calcium and integrin binding 1 (calmyrin) NA NA NA angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to growth factor stimulus (GO:0071363)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to tumor necrosis factor (GO:0071356)|cytoplasmic microtubule organization (GO:0031122)|double-strand break repair (GO:0006302)|endomitotic cell cycle (GO:0007113)|extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|platelet formation (GO:0030220)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of male germ cell proliferation (GO:2000256)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell division (GO:0051302)|regulation of cell proliferation (GO:0042127)|response to ischemia (GO:0002931)|spermatid development (GO:0007286)|thrombopoietin-mediated signaling pathway (GO:0038163) cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|vesicle (GO:0031982) calcium ion binding (GO:0005509)|protein anchor (GO:0043495)|Ras GTPase binding (GO:0017016) lung(1)|prostate(1) 2 Melanoma(11;0.00551)|Lung NSC(78;0.0141)|all_lung(78;0.0303) BRCA - Breast invasive adenocarcinoma(143;0.00269)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217) ATCAAAGTCTAGAGAGCAGACACA 0.588 NA NA NA 2970 0.593051 0.4198 0.6138 5008 , , NA 19737 0.8016 NA 0.5169 False NA ,,, NA NA NA 2504 0.6759 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 703 676.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.47 U82226 CCDS10360.1, CCDS73781.1 15q25.3-q26 2013-01-10 ENSG00000185043 ENSG00000185043 10519 "EF-hand domain containing" 16920 protein-coding gene gene with protein product 602293 NA 9030514, 10826701 Standard NM_006384 NA Approved SIP2-28, CALMYRIN, CIB, KIP uc031qtq.1 Q99828 OTTHUMG00000149808 ENST00000328649.6:c.347-3CTCT>- chr15.hg19:g.90774448_90774451delAGAG 1 2 ref NA False 68 68 PASS 3 PASS ref->het 0 NA 572,577 71,72 66,62 1 1 B5BU40|H6WJF3|O00693|O00735|Q6IB49|Q96J54|Q99971 True hg19 CCDS10360.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CIB1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000313419.1 PASS NA None 703 NA True - AG ENST00000328649.6 SLCO3A1 28232 __UNKNOWN__ __UNKNOWN__ 15 92397615 92397616 __UNKNOWN__ Intron INS - - C rs56403444 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:92397615_92397616insC ENST00000424469.2 + 1 233 SLCO3A1_ENST00000318445.6_Intron NM_001145044.1 NP_001138516.1 Q9UIG8 SO3A1_HUMAN solute carrier organic anion transporter family, member 3A1 NA NA NA sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085) integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) transporter activity (GO:0005215) breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2) 25 Lung NSC(78;0.0158)|all_lung(78;0.0255) BRCA - Breast invasive adenocarcinoma(143;0.0841) Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563) ACTATTCCTCTCCCCCCATAAG 0.634 NA NA NA CCCCCC|CCCCCC|CCCCCCC|insertion 889 0.177516 0.3116 0.1988 5008 , , NA 12515 0.0079 NA 0.2485 False NA ,,, NA NA NA 2504 0.0828 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 161 149.35 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.71 AB031050 CCDS10371.1, CCDS45354.1 15q26 2013-05-22 2003-11-25 2003-11-26 ENSG00000176463 ENSG00000176463 28232 "Solute carriers" 10952 protein-coding gene gene with protein product 612435 "solute carrier family 21 (organic anion transporter), member 11" SLC21A11 NA Standard NM_013272 NM_001145044 NA Approved OATP-D, OATP3A1 uc002bqx.2 Q9UIG8 OTTHUMG00000149846 ENST00000424469.2:c.180+297->C chr15.hg19:g.92397621_92397621dupC 7 7 ref NA False 47 47 PASS 6 PASS ref->het 0 NA 133,135 15,15 13,13 1 1 A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2 True hg19 CCDS45354.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SLCO3A1-002 PUTATIVE basic|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000414816.1 PASS NA None 161 NA True + C ENST00000424469.2 IGF1R 3480 __UNKNOWN__ __UNKNOWN__ 15 99192259 99192260 __UNKNOWN__ 5'UTR INS - - AGG rs536189507|rs533518937|rs45619631|rs139163109 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:99192259_99192260insAGG ENST00000268035.6 + 0 60_61 NM_000875.3 NP_000866.1 P08069 IGF1R_HUMAN insulin-like growth factor 1 receptor NA NA NA axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165) caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235) ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713) NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1) 63 all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163) Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261) """Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)" CGAGCGGAGCCaggaggaggag 0.718 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 76 84.81 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0 M69229 CCDS10378.1, CCDS73785.1 15q26.3 2013-02-11 ENSG00000140443 ENSG00000140443 3480 "CD molecules", "Fibronectin type III domain containing" 5465 protein-coding gene gene with protein product 147370 NA 1316909 Standard NM_000875 XM_006720486 NA Approved JTK13, CD221, IGFIR, MGC18216, IGFR uc002bul.3 P08069 OTTHUMG00000149851 ENST00000268035.6:c.-551->AGG chr15.hg19:g.99192266_99192268dupAGG 7 2 ref NA False 90 89 PASS 6 PASS ref->het 0 NA 37,40 24,24 13,10 1 1 B1B5Y2|Q14CV2|Q9UCC0 True hg19 CCDS10378.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IGF1R-001 KNOWN NAGNAG_splice_site|basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000313537.2 PASS NA None 76 NA True + AGG ENST00000268035.6 LRRC28 123355 __UNKNOWN__ __UNKNOWN__ 15 99926683 99926687 __UNKNOWN__ 3'UTR DEL CTCCC CTCCC - rs67576387|rs77098534|rs544250980|rs3217510 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr15:99926683_99926687delCTCCC ENST00000301981.3 + 0 1720_1724 NM_144598.2 NP_653199.2 Q86X40 LRC28_HUMAN leucine rich repeat containing 28 NA NA NA endometrium(2)|large_intestine(3)|lung(6)|prostate(1) 12 Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00106) TTCCTCTCCTCTCCCCTCCCTTGCT 0.468 NA NA NA 2305 0.460264 0.5499 0.4899 5008 , , NA 20303 0.3958 NA 0.3807 False NA ,,, NA NA NA 2504 0.4663 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 235 223.04 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AK091588 CCDS10380.1, CCDS66873.1 15q26.3 2004-06-29 ENSG00000168904 ENSG00000168904 123355 28355 protein-coding gene gene with protein product NA NA 12975309 Standard NM_144598 XM_005254861 NA Approved MGC24976, FLJ34269, FLJ45242 uc002bva.1 Q86X40 OTTHUMG00000149854 ENST00000301981.3:c.*380CTCCC>- chr15.hg19:g.99926688_99926692delCTCCC 1 7 ref NA False 43 43 PASS 2 PASS ref->het 0 NA 184,184 25,25 25,25 1 1 A8KA22|Q6UY49|Q6ZSS6 True hg19 CCDS10380.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LRRC28-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000313546.1 PASS NA None 235 NA True + CTCCC ENST00000301981.3 TMEM8A 58986 __UNKNOWN__ __UNKNOWN__ 16 422544 422545 __UNKNOWN__ Intron INS - - G rs144177536|rs542545603 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:422544_422545insG ENST00000431232.2 - 12 2180 TMEM8A_ENST00000250930.3_Intron NM_021259.2 NP_067082.2 Q9HCN3 TMM8A_HUMAN transmembrane protein 8A NA NA NA cell adhesion (GO:0007155) extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765) central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1) 14 GAACGTGGCTAGAGCAAGGGGC 0.629 NA NA NA G|G|GG|insertion 205 0.0409345 0.0303 0.0576 5008 , , NA 18572 0.001 NA 0.0875 False NA ,,, NA NA NA 2504 0.0368 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 227 216.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AB045292 CCDS10407.1 16p13.3 2009-06-12 2009-06-12 2009-06-12 ENSG00000129925 ENSG00000129925 58986 17205 protein-coding gene gene with protein product NA "transmembrane protein 6", "transmembrane protein 8 (five membrane-spanning domains)" TMEM6, TMEM8 NA 11006113 Standard NM_021259 NM_021259 NA Approved M83 uc002cgu.4 Q9HCN3 OTTHUMG00000047996 ENST00000431232.2:c.2019+65->C chr16.hg19:g.422545_422545dupG 2 2 ref NA False 47 47 PASS 1 PASS ref->het 0 NA 170,173 41,41 16,15 1 1 D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9 True hg19 CCDS10407.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM8A-001 KNOWN basic|appris_candidate_longest|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000109257.2 PASS NA None 227 NA True - G ENST00000431232.2 WDR90 197335 __UNKNOWN__ __UNKNOWN__ 16 711546 711546 __UNKNOWN__ Intron DEL G G - rs113257271|rs11284424|rs397854898 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:711546delG ENST00000293879.4 + 30 3673 WDR90_ENST00000549091.1_Intron Q96KV7 WDR90_HUMAN WD repeat domain 90 NA NA NA endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2) 37 Hepatocellular(780;0.0218) CCTAGACCCCGGGGGGGGCTG 0.672 NA NA NA gGGGGGG|GGGGGGGG|GGGGGGG|insertion 3456 0.690096 0.8623 0.5937 5008 , , NA 15688 0.9841 NA 0.3698 False NA ,,, NA NA NA 2504 0.5521 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 235 245.78 NA NA 13 24 21 NA NA 16 NA NA NA 711546 1755 4058 5813 SO:0001627 intron_variant 0.18 AB067511 CCDS42092.1 16p13.3 2013-01-09 ENSG00000161996 ENSG00000161996 197335 "WD repeat domain containing" 26960 protein-coding gene gene with protein product NA "chromosome 16 open reading frame 17", "chromosome 16 open reading frame 15", "chromosome 16 open reading frame 16", "chromosome 16 open reading frame 19", "chromosome 16 open reading frame 18" C16orf17, C16orf15, C16orf16, C16orf19, C16orf18 NA 11572484, 11157797 Standard NM_145294 XM_005255160 NA Approved FLJ36483, KIAA1924 uc002cii.1 Q96KV7 OTTHUMG00000048040 ENST00000293879.4:c.3673+45G>- chr16.hg19:g.711546delG 7 8 ref NA False 72 72 PASS 8 PASS ref->het 0 NA 159,159 37,37 36,36 1 1 Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18 True hg19 CCDS42092.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA WDR90-002 NOVEL basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000404335.1 PASS NA None 235 NA True + G ENST00000293879.4 FBXL16 146330 __UNKNOWN__ __UNKNOWN__ 16 743980 743981 __UNKNOWN__ 3'UTR INS - - G rs3833954|rs113541943 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:743980_743981insG ENST00000397621.1 - 0 2065_2066 FBXL16_ENST00000562563.1_3'UTR|FBXL16_ENST00000324361.5_3'UTR NM_153350.3 NP_699181.2 Q8N461 FXL16_HUMAN F-box and leucine-rich repeat protein 16 NA NA NA endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1) 10 Hepatocellular(780;0.0218) GCTGTGGCTGTGGCGTGGCGGA 0.748 NA NA NA GG|GG|GGG|insertion 2810 0.561102 0.8064 0.4438 5008 , , NA 10164 0.7212 NA 0.2714 False NA ,,, NA NA NA 2504 0.4458 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 89 94.27 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.36 BC036680 CCDS10421.1 16p13.3 2011-06-09 2004-06-15 2004-06-16 ENSG00000127585 ENSG00000127585 146330 "F-boxes / Leucine-rich repeats" 14150 protein-coding gene gene with protein product 609082 "chromosome 16 open reading frame 22" C16orf22 NA 11157797 Standard NM_153350 NM_153350 NA Approved MGC33974, Fbl16 uc021taa.1 Q8N461 OTTHUMG00000090420 ENST00000397621.1:c.*295->C chr16.hg19:g.743982_743982dupG 3 3 ref NA False 35 35 PASS 2 PASS ref->het 0 NA 55,56 23,23 10,9 1 1 B3KR59|D3DU60|Q2MHR2|Q96S14|Q9UJI0 True hg19 CCDS10421.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FBXL16-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000206851.2 PASS NA None 89 NA True - G ENST00000397621.1 CLCN7 1186 __UNKNOWN__ __UNKNOWN__ 16 1495487 1495488 __UNKNOWN__ 3'UTR INS - - C rs397743593|rs146690487 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:1495487_1495488insC ENST00000382745.4 - 0 4167_4168 CLCN7_ENST00000448525.1_3'UTR|LA16c-390E6.5_ENST00000566287.1_RNA|CLCN7_ENST00000262318.8_3'UTR NM_001287.5 NP_001278.1 P51798 CLCN7_HUMAN chloride channel, voltage-sensitive 7 NA NA NA chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810) cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020) antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247) breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2) 24 Hepatocellular(780;0.0893) GCCGCACCCAGCCCCCCACGGA 0.708 NA NA NA CCCCcC|CCCCCC|CCCCCCC|insertion 508 0.101438 0.239 0.0908 5008 , , NA 9841 0.0109 NA 0.0517 False NA ,,, NA NA NA 2504 0.0675 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 184 188.75 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.34 Z67743 CCDS32361.1, CCDS45378.1 16p13 2012-09-26 2012-02-23 ENSG00000103249 ENSG00000103249 1186 "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ion channels / Chloride channels : Voltage-sensitive" 2025 protein-coding gene gene with protein product "protein phosphatase 1, regulatory subunit 63" 602727 "chloride channel 7" NA 8543009 Standard NM_001287 NM_001114331 NA Approved CLC-7, OPTA2, CLC7, ClC-7, PPP1R63 uc002clv.3 P51798 OTTHUMG00000044467 ENST00000382745.4:c.*1145->G chr16.hg19:g.1495493_1495493dupC 7 7 ref NA False 34 34 PASS 6 PASS ref->het 0 NA 131,135 28,29 23,18 1 1 A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5 True hg19 CCDS32361.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CLCN7-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000103598.2 PASS NA None 184 NA True - C ENST00000382745.4 TELO2 9894 __UNKNOWN__ __UNKNOWN__ 16 1549344 1549344 __UNKNOWN__ Intron DEL C C - rs397854665|rs11344586 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:1549344delC ENST00000262319.6 + 6 1212 NM_016111.3 NP_057195.2 Q9Y4R8 TELO2_HUMAN telomere maintenance 2 NA NA NA regulation of TOR signaling (GO:0032006) chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932) protein complex binding (GO:0032403) NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1) 19 Hepatocellular(780;0.219) GGTGAGGACGCCACGGAGGGT 0.592 NA NA NA CC|CC|C|deletion 1964 0.392173 0.4955 0.2709 5008 , , NA 15536 0.3363 NA 0.2594 False NA ,,, NA NA NA 2504 0.5327 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 238 219.46 NA 1878,2386 NA 392,1094,646 74 76 75 -4.7 0 16 dbSNP_130 105 2289,5963 NA 307,1675,2144 no intron TELO2 NM_016111.3 699,2769,2790 A1A1,A1R,RR NA 27.7387,44.0432,33.2934 1549344 4167,8349 2194 4295 6489 SO:0001627 intron_variant 0.02 AL080126 CCDS32363.1 16p13.3 2013-08-06 2013-08-06 ENSG00000100726 ENSG00000100726 9894 29099 protein-coding gene gene with protein product 611140 "TEL2, telomere maintenance 2, homolog (S. cerevisiae)" NA 9734811, 11230166, 12670948 Standard NM_016111 NM_016111 NA Approved KIAA0683, hCLK2, TEL2 uc002cly.3 Q9Y4R8 OTTHUMG00000044471 ENST00000262319.6:c.933+10C>- chr16.hg19:g.1549344delC 1 3 ref NA False 56 56 PASS 2 PASS ref->het 0 NA 171,172 43,43 21,20 1 1 D3DU73|O75168|Q7LDV4|Q9BR21 True hg19 CCDS32363.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TELO2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000103602.2 PASS NA None 238 NA True + C ENST00000262319.6 HAGH 3029 __UNKNOWN__ __UNKNOWN__ 16 1876992 1876993 __UNKNOWN__ 5'UTR INS - - GCG rs375347528|rs560980687|rs28364708|rs76260324 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:1876992_1876993insGCG ENST00000566709.1 - 0 165_166 FAHD1_ENST00000382666.4_5'UTR|HAGH_ENST00000397356.3_5'UTR|FAHD1_ENST00000382668.4_5'UTR Q16775 GLO2_HUMAN hydroxyacylglutathione hydrolase NA NA NA glutathione biosynthetic process (GO:0006750) cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739) hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270) kidney(2)|lung(1)|ovary(1)|skin(1) 5 Hepatocellular(780;0.00335) Glutathione(DB00143) CGGGCCTGGGAGCGGCGGCGGC 0.713 NA NA NA 998 0.199281 0.1831 0.2262 5008 , , NA 10611 0.1706 NA 0.1779 False NA ,,, NA NA NA 2504 0.2536 NA NA NA Pancreas(55;1048 1176 25227 40124 41333) PASS NA NA NA 0 NA NA NA NA NA 70 72.83 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 2.34 X90999 CCDS32366.1, CCDS10447.2, CCDS66900.1 16p13.3 2012-10-02 2003-11-04 ENSG00000063854 ENSG00000063854 3029 3.1.2.6 4805 protein-coding gene gene with protein product 138760 "hydroxyacyl glutathione hydrolase" NA 3025077, 7327557 Standard NM_005326 NM_001286249 NA Approved GLO2, GLXII, HAGH1 uc002cna.3 Q16775 OTTHUMG00000128662 ENST00000566709.1:c.-120->CGC chr16.hg19:g.1876999_1877001dupGCG 5 4 ref NA False 55 55 PASS 4 PASS ref->het 0 NA 31,36 11,12 27,21 1 1 A8K290|B4DP33|B4DRA7|E7EN93 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HAGH-003 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000433838.1 PASS NA None 70 NA True - GCG ENST00000566709.1 RP11-473M20.9 0 __UNKNOWN__ __UNKNOWN__ 16 3131940 3131941 __UNKNOWN__ lincRNA INS - - GG rs376824299|rs58826170|rs397977237 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:3131940_3131941insGG ENST00000571404.1 - 0 210 NA NA NA NA CGGAGCCACACGGGGGGCAAGG 0.564 NA NA NA 1246 0.248802 0.0598 0.2277 5008 , , NA 11829 0.2976 NA 0.3509 False NA ,,, NA NA NA 2504 0.364 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 38 56.28 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 NA NA NA NA NA ENST00000571404.1: chr16.hg19:g.3131945_3131946dupGG 8 6 ref NA False 33 33 PASS 6 PASS ref->het 0 NA 14,14 17,39 7,7 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-473M20.9-002 KNOWN basic lincRNA NA lincRNA OTTHUMT00000437122.1 PASS NA None 38 NA True - G ENST00000571404.1 RBFOX1 54715 __UNKNOWN__ __UNKNOWN__ 16 7703785 7703786 __UNKNOWN__ Intron INS - - CT rs397938774|rs3217052|rs34884713 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:7703785_7703786insCT ENST00000552089.1 + 10 922 RBFOX1_ENST00000422070.4_Intron|RBFOX1_ENST00000436368.2_Intron|RBFOX1_ENST00000311745.5_Intron|RBFOX1_ENST00000355637.4_Intron|RBFOX1_ENST00000547338.1_Intron|RBFOX1_ENST00000547372.1_Intron|RBFOX1_ENST00000340209.4_Intron|RBFOX1_ENST00000550418.1_Intron|RBFOX1_ENST00000535565.2_Intron|RBFOX1_ENST00000553186.1_Intron Q9NWB1 RFOX1_HUMAN RNA binding protein, fox-1 homolog (C. elegans) 1 NA NA NA mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658) cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802) nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723) breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2) 55 GACAGCCTGTGCTCTCTCTCTC 0.698 NA NA NA 1950 0.389377 0.2935 0.4006 5008 , , NA 14927 0.373 NA 0.505 False NA ,,, NA NA NA 2504 0.409 NA NA NA Ovarian(157;934 2567 15163 39509) PASS NA NA NA 0 NA NA NA NA NA 79 82.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF107203 CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1 16p13.3 2013-02-12 ENSG00000078328 ENSG00000078328 54715 "RNA binding motif (RRM) containing" 18222 protein-coding gene gene with protein product "ataxin 2-binding protein 1", "hexaribonucleotide binding protein 1" 605104 NA 10814712, 16260614 Standard NM_145891 NM_018723 NA Approved A2BP1, FOX-1, HRNBP1 uc002cyy.2 Q9NWB1 OTTHUMG00000129551 ENST00000552089.1:c.809-31->CT chr16.hg19:g.7703794_7703795dupCT 9 2 ref NA False 43 43 PASS 8 PASS ref->het 0 NA 41,42 24,24 13,12 1 1 Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RBFOX1-006 PUTATIVE not_organism_supported|basic|exp_conf protein_coding NA protein_coding OTTHUMT00000409496.1 PASS NA None 79 NA True + CT ENST00000552089.1 PARN 5073 __UNKNOWN__ __UNKNOWN__ 16 14678349 14678350 __UNKNOWN__ Intron INS - - C rs71373034|rs386384326|rs374880534 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:14678349_14678350insC ENST00000437198.2 - 16 1147 PARN_ENST00000341484.7_Intron|PARN_ENST00000539279.1_Intron|PARN_ENST00000420015.2_Intron NM_001134477.2|NM_002582.3 NP_001127949.1|NP_002573.1 O95453 PARN_HUMAN poly(A)-specific ribonuclease NA NA NA female gamete generation (GO:0007292)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA metabolic process (GO:0016070)|RNA modification (GO:0009451)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503) cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634) metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|nuclease activity (GO:0004518)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(A)-specific ribonuclease activity (GO:0004535)|protein kinase binding (GO:0019901) cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1) 21 AGATTCACTGACCCCCCCAAAA 0.366 NA NA NA ccccCCC|CCCCCCC|CCCCCCCC|insertion 1467 0.292931 0.0885 0.4841 5008 , , NA 17325 0.2024 NA 0.3887 False NA ,,, NA NA NA 2504 0.4284 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 189 188.07 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.41 AJ005698 CCDS45419.1, CCDS45420.1, CCDS58425.1 16p13 2014-08-08 2011-07-07 ENSG00000140694 ENSG00000140694 5073 3.1.13.4 8609 protein-coding gene gene with protein product "deadenylation nuclease" 604212 "poly(A)-specific ribonuclease (deadenylation nuclease)" NA 10640832 Standard NM_002582 NM_002582 NA Approved DAN uc010uzd.2 O95453 OTTHUMG00000173199 ENST00000437198.2:c.1006-70->G chr16.hg19:g.14678356_14678356dupC 8 7 ref NA False 117 100 PASS 7 PASS ref->het 0 NA 98,98 64,64 27,28 1 1 B2RCB3|B4DDG8|B4DWR4|B4E1H6 True hg19 CCDS45419.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PARN-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000422383.1 PASS NA None 189 NA True - C ENST00000437198.2 FOPNL 123811 __UNKNOWN__ __UNKNOWN__ 16 15967361 15967362 __UNKNOWN__ In_Frame_Ins INS - - CTA rs80120167|rs10656021|rs376120465 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:15967361_15967362insCTA ENST00000255759.6 - 4 463_464 c.434_435insTAG c.(433-435)aga>agTAGa p.144_145insS FOPNL_ENST00000575073.1_Intron|FOPNL_ENST00000575744.1_In_Frame_Ins_p.78_79insS|FOPNL_ENST00000573429.1_In_Frame_Ins_p.168_169insS|FOPNL_ENST00000573968.1_Intron|FOPNL_ENST00000573396.1_Intron NM_144600.2 NP_653201.1 Q96NB1 FOPNL_HUMAN FGFR1OP N-terminal like 144 NA NA cilium assembly (GO:0042384)|microtubule anchoring (GO:0034453) centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|motile cilium (GO:0031514)|nucleus (GO:0005634) breast(1)|large_intestine(1)|lung(5)|stomach(4) 11 TTGGCTTTCTTCTACTAGGTTG 0.411 NA NA NA 437 0.0872604 0.0779 0.0879 5008 , , NA 16729 0.2024 NA 0.0457 False NA ,,, NA NA NA 2504 0.0235 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 227 207.33 NA 358,3906 NA 14,330,1788 NA NA NA 5.6 0.2 NA dbSNP_119 74 441,7813 NA 9,423,3695 no coding FOPNL NM_144600.2 23,753,5483 A1A1,A1R,RR NA 5.3429,8.3959,6.3828 NA 799,11719 NA NA NA SO:0001652 inframe_insertion 0 AL832498 CCDS10567.1 16p13.11 2011-03-18 2011-03-18 2011-03-18 ENSG00000133393 ENSG00000133393 123811 26435 protein-coding gene gene with protein product "pluripotent embryonic stem cell-related protein", "FOP-related protein of 20 kDa" NA "chromosome 16 open reading frame 63" C16orf63 NA 12477932 Standard NM_144600 NM_144600 NA Approved DKFZp686N1651, FLJ31153, PHSECRG2, FOR20 uc002dec.1 Q96NB1 OTTHUMG00000129923 ENST00000255759.6:c.432_434dupTAG chr16.hg19:g.15967365_15967367dupCTA ENSP00000255759:p.Ser144_Ser144dup 3 5 ref NA False 83 83 PASS 2 PASS ref->het 0 NA 173,173 39,40 16,16 1 1 B3KPU9 True hg19 CCDS10567.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FOPNL-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000252177.2 PASS NA None 227 NA True - CTA ENST00000255759.6 USP31 57478 __UNKNOWN__ __UNKNOWN__ 16 23076158 23076158 __UNKNOWN__ 3'UTR DEL A A - rs397855750|rs3841243 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:23076158delA ENST00000219689.7 - 0 7267 NM_020718.3 NP_065769.3 Q86UV5 UBP48_HUMAN ubiquitin specific peptidase 31 NA NA NA ubiquitin-dependent protein catabolic process (GO:0006511) cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634) ubiquitin-specific protease activity (GO:0004843) breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2) 57 GBM - Glioblastoma multiforme(48;0.0187) ATGAATGATGAAAACAAGATT 0.463 NA NA NA AAAA|AAAA|AAA|deletion 1213 0.242212 0.1543 0.3876 5008 , , NA 21919 0.1577 NA 0.335 False NA ,,, NA NA NA 2504 0.2495 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 116 109.53 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AB033029 CCDS10607.1 16p12.3 2008-02-05 2005-08-08 ENSG00000103404 ENSG00000103404 57478 "Ubiquitin-specific peptidases" 20060 protein-coding gene gene with protein product NA "ubiquitin specific protease 31" NA 12838346 Standard NM_020718 NM_020718 NA Approved KIAA1203 uc002dll.3 Q70CQ4 OTTHUMG00000094793 ENST00000219689.7:c.*3209T>- chr16.hg19:g.23076158delA 3 6 ref NA False 39 39 PASS 4 PASS ref->het 0 NA 85,86 16,16 14,14 1 1 B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0 True hg19 CCDS10607.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA USP31-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000211607.1 PASS NA None 116 NA True - A ENST00000219689.7 PALB2 79728 __UNKNOWN__ __UNKNOWN__ 16 23649801 23649802 __UNKNOWN__ Intron DEL TC TC - rs201458864 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:23649801_23649802delTC ENST00000261584.4 - 2 201 NM_024675.3 NP_078951.2 Q86YC2 PALB2_HUMAN partner and localizer of BRCA2 NA NA NA DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756) nucleoplasm (GO:0005654)|nucleus (GO:0005634) DNA binding (GO:0003677) breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3) 55 GBM - Glioblastoma multiforme(48;0.0167) CACACTATGTTCTCTGTTTCTC 0.431 NA NA "F, N, Mis" "Wilms tumor, medulloblastoma, AML ,breast" NA Involved in tolerance or repair of DNA crosslinks 36 0.0071885 0.0015 0.0086 5008 , , NA 21513 0 NA 0.0219 False NA ,,, NA NA NA 2504 0.0061 NA NA NA PASS yes Rec "Fanconi anaemia N, breast cancer susceptibility " 16 16p12.1 79728 partner and localizer of BRCA2 NA "L, O, E" 0 NA NA NA NA NA 189 173.97 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS32406.1 16p12.1 2014-09-17 ENSG00000083093 79728 "Fanconi anemia, complementation groups" 26144 protein-coding gene gene with protein product "Fanconi anemia, complementation group N" 610355 NA 16793542, 17200672 Standard NM_024675 NM_024675 NA Approved FLJ21816, FANCN uc002dlx.1 Q86YC2 ENST00000261584.4:c.49-351GA>- chr16.hg19:g.23649803_23649804delTC 1 3 ref NA False 35 35 PASS 2 PASS ref->het 0 NA 152,153 28,28 13,13 1 1 A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1 True hg19 CCDS32406.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PALB2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000435287.2 PASS NA None 189 NA True - TC ENST00000261584.4 GPT2 84706 __UNKNOWN__ __UNKNOWN__ 16 46964358 46964358 __UNKNOWN__ 3'UTR DEL G G - rs201130921|rs3217619 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:46964358delG ENST00000340124.4 + 0 3133 GPT2_ENST00000440783.2_3'UTR NM_133443.2 NP_597700.1 Q8TD30 ALAT2_HUMAN glutamic pyruvate transaminase (alanine aminotransferase) 2 NA NA NA 2-oxoglutarate metabolic process (GO:0006103)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|L-alanine metabolic process (GO:0042851)|small molecule metabolic process (GO:0044281) mitochondrial matrix (GO:0005759) L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170) NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2) 23 all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522) L-Alanine(DB00160)|Phenelzine(DB00780) CCTCTATGCTGTGATTTCCAC 0.542 NA NA NA OREG0023767 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) G|G|-|deletion 2163 0.431909 0.0968 0.5043 5008 , , NA 17684 0.7937 NA 0.325 False NA ,,, NA NA NA 2504 0.5706 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 172 171.72 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.4 CCDS10725.1, CCDS45478.1 16q12.1 2008-02-05 ENSG00000166123 ENSG00000166123 84706 2.6.1.2 18062 protein-coding gene gene with protein product 138210 NA Standard NM_133443 NA Approved ALT2 uc002eel.3 Q8TD30 OTTHUMG00000132541 ENST00000340124.4:c.*1449G>- chr16.hg19:g.46964358delG 0 2 ref 943 False 83 82 PASS 1 PASS ref->het 0 NA 92,93 61,62 20,20 1 1 Q8N9E2 True hg19 CCDS10725.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GPT2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000255741.2 PASS NA None 172 NA True + G ENST00000340124.4 LONP2 83752 __UNKNOWN__ __UNKNOWN__ 16 48388788 48388789 __UNKNOWN__ 3'UTR INS - - AGTT rs34908555|rs5816591|rs3083559 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:48388788_48388789insAGTT ENST00000285737.4 + 0 5727_5728 LONP2_ENST00000564259.1_Intron NM_031490.2 NP_113678.2 lon peptidase 2, peroxisomal NA NA NA breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 31 TTATTTGCAACAGTTAGCTTTC 0.396 NA NA NA 601 0.120008 0.205 0.1311 5008 , , NA 20149 0.0198 NA 0.162 False NA ,,, NA NA NA 2504 0.0573 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 89 83.11 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AJ548761 CCDS10734.1, CCDS73880.1 16q12.1 2010-04-21 ENSG00000102910 ENSG00000102910 83752 "ATPases / AAA-type" 20598 protein-coding gene gene with protein product NA NA 14561759 Standard NM_031490 XM_005256191 NA Approved MGC4840, LONP, LONPL uc002efi.1 Q86WA8 OTTHUMG00000133144 ENST00000285737.4:c.*3076->AGTT chr16.hg19:g.48388789_48388792dupAGTT 2 3 ref NA False 40 40 PASS 1 PASS ref->het 0 NA 62,62 14,14 12,12 1 1 True hg19 CCDS10734.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LONP2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256839.2 PASS NA None 89 NA True + AGTT ENST00000285737.4 Unknown 0 __UNKNOWN__ __UNKNOWN__ 16 48533041 48533042 __UNKNOWN__ IGR INS - - T rs201770479|rs34571725|rs148074609 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:48533041_48533042insT NA snoU13 (6629 upstream) : N4BP1 (39594 downstream) NA NA NA NA GACTTTATCTCCCTTCTGCCCA 0.55 NA NA NA T|-|T|deletion 3087 0.616414 0.587 0.6023 5008 , , NA 18576 0.8423 NA 0.4583 False NA ,,, NA NA NA 2504 0.5961 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 91 86.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0 NA NA NA NA NA chr16.hg19:g.48533041_48533042insT 1 4 ref NA False 45 45 PASS 0 PASS ref->het 0 NA 59,59 19,20 14,14 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 91 NA True T PAPD5 64282 __UNKNOWN__ __UNKNOWN__ 16 50187198 50187200 __UNKNOWN__ Intron DEL GCC GCC - rs534559724 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:50187198_50187200delGCC ENST00000436909.3 + 1 115 NM_001040284.2|NM_001040285.2 NP_001035374.2|NP_001035375.2 Q8NDF8 PAPD5_HUMAN PAP associated domain containing 5 NA NA NA histone mRNA catabolic process (GO:0071044)|mitotic nuclear division (GO:0007067)|mRNA processing (GO:0006397)|rRNA processing (GO:0006364) cytoplasm (GO:0005737)|nucleus (GO:0005634) DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|polynucleotide adenylyltransferase activity (GO:0004652) endometrium(1)|kidney(1)|lung(2) 4 all_cancers(37;0.0452) BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231) tgccgccgctgccgccgccgccg 0.808 NA NA NA 1072 0.214058 0.2345 0.2406 5008 , , NA 1607 0.255 NA 0.1571 False NA ,,, NA NA NA 2504 0.184 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 5 4.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.23 AF089897 CCDS54006.1 16q12.1 2010-11-18 ENSG00000121274 64282 30758 protein-coding gene gene with protein product "TUTase3" 605540 NA 10066793 Standard NM_022447 NM_001040284 NA Approved TRF4-2 uc010vgo.2 Q8NDF8 ENST00000436909.3:c.80+255GCC>- chr16.hg19:g.50187207_50187209delGCC 3 4 ref NA False 41 41 PASS 4 PASS ref->het 0 NA 2,2 3,3 0,0 1 1 B4DV38|Q9NW67|Q9Y6C0 True hg19 CCDS54006.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PAPD5-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000423149.2 PASS NA None 5 NA True + GCC ENST00000436909.3 NUDT21 11051 __UNKNOWN__ __UNKNOWN__ 16 56465661 56465662 __UNKNOWN__ 3'UTR INS - - TA rs74311713|rs368457421 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:56465661_56465662insTA ENST00000300291.5 - 0 1818_1819 NM_007006.2 NP_008937.1 O43809 CPSF5_HUMAN nudix (nucleoside diphosphate linked moiety X)-type motif 21 NA NA NA gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366) centrosome (GO:0005813)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382) AU-rich element binding (GO:0017091)|histone deacetylase binding (GO:0042826)|hydrolase activity (GO:0016787)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803) breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4) 7 TTAAAATTTCGTTTTTCTCTTA 0.327 NA NA NA 461 0.0920527 0.0681 0.0461 5008 , , NA 16276 0.1637 NA 0.0288 False NA ,,, NA NA NA 2504 0.1483 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 140 142.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AJ001810 CCDS10760.1 16q12.2 2013-06-18 2005-07-11 2005-07-11 ENSG00000167005 ENSG00000167005 11051 "Nudix motif containing" 13870 protein-coding gene gene with protein product "cleavage factor Im complex 25 kDa subunit" 604978 "cleavage and polyadenylation specific factor 5, 25 kDa", "cleavage and polyadenylation specific factor 5, 25 kD subunit" CPSF5 NA 9659921 Standard NM_007006 NM_007006 NA Approved CFIM25 uc002eja.3 O43809 OTTHUMG00000133240 ENST00000300291.5:c.*963->TA chr16.hg19:g.56465661_56465662insTA 1 6 ref NA False 74 74 PASS 0 PASS ref->het 0 NA 95,95 31,31 15,15 1 1 Q6IB85|Q6NE84 True hg19 CCDS10760.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NUDT21-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256980.3 PASS NA None 140 NA True - TA ENST00000300291.5 NFAT5 10725 __UNKNOWN__ __UNKNOWN__ 16 69599949 69599950 __UNKNOWN__ 5'UTR INS - - C rs552981185|rs149738655 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:69599949_69599950insC ENST00000354436.2 + 0 63_64 NFAT5_ENST00000349945.1_5'UTR|NFAT5_ENST00000432919.1_5'UTR NM_006599.3 NP_006590.1 O94916 NFAT5_HUMAN nuclear factor of activated T-cells 5, tonicity-responsive NA NA NA cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366) cytoplasm (GO:0005737)|nucleus (GO:0005634) DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700) NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1) 37 CCTTTGGCTCTCCCCCTTCCCC 0.668 NA NA NA ccccc|CCCCC|CCCCCC|insertion 1570 0.313498 0.2595 0.3415 5008 , , NA 8144 0.4187 NA 0.2157 False NA ,,, NA NA NA 2504 0.3589 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 573 558.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 1.23 AF134870 CCDS10881.1, CCDS10882.1, CCDS45519.1 16q22.1 2009-11-24 ENSG00000102908 ENSG00000102908 10725 "Nuclear factor of activated T-cells" 7774 protein-coding gene gene with protein product 604708 NA 10377394 Standard NM_138714 NM_173214 NA Approved TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5 uc002exl.2 O94916 OTTHUMG00000137572 ENST00000354436.2:c.-255->C chr16.hg19:g.69599954_69599954dupC 6 6 ref NA False 389 312 PASS 5 PASS ref->het 0 NA 403,411 118,119 55,50 1 1 A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18 True hg19 CCDS10881.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NFAT5-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000268952.2 PASS NA None 573 NA True + C ENST00000354436.2 PIEZO1 9780 __UNKNOWN__ __UNKNOWN__ 16 88782320 88782320 __UNKNOWN__ Intron DEL C C - rs3214887|rs397756043 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:88782320delC ENST00000301015.9 - 50 7563 PIEZO1_ENST00000327397.7_Intron NM_001142864.2 NP_001136336.2 Q92508 PIEZ1_HUMAN piezo-type mechanosensitive ion channel component 1 NA NA NA cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381) NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1) 10 CTGCGGGGTGCCCCCCCAGCC 0.667 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 296 330.24 NA 361,1603 NA 73,215,694 9 11 11 -2.8 0 16 dbSNP_106 13 1218,2712 NA 266,686,1013 no intron PIEZO1 NM_001142864.2 339,901,1707 A1A1,A1R,RR NA 30.9924,18.3809,26.79 88782320 1579,4315 687 1564 2251 SO:0001627 intron_variant 7.75 D87071 CCDS54058.1 16q24.3 2011-08-31 2011-08-31 2011-08-31 ENSG00000103335 ENSG00000103335 9780 28993 protein-coding gene gene with protein product 611184 "family with sequence similarity 38, member A" FAM38A NA 20813920, 21056836, 21299953, 21696149 Standard NM_014745 NM_001142864 NA Approved KIAA0233 uc010vpb.2 Q92508 OTTHUMG00000156776 ENST00000301015.9:c.7316+20G>- chr16.hg19:g.88782320delC 6 7 ref NA False 48 48 PASS 7 PASS ref->het 0 NA 202,214 43,53 74,56 1 1 A6NHT9|A7E2B7|Q0KKZ9 True hg19 CCDS54058.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PIEZO1-001 NOVEL not_organism_supported|basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000345699.4 PASS NA None 296 NA True - C ENST00000301015.9 PIEZO1 9780 __UNKNOWN__ __UNKNOWN__ 16 88787608 88787610 __UNKNOWN__ In_Frame_Del DEL CTT CTT - rs3217718|rs150376294|rs113773794 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr16:88787608_88787610delCTT ENST00000301015.9 - 39 5878_5880 c.5632_5634delAAG c.(5632-5634)aagdel p.K1878del NM_001142864.2 NP_001136336.2 Q92508 PIEZ1_HUMAN piezo-type mechanosensitive ion channel component 1 1878 NA NA cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391) endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381) p.K1878delK(1) NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1) 10 CTGGGCCCTCCTTCTTCCTTCTT 0.616 NA NA NA 1081 0.215855 0.1452 0.2003 5008 , , NA 19820 0.0774 NA 0.334 False NA ,,, NA NA NA 2504 0.3436 NA NA NA PASS NA NA NA 1 Deletion - In frame(1) breast(1) NA NA NA NA NA 298 275.23 NA 433,2117 NA 88,257,930 NA NA NA 3.8 0.1 NA dbSNP_131 32 1667,3279 NA 392,883,1198 no coding PIEZO1 NM_001142864.2 480,1140,2128 A1A1,A1R,RR NA 33.704,16.9804,28.0149 NA 2100,5396 NA NA NA SO:0001651 inframe_deletion 0.75 D87071 CCDS54058.1 16q24.3 2011-08-31 2011-08-31 2011-08-31 ENSG00000103335 ENSG00000103335 9780 28993 protein-coding gene gene with protein product 611184 "family with sequence similarity 38, member A" FAM38A NA 20813920, 21056836, 21299953, 21696149 Standard NM_014745 NM_001142864 NA Approved KIAA0233 uc010vpb.2 Q92508 OTTHUMG00000156776 ENST00000301015.9:c.5632_5634delAAG chr16.hg19:g.88787611_88787613delCTT ENSP00000301015:p.Lys1878del 1 5 ref NA False 34 34 PASS 2 PASS ref->het 0 NA 222,227 56,57 22,17 1 1 A6NHT9|A7E2B7|Q0KKZ9 True hg19 CCDS54058.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PIEZO1-001 NOVEL not_organism_supported|basic|appris_principal|exp_conf|CCDS protein_coding NA protein_coding OTTHUMT00000345699.4 PASS NA None 298 NA True - CTT ENST00000301015.9 TM4SF5 9032 __UNKNOWN__ __UNKNOWN__ 17 4686463 4686464 __UNKNOWN__ 3'UTR INS - - CGCCTACCTGGCT rs3217068|rs11268672 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:4686463_4686464insCGCCTACCTGGCT ENST00000270560.3 + 0 665_666 NM_003963.2 NP_003954.2 O14894 T4S5_HUMAN transmembrane 4 L six family member 5 NA NA NA integral component of plasma membrane (GO:0005887) large_intestine(2)|lung(3)|ovary(1) 6 TCCTTCCTGGACGCTCACTCCC 0.559 NA NA NA 2044 0.408147 0.2693 0.2882 5008 , , NA 17357 0.4504 NA 0.3936 False NA ,,, NA NA NA 2504 0.6524 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 337 330.31 NA 1309,2955 NA 177,955,1000 NA NA NA 5 1 NA dbSNP_106 94 3196,5058 NA 624,1948,1555 no utr-3 TM4SF5 NM_003963.2 801,2903,2555 A1A1,A1R,RR NA 38.7206,30.6989,35.9882 NA 4505,8013 NA NA NA SO:0001624 3_prime_UTR_variant 0.32 AF027204 CCDS11054.1 17p13.3 2007-01-06 2005-03-21 ENSG00000142484 ENSG00000142484 9032 11857 protein-coding gene gene with protein product 604657 "transmembrane 4 superfamily member 5" NA 9479038 Standard NM_003963 NA Approved uc002fyw.1 O14894 OTTHUMG00000090776 ENST00000270560.3:c.*41->CGCCTACCTGGCT chr17.hg19:g.4686463_4686464insCGCCTACCTGGCT 1 2 ref NA False 30 30 PASS 0 PASS ref->het 0 NA 268,270 29,29 38,36 1 1 Q17RW9|Q6IB79 True hg19 CCDS11054.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TM4SF5-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000207558.2 PASS NA None 337 NA True + CGCCTACCTGGCT ENST00000270560.3 C17orf100 388327 __UNKNOWN__ __UNKNOWN__ 17 6556194 6556195 __UNKNOWN__ 3'UTR INS - - AGAAG rs150414123|rs59663818|rs144808411 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:6556194_6556195insAGAAG ENST00000391428.2 + 0 1224_1225 NM_001105520.1 NP_001098990.1 A8MU93 CQ100_HUMAN chromosome 17 open reading frame 100 NA NA NA NA AAAATAATCTTAGAAAGTGAGA 0.421 NA NA NA 1745 0.348442 0.5492 0.2435 5008 , , NA 18807 0.4256 NA 0.169 False NA ,,, NA NA NA 2504 0.2566 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 145 142.47 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 BC028174, BC038956, BC052606 CCDS73952.1 17p13.2 2014-04-10 ENSG00000212734 ENSG00000256806 388327 34494 protein-coding gene gene with protein product NA NA Standard NM_001105520 NM_001105520 NA Approved LOC388327 uc010clp.1 A8MU93 OTTHUMG00000188340 ENST00000391428.2:c.*467->AGAAG chr17.hg19:g.6556194_6556195insAGAAG 1 4 ref NA False 35 35 PASS 0 PASS ref->het 0 NA 119,122 15,15 12,11 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C17orf100-001 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000255575.2 PASS NA None 145 NA True + AGAAG ENST00000391428.2 GPS2 2874 __UNKNOWN__ __UNKNOWN__ 17 7217498 7217498 __UNKNOWN__ Intron DEL G G - rs3215130 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:7217498delG ENST00000380728.2 - 5 618 RP11-542C16.2_ENST00000575474.1_Intron|GPS2_ENST00000389167.5_Intron|GPS2_ENST00000391950.3_Intron Q13227 GPS2_HUMAN G protein pathway suppressor 2 NA NA NA cell cycle (GO:0007049)|inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122) nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053) GTPase inhibitor activity (GO:0005095)|transcription corepressor activity (GO:0003714) breast(1)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(4) 24 Prostate(122;0.157) AAGGAAGACAGGTCAAAGTCA 0.488 NA NA NA GG|GG|G|deletion 594 0.11861 0.1641 0.1326 5008 , , NA 23568 0.1815 NA 0.0577 False NA ,,, NA NA NA 2504 0.045 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 236 235.04 NA 531,3733 NA 44,443,1645 173 169 171 2.8 0 17 dbSNP_106 181 382,7872 NA 12,358,3757 no intron GPS2 NM_004489.4 56,801,5402 A1A1,A1R,RR NA 4.6281,12.4531,7.2935 7217498 913,11605 2202 4300 6502 SO:0001627 intron_variant 0.73 U28963 CCDS11100.1 17p13.1 2006-04-29 ENSG00000132522 ENSG00000132522 2874 4550 protein-coding gene gene with protein product 601935 NA 8943324 Standard NM_004489 NM_004489 NA Approved uc002gfx.1 Q13227 OTTHUMG00000102198 ENST00000380728.2:c.318-20C>- chr17.hg19:g.7217498delG 1 2 ref NA False 47 47 PASS 2 PASS ref->het 0 NA 187,187 23,24 25,25 1 1 B4DXA1|Q6FHM8 True hg19 CCDS11100.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GPS2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000220048.4 PASS NA None 236 NA True - G ENST00000380728.2 TP53 7157 __UNKNOWN__ __UNKNOWN__ 17 7577599 7577600 __UNKNOWN__ Frame_Shift_Ins INS - - A LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:7577599_7577600insA ENST00000269305.4 - 7 870_871 c.681_682insT c.(679-684)tctgacfs p.D228fs TP53_ENST00000574684.1_5'UTR|TP53_ENST00000359597.4_Frame_Shift_Ins_p.D228fs|TP53_ENST00000455263.2_Frame_Shift_Ins_p.D228fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.D228fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.D228fs|TP53_ENST00000445888.2_Frame_Shift_Ins_p.D228fs NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 228 Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A. NA D -> A (in sporadic cancers; somatic mutation).|D -> E (in sporadic cancers; somatic mutation).|D -> G (in sporadic cancers; somatic mutation).|D -> H (in sporadic cancers; somatic mutation).|D -> N (in sporadic cancers; somatic mutation).|D -> P (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|D -> V (in sporadic cancers; somatic mutation).|D -> Y (in sporadic cancers; somatic mutation). NA apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032) chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657) ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270) p.0?(8)|p.D228N(6)|p.?(5)|p.S227S(3)|p.D228Y(2)|p.?fs(2)|p.V225_S227delVGS(2)|p.S227fs*1(1)|p.G226_D228delGSD(1)|p.D228fs*1(1)|p.V225fs*23(1)|p.D228fs*12(1)|p.D228fs*11(1)|p.S227_I232delSDCTTI(1)|p.D228H(1)|p.D228fs*19(1) NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) Acetylsalicylic acid(DB00945) GTGGTACAGTCAGAGCCAACCT 0.525 NA 111 "Mis, N, F" "breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types" "breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types" NA Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Pancreas(47;798 1329 9957 10801) PASS yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 NA "L, E, M, O" 37 Substitution - Missense(9)|Whole gene deletion(8)|Deletion - Frameshift(5)|Unknown(5)|Deletion - In frame(4)|Insertion - Frameshift(3)|Substitution - coding silent(3) biliary_tract(5)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(4)|breast(4)|bone(4)|oesophagus(2)|lung(2)|ovary(2)|liver(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|pancreas(1) NA NA NA NA NA 128 120.98 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.99 Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; AF307851 CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1 17p13.1 2014-09-17 2008-01-16 ENSG00000141510 ENSG00000141510 7157 11998 protein-coding gene gene with protein product "Li-Fraumeni syndrome" 191170 NA 6396087, 3456488, 2047879 Standard NM_000546 NM_001126115 NA Approved p53, LFS1 uc002gij.3 P04637 OTTHUMG00000162125 ENST00000269305.4:c.682dupT chr17.hg19:g.7577600_7577600dupA ENSP00000269305:p.Asp228fs 2 2 ref NA False 101 83 PASS 1 PASS ref->het 0 NA 35,36 77,78 14,14 1 1 Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61 True hg19 CCDS11118.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TP53-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000367397.1 PASS NA None 128 NA True - A ENST00000269305.4 PER1 5187 __UNKNOWN__ __UNKNOWN__ 17 8045061 8045061 __UNKNOWN__ Intron DEL T T - rs71159549|rs55822222 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:8045061delT ENST00000317276.4 - 22 3838 PER1_ENST00000581082.1_Intron NM_002616.2 NP_002607.2 O15534 PER1_HUMAN period circadian clock 1 NA NA NA circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleus (GO:0005634) chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625) breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 47 AGCTCAATTCTTTTTTCTCCC 0.478 NA NA T ETV6 "AML, CMML" NA Other conserved DNA damage response genes tttttt|TTTTTT|TTTTT|deletion 1136 0.226837 0.2753 0.2219 5008 , , NA 17698 0.1131 NA 0.328 False NA ,,, NA NA NA 2504 0.1779 NA NA NA PASS Dom yes 17 17p13.1-17p12 5187 period homolog 1 (Drosophila) NA L 0 NA NA NA NA NA 198 194.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AB002107 CCDS11131.1 17p13.1 2012-12-13 2012-12-13 ENSG00000179094 5187 8845 protein-coding gene gene with protein product 602260 "period (Drosophila) homolog 1", "period homolog 1 (Drosophila)" PER NA 9323128 Standard NM_002616 NA Approved RIGUI uc002gkd.3 O15534 ENST00000317276.4:c.3600+61A>- chr17.hg19:g.8045061delT 5 8 ref NA False 47 47 PASS 6 PASS ref->het 0 NA 142,144 30,30 28,28 1 1 B2RPA8|B4DI49|D3DTR3 True hg19 CCDS11131.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PER1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000441481.2 PASS NA None 198 NA True - T ENST00000317276.4 RP11-599B13.6 0 __UNKNOWN__ __UNKNOWN__ 17 8065784 8065786 __UNKNOWN__ Intron DEL TCC TCC - rs150206004 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:8065784_8065786delTCC ENST00000498285.1 - 2 98 VAMP2_ENST00000481878.1_Intron|VAMP2_ENST00000404970.3_Intron|VAMP2_ENST00000488857.1_5'UTR|VAMP2_ENST00000316509.6_Intron NA NA NA NA GTCCCTCCAGTCCTCCTTTTCGG 0.685 NA NA NA 42 0.00838658 0.0015 0.0202 5008 , , NA 14208 0 NA 0.0229 False NA ,,, NA NA NA 2504 0.0031 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 120 141.15 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.33 NA NA NA NA NA ENST00000498285.1:c.3-97GGA>- chr17.hg19:g.8065787_8065789delTCC 1 4 ref NA False 75 75 PASS 2 PASS ref->het 0 NA 92,95 17,17 19,19 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RP11-599B13.6-001 PUTATIVE mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript protein_coding NA protein_coding OTTHUMT00000441549.1 PASS NA None 120 NA True - TCC ENST00000498285.1 TMEM107 84314 __UNKNOWN__ __UNKNOWN__ 17 8076912 8076913 __UNKNOWN__ 3'UTR INS - - A rs200531412|rs183982066|rs386795074|rs149176359 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:8076912_8076913insA ENST00000449985.2 - 0 851_852 Q6UX40 TM107_HUMAN transmembrane protein 107 NA NA NA cilium assembly (GO:0042384)|embryonic digit morphogenesis (GO:0042733)|neural tube patterning (GO:0021532) integral component of membrane (GO:0016021) large_intestine(1)|lung(4)|ovary(1) 6 acgatACAGACAAACAGCCGAC 0.46 NA NA NA 42 0.00838658 0.0015 0.0202 5008 , , NA 21809 0 NA 0.0229 False NA ,,, NA NA NA 2504 0.0031 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 505 481.41 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.66 AF311338 CCDS11132.1, CCDS45607.1 17p13.1 2005-12-19 ENSG00000179029 84314 28128 protein-coding gene gene with protein product NA NA 12477932 Standard NM_032354 NM_032354 NA Approved MGC10744 uc002gkh.4 Q6UX40 ENST00000449985.2:c.*658->T chr17.hg19:g.8076915_8076915dupA 4 4 ref NA False 128 128 PASS 3 PASS ref->het 0 NA 399,400 50,50 49,49 1 1 A0PJV7|Q6NSE3|Q6ZRX9|Q96T82 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TMEM107-004 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000388841.1 PASS NA None 505 NA True - A ENST00000449985.2 SREBF1 6720 __UNKNOWN__ __UNKNOWN__ 17 17740165 17740165 __UNKNOWN__ 5'UTR DEL C C - rs60282872 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:17740165delC ENST00000261646.5 - 0 151 SREBF1_ENST00000338854.5_5'UTR|SREBF1_ENST00000355815.4_5'UTR NM_004176.4 NP_004167.3 P36956 SRBP1_HUMAN sterol regulatory element binding transcription factor 1 NA NA NA aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234) chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810) cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1) 14 GCCCGCCGGGCCCGCCGCCTC 0.766 NA NA NA CCC|CCC|CC|deletion 1304 0.260383 0.1029 0.4063 5008 , , NA 8497 0.0704 NA 0.5815 False NA ,,, NA NA NA 2504 0.2352 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 152 178.15 NA , 458,1618 NA 162,134,742 2 2 2 , 0.6 0.2 17 dbSNP_129 2 3046,1734 NA 1262,522,606 no utr-5,utr-5 SREBF1 NM_004176.4,NM_001005291.2 , 1424,656,1348 A1A1,A1R,RR NA 36.2762,22.0617,48.8915 , , 17740165 3504,3352 1110 1837 2947 SO:0001623 5_prime_UTR_variant 0.57 BC057388 CCDS11189.1, CCDS32583.1 17p11.2 2013-05-21 ENSG00000072310 ENSG00000072310 6720 "Basic helix-loop-helix proteins" 11289 protein-coding gene gene with protein product 184756 NA 8402897, 7759101 Standard NM_004176 NM_001005291 NA Approved SREBP1, bHLHd1, SREBP-1c uc002grt.2 P36956 OTTHUMG00000059313 ENST00000261646.5:c.-34G>- chr17.hg19:g.17740165delC 2 5 ref NA False 128 115 PASS 3 PASS ref->het 0 NA 83,89 44,45 26,20 1 1 B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9 True hg19 CCDS11189.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SREBF1-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000131771.1 PASS NA None 152 NA True - C ENST00000261646.5 TOM1L2 146691 __UNKNOWN__ __UNKNOWN__ 17 17773900 17773901 __UNKNOWN__ Intron INS - - T rs140445913 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:17773900_17773901insT ENST00000535933.1 - 7 725 TOM1L2_ENST00000395739.4_Intron|TOM1L2_ENST00000577517.1_Intron|TOM1L2_ENST00000542206.1_Intron|TOM1L2_ENST00000379504.3_Intron|TOM1L2_ENST00000478943.1_Intron|TOM1L2_ENST00000318094.10_Intron|TOM1L2_ENST00000540946.1_Intron|TOM1L2_ENST00000581396.1_Intron Q6ZVM7 TM1L2_HUMAN target of myb1-like 2 (chicken) NA NA NA intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|signal transduction (GO:0007165) extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622) clathrin binding (GO:0030276)|protein kinase binding (GO:0019901) endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(2) 10 all_neural(463;0.228) TGAAGGATAAGTCTCTCCTTCT 0.465 NA NA NA T|T|TT|insertion 4 0.000798722 0 0.0014 5008 , , NA 23003 0 NA 0.003 False NA ,,, NA NA NA 2504 0 NA NA NA Melanoma(192;2505 2909 14455 25269) PASS NA NA NA 0 NA NA NA NA NA 252 241.69 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AJ230803 CCDS32584.1, CCDS42270.1, CCDS74000.1, CCDS74001.1, CCDS74002.1, CCDS74003.1 17p11.2 2008-07-03 2001-11-28 ENSG00000175662 ENSG00000175662 146691 11984 protein-coding gene gene with protein product 615519 "target of myb1 (chicken) homolog-like 1" NA 10036180 Standard NM_001082968 NA Approved uc002grz.4 Q6ZVM7 OTTHUMG00000059353 ENST00000535933.1:c.619-1113->A chr17.hg19:g.17773901_17773901dupT 2 2 ref NA False 45 45 PASS 1 PASS ref->het 0 NA 200,200 27,27 27,27 1 1 B7Z2L7|B7Z7F4|Q86V61|Q8TDE7|Q96M88 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TOM1L2-007 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000443248.1 PASS NA None 252 NA True - T ENST00000535933.1 ALDH3A2 224 __UNKNOWN__ __UNKNOWN__ 17 19561012 19561019 __UNKNOWN__ Intron DEL ACTGAATT ACTGAATT - rs534772670|rs372698552|rs3034928|rs3841513 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:19561012_19561019delACTGAATT ENST00000339618.4 + 5 901 ALDH3A2_ENST00000581518.1_Intron|ALDH3A2_ENST00000395575.2_Intron|ALDH3A2_ENST00000579855.1_Intron|ALDH3A2_ENST00000176643.6_Intron NM_001031806.1 NP_001026976.1 P51648 AL3A2_HUMAN aldehyde dehydrogenase 3 family, member A2 NA NA NA cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714) endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777) aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814) endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1) 13 all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245) TGAATATTTGACTGAATTACTGAATTAT 0.322 NA NA NA 3027 0.604433 0.3336 0.6398 5008 , , NA 18872 0.9018 NA 0.5388 False NA ,,, NA NA NA 2504 0.7065 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 217 237.93 NA , 1623,2635 NA 325,973,831 NA NA NA , -4.3 0 NA dbSNP_107 46 4232,3976 NA 1112,2008,984 no intron,intron ALDH3A2 NM_001031806.1,NM_000382.2 , 1437,2981,1815 A1A1,A1R,RR NA 48.4405,38.1165,46.9678 , , NA 5855,6611 NA NA NA SO:0001627 intron_variant 0 L47162 CCDS11210.1, CCDS32589.1 17p11.2 2010-05-07 ENSG00000072210 ENSG00000072210 224 1.2.1.3 "Aldehyde dehydrogenases" 403 protein-coding gene gene with protein product "fatty aldehyde dehydrogenase" 609523 SLS, ALDH10 NA 7894487 Standard NM_000382 NA Approved FALDH uc002gwa.1 P51648 OTTHUMG00000059471 ENST00000339618.4:c.681-39ACTGAATT>- chr17.hg19:g.19561020_19561027delACTGAATT 1 3 ref NA False 48 48 PASS 2 PASS ref->het 0 NA 177,181 40,40 27,26 1 1 Q6I9T3|Q93011|Q96J37 True hg19 CCDS32589.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ALDH3A2-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000132269.1 PASS NA None 217 NA True + ACTGAATT ENST00000339618.4 ALDH3A2 224 __UNKNOWN__ __UNKNOWN__ 17 19576669 19576669 __UNKNOWN__ Intron DEL G G - rs112169072|rs34160909 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:19576669delG ENST00000571163.1 + 3 226 ALDH3A2_ENST00000581518.1_Intron|ALDH3A2_ENST00000395575.2_Intron|ALDH3A2_ENST00000579855.1_Intron|ALDH3A2_ENST00000574597.1_Intron|ALDH3A2_ENST00000339618.4_Intron|ALDH3A2_ENST00000176643.6_Intron P51648 AL3A2_HUMAN aldehyde dehydrogenase 3 family, member A2 NA NA NA cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714) endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777) aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814) endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1) 13 all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245) Gtttgtttttgtttttgtttt 0.373 NA NA NA |||unknown(STR4?) 3384 0.675719 0.5038 0.67 5008 , , NA 17648 0.9861 NA 0.5537 False NA ,,, NA NA NA 2504 0.7178 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 165 182.19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.04 L47162 CCDS11210.1, CCDS32589.1 17p11.2 2010-05-07 ENSG00000072210 ENSG00000072210 224 1.2.1.3 "Aldehyde dehydrogenases" 403 protein-coding gene gene with protein product "fatty aldehyde dehydrogenase" 609523 SLS, ALDH10 NA 7894487 Standard NM_000382 NA Approved FALDH uc002gwa.1 P51648 OTTHUMG00000059471 ENST00000571163.1:c.227-2202G>- chr17.hg19:g.19576669delG 0 10 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 111,114 27,28 24,21 1 1 Q6I9T3|Q93011|Q96J37 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ALDH3A2-010 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000441026.2 PASS NA None 165 NA True + G ENST00000571163.1 AC090616.2 0 __UNKNOWN__ __UNKNOWN__ 17 30470028 30470029 __UNKNOWN__ Intron INS - - C rs397746343|rs149838766 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:30470028_30470029insC ENST00000398832.2 - 1 111 RHOT1_ENST00000358365.3_Intron|RHOT1_ENST00000545287.2_Intron|RHOT1_ENST00000580976.1_Intron|RHOT1_ENST00000354266.3_Intron|RHOT1_ENST00000394692.2_Intron|RHOT1_ENST00000583994.1_Intron|RHOT1_ENST00000333942.6_Intron|RHOT1_ENST00000581094.1_Intron NA NA NA NA GTCCCTATTAGCCCTAACCGCC 0.629 NA NA NA CCCC|CCC|CCCC|deletion 1608 0.321086 0.5764 0.2334 5008 , , NA 14847 0.2212 NA 0.1918 False NA ,,, NA NA NA 2504 0.274 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 757 724.85 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 1.21 NA NA NA NA NA ENST00000398832.2:c.5+14->G chr17.hg19:g.30470031_30470031dupC 4 3 ref NA False 379 205 PASS 3 PASS ref->het 0 NA 476,482 212,216 66,63 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AC090616.2-001 NOVEL basic|appris_principal protein_coding NA protein_coding OTTHUMT00000256184.2 PASS NA None 757 NA True - C ENST00000398832.2 CISD3 284106 __UNKNOWN__ __UNKNOWN__ 17 36889466 36889467 __UNKNOWN__ Intron INS - - CCTGC rs3066485|rs200582089|rs25605|rs5820264 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:36889466_36889467insCCTGC ENST00000439660.2 + 4 328 CISD3_ENST00000578573.1_Intron NM_001136498.1 NP_001129970.1 P0C7P0 CISD3_HUMAN CDGSH iron sulfur domain 3 NA NA NA mitochondrion (GO:0005739) 2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872) endometrium(2) 2 AGCTCCTGCAGCCTGCCCTGCC 0.604 NA NA NA 2533 0.505791 0.5779 0.5447 5008 , , NA 16669 0.3532 NA 0.5427 False NA ,,, NA NA NA 2504 0.5 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 93 116.8 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AK097047 CCDS45662.1 17q12 2007-08-10 ENSG00000277972 284106 "CDGSH iron sulfur domain containing" 27578 protein-coding gene gene with protein product "mitoNEET related 2" 611933 NA 17376863, 17584744 Standard NM_001136498 NA Approved Miner2 uc010wds.1 P0C7P0 ENST00000439660.2:c.205-62->CCTGC chr17.hg19:g.36889472_36889476dupCCTGC 4 2 ref NA False 30 30 PASS 3 PASS ref->het 0 NA 58,58 15,15 20,20 1 1 True hg19 CCDS45662.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CISD3-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000441921.1 PASS NA None 93 NA True + CCTGC ENST00000439660.2 NT5C3B 115024 __UNKNOWN__ __UNKNOWN__ 17 39991849 39991852 __UNKNOWN__ Intron DEL GCTG GCTG - rs148849516 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:39991849_39991852delGCTG ENST00000521789.1 - 2 79 NT5C3B_ENST00000435506.2_Intron|NT5C3B_ENST00000269534.8_Intron Q969T7 5NT3B_HUMAN 5'-nucleotidase, cytosolic IIIB NA NA NA nucleotide metabolic process (GO:0009117) cytoplasm (GO:0005737) 5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166) NA CTGGGGAGCCGCTGGCTTGGGGAG 0.495 NA NA NA 330 0.0658946 0.0076 0.0432 5008 , , NA 18745 0.0605 NA 0.1123 False NA ,,, NA NA NA 2504 0.1186 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 75 87.72 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS11410.1, CCDS11410.2 17q21.2 2013-01-31 2013-01-31 2013-01-31 ENSG00000141698 ENSG00000141698 115024 3.1.3.5 28300 protein-coding gene gene with protein product NA "5'-nucleotidase, cytosolic III-like" NT5C3L NA 23223233 Standard NM_052935 NM_052935 NA Approved MGC20781 uc021txo.1 Q969T7 OTTHUMG00000133499 ENST00000521789.1:c.13-325CAGC>- chr17.hg19:g.39991849_39991852delGCTG 0 3 ref NA False 34 34 PASS 1 PASS ref->het 0 NA 55,57 14,14 17,16 1 1 A8MWB9|C9JKC4|Q7L3B7 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NT5C3B-017 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000380435.1 PASS NA None 75 NA True - GCTG ENST00000521789.1 SNF8 11267 __UNKNOWN__ __UNKNOWN__ 17 47014652 47014652 __UNKNOWN__ Intron DEL T T - rs112252929|rs5820737 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:47014652delT ENST00000290330.3 - 4 320 SNF8_ENST00000502492.1_Intron NM_007241.2 NP_009172.2 Q96H20 SNF8_HUMAN SNF8, ESCRT-II complex subunit NA NA NA endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351) cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|transcription factor complex (GO:0005667) protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134) breast(1)|endometrium(1)|lung(1) 3 CGGTAACTCCTGCTGAAGAAC 0.502 NA NA NA T|T|-|deletion 1097 0.21905 0.1891 0.3732 5008 , , NA 17260 0.1726 NA 0.2435 False NA ,,, NA NA NA 2504 0.1728 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 454 446.06 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 AF156102 CCDS11541.1 17q21.32 2013-06-05 2013-06-05 ENSG00000159210 ENSG00000159210 11267 17028 protein-coding gene gene with protein product 610904 "SNF8, ESCRT-II complex subunit, homolog (S. cerevisiae)" NA 10419521, 15329733 Standard NM_007241 NM_007241 NA Approved EAP30, VPS22, Dot3 uc002ioj.3 Q96H20 OTTHUMG00000160569 ENST00000290330.3:c.245-166A>- chr17.hg19:g.47014652delT 0 3 ref NA False 47 47 PASS 1 PASS ref->het 0 NA 332,334 59,59 56,54 1 1 Q8IXY3|Q9UN50 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SNF8-002 KNOWN basic|appris_principal protein_coding NA protein_coding OTTHUMT00000361173.1 PASS NA None 454 NA True - T ENST00000290330.3 SPATA20 64847 __UNKNOWN__ __UNKNOWN__ 17 48627861 48627862 __UNKNOWN__ Intron DEL CT CT - rs113990008|rs201592753|rs398119860|rs10586811 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:48627861_48627862delCT ENST00000006658.6 + 10 1218 SPATA20_ENST00000356488.4_Intron|SPATA20_ENST00000393244.3_Intron|SPATA20_ENST00000511937.1_Intron NM_022827.3 NP_073738.2 Q8TB22 SPT20_HUMAN spermatogenesis associated 20 NA NA NA cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283) extracellular region (GO:0005576) catalytic activity (GO:0003824) endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 24 Breast(11;1.23e-18) BRCA - Breast invasive adenocarcinoma(22;9.38e-09) CCCCAGTGACCTCTCTGTTCAC 0.574 NA NA NA OREG0024568 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 1496 0.298722 0.68 0.2349 5008 , , NA 18224 0.0427 NA 0.2525 False NA ,,, NA NA NA 2504 0.1401 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 197 200.44 NA 2613,1651 NA 812,989,331 NA NA NA 1.9 0 NA dbSNP_130 158 2105,6149 NA 256,1593,2278 no intron SPATA20 NM_022827.2 1068,2582,2609 A1A1,A1R,RR NA 25.5028,38.7195,37.6897 NA 4718,7800 NA NA NA SO:0001627 intron_variant 0.02 CCDS11571.1, CCDS58563.1, CCDS58564.1 17q21.33 2011-03-17 ENSG00000006282 ENSG00000006282 64847 26125 protein-coding gene gene with protein product "hypothetical protein FLJ21347" 613939 NA 12477932 Standard NM_022827 NM_022827 NA Approved FLJ21347, SSP411, Tisp78 uc002ird.3 Q8TB22 OTTHUMG00000162162 ENST00000006658.6:c.1099-35CT>- chr17.hg19:g.48627865_48627866delCT 2 3 ref 119 False 34 34 PASS 3 PASS ref->het 0 NA 158,162 25,25 14,13 1 1 Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747 True hg19 CCDS11571.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SPATA20-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000367648.2 PASS NA None 197 NA True + CT ENST00000006658.6 ENDOV 284131 __UNKNOWN__ __UNKNOWN__ 17 78389441 78389443 __UNKNOWN__ Intron DEL TCC TCC - rs199849833 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:78389441_78389443delTCC ENST00000523999.1 + 2 73 ENDOV_ENST00000522751.1_5'UTR|ENDOV_ENST00000518137.1_Intron|ENDOV_ENST00000520367.1_Intron|ENDOV_ENST00000521847.1_3'UTR|ENDOV_ENST00000323854.5_Intron|ENDOV_ENST00000517795.1_Intron|ENDOV_ENST00000518907.1_Intron|ENDOV_ENST00000518644.1_Intron|ENDOV_ENST00000518901.1_Intron|ENDOV_ENST00000520284.1_Intron Q8N8Q3 ENDOV_HUMAN endonuclease V NA NA NA DNA repair (GO:0006281)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502) cytoplasm (GO:0005737)|nucleolus (GO:0005730) endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|endoribonuclease activity, producing 5'-phosphomonoesters (GO:0016891)|magnesium ion binding (GO:0000287)|single-stranded RNA binding (GO:0003727)|structure-specific DNA binding (GO:0043566) endometrium(1)|lung(1)|pancreas(1)|prostate(1) 4 GACGCTTCTGTCCTCCTAGGGAG 0.68 NA NA NA Direct reversal of damage 36 0.0071885 0 0.0202 5008 , , NA 16939 0 NA 0.0219 False NA ,,, NA NA NA 2504 0 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 190 173.53 NA ,, 16,3928 NA 3,10,1959 NA NA NA ,, -9.2 0 NA 29 111,7909 NA 4,103,3903 no intron,intron,intron ENDOV NM_173627.3,NM_001164638.1,NM_001164637.1 ,, 7,113,5862 A1A1,A1R,RR NA 1.384,0.4057,1.0615 ,, ,, NA 127,11837 NA NA NA SO:0001627 intron_variant 0.04 CCDS54172.1, CCDS54173.1, CCDS54174.1 17q25.3 2011-05-05 ENSG00000173818 ENSG00000173818 284131 26640 protein-coding gene gene with protein product NA NA 12853604 Standard NM_173627 NM_001164638 NA Approved FLJ35220 uc021ueo.1 Q8N8Q3 OTTHUMG00000164638 ENST00000523999.1:c.57-7TCC>- chr17.hg19:g.78389444_78389446delTCC 1 4 ref NA False 45 45 PASS 2 PASS ref->het 0 NA 156,156 22,22 17,17 1 1 I3L3S4|Q6P2G2|Q86X99|Q8NAK0 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ENDOV-003 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000379489.1 PASS NA None 190 NA True + TCC ENST00000523999.1 DCXR 51181 __UNKNOWN__ __UNKNOWN__ 17 79995490 79995491 __UNKNOWN__ Intron INS - - TT rs113364103 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr17:79995490_79995491insTT ENST00000306869.2 - 1 102 NM_001195218.1|NM_016286.3 NP_001182147.1|NP_057370.1 Q7Z4W1 DCXR_HUMAN dicarbonyl/L-xylulose reductase NA NA NA D-xylose metabolic process (GO:0042732)|glucose metabolic process (GO:0006006)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|xylulose metabolic process (GO:0005997) brush border (GO:0005903)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634) L-xylulose reductase (NADP+) activity (GO:0050038)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655) kidney(1)|lung(3) 4 all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246) BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191) CTTTGCCCACCTTTCCCCGCCG 0.748 NA NA NA 927 0.185104 0.5189 0.0821 5008 , , NA 10523 0.0655 NA 0.1004 False NA ,,, NA NA NA 2504 0.0174 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 176 180.22 NA , 1814,1884 NA 600,614,635 NA NA NA , 3.5 0 NA dbSNP_132 5 881,6617 NA 149,583,3017 no intron,intron DCXR NM_016286.3,NM_001195218.1 , 749,1197,3652 A1A1,A1R,RR NA 11.7498,49.0535,24.0711 , , NA 2695,8501 NA NA NA SO:0001627 intron_variant 0.49 AB013846 CCDS11799.1 17q25.3 2011-09-14 ENSG00000169738 51181 1.1.1.10 "Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1" 18985 protein-coding gene gene with protein product "short chain dehydrogenase/reductase family 20C, member 1" 608347 NA 11882650, 19027726 Standard NM_016286 NA Approved KIDCR, DCR, SDR20C1 uc002kdg.3 Q7Z4W1 ENST00000306869.2:c.52+15->AA chr17.hg19:g.79995491_79995492dupTT 5 5 ref NA False 67 67 PASS 3 PASS ref->het 0 NA 137,143 20,21 18,13 1 1 Q9BTZ3|Q9UHY9 True hg19 CCDS11799.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DCXR-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000442153.2 PASS NA None 176 NA True - T ENST00000306869.2 MPPE1 65258 __UNKNOWN__ __UNKNOWN__ 18 11883216 11883217 __UNKNOWN__ 3'UTR INS - - A rs397781575|rs35302696 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:11883216_11883217insA ENST00000588072.1 - 0 3639_3640 GNAL_ENST00000334049.6_3'UTR NM_023075.5 NP_075563.3 Q53F39 MPPE1_HUMAN metallophosphoesterase 1 NA NA NA ER to Golgi vesicle-mediated transport (GO:0006888)|GPI anchor biosynthetic process (GO:0006506) cis-Golgi network (GO:0005801)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021) GPI anchor binding (GO:0034235)|manganese ion binding (GO:0030145)|phosphoric diester hydrolase activity (GO:0008081) endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1) 5 ATCACCGTCTTACTGCCTCCCC 0.361 NA NA NA A|A|AA|insertion 1200 0.239617 0.3631 0.1182 5008 , , NA 16651 0.3948 NA 0.1093 False NA ,,, NA NA NA 2504 0.1329 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 480 454.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.92 BC002877 CCDS11853.1, CCDS56054.1 18p11.21 2004-04-30 ENSG00000154889 ENSG00000154889 65258 15988 protein-coding gene gene with protein product 611900 NA 11978971 Standard NM_023075 NM_001242904 NA Approved uc002kqf.3 Q53F39 OTTHUMG00000131661 ENST00000588072.1:c.*1228->T chr18.hg19:g.11883217_11883217dupA 2 3 ref NA False 48 48 PASS 1 PASS ref->het 0 NA 367,368 71,72 39,37 1 1 B0YJ39|B0YJ40|B0YJ41|B5ME53|B7WNJ3|D3DUI5|D3DUI7|Q6GMP1|Q8TAD6|Q8TE26|Q8WZ32|Q9BU58|Q9H958|Q9HAI4 True hg19 CCDS11853.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MPPE1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254562.2 PASS NA None 480 NA True - A ENST00000588072.1 MPPE1 65258 __UNKNOWN__ __UNKNOWN__ 18 11883224 11883225 __UNKNOWN__ 3'UTR INS - - T rs111393316|rs35697185|rs72122319|rs386801311|rs560964616 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:11883224_11883225insT ENST00000588072.1 - 0 3631_3632 GNAL_ENST00000334049.6_3'UTR NM_023075.5 NP_075563.3 Q53F39 MPPE1_HUMAN metallophosphoesterase 1 NA NA NA ER to Golgi vesicle-mediated transport (GO:0006888)|GPI anchor biosynthetic process (GO:0006506) cis-Golgi network (GO:0005801)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021) GPI anchor binding (GO:0034235)|manganese ion binding (GO:0030145)|phosphoric diester hydrolase activity (GO:0008081) endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1) 5 CTTACTGCCTCCCCATCCACTG 0.366 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 469 447.61 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.92 BC002877 CCDS11853.1, CCDS56054.1 18p11.21 2004-04-30 ENSG00000154889 ENSG00000154889 65258 15988 protein-coding gene gene with protein product 611900 NA 11978971 Standard NM_023075 NM_001242904 NA Approved uc002kqf.3 Q53F39 OTTHUMG00000131661 ENST00000588072.1:c.*1220->A chr18.hg19:g.11883224_11883225insT 1 6 ref NA False 48 48 PASS 0 PASS ref->het 0 NA 368,369 70,71 30,28 1 1 B0YJ39|B0YJ40|B0YJ41|B5ME53|B7WNJ3|D3DUI5|D3DUI7|Q6GMP1|Q8TAD6|Q8TE26|Q8WZ32|Q9BU58|Q9H958|Q9HAI4 True hg19 CCDS11853.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MPPE1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000254562.2 PASS NA None 469 NA True - T ENST00000588072.1 MEX3C 51320 __UNKNOWN__ __UNKNOWN__ 18 48723146 48723154 __UNKNOWN__ Intron DEL GCCGCCGCG GCCGCCGCG - rs78074704|rs530394988|rs147438518|rs201868643|rs62092914|rs530602218 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:48723146_48723154delGCCGCCGCG ENST00000591040.1 - 2 43 Q5U5Q3 MEX3C_HUMAN mex-3 RNA binding family member C NA NA NA chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598) cytoplasm (GO:0005737)|nucleus (GO:0005634) ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270) endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1) 17 Colorectal(6;0.003)|all_epithelial(6;0.0473) Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15) CCccgccgccgccgccgcggccgccgccT 0.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 188 183.99 NA 429,1467 NA 144,141,663 NA NA NA -0.2 0.9 NA dbSNP_131 4 2100,2286 NA 804,492,897 no coding MEX3C NM_016626.4 948,633,1560 A1A1,A1R,RR NA 47.8796,22.6266,40.2579 NA 2529,3753 NA NA NA SO:0001627 intron_variant 0.21 BC041122 CCDS11951.2 18q21.1 2013-08-21 2013-08-21 2007-07-18 ENSG00000176624 ENSG00000176624 51320 "RING-type (C3HC4) zinc fingers", "Mex-3 homologs" 28040 protein-coding gene gene with protein product 611005 "ring finger and KH domain containing 2", "mex-3 homolog C (C. elegans)" RKHD2 NA 17267406 Standard NM_016626 NM_016626 NA Approved FLJ38871, RNF194 uc002lfc.4 Q5U5Q3 OTTHUMG00000132693 ENST00000591040.1:c.757-19200CGCGGCGGC>- chr18.hg19:g.48723146_48723154delGCCGCCGCG 0 4 ref NA False 73 73 PASS 1 PASS ref->het 0 NA 141,144 25,25 27,25 1 1 A1L022|Q9NZE3 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MEX3C-003 KNOWN mRNA_end_NF|basic processed_transcript NA protein_coding OTTHUMT00000449559.1 PASS NA None 188 NA True - GCCGCCGCG ENST00000591040.1 C18orf54 162681 __UNKNOWN__ __UNKNOWN__ 18 51907707 51907707 __UNKNOWN__ 3'UTR DEL T T - rs34057877|rs398100887 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:51907707delT ENST00000300091.5 + 0 4542 NM_173529.4 NP_775800.3 Q8IYD9 LAS2_HUMAN chromosome 18 open reading frame 54 NA NA NA extracellular region (GO:0005576) breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1) 15 Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186) CCCTTCTGTGTTAACAGTTTT 0.358 NA NA NA T|TT|T|insertion 3809 0.760583 0.8979 0.7378 5008 , , NA 19269 0.7044 NA 0.6799 False NA ,,, NA NA NA 2504 0.7321 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 369 338.58 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AK126503 CCDS11956.1, CCDS74223.1 18q21 2012-10-24 ENSG00000166845 ENSG00000166845 162681 13796 protein-coding gene gene with protein product "lung adenoma susceptibility protein 2" 613258 NA Standard NM_173529 XM_005258201 NA Approved MGC33382, LAS2 uc031rij.1 Q8IYD9 OTTHUMG00000132703 ENST00000300091.5:c.*3091T>- chr18.hg19:g.51907707delT 1 3 ref NA False 38 38 PASS 2 PASS ref->het 0 NA 299,302 46,48 24,24 1 1 I7HFJ6|Q6MZU3|Q6ZTL6 True hg19 CCDS11956.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C18orf54-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000256001.1 PASS NA None 369 NA True + T ENST00000300091.5 ZCCHC2 54877 __UNKNOWN__ __UNKNOWN__ 18 60212014 60212015 __UNKNOWN__ Intron DEL TG TG - rs143702074 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:60212014_60212015delTG ENST00000269499.5 + 4 1546 ZCCHC2_ENST00000586834.1_Intron NM_017742.4 NP_060212.4 Q9C0B9 ZCHC2_HUMAN zinc finger, CCHC domain containing 2 NA NA NA cytoplasm (GO:0005737) nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270) breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1) 25 CCATATAATATGTGTGTTTTTT 0.332 NA NA NA 1178 0.235224 0.1505 0.2882 5008 , , NA 14091 0.2331 NA 0.2266 False NA ,,, NA NA NA 2504 0.3231 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 71 69.81 NA 518,2882 NA 77,364,1259 NA NA NA 0 0.8 NA dbSNP_134 35 1549,6119 NA 236,1077,2521 no intron ZCCHC2 NM_017742.4 313,1441,3780 A1A1,A1R,RR NA 20.2008,15.2353,18.6755 NA 2067,9001 NA NA NA SO:0001627 intron_variant 0 AB051531 CCDS45880.1 18q21.33 2012-04-19 ENSG00000141664 ENSG00000141664 54877 "Zinc fingers, CCHC domain containing" 22916 protein-coding gene gene with protein product NA "chromosome 18 open reading frame 49" C18orf49 NA 11214970 Standard NM_017742 NM_017742 NA Approved FLJ20281, KIAA1744, FLJ20222 uc002lip.4 Q9C0B9 ENST00000269499.5:c.1129-20TG>- chr18.hg19:g.60212018_60212019delTG 2 3 ref NA False 43 43 PASS 3 PASS ref->het 0 NA 50,51 18,18 4,3 1 1 B2RPG6|Q8N3S1|Q9NXF6 True hg19 CCDS45880.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZCCHC2-005 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000450083.1 PASS NA None 71 NA True + TG ENST00000269499.5 AC139100.2 0 __UNKNOWN__ __UNKNOWN__ 18 77921332 77921333 __UNKNOWN__ Intron DEL AG AG - rs33942860 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr18:77921332_77921333delAG ENST00000586421.1 + 2 418 AC139100.2_ENST00000585422.1_Intron|PARD6G_ENST00000353265.3_Intron|AC139100.2_ENST00000589574.1_Intron|AC139100.2_ENST00000587254.1_Intron NA NA NA NA ACTGACTCACAGAGTTTGAGGT 0.584 NA NA NA 1840 0.367412 0.6694 0.3213 5008 , , NA 20987 0.1042 NA 0.3628 False NA ,,, NA NA NA 2504 0.2679 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 217 201.86 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.97 NA NA NA NA NA ENST00000586421.1:c.184+846AG>- chr18.hg19:g.77921334_77921335delAG 1 2 ref NA False 55 55 PASS 2 PASS ref->het 0 NA 140,141 52,52 25,24 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AC139100.2-001 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000451060.1 PASS NA None 217 NA True + AG ENST00000586421.1 MKNK2 2872 __UNKNOWN__ __UNKNOWN__ 19 2046294 2046294 __UNKNOWN__ Intron DEL C C - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:2046294delC ENST00000591601.1 - 4 277 MKNK2_ENST00000250896.3_Intron|MKNK2_ENST00000541165.1_Intron|MKNK2_ENST00000309340.7_Intron Q9HBH9 MKNK2_HUMAN MAP kinase interacting serine/threonine kinase 2 NA NA NA cell surface receptor signaling pathway (GO:0007166)|cellular response to arsenic-containing substance (GO:0071243)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|hemopoiesis (GO:0030097)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417) cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634) ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674) breast(1)|kidney(3)|large_intestine(3)|lung(3) 10 Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) TGCCGGGCAGCGGGGCGGGCG 0.667 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 210 223.33 NA NA 43 50 48 NA NA 19 NA NA NA 2046294 2203 4299 6502 SO:0001627 intron_variant 0.05 AF125532 CCDS12079.1, CCDS12080.1 19p13.3 2012-12-20 ENSG00000099875 ENSG00000099875 2872 7111 protein-coding gene gene with protein product "Putative map kinase interacting kinase" 605069 "G protein-coupled receptor kinase 7" GPRK7 NA 11013076 Standard NM_199054 NM_199054 NA Approved MNK2 uc002lus.2 Q9HBH9 OTTHUMG00000180020 ENST00000591601.1:c.242-12G>- chr19.hg19:g.2046294delC 0 7 ref NA False 185 146 PASS 1 PASS ref->het 0 NA 126,127 53,53 35,34 1 1 Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6 True hg19 CCDS12080.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MKNK2-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding NA protein_coding OTTHUMT00000449312.1 PASS NA None 210 NA True - C ENST00000591601.1 NFIC 4782 __UNKNOWN__ __UNKNOWN__ 19 3381646 3381646 __UNKNOWN__ Intron DEL C C - rs67426967 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:3381646delC ENST00000443272.2 + 2 81 NFIC_ENST00000589123.1_Intron|NFIC_ENST00000395111.3_Intron|NFIC_ENST00000341919.3_Intron|NFIC_ENST00000590282.1_Intron|NFIC_ENST00000346156.5_Intron|NFIC_ENST00000586919.1_Intron NM_001245002.1 NP_001231931.1 P08651 NFIC_HUMAN nuclear factor I/C (CCAAT-binding transcription factor) NA NA NA DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366) nucleolus (GO:0005730)|nucleus (GO:0005634) core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700) NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1) 21 Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191) GCCTTCGGGGCCGGGCAGTGG 0.726 NA NA NA CC|CC|C|deletion 952 0.190096 0.2579 0.1556 5008 , , NA 13578 0.0188 NA 0.2296 False NA ,,, NA NA NA 2504 0.2587 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 237 241.09 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.36 X12492 CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1 19p13.3 2008-02-05 ENSG00000141905 4782 7786 protein-coding gene gene with protein product 600729 NFI NA 3398920, 7590749 Standard NM_005597 NM_205843 NA Approved CTF, NF-I, CTF5 uc010xhi.2 P08651 ENST00000443272.2:c.31-64C>- chr19.hg19:g.3381646delC 1 4 ref NA False 145 145 PASS 2 PASS ref->het 0 NA 174,176 41,41 29,27 1 1 A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1 True hg19 CCDS59330.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NFIC-006 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000452834.1 PASS NA None 237 NA True + C ENST00000443272.2 SAFB2 9667 __UNKNOWN__ __UNKNOWN__ 19 5613397 5613398 __UNKNOWN__ Intron DEL AT AT - rs145997637 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:5613397_5613398delAT ENST00000252542.4 - 5 871 NM_014649.2 NP_055464.1 Q14151 SAFB2_HUMAN scaffold attachment factor B2 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634) DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822) endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 29 UCEC - Uterine corpus endometrioid carcinoma (162;0.000228) TTCCATACACATACACACTGCT 0.46 NA NA NA 260 0.0519169 0.0212 0.0533 5008 , , NA 23755 0.0169 NA 0.0626 False NA ,,, NA NA NA 2504 0.1176 NA NA NA Ovarian(127;888 1728 23957 44128 52668) PASS NA NA NA 0 NA NA NA NA NA 169 154.65 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 D50928 CCDS32879.1 19p13.3 2013-02-12 ENSG00000130254 9667 "RNA binding motif (RRM) containing" 21605 protein-coding gene gene with protein product 608066 NA 12660241 Standard NM_014649 NM_014649 NA Approved KIAA0138 uc002mcd.3 Q14151 ENST00000252542.4:c.606+77AT>- chr19.hg19:g.5613397_5613398delAT 0 2 ref NA False 91 91 PASS 1 PASS ref->het 0 NA 108,109 48,50 14,14 1 1 B4DKG3|Q8TB13 True hg19 CCDS32879.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SAFB2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000451016.1 PASS NA None 169 NA True - AT ENST00000252542.4 CERS4 79603 __UNKNOWN__ __UNKNOWN__ 19 8320657 8320666 __UNKNOWN__ Intron DEL GGGGCGGGGC GGGGCGGGGC - rs2913986|rs558805981|rs71786313|rs201732874|rs144397154 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:8320657_8320666delGGGGCGGGGC ENST00000559336.1 + 6 692 CERS4_ENST00000559450.1_Intron|CERS4_ENST00000251363.5_Intron|CERS4_ENST00000595722.1_Intron|CERS4_ENST00000558331.1_Intron Q9HA82 CERS4_HUMAN ceramide synthase 4 NA NA NA ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665) endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634) DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291) NA GGGCCGGGGTGGGGCGGGGCGGGTGTCTGC 0.638 NA NA NA 1010 0.201677 0.0741 0.2939 5008 , , NA 15521 0.1538 NA 0.4016 False NA ,,, NA NA NA 2504 0.1524 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 103 101.18 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 CCDS12197.1 19p13.2 2014-09-11 2011-07-08 2011-07-08 ENSG00000090661 ENSG00000090661 79603 "Homeoboxes / CERS class" 23747 protein-coding gene gene with protein product 615334 "LAG1 longevity assurance homolog 4 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 4" LASS4 NA Standard NM_024552 NM_024552 NA Approved FLJ12089, Trh1 uc002mjg.3 Q9HA82 OTTHUMG00000172570 ENST00000559336.1:c.411-40GGGGCGGGGC>- chr19.hg19:g.8320657_8320666delGGGGCGGGGC 0 8 ref NA False 60 60 PASS 2 PASS ref->het 0 NA 48,51 52,52 18,17 1 1 D6W665 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CERS4-003 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000419202.1 PASS NA None 103 NA True + GGGGC ENST00000559336.1 EIF3G 8666 __UNKNOWN__ __UNKNOWN__ 19 10226341 10226344 __UNKNOWN__ Intron DEL TGCC TGCC - rs150759321|rs71188883 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:10226341_10226344delTGCC ENST00000253108.4 - 9 883 NM_003755.3 NP_003746.2 eukaryotic translation initiation factor 3, subunit G NA NA NA central_nervous_system(1)|lung(1) 2 OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05) AGCCCCACCGTGCCTGCCTGCCTG 0.637 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Colon(124;1100 1638 3822 4510 4876) PASS NA NA NA 0 NA NA NA NA NA 251 237.52 NA 1,936,3327 NA 0,0,1,99,738,1294 NA NA NA -4.7 0 NA dbSNP_134 91 0,3715,4539 NA 0,0,0,842,2031,1254 no intron EIF3G NM_003755.3 0,0,1,941,2769,2548 A1A1,A1A2,A1R,A2A2,A2R,RR NA 45.0085,21.9747,37.1625 NA 1,4651,7866 NA NA NA SO:0001627 intron_variant 0 U96074 CCDS12227.1 19p13.2 2013-02-12 2007-07-27 2007-07-27 ENSG00000130811 8666 "RNA binding motif (RRM) containing" 3274 protein-coding gene gene with protein product 603913 "eukaryotic translation initiation factor 3, subunit 4 delta, 44kDa" EIF3S4 NA 9822659 Standard NM_003755 NA Approved eIF3-delta, eIF3-p44, eIF3g uc002mnd.3 O75821 ENST00000253108.4:c.840+15GGCA>- chr19.hg19:g.10226349_10226352delTGCC 3 2 ref NA False 43 43 PASS 4 PASS ref->het 0 NA 161,163 56,56 34,32 1 1 True hg19 CCDS12227.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EIF3G-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000451144.1 PASS NA None 251 NA True - TGCC ENST00000253108.4 EIF3G 8666 __UNKNOWN__ __UNKNOWN__ 19 10229727 10229747 __UNKNOWN__ Intron DEL GGCAGTCCTCACTCACCTCCC GGCAGTCCTCACTCACCTCCC - rs3217685|rs149991692 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:10229727_10229747delGGCAGTCCTCACTCACCTCCC ENST00000253108.4 - 3 194 EIF3G_ENST00000587168.1_Intron NM_003755.3 NP_003746.2 eukaryotic translation initiation factor 3, subunit G NA NA NA central_nervous_system(1)|lung(1) 2 OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05) GACACCGAGTGGCAGTCCTCACTCACCTCCCGGCAGTCCTC 0.629 NA NA NA 1640 0.327476 0.171 0.4409 5008 , , NA 12964 0.3065 NA 0.4165 False NA ,,, NA NA NA 2504 0.3885 NA NA NA Colon(124;1100 1638 3822 4510 4876) PASS NA NA NA 0 NA NA NA NA NA 141 129.39 NA 675,3521 NA 111,453,1534 NA NA NA -7 0 NA dbSNP_130 26 2586,5314 NA 711,1164,2075 no intron EIF3G NM_003755.3 822,1617,3609 A1A1,A1R,RR NA 32.7342,16.0867,26.9593 NA 3261,8835 NA NA NA SO:0001627 intron_variant 0 U96074 CCDS12227.1 19p13.2 2013-02-12 2007-07-27 2007-07-27 ENSG00000130811 8666 "RNA binding motif (RRM) containing" 3274 protein-coding gene gene with protein product 603913 "eukaryotic translation initiation factor 3, subunit 4 delta, 44kDa" EIF3S4 NA 9822659 Standard NM_003755 NA Approved eIF3-delta, eIF3-p44, eIF3g uc002mnd.3 O75821 ENST00000253108.4:c.151+16GGGAGGTGAGTGAGGACTGCC>- chr19.hg19:g.10229727_10229747delGGCAGTCCTCACTCACCTCCC 1 5 ref NA False 32 32 PASS 2 PASS ref->het 0 NA 74,78 9,9 73,70 1 1 True hg19 CCDS12227.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA EIF3G-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000451144.1 PASS NA None 141 NA True - GGCAGTCCTCACTCACCTCCC ENST00000253108.4 ZNF440 126070 __UNKNOWN__ __UNKNOWN__ 19 11944367 11944368 __UNKNOWN__ 3'UTR INS - - CT rs34722409|rs35549963 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:11944367_11944368insCT ENST00000304060.5 + 0 2540_2541 NM_152357.2 NP_689570.2 Q8IYI8 ZN440_HUMAN zinc finger protein 440 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 27 TCATGAAAGAACACACTAGGGA 0.381 NA NA NA 1678 0.335064 0.5272 0.3285 5008 , , NA 21504 0.1597 NA 0.3628 False NA ,,, NA NA NA 2504 0.2321 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 423 445.51 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.92 AK095252 CCDS42503.1 19p13.13 2013-01-08 2006-08-14 2006-08-14 ENSG00000171295 ENSG00000171295 126070 "Zinc fingers, C2H2-type", "-" 20874 protein-coding gene gene with protein product NA NA Standard NM_152357 NM_152357 NA Approved FLJ37933 uc002msp.1 Q8IYI8 OTTHUMG00000156403 ENST00000304060.5:c.*589->CT chr19.hg19:g.11944367_11944368insCT 1 5 ref NA False 31 31 PASS 0 PASS ref->het 0 NA 322,328 43,44 54,51 1 1 Q8N1R9 True hg19 CCDS42503.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF440-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000344508.1 PASS NA None 423 NA True + CT ENST00000304060.5 ZNF493 284443 __UNKNOWN__ __UNKNOWN__ 19 21607879 21607882 __UNKNOWN__ 3'UTR DEL TAAT TAAT - rs397728603|rs34723025 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:21607879_21607882delTAAT ENST00000392288.2 + 0 2527_2530 ZNF493_ENST00000355504.4_3'UTR|CTD-2561J22.3_ENST00000600810.1_Intron NM_001076678.2 NP_001070146.1 Q6ZR52 ZN493_HUMAN zinc finger protein 493 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1) 30 ACACATAAGATAATTAATGCTGGA 0.338 NA NA NA 1454 0.290335 0.2421 0.3429 5008 , , NA 18679 0.3403 NA 0.2843 False NA ,,, NA NA NA 2504 0.273 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 700 702.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AK093823, BC006408, BC022394 CCDS12412.1, CCDS42536.1, CCDS12411.1 19p12 2013-01-08 ENSG00000196268 ENSG00000196268 284443 "Zinc fingers, C2H2-type", "-" 23708 protein-coding gene gene with protein product NA NA Standard NM_175910 NM_001076678 NA Approved FLJ36504 uc002npw.3 Q6ZR52 OTTHUMG00000141297 ENST00000392288.2:c.*96TAAT>- chr19.hg19:g.21607883_21607886delTAAT 1 3 ref NA False 100 100 PASS 2 PASS ref->het 0 NA 509,515 129,130 67,68 1 1 G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99 True hg19 CCDS42536.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF493-002 NOVEL basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000280562.1 PASS NA None 700 NA True + TAAT ENST00000392288.2 PHLDB3 653583 __UNKNOWN__ __UNKNOWN__ 19 44005877 44005880 __UNKNOWN__ Intron DEL CAAA CAAA - rs71336868|rs201991650|rs10562543|rs112058634 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:44005877_44005880delCAAA ENST00000292140.5 - 4 895 PHLDB3_ENST00000599242.1_Intron NM_198850.3 NP_942147.3 Q6NSJ2 PHLB3_HUMAN pleckstrin homology-like domain, family B, member 3 NA NA NA enzyme binding (GO:0019899) breast(1)|central_nervous_system(1)|lung(5) 7 Prostate(69;0.0153) CCCGGTGAGCCAAACAGACCTGTT 0.672 NA NA NA 761 0.151957 0.1747 0.085 5008 , , NA 13335 0.1329 NA 0.1988 False NA ,,, NA NA NA 2504 0.1401 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 363 321.63 NA 709,3535 NA 62,585,1475 NA NA NA -6.8 0 NA dbSNP_132 26 1495,6721 NA 167,1161,2780 no intron PHLDB3 NM_198850.3 229,1746,4255 A1A1,A1R,RR NA 18.1962,16.7059,17.6886 NA 2204,10256 NA NA NA SO:0001627 intron_variant 0.89 CCDS12621.2 19q13.31 2013-01-10 ENSG00000176531 ENSG00000176531 653583 "Pleckstrin homology (PH) domain containing" 30499 protein-coding gene gene with protein product NA NA Standard NM_198850 NA Approved FLJ40193 uc002own.4 Q6NSJ2 OTTHUMG00000150693 ENST00000292140.5:c.534+5TTTG>- chr19.hg19:g.44005877_44005880delCAAA 0 4 ref NA False 167 137 PASS 1 PASS ref->het 0 NA 242,247 89,91 32,27 1 1 Q8N7Z4 True hg19 CCDS12621.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PHLDB3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000319643.2 PASS NA None 363 NA True - CAAA ENST00000292140.5 SEPW1 6415 __UNKNOWN__ __UNKNOWN__ 19 48282077 48282078 __UNKNOWN__ Intron INS - - GCAGCGG rs34940677|rs111841672|rs3074137 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:48282077_48282078insGCAGCGG ENST00000601048.1 + 1 243 SEPW1_ENST00000601419.1_Intron|SEPW1_ENST00000509570.2_Intron|SEPW1_ENST00000593892.1_Intron|SEPW1_ENST00000595615.1_Intron NM_003009.2 NP_003000.1 P63302 SELW_HUMAN selenoprotein W, 1 NA NA NA cell redox homeostasis (GO:0045454) cytoplasm (GO:0005737) antioxidant activity (GO:0016209)|selenium binding (GO:0008430) endometrium(1)|kidney(1)|lung(2) 4 all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133) all cancers(93;0.000291)|OV - Ovarian serous cystadenocarcinoma(262;0.000305)|Epithelial(262;0.0146)|GBM - Glioblastoma multiforme(486;0.0273) TATTGGTAAGCCCAGCGGCCAG 0.713 NA NA NA 3000 0.599042 0.528 0.6412 5008 , , NA 10503 0.5258 NA 0.6511 False NA ,,, NA NA NA 2504 0.6871 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 197 189.97 NA 2049,1507 NA 619,811,348 NA NA NA 2.3 0.1 NA dbSNP_102 13 5169,2585 NA 1778,1613,486 no intron SEPW1 NM_003009.2 2397,2424,834 A1A1,A1R,RR NA 33.3376,42.3791,36.1804 NA 7218,4092 NA NA NA SO:0001627 intron_variant 0.63 U67171 CCDS59402.1 19q13.33 2012-05-22 ENSG00000178980 ENSG00000178980 6415 10752 protein-coding gene gene with protein product 603235 NA 9256076 Standard NM_003009 NM_003009 NA Approved selW uc021uwp.1 P63302 ENST00000601048.1:c.29+6->GCAGCGG chr19.hg19:g.48282077_48282078insGCAGCGG 1 3 ref NA False 110 110 PASS 0 PASS ref->het 0 NA 148,150 24,24 24,22 1 1 A8MRR7|O15532|O19096|Q86TI9|Q96KM5 True hg19 CCDS59402.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SEPW1-001 KNOWN upstream_ATG|basic|appris_candidate|CCDS|seleno protein_coding NA protein_coding OTTHUMT00000464884.1 PASS NA None 197 NA True + GCAGCGG ENST00000601048.1 CTC-273B12.7 0 __UNKNOWN__ __UNKNOWN__ 19 48972614 48972614 __UNKNOWN__ Intron DEL A A - rs11292058 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:48972614delA ENST00000595676.1 + 2 121 CYTH2_ENST00000427476.1_5'UTR|CYTH2_ENST00000452733.2_5'UTR|CTC-273B12.5_ENST00000600650.1_RNA|CTC-273B12.5_ENST00000593476.1_RNA NA NA NA NA CGACGAAGGGAAGAGTCTTTT 0.672 NA NA NA A|AA|A|insertion 670 0.133786 0.416 0.0533 5008 , , NA 13081 0.0546 NA 0.0099 False NA ,,, NA NA NA 2504 0.0184 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 69 81.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.26 NA NA NA NA NA ENST00000595676.1:c.-29-996A>- chr19.hg19:g.48972614delA 1 3 ref NA False 37 37 PASS 2 PASS ref->het 0 NA 47,48 13,13 6,5 2 2 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CTC-273B12.7-001 PUTATIVE mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript protein_coding NA protein_coding OTTHUMT00000466132.1 PASS NA None 69 NA True + A ENST00000595676.1 DBP 1628 __UNKNOWN__ __UNKNOWN__ 19 49138657 49138658 __UNKNOWN__ Intron INS - - AAGACCAA rs572773395|rs386810053 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:49138657_49138658insAAGACCAA ENST00000222122.5 - 2 994 DBP_ENST00000601104.1_Intron NM_001352.3 NP_001343.2 Q10586 DBP_HUMAN D site of albumin promoter (albumin D-box) binding protein NA NA NA liver development (GO:0001889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|rhythmic process (GO:0048511) nucleus (GO:0005634) RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977) endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1) 5 all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113) OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000112)|GBM - Glioblastoma multiforme(486;0.00615)|Epithelial(262;0.0155) TGGATCCATTGGTCCCTGACCC 0.554 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 375 350.79 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0 U06936 CCDS12728.1 19q13.33 2013-09-20 ENSG00000105516 ENSG00000105516 1628 2697 protein-coding gene gene with protein product 124097 NA 1535333, 7835883 Standard NM_001352 XR_243907 NA Approved DABP uc002pjx.4 Q10586 OTTHUMG00000183319 ENST00000222122.5:c.550+178->TTGGTCTT chr19.hg19:g.49138657_49138658insAAGACCAA 1 2 ref NA False 180 180 PASS 0 PASS ref->het 0 NA 309,310 27,28 39,37 1 1 A2I2P4 True hg19 CCDS12728.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DBP-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000466167.1 PASS NA None 375 NA True - AAGACCAA ENST00000222122.5 CA11 770 __UNKNOWN__ __UNKNOWN__ 19 49142288 49142296 __UNKNOWN__ In_Frame_Del DEL CTCAGGAGT CTCAGGAGT - rs147254552 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:49142288_49142296delCTCAGGAGT ENST00000084798.4 - 8 1489_1497 c.810_818delACTCCTGAG c.(808-819)agactcctgagc>agc p.RLL270del SEC1P_ENST00000430145.2_RNA NM_001217.3 NP_001208.2 O75493 CAH11_HUMAN carbonic anhydrase XI 270 NA NA basolateral plasma membrane (GO:0016323)|extracellular region (GO:0005576) breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8) 14 all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261) OV - Ovarian serous cystadenocarcinoma(262;0.000103)|all cancers(93;0.000119)|GBM - Glioblastoma multiforme(486;0.00634)|Epithelial(262;0.016) Zonisamide(DB00909) AGGATTCTGGCTCAGGAGTCTCAGGGAGT 0.622 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 125 118.74 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001651 inframe_deletion 0 AF067662 CCDS12729.1 19q13.3 2012-07-02 ENSG00000063180 ENSG00000063180 770 "Carbonic anhydrases" 1370 protein-coding gene gene with protein product "CA-RP XI", "carbonic anhydrase-related protein XI", "carbonic anhydrase-related protein 2" 604644 NA 9878252 Standard NM_001217 XR_243956 NA Approved CARP2, CARPX1 uc002pjz.1 O75493 ENST00000084798.4:c.810_818delACTCCTGAG chr19.hg19:g.49142288_49142296delCTCAGGAGT ENSP00000084798:p.Arg270_Leu272del 0 2 ref NA False 52 52 PASS 1 PASS ref->het 0 NA 110,110 5,5 19,19 1 1 O60596|Q6FHI1|Q9UEC4 True hg19 CCDS12729.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CA11-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000466172.1 PASS NA None 125 NA True - CTCAGGAGT ENST00000084798.4 LIN7B 64130 __UNKNOWN__ __UNKNOWN__ 19 49618682 49618684 __UNKNOWN__ Intron DEL ATG ATG - rs55891932|rs5828374 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:49618682_49618684delATG ENST00000391864.3 + 3 309 LIN7B_ENST00000221459.2_Intron Q9HAP6 LIN7B_HUMAN lin-7 homolog B (C. elegans) NA NA NA exocytosis (GO:0006887)|neurotransmitter secretion (GO:0007269)|protein transport (GO:0015031) neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923) protein domain specific binding (GO:0019904) central_nervous_system(1)|endometrium(1)|prostate(1) 3 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261) all cancers(93;5e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000191)|GBM - Glioblastoma multiforme(486;0.00449)|Epithelial(262;0.01) TTCCTCCCTCATGATTTTTGCTA 0.409 NA NA NA 1282 0.25599 0.3601 0.1715 5008 , , NA 21725 0.0585 NA 0.3072 False NA ,,, NA NA NA 2504 0.3262 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 378 347.9 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.69 AF311862 CCDS12757.1 19q13.3 2008-07-17 ENSG00000104863 ENSG00000104863 64130 17788 protein-coding gene gene with protein product 612331 NA 10341223 Standard NM_022165 XR_243950 NA Approved MALS-2, LIN-7B, VELI2 uc002pmp.3 Q9HAP6 OTTHUMG00000134288 ENST00000391864.3:c.228+94ATG>- chr19.hg19:g.49618682_49618684delATG 0 5 ref NA False 43 43 PASS 1 PASS ref->het 0 NA 308,310 38,38 31,30 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LIN7B-002 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000258981.1 PASS NA None 378 NA True + ATG ENST00000391864.3 AC018755.1 0 __UNKNOWN__ __UNKNOWN__ 19 52097560 52097561 __UNKNOWN__ Frame_Shift_Ins INS - - A rs141848717 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:52097560_52097561insA ENST00000301439.3 - 1 69_70 c.14_15insT c.(13-15)ttcfs p.F5fs NA NA NA NA CAGAAAATCTGAAAAAAAAGTC 0.515 NA NA NA |||unknown(LONG_INSERTION) 438 0.0874601 0.1112 0.0562 5008 , , NA 20252 0.0228 NA 0.0825 False NA ,,, NA NA NA 2504 0.1493 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 1208 1152.99 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 1.2 NA NA NA NA NA ENST00000301439.3:c.15dupT chr19.hg19:g.52097568_52097568dupA ENSP00000301439:p.Phe5fs 9 8 ref NA False 129 129 PASS 8 PASS ref->het 0 NA 920,930 147,147 137,132 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AC018755.1-201 KNOWN basic|appris_principal|exp_conf protein_coding NA protein_coding PASS NA None 1208 NA True - A ENST00000301439.3 ZNF525 170958 __UNKNOWN__ __UNKNOWN__ 19 53886566 53886567 __UNKNOWN__ Intron INS - - ACCTT rs141866835|rs202180915|rs34940021|rs111991162 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr19:53886566_53886567insACCTT ENST00000475179.1 + 4 256 ZNF525_ENST00000467003.1_3'UTR|ZNF525_ENST00000593918.1_Intron|ZNF525_ENST00000474037.1_3'UTR Q8N782 ZN525_HUMAN zinc finger protein 525 NA NA NA regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351) nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700) endometrium(3)|kidney(3)|lung(3) 9 ACTGGAGAGAAACAAGCGTAAT 0.386 NA NA NA 3463 0.691494 0.6853 0.7997 5008 , , NA 21253 0.6131 NA 0.7207 False NA ,,, NA NA NA 2504 0.6738 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 709 669.16 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.97 AB075859 19q13.42 2013-01-16 ENSG00000203326 ENSG00000203326 170958 "Zinc fingers, C2H2-type", "-" 29423 protein-coding gene gene with protein product NA NA 11853319 Standard NR_003699 NR_003699 NA Approved KIAA1979 uc010eqn.3 Q8N782 OTTHUMG00000158277 ENST00000475179.1:c.143-1656->ACCTT chr19.hg19:g.53886566_53886567insACCTT 1 5 ref NA False 90 90 PASS 0 PASS ref->het 0 NA 518,524 114,117 72,72 1 1 Q8TF23 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZNF525-003 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000350553.1 PASS NA None 709 NA True + ACCTT ENST00000475179.1 SIGLEC1 6614 __UNKNOWN__ __UNKNOWN__ 20 3667748 3667749 __UNKNOWN__ 3'UTR INS - - G rs11483963|rs386393131 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:3667748_3667749insG ENST00000344754.4 - 0 6587_6588 SIGLEC1_ENST00000202578.4_3'UTR NM_023068.3 NP_075556.1 Q9BZZ2 SN_HUMAN sialic acid binding Ig-like lectin 1, sialoadhesin NA NA NA cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337) extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886) carbohydrate binding (GO:0030246) NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1) 70 AAAGTTCACCCGCCCCCAACTG 0.559 NA NA NA GG|G|GG|deletion 2401 0.479433 0.534 0.5159 5008 , , NA 18764 0.3492 NA 0.4404 False NA ,,, NA NA NA 2504 0.5542 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 391 387.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.79 AF230073 CCDS13060.1 20p13 2013-01-29 2006-01-19 2006-01-19 ENSG00000088827 ENSG00000088827 6614 "CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing" 11127 protein-coding gene gene with protein product 600751 "sialoadhesin" SN NA 8530048 Standard NM_023068 XM_006723610 NA Approved SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin uc002wja.3 Q9BZZ2 OTTHUMG00000031757 ENST00000344754.4:c.*1459->C chr20.hg19:g.3667749_3667749dupG 2 8 ref NA False 98 98 PASS 1 PASS ref->het 0 NA 293,299 51,51 44,40 2 2 Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7 True hg19 CCDS13060.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SIGLEC1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000077761.2 PASS NA None 391 NA True - G ENST00000344754.4 LINC00493 388789 __UNKNOWN__ __UNKNOWN__ 20 18548294 18548294 __UNKNOWN__ lincRNA DEL C C - rs398088350|rs11475009|rs368112353 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:18548294delC ENST00000608034.1 + 0 150 long intergenic non-protein coding RNA 493 NA NA NA NA GATGAGAGTTCCCCGGGGGTC 0.517 NA NA NA CCCC|CCCC|CCC|deletion 1264 0.252396 0.1868 0.2968 5008 , , NA 15009 0.1399 NA 0.3907 False NA ,,, NA NA NA 2504 0.2832 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 349 355.13 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0.08 20p11.23 2012-10-12 ENSG00000232388 ENSG00000232388 388789 "Long non-coding RNAs" 43430 non-coding RNA RNA, long non-coding NA NA Standard NR_015432 NR_015432 NA Approved uc002wre.4 OTTHUMG00000031978 ENST00000608034.1: chr20.hg19:g.18548294delC 3 4 ref NA False 89 89 PASS 4 PASS ref->het 0 NA 276,278 45,45 25,25 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA LINC00493-003 KNOWN basic lincRNA NA lincRNA OTTHUMT00000472199.1 PASS NA None 349 NA True + C ENST00000608034.1 RIN2 54453 __UNKNOWN__ __UNKNOWN__ 20 19983023 19983023 __UNKNOWN__ 3'UTR DEL T T - rs10715070 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:19983023delT ENST00000255006.6 + 0 4427 RIN2_ENST00000484638.1_3'UTR NM_001242581.1|NM_018993.3 NP_001229510.1|NP_061866.1 Q8WYP3 RIN2_HUMAN Ras and Rab interactor 2 NA NA NA endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264) cytoplasm (GO:0005737) GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083) autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2) 27 TTGTAAATGATTTTTTAAATG 0.299 NA NA NA TTTTTT|TTTTTT|TTTTT|deletion 1123 0.224241 0.2156 0.2867 5008 , , NA 19832 0.121 NA 0.2962 False NA ,,, NA NA NA 2504 0.2239 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 272 279.24 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.11 AB060339 CCDS56182.1 20p11.22 2008-07-30 ENSG00000132669 ENSG00000132669 54453 18750 protein-coding gene gene with protein product 610222 NA 11733506, 1849280, 16423831 Standard NM_018993 NA Approved RASSF4 uc002wro.2 Q8WYP3 OTTHUMG00000031996 ENST00000255006.6:c.*1443T>- chr20.hg19:g.19983023delT 5 6 ref NA False 54 54 PASS 6 PASS ref->het 0 NA 212,213 43,43 15,15 1 1 Q00425|Q5TFT8|Q9BQL3|Q9H071 True hg19 CCDS56182.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RIN2-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000078212.1 PASS NA None 272 NA True + T ENST00000255006.6 CRNKL1 51340 __UNKNOWN__ __UNKNOWN__ 20 20015192 20015193 __UNKNOWN__ 3'UTR INS - - AAAC rs200155428|rs56296396|rs397725179|rs146345717|rs386393496 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:20015192_20015193insAAAC ENST00000536226.1 - 0 3833_3834 CRNKL1_ENST00000377327.4_3'UTR|CRNKL1_ENST00000377340.2_3'UTR Q9BZJ0 CRNL1_HUMAN crooked neck pre-mRNA splicing factor 1 NA NA NA mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245) catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681) poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723) breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6) 45 TCATGCAACATAAACAGATAAT 0.371 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 279 282.14 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.16 AF255443 CCDS33446.1, CCDS63238.1, CCDS63239.1 20p11.2 2013-10-03 2013-10-03 ENSG00000101343 ENSG00000101343 51340 15762 protein-coding gene gene with protein product "SYF3 pre-mRNA-splicing factor" 610952 "crooked neck (Drosophila Crn homolog)-like 1", "Crn, crooked neck-like 1 (Drosophila)", "crooked neck pre-mRNA splicing factor-like 1 (Drosophila)" NA Standard NM_016652 NA Approved CRN, CLF, SYF3, Clf1 uc002wrs.3 Q9BZJ0 OTTHUMG00000032000 ENST00000536226.1:c.*1647->GTTT chr20.hg19:g.20015193_20015196dupAAAC 2 4 ref NA False 41 41 PASS 1 PASS ref->het 0 NA 202,202 43,43 30,30 1 1 A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CRNKL1-007 PUTATIVE basic|appris_principal protein_coding NA protein_coding OTTHUMT00000378075.1 PASS NA None 279 NA True - AAAC ENST00000536226.1 Unknown 0 __UNKNOWN__ __UNKNOWN__ 20 30946139 30946142 __UNKNOWN__ IGR DEL CACT CACT - LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:30946139_30946142delCACT NA KIF3B (23325 upstream) : ASXL1 (12 downstream) NA NA NA NA TCTTCACACACACTCACACACACC 0.618 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 331 306.2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 3.78 NA NA NA NA NA chr20.hg19:g.30946139_30946142delCACT 0 2 ref NA False 187 187 PASS 1 PASS ref->het 0 NA 240,250 46,48 66,54 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 331 NA True CACT C20orf112 0 __UNKNOWN__ __UNKNOWN__ 20 31034031 31034032 __UNKNOWN__ 3'UTR INS - - ATCA rs71299231|rs372923363|rs574826666 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:31034031_31034032insATCA ENST00000359676.5 - 0 2820_2821 NM_001256798.1|NM_080616.4 NP_001243727.1|NP_542183.2 Q96MY1 NOL4L_HUMAN NA NA NA cytoplasm (GO:0005737)|nucleus (GO:0005634) endometrium(3)|kidney(2)|large_intestine(5)|lung(5) 15 AGGAAGTGCCTATCAATCAATC 0.55 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 371 356.36 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.23 NA NA NA NA NA ENST00000359676.5:c.*1368->TGAT chr20.hg19:g.31034036_31034039dupATCA 5 2 ref NA False 31 31 PASS 4 PASS ref->het 0 NA 263,266 49,49 55,55 2 2 Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6 True hg19 CCDS13202.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA C20orf112-001 KNOWN basic|CCDS protein_coding NA protein_coding OTTHUMT00000078628.2 PASS NA None 371 NA True - ATCA ENST00000359676.5 MAP1LC3A 84557 __UNKNOWN__ __UNKNOWN__ 20 33147980 33147987 __UNKNOWN__ 3'UTR DEL CTGCCTGT CTGCCTGT - rs6479|rs78112782|rs112954375|rs8115693|rs75881564 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:33147980_33147987delCTGCCTGT ENST00000360668.3 + 0 1405_1412 MAP1LC3A_ENST00000476428.1_3'UTR|MAP1LC3A_ENST00000397709.1_3'UTR|MAP1LC3A_ENST00000374837.3_3'UTR Q9H492 MLP3A_HUMAN microtubule-associated protein 1 light chain 3 alpha NA NA NA autophagic vacuole assembly (GO:0000045)|mitochondrion degradation (GO:0000422) autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|late endosome (GO:0005770)|microtubule (GO:0005874)|organelle membrane (GO:0031090) phosphatidylethanolamine binding (GO:0008429)|phospholipid binding (GO:0005543) cervix(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(2) 5 TTTTAGGCCCCTGCCTGTCTGCCCATCT 0.668 NA NA NA 1964 0.392173 0.4085 0.598 5008 , , NA 13027 0.4157 NA 0.3857 False NA ,,, NA NA NA 2504 0.2065 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 291 288.89 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 1.06 CCDS13237.1, CCDS13238.1 20q11.22 2014-02-12 ENSG00000101460 ENSG00000101460 84557 6838 protein-coding gene gene with protein product 601242 NA 8833088, 17580304 Standard NM_181509 NM_032514 NA Approved MAP1BLC3, MAP1ALC3, LC3, LC3A, ATG8E uc002xaq.2 Q9H492 OTTHUMG00000032306 ENST00000360668.3:c.*285CTGCCTGT>- chr20.hg19:g.33147980_33147987delCTGCCTGT 0 4 ref NA False 60 60 PASS 1 PASS ref->het 0 NA 250,253 26,26 37,35 1 1 E1P5P4|E1P5P5|Q9BXW5 True hg19 CCDS13238.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAP1LC3A-002 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000078801.2 PASS NA None 291 NA True + CTGCCTGT ENST00000360668.3 RBM39 9584 __UNKNOWN__ __UNKNOWN__ 20 34329910 34329915 __UNKNOWN__ 5'UTR DEL TGCTGC TGCTGC - rs72096088 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:34329910_34329915delTGCTGC ENST00000361162.6 - 0 319_324 RBM39_ENST00000463098.1_5'UTR|RBM39_ENST00000407261.4_5'UTR|RBM39_ENST00000528062.3_5'UTR|RBM39_ENST00000397370.3_5'UTR NM_004902.3|NM_184234.2 NP_004893.1|NP_909122.1 Q14498 RBM39_HUMAN RNA binding motif protein 39 NA NA NA mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351) microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822) breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1) 35 all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676) GGGAAGAGATtgctgctgctgctgct 0.641 NA NA NA 1432 0.285942 0.4418 0.1888 5008 , , NA 16604 0.1835 NA 0.1918 False NA ,,, NA NA NA 2504 0.3466 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 143 135.73 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.8 L10910 CCDS13265.1, CCDS13266.1, CCDS56186.1 20q11.22 2014-07-03 2006-07-11 2006-07-11 ENSG00000131051 ENSG00000131051 9584 "RNA binding motif (RRM) containing" 15923 protein-coding gene gene with protein product "coactivator of activating protein-1 and estrogen receptors", "functional spliceosome-associated protein 59" 604739 "RNA-binding region (RNP1, RRM) containing 2" RNPC2 NA 8227358, 15694343, 21551269 Standard NM_184237 NM_184234 NA Approved CC1.3, HCC1, CAPER, fSAP59, CAPERalpha uc002xeb.3 Q14498 OTTHUMG00000032358 ENST00000361162.6:c.-66GCAGCA>- chr20.hg19:g.34329916_34329921delTGCTGC 6 2 ref NA False 85 85 PASS 8 PASS ref->het 0 NA 97,102 20,20 36,31 1 1 A2RRD3|A5D8W2|B0BLV3|E1P5S0|E1P5S1|Q14499 True hg19 CCDS13265.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA RBM39-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000078930.2 PASS NA None 143 NA True - TGC ENST00000361162.6 Unknown 0 __UNKNOWN__ __UNKNOWN__ 20 49411366 49411367 __UNKNOWN__ IGR INS - - A rs145015809 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:49411366_49411367insA NA PARD6B (38034 upstream) : BCAS4 (63 downstream) NA NA NA NA ctgccatctgcaagcgagtttg 0.624 NA NA NA AA|AA|AAA|insertion 791 0.157947 0.093 0.1585 5008 , , NA 9140 0.1458 NA 0.1968 False NA ,,, NA NA NA 2504 0.2178 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 205 188.17 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001628 intergenic_variant 0.4 NA NA NA NA NA chr20.hg19:g.49411368_49411368dupA 3 2 ref NA False 98 98 PASS 2 PASS ref->het 0 NA 146,147 37,38 19,18 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 PASS NA None 205 NA True A AC005220.3 0 __UNKNOWN__ __UNKNOWN__ 20 52557950 52557951 __UNKNOWN__ RNA INS - - TTGTGTGTGCGCGC rs78057394|rs141488543|rs2870294 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr20:52557950_52557951insTTGTGTGTGCGCGC ENST00000450473.1 + 0 550 NA NA NA NA tgtgtgtgtgtgtgtgtgcgcg 0.505 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 238 265.67 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 3.03 NA NA NA NA NA ENST00000450473.1: chr20.hg19:g.52557950_52557951insTTGTGTGTGCGCGC 1 2 ref NA False 54 54 PASS 0 PASS ref->het 0 NA 177,186 30,33 52,46 1 1 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AC005220.3-001 KNOWN basic|exp_conf antisense NA antisense OTTHUMT00000079763.1 PASS NA None 238 NA True + TTGTGTGTGCGCGC ENST00000450473.1 GRIK1 2897 __UNKNOWN__ __UNKNOWN__ 21 30909636 30909645 __UNKNOWN__ Frame_Shift_Del DEL TTTTTCTTTA TTTTTCTTTA - rs116002269 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:30909636_30909645delTTTTTCTTTA ENST00000389125.3 - 16 2748_2757 c.2624_2633delTAAAGAAAAA c.(2623-2634)ataaagaaaaagfs p.IKKK875fs GRIK1_ENST00000399913.1_Frame_Shift_Del_p.IKKK890fs|GRIK1_ENST00000535441.1_Frame_Shift_Del_p.IKKK892fs|GRIK1_ENST00000399914.1_Frame_Shift_Del_p.IKKK904fs|GRIK1_ENST00000327783.4_Frame_Shift_Del_p.IKKK919fs NM_175611.2 NP_783300.1 P39086 GRIK1_HUMAN glutamate receptor, ionotropic, kainate 1 0 NA NA adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810) cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734) extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277) p.K876N(1) NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1) 45 Topiramate(DB00273) AGTTCTTGACTTTTTCTTTATTTTTTTCTG 0.405 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 1 Substitution - Missense(1) lung(1) NA NA NA NA NA 194 196.91 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001589 frameshift_variant 0.04 CCDS33530.1, CCDS42913.1 21q22 2012-08-29 ENSG00000171189 ENSG00000171189 2897 "Ligand-gated ion channels / Glutamate receptors, ionotropic", "Glutamate receptors" 4579 protein-coding gene gene with protein product 138245 GLUR5 NA 8468067 Standard XM_005260942 NA Approved GluK1 uc002yno.1 P39086 OTTHUMG00000078879 ENST00000389125.3:c.2624_2633delTAAAGAAAAA chr21.hg19:g.30909636_30909645delTTTTTCTTTA ENSP00000373777:p.Ile875fs 0 10 ref NA False 35 35 PASS 1 PASS ref->het 0 NA 134,134 39,40 23,23 1 1 Q13001|Q86SU9 True hg19 CCDS33530.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA GRIK1-001 KNOWN basic|appris_candidate|CCDS protein_coding NA protein_coding OTTHUMT00000171978.1 PASS NA None 194 NA True - TTTTTCTTTA ENST00000389125.3 PSMG1 8624 __UNKNOWN__ __UNKNOWN__ 21 40555616 40555617 __UNKNOWN__ 5'UTR INS - - GG rs34006192|rs563523008|rs146767384|rs386394756 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:40555616_40555617insGG ENST00000331573.3 - 0 160_161 NM_001261824.1|NM_003720.3 NP_001248753.1|NP_003711.1 O95456 PSMG1_HUMAN proteasome (prosome, macropain) assembly chaperone 1 NA NA NA cerebellar granule cell precursor proliferation (GO:0021930)|proteasome assembly (GO:0043248)|proteasome core complex assembly (GO:0080129) cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634) autonomic_ganglia(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2) 8 Prostate(19;8.44e-08) agattgggggagggggtctcgc 0.594 NA NA NA OREG0003859 type=REGULATORY REGION|Gene=DSCR2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay 767 0.153155 0.0794 0.2061 5008 , , NA 14084 0.0367 NA 0.3151 False NA ,,, NA NA NA 2504 0.1687 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 88 104.37 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.68 AJ006291 CCDS13660.1, CCDS13661.1 21q22.3 2007-10-23 2007-10-23 2007-10-23 ENSG00000183527 ENSG00000183527 8624 3043 protein-coding gene gene with protein product 605296 "Down syndrome critical region gene 2" DSCR2 NA 10872820, 17189198 Standard NM_003720 NM_003720 NA Approved c21-LRP, LRPC21, PAC1 uc002yxi.4 O95456 OTTHUMG00000066034 ENST00000331573.3:c.-306->CC chr21.hg19:g.40555619_40555620dupGG 7 10 ref 894 False 30 30 PASS 5 PASS ref->het 0 NA 66,68 10,10 10,10 1 1 B5BUN2|Q6FHA3|Q6FHD3|Q6S713 True hg19 CCDS13660.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PSMG1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000141404.2 PASS NA None 88 NA True - G ENST00000331573.3 BRWD1 54014 __UNKNOWN__ __UNKNOWN__ 21 40558600 40558604 __UNKNOWN__ 3'UTR DEL TTCAC TTCAC - rs201318348|rs72527929|rs71330348 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:40558600_40558604delTTCAC ENST00000333229.2 - 0 7638_7642 NM_018963.4 NP_061836.2 Q9NSI6 BRWD1_HUMAN bromodomain and WD repeat domain containing 1 NA NA NA cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleus (GO:0005634) cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2) 58 Prostate(19;8.44e-08)|all_epithelial(19;0.223) TTGAAATTTGTTCACTTCAAGTTCT 0.366 NA NA NA 1051 0.209864 0.2852 0.2147 5008 , , NA 20465 0.0367 NA 0.3131 False NA ,,, NA NA NA 2504 0.1769 NA NA NA Melanoma(170;988 1986 4794 16843 39731) PASS NA NA NA 0 NA NA NA NA NA 194 195.4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 AJ002572 CCDS13662.1, CCDS13663.1, CCDS33557.1 21q22.2 2013-05-21 2005-05-13 2005-05-13 ENSG00000185658 ENSG00000185658 54014 "WD repeat domain containing" 12760 protein-coding gene gene with protein product NA "chromosome 21 open reading frame 107", "WD repeat domain 9" C21orf107, WDR9 NA Standard NM_033656 NM_033656 NA Approved FLJ11315, N143 uc002yxk.2 Q9NSI6 OTTHUMG00000066030 ENST00000333229.2:c.*352GTGAA>- chr21.hg19:g.40558600_40558604delTTCAC 0 5 ref NA False 30 30 PASS 1 PASS ref->het 0 NA 164,165 15,15 24,23 1 1 C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1 True hg19 CCDS13662.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BRWD1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000141398.3 PASS NA None 194 NA True - TTCAC ENST00000333229.2 COL6A2 1292 __UNKNOWN__ __UNKNOWN__ 21 47546390 47546391 __UNKNOWN__ Intron INS - - GGCCCGGCCCGGCCC rs371824276|rs370256484|rs200215200|rs138363207 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr21:47546390_47546391insGGCCCGGCCCGGCCC ENST00000300527.4 + 27 2526 COL6A2_ENST00000409416.1_Intron|COL6A2_ENST00000310645.5_Intron|COL6A2_ENST00000397763.1_Intron|COL6A2_ENST00000357838.4_Intron NM_001849.3 NP_001840.3 P12110 CO6A2_HUMAN collagen, type VI, alpha 2 NA NA NA axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749) collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982) NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1) 43 Breast(49;0.245) Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649) GACCCTGGCCTGGCCCGGCCTC 0.649 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 302 303.9 NA ,, 0,91,243,3930 NA 0,0,0,0,0,9,82,10,214,1817 NA NA NA ,, -2.5 0 NA dbSNP_134 72 6,717,6,7523 NA 0,1,0,5,25,0,666,0,6,3423 no intron,intron,intron COL6A2 NM_058175.2,NM_058174.2,NM_001849.3 ,, 0,1,0,5,25,9,748,10,220,5240 A1A1,A1A2,A1A3,A1R,A2A2,A2A3,A2R,A3A3,A3R,RR NA 8.8342,7.833,8.4931 ,, ,, NA 6,808,249,11453 NA NA NA SO:0001627 intron_variant 0 M20777 CCDS13728.1, CCDS13729.1, CCDS13730.1 21q22.3 2014-09-17 ENSG00000142173 ENSG00000142173 1292 "Collagens" 2212 protein-coding gene gene with protein product 120240 NA Standard NM_001849 NA Approved uc002zia.1 P12110 OTTHUMG00000090489 ENST00000300527.4:c.2423-26->GGCCCGGCCCGGCCC chr21.hg19:g.47546390_47546391insGGCCCGGCCCGGCCC 4 2 ref NA False 38 38 PASS 1 PASS ref->het 0 NA 206,208 32,33 67,66 1 1 Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8 True hg19 CCDS13728.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA COL6A2-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000206971.1 PASS NA None 302 NA True + GGCCC ENST00000300527.4 DGCR2 9993 __UNKNOWN__ __UNKNOWN__ 22 19109747 19109748 __UNKNOWN__ 5'UTR INS - - GCTGCGTGACCCC LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:19109747_19109748insGCTGCGTGACCCC ENST00000263196.7 - 0 219_220 AC004471.9_ENST00000456035.1_RNA|DGCR2_ENST00000545799.1_5'UTR|DGCR2_ENST00000537045.1_5'UTR NM_001184781.1|NM_005137.2 NP_001171710.1|NP_005128.1 P98153 IDD_HUMAN DiGeorge syndrome critical region gene 2 NA NA NA cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887) integral component of membrane (GO:0016021) carbohydrate binding (GO:0030246) breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1) 18 Colorectal(54;0.0993) TCCCCGGGGCGGCTGGAAGGCC 0.693 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 253 249.73 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.92 D79985 CCDS33598.1, CCDS54496.1 22q11.21 2008-06-12 ENSG00000070413 ENSG00000070413 9993 2845 protein-coding gene gene with protein product "integral membrane protein DGCR2" 600594 NA 7655455, 8630060 Standard NM_005137 NM_005137 NA Approved KIAA0163, LAN, IDD, DGS-C, SEZ-12 uc002zoq.1 P98153 OTTHUMG00000150141 ENST00000263196.7:c.-29->GGGGTCACGCAGC chr22.hg19:g.19109747_19109748insGCTGCGTGACCCC 1 6 ref NA False 58 58 PASS 0 PASS ref->het 0 NA 201,202 9,9 40,39 1 1 A6NIB5|A8K6K5|B5TY34|B7Z935 True hg19 CCDS33598.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA DGCR2-001 KNOWN non_canonical_conserved|basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000316504.1 PASS NA None 253 NA True - GCTGCGTGACCCC ENST00000263196.7 CDC42EP1 11135 __UNKNOWN__ __UNKNOWN__ 22 37964409 37964429 __UNKNOWN__ In_Frame_Del DEL CAGCGCCTGCTGCAAACCCCT CAGCGCCTGCTGCAAACCCCT - rs13056859|rs13055845|rs77417880|rs62235033|rs62235034|rs187761157|rs66468174|rs200195385 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:37964409_37964429delCAGCGCCTGCTGCAAACCCCT ENST00000249014.4 + 3 1178_1198 c.758_778delCAGCGCCTGCTGCAAACCCCT c.(757-780)ccagcgcctgctgcaaacccctca>cca p.APAANPS254del NM_152243.2 NP_689449.1 Q00587 BORG5_HUMAN CDC42 effector protein (Rho GTPase binding) 1 254 8 X 7 AA tandem repeats of [PT]-[AT]-A- [ENT]-[PT]-[PTS]-[AG]. NA NA positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266) actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886) p.N258_A264delNPSAPAA(3) endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5) 15 Melanoma(58;0.0574) GCAAACCCCCCAGCGCCTGCTGCAAACCCCTCAGCACCTGC 0.665 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 3 Deletion - In frame(3) large_intestine(2)|haematopoietic_and_lymphoid_tissue(1) NA NA NA NA NA 96 106.14 NA 868,3338 NA 98,672,1333 NA NA NA 1.5 0 NA dbSNP_130 10 4310,3696 NA 1298,1714,991 no coding CDC42EP1 NM_152243.2 1396,2386,2324 A1A1,A1R,RR NA 46.1654,20.6372,42.4009 NA 5178,7034 NA NA NA SO:0001651 inframe_deletion 2.6 M88338 CCDS13949.1 22q13.1 2008-06-11 ENSG00000128283 ENSG00000128283 11135 17014 protein-coding gene gene with protein product "55 kDa bone marrow stromal/endothelial cell protein", "serum constituent protein" 606084 NA 1629197, 10430899 Standard NM_152243 NM_152243 NA Approved MSE55, CEP1, Borg5 uc003asz.4 Q00587 OTTHUMG00000150591 ENST00000249014.4:c.758_778delCAGCGCCTGCTGCAAACCCCT chr22.hg19:g.37964409_37964429delCAGCGCCTGCTGCAAACCCCT ENSP00000249014:p.Ala254_Ser260del 0 6 ref NA False 69 69 PASS 1 PASS ref->het 0 NA 83,85 28,29 18,18 1 1 A8K825|Q96GN1 True hg19 CCDS13949.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CDC42EP1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000318993.1 PASS NA None 96 NA True + CAGCGCCTGCTGCAAACCCCT ENST00000249014.4 MKL1 57591 __UNKNOWN__ __UNKNOWN__ 22 40806939 40806940 __UNKNOWN__ 3'UTR INS - - G rs368523135|rs398101769|rs1543322|rs150999789|rs5845460 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:40806939_40806940insG ENST00000402042.1 - 0 3696_3697 MKL1_ENST00000407029.1_3'UTR|MKL1_ENST00000396617.3_3'UTR|MKL1_ENST00000355630.3_3'UTR NM_001282661.1 NP_001269590.1 Q969V6 MKL1_HUMAN megakaryoblastic leukemia (translocation) 1 NA NA NA negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351) cytoplasm (GO:0005737)|nucleus (GO:0005634) actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976) breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1) 30 ACACAGGGAATAGGGGGTAGAG 0.51 NA NA T RBM15 acute megakaryocytic leukemia NA -|-|G|insertion 791 0.157947 0.0212 0.4107 5008 , , NA 16298 0.249 NA 0.1213 False NA ,,, NA NA NA 2504 0.1074 NA NA NA PASS Dom yes 22 22q13 57591 megakaryoblastic leukemia (translocation) 1 NA L 0 NA NA NA NA NA 129 136.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.47 AB037859 CCDS14003.1, CCDS74865.1, CCDS74866.1 22q13 2008-06-12 ENSG00000196588 ENSG00000196588 57591 14334 protein-coding gene gene with protein product "megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain" 606078 NA 11431691, 12019265, 14970199 Standard NM_020831 XM_005261692 NA Approved KIAA1438, MAL, MRTF-A, BSAC uc003ayw.1 Q969V6 OTTHUMG00000151146 ENST00000402042.1:c.*455->C chr22.hg19:g.40806939_40806940insG 1 5 ref NA False 37 37 PASS 0 PASS ref->het 0 NA 89,91 22,22 16,16 1 1 Q8TCL1|Q96SC5|Q96SC6|Q9P2B0 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MKL1-002 NOVEL basic|exp_conf protein_coding NA protein_coding OTTHUMT00000321523.1 PASS NA None 129 NA True - G ENST00000402042.1 POLDIP3 84271 __UNKNOWN__ __UNKNOWN__ 22 42980417 42980418 __UNKNOWN__ 3'UTR INS - - C rs137084|rs199670274|rs143045108|rs201936394 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:42980417_42980418insC ENST00000252115.5 - 0 2749_2750 POLDIP3_ENST00000348657.2_3'UTR NM_032311.3 NP_115687.2 Q9BY77 PDIP3_HUMAN polymerase (DNA-directed), delta interacting protein 3 NA NA NA poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727) cytoplasm (GO:0005737)|nuclear speck (GO:0016607) nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822) biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1) 16 CTCTGGTTTTTTTCACTGGGCT 0.53 NA NA NA |||unknown(NO_COVERAGE) 2968 0.592652 0.8722 0.4035 5008 , , NA 19783 0.7659 NA 0.3002 False NA ,,, NA NA NA 2504 0.4714 NA NA NA Ovarian(52;967 1128 5875 19997 42537) PASS NA NA NA 0 NA NA NA NA NA 125 115.57 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.72 CCDS14038.1, CCDS14039.1, CCDS74873.1 22q13.31 2013-02-12 ENSG00000100227 ENSG00000100227 84271 "RNA binding motif (RRM) containing" 23782 protein-coding gene gene with protein product 611520 NA 12522211 Standard NM_032311 NM_032311 NA Approved PDIP46, KIAA1649 uc003bcu.3 Q9BY77 OTTHUMG00000150887 ENST00000252115.5:c.*1380->G chr22.hg19:g.42980417_42980418insC 1 7 ref NA False 48 48 PASS 0 PASS ref->het 0 NA 92,95 22,22 10,7 1 1 A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6 True hg19 CCDS14038.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA POLDIP3-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000320433.1 PASS NA None 125 NA True - C ENST00000252115.5 TTLL12 23170 __UNKNOWN__ __UNKNOWN__ 22 43576075 43576075 __UNKNOWN__ Intron DEL A A - rs376045650|rs111515672 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:43576075delA ENST00000216129.6 - 4 610 NM_015140.3 NP_055955.1 Q14166 TTL12_HUMAN tubulin tyrosine ligase-like family, member 12 NA NA NA cellular protein modification process (GO:0006464) central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1) 13 Ovarian(80;0.221)|Glioma(61;0.222) TCCGGAACCCAGACATCGACC 0.587 NA NA NA 592 0.118211 0.0877 0.0346 5008 , , NA 17469 0.2946 NA 0.0527 False NA ,,, NA NA NA 2504 0.1043 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 320 326.52 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001627 intron_variant 0.81 D63487 CCDS14047.1 22q13.31 2013-02-14 2006-02-02 ENSG00000100304 ENSG00000100304 23170 "Tubulin tyrosine ligase-like family" 28974 protein-coding gene gene with protein product NA NA 15890843 Standard NM_015140 NM_015140 NA Approved KIAA0153 uc003bdp.3 Q14166 OTTHUMG00000150682 ENST00000216129.6:c.547-69T>- chr22.hg19:g.43576075delA 0 3 ref NA False 56 56 PASS 1 PASS ref->het 0 NA 224,225 55,56 36,36 1 1 Q20WK5|Q9UGU3 True hg19 CCDS14047.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TTLL12-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000319611.1 PASS NA None 320 NA True - A ENST00000216129.6 NUP50 10762 __UNKNOWN__ __UNKNOWN__ 22 45580569 45580570 __UNKNOWN__ 3'UTR INS - - TT rs369753596 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:45580569_45580570insTT ENST00000347635.4 + 0 1906_1907 NUP50_ENST00000407019.2_3'UTR|NUP50_ENST00000396096.2_3'UTR|NUP50_ENST00000425733.2_3'UTR NM_007172.3 NP_009103.2 Q9UKX7 NUP50_HUMAN nucleoporin 50kDa NA NA NA carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intracellular transport (GO:0046907)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032) nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634) endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1) 9 Ovarian(80;0.00965)|all_neural(38;0.0244) UCEC - Uterine corpus endometrioid carcinoma (28;0.0178) TTATTGCCAAGTTGCTGCTGCT 0.406 NA NA NA 1323 0.264177 0.1551 0.3401 5008 , , NA 17413 0.2778 NA 0.2823 False NA ,,, NA NA NA 2504 0.3252 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 344 307.76 NA , 677,3577 NA 65,547,1515 NA NA NA , 0.3 0 NA 25 2264,5956 NA 404,1456,2250 no utr-3,utr-3 NUP50 NM_153645.2,NM_007172.3 , 469,2003,3765 A1A1,A1R,RR NA 27.5426,15.9144,23.577 , , NA 2941,9533 NA NA NA SO:0001624 3_prime_UTR_variant 1.46 AF107840 CCDS14062.1, CCDS14063.1 22q13.3 2007-01-22 2002-08-29 ENSG00000093000 ENSG00000093000 10762 8065 protein-coding gene gene with protein product 604646 "nucleoporin 50kD" NPAP60L NA 10449902 Standard XM_005261312 NA Approved uc003bfr.3 Q9UKX7 OTTHUMG00000151265 ENST00000347635.4:c.*34->TT chr22.hg19:g.45580570_45580571dupTT 4 2 ref NA False 62 62 PASS 2 PASS ref->het 0 NA 272,275 37,37 34,33 1 1 B1AHA4|B2RB15|O75644|Q8N6V5|Q9NPM9|Q9NPR6|Q9P1K5 True hg19 CCDS14062.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NUP50-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000321993.2 PASS NA None 344 NA True + T ENST00000347635.4 FBLN1 2192 __UNKNOWN__ __UNKNOWN__ 22 45929595 45929595 __UNKNOWN__ Intron DEL G G - rs3216851 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:45929595delG ENST00000262722.7 + 7 749 FBLN1_ENST00000348697.2_Intron|FBLN1_ENST00000442170.2_Intron|FBLN1_ENST00000327858.6_Intron|FBLN1_ENST00000402984.3_Intron|FBLN1_ENST00000340923.5_Intron NM_001996.3 NP_001987 P23142 FBLN1_HUMAN fibulin 1 NA NA NA embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032) basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578) calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504) biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1) 30 Ovarian(80;0.00965)|all_neural(38;0.0416) UCEC - Uterine corpus endometrioid carcinoma (28;0.0182) GTATTAGGATGGGTCGTTCTT 0.567 NA NA NA GGG|GGG|GG|deletion 1367 0.272963 0.2405 0.1499 5008 , , NA 19728 0.4861 NA 0.1769 False NA ,,, NA NA NA 2504 0.2832 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 135 133.83 NA ,,, 1004,3258 NA 123,758,1250 35 37 36 ,,, -0.7 0 22 dbSNP_134 43 1366,6888 NA 129,1108,2890 no intron,intron,intron,intron FBLN1 NM_006487.2,NM_006486.2,NM_006485.3,NM_001996.3 ,,, 252,1866,4140 A1A1,A1R,RR NA 16.5496,23.557,18.9358 ,,, ,,, 45929595 2370,10146 2174 4264 6438 SO:0001627 intron_variant 0.49 CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1 22q13.31 2010-06-15 ENSG00000077942 ENSG00000077942 2192 "Fibulins" 3600 protein-coding gene gene with protein product 135820 NA 2269669, 1400330 Standard NM_006486 NM_006485 NA Approved FBLN uc003bgj.1 P23142 OTTHUMG00000151340 ENST00000262722.7:c.647-46G>- chr22.hg19:g.45929595delG 2 3 ref NA False 76 76 PASS 3 PASS ref->het 0 NA 96,102 27,27 13,8 2 2 B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41 True hg19 CCDS14069.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA FBLN1-003 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000322289.1 PASS NA None 135 NA True + G ENST00000262722.7 ZBED4 9889 __UNKNOWN__ __UNKNOWN__ 22 50277240 50277240 __UNKNOWN__ 5'UTR DEL G G - rs66694531|rs190460964 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:50277240delG ENST00000216268.5 + 0 407 NM_014838.2 NP_055653.2 O75132 ZBED4_HUMAN zinc finger, BED-type containing 4 NA NA NA cytoplasm (GO:0005737)|nucleus (GO:0005634) DNA binding (GO:0003677)|metal ion binding (GO:0046872) breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1) 44 all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164) UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247) ATCTACATTCGGGGGCACAAA 0.358 NA NA NA GGGGG|GGGGG|GGGG|deletion 874 0.174521 0.5303 0.0605 5008 , , NA 21966 0.0675 NA 0.0199 False NA ,,, NA NA NA 2504 0.044 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 163 165.78 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.48 AB014537 CCDS33677.1 22q13.33 2013-05-03 ENSG00000100426 ENSG00000100426 9889 "Zinc fingers, BED-type" 20721 protein-coding gene gene with protein product 612552 NA 23533661 Standard NM_014838 NM_014838 NA Approved KIAA0637 uc003bix.2 O75132 OTTHUMG00000150291 ENST00000216268.5:c.-71G>- chr22.hg19:g.50277240delG 4 5 ref NA False 31 31 PASS 5 PASS ref->het 0 NA 127,128 23,23 21,20 1 1 B2RZH1|Q1ECU0|Q9UGG8 True hg19 CCDS33677.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ZBED4-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000317408.2 PASS NA None 163 NA True + G ENST00000216268.5 MLC1 23209 __UNKNOWN__ __UNKNOWN__ 22 50498030 50498031 __UNKNOWN__ 3'UTR INS - - C rs145385166 byFrequency LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chr22:50498030_50498031insC ENST00000311597.5 - 0 3721_3722 MLC1_ENST00000395876.2_3'UTR NM_015166.3 NP_055981.1 Q15049 MLC1_HUMAN megalencephalic leukoencephalopathy with subcortical cysts 1 NA NA NA caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192) apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037) protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215) endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3) 18 all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113) READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216) ACATCAGCCCGCCCCGGGTCGT 0.594 NA NA NA CCCC|CCCC|CCCCC|insertion 662 0.132188 0.059 0.1888 5008 , , NA 12856 0.0863 NA 0.1322 False NA ,,, NA NA NA 2504 0.2382 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 262 248.43 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0.79 D25217 CCDS14083.1 22q13.33 2007-03-20 ENSG00000100427 ENSG00000100427 23209 17082 protein-coding gene gene with protein product 605908 NA 7584026, 7584028 Standard NM_015166 XR_430476 NA Approved MLC, KIAA0027, LVM, VL uc003bjg.1 Q15049 OTTHUMG00000150236 ENST00000311597.5:c.*1982->G chr22.hg19:g.50498034_50498034dupC 5 7 ref NA False 50 49 PASS 4 PASS ref->het 0 NA 194,195 49,50 22,21 1 1 B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8 True hg19 CCDS14083.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA MLC1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000316979.2 PASS NA None 262 NA True - C ENST00000311597.5 ERCC6L 54821 __UNKNOWN__ __UNKNOWN__ X 71458793 71458794 __UNKNOWN__ 5'UTR INS - - GGAGTTT rs202000886 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:71458793_71458794insGGAGTTT ENST00000373657.1 - 0 83_84 ERCC6L_ENST00000334463.3_5'UTR|PIN4_ENST00000423432.2_Intron Q2NKX8 ERC6L_HUMAN excision repair cross-complementation group 6-like NA NA NA mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067) cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020) ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386) breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1) 38 Renal(35;0.156) TTACCCCGGCGggagtttggag 0.599 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA PASS NA NA NA 0 NA NA NA NA NA 509 473.95 NA , 624,3049 NA 9,550,56,1021,457 NA NA NA , -5.4 0 NA 20 327,6047 NA 9,235,74,2088,1636 no utr-5,intron PIN4,ERCC6L NM_017669.2,NM_001170747.1 , 18,785,130,3109,2093 A1A1,A1R,A1,RR,R NA 5.1302,16.9888,9.4655 , , NA 951,9096 NA NA NA SO:0001623 5_prime_UTR_variant 0.16 AK000112 CCDS35329.1 Xq13.1 2014-03-07 2014-03-07 ENSG00000186871 ENSG00000186871 54821 20794 protein-coding gene gene with protein product "PLK1-interacting checkpoint helicase" 300687 "excision repair cross-complementing rodent repair deficiency, complementation group 6-like" NA 17218258 Standard NM_017669 NM_017669 NA Approved FLJ20105, PICH, RAD26L uc004eaq.1 Q2NKX8 OTTHUMG00000021810 ENST00000373657.1:c.-520->AAACTCC chrX.hg19:g.71458794_71458800dupGGAGTTT 2 5 ref NA False 49 49 PASS 1 PASS ref->het 0 NA 378,380 51,51 72,71 1 1 Q8NCI1|Q96H93|Q9NXQ8 True hg19 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ERCC6L-001 PUTATIVE basic|exp_conf protein_coding NA protein_coding OTTHUMT00000057173.1 PASS NA None 509 NA True - GGAGTTT ENST00000373657.1 IL13RA1 3597 __UNKNOWN__ __UNKNOWN__ X 117926720 117926721 __UNKNOWN__ 3'UTR INS - - ATG rs111653614|rs72012187 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:117926720_117926721insATG ENST00000371666.3 + 0 2254_2255 NM_001560.2 NP_001551.1 P78552 I13R1_HUMAN interleukin 13 receptor, alpha 1 NA NA NA cell surface receptor signaling pathway (GO:0007166)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin production (GO:0002639) interleukin-13 receptor complex (GO:0005898)|plasma membrane (GO:0005886) interleukin-13 receptor activity (GO:0016515) endometrium(2)|kidney(1)|large_intestine(2)|lung(7) 12 CAGTGTTGGCCATGATGACAAC 0.426 NA NA NA 935 0.247682 0.0401 0.3112 3775 , , NA 14645 0.3284 NA 0.1252 False NA ,,, NA NA NA 2504 0.2137 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 189 170.55 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001624 3_prime_UTR_variant 0 U62858 CCDS14573.1 Xq24 2008-02-05 ENSG00000131724 ENSG00000131724 3597 "Interleukins and interleukin receptors", "CD molecules" 5974 protein-coding gene gene with protein product "IL13 receptor alpha-1 chain", "CD213a1 antigen" 300119 NA 8910586, 9013879 Standard NM_001560 NM_001560 NA Approved IL-13Ra, NR4, CD213a1 uc004eqs.3 P78552 OTTHUMG00000022258 ENST00000371666.3:c.*904->ATG chrX.hg19:g.117926724_117926726dupATG 3 2 ref NA False 35 35 PASS 2 PASS ref->het 0 NA 150,152 20,20 20,20 1 1 O95646|Q5JSL4|Q99656|Q9UDY5 True hg19 CCDS14573.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA IL13RA1-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000058009.1 PASS NA None 189 NA True + ATG ENST00000371666.3 ARHGEF6 9459 __UNKNOWN__ __UNKNOWN__ X 135864093 135864095 __UNKNOWN__ 5'UTR DEL CAA CAA - rs201033020 LTS-041_T LTS-041_N __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ TUMOR TUMOR g.chrX:135864093_135864095delCAA ENST00000250617.6 - 0 152_154 NM_004840.2 NP_004831.1 Q15052 ARHG6_HUMAN Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 NA NA NA apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264) cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027) GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089) cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1) 38 Acute lymphoblastic leukemia(192;0.000127) CTTATTTTCCCAACAACAACAAC 0.31 NA NA NA 23 0.00609272 8e-04 0.0043 3775 , , NA 19327 0 NA 0.0109 False NA ,,, NA NA NA 2504 0.0082 NA NA NA PASS NA NA NA 0 NA NA NA NA NA 198 181.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA SO:0001623 5_prime_UTR_variant 0.37 D13631 CCDS14660.1 Xq26 2013-01-10 2002-05-23 ENSG00000129675 ENSG00000129675 9459 "Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing" 685 protein-coding gene gene with protein product "Rac/Cdc42 guanine exchange factor (GEF) 6", "PAK-interacting exchange factor, alpha", "rho guanine nucleotide exchange factor 6" 300267 "mental retardation, X-linked 46" MRX46 NA 7584048, 9659915 Standard NM_004840 NM_004840 NA Approved alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2 uc004fab.3 Q15052 OTTHUMG00000022518 ENST00000250617.6:c.-1054TTG>- chrX.hg19:g.135864102_135864104delCAA 5 4 ref NA False 35 35 PASS 6 PASS ref->het 0 NA 155,156 19,21 26,25 1 1 A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0 True hg19 CCDS14660.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ARHGEF6-001 KNOWN basic|appris_principal|CCDS protein_coding NA protein_coding OTTHUMT00000058511.2 PASS NA None 198 NA True - CAA ENST00000250617.6