Table 1. Homozygous variants that putatively affect protein function and are absent in the 1000 Genomes and the ESP5400a.
| Gene nameb | Change type | AA impactc | Unique identifierd | SNP ide | SIFT scoref | Polypheng | Accession #h | Cell lines in which variants occur |
| TP53 | SpliceSence | - | chr17:7577610_T_C | - | NA | NA | NM_001126114 | LC:HOP_62 |
| MLH1 | SpliceSence | - | chr3:37038108_A_T | - | NA | NA | NM_000249 | PR:DU_145 |
| FANCM | SpliceSence | - | chr14:45628296_*_-TA | - | NA | NA | null | ME:LOXIMVI |
| TRAF1 | SpliceSence | - | chr9:123667518_T_G | - | NA | NA | NM_005658 | LC:EKVX |
| FLT3 | SpliceSence | - | chr13:28622411_C_A | - | NA | NA | NM_004119 | LC:NCI_H322M |
| RB1 | Frameshift | 116_117del | chr13:48916816_*_-ACTT | - | NA | NA | NM_000321 | CNS:SF_539 |
| APC | Frameshift | G1398fs | chr5:112175539_*_-C | - | NA | NA | NM_001127511 | CO:HCT_15 |
| PTEN | Frameshift | K267fs | chr10:89717775_*_-A | rs121913289 | NA | NA | NM_000314 | LE:MOLT_4 |
| VHL | Frameshift | G104fs | chr3:10183842_*_-G | - | NA | NA | NM_000551 | RE:786_0 |
| CASP10 | Frameshift | 334_336del | chr2:202074072_*_-GCCAAGG | - | NA | NA | NM_001206524 | BR:BT_549 |
| SMAD4 | Premature Stop | Q311X | chr18:48586262_C_T | - | 0.35 | 0.735 | NM_005359 | CO:HT29 |
| CDKN2A | Premature Stop | R80X | chr9:21971120_G_A | rs121913388 | 0.84 | 0.737 | NM_000077 | LE:HL_60 |
| MAP3K5 | Premature Stop | S1240X | chr6:136888811_G_C | - | 0.04 | 0.735 | NM_005923 | LC:NCI_H322M |
| CDH4 | Premature Stop | Q383X | chr20:60485547_C_T | - | 0.13 | 0.735 | NM_001252338 | LC:NCI_H322M |
| NF2 | Premature Stop | R57X | chr22:30032794_C_T | rs121434259 | 1 | 0.735 | NM_000268 | RE:ACHN |
| ABCB1 | SIFT and PolyPhen | A1217T | chr7:87133753_C_T | - | 0.00 | 0.968 | NM_000927 | ME:SK_MEL_28 |
| ABL1 | SIFT and PolyPhen | K7R | chr9:133589726_A_G | - | 0.00 | 0.956 | NM_007313 | BR:HS578T |
| AXL | SIFT and PolyPhen | H292Q | chr19:41743941_T_A | - | 0.05 | 0.992 | NM_001699 | OV:OVCAR_8;OV:NCI_ADR_RES |
| EGFR | SIFT and PolyPhen | P753S | chr7:55242487_C_T | rs121913231 | 0.00 | 0.996 | NM_005228 | ME:SK_MEL_28 |
| KRAS | SIFT and PolyPhen | G12V | chr12:25398284_C_A | rs121913529 | 0.01 | 0.91 | NM_004985 | CO:SW_620;OV:OVCAR_5 |
| NRAS | SIFT and PolyPhen | Q61L | chr1:115256529_T_A | rs11554290 | 0.00 | 0.868 | NM_002524 | LE:HL_60 |
| PIK3R2 | SIFT and PolyPhen | N561D | chr19:18278061_A_G | - | 0.02 | 0.991 | NM_005027 | ME:LOXIMVI |
| TDP1 | SIFT and PolyPhen | K292E | chr14:90446966_A_G | - | 0.00 | 0.999 | NM_001008744 | LC:NCI_H522 |
| BRAF | SIFT | V600E | chr7:140453136_A_T | rs113488022 | 0.00 | 0.796 | NM_004333 | ME:SK_MEL_28;ME:UACC_62 |
| WT1 | SIFT | S204R | chr11:32456280_G_T | - | 0.00 | 0.023 | NM_000378 | PR:DU_145 |
Variants called as homozygous by Annovar (http://www.openbioinformatics.org/annovar/). Variants absent in both the 1000 Genomes catalog of human genetic variation (http://www.1000genomes.org/) and the ESP5400 (http://evs.gs.washington.edu/EVS/).
Official gene names as defined by the HUGO Gene Nomenclature Committee (http://www.genenames.org/).
Amino acid impact. 116_117del indicates a deletion affecting amino acids 116 and 117. G13981fs indicates a change from an amino acid to a frameshift. R80X indicates a change from an amino acid to a stop. K7RD indicates a change in amino acids.
Denotes the chromosome number, start location, and the nucleotide change. _* indicates that there has been either an addition (+) or a deletion (−) of nucleotides.
Single nucleotide polymorphisms identifiers as defined at dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/).
Percent presense of the variant in the 1000 Genomes catalog of human genetic variation (http://www.1000genomes.org/).
Sorting Intolerant From Tolerent (http://sift.bii.a-star.edu.sg/index.html).
Prediction of functional effects of human nsSNPs, or PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/).
Reference sequence accession number from the National Center for Biotechnology Information, NCBI (http://www.ncbi.nlm.nih.gov/).