Table 2.
Diseases associated with genes containing nsSNPs
| General Category | # Associated Deleterious SNPs | Gene names | Diseases | ||
|---|---|---|---|---|---|
| Apoptosis | 8 | CYCS; | Huntington's disease | DNA damage | Alzheimer's disease |
| TNFRSF10D; | Thrombocytopenia | Bipolar | Rheumatoid arthritis | ||
| CASP7; MAP3K1; | Diabetes mellitus type I | Renal cell carcinoma | Myeloproliferative disorders | ||
| PRKCZ; MPL; | |||||
| TNFRSF19 | Leukemia | Diabetes mellitus type II | Amyotrophic lateral Sclerosis | ||
| Pancreatitis | Carcinoma (multiple types) | Multiple sclerosis | |||
| Cell cycle | 20 | BRCA2; POLD2; | Spontaneous abortion | Genomic instability | Drug toxicity |
| CDC14A; CDT1; | |||||
| CHAF1A; WRN; | Endometriosis | Anemia | Li-Fraumeni Syndrome | ||
| IPO5; KIF23; TTK; | Aneuploidy | Amyotrophic lateral Sclerosis | Diabetes mellitus type I | ||
| MSH2; CASC5; | |||||
| PRKCZ; CASP7; | Carcinoma (multiple types) | Diabetes mellitus type II | Werner Syndrome | ||
| SERPINB13; | |||||
| LATS1 | Male infertility | Rheumatoid arthritis | osteoporosis | ||
| Development | 11 | NCOA6; PABPN1; | Carcinoma (multiple types) | Endometriosis | Asthma |
| LTF; MAP3K1; | |||||
| TLL1; YAP1; SPEN; | Deglutition disorders | Male infertility | Coronary disease | ||
| IL18R1 | Oculopharyngeal Muscular dystrophy | Li-Fraumeni Syndrome | Idiopathic pulmonary fibrosis | ||
| DNA repair | 9 | BRCA2; CHAF1A; | Genomic instability | Werner Syndrome | Fanconi anemia |
| FANCM; RAD51L1; | Carcinoma (multiple types) | Diabetes mellitus type I | Drug toxicity | ||
| WRN; MSH2 | |||||
| Inflammation | 22 | CYCS; SOCS6; | Huntington's disease | Severe combined Immunodeficiency | Stomach ulcer |
| BDKRB1; HPRT1; | |||||
| IL18R1; IL7R; | Thrombocytopenia | Multiple sclerosis | Ataxia | ||
| MAP3K1; 1L27RA; | Asthma | Rheumatoid arthritis | Leukemia | ||
| PRKCZ; OAS2; | Diabetes mellitus type I | Myeloproliferative disorders | Sarcoidosis | ||
| CD53; LAMA3; | |||||
| LAMA4; IL174A; | Diabetic nephropathies | Crohn's disease | Carcinoma (multiple types) | ||
| HABP2; KLKB1 | |||||
| Autosomal dominant polycystic kidney | Sjogren's syndrome | Gout | |||
| Rhinitis | Nasal polyps | Telangiectasis | |||
| Lesch-Nyhan syndrome | Arteriosclerosis | Genome instability | |||
| Metabolism | 4 | P2RX2; LTF; | Anoxia | Encephalitis | Rheumatoid arthritis |
| ACACB; PRKCZ | Carcinoma (multiple types) | Diabetes mellitus type II | Glomberulonephritis | ||
| Nervous System | 17 | CDK5RAP2; | Microcephaly | Lipodystrophy | Rheumatoid arthritis |
| P2RX2; | Anoxia | Mucolipidoses | Fragile X Syndrome | ||
| ST8S1A2; HTR1F; | Schizophrenia | Pain | Liver cirrhosis | ||
| SCN10A; SLC28A2; | Parkinson's disease | Asthma | Diabetes mellitus type I | ||
| MCOLN1; DLGAP4; | Glioma | Acquired immunodeficiency | |||
| SYT8; ATP2B3; | |||||
| MAP1A; LAMA4; | |||||
| MAP3K1; AHNAK; | |||||
| AFF2; CASP7 | |||||
| Protein folding | 4 | CHAF1A; GRPEL1; | Aneurysm | Pulmonary fibrosis | Diabetes mellitus type I |
| HSPA4; EEF1A2; | |||||
| Carcinoma (multiple types) | Graft vs. host disease | Paralysis | |||
| Reproduction | 13 | SPDY1; CENPI; | Gastrointestinal diseases | Hyperaldosteronism | Genomic instability |
| BRCA2; NCOA4; | |||||
| RBAK; CASC5; | Carcinoma (multiple types) | Diabetes mellitus type II | Oligospermia | ||
| PRKCZ; MAP3K1 | |||||
| anemia | |||||
| Signal transduction | 19 | BRCA2; CASP7; | Spontaneous abortion | Arteriosclerosis | Dilated cardiomyopathy |
| NCOA6;IL7R; | |||||
| CYCS; BAMBI; | Carcinoma (multiple types) | Hypertension | Asthma | ||
| KLKB1; IL17RA; | |||||
| MAP3K1; DSG2; | Huntington's disease | Severe combined immunodeficiency | Sarcoidosis | ||
| PRKCZ; IFI44; | |||||
| IL18R1; HABP2; | Thrombocytopenia | Multiple sclerosis | Diabetes mellitus type I | ||
| Rheumatoid arthritis | Alzheimer's disease | Arrhythmogenic right ventricular dysplasia | |||
| Transcription | 8 | NCOA6; BRCA2; | Retinoblastoma | Oculopharyngeal muscular dystrophies | Rheumatoid arthritis |
| MAP3K1; TAF3; | |||||
| PABPN1 | Spontaneous abortion | Aneuploidy | Deglutition disorders | ||
| Carcinoma (multiple types) | Infertility | ||||
| Transport | 11 | KCNH3; LTF; | Anemia | Genomic instability | Liver cirrhosis |
| MSH2;NCOA4; | Alzheimer's disease | Crohn's disease | Obesity | ||
| PPARGC1B; | Epilepsy | Diabetes mellitus type II | Barrett esophagus | ||
| ZNF217; | Carcinoma (multiple types) | Gastritis | progeria | ||
| ME2;P2RX2;ANK3; | |||||
| LATS1; MAT2A | |||||
A list of genes containing probably or possibly damaging nsSNPs as predicted by PolyPhen-2 was submitted for network analysis in GeneGo. Characterization of the genes containing nsSNPs is achieved by listing the general cellular process (column 1), the total number of deleterious nsSNPs in the genes that GeneGo annotated (column 2), the genes associated with the cellular process (column 3), and the specific diseases that have been associated by GeneGo with the genes in question (columns 4-6).