Table 2.
Predicted deleterious non-synonymous TASPs with p < 5 × 10−8. Sixteen nonsynonymous trait/disease associated SNPs and their strong linkage disequilibrium partners (TASPs defined here as r2 > 0.9), are predicted to be deleterious according to both PolyPhen (PP) and CDPred (CDP), 7 only by PP and 7 only by CDP
| Non-synonymous TASP | Amino acid change | Index TAS from GWAS | Affected gene | Reported gene | Trait/disease | Program |
|---|---|---|---|---|---|---|
| rs1046934 | Q59H | rs2274432 | TSEN15 | GLT25S2 | Height | PP & CDP |
| rs2305479 | G282R | rs7216389 | GSDMB | ORMDL3 | Asthma | PP & CDP |
| rs2305480 | P289S | rs2872507 | GSDMB | ORMDL3 | Crohn's disease | PP & CDP |
| rs3197999 | R689C | rs3197999 | MST1 | MST1 | Crohn's disease | PP & CDP |
| rs2476601 | R620W | rs2476601 | PTPN22 | PTPN22 | Rheumatoid arthritis | PP & CDP |
| rs2395029 | V112G | rs2395029 | HLA-C | HLA-C | Psoriasis | PP & CDP |
| rs4149056 | V174A | rs4149056 | SLCO1B1 | SLCO1B1 | Myopathy | PP & CDP |
| rs7578597 | T1187A | rs7578597 | THADA | THADA | T2D | PP & CDP |
| rs229527 | G21V | rs229541 | C1QTNF6 | C1QTNF6 | T1D | PP & CDP |
| rs11820589 | P148L | rs12272004 | BUD13 | APOA | LDL/TG | PP & CDP |
| rs676210 | P2739L | rs673548 | APOB | APOB | Metabolic traits | PP & CDP |
| rs1799990 | M129V | rs1799990 | PRNP | PRNP | Creutzfeldt-Jacob disease | PP & CDP |
| rs6756629 | R50C | rs6756629 | ABCG5 | ABCG5 | LDL | PP & CDP |
| rs1800562 | C282Y | rs1800562 | HFE | HFE | Serum markers of iron status | PP & CDP |
| rs328 | Nonsense | rs10503669 | LPL | LPL | HDL/TG | PP & CDP |
| rs601338 | Nonsense | rs492602 | FUT2 | FUT2 | Vitamin B12 | PP & CDP |
| rs2274432 | G19D | rs2274432 | TSEN15 | GLT25D2 | Height | PP only |
| rs11591147 | R46L | rs11591147 | PCSK9 | PCSK9 | LDL | PP only |
| rs11887534 | D19H | rs11887534 | ABCG8 | ABCG8 | Gallstones | PP only |
| rs1799969 | G241R | rs1799969 | ICAM1 | ICAM1 | Soluble ICAM1 | PP only |
| rs17467284 | R911L | rs11175593 | Predicted | LRRK2 / MUC19 | Crohn's disease | PP only |
| rs1260326 | P446L | rs1260326 | GCKR | GCKR | TG | PP only |
| rs1064608 | P290A | rs10838738 | MTCH2 | MTCH2 | BMI | PP only |
| rs1042602 | S192Y | rs1042602 | TYR | TYR | Freckles | CDP only |
| rs6046 | R413Q | rs561241 | Factor VII | Factor VII | Factor VII level | CDP only |
| rs16969968 | D398N | rs8034191 | CHRNA5 | CHRNA5 | Lung cancer | CDP only |
| rs16890979 | V282I | rs16890979 | SLC2A9 | SLC2A9 | Serum uric acid | CDP only |
| rs2231142 | Q141K | rs2231142 | ABCG2 | ABCG2 | Serum uric acid | CDP only |
| rs3761472 | D110G | rs2281135 | SAMM50 | SAMM50 | Plasma level of liver enzymes | CDP only |
| rs1169288 | I27L | rs2650000 | HNF1A | HNF1A | LDL | CDP only |