Table 3 HCAR rare non-synonymous variants detected in TCGA
Gene | GRCh38 Position | rs ID | Alleles | GVS Function | cDNA Change | Protein Change | Polyphen2 (missense variants) | TCGA | EVS | Single variant P-values | Gene based aggregation analysis—non-synonymous variants | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EA Minor Allele # | EA Major Allele # | MAF (%) (EA) | EA Minor Allele # | EA Major Allele # | MAF (%) (EA) | ||||||||||
HCAR1 | 12:122729570 | rs141008238 | T > C | missense | c.770A > G | p.H257R | Benign | 1 | 1295 | 0.08 | 0 | 8600 | 0.00 | 0.131 | 1 |
12:122729619 | rs140482291 | G > A | missense | c.721C > T | p.L241F | Probably damaging | 4 | 1292 | 0.31 | 13 | 8587 | 0.15 | 0.266 | ||
12:122729825 | rs61742326 | G > A | missense | c.515C > T | p.S172L | Benign | 6 | 1290 | 0.46 | 31 | 8569 | 0.36 | 0.622 | ||
12:122730006 | rs749553547 | C > T | missense | c.334G > A | p.D112N | Probably damaging | 1 | 1295 | 0.08 | 0 | 8600 | 0.00 | 0.131 | ||
12:122730119 | rs201991947 | T > C | missense | c.221A > G | p.Y74C | Probably damaging | 2 | 1294 | 0.15 | 5 | 8595 | 0.06 | 0.231 | ||
HCAR2 | 12:122702194 | rs63475561 | AAGGA > - | frameshift | c.1086_1090del | p.P363Nfs*26 | - | 2 | 1294 | 0.15 | 0 | 8600 | 0.00 | 0.017 | 0.238 |
12:122702236 | rs148160325 | C > T | missense | c.1048G > A | p.G350S | Benign | 1 | 1295 | 0.08 | 1 | 8599 | 0.01 | 0.131 | ||
12:122702248 | rs145934041 | T > C | missense | c.1036A > G | p.M346V | Benign | 3 | 1293 | 0.23 | 1 | 8599 | 0.01 | 0.002 | ||
12:122702352 | rs780477417 | C > T | missense | c.932G > A | p.R311H | Probably damaging | 1 | 1295 | 0.08 | 0 | 8600 | 0.00 | 0.131 | ||
12:122702766 | rs144376493 | C > G | missense | c.517_518delinsAC | p.G173T | Benign | 4 | 1292 | 0.31 | 0 | 8600 | 0.00 | 2.93e-4 | ||
12:122702781 | rs145014727 | G > A | missense | c.503C > T | p.P168L | Benign | 4 | 1292 | 0.31 | 26 | 8574 | 0.30 | 1 | ||
12:122702785 | rs147573131 | T > A | missense | c.499A > T | p.M167L | Benign | 4 | 1292 | 0.31 | 28 | 8572 | 0.33 | 1 | ||
12:122702860 | rs151172149 | T > C | missense | c.424C > T | p.R142W | Benign | 3 | 1293 | 0.23 | 1 | 8599 | 0.01 | 0.002 | ||
12:122703252 | rs755259236 | C > T | missense | c.32 T > C | p.L11P | Benign | 1 | 1295 | 0.08 | 1 | 8599 | 0.01 | 0.131 | ||
HCAR3 | 12:122716092 | rs200839014 | G > A | missense | c.646C > T | p.R216W | Possibly damaging | 1 | 1295 | 0.08 | 0 | 8600 | 0.00 | 0.131 | 1 |
12:122716658 | rs148858491 | G > A | missense | c.80C > T | p.A27V | Benign | 4 | 1292 | 0.31 | 12 | 8588 | 0.14 | 0.148 | ||
12:122716731 | rs190370423 | G > A | missense | c.7C > T | p.R3W | Benign | 1 | 1295 | 0.08 | 1 | 8599 | 0.01 | 0.245 | ||