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Table 3 HCAR rare non-synonymous variants detected in TCGA

From: Rare and potentially pathogenic variants in hydroxycarboxylic acid receptor genes identified in breast cancer cases

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