Table 1 SNVs after quality filtration having low frequencies (<0.2) in European population causing nonsynonymous changes in protein products
From: Study of Alzheimer family case reveals hemochromotosis-associated HFE mutation
Chromosome | Position | Reference allele | Alternative | Function | Gene | Exonic function | Amino-acid | Frequency in 1,000 g | dbSNP (snp135) | Clinvar annotation | gwascatalog annotation | Genotypes | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
allele | change | (CEU population) | P3D illumina | P3D SOLiD | P4A SOLiD | P4C SOLiD | P3C illumina | P3C SOLiD | P3B illumina | P3B SOLiD | P4B SOLiD | P3A illumina | P3A SOLiD | |||||||||
1 | 226555302 | A | G | Exonic | PARP1 | Nonsynonymous | V762A | 0.17 | rs1136410 | — | — | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 |
6 | 26093141 | G | A | Exonic | HFE | Nonsynonymous | C102Y | 0.05 | rs1800562 | Pathogenic; hereditary hemochromatosis | Hemoglobin, … (1) | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 1 |
6 | 29796376 | C | A | Exonic | HLA-G | Nonsynonymous | L134I | 0.09 | rs12722477 | — | — | 1 | 1 | 0 | — | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
6 | 29910759 | T | C | Exonic | HLA-A | Nonsynonymous | V100A | — | rs1071742 | — | — | 2 | — | 1 | 0 | 1 | 2 | 2 | 2 | 0 | 1 | — |
6 | 29911056 | A | C | Exonic | HLA-A | Nonsynonymous | I119L | 0.13 | rs1071743 | — | — | 1 | 1 | 0 | 0 | 1 | 1 | 2 | 2 | 1 | 1 | 1 |
6 | 29911069 | A | T | Exonic | HLA-A | Nonsynonymous | Y123F | 0.1 | rs1136697 | — | — | 1 | 1 | 0 | 0 | 1 | 1 | 2 | 2 | 1 | 1 | 1 |
6 | 29912348 | A | G | Exonic | HLA-A | Nonsynonymous | T323A | 0.16 | rs1137078 | — | — | 2 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 1 |
6 | 29912386 | G | C | Exonic | HLA-A | Nonsynonymous | K335N | 0.1 | rs1137160 | — | — | 1 | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 2 |
6 | 31238930 | A | T | Exonic | HLA-C | Nonsynonymous | L180Q | — | rs2308592 | — | — | 1 | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
6 | 31324200 | G | C | Exonic | HLA-B | Nonsynonymous | S121R | — | rs1140412 | — | — | 2 | — | 1 | 2 | 2 | 2 | 2 | 2 | 1 | 2 | 2 |
20 | 56138648 | G | A | Exonic | PCK1 | Nonsynonymous | E276K | 0.16 | rs11552145 | — | — | 2 | 2 | 1 | 0 | 1 | 1 | 2 | 1 | 1 | 2 | 2 |
