Table 3. Identified variants and scores of pathogenicity prediction tools.
| Gene | GenBank accession number |
Substitution
|
Variant ID |
MAF
|
PolyPhen2 | GERP | ||
|---|---|---|---|---|---|---|---|---|
| HGVD | 1000 Genomes | |||||||
| PAX9 | NM_006194 | c.398A>G | p.Asn133Ser | 0 | 0 | 0.985 | 4.90 | |
| AXIN2 | NM_004655 | c.1250C>T | p.Ala417Val | 0.0141 | 0.0032 | 0.001 | −4.86 | |
| NM_004655 | c.1807G>C | p.Ala603Pro | rs145353986 | 0.0492 | 0.0100 | 0.000 | −2.26 | |
| NM_004655 | c.1853A>G | p.Asp618Gly | 0 | 0 | 0.028 | 3.95 | ||
| NM_004655 | c.2213C>T | p.Ser738Phe | rs139209450 | 0.0150 | 0.0032 | 0.004 | 1.02 | |
| EDA | NM_001005613 | c.428G>C | p.Gly143Ala | rs61761321 | 0 | 0 | 0.364 | 4.82 |
| NM_001005613 | c.436G>T | p.Gly146Cys | 0 | 0 | Unknown | 0.00 | ||
| NM_001005609 | c.555T>A | p.Asn185Lys | 0 | 0 | 0.616 | 2.59 | ||
| EDAR | NM_022336 | c.319A>G | p.Met107Val | rs61761321 | 0.0485 | 0.0200 | 0.364 | 4.82 |
| NM_022336 | c.701G>T | p.Ser234Ile | 0 | 0 | 0.201 | 1.23 | ||
| NM_022336 | c.1138A>C | p.Ser380Arg | rs146567337 | 0.0282 | 0.0100 | 0.978 | 5.18 | |
| NM_022336 | c.1166G>C | p.Gly389Ala | 0 | 0 | 0.888 | 4.91 | ||
| NM_022336 | c.1270G>A | p.Val424Met | 0 | 0 | 0.888 | 4.91 | ||
| WNT10A | NM_025216 | c.511C>T | p.Arg171Cys | rs116998555 | 0.0158 | 0.0046 | 0.999 | 1.57 |
| NM_025216 | c.637G>A | p.Gly213Ser | rs147680216 | 0.0156 | 0.0046 | 0.988 | 4.41 | |
| NM_025216 | c.874A>G | p.Ser292Gly | 0.0040 | 0 | 0.001 | 2.25 | ||
| NM_025216 | c.909C>A | p.H303Gln | 0.0132 | 0 | 0.999 | 3.93 | ||
| BMP2 | NM_001200 | c.389G>A | p.R130Gln | 0.0012 | 0 | 0.023 | 5.70 | |
| FAM65A | NM_001193522 | c.137C>T | p.Pro46Leu | 0.0068 | 0.0009 | 0.793 | 4.82 | |
| NM_001193522 | c.148C>T | p.Pro50Ser | rs140402307 | 0.0037 | 0.0009 | 0.679 | 4.82 | |
| NM_001193522 | c.1117C>A | p.Leu373Met | 0.0014 | 0.0009 | 0.009 | 1.17 | ||
| NM_001193522 | c.1994C>T | p.Thr665Ile | rs28364801 | 0.0167 | 0.0018 | 0.212 | 2.30 | |
| NM_001193522 | c.2542G>A | p.Glu848Lys | 0 | 0 | 0.676 | 4.91 | ||
| NM_001193522 | c.2668C>T | p.Arg890Cys | rs61744916 | 0.0107 | 0.0600 | 0.038 | 1.96 | |
| NM_001193522 | c.2734C>A | p.Arg912Ser | 0 | 0 | 0.026 | 1.18 | ||
| NM_001193522 | c.2771G>A | p.Arg924His | rs145721165 | 0.0268 | 0.0032 | 0.983 | 5.15 | |
| NFATC3 | NM_004555 | c.244A>G | p.Ser82Gly | rs56326642 | 0.0215 | 0.0014 | 0.000 | 1.65 |
| NM_004555 | c.281A>C | p.Glu94Ala | rs3743736 | 0.0156 | 0.0018 | 0.963 | 5.57 | |
| NM_004555 | c.1043C>T | p.Ala348Val | rs146091507 | 0.0156 | 0.0018 | 0.001 | 5.25 | |
| NM_004555 | c.1279C>G | p.His427Asp | 0 | 0 | 0.996 | 5.13 | ||
| CDH23 | NM_001171933 | c.127G>A | p.Val43Ile | rs41281334 | 0.0248 | 0.0400 | 0.014 | 3.21 |
| NM_001171933 | c.141T>G | p.Asn47Lys | 0 | 0 | 1 | 5.49 | ||
| NM_001171930 | c.1637G>C | p.Arg546Pro | 0 | 0 | 0.976 | 0.49 | ||
| NM_001171933 | c.1681T>G | p.Phe561Val | rs3802707 | 0.0175 | 0.0014 | 0.011 | 3.09 | |
| NM_001171930 | c.3179G>A | p.Arg1060Gln | 0 | 0 | 1.000 | 5.49 | ||
| NM_001171930 | c.3352G>A | p.Gly1118Ser | 0.0055 | 0 | 0.272 | 4.92 | ||
| NM_001171930 | c.3397G>A | p.Glu1133Lys | 0 | 0 | 0.668 | 4.89 | ||
| NM_001171930 | c.3656G>A | p.Arg1219Gln | 0 | 0 | 1.000 | 4.32 | ||
| NM_001171930 | c.4009G>A | p.Ala1337Thr | 0 | 0 | 1.000 | 4.81 | ||
| NM_022124 | c.4135C>T | p.Arg1379Cys | 0 | 0 | 0.028 | 0.91 | ||
| NM_022124 | c.4346G>A | p.Gly1449Asp | 0 | 0 | 0.045 | 1.01 | ||
| NM_022124 | c.4762C>T | p.Arg1588Trp | rs137937502 | 0.0051 | 0.0018 | 1.000 | 3.24 | |
| NM_022124 | c.5418C>G | p.Asp1806Glu | rs74145660 | 0.0918 | 0.0300 | 0.998 | −5.31 | |
| NM_022124 | c.5722G>A | p.Val1908Ile | 0.0040 | 0 | 0.028 | −0.78 | ||
| NM_022124 | c.6023G>T | p.Gly2008Val | 0 | 0 | 0.045 | 1.01 | ||
Abbreviations: GERP, Genomic Evolutionary Rate Profiling; HGVD, Human Genetic Variation database; MAF, minor allele frequency (based on 1000 Genomes allele frequencies for Japanese and European populations); PolyPhen2, Polymorphism Phenotyping v2.