Table 3.
Allelic frequencies of the variants found in the individuals with Thalidome Embryopathy compared to the ones of different databases.
| Gene | Polymorphism | DNA variation | Aminoacid variation | Position | MAF in the TE | MAF in the ExAC | p a | MAF in the 1000 Genomes | p a | MAF in the ABraOM | p a |
|---|---|---|---|---|---|---|---|---|---|---|---|
| ESCO2 | rs35430328 | c.-151G > A | Exon 1 (UTR) | 0.259 | 0.354 (A) | 0.532 | 0.273 | 0.986 | |||
| rs2272730 | c.-17 + 19 C > T | Intron | 0.463 | 0.424 (T) | 0.938 | 0.379 | 0.742 | ||||
| rs4732748 | c.239 C > T | p.Ala80Val | Exon 3 | 0.056 | 0.099 | 0.736 | 0.107 (T) | 0.655 | 0.102 | 0.747 | |
| rs182074852 | c.346 G > A | p.Asp116Asn | Exon 3 | 0.019 | <0.001 (A) | 0.209 | |||||
| rs1824449 | c.1013 + 35 G > A | Intron | 0.111 | <0.001 | <0.003 | <0.001 (G) | <0.018 | 0.015 | <0.013 | ||
| rs533417099 | c.*71_*74delTATT | 3′UTR | 0.056 | <0.001 (-) | <0.018 | 0.002 | 0.013 | ||||
| rs62498042 | c.*130 G > A | 3′UTR | 0.241 | 0.458 (G) | 0.020 | 0.244 | 1.000 | ||||
| rs114667641 | c.*1489 A > T | 3′UTR | 0.019 | <0.001 (T) | 0.209 | 0.045 | 0.760 | ||||
| SALL4 | rs11697572 | c.131–316 C > T | Intron | 0.056 | 0.037 (T) | 0.696 | |||||
| rs190593855 | c.131–260 G > A | Intron | 0.019 | 0.007 (A) | 0.655 | ||||||
| rs146597375 | c.131–226 T > C | Intron | 0.019 | 0.017 (C) | 0.782 | ||||||
| rs6013281 | c.540 T > C | p.Asn180= | Exon 2 | 0.019 | 0.005 | 0.847 | 0.004 (T) | 0.567 | 0.002 | 0.470 | |
| rs61737139 | c.645 C > G | p.Leu215= | Exon 2 | 0.037 | 0.025 | 0.969 | 0.022 (C) | 0.655 | 0.020 | 0.743 | |
| rs13038893 | c.1056 G > A | p.Ala352= | Exon 2 | 0.333 | 0.313 | 0.969 | 0.328 (A) | 1.000 | 0.266 | 0.742 | |
| rs140110863 | c.1353 C > T | p.Ala451= | Exon 2 | 0.019 | <0.001 | <0.003 | <0.001 (T) | 0.209 | |||
| rs6126344 | c.1520 T > G | p.Leu507Arg | Exon 2 | 0.315 | 0.350 | 0.474 | 0.335 (G) | 0.938 | 0.350 | 0.813 | |
| rs6021437 | c.1860 A > G | p.Thr620= | Exon 2 | 0.315 | 0.350 | 0.847 | 0.336 (G) | 0.938 | 0.362 | 0.760 | |
| rs13043248 | c.2037 C > T | p.Thr679= | Exon 2 | 0.148 | 0.102 | 0.736 | 0.115 (T) | 0.757 | 0.069 | 0.351 | |
| rs6091375 | c.2392 A > C | p.Ile798Leu | Exon 2 | 0.074 | 0.052 | 0.847 | 0.065 (C) | 0.898 | 0.073 | 1.000 | |
| rs17802735 | c.2640 G > C | p.Ser880= | Exon 3 | 0.093 | 0.089 | 1.000 | 0.127 (G) | 0.828 | 0.083 | 0.939 | |
| rs138891224 | c.2977 G > C | p.Gly993Arg | Exon 4 | 0.019 | <0.001 | <0.003 | <0.001 (C) | 0.049 | |||
| rs3171177 | c.*125 T > A | 3′UTR | 0.019 | 0.041 (T) | 1.000 | 0.057 | 0.747 | ||||
| rs150300174 | c.*497 T > C | Downstream | 0.019 | 0.004 (C) | 0.567 | ||||||
| TBX5 | rs143563344 | c.-712 C > T | 5′UTR | 0.019 | 0.014 (T) | 0.214 | |||||
| rs186960328 | c.-664 G > A | Exon 1 (UTR) | 0.037 | <0.001 (A) | 0.777 | ||||||
| rs1248046 | c.-39 + 113 A > G | Intron | 0.398 | 0.416 (G) | 0.898 | 0.339 | 0.760 | ||||
| rs12423887 | c.-38–1865 G > A | Intron | 0.167 | 0.130 (A) | 0.662 | 0.123 | 0.760 | ||||
| rs571924700 | c.147 + 107 C > A | Intron | 0.037 | <0.001 (A) | 0.022 | ||||||
| Novel variant | c.420 C > T | p. Asp140= | Exon 5 | 0.019 | |||||||
| rs185924249 | c.511–56 T > C | Intron | 0.019 | 0.008 (C) | 0.655 | <0.001 | 0.448 | ||||
| rs2236017 | c.663 + 36 G > T | Intron | 0.352 | 0.390 | 0.847 | 0.395 (G) | 0.781 | 0.403 | 0.760 | ||
| rs2277377 | c.755 + 94 C > A | Intron | 0.241 | 0.307 (A) | 0.655 | 0.251 | 1.000 | ||||
| rs78344365 | c.756–26 G > A | Intron | 0.019 | <0.001 | <0.003 | 0.001 (A) | 0.333 | 0.004 | 0.742 | ||
| rs147405081 | c.787 G > A | p.Val263Met | Exon 8 | 0.037 | <0.001 | <0.003 | <0.001 (A) | 0.022 | 0.002 | 0.090 | |
| rs28730761 | c.*77 A > G | 3′UTR | 0.074 | 0.169 | 0.225 | 0.123 (G) | 0.655 | 0.100 | 0.813 | ||
| rs883079 | c.*97 G > A | 3′UTR | 0.389 | 0.258 | 0.113 | 0.285 (G) | 0.379 | 0.349 | 0.760 | ||
| rs143511878 | c.*812 C > T | 3′UTR | 0.019 | 0.008 (T) | 0.655 | 0.012 | 0.760 | ||||
| rs6489956 | c.*1101 A > G | 3′UTR | 0.222 | 0.190 (A) | 0.782 | 0.333 | 0.463 |
Reference sequences are: ESCO2 transcript NM_001017420, SALL4 transcript NM_020436 and TBX5 transcript NM_000192. aWith FDR correction.