Table 1.
Rare sequence variants predicted to be pathogenic by at least one computational program.
| CHD7 variant | Population allele frequency (ExAC/Portuguese)(a) | Computational programs that support a pathogenic effect(b) | Additional genetic variants |
|---|---|---|---|
| Missense | |||
| c.1163 G > A; p.Gly388Glu | 0.0008%/0% | SIFT, PP2, MT | |
| c.2708 A > C; p.His903Pro | 0%/0% | SIFT, PP2, MT | |
| c.3245 C > T; p.Thr1082Ile | 0%/0% | SIFT, PP2, MT | FGFR1 c.12 G > T and PROKR2 c.802 C > T(c) |
| c.4354 G > T; p.Val1452Leu | 0%/0% | MT | |
| c.5561 A > G; p.Asp1854Gly | 0%/0% | SIFT, PP2, MT | FGFR1 c.177 C > T |
| c.6194 G > A; p.Arg2065His | 0%/0% | SIFT, PP2, MT | |
| Synonymous | |||
| c.1677G > A; p.Ser559Ser | 0.0036%/0% | MT, HSF | |
| c.8355 C > T; p.Ala2785Ala | 0.0074%/0% | MT, HSF | FGFR1 c.600 C > T and PROKR2 c.528 G > C |
(a)ExAC Exome Aggregation Consortium frequency/Portuguese control population. (b)SIFT, Sorting Tolerant From Intolerant; PP2, PolyPhen-2; MT, Mutation Taster; HSF, Human Splicing Finder. (c)Patient previously reported by Gonçalves et al.15.