Table 2. In silico evaluation of NLGN1 variants.
| Amino acid change | MAF | in silico prediction | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1000 Genomes | ESP 6500 | ExAc | CADD | SIFT | Poly-Phen2 | Mutation Taster | LRT | Mutation Assessor | FATHMM | Number of "deleterious" | Classification | |
| P89L | NA | NA | NA | 22.2 | D | D | D | D | H | D | 7 | High-risk |
| L269P | NA | NA | NA | 20.9 | D | D | D | D | H | T | 6 | High-risk |
| G297E | NA | NA | NA | 22.8 | D | D | D | D | H | D | 7 | High-risk |
| H795Y | NA | NA | 0.000008 | 13.6 | D | B | D | D | M | T | 3 | Low-risk |
| T90I | NA | NA | 0.00008 | 5.7 | T | B | D | D | N | T | 2 | Low-risk |
MAF: minor allele frequency. 1000 genome European ancestry and ESP 6500 European ancestry are used.
D and H indicate the highest probability (e.g. damaging or deleterious),
B, N and T indicate the lowest probability (e.g. benign or neutral or tolerated),
M indicates the intermediate probability of pathogenic effect, respectively.
We defined the variant as “deletrious” if 1) the variant was not found in 1000 Genomes, ESP 6500 and ExAc, 2) CADD score > 20, 3) the evaluation by each in silico tool was “D” or “H”.