Table 4.
Predicted consequences of identified missense mutations
| Gene | Protein change | Align-GVGD class | PolyPhen-2 (score) | SIFT (score) | Mutation Taster (P-value) | SSF (scale 1–100, wt:mut [% diff]) | MaxEnt (scale 1–12, wt:mut [% diff]) | NNSPLICE (scale 0–1, wt:mut [% diff]) | HSF (scale 1–100, wt:mut [% diff]) |
|---|---|---|---|---|---|---|---|---|---|
| SOX2 | p.(His101Arg) | C25 | Probably damaging (0.996) | Deleterious (0.00) | Disease causing (1.0) | ||||
| SOX2 | p.(Asp123Gly) | C65 | Possibly damaging (0.616) | Deleterious (0.00) | Disease causing (1.0) | ||||
| OTX2 | p.(Gln83His) | C15 | Probably damaging (1.000) | Deleterious (0.00) | Disease causing (1.0) | 84.9:72.3 (−14.9%) | 9.5:2.2 (−77.2%) | 0.75:0 | 89.7:78.9 (−12.1%) |
wt:mut, the ratio of scores between wild-type and mutant alleles, respectively; % diff, the percentage difference between the wild-type and mutant allele score. Align-GVGD, align with Grantham variation (GV), Grantham deviation (GD); HSF, human splicing finder; MaxEnt, maximum entropy modeling of short sequence motifs; NNSPLICE, neural network splice site analysis; PolyPhen-2, polymorphism phenotyping v2; SIFT, sorting intolerant from tolerant; SSF, splicing sequences finder.