Table 2 Pathogenicity prediction of variants using bioinformatics tool
Gene | Transcript | Variant position | Nucleotide change | Amino acid change | Mutation frequency | Polyphen2 | MutationTaster | M-CAP | Pathogenicity (ACMG) | Evidence (ACMG) | Phenotypic effect of variant | Reference |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
FLG | NM_002016.1 | Exon 3 | c.12064A > T | p.Lys4022Ter | 0.0049 | / | Disease causing | Likely benign | Moderate pathogenicity | PM2, PP5 | Ichthyosis vulgaris | |
BCR | NM_004327.3 | Exon 19 | c.3275_3278dupCCGG | p.Val1094ArgfsTer17 | / | / | Disease causing | / | Moderate pathogenicity | PM2, PP5 | / | / |
GIGYF2 | NM_001103146.1 | Exon 29 | c.3463C > A | p.Pro1155Thr | 0.0000 | Probably damaging, 1.000 | Polymorphism | / | Supporting benign | BP4, BP6 | Early-onset Parkinson disease | [25] |
ITK | NM_005546.3 | Exon 16 | c.1741C > T | p.Arg581Trp | 0.0005 | Probably damaging, 1.000 | Disease causing | / | Moderate pathogenicity | PM2, PP5 | Autoinflammatory syndrome; lymphoproliferative syndrome 1 | |
SLC26A4 | NM_000441.1 | Intron 7 | c.919-2A > G | / | 0.0000 | / | Disease causing | Possibly pathogenic | Moderate pathogenicity | PP5 | / | / |