Table 3 Pathogenicity analyses of variants and classification in the 6 Chinese families with IRD.
Family4 | Family7 | Family8 | Family12 | Family13 | Family14 | |
|---|---|---|---|---|---|---|
Gene | USH2A | PROM1 | PROM1 | CNGA1 | CNGA1 | PRPH2 |
Nucleotide | c.10179del | c.544dupC | c.1363G > C | c.265del | c.253del | c.640T > A |
Amino acid | p. (Met3393*) | p. (Gln182*) | p. (Gly455Arg) | p. (Leu89Phefs*4) | p. (Leu85Phefs*) | p. (Cys214Ser) |
Chromosome | chr12: 15,963,403 | chr4:16026900 | chr4:16008252 | chr4: 47,951,884 | chr4:47951884 | chr6: 42,672,291 |
Exon | Exon51 | Exon4 | Exon13 | Exon6 | Exon6 | Exon2 |
Source | Father and mother | Father and mother | Father and mother | Father and mother | Father and mother | Father and mother |
LRT | - | - | D | - | - | D |
Variant taster | - | - | D | - | - | D |
Variant assessor | - | M | - | M | ||
SIFT | - | - | D | - | - | D |
Variant taster | - | - | D | - | - | D |
PolyPhen_2 | - | - | D | - | - | D |
CADD raw | - | - | 4.046 | - | - | 1.784968 |
PhyloP100way | - | - | 7.798 | - | - | 0.95719 |
GERP++ | - | - | 5.37 | - | - | 0.69264 |
Evidence of pathogenicity | PVS1 + PM2 + PP4 | PVS1 + PM2 + PP4 | PM2 + PP3 + PP1+ PP4 + PP5 | PVS1 + PM2 + PP1 + PP4 | PVS1 + PM2 + PP4 | PM2 + PP1 + PP3 +PP4 + PP5 |
Variant classification | Pathogenic | Pathogenic | Pathogenic | Pathogenic | Pathogenic | Pathogenic |
