Table 3.
Various online databases that used to predict the pathogenicity of the exonic variants
| Family 1 | Family 2 | Family 3 | Family 4 | Family 5 | Family 6 | Family 7 | Family 8 | Family 9 | ||
|---|---|---|---|---|---|---|---|---|---|---|
| Gene | CDH23 | CDH23 bvn | GIPC3 | MYO7A | MYO7A | TECTA | OTOF | MYO7A | TRIOBP | GIPC3 |
| Nucleic acid alternation | c.5908G>A | c.3215C>A | c.245A>G | c.1368C>T | c.2122A>G | c.49_50insT | c.1392+1G>A | c.487G>A | c.3202C>T | c.122C>A |
| Mutation type | Nonsynonymous | Nonsynonymous | Nonsynonymous | Synonymous | Nonsynonymous | Frameshift | Intronic | Nonsynonymous | Stop Gain | Nonsynonymous |
| Mutation function (ACMG) | Variant of uncertain significance | Variant of uncertain significance | Variant of uncertain significance | Variant of uncertain significance | Variant of uncertain significance | Likely pathogenic | Likely pathogenic | Pathogenic | Pathogenic | Likely pathogenic |
| SIFT | Damaging | Damaging | Tolerated | – | Damaging | – | – | Damaging | – | Tolerated |
| Polyphen | Probable damaging | Probable damaging | Probable damaging | – | Benign | – | – | Probable damaging | – | Polymorphism |
| MutationTaster | Disease causing | Disease causing | Disease causing | Disease causing | Disease causing | Disease causing | Disease causing | Disease causing | Disease causing | Disease causing |
| 1000 Genome | N.R | N.R | N.R |
Homozygous: 0 Heterozygous: 1 |
Homozygous: 0 Heterozygous: 2 |
N.R | N.R | N.R | N.R | N.R |
| EXAC all MAF | N.R | N.R | 0.000041 | 0.000223 | 0.000258 | N.R | N.R | N.R | 0.000008 | N.R |
| Varsome | Uncertain significance | Uncertain significance | Uncertain significance | Likely benign | Uncertain significance | Pathogenic | – | Pathogenic | Pathogenic | Uncertain significance |
| Spliceview | – | – | – | – | – | – | Mutant N.R | – | – | – |
| NetGene2 2.3 | – | – | – | – | – | – | Mutant N.R | – | – | – |
| BDGP | – | – | – | – | – | – | Mutant N.R | – | – | – |
| HSF | – | – | – |
New ESS site ESE site broken |
||||||
| Segregates in the family | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
Abbreviations: ACMG, American College of Medical Genetics and Genomics; ExAC, Exome Aggregation Consortium; MAF, Minor Allele Frequency; NR, not reported.