Table 4. Probable effects of splice site mutations using HSF 2.4.1 and Mutation Taster and effects of missense mutations using PolyPhen and SIFT.
| S.No | Family ID | Gene | Mutation identified | HSF Wild type Consensous value (CV) | HSF Mutant consensous value (CV) | HSF delta CV (%) | MT Wild type scoring | MT Mutant scoring | MT Splice site change | cDNA Analysis | PolyPhen score | Polyphen predicted effect | SIFT score | SIFT Predicted effect |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1. | LCA-1 | RPE65 | c.858+1G>T | - | - | - | - | - | Likely to Disturb Normal Splicing, sequence motif lost | Not done | NA | NA | NA | NA |
| 2. | LCA-4 | IQCB1 | c.1278+6T>A | 79.28 | 75.78 | -4.42 | 0.36 | 0.95 | Donor increased | r.[1131_1278 del,1131_1278del]Exon12 skipping | NA | NA | NA | NA |
| 3. | LCA-7 | RDH12 | c.344-8C>T | 73.62 | 70.25 | -4.57 | 0.55 | 0.76 | Acceptor increased | Not done | NA | NA | NA | NA |
| 4. | LCA-11 | SPATA7 | c.913-2A>G | 86.72 | 57.09 | Site broken | 0.53 | 0.84 | Acceptor increased | Not done | NA | NA | NA | NA |
| 5. | LCA-2 | CRB1 | c.3307G>Ap.(Gly1103Arg) | NA | NA | NA | NA | NA | NA | NA | 0.91 | Probably damaging | 0 | Deleterious |
| 6. | LCA-8 | AIPL1 | c.247G>A p.(Glu83Lys) | NA | NA | NA | NA | NA | NA | NA | 1.0 | Probably damaging | 0 | Deleterious |
NA-not applicable
The human splice finder presents consensous value (CV) which indicate strength of the splice site range from 0 to 100. The splice sites of CV higher than 80 are considered as strong splice sites, 70–80 as less strong and 65–70 as weak, and a CV below 70 is considered to be non-functional [41]. The mutation taster (MT) scores the wild type and the mutant and a confidence score of >0.3 for the mutant indicates gain of completely new splice site [43].