Table 2.
Pathogenicity predictions for missense and splice site mutations based on in silico analyses.
| Amino acid change predictions | |||||||
|---|---|---|---|---|---|---|---|
| DNA change | Mutation consequence | Exome variant server1 | PhyloP | Grantham score | SIFT | PolyPhen | References |
| c.242C>G | p.(Thr81Arg) | – | 2.55 | 71 | Tolerated | Benign | Novel |
| c.332T>C | p.(Ile111Thr) | – | 4.56 | 89 | Deleterious | Probably damaging | Li et al. (2004) |
| c.604G>A | p.(Glu202Lys) | – | 5.61 | 56 | Deleterious | Probably damaging | Novel |
| c.1198C>T | p.(Arg400Cys) | 2/13004 MAF 0.0154 | 4.48 | 180 | Deleterious | Probably damaging | Lai et al. (2007) |
| c.1393A>G | p.(Arg465Gly) | 2/13004 MAF 0.0077 | 1.25 | 125 | Deleterious | Probably damaging | Rossi et al. (2013) |
| Splicing prediction | |||||||
|---|---|---|---|---|---|---|---|
| DNA change | Mutation consequence | Position | SSF (0–100) | MaxEnt (0–12) | NNSPLICE (0–1) | HSF (0–100) | Reference |
| c.604+4A>G | Altered splicing | c.604 | 84.07 ⇒ 73.99 (−12.0%) | 8.95 ⇒ 4.29 (−52.1%) | 0.98 ⇒ 0 (−100%) | 92.33 ⇒ 83.99 (−9.0%) | Novel |
List of missense and splice site mutations identified in this study and predictions of their consequences with the use of in silico program (SIFT and PolyPhen). Splicing prediction shows the percent decrease in comparison to the original splice donor site scores. In addition, HSF predicted a novel splice donor site in position c.604+4. SIFT, sorting intolerant from tolerant; MAF, minor allele frequency; HSF, Human Splicing Finder; SSF, Splice Sequence Finder; NNSPLICE, Splice Site Prediction by Neural Network.
1
Heterozygous alleles of total number of chromosomes.