Table 3 In silico analysis of novel mutation MSH2, p.Arg711Pro located in exon 13.
Methods of in silico analysis | Result | Comments |
|---|---|---|
SIFT score | 0.00 →pathogenic | If SIFT score < .05 then the aa substitution is predicted to affect protein function |
PolyPhen | Probably damaging (3.071) →pathogenic | If PolyPhen score > 2 then the aa substitution is predicted to affect protein function |
MAPP-MMR | 40.700→pathogenic | If MAPP-MMR score > 4.55 then the aa substitution is predicted to affect protein function |
NNSplice (0.9) | SD: 1.00/1.00 No SA: 0.95/0.95 Change | Scores predicted for the wt seq/score predicted for the mut seq |
NetGene2 Server | SD: 0.58/0.62 No SA: 0.71/0.71 Change | Scores predicted for the wt seq/score predicted for the mut seq |
Human Splice Finder v2.4 (HSF) ** Rescue ESE PESE octamers No difference ESS (Wang et al) Fas-Ess hexamers PESS octamers IIEs (Zhang et al) hnRP motifs | SD: 74.29/74.4 SA (c.2123):76.67/86.97 SA (c.2126):75.87/79.36 BP:81.68/86.61 | Scores predicted for the wt seq/score predicted for the mut seq |
|  | ESE Finder:c.2129 SF2/ASF (IgM-BRCA1)→new site EIEs (Zhang et al): c.2127→new site ESE from HSF: c.2132 9G8)→broken site Silencer motifs (Sironi et al): c.2127→new site Other splicing motifs (Goren et al): c.2130→new site |  |