Table 4.
In silico analysis of novel sequence variations.
| Gene (exon/intron) | Nucleotide change | Method | Result | Comments |
|---|---|---|---|---|
| MSH2 (exon 7) | c.1276G > A |
Human Splice Finder (v.2.4) (HSF) (*) EIEs (Zhang et al) No Rescue ESE change PESE octamers/no ESS (Wang et al) motif PESS octamers found IIEs (Zhang et al) Other splicing motifs (Goren et al) |
"wt" donor site broken (84.7/73.68) | Scores predicted for the wt seq/score predicted for the mut seq |
| ESE Finder: c.1274 (SRp55)→ new site | ||||
| Rescue ESE: c.1271/c.1272→ site broken | ||||
| ESE from HSF: c.1273/c.1276 (9G8)→site broken | ||||
| Silencer motifs (Sironi et al): c.1271/c.1272→site broken | ||||
| Fas-Ess hexamers: c.1275→ site broken | ||||
| hnRNP motifs: c.1273/c.1274 (hnRNP A1)→site broken | ||||
| NNSplice (0.9) | "wt" donor site broken (0.91/-) | Scores predicted for the wt seq/score predicted for the mut seq | ||
| NetGene2 Server | "wt" donor site broken (0.83/-) | Scores predicted for the wt seq/score predicted for the mut seq | ||
| MSH2 (intron 3) | c.646/46delC |
Human Splice Finder (v.2.4) (HSF) (*) ESE Finder Rescue ESE PESE octamers EIEs (Zhang et al) No ESE from HSF change Silencer motifs/no (Sironi et al) motif ESS (Wang et al) found IIEs (Zhang et al) hnRNP motifs Other splicing motifs (Goren et al) |
Variation in one of the potential branch points (c.646-48) (79.39/23.83) | Scores predicted for the wt seq/score predicted for the mut seq |
| PESS octamers: c.646-49 (46.39/87.56)/c.646-46→ new site | ||||
| NNSplice (0.9) | SD: 0.90/0.90 No SA: 0.90/0.91 change |
Scores predicted for the wt seq/score predicted for the mut seq | ||
| NetGene2 Server | SD: 0.76/0.76 No SA: 0.23/0.25 change |
Scores predicted for the wt seq/score predicted for the mut seq |
(*) these algorithms are included in the HSF analysis