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


* SD: splice donor, SA: splice acceptor, BP: branch point aa: aminoacid

** These algorithms are included in the HSF analysis

Thodi et al. BMC Cancer 2010 10:544   doi:10.1186/1471-2407-10-544

Open Data