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. Author manuscript; available in PMC: 2010 Jan 15.
Published in final edited form as: Mutat Res. 2008 Oct 17;660(1-2):1–11. doi: 10.1016/j.mrfmmm.2008.09.017

Table 3.

Bioinformatics predictions of the impact of BRCA1 variants in the BRCT domains.

Variant LS-SNP SIFT PolyPhen nsSNPanalyzer PMUT Panther
M1652I Neutral Tolerated Benign Disease Pathological Not deleterious
A1669S Neutral Tolerated Benign Neutral Neutral Not deleterious
T1685I Deleterious Not Tolerated Probably Damaging Disease Pathological Deleterious
M1689R Deleterious Tolerated Probably Damaging Disease Pathological Deleterious
R1699W Deleterious Not Tolerated Probably Damaging Disease Pathological Deleterious
R1699Q Deleterious Tolerated Probably Damaging Disease Pathological Deleterious
G1706E Deleterious Not Tolerated Probably Damaging Disease Pathological Deleterious
A1708E Deleterious Not Tolerated Probably Damaging Neutral Pathological Deleterious
S1715R Deleterious Not Tolerated Probably Damaging Disease Pathological Deleterious
T1720A Neutral Not Tolerated Possibly Damaging Neutral Neutral Not deleterious
V1736A Deleterious Tolerated Possibly Damaging Disease Pathological Deleterious
G1738R Deleterious Tolerated Probably Damaging Disease Pathological Deleterious
L1764P Deleterious Not Tolerated Probably Damaging Disease Pathological Deleterious
I1766S Deleterious Not Tolerated Probably Damaging Disease Pathological Deleterious
M1775K Deleterious Tolerated Probably Damaging Disease Pathological Deleterious
M1775R Deleterious Tolerated Probably Damaging Disease Pathological Deleterious
G1788V Deleterious Tolerated Probably Damaging Disease Pathological Deleterious
V1804D Neutral Not Tolerated Benign Neutral Pathological Not deleterious
Q1826H Neutral Tolerated Probably Damaging Neutral Pathological Deleterious
V1833M Deleterious Tolerated Benign Disease Neutral Deleterious

The three BRCT missense variants analyzed in this study are shaded in gray. We also show predictions of 17 additional BRCA1 variants for which there is a genetic or integrative classification available (“Validation set”, Table 2). Red in the “Variant” column indicates that the genetic or integrative classification is deleterious; Blue that it is neutral. We compare the predictions of our LS-SNP method [18,25] with SIFT [40], PolyPhen [41], nsSNPanalyzer [42], PMUT [43] and Panther [44].