Protein Function by Gene.

Overlap of SIFT [13], T - Tolerated, I - Intolerant (tolerance index score , as suggested by the software documentation), I-LC - Intolerant with Low Confidence (tolerance index score , but median sequence conservation score ); PMUT [14], Neut - Neutral, Path - Pathological; and PolyPhen [15], Ben - Benign, Poss = Possibly Damaging, Prob = Probably Damaging. Bolded counts indicate where one method is the opposite of the other, where we allow I-LC and Poss to go either way. There was a pairwise concordance between SIFT and PMUT, where we allowed SIFT I-LC to match to either PMUT pathological or PMUT neutral; concordance between SIFT and PolyPhen, where we allowed SIFT I-LC to match to anything PolyPhen; and concordance between PMUT and PolyPhen where we allowed SIFT I-LC to match to anything and PolyPhen Poss to match to anything.