Table 1.

Summary of Mutation Datasets

Dataset	Proteins	Amino acid substitutions	Description
HGMD	2,298	49,532	Inherited disease-causing mutations from HGMD used to calculate our pathogenicity weights
UniProt	11,548	36,928	Inherited putative functionally neutral mutations from UniProt used to calculate our pathogenicity weights
VariBench	9,684	40,470	Benchmarking dataset used in a review of nine alternative computational prediction algorithms [Thusberg et al., 2011]
Hicks et al. 2011	4	267	Benchmarking dataset consisting of both disease-causing and functionally neutral mutations in four well-characterized genes (BRCA1, MSH2, MLH1, TP53) used in a recent review of four alternative prediction algorithms [Hicks et al., 2011]
SwissVar	11,986	59,976	Benchmarking dataset used as an independent benchmark of eight alternative prediction algorithms