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| SIFT/PolyPhen Data |
Putative functional changes in a candidate gene's protein function were assessed by taking the nonsynonymous coding SNPs (cSNPs) for each gene and using both SIFT and Polyphen. Generally, each nonsynonymous amino acid change is analyzed in the context of other evolutionarily similar proteins to determine the likelihood of the polymorphic nonsynonymous change, and then statistically classified. Each of these programs classifies each coding SNP as tolerant or intolerant (SIFT), or benign, possibly damaging, probably damaging (Polyphen). For literature references detailing the specific algorithms implemented by SIFT and Polyphen, see:
Ng and Henikoff, "Accounting for Human Polymorphisms Predicted to Affect Protein Function", Genome Research, 12:436-446, 2002
Ramensky, et al., "Human non-synonymous SNPs: server and survey", Nucleic Acids Research, 30:17:3894-3900, 2002
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