A tool to predict the effect of missense variants Polyphen, now available in its version Polyphen-2, predicts the impact of a missense variant (also referred to as nsSNP: non synonymous single nucleotide polymorphism) based on (1) protein sequence (2) phylogenetic information and (3) structural information. So Polyphen is able to do the so called functional annotation of missense variants.

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