This document summarizes methods for predicting the functional effects of amino acid substitutions, including SIFT (Sorts Intolerant From Tolerant), which uses sequence conservation to predict whether an amino acid substitution will affect protein function. SIFT has similar prediction accuracy to tools using protein structure. Case studies on disease genes like MSHR, PPARα, and MTHFR show SIFT can distinguish pathogenic from benign variants and detect variants under balancing selection. Focusing genetic association studies on predicted functional variants in genes and conserved non-coding regions improves the direct approach to finding disease loci.