Many diseases,both Mendelian and complex,have been associated with single-nucleotide changes (SNPs) that lead to an amino acid substitution in the encoded protein (nonsynonymous SNPs,or nsSNPs).Because of ascertainment bias,nsSNPs may not necessarily be the dominant cause of human disease.Nevertheless,nsSNPs provide an excellent testing ground for using evolutionary analysis to predict the functional effects of genetic variation,as computational methods for inferring selective pressure in protein-coding sequences are well-established.We have applied models of both negative and positive selection.One signature of negative selection is that in groups of related protein sequences,many positions in the protein are "conserved",for instance,all serine proteases must possess the catalytic serine residue.To quantify this negative selection,we developed a "substitution position-specific evolutionary conservation" (subPSEC) score,a statistical measure of the likelihood of a particular amino acid substitution being deleterious.