Genetic intolerance analysis as a tool for protein science.

Abstract Recent advances in whole genome and exome sequencing have dramatically increased the database of human gene variations. There are now enough sequenced human exomes and genomes to begin to identify gene variations that are notable because they are NOT observed in sequenced human genomes, apparently because they are subject to “purifying selection”, exemplifying genetic intolerance. Such “dysprocreative” gene variations are embryonic lethal or prevent reproduction through any one of a number of possible mechanisms. Here we review an emerging quantitative approach, “Missense Tolerance Ratio” (MTR) analysis, that is used to assess protein-encoding gene (cDNA) sequence intolerance to missense mutations based on analysis of the >100 K currently available human genome and exome sequences. This approach is already useful for analyzing intolerance to mutations in cDNA segments with a resolution on the order of 90 residues. Moreover, as the number of sequenced genomes/exomes increases by orders of magnitude it may eventually be possible to assess mutational tolerance in a statistically robust manner at or near single site resolution. Here we focus on how cDNA intolerance analysis complements other bioinformatic methods to illuminate structure-folding-function relationships for the encoded proteins. A set of disease-linked membrane proteins is employed to provide examples.