The 3D mutational constraint on amino acid sites in the human proteome

Quantification of the tolerance of protein sites to genetic variation has become a cornerstone of variant interpretation. We hypothesize that the constraint on missense variation at individual amino acid sites is largely shaped by direct interactions with 3D neighboring sites. To quantify this constraint, we introduce a framework called COntact Set MISsense tolerance (or COSMIS) and comprehensively map the landscape of 3D mutational constraint on 6.1 million amino acid sites covering 16,533 human proteins. We show that 3D mutational constraint is pervasive and that the level of constraint is strongly associated with disease relevance both at the site and the protein level. We demonstrate that COSMIS performs significantly better at variant interpretation tasks than other population-based constraint metrics while also providing structural insight into the functional roles of constrained sites. We anticipate that COSMIS will facilitate the interpretation of protein-coding variation in evolution and prioritization of sites for mechanistic investigation. Here, Li et al. integrate population genetic and protein structural perspectives to map the landscape of 3D constraint on 80% of human proteins. They show that 3D mutational constraint is pervasive and strongly associated with functional relevance.

Automated summary

In this study, Li et al. map the landscape of 3D constraint on 80% of human proteins using population genetic and protein structural perspectives. They demonstrate that 3D mutational constraint is pervasive and strongly associated with functional relevance.