Interpretation of the colossal number of genetic variants identified from sequencing applications is one of the major bottlenecks in clinical genetics, with the inference of the effect of amino acid-substituting missense variations on protein structure and function being especially challenging. Here we characterize the three-dimensional (3D) amino acid positions affected in pathogenic and population variants from 1,330 disease-associated genes using over 14,000 experimentally solved human protein structures. By measuring the statistical burden of variations (i.e., point mutations) from all genes on 40 3D protein features, accounting for the structural, chemical, and functional context of the variations' positions, we identify features that are generally associated with pathogenic and population missense variants. We then perform the same amino acid-level analysis individually for 24 protein functional classes, which reveals unique characteristics of the positions of the altered amino acids: We observe up to 46% divergence of the class-specific features from the general characteristics obtained by the analysis on all genes, which is consistent with the structural diversity of essential regions across different protein classes. We demonstrate that the function-specific 3D features of the variants match the readouts of mutagenesis experiments for BRCA1 and PTEN, and positively correlate with an independent set of clinically interpreted pathogenic and benign missense variants. Finally, we make our results available through a web server to foster accessibility and downstream research. Our findings represent a crucial step toward translational genetics, from highlighting the impact of mutations on protein structure to rationalizing the variants' pathogenicity in terms of the perturbed molecular mechanisms.

Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA 02114

Center for the Development of Therapeutics Broad Institute of MIT and Harvard Cambridge MA 02142

Center for the Development of Therapeutics Broad Institute of MIT and Harvard Cambridge MA 02142;

Cologne Center for Genomics University of Cologne 50931 Cologne Germany

Computer Science and Engineering Bangladesh University of Engineering and Technology Dhaka 1205 Bangladesh

Department of Bio and Health Informatics Technical University of Denmark 2800 Kgs Lyngby Denmark

Department of Software Engineering Faculty of Mathematics and Physics Charles University Prague 11636 Czech Republic

Department of Surgery Massachusetts General Hospital Boston MA 02114

Epilepsy Center Neurological Institute Cleveland Clinic Cleveland OH 44195

Genomic Medicine Institute Lerner Research Institute Cleveland Clinic Cleveland OH 44195

Institute for Molecular Medicine Finland University of Helsinki 00100 Helsinki Finland

Luxembourg Centre for Systems Biomedicine University of Luxembourg 4365 Esch sur Alzette Luxembourg

Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA 02142

Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA 02142

Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA 02142;

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