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.

对测序应用中鉴定出的大量遗传变异的解释是临床遗传学的主要瓶颈之一，推断氨基酸取代错义变异对蛋白质结构和功能的影响尤其具有挑战性。在这里，我们使用超过 14,000 个经过实验解决的人类蛋白质结构，描述了 1,330 个疾病相关基因的致病性和群体变异中受影响的三维 (3D) 氨基酸位置。通过测量 40 个 3D 蛋白质特征上所有基因的变异（即点突变）的统计负担，考虑变异位置的结构、化学和功能背景，我们识别出通常与致病性和群体错义相关的特征变种。然后，我们对 24 个蛋白质功能类别分别进行相同的氨基酸水平分析，这揭示了改变的氨基酸位置的独特特征：我们观察到类别特异性特征与通过对所有基因的分析，这与不同蛋白质类别的重要区域的结构多样性一致。我们证明，变体的功能特异性 3D 特征与 BRCA1 和 PTEN 诱变实验的读数相匹配，并与一组独立的临床解释的致病性和良性错义变体呈正相关。最后，我们通过网络服务器提供我们的结果，以促进可访问性和下游研究。 我们的研究结果代表了转化遗传学的关键一步，从强调突变对蛋白质结构的影响到根据扰动的分子机制合理化变异的致病性。