Pervasive mislocalization of pathogenic coding variants underlying human disorders

Widespread sequencing has yielded thousands of missense variants predicted or confirmed as disease causing. This creates a new bottleneck: determining the functional impact of each variant—typically a painstaking, customized process undertaken one or a few genes and variants at a time. Here, we established a high-throughput imaging platform to assay the impact of coding variation on protein localization, evaluating 3,448 missense variants of over 1,000 genes and phenotypes. We discovered that mislocalization is a common consequence of coding variation, affecting about one-sixth of all pathogenic missense variants, all cellular compartments, and recessive and dominant disorders alike. Mislocalization is primarily driven by effects on protein stability and membrane insertion rather than disruptions of trafficking signals or specific interactions. Furthermore, mislocalization patterns help explain pleiotropy and disease severity and provide insights on variants of uncertain significance. Our publicly available resource extends our understanding of coding variation in human diseases. [Display omitted] •Screen for missense variant mislocalization for 3,448 variants across 1,269 genes•16% of pathogenic or likely pathogenic variants are mislocalized•Mislocalization is mainly caused by disruption of protein stability•Distinct localization patterns are associated with pleiotropy and disease severity Pathogenic missense variation can affect protein function in many ways, but the role of protein mislocalization has not been systematically assessed. By characterizing the localization of 3,400 missense variants of over 1,000 genes, we discovered that mislocalization is an unexpectedly common molecular phenotype of coding variation.