Missense variants pathogenicity annotation from homologous proteins

Abstract

Motivation: High-throughput DNA sequencing has revealed millions of single nucleotide variants (SNVs) in the human genome, with a small fraction linked to disease. The effect of missense variants, which alter the protein sequence, is particularly challenging to interpret due to the scarcity of clinical annotations and experimental information. While using conservation and structural information, current prediction tools still struggle to predict variant pathogenicity. In this study, we explored the pathogenicity of homologous missense variants—variants in equivalent positions across homologous proteins—focusing on proteins involved in autosomal dominant diseases. Results: Our analysis of 2976 pathogenic and 17 555 non-pathogenic homologous variants demonstrated that pathogenicity can be extrapolated with 95% accuracy within a family, or up to 98% for closer homologs. Remarkably, the evaluation of 27 commonly used mutation predictor methods revealed that they were not fully capturing this biological feature. To facilitate the exploration of homologous variants, we created HomolVar, a web server that computationally predicts the pathogenesis of missense variants using annotations from homologous variants, freely available at https://rarevariants.org/HomolVar. Overall, these findings and the accompanying tool offer a robust method for predicting the pathogenicity of unannotated variants, enhancing genotype-phenotype correlations, and contributing to diagnosing rare genetic disorders. Availability and implementation: HomolVar is freely available at https://rarevariants.org/HomolVar.