A comprehensive map of missense trafficking mutations in rhodopsin and their response to pharmacologic correction
In this study, we present systematic quantification of surface expression for all possible single residue missense variants (6,612), nonsense variants (348), and synonymous variants of RHO. We measure pathogenic levels of surface trafficking for 11.4% of all missense variants, including annotated Class 2 variants, as expected, as well as several annotated Class 3 variants and no other mechanistic classes. These mistrafficking variants are spatially concentrated in the N-terminus and extracellular loop 2 (ECL2), which form a cap over the retinal-binding pocket, and are enriched for likely pathogenic and pathogenic ClinVar clinical significance annotations, strongly suggesting that VUS with trafficking defects as measured in these assays likely have pathogenic misfolding. Our trafficking DMS scores outperform most computational predictors in their ability to predict pathogenicity despite being designed to measure only one of the seven disease mechanisms (misfolding). Treatment with the literature small molecule corrector YC-001 significantly rescues trafficking for more than 50% of these misfolding and mistrafficking variants. Taken together, our results provide functional in vitro data for all possible RHO missense variants that improve our understanding of RHO biology, suggest updated mechanistic class and clinical significance variant annotations, and support the development of a precision medicine correctors approach for RP caused by misfolding and mistrafficking RHO variants.