Comprehensive Variant Effect Map of Parkin-Mediated Mitophagy in Parkinson’s Disease

Abstract The development of Parkinson’s disease (PD) has a substantial genetic basis. Variants in the PRKN gene account for roughly half of autosomal-recessive PD cases, yet most variants remain classified as variants of uncertain significance. PRKN encodes the E3 ubiquitin-protein ligase, Parkin, that plays a key role in mitochondrial quality control by initiating mitophagy. In this work, we introduce a multiplexed mitophagy assay and measure the activity of more than 99% of all possible single–amino acid substitution and nonsense variants of Parkin. We also demonstrate that misfolded, rapidly degraded variants autonomously trigger Parkin-independent mitophagy. The obtained activity landscape closely reflects known structural and functional aspects of Parkin while revealing new insights into specific functional effects across the protein. This dataset near-perfectly distinguishes pathogenic from benign variants and surpasses both computational predictors and abundance-based metrics in pathogenicity assessment. Finally, the data pinpoint hypomorphic variants that could be amenable to rescue in future personalized therapeutic approaches for PD.