Challenges in Classification of PKD1 Missense Variation in Autosomal Dominant Polycystic Kidney Disease
TL;DR
A large majority of PKD1 missense variants are classified as VUS with current pathogenicity criteria, and commonly used silico tools, applied with established genome-wide thresholds, do not reliably distinguish pathogenic and benign missense variants in PKD1.
Abstract
Purpose: Autosomal Dominant Polycystic Kidney Disease is the most common monogenic kidney disease and largely due to variants in PKD1. We aimed to assess pathogenicity evidence for PKD1 missense variants in disease databases and evaluate in silico pathogenicity prediction tool performance. Methods: PKD1 missense variants reported as pathogenic, likely pathogenic or likely benign were extracted from ClinVar and PKDB. Variants were re-classified using ACMG/AMP criteria to identify "truth sets" of pathogenic and benign variants. In silico scores were obtained from five tools (SIFT, PolyPhen-2, CADD, REVEL, AlphaMissense) and evaluated using established thresholds. A Receiver Operating Characteristic curve analysis was performed using the PKD1 variant truth sets. Results: 346/389 (89%) reported disease-causing missense variants in PKD1 were downgraded to Variants of Unknown Significance (VUS) using current classification criteria. Based on current thresholds, REVEL achieved the highest sensitivity of 62%, with specificity of 79%. AlphaMissense was the only tool not to misclassify any truth set variants, but many of the variant scores were between the pathogenic and benign thresholds. Conclusion: A large majority of PKD1 missense variants are classified as VUS with current pathogenicity criteria. Commonly used in silico tools, applied with established genome-wide thresholds, do not reliably distinguish pathogenic and benign missense variants in PKD1.