Likely Pathogenicity of Uncharacterized KCNQ1 and KCNE1 Variants

Background: Voltage-gated potassium channels Kv7.1 encoded by gene KCNQ1 play critical roles in various physiological processes. In cardiomyocytes, complex Kv7.1-KCNE1 mediates the slow component of delayed rectifier potassium current that is essential for the action potential repolarization. Over 1,000 KCNQ1 missense variants, many of which are associated with long QT syndrome, are reported in ClinVar and other databases. However, over 600 variants are of uncertain clinical significance (VUS), have conflicting interpretations of pathogenicity or lack germline information. Computational prediction of damaging potential of such variants is important for diagnostics and treatment of cardiac disease. Methods and Results: We collected 1,750 benign and pathogenic missense variants of Kv channels from databases ClinVar, Humsavar and Ensembl Variation and tested 26 bioinformatics tools in their ability to identify known damaging variants. The best-performing tool, AlphaMissense, correctly predicted pathogenicity of 195 VUSs in Kv7.1. Among these, 79 variants of 66 wildtype residues (WTRs) are also reported as pathogenic or likely pathogenic (P/LP) in sequentially matching positions of at least one paralogue of hKv7.1. In available cryoEM structures of Kv7.1 with activated and deactivated voltage sensing domains, 52 WTRs form intersegment contacts with WTRs of ClinVar-listed variants, including 21 WTRs with P/LP variants. Analysis of state-dependent contacts suggests atomic mechanisms of dysfunction for some variants. ClinPred and paralogues annotation methods consensually predicted that 21 WTRs of KCNE1 have 34 VUSs with damaging potential. Among these, eight WTRs are contacting 23 Kv7.1 WTRs with 13 ClinVar-listed variants in AplhaFold3 model. Conclusions: Bioinformatics tools, including the paralogue annotation method, predicted likely pathogenicity of 79 VUSs in Kv7.1 and 34 VUSs in KCNE1. Analysis of intersegment contacts in CryoEM and AplhaFold3 structures suggests atomic mechanism of dysfunction for some VUSs.