Prognostic Value of Multiplexed Assays of Variant Effect and Automated Patch-clamping for KCNH2-LQTS Risk Stratification

Background Long QT syndrome (LQTS) is a lethal arrhythmia condition, frequently caused by rare loss-of-function variants in the cardiac potassium channel encoded by KCNH2 . Variant-based risk stratification is complicated by heterogenous clinical data, incomplete penetrance, and low-throughput functional data. Objective To test the utility of variant-specific features, including high-throughput functional data, to predict cardiac events among KCNH2 variant heterozygotes. Methods We quantified cell-surface trafficking of 18,323 variants in KCNH2 and recorded potassium current densities for 506 KCNH2 variants. Next, we deeply phenotyped 1150 KCNH2 missense variant patients, including ECG features, cardiac event history (528 total cardiac events), and mortality. We then assessed variant functional, in silico , structural, and LQTS penetrance data to stratify event-free survival for cardiac events in the study cohort. Results Variant-specific current density (HR 0.28 [0.13-0.60]) and estimates of LQTS penetrance incorporating MAVE data (HR 3.16 [1.59-6.27]) were independently predictive of severe cardiac events when controlling for patient-specific features. Risk prediction models incorporating these data significantly improved prediction of 20 year cardiac events (AUC 0.79 [0.75-0.82]) over patient-only covariates (QTc and sex) (AUC 0.73 [0.70-0.77]). Conclusion We show that high-throughput functional data, and other variant-specific features, meaningfully contribute to both diagnosis and prognosis of a clinically actionable monogenic disease. Graphical Abstract Implementation of KCNH2 variant functional studies, deep clinical phenotyping, and cardiac event risk stratification. ![Figure][1] ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was funded by the National Institutes of Health: F30HL163923-01 (MJO), T32GM007347 (MJO), R01HL164675 (AMG, DMR, and BMK), and R01HL160863 (BMK); by the Leducq Transatlantic Network of Excellence Program 18CVD05 (LS, LC, PJS, and BMK); by the New South Wales Cardiovascular Disease Senior Scientist grant (JIV), and a MRFF Genomics Health Futures Mission grant (CAN/JIV). Flow cytometry experiments were performed in the Vanderbilt Flow Cytometry Shared Resource. The Vanderbilt Flow Cytometry Shared Resource is supported by the Vanderbilt Ingram Cancer Center (P30 CA68485) and the Vanderbilt Digestive Disease Research Center (DK058404). We also acknowledge support from the Victor Chang Cardiac Research Institute Innovation Centre, funded by the NSW Government. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: IRB of Vanderbilt University Medical Center gave ethical approval for this work under #191563 "Estimating LQT2 Penetrance Caused by Common and Rare Variants in KCNH2". I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All non-participant-level data are contained in the manuscript. Data analysis pipelines are fully available at https://github.com/kroncke-lab. Prospective data for KCNH2 variant interpretation are hosted at https://variantbrowser.org/. [1]: pending:yes