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Utilization of the genome aggregation database, in silico tools, and heterologous expression patch-clamp studies to identify and demote previously published type 2 long QT syndrome: Causative variants from pathogenic to likely benign

  • Connor L. Mattivi
    Affiliations
    Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology & Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
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  • Dan Ye
    Affiliations
    Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology & Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
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  • David J. Tester
    Affiliations
    Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology & Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota

    Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Mayo Clinic, Rochester, Minnesota
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  • Daniel J. Clemens
    Affiliations
    Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology & Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
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  • Wei Zhou
    Affiliations
    Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology & Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota
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  • John R. Giudicessi
    Affiliations
    Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Mayo Clinic, Rochester, Minnesota
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  • Michael J. Ackerman
    Correspondence
    Address reprint requests and correspondence: Dr Michael J. Ackerman, Mayo Clinic Windland Smith Rice Sudden Death Genomics Laboratory, Guggenheim 501, Mayo Clinic, 200 First St SW, Rochester, MN 55905.
    Affiliations
    Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology & Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota

    Department of Pediatric and Adolescent Medicine, Division of Pediatric Cardiology, Mayo Clinic, Rochester, Minnesota
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Published:September 05, 2019DOI:https://doi.org/10.1016/j.hrthm.2019.08.014

      Background

      Loss-of-function variants in the KCNH2-encoded Kv11.1 potassium channel cause long QT syndrome (LQTS) type 2 (LQT2). Presently, hundreds of KCNH2 missense variants (MVs) have been published as “disease-causative.” However, an estimated 10% of rare published LQTS MVs may be “false positives.”

      Objective

      The purpose of this study was to determine which published KCNH2 MVs are likely false positives and warrant demotion to “likely benign” status.

      Methods

      A list of 337 LQT2-associated MVs from 6 large compendia was compiled. MV frequency within the Genome Aggregation Database (gnomAD) (n = 141,352 individuals) was assessed, and MVs were analyzed with 8 in silico tools. Variants with minor allele frequency (MAF) >7*10E-6, the calculated maximum credible frequency of LQT2, and predicted “benign” by all tools were demoted to “likely benign.” Ultra-rare variants (n = 8) absent in gnomAD but predicted “benign” by all tools were considered as potential false positives and were characterized functionally using whole-cell patch clamp.

      Results

      Overall, 14 of 337 published KCNH2 MVs (4%) were observed at MAF >7*10E-6, whereas 252 of 337 (75%) were absent in gnomAD. Among the latter, 8 variants (I96V, G187S, A203T, P241L, H254Q, G314S, P935S, P963T) were predicted benign by 8 tools and lacked characterization. Patch clamp showed no functional perturbation for these 8 MVs.

      Conclusion

      This study offers compelling evidence for the demotion of 22 of 337 KCNH2 variants (6.5%) in the literature. Meticulous “pruning” of compendia using exome/genome databases, in silico tools, and in vitro functional studies must be conducted not only for putatively pathogenic LQTS MVs but for the entire field of genetic heart disease.

      Keywords

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