Using the genome aggregation database, computational pathogenicity prediction tools, and patch clamp heterologous expression studies to demote previously published long QT syndrome type 1 mutations from pathogenic to benign

Abstract

<div class="section"> <a class="named-anchor" id="S1"> <!-- named anchor --> </a> <h5 class="section-title" id="d5709127e189">Background:</h5> <p id="P1">Mutations in the <i>KCNQ1</i>-encoded Kv7.1 potassium channel cause type 1 long QT syndrome (LQT1). It has been suggested that ~10-20% of rare LQTS case-derived variants in the literature may have been published erroneously as LQT1-causative mutations and may be “false positives.” </p> </div><div class="section"> <a class="named-anchor" id="S2"> <!-- named anchor --> </a> <h5 class="section-title" id="d5709127e197">Objective:</h5> <p id="P2">To determine which previously published <i>KCNQ1</i> case variants are likely false positives. </p> </div><div class="section"> <a class="named-anchor" id="S3"> <!-- named anchor --> </a> <h5 class="section-title" id="d5709127e205">Methods:</h5> <p id="P3">A list of all published, case-derived <i>KCNQ1</i> missense variants (MVs) was compiled. The occurrence of each MV within the Genome Aggregation Database (gnomAD) was assessed. Eight <i>in silico</i> tools were used to predict each variant’s pathogenicity. Case-derived variants that either i) were too frequently found in gnomAD or ii) were absent in gnomAD but predicted to be pathogenic by ≤ 2 tools were considered potential false positives. Three of these variants were characterized functionally using whole cell patch clamp technique. </p> </div><div class="section"> <a class="named-anchor" id="S4"> <!-- named anchor --> </a> <h5 class="section-title" id="d5709127e216">Results:</h5> <p id="P4">Overall, there were 244 <i>KCNQ1</i> case-derived MVs. Of these, 29 (12%) were seen in ≥ 10 individuals in gnomAD and are demotable. However, 157/244 (64%) MVs were absent in gnomAD. Of these, 7 (4%) were predicted to be pathogenic by ≤ 2 tools, 3 of which we characterized functionally. There was no significant difference in current density between heterozygous KCNQ1-F127L, -P477L, or -L619M variant-containing channels compared to KCNQ1-WT. </p> </div><div class="section"> <a class="named-anchor" id="S5"> <!-- named anchor --> </a> <h5 class="section-title" id="d5709127e224">Conclusion:</h5> <p id="P5">Here, we offer preliminary evidence for the demotion of 32 (13%) previously published LQT1 MVs. Of these, 29 MVs were demoted because of their frequent sighting in gnomAD. Additionally, <i>in silico</i> analysis and <i>in vitro</i> functional studies have facilitated the demotion of three ultra-rare MVs (F127L, P477L, and L619M). </p> </div>