Reclassification of a likely pathogenic Dutch founder variant in KCNH2; implications of reduced penetrance

Abstract

Background: Variants in KCNH2, encoding the hERG channel which is responsible for the rapid component of the cardiac delayed rectifier K+ current (IKr), are causal to Long QT Syndrome type 2 (LQTS2). We identified eight index patients with a new variant of unknown significance (VUS), KCNH2:c.2717C>T:p.(Ser906Leu). We aimed to elucidate the biophysiological effect of this variant, to enable reclassification and consequent clinical decision-making. Methods: A genotype-phenotype overview of the patients and relatives was created. The biophysiological effects were assessed by manual whole-cell patch-clamp using HEK293a cells expressing: (I) wild type (WT) KCNH2, (II) KCNH2-p.S906L alone (homozygous, Hm) or (III) KCNH2-p.S906L in combination with WT (1:1) (heterozygous, Hz). A calibrated automated patch-clamp assay using Flp-In HEK293 was used to follow up on the functional data. Results: Incomplete penetrance of LQTS2 in KCNH2:p.(Ser906Leu) carriers was observed. In addition, some patients were heterozygous for other VUSs in CACNA1C, PKP2, RYR2, or AKAP9. The phenotype of carriers of KCNH2:p.(Ser906Leu) ranged from asymptomatic to life-threatening arrhythmic events. Manual patch-clamp showed a reduced current density by 69.8%, and 60.4% in KCNH2-p.S906L-Hm and KCNH2-p.S906L-Hz, respectively. The time constant of activation was significantly increased with 80.1% in KCNH2-p.S906L-Hm compared to KCNH2-WT. Assessment of KCNH2-p.S906L-Hz, by calibrated automatic patch-clamp showed a reduction in current density by 35.6%. Conclusion: The reduced current density in the KCNH2-p.S906L-Hz indicates a moderate loss of function. Combined with the reduced penetrance and variable phenotype, we conclude that KCNH2:p.(Ser906Leu) is a low penetrant likely pathogenic variant for LQTS2.

Validation of the ACMG/AMP guidelines-based seven-category variant classification system

“…Over the past years, we have witnessed near continuous revolution in terms of the standards and rules governing how to weigh and combine evidence with a view to improving our classification of variants, as reflected by the abovementioned works that have attempted to adapt or refine the ACMG/AMP guidelines [2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17]. Directly or indirectly related to these adaptations or refinements, variant reclassifications (either upgrades or downgrades) have been a frequent occurrence in the literature (e.g., see recent reports [108][109][110][111][112][113][114][115][116][117][118]. It is our hope that our proposed general variant classification framework will stimulate discussion and debate and lead to further improvements in variant classification.…”