Patch-clamp dataset (SyncroPatch384PE) for control variants used in a calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome

Modern sequencing technologies have revolutionised our detection of gene
variants. However, in most genes, including KCNH2, the majority
of missense variants are currently classified as variants of
uncertain significance (VUS). The aim of this study was to
investigate the utility of an automated patch-clamp assay for aiding
clinical variant classification in
the KCNH2 gene. The assay was designed
according to recommendations proposed by the ClinGen Sequence Variant
Interpretation Working Group. Thirty-one variants (17 pathogenic/likely
pathogenic, 14 benign/likely benign) were classified internally as variant
controls. They were heterozygously expressed in Flp-In HEK293 cells for
assessing the effects of variant on current density and channel gating in
order to determine the sensitive and specificity of the assay. All 17
pathogenic variant controls had reduced current density and 13/14 benign
variant controls had normal current density, which enabled determination
of normal and abnormal ranges for applying moderate or supporting evidence
strength for VUS reclassification. Inclusion
of KCNH2 functional assay evidence enabled us to
reclassify 6 out of 44 VUS as likely pathogenic. The high-throughput patch
clamp assay can provide moderate strength evidence for clinical
interpretation of clinical KCNH2 variants
and demonstrates the value of developing automated patch clamp
assays for functional characterisation of ion channel gene variants.