Likelihood ratio calibration aligns MAVE and automated patch-clamp functional evidence for KCNH2 variants in long QT syndrome.

KCNH2

Conversion of automated patch-clamp results into likelihood ratios using reference sets of pathogenic and benign KCNH2 variants, then mapping to ACMG/AMP functional evidence categories and comparison with previously calibrated MAVE data

Many people with long QT syndrome carry missense variants classified as variants of uncertain significance, and functional evidence from laboratory experiments needs proper validation before use in a clinical interpretation framework. The authors compared two functional datasets for KCNH2: a high-throughput assay (MAVE) that measures how much Kv11.1 channel reaches the cell surface, and automated patch clamp, which measures potassium current in HEK293 cells. Patch-clamp results were converted into likelihood ratios using reference sets of pathogenic and benign KCNH2 variants, mapped to ACMG/AMP functional evidence categories, and compared with previously calibrated MAVE evidence for 495 single-nucleotide KCNH2 variants found in individuals with long QT syndrome. Interpretations were concordant for 392 of the 495 variants (79%); of the remaining 103, 49 shifted between normal and abnormal functional evidence and 54 between a functional evidence category and an indeterminate result. Among variants assigned strong abnormal evidence by both assays, 54 were absent from ClinVar, and 92 of the 111 unresolved or conflicting ClinVar variants would reach an evidence combination sufficient for a likely pathogenic classification when strong functional evidence was combined with supporting computational and population-frequency evidence.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

Likelihood ratio calibration is what makes the two assays usable within the ACMG/AMP framework: without it they measure different quantities, with it they are expressed as comparable levels of evidence. With 103 discordances among 495 variants, the choice of assay changes the functional weight of roughly one variant in five, and the 92 possible likely pathogenic classifications remain conditional on supporting computational and frequency evidence, not on function alone. On an exome or a genome, where KCNH2 is already sequenced, this interpretation step decides the reported result, and the abstract does not say which assay to favour when the two diverge.

Analysis by Dr Thibaut Benquey