Clinical interpretation of KCNH2 variants using a robust PS3/BS3 functional patch-clamp assay

Area of Science:

• Cardiovascular Genetics
• Molecular Cardiology
• Genetic Variant Interpretation

Background:

• Long QT syndrome (LQTS) is a genetic disorder affecting cardiac ion channels, increasing sudden death risk.
• Genetic diagnosis for LQTS is challenging due to insufficient evidence for many gene variants.
• KCNH2 is a key gene implicated in LQTS pathogenesis.

Purpose of the Study:

• To develop and validate a robust functional assay for classifying missense variants in the KCNH2 gene.
• To establish a quantitative measure (Z score) for ion channel dysfunction.
• To integrate functional data into genetic variant classification frameworks.

Main Methods:

• Established a functional patch-clamp assay using a curated set of benign and pathogenic KCNH2 missense variants.
• Quantified protein function reduction using Z scores relative to normal controls.
• Validated the assay in a cohort of childhood LQTS patients by correlating Z scores with clinical parameters.

Main Results:

• The assay reliably distinguished between benign and pathogenic KCNH2 variants.
• A Z score threshold of -2 was established, indicating significant loss of function (below 55% wild-type).
• Functional assay results correlated with clinical LQTS scores (Schwartz score) and QTc interval length.

Conclusions:

• The developed functional assay provides a quantitative method for KCNH2 variant classification.
• Z scores can inform genetic variant interpretation within established frameworks (ACMG PS3/BS3 criteria).
• This approach aids in diagnosing LQTS and assessing patient risk.