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bioRxiv · 10.1101/2021.07.10.451881

A Massively Parallel Trafficking Assay Accurately Predicts Loss of Channel Function in KCNH2 Variants

Ng, C. A.·Ullah, R.·Farr, J.·Hill, A. P.·Kozek, K. A.·Vanags, L. R.·Mitchell, D. W.·Kroncke, B. M.·Vandenberg, J. I.
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Abstract

High throughput genomics has greatly facilitated identification of genetic variants. However, determining which variants contribute to disease causation is challenging with more than half of all missense variants now classified as variants of uncertain significance (VUS). A VUS leaves patients and their clinicians unable to utilize the variant information in clinical decision-making. In long QT syndrome type 2, KCNH2 channel function is directly associated with disease presentation. Therefore, functional phenotyping of KCNH2 variants can provide direct evidence to aid variant classification. Here, we investigated the expression of all codon variants in exon 2 of KCNH2 using a massively parallel trafficking assay and for a subset of 458 single nucleotide variants compared the results with peak tail current density and gating using automated patch clamp electrophysiology. Trafficking could correctly classify loss of peak tail current density variants with an AUC reaching 0.94 compared to AUCs of 0.75 to 0.8 for in silico variant classifiers. We suggest massively parallel trafficking assays can provide prospective and accurate functional assessment for all missense variants in KCNH2 and most likely many other ion channels and membrane proteins.

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Ng, C. A., Ullah, R., Farr, J., Hill, A. P., Kozek, K. A., Vanags, L. R., Mitchell, D. W., Kroncke, B. M., Vandenberg, J. I.. 2021-07-11. A Massively Parallel Trafficking Assay Accurately Predicts Loss of Channel Function in KCNH2 Variants. https://doi.org/10.1101/2021.07.10.451881

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