Utilizing the Genome Aggregation Database, Computational Pathogenicity Prediction Tools, and Patch Clamp Heterologous Expression Studies to Demote Previously Published Type 1 Long QT Syndrome Mutations from Pathogenic to Benign

Abstract

Background:

Mutations in the KCNQ1-encoded Kv7.1 potassium channel cause type 1 long QT syndrome (LQT1). It has been suggested that ~10-20% of rare LQTS case-derived variants in the literature may have been published erroneously as LQT1-causative mutations and may be “false positives.”

Objective:

To determine which previously published KCNQ1 case variants are likely false positives.

Methods:

A list of all published, case-derived KCNQ1 missense variants (MVs) was compiled. The occurrence of each MV within the Genome Aggregation Database (gnomAD) was assessed. Eight in silico tools were used to predict each variant’s pathogenicity. Case-derived variants that either i) were too frequently found in gnomAD or ii) were absent in gnomAD but predicted to be pathogenic by ≤ 2 tools were considered potential false positives. Three of these variants were characterized functionally using whole cell patch clamp technique.

Results:

Overall, there were 244 KCNQ1 case-derived MVs. Of these, 29 (12%) were seen in ≥ 10 individuals in gnomAD and are demotable. However, 157/244 (64%) MVs were absent in gnomAD. Of these, 7 (4%) were predicted to be pathogenic by ≤ 2 tools, 3 of which we characterized functionally. There was no significant difference in current density between heterozygous KCNQ1-F127L, -P477L, or -L619M variant-containing channels compared to KCNQ1-WT.

Conclusion:

Here, we offer preliminary evidence for the demotion of 32 (13%) previously published LQT1 MVs. Of these, 29 MVs were demoted because of their frequent sighting in gnomAD. Additionally, in silico analysis and in vitro functional studies have facilitated the demotion of three ultra-rare MVs (F127L, P477L, and L619M).