Functional Invalidation of Putative Sudden Infant Death Syndrome-Associated Variants in the KCNH2-Encoded Kv11.1 Channel

H1153Y-KCNH2 Mutation Identified in a Sudden Arrhythmic Death Syndrome Case Alters Channel Gating

Long QT syndrome is one of the most common hereditary channelopathies inducing fatal arrhythmias and sudden cardiac death. We identified in a sudden arrhythmic death syndrome case a C-term KCNH2 mutation (c.3457C > T; p.His1153Tyr) classified as variant of unknown significance and functional impact. Heterologous expression in HEK293 cells combined with western-blot, flow-cytometry, immunocytochemical and microscope analyses shows no modification of channel trafficking to the cell membrane. Electrophysiological studies reveal that the mutation causes a loss of HERG channel function through an alteration of channel biophysical properties that reduces the current density leading to LQT2. These results provide the first functional evidence for H1153Y-KCNH2 mutation-induced abnormal channel properties. They concur with previous biophysical and clinical presentations of a survived patient with another variant that is G1036D. Therefore, the present report importantly highlights the potential severity of variants that may have useful implications for treatment, surveillance, and follow-up of LQT2 patients.

Functional evaluation of gene mutations in Long QT Syndrome: strength of evidence from in vitro assays for deciphering variants of uncertain significance

Background

Genetic screening is now commonplace for patients suspected of having inherited cardiac conditions. Variants of uncertain significance (VUS) in disease-associated genes pose problems for the diagnostician and reliable methods for evaluating VUS function are required. Although function is difficult to interrogate for some genes, heritable channelopathies have established mechanisms that should be amenable to well-validated evaluation techniques.

The cellular electrophysiology techniques of ‘voltage-’ and ‘patch-’ clamp have a long history of successful use and have been central to identifying both the roles of genes involved in different forms of congenital Long QT Syndrome (LQTS) and the mechanisms by which mutations lead to aberrant ion channel function underlying clinical phenotypes. This is particularly evident for KCNQ1, KCNH2 and SCN5A, mutations in which underlie > 90% of genotyped LQTS cases (the LQT1-LQT3 subtypes). Recent studies utilizing high throughput (HT) planar patch-clamp recording have shown it to discriminate effectively between rare benign and pathological variants, studied through heterologous expression of recombinant channels. In combination with biochemical methods for evaluating channel trafficking and supported by biophysical modelling, patch clamp also provides detailed mechanistic insight into the functional consequences of identified mutations. Whilst potentially powerful, patient-specific stem-cell derived cardiomyocytes and genetically modified animal models are currently not well-suited to high throughput VUS study.

Conclusion

The widely adopted 2015 American College of Medical Genetics (ACMG) and Association for Molecular Pathology (AMP) guidelines for the interpretation of sequence variants include the PS3 criterion for consideration of evidence from well-established in vitro or in vivo assays. The wealth of information on underlying mechanisms of LQT1-LQT3 and recent HT patch clamp data support consideration of patch clamp data together (for LQT1 and LQT2) with information from biochemical trafficking assays as meeting the PS3 criterion of well established assays, able to provide ‘strong’ evidence for functional pathogenicity of identified VUS.

Trajectory of exonic variant discovery in a large clinical population: implications for variant curation

PURPOSE

Precision health initiatives and reduced sequencing costs are driving large-scale human genome analyses. Genetic variant curation is a bottleneck in clinical applications. The burden of variant curation can be high for newly discovered variants because they are less likely to have undergone previous clinical annotation; the rate of discovery of genetic variants in large clinical populations has not been empirically determined.

METHODS

We determined the rate of accrual of unique sequence variants in 90,000 exome sequences. Separate analyses were done for 17,267 autosomal genes and a subset of 74 actionable genes; the effect of relatedness in the cohort was also determined.

RESULTS

Variant discovery showed a nonlinear growth pattern. The rate of unique variant accrual decreased as the database size increased; by 90,000 exomes 97% of all projected coding and splicing variants had been observed. Variants in 74 actionable genes showed a similar pattern. Family relatedness slightly reduced the rate of discovery of unique variants.

CONCLUSION

The heaviest burden of interpretation for genetic variants occurs early and diminishes as the database size increases. Our data provide a framework for scaling pathogenic genetic variant discovery and curation, a critical element of patient care in the era of precision health.