Coexistence of Two Rare Genetic Variants in Canonical and Non-canonical Exons of SCN5A: A Potential Source of Misinterpretation

Abstract

Primary cardiac channelopathies are a group of diseases wherein the role of DNA testing in aiding diagnosis and treatment-based decision-making is gaining increasing attention. However, in some cases, evaluating the pathogenicity of new variants is still challenging. We report an accurate multistage assessment of a rare genetic variant in the SCN5A gene using next-generation sequencing (NGS) techniques and Sanger sequencing. Female sportsman (14 years old) underwent genetic counseling and DNA testing due to QT interval prolongation registered during ECG Holter monitoring. Genetic testing of the proband was performed in two independent laboratories. Primary DNA testing was performed by WES using the Ion ProtonTM System. Target panel sequencing of 11 genes was performed using PGM Ion Torrent. Search for variants in non-canonical and canonical exons 6 was performed by Sanger sequencing. The cascade familial screening and control re-sequencing were provided for proband with identified genetic variant p.S216L (g.38655290G>A, NM_198056.2:c.647C>T, and rs41276525) in the canonical exon 6 of the SCN5A gene after receiving data from another laboratory. Control Sanger and NGS sequencing revealed the absence p.S216L in the canonical exon 6 and confirmed the presence of p.S216L (g.38655522G>A, c.647C>T, and rs201002736) in the non-canonical exon 6 of the SCN5A gene. The identified variant was re-interpreted. The non-canonical transcripts of the exon 6 of the SCN5A gene is poorly represented in cardiac tissue (gnomAD). The detected variant was found in proband’s healthy mother. The correct interpretation of genetic data requires close cooperation between clinicians and researchers. It can help to avoid financial costs and stress for proband’s and families.

Multi-site validation of a functional assay to adjudicateSCN5ABrugada Syndrome-associated variants

“…39 p.Ser216Leu is present in the population at a much higher than expected frequency for a highly penetrant disease-associated variant (allele frequency > 0.05% in gnomAD). 40 However, p.Ser216Leu has also been observed in multiple patients with arrhythmia phenotypes, including BrS, 38,41,42 Type 3 Long QT syndrome, 43,44 Sudden Infant Death Syndrome, 39,45,46 and atrial fibrillation. 47,48 Given the multiple arrhythmia reports and the borderline partial LOF phenotype of the variant, p.Ser216Leu may be a risk allele for arrhythmia phenotypes, analogous to KCNE1 p.Asp85Asn.…”