KCNQ1 p.L353L affects splicing and modifies the phenotype in a founder population with long QT syndrome type 1.

Abstract

Variable expressivity and incomplete penetrance between individuals with identical long QT syndrome (LQTS) causative mutations largely remain unexplained. Founder populations provide a unique opportunity to explore modifying genetic effects. We examined the role of a novel synonymous <i>KCNQ1</i> p.L353L variant on the splicing of exon 8 and on heart rate corrected QT interval (QTc) in a population known to have a pathogenic LQTS type 1 (LQTS1) causative mutation, p.V205M, in <i>KCNQ1</i>-encoded Kv7.1. 419 adults were genotyped for p.V205M, p.L353L and a previously described QTc modifier (<i>KCNH2-</i>p.K897T). Adjusted linear regression determined the effect of each variant on QTc, alone and in combination. In addition, peripheral blood RNA was extracted from three controls and three p.L353L-positive individuals. The mutant transcript levels were assessed via qPCR and normalised to overall <i>KCNQ1</i> transcript levels to assess the effect on splicing. For women and men, respectively, p.L353L alone conferred a 10.0 (p=0.064) ms and 14.0 (p=0.014) ms increase in QTc and in men only a significant interaction effect in combination with the p.V205M (34.6 ms, p=0.003) resulting in a QTc of ∼500 ms. The mechanism of p.L353L's effect was attributed to approximately threefold increase in exon 8 exclusion resulting in ∼25% mutant transcripts of the total <i>KCNQ1</i> transcript levels. Our results provide the first evidence that synonymous variants outside the canonical splice sites in <i>KCNQ1</i> can alter splicing and clinically impact phenotype. Through this mechanism, we identified that p.L353L can precipitate QT prolongation by itself and produce a clinically relevant interactive effect in conjunction with other LQTS variants.