Background 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 KCNQ1 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 KCNQ1-encoded Kv7.1.
Methods 419 adults were genotyped for p.V205M, p.L353L and a previously described QTc modifier (KCNH2-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 KCNQ1 transcript levels to assess the effect on splicing.
Results 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 KCNQ1 transcript levels.
Conclusions Our results provide the first evidence that synonymous variants outside the canonical splice sites in KCNQ1 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.
- long QT syndrome
- exon skipping
- First Nations
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LA and MJA are co-corresponding senior authors.
Contributors JDK was responsible for the data collection and laboratory analysis with regard to the L353L variant, wrote the first draft of the manuscript and contributed to subsequent drafts. AE developed the methods for the regression analysis and carried them out. SA contributed to literature review, created tables, figures and contributed to subsequent drafts of the manuscript. DJT contributed to the lab experiments and to the drafting of the manuscript. SM assisted in collection of clinical data and editing of final manuscript. CRK was responsible for the clinical cardiology phenotyping of adults and the QTc assessments. JM was the community partner responsible for review of the study, results and manuscript. AT contributed to the design of the study, funding and manuscript development. SS contributed to the design of the project and assisted in the development of the project and manuscript at all stages. LA conceived of the design of the clinical study, supervised the clinical data collection and analysis, contributed to editing of manuscripts and was responsible for funding of the project for the collection and genetic testing of the clinical cohort. MJA contributed to the funding, design of the laboratory experiments, assessment of results and drafting of the manuscript.
Funding This work was supported by the Windland Smith Rice Comprehensive Sudden Cardiac Death Program, Rochester, Minnesota (JDK, DJT, MJA). JDK is supported by a National Institutes of Health (NIH)/National Heart, Lung, and Blood Institute (NHLBI) National Research Service Awards (NRSA) Ruth L. Kirschstein individual predoctoral MD/PhD fellowship (F30HL127904) by the NIH grant GM72474-08. The clinical cohort work (LA, SA, AE, CRK, SS, AT) was funded through the Canadian Institutes of Health Research, Ottawa, Ontario, Research grant no. 81197 to LA and AT.
Competing interests MJA is a consultant for Boston Scientific, Gilead Sciences, Medtronic and St. Jude Medical. MJA and Mayo Clinic receive royalties from Transgenomic for their FAMILION-LQTS and FAMILION-CPVT genetic tests. However, none of these commercial entities supported this research work.
Ethics approval University of British Columbia Research Ethics Board, BC Northern Health Authority Research Ethics Board.
Provenance and peer review Not commissioned; externally peer reviewed.
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