Tobert KE, Tester DJ, Zhou W, Haglund-Turnquist CM, Giudicessi JR, Ackerman MJ. Genome Sequencing in a Genetically Elusive Multi-Generational Long QT Syndrome Pedigree Identifies a Novel LQT2-Causative Deeply Intronic KCNH2 Variant.
Heart Rhythm 2022;
19:998-1007. [PMID:
35144019 DOI:
10.1016/j.hrthm.2022.02.004]
[Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND
Most of long QT syndrome (LQTS) stems from pathogenic variants in KCNQ1, KCNH2, or SCN5A. However, ∼10-20% of LQTS index cases remain genotype-negative.
OBJECTIVE
Here, we identified and characterized functionally a novel LQTS genetic substrate in a multi-generational, "genotype-negative" LQTS pedigree.
METHODS
The patient was a 40-year-old female with a history of syncope, seizures, ventricular fibrillation, and a family history of LQTS and sudden death. Commercial genetic testing of all LQTS-causative genes was negative. Genome sequencing was performed on 6 affected family members. Patient-specific and CRISPR/Cas9 "gene-corrected" isogenic control induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) were generated.
RESULTS
No ultra-rare, nonsynonymous heterozygous variants co-segregated among the 6 LQTS phenotype-positive individuals. Instead, a deep intronic KCNH2 variant (c.3331-316G>T) was present in all affected individuals. RT-PCR analysis of patient-specific iPSC-CM-derived RNA revealed that c.3331-316G>T creates a novel 89 base-pair exon that results in a frame-shift variant (p.S1112Pfs*171). The action potential duration (APD90) was significantly longer in p.S1112Pfs*171-iPSC-CMs (602.4 ± 12.2 ms, n=70) compared to isogenic control iPSC-CMs (425.7 ± 9.3 ms, n=61, p<0.0001). Further, the field potential duration (FPD) was significantly longer in p.S1112Pfs*171-iPSC-CMs (358.9 ± 7.7 ms, n=65) compared to isogenic control iPSC-CMs (282.2 ± 10.8 ms, n=51, p<0.0001).
CONCLUSIONS
A novel deep intronic KCNH2 variant was identified in a multi-generational, genetically elusive LQTS pedigree. The iPSC-CMs establish that the variant is the monogenetic cause for this family's LQTS. Deep intronic variants within the two most common LQTS-susceptibility genes should be considered in patients with seemingly, genetically elusive LQTS.
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