Phenotype-guided whole genome analysis in a patient with genetically elusive long QT syndrome yields a novel TRDN-encoded triadin pathogenetic substrate for triadin knockout syndrome and reveals a novel primate-specific cardiac TRDN transcript

Background: Triadin knockout syndrome (TKOS) is a rare arrhythmia syndrome caused by recessive null variants in TRDN-encoded cardiac triadin 1. TKOS has presented frequently with cardiac arrest in childhood. Objective: The purpose of this study was to elucidate the underlying genetic mechanism of disease in a genetically elusive patient displaying a characteristic TKOS phenotype. Methods: Genome sequencing and a TRDN gene–specific trio analysis were completed on the patient. RNA and protein isolated from patient-specific human-induced pluripotent stem cell-derived cardiomyocytes were used to determine the effects of the identified variants using reverse transcription polymerase chain reaction (RT-PCR) and Western blot. Results: Genome sequencing revealed compound heterozygous putative splice-error variants (maternal c.22+29A>G and paternal c.484+1189G>A). The novel paternally derived c.484+1189G>A variant is located within 24 base pairs of a predicted alternative exon 6 (exon 6a), which resides within the intron between canonical exons 5 and 6. We determined that this previously unrecognized exon 6a produces a short TRDN transcript and potentially a novel protein isoform in the normal human heart. The c.484+1189G>A variant not only results in abnormal splicing of the exon 6a–containing transcript leading to a frameshift mutation but also results in the abolishment of the 8-exon cardiac triadin 1 transcript. Conclusion: Here, we present evidence for a novel alternative exon 6a–containing TRDN transcript in the normal heart. The novel deep intronic TRDN variant identified in a patient with TKOS leads to splicing error of a newly recognized exon 6a and loss of triadin. Considering that both TRDN variants in this patient were missed after commercial testing, these results highlight the importance of using genome sequencing when identifying patients with TKOS.