Expanding the Recessive Spectrum of Dilated Cardiomyopathy: RNA‐Level Validation of a Homozygous CTNNA3 Splice‐Site Variant

Abstract

CTNNA3 encodes αT‐catenin, an intercalated disc (ICD) protein essential for cardiomyocyte coupling. Human omics studies have shown reduced CTNNA3 expression, ICD ultrastructural disruption, and dilated cardiomyopathy (DCM)–associated hyperphosphorylation of αT‐catenin. Direct RNA‐level evidence linking biallelic CTNNA3 variants to human cardiomyopathy has been lacking. Clinical exome sequencing was performed in a 21‐year‐old man with DCM, severe left ventricular systolic dysfunction (LVEF 20%), and atrial fibrillation (AF). The identified homozygous variant (NM_013266.4 : c.1733 − 1G > C) was assessed with multiple splicing prediction tools and functionally validated via a minigene hybrid assay in HEK293 cells. Splicing predictors indicated loss of the canonical acceptor site. The minigene assay confirmed three aberrant transcripts: out‐of‐frame exon 13 skipping with a premature stop codon, a 24‐nucleotide in‐frame deletion, and partial intron retention, resulting in a possibly nonfunctional protein. Under guideline‐directed medical therapy, LVEF normalized, but a persistent arrhythmic phenotype remained, with recurrent AF, frequent ventricular ectopic beats, and nonsustained ventricular tachycardia. We report a recessive form of DCM associated with a homozygous canonical splice‐site variant in CTNNA3, encoding the ICD protein αT‐catenin. Our results are consistent with human omics studies. Altogether, these data provide evidence that biallelic CTNNA3 splice‐disrupting variants can cause human cardiomyopathy driven by ICD dysfunction. The dissociation between ventricular recovery and persistent arrhythmia highlights the complex phenotypic spectrum of CTNNA3‐related disease.