Jan 2026· Human Mutation· Vol 2026· 0 citations· 28 references
Medicine
TL;DR
Evidence is provided that biallelic CTNNA3 splice‐disrupting variants can cause human cardiomyopathy driven by ICD dysfunction, and the dissociation between ventricular recovery and persistent arrhythmia highlights the complex phenotypic spectrum of CTNNA3‐related disease.
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.
Background Osteogenesis imperfecta (OI) is a clinical and genetic disorder characterised by bone fragility, growth deficiency and skeletal deformity. Ninety per cent of OI cases are attributable to autosomal dominant variants in the COL1A1 and COL1A2 genes. Methods Candidate variants were identified and verified through trio whole‐exome sequencing (trio‐WES), copy number variation sequencing (CNV‐seq) and Sanger sequencing. Minigene splicing assays were performed in HeLa and HEK293T cells with pcDNA3.1 and pcMINI‐C vectors to investigate the function of the candidate variants. A systematic review of COL1A1 splicing variants and the corresponding genotype–phenotype spectrum was performed. Results Trio‐WES revealed a novel heterozygous variant in the C‐terminal region of the COL1A1 gene: NM_000088.4:c.3423+5G>A. Sanger sequencing confirmed the variant in both the proband (II‐2) and her foetus (III‐1) who were clinically suspected of having OI. The c.3423+5G>A variant causes complete skipping of Exon 46, as demonstrated by a minigene splicing assay. We retrieved 419 COL1A1 splicing variants from PubMed, excluded 15 without phenotypic data and 2 linked to Ehlers–Danlos syndrome and stratified the remaining 402 variants into three types on the basis of splice site location: (1) Variants at canonical splicing sites (77.8%, 313/402) mostly cause mild phenotypes, whereas a minority may be severe. (2) Intron variants in other locations, such as splice region variants (17.9%, 72/402), usually cause mild clinical phenotypes, and deep intronic splice variants (0.4%, 2/402) that may result in severe phenotypes. (3) Other variants (3.7%, 15/402), such as exon variants or fragment loss, are extremely rare. We also preliminarily discuss the mechanisms underlying phenotypic variability and the characteristics of C‐terminal variants. Conclusions This intron variant in COL1A1 was classified as likely pathogenic and was confirmed to disrupt COL1A1 expression. The summary analysis results also revealed a correlation among splicing variants, C‐terminal region variants and disease, suggesting that variant location provides a useful framework for prognosis prediction.
Yujun Zhang, Huibing Liu, Ai-lan Yin et al.· Human Mutation· 0 citations
The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) research consortium conducted a comprehensive study to characterize spliceogenic variants in BRCA1 exon 18. The absence of systematic RNA-based assessment for these variants has led to inconsistent interpretation, limiting accurate classification and management of individuals and their families. The splicing profile of 166 variants was assessed using minigene assays; 32 were additionally analyzed in blood-derived RNA from 51 individuals and 18 in mouse embryonic stem cell (mESC)-based assays to evaluate homology-directed repair (HDR) capacity. mRNA assessment by RT-PCR in blood samples and minigene assays showed a significant positive correlation, with splicing analysis in mESCs displaying highly concordant results. The mESC-based HDR assay showed that the in-frame exon 18 skipping (Δ18) transcript encodes a non-functional protein lacking rescue activity. Linear regression analysis using mESC splicing and functional data indicated that ≥59% of full-length (FL) levels and <34% of Δ18 were associated with benign HDR activity. These thresholds differ from those recommended by the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) specifications for applying BP7_strong(RNA): >30% functional transcripts or <70% non-functional transcripts. Incorporation of RNA splicing evidence into variant interpretation increased pathogenic (28.6%-31.7%) and benign (3.7%-24.4%) classifications while reducing likely pathogenic (19.5%-17.7%), uncertain (18.9%-8.5%), and likely benign (29.3%-17.7%) categories. Experimental mRNA profiling impacted the interpretation of 34% of variants and resolved uncertainty in approximately 10% of cases. Exon 18 skipping was less tolerated, indicating that the degree of splice perturbation required to impair BRCA1 function may depend on the nature of the resulting non-functional transcript.
Joanna Domènech-Vivó, Hélène Tubeuf, Romy L. S. Mesman et al.· American Journal of Human Ge...· 0 citations
Parkinsonism–dystonia Type 2 (PKDYS2) is a rare autosomal recessive disorder caused by SLC18A2 variants affecting the vesicular monoamine transporter 2 (VMAT2). We report the first genetically confirmed Iranian patient, an 18‐month‐old boy presenting with profound developmental delay, axial hypotonia, limb hypertonia, dystonia, oculogyric crises, ptosis, and autonomic dysfunction. Brain MRI, metabolic studies, and neurophysiological evaluations were normal. Whole‐exome sequencing identified a novel homozygous canonical splice‐site variant in SLC18A2 (NM_003054.6:c.1071‐2A > G), confirmed by Sanger sequencing and absent from population databases. SpliceAI predicted loss of the native splice acceptor site (DS_AL = 0.74), supporting a deleterious effect on RNA splicing. According to ACMG criteria, the variant was classified as likely pathogenic. Levodopa–benserazide failed to provide sustained benefit and caused irritability and insomnia, whereas pramipexole produced modest improvement in bradykinesia, ptosis, and sweating with persistence of dystonia and oculogyric crises. Comparison with reported international cases shows a consistent phenotype and limited therapeutic response. This case expands the mutational spectrum of SLC18A2‐related disease and highlights the importance of early genetic diagnosis.
Ali Nikkhah, R. Badv, S. Habibi et al.· Case Reports in Neurological...· 0 citations
The first functional characterization of the cardiomyopathy-associated SMYD1 N101S variant identified in a child with severe infantile cardiomyopathy is provided, establishing a mechanistic link between SMYD1 dysfunction and infantile cardiomyopathy and highlighting the importance of integrating genomic and functional approaches in rare cardiovascular disease.
Marta W. Szulik, Clint Gwynn, Magnus Creed et al.· bioRxiv· 0 citations
Arrhythmogenic cardiomyopathy is an inherited myocardial disease frequently associated with variants in desmosomal genes. DSC2 encodes desmocollin-2, a cadherin involved in cardiomyocyte adhesion at the intercalated disc; disruption of desmosomal integrity may contribute to myocardial remodeling and arrhythmogenic susceptibility. We describe a Panamanian family in which the DSC2 splice-site variant c.354+1G>T (NM_024422.6) was identified during evaluation for suspected inherited cardiac disease. The proband was a 66- year-old woman with hypertrophic cardiomyopathy, concentric hypertrophy on echocardiography, and high-risk syncope. Her 86-year-old mother had cardiac conduction disease requiring pacemaker implantation, and the proband’s daughter was identified as a carrier. The variant affects the canonical +1 donor splice site and is predicted to alter pre-mRNA splicing, with SpliceAI donor-loss score of 0.96, Pangolin splice-loss score of 0.64, CADD PHRED score of 33, and PhyloP score of 8.87. ClinVar classifies the variant as likely pathogenic. These findings support genetic counseling, cascade testing, and cardiovascular surveillance. However, the current clinical and segregation data do not establish definitive causality for hypertrophic cardiomyopathy or conduction disease.
JoseCedeno, Carlos Chellaram, Carolina Vega et al.· Frontiers in Medical Case Re...· 0 citations
The findings expand the phenotypic spectrum of VPS41‐related disease and highlight the value of long‐read allelic resolution in clarifying pathogenic mechanisms in rare genetic disorders.
Natsuki Nakamura, Y. Nishio, Hiromi Nyuzuki et al.· Molecular Genetics & Genomic...· 0 citations