A synonymous NPR2 variant causes acromesomelic dysplasia through aberrant pre-mRNA splicing.

A novel pathogenic synonymous DHCR7 variant unveiled by aberrant splicing in Smith-Lemli-Opitz syndrome

In-frame exon skipping induced by the c.14510delA variant in RYR1.

RNA splicing is a crucial step in eukaryotic gene expression, ensuring the accurate removal of introns and joining of exons to produce mature transcripts. Mutations that alter canonical splice sites or splicing regulatory elements can profoundly affect this process, resulting in aberrant mRNA species and disease. Genetic screening for Malignant Hyperthermia Susceptibility (MHS), resulted in the identified of a frameshift variant in RYR1 (c.14510delA, rs193922877) associated with MHS and core-like structures in skeletal muscle biopsies. The c.14510delA variant causes a frameshift leading to premature truncation of the protein and loss of the C-terminal transmembrane domains. Splice site prediction analysis suggested that this variant could also impact mRNA splicing. Transcript analysis confirmed that the variant induces in-frame skipping of exon 100, resulting in a shorter RYR1 transcript where exon 101 follows exon 99. To our knowledge, this represents the first description of an in-frame exon skipping event in RYR1. Although the functional impact of the resulting channel isoform remains to be fully elucidated, our findings emphasize the importance of mRNA-level investigations in the molecular diagnosis of RYR1-related myopathies.

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

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.

ASXL3 truncating patient variants mediate transcriptional gain-of-function and are antisense oligonucleotide-responsive

ASXL3 patient truncations in neurodevelopmental condition Bainbridge-Ropers syndrome are shown to mediates gain-of-function (GOF) by escaping nonsense-mediated decay and Cullin 4-dependent degradation, resulting in aberrant protein accumulation, widespread transcriptional dysregulation, and altered chromatin accessibility.

Isoform-specific regulation of SMARCAD1 dosage in ectodermal homeostasis and dysplasia

Missense but mis-spliced: germline TP53 variant c.671A > C (p.E224A) and the path from uncertainty to pathogenicity.

The TP53 gene encodes the well-known p53 tumor suppressor protein, which plays a crucial role in preventing cancer development. Germline TP53 variants cause Li-Fraumeni Syndrome (LFS), an autosomal dominant disorder associated with early-onset cancers, including breast cancer, brain tumors, leukemias, bone cancers, and soft tissue sarcomas. Here, we described a germline TP53 variant c.671A>C, located at the penultimate nucleotide of exon 6 and predicted to result in the missense substitution p.E224A. The variant was identified in a 2-year-old child with retroperitoneal rhabdomyosarcoma and with a strong family history suggestive of LFS. Functional assays in yeast and human cells demonstrated wild type-like activity of the protein p.E224A; however, in silico splicing analysis indicated potential splice defects (e.g., SpliceAI score = 0.77). Given this discrepancy, we further investigated this variant using a minigene approach, demonstrating that it causes the skipping of exon 6, likely resulting in a frameshift and the introduction of a premature stop codon. These findings supported the classification of the TP53 germline variant c.671A>C (p.E224A) as likely pathogenic, providing a definitive molecular diagnosis for family counselling. Additionally, the present results sheds light on how certain predicted TP53 missense variants can be linked to disease mechanisms through RNA splicing disruption.