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

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

A homozygous synonymous NPR2 variant is identified in an individual with AMDM and aberrant splicing induced by a synonymous variant as a disease-causing mechanism affecting a core developmental signaling pathway is established.

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

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.

Human-specific sequence features in HTT exon 1 promote toxic misprocessing via splicing factor SRSF7

Expansion of CAG repeats in HTT exon 1 is the acknowledged driver of Huntington’s disease. Alternative processing of HTT pre-mRNA generates the truncated HTT1a transcript, translated into a toxic peptide. While its dependence on CAG length is well documented, the role of adjacent sequences - particularly the Proline-Rich Domain (PRD) - remains unexplored. Using our HuntEx1-engineered mouse embryonic stem cell platform, we show that human PRD promotes HTT1a production, whereas its replacement with mouse PRD in an otherwise human exon 1 markedly reduces HTT1a levels. Mechanistically, we find that the PRD shapes mRNA structure, and motif analysis identifies Serine-Arginine Splicing Factor 7 (SRSF7) binding sites in mouse but not in human PRD. Their targeted mutation confirms SRSF7’s regulatory role in suppressing HTT1a production. Our findings establish the PRD as a key cis-regulator of HTT1a biogenesis, demonstrating that HTT toxicity also depends on sequence context, and highlighting splicing-based, PRD-focused therapeutic avenues. CAG repeat expansion drives Huntington’s disease, but additional sequence features influencing HTT toxicity are less defined. Here, the authors show that the proline‑rich domain regulates HTT1a transcript production via mRNA structure and SRSF7 binding, revealing sequence context-dependent control of toxic HTT generation.

Translational reading frame predicts the pathogenicity of C-terminal frameshift deletions in MeCP2

Mutations in the MECP2 gene cause the severe neurological disorder Rett syndrome. A cluster of frameshift-causing C-terminal deletions (CTDs) removes ~100 amino acids and accounts for approximately 10% of RTT-causing mutations. Their pathogenicity is unexpected because this C-terminal domain is dispensable in mice. Analysis of pathogenic and benign human MECP2 variants reveals that some individuals with apparently typical CTDs do not develop Rett syndrome, confirming that C-terminal truncations are not intrinsically pathogenic. Using human sequence data and mouse models we show that pathogenicity results from a marked reduction in MeCP2 levels and depends on the presence of a proline proline stop motif (-PPX) generated by a shift to the +2 reading frame. CTDs that shift to the +1 frame avoid this motif and are benign. Replacing the stop codon of the PPX motif with tryptophan restores MeCP2 expression and rescues RTT-like phenotypes in a CTD mouse model. An adenine base editor efficiently introduces this substitution in cultured cells. These findings define a reliable prognostic distinction between benign and pathogenic CTDs and establish a potential editing strategy for correcting disease-causing CTD mutations.

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

RNA splicing evidence enables robust classification of BRCA1 exon 18 variants: Results from the ENIGMA consortium.

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.