Natural Missplicing Events Amplified by an Elusive Deep-Intronic MYBPC3 Variant Cause Hypertrophic Cardiomyopathy.

MYBPC3

Deep-intronic MYBPC3 c.2308+227G>A variant that amplifies the use of pre-existing cryptic splice sites without creating a new essential site, generating two misspliced mRNAs encoding truncated proteins

The deep-intronic MYBPC3 c.2308+227G>A variant was identified by massively parallel sequencing in a cohort of genotype-negative hypertrophic cardiomyopathy patients from Salamanca, Spain, even though SpliceAI predicted a benign effect (delta score 0.03). The authors report 35 unrelated probands plus 46 relatives from 27 families, yielding 81 confirmed carriers, of whom 56 (69%) met diagnostic criteria for hypertrophic cardiomyopathy; cumulative penetrance by age 60 was estimated at 81% in women and 96% in men, with a combined LOD score of 5.51 across 20 informative families. Blood splicing assays, confirmed in cardiac tissue, show that the variant hijacks pre-existing cryptic donor and acceptor sites, producing partial intron retention or cryptic exon inclusion. A shared haplotype among probands explains the recurrence of the variant and points to an ancient founder effect. During follow-up, no significant differences in heart failure, arrhythmic events, atrial fibrillation or mortality were seen compared with carriers of other pathogenic MYBPC3 variants.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

This is the most useful counterexample of the year for splice predictors: a SpliceAI score of 0.03 excludes nothing when the mechanism is amplification of natural missplicing rather than creation of a new site. The practical lesson is twofold — in unresolved hypertrophic cardiomyopathy the intronic coverage of the gene deserves a second look, and a variant recurring across several probands warrants an RNA splicing assay before being called benign. With penetrance of 81 to 96% by age 60, cascade family screening becomes immediately justified in affected families.

Analysis by Dr Thibaut Benquey