A novel SEMA6B splice-site variant (c.1680-2A>G) causes incompletely penetrant epilepsy via diverse aberrant transcripts.

BACKGROUND: While truncating variants in the SEMA6B gene are an established cause of Progressive Myoclonus Epilepsy-1(EPM11), the pathogenic mechanisms of non-last-exon splicing variants, particularly those underlying the frequent yet elusive phenomenon of incomplete penetrance, remain a critical knowledge gap. Elucidating these mechanisms is essential for accurate molecular diagnosis and genetic counseling METHODS: We combined whole-exome sequencing in a proband, familial co-segregation analysis, and an in vitro minigene splicing assay in HEK-293T cells to characterize a novel candidate variant. Long-term clinical follow-up assessed phenotypic trajectory. RESULTS: We identified a novel heterozygous donor splice-site variant NM_032108.4 (SEMA6B): c.1680-2A>G segregating with autosomal dominant EPM1in a family exhibiting marked incomplete penetrance. The minigene assay demonstrated that this single variant drives the production of three distinct aberrant transcripts (exon 16 skipping, intron 15 retention, and partial exon 16 deletion), confirming its strong splice-disrupting effect. Notably, effective anti-seizure medication was associated with improved neurodevelopmental outcomes. CONCLUSION: This study provides the first functional validation of the c.1680-2A>G variant, demonstrating that complex transcript heterogeneity from a single splice-site mutation is a key molecular feature. Our findings propose a plausible link between this heterogeneity and the observed incomplete penetrance, thereby refining the genetic architecture of SEMA6B-related disorders and underscoring the necessity of functional assays for the interpretation of splicing variants.