Pontocerebellar hypoplasia type 2D in two Acadian families: functional RNA characterization of the recurrent SEPSECS c.388+3A>G variant

Abstract

Pontocerebellar hypoplasia type 2D (PCH2D, OMIM #613811) is an ultra-rare autosomal recessive neurodevelopmental disorder caused by biallelic pathogenic variants in SEPSECS , which encodes a key enzyme required for selenoprotein biosynthesis. An extensive literature review conducted for this report identified approximately 34 genetically confirmed patients from 26 families with SEPSECS -related disease across the published literature, underscoring the extreme rarity of PCH2D. Intronic splice-altering variants with functional RNA confirmation remain poorly characterized, and no population-specific founder variant has been established for SEPSECS -related PCH2D. We performed detailed clinical, molecular, and transcriptomic analyses in three affected individuals from two unrelated Acadian families originating from the Canadian Maritime provinces. All individuals underwent exome sequencing, followed by RNA-based analyses of patient-derived samples to assess the functional impact of the recurrent intronic SEPSECS variant. Exome sequencing identified the same homozygous intronic SEPSECS variant, c.388 + 3A>G, in all three affected individuals. The variant was initially classified as a variant of uncertain significance in patients 1 and 2 and as likely pathogenic in patient 3 by different diagnostic laboratories. RNA analysis demonstrated aberrant splicing with exon 3 skipping, generating an out-of-frame transcript consistent with a loss-of-function mechanism. Residual normally spliced transcript was also detected in blood-derived RNA, consistent with a partial or “leaky” splice defect at the transcript level. These findings supported pathogenic reclassification and established a molecular diagnosis of PCH2D. Clinically, the patients presented with early-onset lower-extremity spasticity, gait abnormalities, nystagmus, and mild neurodevelopmental delay, but had an attenuated clinical course compared to classical severe PCH2D. This case series expands the molecular and clinical spectrum of SEPSECS -related PCH2D by providing functional RNA evidence for a recurrent non-canonical intronic splice variant and documenting an attenuated infantile-onset presentation. The recurrence of c.388 + 3A>G in individuals of Acadian ancestry raises the possibility of a candidate Acadian founder allele. These findings underscore the importance of transcript-level analyses for interpreting intronic variants and improving diagnosis in ultra-rare neurodevelopmental disorders.