A novel intronic variant in the ASAH1 gene enhances aberrant splicing, causing spinal muscular atrophy with progressive myoclonic epilepsy.

Background: Spinal muscular atrophy with progressive myoclonic epilepsy (SMA-PME) is a rare autosomal recessive disorder caused by ASAH1 gene variants. Although ASAH1 coding variants cause SMA-PME, the impact of noncoding variants, particularly noncanonical splice-site variants, is less clear.

Methods: Whole-exome sequencing (WES) was performed on the proband, and Sanger sequencing was used to confirm the carrier status of the variants in the core family members. Complementary DNA (cDNA) and minigene splicing assays were performed to validate the splicing effects.

Results: Two heterozygous ASAH1 variants were identified through WES: c.304dupA (p.Thr102Asnfs*14) and c.264 + 11A > G. Sanger sequencing confirmed that the variants were bi-parentally segregated in trans: c.304dupA was inherited from the father, and c.264 + 11A > G was inherited from the mother. The c.304dupA variant was classified as pathogenic according to the ACMG guidelines. However, the c.264 + 11A > G variant in intron 3 was reported for the first time, and its functional impact has not yet been fully elucidated. Complementary DNA (cDNA) and minigene splicing assays indicated that the c.264 + 11A > G variant generated two transcripts. Approximately 10% of the ASAH1 transcripts from the allele carrying c.264 + 11A > G were full length, whereas the remaining transcripts lacked exon 3. Exon skipping results from aberrant splicing, which potentially leads to a premature termination codon (PTC, p.Tyr59Ter).

Conclusion: To the best of our knowledge, the c.264 + 11A > G is the first likely pathogenic noncanonical splice-site variant identified in this gene. This drives the pathogenesis of SMA-PME through exon 3 skipping. Our findings provide new insights into the intricate splicing mechanisms of noncanonical splice-site variants, emphasizing the unique role of cDNA analysis and minigene splicing assays in the precise diagnosis and genetic counseling of SMA-PME cases.