Case Report: A novel deep intronic MFSD8 splice-altering variant causes CLN7 disease through pseudoexon inclusion

Pathogenic deep intronic variants are an underrecognized cause of inherited disorders because they are typically missed by exon-focused sequencing and often require functional validation. We describe a patient with classic CLN7 disease caused by a previously unreported deep intronic variant in MFSD8. The patient presented with developmental regression, progressive epilepsy, cerebellar ataxia, and cerebral and cerebellar atrophy. Trio whole-genome sequencing identified a homozygous MFSD8 variant, NM_001371596.2:c.999-556C>G, absent from population databases and previous reports. SpliceAI predicted activation of cryptic splice sites leading to inclusion of a 98-nt pseudoexon. RNA analysis of patient-derived fibroblasts confirmed aberrant pseudoexon inclusion, resulting in a frameshift and premature termination codon, with the aberrant transcript accounting for 84% of total MFSD8 transcripts. A minigene assay independently reproduced the splicing defect, confirming that the variant disrupts normal MFSD8 splicing. This study expands the mutational spectrum of MFSD8 and provides functional evidence supporting the pathogenicity of a novel deep intronic splice-altering variant. Our findings further demonstrate the value of combining whole-genome sequencing with transcript analysis for the molecular diagnosis of unsolved rare neurogenetic disorders.