A Homozygous Deep Intronic SNX14 Variant Activates Pseudo-Exon Inclusion in a Patient with SCAR20

Background: The contribution of intronic variants to the etiology of Mendelian diseases is still underrecognized, impacting the diagnostic yield. Whole genome sequencing (WGS) detects intronic variants, but beside canonical splice-sites, intronic variants are frequently excluded from the interpretation step or are classified as variants of uncertain significance (VUS). In fact, assessing their clinical significance often requires validation via RNA-sequencing or in vitro studies. Methods: We studied a 31-year-old patient with spinocerebellar ataxia who lacked a molecular diagnosis after WGS analysis. We applied the Detection of RNA Outliers Pipeline (DROP) to analyze RNA-sequencing (RNA-seq) data from patient fibroblasts. DROP integrates OUTRID-ER and FRASER 2.0 algorithms designed to identify aberrant gene expression and splicing, respectively. Results: DROP identified SNX14 as an outlier with significantly reduced gene expression and aberrant splicing. Retrospective WGS data inspection revealed a homozygous deep intronic variant NM_153816.6(SNX14):c.867+288A>G, which caused the splicing defect. Biallelic loss of function variants in SNX14 cause autosomal recessive spinocerebellar ataxia type 20 (SCAR20; OMIM 616354), and the patient’s clinical presentation was compatible with this disease. Conclusion: We present a deep intronic SNX14 variant as the cause of SCAR20. Integration of RNA-sequencing increases the diagnostic yield specifically by identifying and resolving the pathogenicity of deep intronic variants. Identification of aberrant splicing events can be therapeutically relevant, as these mechanisms are targets for antisense oligonucleotide (ASO) based interventions.