SNUPN variants cause spinocerebellar atrophy by disrupting global splicing in cerebellar Purkinje cells

Mutations in the SNUPN gene, which encodes snurportin-1, a nuclear import adaptor for U1 small nuclear ribonucleoproteins (snRNP), have recently been implicated in limb-girdle muscular dystrophy, attributed to disrupted pre-messenger RNA splicing in skeletal muscle. U1 small nuclear ribonucleoproteins play a vital role in pre-messenger RNA splicing, a process essential for transcript fidelity and the regulation of gene expression across tissues. However, the impact of SNUPN mutations on the CNS remains unclear. We identified pathogenic variants in the SNUPN gene in two families with spinocerebellar atrophy. One patient exhibited mild changes in skeletal muscle, while the other did not. To elucidate the pathogenic mechanisms, nuclear transport of the mutated snurpotin-1, and its interaction with importin beta were analysed in vitro. Then, we generated a knock-in mouse carrying the patients' variants and assessed its motor function and cerebellar morphology in vivo. Furthermore, we analysed U1 snRNP localization and RNA splicing in cerebellar Purkinje cells by both RNA- and single-cell RNA sequencing. Mutated snurportin-1 displayed impaired nuclear transport and reduced binding to importin beta. The knock-in mouse mimicking the compound heterozygous variants exhibited cerebellar ataxia, cerebellar atrophy and dendritic abnormalities in Purkinje cells. Abnormal RNA splicing and reduced expression were observed in many genes related to neuronal development and synaptic organization in Purkinje cells, leading to an immature cytoskeleton and reduced secretion of sonic hedgehog. The defects in Purkinje cells caused secondary abnormalities in granule cell migration and interneuron development. Our findings suggest that snurportin-1 plays a critical role in cerebellar development through U1 snRNP-mediated RNA processing and that its dysfunction may contribute to spinocerebellar ataxia. These results expand the clinical spectrum of SNUPN-related disorders beyond skeletal muscle and highlight splicing dysregulation as a potential mechanism underlying cerebellar atrophy.