De novo variants in the splicing factor gene SF3B1 are associated with neurodevelopmental disorders

TL;DR

New genetic variants in SF3B1 are linked to neurodevelopmental disorders, showing how this gene affects development and splicing.

Contribution

Identifies de novo SF3B1 missense variants as a cause of neurodevelopmental disorders, distinct from cancer-related mutations.

Findings

De novo SF3B1 missense variants are associated with neurodevelopmental disorders and facial dysmorphia.

Missense variants in SF3B1 disrupt RNA splicing more subtly than cancer-related somatic variants.

SF3B1 is implicated in both cancer and neurodevelopmental disorders, highlighting its multifaceted role.

Abstract

SF3B1 is an essential and ubiquitous splicing factor that plays a pivotal role in the early steps of pre-mRNA splicing. Recurrent somatic missense mutations in SF3B1 are frequent in cancers, but no constitutional variant has been reported so far. We describe here a cohort of 26 individuals with neurodevelopmental disorders, harbouring SF3B1 constitutional heterozygous variants that appeared mostly de novo. Patients present with a global developmental delay, associated with variable neurological and facial dysmorphic traits. A dichotomy may emerge between patients harbouring predicted loss of function (n = 9) and missense variants (n = 17), the latter being associated with a more severe and syndromic phenotype, including heart and gastrointestinal anomalies. We focused on de novo SF3B1 missense variants, which were largely distinct from those reported in cancer. Functional complementation assays show that de novo SF3B1 missense variants did not cause a loss of function of the protein. Targeted and genome-wide analysis of RNA splicing reveal that they affect canonical and alternative splicing more moderately than somatic variants, and subtly modify the splicing of many transcripts. These findings place SF3B1 among the rare U2 snRNP components implicated in both cancer and neurodevelopmental disorders, highlighting its critical and multifaceted role in human disease.

This study reports that de novo germline missense variants in SF3B1, distinct from the somatic variants frequently observed in cancer, cause a neurodevelopmental disorder and disrupt global RNA splicing.

Figures