Novel variants in the splicing factor gene SF3B1 are associated with neurodevelopmental disorders
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, some of which are involved in neurodevelopmental disorders. SF3B1 joins the short list of U2 snRNP components involved in both cancer and neurodevelopmental disorders. Overall design: RNA-seq profiling of K562 cells stably expressing wild type or variant SF3B1 (K700E, E722K, P780L, N829S) upon induction with 2 microg/mL of doxycycline for 7 days (in RPMI, 10% FBS, 2mM Gln). Biological independent replicates (n=3) were realised for each condition. RNA sequencing was performed by Novogene on an Illumina NovaSeq platform, using a 150-bp paired-end sequencing strategy.