De novo variants in the essential splicing factor gene SRSF3 cause variable developmental phenotypes

Abstract

SRSF3 (SRp20), a member of the serine/arginine-rich protein family of splicing factors, plays a central role in constitutive and alternative splicing. The C-terminal arginine/serine-rich domain of SRSF3 undergoes dynamic phosphorylation cycles that regulate its subcellular localization, protein-protein interactions, and nuclear mRNA export while also indirectly modulating the RNA-binding capability. We report nine individuals with variable developmental phenotypes, including developmental delay and/or mild to moderate intellectual disability as the most consistent feature, and de novo SRSF3 variants. These variants comprise c.181G>C (p.Asp61His) and c.242C>G (p.Ser81Trp), affecting highly conserved residues within the RNA recognition motif, c.330_331del (p.Pro111Serfs∗20), c.402_403del (p.Arg137Ilefs∗16), c.477dup (p.Ser160Valfs∗3), and a recurrent nonsense variant c.445C>T (p.Arg149∗). For c.330_331del, nonsense-mediated mRNA decay (NMD) was predicted. Qualitative RT-PCR followed by Sanger sequencing and RNA sequencing (RNA-seq) of fibroblasts from this individual demonstrated NMD of SRSF3 transcripts containing the variant. However, overall SRSF3 mRNA and protein levels were comparable to control cells, suggestive of a compensatory mechanism acting in these cells. Comprehensive functional studies of ectopically expressed SRSF3Asp61His, SRSF3Ser81Trp, SRSF3Arg137Ilefs∗16, SRSF3Arg149∗, and SRSF3Ser160Valfs∗3 in HEK293T cells revealed reduced complex formation with polyadenylated RNA as well as intrinsic instability of C-terminally truncated variant proteins, correlating with decreased C-terminal phosphorylation. Complex formation with the nuclear export proteins YTHDC1 and NXF1 was reduced for SRSF3Arg137Ilefs∗16 and SRSF3Arg149∗ and increased for SRSF3Ser81Trp. Additionally, nucleocytoplasmic shuttling, assessed in HeLa cells, was reduced for the C-terminally truncated SRSF3 variant proteins. Together, our data demonstrate distinct functional defects for the disease-associated SRSF3 variants, which may underlie phenotypic variability in affected individuals.