Monoallelic and biallelic RNU4-2 variants in neurodevelopmental disorders

The accurate removal of intronic sequences from pre-mRNA by the spliceosome is essential for correct gene expression, with small nuclear RNAs (snRNAs) such as U4 playing structural and regulatory roles in catalyzing this. De novo variants in the highly constrained critical region including the T-loop region of RNU4-2 have been linked to ReNU syndrome, a neurodevelopmental disorder, but the broader mutational spectrum remains uncharacterized. Here, we show that, in a cohort of unresolved cases with neurodevelopmental disorder, monoallelic and biallelic RNU4-2 variants were identified in 16 affected individuals, expanding the genetic basis beyond the critical region: 12 with de novo T-loop variants and 4 from two families with compound heterozygous variants in non-critical regions (stem II, the k-turn, and the Sm-binding site). Previously reported functional mapping by saturation genome editing confirmed that most of the variant positions in this study are highly functionally constrained. Clinically, individuals with biallelic variants exhibited developmental delay and intellectual disability that were similar to but milder than those with monoallelic variants, notably lacking extracerebral organ involvement. These results suggest that pathogenic RNU4-2 variants act in both dominant and recessive manners, and that non-critical regions may also harbor disease-causing variants. More broadly, this study underscores the diagnostic importance of non-coding RNA genes in neurodevelopmental disorders and demonstrates the need to distinguish pathogenic variants from benign ones, together with their inheritance patterns.