Biallelic variants in RNU2-2 cause the most prevalent known recessive neurodevelopmental disorder

Abstract

We recently showed that mutations in RNU4-2 and RNU2-2, two genes that are transcribed into small nuclear RNA (snRNA) components of the major spliceosome, are prevalent causes of dominant neurodevelopmental disorders (NDDs). By genetic association comparing 12,776 NDD cases with 56,064 controls, we now demonstrate the existence of a recessive form of RNU2-2 syndrome that, in England, is even more common than the dominant form. We inferred log Bayes factors for dominant and recessive models of association of 14.0 and 18.2, respectively, and observed 17 rare variants with a posterior probability of pathogenicity conditional on recessive association >0.8. This conservative threshold identified 18 probands (all with unaffected parents) and five affected siblings, each carrying two alleles in trans at these variants. A relaxed threshold of >0.6 identified a further 13 candidate probands. We estimate that recessive RNU2-2 syndrome accounts for 7-10% of families with a diagnosed recessive NDD, and is 36-62% as prevalent as the dominant RNU4-2-related disorder ReNU syndrome. We identified a further seven cases in five pedigrees in two replication collections. Cases are characterized by intellectual disability, global developmental delay and seizures. The variants are predicted to destabilize stem loops and binding domains of the U2-2 snRNA that contribute to spliceosome quaternary structure, intron recognition and catalytic function. Despite this, whole-blood derived RNA-seq data from three patients did not reveal splicing defects, in line with previous analogous observations for dominant RNU2-2 syndrome.