Phenotypic and transcriptomic characterisation of a novel biallelic RNU2-2 developmental and epileptic encephalopathy

A significant proportion of individuals with suspected genetic developmental and epileptic encephalopathies (DEEs) remain unsolved following whole genome sequencing (WGS). We screened individuals who received WGS analyses at Genomic Medicine Centre Karolinska for Rare Diseases for biallelic RNU2-2 variants. Deep phenotyping was performed and phenotypic traits were transcribed to their corresponding Human Phenotype Ontology (HPO) term. HPO terms were used to generate pairwise phenotypic similarity scores and assess for significant phenotypic enrichment in the RNU2-2 sub-cohort. RNA sequencing analyses were performed in fibroblast and blood tissues to compare splicing events between RNU2-2 individuals and two independent control groups. We identified 14 individuals with 12 ultra-rare biallelic RNU2-2 variants clustering in the conserved 5 domains. All individuals presented with a highly concordant, severe DEE, characterised by severe to profound intellectual disability, inability to walk or communicate, hyperkinesia and refractory seizures. Infantile spasms and tonic seizures were the predominant seizure types and a Lennox-Gastaut syndrome-like phenotype was common. These individuals had a significantly similar phenotypic signature when compared with 703 individuals with paediatric epilepsy (two-sided Monte Carlo permutation test, p=0.005). RNA sequencing analyses in fibroblast tissues showed a clear separation of aberrant mutually exclusive exon and alternate 3 splice site events between RNU2-2 individuals and controls, which was not detectable in blood. In summary, we present deep phenotyping data and transcriptomic analyses which provide support for rare, 5 clustering biallelic RNU2-2 variants causing a novel, severe DEE. We propose an RNA sequencing methodology on fibroblast tissue for future validation of RNU2-2 variants.