Oral Presentation GENEMAPPERS 2026

Pathogenic variants in the small nuclear RNA RNU2-2 are enriched in developmental and epileptic encephalopathies (#33)

Mark F Bennett 1 2 3 , Harshini Thiyagarajah 3 , Sian Macdonald 3 , Tom Witkowski 3 , Annie TG Chiu 3 , Amy Schneider 3 , Talia Allan 3 , Nico Lieffering 3 , Edith P Almanza Fuerte 4 , Blake Robinson 4 , Christy LaFlamme 4 , Soham Sengupta 4 , Piero Perucca 3 , Samuel F Berkovic 3 , Melanie Bahlo 1 2 , Heather C Mefford 4 , Ingrid E Scheffer 3 5 6 7 , Michael S Hildebrand 3 5
  1. Genetics and Gene Regulation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
  2. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
  3. Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
  4. Department of Cell and Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
  5. Neuroscience Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
  6. Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
  7. The Florey Institute of Neurosciences and Mental Health, Parkville, Victoria, Australia

Objectives: Small nuclear RNAs (snRNAs) play a critical role in gene splicing. Recurrent variants in genes RNU4-2 and RNU2-2, encoding snRNAs involved in the major spliceosome, were recently found to be a frequent cause of neurodevelopmental disorders (NDDs). We investigated a large cohort of individuals with developmental and epileptic encephalopathies (DEEs), the most severe group of epilepsies, for causal variants in snRNA genes.

Methods: We searched for pathogenic variants in snRNA genes, focusing on RNU4-2, RNU2-2, RNU5A-1, RNU5B-1, RNU5E-1, and RNU5F-1, where de novo variants have recently been reported in NDDs. RNA-seq data from individuals with pathogenic snRNA variants was interrogated for evidence of abnormal splicing to understand the disease mechanism.

Results: We identified recurrent de novo pathogenic RNU2-2 variants in four individuals with DEEs (4/672; 0.6%). We did not identify any causal variants in other snRNA genes implicated in NDDs. Individuals with pathogenic RNU2-2 variants had a distinctive phenotype including onset of drug-resistant epilepsy at median age of 21 months and profound to severe developmental impairment. In addition, four individuals were found with compound heterozygous RNU2-2 variants, suggesting biallelic variants also contribute to disease. In contrast to RNU4-2, RNA-seq analysis did not reveal a strong signature of widespread abnormal splicing, consistent with recently reported data, however suggests that pathogenic RNU2-2 variants have more subtle effects on splicing.

Conclusions: Our findings indicate variants in RNU2-2 account for 0.6% of DEEs. Pathogenic de novo variants in RNU2-2 cause a DEE with a distinctive phenotype. Biallelic variants may also cause DEEs with similar frequency. Strikingly the diagnostic yield of pathogenic RNU2-2 variants in our DEE cohort is six times that for NDDs.