De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome
Authors: Chen Yuyang , Dawes Ruebena , Kim Hyung Chul , Ljungdahl Alicia , Stenton Sarah L. , Walker Susan , Lord Jenny , Lemire Gabrielle , Martin-Geary Alexandra C. , Ganesh Vijay S. , Ma Jialan , Ellingford Jamie M. , Delage Erwan , D’Souza Elston N. , Dong Shan , Adams David R. , Allan Kirsten , Bakshi Madhura , Baldwin Erin E. , Berger Seth I. , Bernstein Jonathan A. , Bhatnagar Ishita , Blair Ed , Brown Natasha J. , Burrage Lindsay C. , Chapman Kimberly , Coman David J. , Compton Alison G. , Cunningham Chloe A. , D’Souza Precilla , Danecek Petr , Délot Emmanuèle C. , Dias Kerith-Rae , Elias Ellen R. , Elmslie Frances , Evans Care-Anne , Ewans Lisa , Ezell Kimberly , Fraser Jamie L. , Gallacher Lyndon , Genetti Casie A. , Goriely Anne , Grant Christina L. , Haack Tobias , Higgs Jenny E. , Hinch Anjali G. , Hurles Matthew E. , Kuechler Alma , Lachlan Katherine L. , Lalani Seema R. , Lecoquierre François , Leitão Elsa , Fevre Anna Le , Leventer Richard J. , Liebelt Jan E. , Lindsay Sarah , Lockhart Paul J. , Ma Alan S. , Macnamara Ellen F. , Mansour Sahar , Maurer Taylor M. , Mendez Hector R. , Metcalfe Kay , Montgomery Stephen B. , Moosajee Mariya , Nassogne Marie-Cécile , Neumann Serena , O’Donoghue Michael , O’Leary Melanie , Palmer Elizabeth E. , Pattani Nikhil , Phillips John , Pitsava Georgia , Pysar Ryan , Rehm Heidi L. , Reuter Chloe M. , Revencu Nicole , Riess Angelika , Rius Rocio , Rodan Lance , Roscioli Tony , Rosenfeld Jill A. , Sachdev Rani , Shaw-Smith Charles J. , Simons Cas , Sisodiya Sanjay M. , Snell Penny , St Clair Laura , Stark Zornitza , Stewart Helen S. , Tan Tiong Yang , Tan Natalie B. , Temple Suzanna E. L. , Thorburn David R. , Tifft Cynthia J. , Uebergang Eloise , VanNoy Grace E. , Vasudevan Pradeep , Vilain Eric , Viskochil David H. , Wedd Laura , Wheeler Matthew T. , White Susan M. , Wojcik Monica , Wolfe Lynne A. , Wolfenson Zoe , Wright Caroline F. , Xiao Changrui , Zocche David , Rubenstein John L. , Markenscoff-Papadimitriou Eirene , Fica Sebastian M. , Baralle Diana , Depienne Christel , MacArthur Daniel G. , Howson Joanna M. M. , Sanders Stephan J. , O’Donnell-Luria Anne , Whiffin Nicola 
Published: July 2024

Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes1. Large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here we identify the non-coding RNA RNU4-2 as a syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome2. We identify an 18 base pair region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 115 individuals with NDD. Most individuals (77.4%) have the same highly recurrent single base insertion (n.64_65insT). In 54 individuals in whom it could be determined, the de novo variants were all on the maternal allele. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to RNU4-1 and other U4 homologues. Using RNA sequencing, we show how 5′ splice-site use is systematically disrupted in individuals with RNU4-2 variants, consistent with the known role of this region during spliceosome activation. Finally, we estimate that variants in this 18 base pair region explain 0.4% of individuals with NDD. This work underscores the importance of non-coding genes in rare disorders and will provide a diagnosis to thousands of individuals with NDD worldwide.