De novo variants in the non-coding spliceosomal snRNA gene RNU4-2 are a frequent cause of syndromic neurodevelopmental disorders

Yuyang Chen; Ruebena Dawes; Hyung Chul Kim; Sarah L Stenton; Susan Walker; Alicia Ljungdahl; Jenny Lord; Vijay S Ganesh; Jialan Ma; Alexandra C Martin-Geary; Gabrielle Lemire; Elston N D'Souza; Shan Dong; Jamie M Ellingford; David R Adams; Kirsten Allan; Madhura Bakshi; Erin E Baldwin; Seth I Berger; Jonathan A Bernstein; Natasha J Brown; Lindsay C Burrage; Kimberly Chapman; Alison G Compton; Chloe A Cunningham; Precilla D'Souza; Emmanuèle C Délot; Kerith-Rae Dias; Ellen R Elias; Carey-Anne Evans; Lisa Ewans; Kimberly Ezell; Jamie L Fraser; Lyndon Gallacher; Casie A Genetti; Christina L Grant; Tobias Haack; Alma Kuechler; Seema R Lalani; Elsa Leitão; Anna Le Fevre; Richard J Leventer; Jan E Liebelt; Paul J Lockhart; Alan S Ma; Ellen F Macnamara; Taylor M Maurer; Hector R Mendez; Stephen B Montgomery; Marie-Cécile Nassogne; Serena Neumann; Melanie O'Leary; Elizabeth E Palmer; John Phillips; Georgia Pitsava; Ryan Pysar; Heidi L Rehm; Chloe M Reuter; Nicole Revencu; Angelika Riess; Rocio Rius; Lance Rodan; Tony Roscioli; Jill A Rosenfeld; Rani Sachdev; Cas Simons; Sanjay M Sisodiya; Penny Snell; Laura Clair; Zornitza Stark; Tiong Yang Tan; Natalie B Tan; Suzanna El Temple; David R Thorburn; Cynthia J Tifft; Eloise Uebergang; Grace E VanNoy; Eric Vilain; David H Viskochil; Laura Wedd; Matthew T Wheeler; Susan M White; Monica Wojcik; Lynne A Wolfe; Zoe Wolfenson; Changrui Xiao; David Zocche; John L Rubenstein; Eirene Markenscoff-Papadimitriou; Sebastian M Fica; Diana Baralle; Christel Depienne; Daniel G MacArthur; Joanna Mm Howson; Stephan J Sanders; Anne O'Donnell-Luria; Nicola Whiffin

doi:10.1101/2024.04.07.24305438

De novo variants in the non-coding spliceosomal snRNA gene RNU4-2 are a frequent cause of syndromic neurodevelopmental disorders

medRxiv [Preprint]. 2024 Apr 9:2024.04.07.24305438. doi: 10.1101/2024.04.07.24305438.

Authors

Yuyang Chen^{1

2}, Ruebena Dawes^{1

2}, Hyung Chul Kim^{1

2}, Sarah L Stenton^{3

4}, Susan Walker⁵, Alicia Ljungdahl^{6

7}, Jenny Lord⁸, Vijay S Ganesh^{3

4

9}, Jialan Ma³, Alexandra C Martin-Geary^{1

2}, Gabrielle Lemire^{3

4}, Elston N D'Souza^{1

2}, Shan Dong^{6

7}, Jamie M Ellingford^{5

10

11}, David R Adams¹², Kirsten Allan¹³, Madhura Bakshi¹⁴, Erin E Baldwin¹⁵, Seth I Berger^{16

17}, Jonathan A Bernstein^{18

19

20}, Natasha J Brown^{13

21}, Lindsay C Burrage²², Kimberly Chapman¹⁷, Alison G Compton^{13

21

23}, Chloe A Cunningham^{13

21}, Precilla D'Souza¹², Emmanuèle C Délot¹⁶, Kerith-Rae Dias^{24

25}, Ellen R Elias^{26

27}, Carey-Anne Evans^{24

28}, Lisa Ewans^{29

30

31}, Kimberly Ezell³², Jamie L Fraser^{16

17}, Lyndon Gallacher^{13

21}, Casie A Genetti^{4

33}, Christina L Grant¹⁷, Tobias Haack^{34

35}, Alma Kuechler³⁶, Seema R Lalani²², Elsa Leitão³⁶, Anna Le Fevre¹³, Richard J Leventer^{21

23

37}, Jan E Liebelt^{38

39}, Paul J Lockhart^{21

40}, Alan S Ma^{41

42}, Ellen F Macnamara¹², Taylor M Maurer^{19

20

43}, Hector R Mendez^{19

20

44}, Stephen B Montgomery^{19

20

45}, Marie-Cécile Nassogne^{46

47}, Serena Neumann³², Melanie O'Leary³, Elizabeth E Palmer^{29

30}, John Phillips³², Georgia Pitsava⁴⁸, Ryan Pysar^{29

30

49}, Heidi L Rehm^{3

50}, Chloe M Reuter^{19

20

44}, Nicole Revencu⁵¹, Angelika Riess³⁴, Rocio Rius^{21

52

53}, Lance Rodan⁴, Tony Roscioli^{24

25

28}, Jill A Rosenfeld²², Rani Sachdev^{29

30}, Cas Simons^{52

53}, Sanjay M Sisodiya^{54

55}, Penny Snell⁴⁰, Laura Clair⁴¹, Zornitza Stark^{13

21}, Tiong Yang Tan^{13

21}, Natalie B Tan¹³, Suzanna El Temple^{14

56}, David R Thorburn^{13

21

23}, Cynthia J Tifft¹², Eloise Uebergang²³, Grace E VanNoy³, Eric Vilain⁵⁷, David H Viskochil¹⁵, Laura Wedd^{52

53}, Matthew T Wheeler^{19

20

44}, Susan M White^{13

21}, Monica Wojcik^{4

33

58}, Lynne A Wolfe¹², Zoe Wolfenson¹², Changrui Xiao⁵⁹, David Zocche⁶⁰, John L Rubenstein⁷, Eirene Markenscoff-Papadimitriou⁶¹, Sebastian M Fica⁶², Diana Baralle^{63

64}, Christel Depienne³⁶, Daniel G MacArthur^{52

53}, Joanna Mm Howson⁶⁵, Stephan J Sanders^{6

7}, Anne O'Donnell-Luria^{3

4

50}, Nicola Whiffin^{1

2

3}

Affiliations

¹ Big Data Institute, University of Oxford, Oxford, UK.
² Centre for Human Genetics, University of Oxford, Oxford, UK.
³ Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁴ Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
⁵ Genomics England, London, UK.
⁶ Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK.
⁷ Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA.
⁸ Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK.
⁹ Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
¹⁰ Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK.
¹¹ Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK.
¹² Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA.
¹³ Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
¹⁴ Department of Clinical Genetics, Liverpool Hospital, Sydney, NSW, Australia.
¹⁵ Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA.
¹⁶ Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA.
¹⁷ Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA.
¹⁸ Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
¹⁹ GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA.
²⁰ Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.
²¹ Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.
²² Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
²³ Murdoch Children's Research Institute, Melbourne, VIC, Australia.
²⁴ Neuroscience Research Australia, Sydney, NSW, Australia.
²⁵ Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
²⁶ Department of Pediatrics, Children's Hospital Colorado, Aurora, CO, USA.
²⁷ University of Colorado School of Medicine, University of Colorado, Aurora, CO, USA.
²⁸ New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia.
²⁹ Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.
³⁰ Centre for Clinical Genetics, Sydney Children's Hospitals Network, Randwick, NSW, Australia.
³¹ Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
³² Division of Medical Genetics & Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
³³ Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
³⁴ Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
³⁵ Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany.
³⁶ Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
³⁷ Royal Children's Hospital, Melbourne, VIC, Australia.
³⁸ Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, SA, Australia.
³⁹ Repromed, Dulwich, SA, Australia.
⁴⁰ Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
⁴¹ Department of Clinical Genetics, Sydney Children's Hospitals Network Westmead, Sydney, NSW, Australia.
⁴² Specialty of Genomic Medicine, University of Sydney, Sydney, NSW, Australia.
⁴³ Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
⁴⁴ Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
⁴⁵ Department of Pathology, Department of Genetics, Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA.
⁴⁶ Service de Neurologie Pédiatrique, Cliniques Universitaires Saint-Luc, UCLouvain, B-1200, Brussels, Belgium.
⁴⁷ Institut des Maladies Rares, Cliniques Universitaires Saint-Luc, UCLouvain, B-1200, Brussels, Belgium.
⁴⁸ Institute for Clinical and Translational Research, University of California, Irvine, CA, USA.
⁴⁹ Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia.
⁵⁰ Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
⁵¹ Center for Human Genetics, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium.
⁵² Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia.
⁵³ Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
⁵⁴ Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.
⁵⁵ UK and Chalfont Centre for Epilepsy, Bucks, UK.
⁵⁶ School of Women's and Childrens's Health, University of New South Wales, Sydney, NSW, Australia.
⁵⁷ Institute for Clinical and Translational Science, University of California, Irvine, CA, USA.
⁵⁸ Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
⁵⁹ Department of Neurology, University of California, Irvine, CA, USA.
⁶⁰ North West Thames Regional Genetics Service, Northwick Park & St Mark's Hospitals, London, UK.
⁶¹ Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA.
⁶² Department of Biochemistry, University of Oxford, Oxford, UK.
⁶³ School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.
⁶⁴ National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, UK.
⁶⁵ Human Genetics Centre of Excellence, Novo Nordisk Research Centre, Oxford, UK.

Abstract

Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes¹. Increasingly, 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 novel 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 bp 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 119 individuals with NDD. The vast majority of individuals (77.3%) have the same highly recurrent single base-pair insertion (n.64_65insT). We estimate that variants in this region explain 0.41% of individuals with NDD. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to its contiguous counterpart RNU4-1 and other U4 homologs, supporting RNU4-2's role as the primary U4 transcript in the brain. Overall, this work underscores the importance of non-coding genes in rare disorders. It will provide a diagnosis to thousands of individuals with NDD worldwide and pave the way for the development of effective treatments for these individuals.

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Abstract

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