Dominant variants in major spliceosome U4 and U5 small nuclear RNA genes cause neurodevelopmental disorders through splicing disruption
Caroline Nava, Benjamin Cogné, Amandine Santini, Elsa Leitão, François Lecoquierre, Yuyang Chen, Sarah L. Stenton, Thomas Besnard, Solveig Heide, Sarah Baer, Abhilasha Jakhar, Sonja Neuser, Boris Keren, Anne Faudet, Sylvie Forlani, Marie Faoucher, Kévin Uguen, Konrad Platzer, Alexandra Afenjar, Jean‐Luc Alessandri, Stephanie Andres, Chloé Angelini, Bernard Aral, Benoı̂t Arveiler, Tania Attié‐Bitach, Marion Aubert‐Mucca, Guillaume Banneau, Tahsin Stefan Barakat, Giulia Barcia, Stéphanie Baulac, Claire Bénéteau, Fouzia Benkerdou, Virginie Bernard, Stéphane Bezieau, Dominique Bonneau, Marie-Noelle Bonnet-Dupeyron, Simon Boussion, Odile Boute, Elise Brischoux‐Boucher, Samantha J. Bryen, Julien Buratti, Tiffany Busa, Almuth Caliebe, Yline Capri, Kévin Cassinari, Roseline Caumes, Camille Cenni, Pascal Chambon, Perrine Charles, John Christodoulou, Cindy Colson, Solène Conrad, Auriane Cospain, Juliette Coursimault, Thomas Courtin, Madeline Couse, Charles Coutton, Isabelle Creveaux, Alissa M. D’Gama, Benjamin Dauriat, Jean‐Madeleine de Sainte Agathe, Giulia Gobbo, Andrée Delahaye‐Duriez, Julian Delanne, Anne‐Sophie Denommé‐Pichon, Anne Dieux‐Coëslier, Laura Do Souto Ferreira, Martine Doco‐Fenzy, Stephan Drukewitz, Véronique Duboc, Christèle Dubourg, Yannis Duffourd, David A. Dyment, Salima El Chehadeh, Monique Elmaleh, Laurence Faivre, Samuel Fennelly, Hanna Fischer, Mélanie Fradin, Camille Galludec Vaillant, Benjamin Ganne, Jamal Ghoumid, Himanshu Goel, Zeynep Gokce‐Samar, Alice Goldenberg, Romain Gonfreville Robert, Svetlana Gorokhova, Louise Goujon, Victoria Granier, Mathilde Gras, John M. Greally, Bianca Greiten, Paul Gueguen, Anne‐Marie Guerrot, Saurav Guha, Anne Guimier, Tobias B. Haack, Hamza Hadj Abdallah, Yosra Halleb, Radu Harbuz
Abstract
The major spliceosome contains five small nuclear RNAs (snRNAs; U1, U2, U4, U5 and U6) essential for splicing. Variants in RNU4-2, encoding U4, cause a neurodevelopmental disorder called ReNU syndrome. We investigated de novo variants in 50 snRNA-encoding genes in a French cohort of 23,649 individuals with rare disorders and gathered additional cases through international collaborations. Altogether, we identified 145 previously unreported probands with (likely) pathogenic variants in RNU4-2 and 21 individuals with de novo and/or recurrent variants in RNU5B-1 and RNU5A-1, encoding U5. Pathogenic variants typically arose de novo on the maternal allele and cluster in regions critical for splicing. RNU4-2 variants mainly localize to two structures, the stem III and T-loop/quasi-pseudoknot, which position the U6 ACAGAGA box for 5' splice site recognition and associate with different phenotypic severity. RNU4-2 variants result in specific defects in alternative 5' splice site usage and methylation patterns (episignatures) that correlate with variant location and clinical severity. This study establishes RNU5B-1 as a neurodevelopmental disorder gene, suggests RNU5A-1 as a strong candidate and highlights the role of de novo variants in snRNAs.