Monoallelic variation inDHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease
Authors: Calame Daniel G. , Guo Tianyu , Wang Chen , Garrett Lillian , Jolly Angad , Dawood Moez , Kurolap Alina , Henig Noa Zunz , Fatih Jawid M. , Herman Isabella , Du Haowei , Mitani Tadahiro , Becker Lore , Rathkolb Birgit , Gerlini Raffaele , Seisenberger Claudia , Marschal Susan , Hunter Jill V. , Gerard Amanda , Heidlebaugh Alexis , Challman Thomas , Spillmann Rebecca C. , Jhangiani Shalini N. , Coban-Akdemir Zeynep , Lalani Seema , Liu Lingxiao , Revah-Politi Anya , Iglesias Alejandro , Guzman Edwin , Baugh Evan , Boddaert Nathalie , Rondeau Sophie , Clothide Ormieres , Barcia Giulia , Tan Queenie K.G. , Thiffault Isabelle , Pastinen Tomi , Sheikh Kazim , Biliciler Suur , Mei Davide , Melani Federico , Shashi Vandana , Yaron Yuval , Steele Mary , Wakeling Emma , Østergaard Elsebet , Nazaryan-Petersen Lusine ,   Network Undiagnosed Diseases, Millan Francisca , Santiago-Sim Teresa , Thevenon Julien , Bruel Ange-Line , Thauvin-Robinet Christel , Popp Denny , Platzer Konrad , Gawlinski Pawel , Wiszniewski Wojciech , Marafi Dana , Pehlivan Davut , Posey Jennifer E. , Gibbs Richard A. , Gailus-Durner Valerie , Guerrini Renzo , Fuchs Helmut , de Angelis Martin Hrabě , Hölter Sabine M. , Cheung Hoi-Hung , Gu Shen , Lupski James R. 
Published: March 2023

DExD/H-box RNA helicases (DDX/DHX) are encoded by a large paralogous gene family; in a subset of these human helicase genes, pathogenic variation causes neurodevelopmental disorder (NDD) traits and cancer.DHX9encodes a BRCA1-interacting nuclear helicase regulating transcription, R-loops, and homologous recombination and exhibits the highest mutational constraint of all DDX/DHX paralogs but remains without disease trait associations. Using exome sequencing and family-based rare variant analysis, we identified 20 individuals withde novo, ultra-rare, heterozygous missense or loss-of-function (LoF)DHX9variant alleles. Phenotypes ranged from NDDs to the distal symmetric polyneuropathy axonal Charcot-Marie-Tooth disease (CMT2). Quantitative HPO analysis demonstrated genotype-phenotype correlations with LoF variants causing mild NDD phenotypes and nuclear localization signal (NLS) missense variants causing severe NDD. We investigatedDHX9variant-associated cellular phenotypes in human cell lines. Whereas wild-type DHX9 restricted to the nucleus, NLS missense variants abnormally accumulated in the cytoplasm. Fibroblasts from a patient with an NLS variant also showed abnormal cytoplasmic DHX9 accumulation. CMT2-associated missense variants caused aberrant nucleolar DHX9 accumulation, a phenomenon previously associated with cellular stress. Two NDD-associated variants, p.(Gly411Glu) and p.(Arg761Gln), altered DHX9 ATPase activity. The severe NDD-associated variant p.(Arg141Gln) did not impact DHX9 localization but instead increased R-loop levels and double-stranded DNA breaks.Dhx9-/-mice exhibit hypoactivity in novel environments, tremor, and sensorineural hearing loss. Taken together, these results establishDHX9as a critical regulator of mammalian neurodevelopment and neuronal homeostasis.