Deleterious, protein-altering variants in the X-linked transcriptional coregulator ZMYM3 in 22 individuals with a neurodevelopmental delay phenotype

Neurodevelopmental disorders (NDDs) often result from highly penetrant variation in one of many genes, including genes not yet characterized. Using the MatchMaker Exchange, we assembled a cohort of 22 individuals with rare, protein-altering variation in the X-linked transcriptional coregulator gene ZMYM3 . Most (n=19) individuals were males; 15 males had maternally-inherited alleles, three of the variants in males arose de novo , and one had unknown inheritance. Overlapping features included developmental delay, intellectual disability, behavioral abnormalities, and a specific facial gestalt in a subset of males. Variants in almost all individuals (n=21) are missense, two of which are recurrent. Three unrelated males were identified with inherited variation at R441, a site at which variation has been previously reported in NDD-affected males, and two individuals have de novo variation at R1294. All variants affect evolutionarily conserved sites, and most are predicted to damage protein structure or function. ZMYM3 is relatively intolerant to variation in the general population, is highly expressed in the brain, and encodes a component of the KDM1A-RCOR1 chromatin-modifying complex. ChIP-seq experiments on one mutant, ZMYM3R1274W, indicate dramatically reduced genomic occupancy, supporting a hypomorphic effect. While we are unable to perform statistical evaluations to support a conclusive causative role for variation in ZMYM3 in disease, the totality of the evidence, including the presence of recurrent variation, overlapping phenotypic features, protein-modeling data, evolutionary constraint, and experimentally-confirmed functional effects, strongly supports ZMYM3 as a novel NDD gene. ### Competing Interest Statement JLB, YC, BRL, AGN and HZE are employees of GeneDx, LLC. SEA is a cofounder and CEO of MediGenome, the Swiss Institute of Genomic Medicine. All other authors declare no competing interests. ### Funding Statement This study was funded by multiple sources. SMH, AC, ACEH, MD and GMC were supported by a grant from the Alabama Genomic Health Initiative (an Alabama-State earmarked project F170303004) through the University of Alabama in Birmingham. LN was supported by the project National Institute for Neurological Research (Programme EXCELES, ID Project No. LX22NPO5107), Funded by the European Union, Next Generation EU and by institutional program UNCE/MED/007 of Charles University in Prague. SK was supported by grant NV19-07-00136 from the Ministry of Health of the Czech Republic. LN and SK thank the National Center for Medical Genomics (LM2018132) for WES analyses. Sequencing and analysis of one individual in this study was made possible by the generous gifts to Children's Mercy Research Institute and Genomic Answers for Kids program at Children's Mercy Kansas City. This work was also supported by the Italian Ministry of Health (Ricerca 5×1000, RCR-2020-23670068\_001, and RCR-2021-23671215 to MT), and Italian Ministry of Research (FOE 2019, to MT), and PRIN2020 (code 20203P8C3X, to AB). Reanalysis of exome sequencing for individual 14 was performed on a research basis by the Care4Rare Canada Consortium. This work was supported by grants from the Swiss National Science Foundation (31003A\_182632 to AR) and the Blackswan Foundation (to AR), and the ChildCare Foundation to SEA. This work was also funded through the CRT Foundation (Progam "Erogazioni Ordinarie" 2019) and the Italian Ministry of University and Research (Assegni, Tornata 2022, Bando: BMSS.2022.06/XXIV), to MRS, GC and GE. MM was supported by RVO VFN 64165, Czech Ministry of Health. This work was also supported by a Swiss National Science Foundation grant 320030_179547 to AR. CN and JD were supported by The Genesis Foundation for Children. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This study was a GeneMatcher-facilitated collaboration involving over 20 different groups. Informed consent for publication of de-identified data or publication of images (where applicable) was obtained through the referring clinical teams. All human subject studies included here were approved or exempted by their local IRBs or institutions, including Arkansas Children's Hospital, Boston Children's Hospital, Children's Hospital of Eastern Ontario Research Institute, Children's Mercy Kansas City, Childrens Hospital of Philadelphia, Cleveland Clinic, Erasmus MC University Medical Center, Ospedale Pediatrico Bambino Gesu, Saints Cyril and Methodius University, The University of Alabama at Birmingham, UCSF/Fresno, University Clinic for Children's Diseases, University Hospital of Rennes, University of Texas Southwestern Medical Center. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The published article includes all variant information pertinent to this study. ChIP-seq data will be made available via the NCBI Gene Expression Omnibus (GEO, ).