1756-994X1612024Apr03Genome MedNODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy.53535310.1186/s13073-024-01312-9NODAL signaling plays a critical role in embryonic patterning and heart development in vertebrates. Genetic variants resulting in perturbations of the TGF-β/NODAL signaling pathway have reproducibly been shown to cause laterality defects in humans. To further explore this association and improve genetic diagnosis, the study aims to identify and characterize a broader range of NODAL variants in a large number of individuals with laterality defects.We re-analyzed a cohort of 321 proband-only exomes of individuals with clinically diagnosed laterality congenital heart disease (CHD) using family-based, rare variant genomic analyses. To this cohort we added 12 affected subjects with known NODAL variants and CHD from institutional research and clinical cohorts to investigate an allelic series. For those with candidate contributory variants, variant allele confirmation and segregation analysis were studied by Sanger sequencing in available family members. Array comparative genomic hybridization and droplet digital PCR were utilized for copy number variants (CNV) validation and characterization. We performed Human Phenotype Ontology (HPO)-based quantitative phenotypic analyses to dissect allele-specific phenotypic differences.Missense, nonsense, splice site, indels, and/or structural variants of NODAL were identified as potential causes of heterotaxy and other laterality defects in 33 CHD cases. We describe a recurrent complex indel variant for which the nucleic acid secondary structure predictions implicate secondary structure mutagenesis as a possible mechanism for formation. We identified two CNV deletion alleles spanning NODAL in two unrelated CHD cases. Furthermore, 17 CHD individuals were found (16/17 with known Hispanic ancestry) to have the c.778G > A:p.G260R NODAL missense variant which we propose reclassification from variant of uncertain significance (VUS) to likely pathogenic. Quantitative HPO-based analyses of the observed clinical phenotype for all cases with p.G260R variation, including heterozygous, homozygous, and compound heterozygous cases, reveal clustering of individuals with biallelic variation. This finding provides evidence for a genotypic-phenotypic correlation and an allele-specific gene dosage model.Our data further support a role for rare deleterious variants in NODAL as a cause for sporadic human laterality defects, expand the repertoire of observed anatomical complexity of potential cardiovascular anomalies, and implicate an allele specific gene dosage model.© 2024. The Author(s).DardasZainZ0000-0003-2387-3122Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.FatihJawid MJMDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.JollyAngadADepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.DawoodMoezMDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA.DuHaoweiHDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.GrochowskiChristopher MCMDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.JonesEdward GEGDivision of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA.JhangianiShalini NSNDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.WehrensXander H TXHTDivision of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA.Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA.Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA.Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.LiuPengfeiPDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.Baylor Genetics, Houston, TX, 77021, USA.BiWeiminWDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.Baylor Genetics, Houston, TX, 77021, USA.BoerwinkleEricEHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.PoseyJennifer EJEDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.MuznyDonna MDMDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.GibbsRichard ARADepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.LupskiJames RJR0000-0001-9907-9246Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.Texas Children's Hospital, Houston, Houston, TX, 77030, USA.Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.Coban-AkdemirZeynepZ0000-0001-9928-9032Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. zeynep.h.cobanakdemir@uth.tmc.edu.Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. zeynep.h.cobanakdemir@uth.tmc.edu.MorrisShaine ASA0000-0002-8056-0934Division of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA. shainem@bcm.edu.engUM1 HG006542HGNHGRI NIH HHSUnited StatesR35 NS105078NSNINDS NIH HHSUnited StatesR01 HD039056HDNICHD NIH HHSUnited StatesR01 HL091771HLNHLBI NIH HHSUnited StatesU01 HG011758HGNHGRI NIH HHSUnited StatesJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, N.I.H., Extramural20240403