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      Pathogenic variants in the DEAH-box RNA helicase DHX37 are a frequent cause of 46,XY gonadal dysgenesis and 46,XY testicular regression syndrome

      research-article
      , PhD 1 , , , PhD 2 , , PhD 1 , , MSc 1 , , BSc 1 , , BSc 3 , , PhD 1 , , PhD 4 , , PhD 5 , , PhD 5 , , MD, PhD 6 , 7 , 8 , , MD, PhD 6 , , MD 9 , , MD, PhD 4 , , MD 10 , , MD, PhD 11 , , MD 12 , , MD, PhD 11 , , MD, PhD 11 , , MD 13 , , MD, PhD 14 , , MD 15 , , MD, PhD 16 , , MD, PhD 17 , , MD, PhD 18 , , MD, PhD 19 , , PhD 3 , , PhD 20 , , PhD 5 , , PhD 1 ,
      Genetics in Medicine
      Nature Publishing Group US
      disorders of sex development (DSD), testicular regression syndrome, DHX37, RNA helicase, ribosomopathy

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          Abstract

          Purpose

          XY individuals with disorders/differences of sex development (DSD) are characterized by reduced androgenization caused, in some children, by gonadal dysgenesis or testis regression during fetal development. The genetic etiology for most patients with 46,XY gonadal dysgenesis and for all patients with testicular regression syndrome (TRS) is unknown.

          Methods

          We performed exome and/or Sanger sequencing in 145 individuals with 46,XY DSD of unknown etiology including gonadal dysgenesis and TRS.

          Results

          Thirteen children carried heterozygous missense pathogenic variants involving the RNA helicase DHX37, which is essential for ribosome biogenesis. Enrichment of rare/novel DHX37 missense variants in 46,XY DSD is highly significant compared with controls ( P value = 5.8 × 10 −10). Five variants are de novo ( P value = 1.5 × 10 −5). Twelve variants are clustered in two highly conserved functional domains and were specifically associated with gonadal dysgenesis and TRS. Consistent with a role in early testis development, DHX37 is expressed specifically in somatic cells of the developing human and mouse testis.

          Conclusion

          DHX37 pathogenic variants are a new cause of an autosomal dominant form of 46,XY DSD, including gonadal dysgenesis and TRS, showing that these conditions are part of a clinical spectrum. This raises the possibility that some forms of DSD may be a ribosomopathy.

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          Most cited references41

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          UCSF Chimera--a visualization system for exploratory research and analysis.

          The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.
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            SWISS-MODEL: homology modelling of protein structures and complexes

            Abstract Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. Recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. Starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. Other major improvements include the implementation of a new modelling engine, ProMod3 and the introduction a new local model quality estimation method, QMEANDisCo. SWISS-MODEL is freely available at https://swissmodel.expasy.org.
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              Analysis of protein-coding genetic variation in 60,706 humans

              Summary Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. We describe the aggregation and analysis of high-quality exome (protein-coding region) sequence data for 60,706 individuals of diverse ethnicities generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of truncating variants with 72% having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human “knockout” variants in protein-coding genes.
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                Author and article information

                Contributors
                kenmce@pasteur.fr
                anu.bashamboo@pasteur.fr
                Journal
                Genet Med
                Genet. Med
                Genetics in Medicine
                Nature Publishing Group US (New York )
                1098-3600
                1530-0366
                24 July 2019
                24 July 2019
                2020
                : 22
                : 1
                : 150-159
                Affiliations
                [1 ]ISNI 0000 0001 2353 6535, GRID grid.428999.7, Human Developmental Genetics Unit, Institut Pasteur, ; Paris, France
                [2 ]GRID grid.475435.4, Department of Growth and Reproduction, , Rigshospitalet, ; Copenhagen, Denmark
                [3 ]ISNI 0000000121742757, GRID grid.194645.b, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, , The University of Hong Kong, ; Hong Kong, China
                [4 ]ISNI 0000000121901201, GRID grid.83440.3b, Genetics and Genomic Medicine, , UCL GOS Institute of Child Health, UCL, ; London, UK
                [5 ]ISNI 0000 0001 0440 1651, GRID grid.420006.0, Mammalian Genetics Unit, , Medical Research Council Harwell Institute, ; Oxfordshire, UK
                [6 ]ISNI 0000 0001 2308 1657, GRID grid.462844.8, AP-HP, Hôpital d’Enfants Armand-Trousseau, Genetics and Embryology Department; Sorbonne Université; INSERM UMRS_933, ; Paris, France
                [7 ]ISNI 0000 0001 2171 2558, GRID grid.5842.b, AP-HP, Hôpital Universitaire Robert-Debré, Pediatric Urology Department,; Reference Center for Rare Diseases (CRMR) Malformations Rares des Voies Urinaires (MARVU), , Université de Paris, ; Paris, France
                [8 ]ISNI 0000 0001 2287 3919, GRID grid.257413.6, Riley Children Hospital, Pediatric Urology Department; Indiana University, School of Medicine, ; Indianapolis, USA
                [9 ]ISNI 0000 0001 2151 8157, GRID grid.419725.c, Genetics Department, National Research Center, ; Cairo, Egypt
                [10 ]National Hospital, OHMATDYT, Kyiv, Ukraine
                [11 ]ISNI 0000 0004 1937 0589, GRID grid.413235.2, Endocrinology et Diabetic Pediatrics, , Hospital Robert Debre, ; Paris, France
                [12 ]ISNI 0000 0001 0942 9821, GRID grid.11804.3c, Second Department of Paediatrics, , Semmelweis University, ; Budapest, Hungary
                [13 ]Department of Pathology, University Hospital, University of Franche-Comté, Besançon, France
                [14 ]ISNI 0000000121901201, GRID grid.83440.3b, Reproductive Medicine Unit, , Institute for Women’s Health UCL, ; London, UK
                [15 ]Department of Pediatrics, University Hospital, University of Franche-Comté, Besançon, France
                [16 ]Human Genetics Center, University Hospital, University of Franche-Comté, Besançon, France
                [17 ]ISNI 0000 0001 0942 9821, GRID grid.11804.3c, First Department of Paediatrics, , Semmelweis University, ; Budapest, Hungary
                [18 ]Ukrainian Center of Endocrine Surgery Endocrine Organs and Tissue Transplantation, MoH of Ukraine, Kyiv, Ukraine
                [19 ]ISNI 0000 0001 2177 525X, GRID grid.417888.a, Fondation Ophtalmologique Adolphe de Rothschild and Université Paris Descartes, ; Paris, France
                [20 ]ISNI 0000 0001 2322 4988, GRID grid.8591.5, Department of Genetic Medicine and Development University of Geneva, ; Geneva, Switzerland
                Author information
                http://orcid.org/0000-0001-6582-1801
                http://orcid.org/0000-0002-6409-198X
                http://orcid.org/0000-0002-8536-9039
                http://orcid.org/0000-0002-8274-7241
                http://orcid.org/0000-0003-0767-1360
                http://orcid.org/0000-0003-3617-4849
                http://orcid.org/0000-0001-8787-6272
                http://orcid.org/0000-0001-5470-7165
                http://orcid.org/0000-0002-0424-6767
                http://orcid.org/0000-0001-8880-5214
                http://orcid.org/0000-0001-7885-8195
                http://orcid.org/0000-0002-6590-9579
                http://orcid.org/0000-0001-5462-0676
                Article
                606
                10.1038/s41436-019-0606-y
                6944638
                31337883
                6bdac085-9522-425f-adbd-eaf8e29c8d39
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 18 April 2019
                : 1 July 2019
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001665, Agence Nationale de la Recherche;
                Award ID: ANR-17-CE14-0038-01
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100004440, Wellcome Trust;
                Award ID: 098513/Z/12/Z
                Award Recipient :
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                © American College of Medical Genetics and Genomics 2020

                Genetics
                disorders of sex development (dsd),testicular regression syndrome,dhx37,rna helicase,ribosomopathy

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