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Al-Kurbi AA, Da'as SI, Aamer W, Krishnamoorthy N, Poggiolini I, Abdelrahman D, Elbashir N, Al-Shabeeb Akil A, Glass GE, Fakhro KA. A recessive variant in SIM2 in a child with complex craniofacial anomalies and global developmental delay. Eur J Med Genet 2022; 65:104455. [PMID: 35182808 DOI: 10.1016/j.ejmg.2022.104455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 11/26/2022]
Abstract
Rare deletions and duplications on the long arm of Chromosome 21 have previously been reported in many patients with craniofacial and developmental phenotypes. However, this Down Syndrome Critical Region (DSCR) contains multiple genes, making identifying a single causative gene difficult. Here, we report a case of a boy with bicoronal craniosynostosis, facial dysmorphism, developmental delay, and intellectual impairment who was found by whole genome sequencing to have a homozygous missense mutation in the Single-Minded Homolog 2 (SIM2) gene (c.461 A > G, p.Tyr154Cys) within the DSCR. SIM2 encodes an essential bHLH and PAS domain transcription factor expressed during fetal brain development and acts as a master regulator of neurogenesis. This variant is globally very rare, segregates in the family, and is predicted to be highly deleterious by in silico analysis, 3D molecular modeling of protein structure, and functional analysis of zebrafish models. Zebrafish expressing the human SIM2p.Y154C variant displayed a progressed microcephaly-like phenotype and head shape abnormalities. When combined with careful phenotyping of the patient vis-à-vis previously reported cases harboring structural variants in this critical 21q22 region, the data support a pathogenic role of SIM2 in this complex syndrome and demonstrates the utility of next-generation sequencing in prioritizing genes in contiguous deletions/duplications syndromes and diagnosing microarray-negative patients in the craniofacial clinic.
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Affiliation(s)
- Alya A Al-Kurbi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar; Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | - Sahar Isa Da'as
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar; Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | | | | | - Doua Abdelrahman
- Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | - Najwa Elbashir
- Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | | | - Graeme E Glass
- Division of Plastic and Craniofacial Surgery, Sidra Medicine, 26999, Doha, Qatar
| | - Khalid A Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar; Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar; Department of Genetic Medicine, Weill Cornell Medical College, Doha, 24144, Qatar.
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A de novo 2.78-Mb duplication on chromosome 21q22.11 implicates candidate genes in the partial trisomy 21 phenotype. NPJ Genom Med 2016; 1. [PMID: 27840696 PMCID: PMC5102301 DOI: 10.1038/npjgenmed.2016.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Down syndrome (DS) is the most common genetic cause of intellectual disability (ID) and in the majority of cases is the result of complete trisomy 21. The hypothesis that the characteristic DS clinical features are due to a single DS critical region (DSCR) at distal chromosome 21q has been refuted by recently reported segmental trisomy 21 cases characterised by microarray-based comparative genomic hybridisation (aCGH). These rare cases have implicated multiple regions on chromosome 21 in the aetiology of distinct features of DS; however, the map of chromosome 21 copy-number aberrations and their associated phenotypes remains incompletely defined. We report a child with ID who was deemed very high risk for DS on antenatal screening (1 in 13) and has partial, but distinct, dysmorphologic features of DS without congenital heart disease (CHD). Oligonucleotide aCGH testing of the proband detected a previously unreported de novo 2.78-Mb duplication on chromosome 21q22.11 that includes 16 genes; however, this aberration does not harbour any of the historical DSCR genes (APP, DSCR1, DYRK1A and DSCAM). This informative case implicates previously under-recognised candidate genes (SOD1, SYNJ1 and ITSN1) in the pathogenesis of specific DS clinical features and supports a critical region for CHD located more distal on chromosome 21q. In addition, this unique case illustrates how the increasing resolution of microarray and high-throughput sequencing technologies can continue to reveal new biology and enhance understanding of widely studied genetic diseases that were originally described over 50 years ago.
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A de novo duplication of chromosome 21q22.11→qter associated with Down syndrome: Prenatal diagnosis, molecular cytogenetic characterization and fetal ultrasound findings. Taiwan J Obstet Gynecol 2011; 50:492-8. [DOI: 10.1016/j.tjog.2011.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2010] [Indexed: 11/22/2022] Open
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Duchon A, Pothion S, Brault V, Sharp AJ, Tybulewicz VL, Fisher EM, Herault Y. The telomeric part of the human chromosome 21 from Cstb to Prmt2 is not necessary for the locomotor and short-term memory deficits observed in the Tc1 mouse model of Down syndrome. Behav Brain Res 2011; 217:271-81. [PMID: 21047530 PMCID: PMC3590452 DOI: 10.1016/j.bbr.2010.10.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2010] [Revised: 10/06/2010] [Accepted: 10/17/2010] [Indexed: 11/19/2022]
Abstract
Trisomy 21 or Down syndrome (DS) is the most common form of human aneuploid disorder. Increase in the copy number of human chromosome 21 genes leads to several alterations including mental retardation, heart and skeletal dysmorphologies with additional physiological defects. To better understand the genotype and phenotype relationships, several mouse models have been developed, including the transchromosomic Tc1 mouse, which carries an almost complete human chromosome 21, that displays several locomotor and cognitive alterations related to DS. In this report we explore the contribution of the genetic dosage of 47 mouse genes located in the most telomeric part of Hsa21, using a novel model, named Ms4Yah, carrying a deletion of the 2.2Mb Ctsb-Prmt2 genetic interval. We combine this deletion with the Tc1 Hsa21 in a rescue experiment. We could recapitulate most of the Tc1 phenotypes but we found no phenotypes induced by the Ms4Yah and no contribution to the Tc1-induced phenotypes even if we described new alteration in social preference but not in olfaction. Thus we conclude that the genes conserved between mouse and human, found in the most telomeric part of Hsa21, and trisomic in Tc1, are not contributing to the major Tc1 phenotypes, suggesting that the Cstb-Prmt2 region is not playing a major role in locomotor and cognitive deficits found in DS.
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Affiliation(s)
- Arnaud Duchon
- Institut de Génétique Biologie Moléculaire et Cellulaire, Translational Medicine and Neuroscience Program, IGBMC, CNRS, INSERM, Université de Strasbourg, UMR7104, UMR964, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Stéphanie Pothion
- Transgenese et Archivage Animaux Modèles, TAAM, CNRS, UPS44, 3B rue de la Férollerie 45071 Orléans, France
| | - Véronique Brault
- Institut de Génétique Biologie Moléculaire et Cellulaire, Translational Medicine and Neuroscience Program, IGBMC, CNRS, INSERM, Université de Strasbourg, UMR7104, UMR964, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, Room 14-75B, Box 1498, New York, NY 10029, USA
| | | | | | - Yann Herault
- Institut de Génétique Biologie Moléculaire et Cellulaire, Translational Medicine and Neuroscience Program, IGBMC, CNRS, INSERM, Université de Strasbourg, UMR7104, UMR964, 1 rue Laurent Fries, 67404 Illkirch, France
- Transgenese et Archivage Animaux Modèles, TAAM, CNRS, UPS44, 3B rue de la Férollerie 45071 Orléans, France
- Institut Clinique de la Souris, ICS, 1 rue Laurent Fries, 67404 Illkirch, France
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