1
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Sundaramurthi JC, Bagley AM, Blau H, Carmody L, Crandall A, Danis D, Gargano MA, Gustafson AG, Raney EM, Shingle M, Davids JR, Robinson PN. De novo TRPM3 missense variant associated with neurodevelopmental delay and manifestations of cerebral palsy. Cold Spring Harb Mol Case Stud 2023; 9:a006293. [PMID: 37684057 PMCID: PMC10815282 DOI: 10.1101/mcs.a006293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
We identified a de novo heterozygous transient receptor potential cation channel subfamily M (melastatin) member 3 (TRPM3) missense variant, p.(Asn1126Asp), in a patient with developmental delay and manifestations of cerebral palsy (CP) using phenotype-driven prioritization analysis of whole-genome sequencing data with Exomiser. The variant is localized in the functionally important ion transport domain of the TRPM3 protein and predicted to impact the protein structure. Our report adds TRPM3 to the list of Mendelian disease-associated genes that can be associated with CP and provides further evidence for the pathogenicity of the variant p.(Asn1126Asp).
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Affiliation(s)
| | - Anita M Bagley
- Shriners Children's Northern California, Sacramento, California 95817, USA
| | - Hannah Blau
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Leigh Carmody
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Amy Crandall
- Shriners Children's, Portland, Oregon 97239, USA
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Michael A Gargano
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | | | | | - Mallory Shingle
- Shriners Children's Northern California, Sacramento, California 95817, USA
| | - Jon R Davids
- Shriners Children's Northern California, Sacramento, California 95817, USA
- Department of Orthopaedic Surgery, University of California Davis Health, Sacramento, California 95817, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA;
- Institute for Systems Genomics, University of Connecticut, Farmington, Connecticut 06032, USA
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2
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Kleyner R, Ung N, Arif M, Marchi E, Amble K, Gavin M, Madrid R, Lyon G. ITPR1-associated spinocerebellar ataxia with craniofacial features-additional evidence for germline mosaicism. Cold Spring Harb Mol Case Stud 2023; 9:a006303. [PMID: 37821226 PMCID: PMC10815276 DOI: 10.1101/mcs.a006303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
Inositol 1,4,5-triphosphate receptor type 1 (ITPR1) is an endoplasmic reticulum-bound intracellular inositol triphosphate receptor involved in the regulation of intracellular calcium. Pathogenic variants in ITPR1 are associated with spinocerebellar ataxia (SCA) types 15/16 and 29 and have recently been implicated in a facial microsomia syndrome. In this report, we present a family with three affected individuals found to have a heterozygous missense c.800C > T (predicted p.Thr267Met) who present clinically with a SCA29-like syndrome. All three individuals presented with varying degrees of ataxia, developmental delay, and apparent intellectual disability, as well as craniofacial involvement-an uncommon finding in patients with SCA29. The variant was identified using clinical exome sequencing and validated with Sanger sequencing. It is presumed to be inherited via parental germline mosaicism. We present our findings to provide additional evidence for germline mosaic inheritance of SCA29, as well as to expand the clinical phenotype of the syndrome.
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Affiliation(s)
- Robert Kleyner
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
- Department of Neurological Surgery, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York 11794-8122, USA
| | - Nathaniel Ung
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
| | - Mohammad Arif
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
- Division of Cytogenetics and Molecular Pathology, North Shore University Hospital, Manhasset, New York 11030, USA
| | - Elaine Marchi
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
| | - Karen Amble
- George A. Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
| | - Maureen Gavin
- George A. Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
| | - Ricardo Madrid
- George A. Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
| | - Gholson Lyon
- Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA;
- George A. Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
- Biology PhD Program, The Graduate Center, The City University of New York, New York, New York 10016, USA
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3
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Devries S, Mulder M, Charron JG, Prokop JW, Mark PR. SLC6A1 G443D associated with developmental delay and epilepsy. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005371. [PMID: 32660967 PMCID: PMC7476406 DOI: 10.1101/mcs.a005371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/29/2020] [Indexed: 11/26/2022] Open
Abstract
SLC6A1 is associated with an autosomal dominant early-onset seizure and epileptic encephalopathy associated with intellectual disability. We present a 2-yr-old girl with developmental delay and epilepsy, using a new computational filtering impact score to show the patient's variant ranks with other pathogenic variants. Genomic studies within the patient revealed a G443D variant of uncertain significance. Structural and evolutionary assessments establish this variant as a loss of function to the protein. Compiled metrics through our custom tools on sequence, structure, and protein dynamics combined with PolyPhen-2, PROVEAN, SIFT, and Align-GVGD reveal this variant to rank in the top functional outcome changes relative to gnomAD, TOPMed, and ClinVar variants known to date. The patient was resistant to multiple epileptic drugs, finally finding that valproic acid controls the seizures. This is consistent with additional groups studying SLC6A1 variants within patients.
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Affiliation(s)
- Seth Devries
- Pediatric Neurology, Helen DeVos Children's Hospital, Grand Rapids, Michigan 49503, USA
| | - Monica Mulder
- Pediatric Neurology, Helen DeVos Children's Hospital, Grand Rapids, Michigan 49503, USA
| | - Jacob G Charron
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, USA.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing Michigan 48824, USA
| | - Paul R Mark
- Spectrum Health Division of Medical Genetics, Grand Rapids, Michigan 49503, USA
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4
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Lyon GJ, Marchi E, Ekstein J, Meiner V, Hirsch Y, Scher S, Yang E, De Vivo DC, Madrid R, Li Q, Wang K, Haworth A, Chilton I, Chung WK, Velinov M. VAC14 syndrome in two siblings with retinitis pigmentosa and neurodegeneration with brain iron accumulation. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003715. [PMID: 31387860 PMCID: PMC6913149 DOI: 10.1101/mcs.a003715] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/09/2019] [Indexed: 01/10/2023] Open
Abstract
Whole-exome sequencing was used to identify the genetic etiology of a rapidly progressing neurological disease present in two of six siblings with early childhood onset of severe progressive spastic paraparesis and learning disabilities. A homozygous mutation (c.2005G>T, p, V669L) was found in VAC14, and the clinical phenotype is consistent with the recently described VAC14-related striatonigral degeneration, childhood-onset syndrome (SNDC) (MIM#617054). However, the phenotype includes a distinct clinical presentation of retinitis pigmentosa (RP), which has not previously been reported in association with VAC14 mutations. Brain magnetic resonance imaging (MRI) revealed abnormal magnetic susceptibility in the globus pallidus, which can be seen in neurodegeneration with brain iron accumulation (NBIA). RP is a group of inherited retinal diseases with phenotypic/genetic heterogeneity, and the pathophysiologic basis of RP is not completely understood but is thought to be due to a primary retinal photoreceptor cell degenerative process. Most cases of RP are seen in isolation (nonsyndromic); this is a report of RP in two siblings with VAC14-associated syndrome, and it is suggested that a connection between RP and VAC14-associated syndrome should be explored in future studies.
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Affiliation(s)
- Gholson J Lyon
- NYS Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, New York 10314, USA
| | - Elaine Marchi
- NYS Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, New York 10314, USA
| | - Joseph Ekstein
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, New York 11211, USA
| | - Vardiella Meiner
- Faculty of Medicine, Hebrew University, Jerusalem 9112001, Israel.,Department of Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem 9112001, Israel
| | - Yoel Hirsch
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, New York 11211, USA
| | - Sholem Scher
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, New York 11211, USA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Darryl C De Vivo
- Columbia University Irving Medical Center, The Neurological Institute, New York, New York 10032, USA
| | - Ricardo Madrid
- NYS Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, New York 10314, USA
| | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario M5G 2C1, Canada
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Andrea Haworth
- Congenica Ltd, Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Ilana Chilton
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, New York 10032, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, New York 10032, USA
| | - Milen Velinov
- NYS Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, New York 10314, USA
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5
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Okur V, LeDuc CA, Guzman E, Valivullah ZM, Anyane-Yeboa K, Chung WK. Homozygous noncanonical splice variant in LSM1 in two siblings with multiple congenital anomalies and global developmental delay. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004101. [PMID: 31010896 PMCID: PMC6549555 DOI: 10.1101/mcs.a004101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022] Open
Abstract
Two siblings, one male and one female, ages 6 and 13 yr old, have similar clinical features of global developmental delay, multiple congenital anomalies affecting the cardiac, genitourinary, and skeletal systems, and abnormal eye movements. Whole-genome sequencing revealed a homozygous splice variant (NM_014462.3:c.231+4A>C) in LSM1 that segregated with the phenotype in the family. LSM1 has a role in pre-mRNA splicing and degradation. Expression studies revealed absence of expression of the canonical isoform in the affected individuals. The Lsm1 knockout mice have a partially overlapping phenotype that affects the brain, heart, and eye. To our knowledge, LSM1 has not been associated with any human disorder; however, the tissue expression pattern, gene constraint, and the similarity of the phenotype in our patients and the knockout mice models suggest it has a role in the development of multiple organ systems in humans.
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Affiliation(s)
- Volkan Okur
- Department of Pediatrics, Columbia University, New York, New York 10032, USA
| | - Charles A LeDuc
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
| | - Edwin Guzman
- Department of Pediatrics, Columbia University, New York, New York 10032, USA
| | - Zaheer M Valivullah
- Center for Mendelian Genomics at the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Columbia University, New York, New York 10032, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York 10032, USA.,Department of Medicine, Columbia University, New York, New York 10032, USA
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6
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Qian Y, Wu B, Lu Y, Dong X, Qin Q, Zhou W, Wang H. Early-onset infant epileptic encephalopathy associated with a de novo PPP3CA gene mutation. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002949. [PMID: 30455226 PMCID: PMC6318765 DOI: 10.1101/mcs.a002949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/14/2018] [Indexed: 12/13/2022] Open
Abstract
Epileptic encephalopathies are severe seizure disorders accompanied by intellectual disability. Whole-exome sequencing technology has enabled the discovery of genetic mutations responsible for a wide range of diseases, and severe epilepsy and neurodevelopmental diseases are often associated with rare de novo mutations. We identified a novel de novo frameshift mutation in the PPP3CA gene encoding calcium-dependent protein phosphatase (calcineurin) catalytic subunit A (c.1255_1256del, p.Ser419Cysfs*31) in an 11.5-mo-old female with early-onset refractory epilepsy and developmental delay. This finding expands the list of PPP3CA mutations associated with early-onset severe neurodevelopmental disease with seizures and provides further details on clinical features.
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Affiliation(s)
- Yanyan Qian
- Children's Hospital of Fudan University, The Translational Medicine Center of Children Development and Disease of Fudan University, Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Bingbing Wu
- Children's Hospital of Fudan University, The Translational Medicine Center of Children Development and Disease of Fudan University, Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Yulan Lu
- Children's Hospital of Fudan University, The Translational Medicine Center of Children Development and Disease of Fudan University, Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Xinran Dong
- Children's Hospital of Fudan University, The Translational Medicine Center of Children Development and Disease of Fudan University, Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Qian Qin
- Children's Hospital of Fudan University, The Translational Medicine Center of Children Development and Disease of Fudan University, Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Wenhao Zhou
- Children's Hospital of Fudan University, The Translational Medicine Center of Children Development and Disease of Fudan University, Key Laboratory of Birth Defects, Shanghai 201102, China.,Department of Neonatology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Huijun Wang
- Children's Hospital of Fudan University, The Translational Medicine Center of Children Development and Disease of Fudan University, Key Laboratory of Birth Defects, Shanghai 201102, China
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7
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Furey C, Antwi P, Duran D, Timberlake AT, Nelson-Williams C, Matouk CC, DiLuna ML, Günel M, Kahle KT. 9p24 triplication in syndromic hydrocephalus with diffuse villous hyperplasia of the choroid plexus. Cold Spring Harb Mol Case Stud 2018; 4:a003145. [PMID: 29895553 PMCID: PMC6169828 DOI: 10.1101/mcs.a003145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/06/2018] [Indexed: 12/19/2022] Open
Abstract
Hydrocephalus, a disorder of impaired cerebrospinal fluid (CSF) homeostasis, often results from an imbalance between CSF production and reabsorption. Rarely, hydrocephalus is the consequence of CSF hypersecretion in the context of diffuse villous hyperplasia of the choroid plexus (DVHCP). The limited genetic information in previously reported cases suggests a high prevalence of gains of Chromosome 9p in this disease, although the critical genes involved in DVHCP pathogenesis have not been identified. Here, we report a patient with syndromic hydrocephalus with DVHCP associated with a novel 9p24.3-11.2 triplication and 15q13.2-q13.3 microdeletion. We review the clinical, radiological, and pathological features of DVHCP, as well as its surgical management. A better understanding of the genetic basis of DVHCP could spur the development of rational, targeted nonsurgical hydrocephalus treatments.
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Affiliation(s)
- Charuta Furey
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Prince Antwi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Daniel Duran
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Andrew T Timberlake
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Surgery, Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Carol Nelson-Williams
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Charles C Matouk
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Michael L DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Murat Günel
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Kristopher T Kahle
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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8
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Polonis K, Blackburn PR, Urrutia RA, Lomberk GA, Kruisselbrink T, Cousin MA, Boczek NJ, Hoppman NL, Babovic-Vuksanovic D, Klee EW, Pichurin PN. Co-occurrence of a maternally inherited DNMT3A duplication and a paternally inherited pathogenic variant in EZH2 in a child with growth retardation and severe short stature: atypical Weaver syndrome or evidence of a DNMT3A dosage effect? Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002899. [PMID: 29802153 PMCID: PMC6071565 DOI: 10.1101/mcs.a002899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/18/2018] [Indexed: 11/24/2022] Open
Abstract
Overgrowth syndromes are a clinically heterogeneous group of disorders characterized by localized or generalized tissue overgrowth and varying degrees of developmental and intellectual disability. An expanding list of genes associated with overgrowth syndromes include the histone methyltransferase genes EZH2 and NSD1, which cause Weaver and Sotos syndrome, respectively, and the DNA methyltransferase (DNMT3A) gene that results in Tatton-Brown–Rahman syndrome (TBRS). Here, we describe a 5-year-old female with a paternally inherited pathogenic mutation in EZH2 (c.2050C>T, p.Arg684Cys) and a maternally inherited 505-kb duplication of uncertain significance at 2p23.3 (encompassing five genes, including DNMT3A) who presented with intrauterine growth restriction, slow postnatal growth, short stature, hypotonia, developmental delay, and neuroblastoma diagnosed at the age of 8 mo. Her father had tall stature, dysmorphic facial features, and intellectual disability consistent with Weaver syndrome, whereas her mother had short stature, cognitive delays, and chronic nonprogressive leukocytosis. It has been previously shown that EZH2 directly controls DNA methylation through physical association with DNMTs, including DNMT3A, with concomitant H3K27 methylation and CpG promoter methylation leading to repression of EZH2 target genes. Interestingly, NSD1 is involved in H3K36 methylation, a mark associated with transcriptional activation, and exhibits exquisite dosage sensitivity leading to overgrowth when deleted and severe undergrowth when duplicated in vivo. Although there is currently no evidence of dosage effects for DNMT3A, the co-occurrence of a duplication involving this gene and a pathogenic alteration in EZH2 in a patient with severe undergrowth is suggestive of a similar paradigm and further study is warranted.
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Affiliation(s)
- Katarzyna Polonis
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Patrick R Blackburn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Raul A Urrutia
- Laboratory of Epigenetics and Chromatin Dynamics, Epigenomics Translational Program, Mayo Clinic, Rochester, Minnesota 55905, USA.,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Gwen A Lomberk
- Laboratory of Epigenetics and Chromatin Dynamics, Epigenomics Translational Program, Mayo Clinic, Rochester, Minnesota 55905, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Teresa Kruisselbrink
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Margot A Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Nicole J Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric W Klee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
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9
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Sweeney NM, Nahas SA, Chowdhury S, Campo MD, Jones MC, Dimmock DP, Kingsmore SF; RCIGM Investigators. The case for early use of rapid whole-genome sequencing in management of critically ill infants: late diagnosis of Coffin-Siris syndrome in an infant with left congenital diaphragmatic hernia, congenital heart disease, and recurrent infections. Cold Spring Harb Mol Case Stud 2018; 4:a002469. [PMID: 29549119 DOI: 10.1101/mcs.a002469] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/09/2018] [Indexed: 11/25/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) results from incomplete formation of the diaphragm leading to herniation of abdominal organs into the thoracic cavity. CDH is associated with pulmonary hypoplasia, congenital heart disease, and pulmonary hypertension. Genetically, it is associated with aneuploidies, chromosomal copy-number variants, and single gene mutations. CDH is the most expensive noncardiac congenital defect. Management frequently requires implementation of extracorporeal membrane oxygenation (ECMO), which increases management expenditures 2.4–3.5-fold. The cost of management of CDH has been estimated to exceed $250 million per year. Despite in-hospital survival of 80%–90%, current management is imperfect, as a great proportion of surviving children have long-term functional deficits. We report the case of a premature infant prenatally diagnosed with CDH and congenital heart disease, who had a protracted and complicated course in the intensive care unit with multiple surgical interventions, including postcardiac surgery ECMO, gastrostomy tube placement with Nissen fundoplication, tracheostomy for respiratory failure, recurrent infections, and developmental delay. Rapid whole-genome sequencing (rWGS) identified a de novo, likely pathogenic, c.3096_ 3100delCAAAG (p.Lys1033Argfs*32) variant in ARID1B, providing a diagnosis of Coffin–Siris syndrome. Her parents elected palliative care and she died later that day.
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10
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Tanaka AJ, Cho MT, Willaert R, Retterer K, Zarate YA, Bosanko K, Stefans V, Oishi K, Williamson A, Wilson GN, Basinger A, Barbaro-Dieber T, Ortega L, Sorrentino S, Gabriel MK, Anderson IJ, Sacoto MJG, Schnur RE, Chung WK. De novo variants in EBF3 are associated with hypotonia, developmental delay, intellectual disability, and autism. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a002097. [PMID: 29162653 PMCID: PMC5701309 DOI: 10.1101/mcs.a002097] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/05/2017] [Indexed: 01/07/2023] Open
Abstract
Using whole-exome sequencing, we identified seven unrelated individuals with global developmental delay, hypotonia, dysmorphic facial features, and an increased frequency of short stature, ataxia, and autism with de novo heterozygous frameshift, nonsense, splice, and missense variants in the Early B-cell Transcription Factor Family Member 3 (EBF3) gene. EBF3 is a member of the collier/olfactory-1/early B-cell factor (COE) family of proteins, which are required for central nervous system (CNS) development. COE proteins are highly evolutionarily conserved and regulate neuronal specification, migration, axon guidance, and dendritogenesis during development and are essential for maintaining neuronal identity in adult neurons. Haploinsufficiency of EBF3 may affect brain development and function, resulting in developmental delay, intellectual disability, and behavioral differences observed in individuals with a deleterious variant in EBF3.
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Affiliation(s)
- Akemi J Tanaka
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
| | | | | | | | - Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Katie Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Vikki Stefans
- Departments of Pediatrics and Physical Medicine and Rehabilitation, Arkansas Children's Hospital, Little Rock, Arkansas 72202, USA
| | - Kimihiko Oishi
- Department of Genetics and Genomic Sciences, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Amy Williamson
- Department of Genetics and Genomic Sciences, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Golder N Wilson
- KinderGenome Genetics, Medical City Hospital Dallas, Dallas, Texas 75230, USA, and Department of Pediatrics, Texas Tech University Health Science Center, Lubbock, Texas 79430, USA
| | | | | | - Lucia Ortega
- Cook Children's Genetics, Fort Worth, Texas 76102, USA
| | - Susanna Sorrentino
- Department of Genetics and Metabolism, Valley Children's Hospital, Madera, California 93636, USA
| | - Melissa K Gabriel
- Children's Hospital of Los Angeles, Los Angeles, California 90027, USA
| | - Ilse J Anderson
- Department of Genetics, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA.,Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA
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Blackburn PR, Barnett SS, Zimmermann MT, Cousin MA, Kaiwar C, Pinto E Vairo F, Niu Z, Ferber MJ, Urrutia RA, Selcen D, Klee EW, Pichurin PN. Novel de novo variant in EBF3 is likely to impact DNA binding in a patient with a neurodevelopmental disorder and expanded phenotypes: patient report, in silico functional assessment, and review of published cases. Cold Spring Harb Mol Case Stud 2017; 3:a001743. [PMID: 28487885 DOI: 10.1101/mcs.a001743] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pathogenic variants in EBF3 were recently described in three back-to-back publications in association with a novel neurodevelopmental disorder characterized by intellectual disability, speech delay, ataxia, and facial dysmorphisms. In this report, we describe an additional patient carrying a de novo missense variant in EBF3 (c.487C>T, p.(Arg163Trp)) that falls within a conserved residue in the zinc knuckle motif of the DNA binding domain. Without a solved structure of the DNA binding domain, we generated a homology-based atomic model and performed molecular dynamics simulations for EBF3, which predicted decreased DNA affinity for p.(Arg163Trp) compared with wild-type protein and control variants. These data are in agreement with previous experimental studies of EBF1 showing the paralogous residue is essential for DNA binding. The conservation and experimental evidence existing for EBF1 and in silico modeling and dynamics simulations to validate comparable behavior of multiple variants in EBF3 demonstrates strong support for the pathogenicity of p.(Arg163Trp). We show that our patient presents with phenotypes consistent with previously reported patients harboring EBF3 variants and expands the phenotypic spectrum of this newly identified disorder with the additional feature of a bicornuate uterus.
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Gupta S, Fahiminiya S, Wang T, Dempsey Nunez L, Rosenblatt DS, Gibson WT, Gilfix B, Bergeron JJM, Jerome-Majewska LA. Somatic overgrowth associated with homozygous mutations in both MAN1B1 and SEC23A. Cold Spring Harb Mol Case Stud 2016; 2:a000737. [PMID: 27148587 PMCID: PMC4853519 DOI: 10.1101/mcs.a000737] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Using whole-exome sequencing, we identified homozygous mutations in two unlinked genes, SEC23A c.1200G>C (p.M400I) and MAN1B1 c.1000C>T (p.R334C), associated with congenital birth defects in two patients from a consanguineous family. Patients presented with carbohydrate-deficient transferrin, tall stature, obesity, macrocephaly, and maloccluded teeth. The parents were healthy heterozygous carriers for both mutations and an unaffected sibling with tall stature carried the heterozygous mutation in SEC23A only. Mutations in SEC23A are responsible for craniolenticosultura dysplasia (CLSD). CLSD patients are short, have late-closing fontanels, and have reduced procollagen (pro-COL1A1) secretion because of abnormal pro-COL1A1 retention in the endoplasmic reticulum (ER). The mutation we identified in MAN1B1 was previously associated with reduced MAN1B1 protein and congenital disorders of glycosylation (CDG). CDG patients are also short, are obese, and have abnormal glycan remodeling. Molecular analysis of fibroblasts from the family revealed normal levels of SEC23A in all cells and reduced levels of MAN1B1 in cells with heterozygous or homozygous mutations in SEC23A and MAN1B1. Secretion of pro-COL1A1 was increased in fibroblasts from the siblings and patients, and pro-COL1A1 was retained in Golgi of heterozygous and homozygous mutant cells, although intracellular pro-COL1A1 was increased in patient fibroblasts only. We postulate that increased pro-COL1A1 secretion is responsible for tall stature in these patients and an unaffected sibling, and not previously discovered in patients with mutations in either SEC23A or MAN1B1. The patients in this study share biochemical and cellular characteristics consistent with mutations in MAN1B1 and SEC23A, indicating a digenic disease.
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Affiliation(s)
- Swati Gupta
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Somayyeh Fahiminiya
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Tracy Wang
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Laura Dempsey Nunez
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - David S Rosenblatt
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 1B1, Canada;; Department of Pediatrics, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - William T Gibson
- Department of Medical Genetics, Child and Family Research Institute, Vancouver, British Columbia V6H 3V4, Canada
| | - Brian Gilfix
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - John J M Bergeron
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Loydie A Jerome-Majewska
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 1B1, Canada;; Department of Pediatrics, McGill University, Montreal, Quebec H4A 3J1, Canada;; Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
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