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Togi S, Ura H, Niida Y. Qualitative and quantitative analysis of MED12 c.887G>A causing both missense and splicing variants in X-linked Ohdo syndrome. Am J Med Genet A 2024; 194:e63628. [PMID: 38655688 DOI: 10.1002/ajmg.a.63628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/24/2024] [Accepted: 03/29/2024] [Indexed: 04/26/2024]
Abstract
The phenotypes associated with MED12 pathogenic variants are diverse. Male patients usually have missense variants, but the effects of base substitutions on mRNA splicing have not been investigated. Here, we report a Japanese brother with intellectual disability, characteristic facial appearance with blepharophimosis, cleft palate, Fallot tetralogy, vesicoureteral reflux, and deafness. A known missense pathogenic variant was detected in MED12, NM_005120.3:c.887G>A p.(Arg296Gln), and X-linked Ohdo syndrome was diagnosed in combination with their phenotype. mRNA splicing of MED12 was evaluated qualitatively and quantitatively using long-range PCR-based targeted RNA sequencing (reverse transcribed long amplicon sequencing), and it was shown that this missense variant simultaneously causes aberrant splicing of the 42-bp in-frame deletion in exon 7, r.847_888del, which accounts for approximately 30% of the mRNAs in both siblings. The X chromosome inactivation study showed that the X chromosome carrying the mutant allele was 100% inactivated in the carrier mothers. mRNA level analysis is essential for the accurate interpretation of the effects of variants. In this case, the MED12 protein function may be reduced by more than just an amino acid substitution, resulting in the patients with the most severe phenotype of MED12-related syndrome in males.
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Affiliation(s)
- Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
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Margot H, Pizano A, Amestoy A, Lacombe D, Berges C, Beneteau C, Innes AM. Investigations of an individual with a Marfanoid habitus, mild intellectual disability, and severe social anxiety identifies PCDHGA5 as a candidate neurodevelopmental disorder gene. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2024:e32087. [PMID: 38591859 DOI: 10.1002/ajmg.c.32087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/23/2024] [Accepted: 03/31/2024] [Indexed: 04/10/2024]
Abstract
Marfanoid habitus and intellectual disability (MHID) co-occur in multiple neurodevelopmental disorders (NDD). Among those, Lujan-Fryns, an X-linked genetic disorder associated with variants in MED12 was the first such syndrome identified. Accurate molecular diagnosis for these MHID syndromes remains a challenge due to significant clinical and genetic heterogeneity. We present a case report of a 20-year-old male patient with MHID and severe social anxiety. A comprehensive clinical evaluation, including morphotype assessment, cognitive, and psychometric and genetic testing, was conducted to provide a detailed understanding of the patient's complex clinical presentation. Psychometric assessments revealed severe social anxiety and various cognitive and emotional challenges. Despite some autism-like symptoms, the patient's clinical presentation was more aligned with mild intellectual disability. Exome sequencing was inconclusive but identified a heterozygous de novo missense variant in the PCDHGA5 gene. This gene is not known in human pathology yet, but we also report a second patient with a syndromic neurodevelopmental disorder and a rare de novo variant which leads us to propose this as a candidate gene. Our findings emphasize the importance of multidisciplinary approach in the diagnosis and management of MHID. This case report underscores the need for objective clinical evaluations and standardized tools to better understand the complex clinical profiles of patients with NDDs. The identification of novel PCDHGA5 gene variants adds this gene's candidacy to the genetic landscape of MHID-NDD, warranting further investigation to determine its potential contribution.
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Affiliation(s)
- Henri Margot
- Univ. Bordeaux, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Adrien Pizano
- Aquitaine Autism Resources Centre, Centre Hospitalier Charles-Perrens, University Pole of Child and Adolescent Psychiatry, Bordeaux, France
| | - Anouck Amestoy
- Aquitaine Autism Resources Centre, Centre Hospitalier Charles-Perrens, University Pole of Child and Adolescent Psychiatry, Bordeaux, France
| | - Didier Lacombe
- Univ. Bordeaux, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Camille Berges
- Univ. Bordeaux, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Claire Beneteau
- Univ. Bordeaux, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - A Micheil Innes
- Department of Medical Genetics and Pediatrics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
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3
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Ilchuk LA, Kubekina MV, Okulova YD, Silaeva YY, Tatarskiy VV, Filatov MA, Bruter AV. Genetically Engineered Mice Unveil In Vivo Roles of the Mediator Complex. Int J Mol Sci 2023; 24:ijms24119330. [PMID: 37298278 DOI: 10.3390/ijms24119330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The Mediator complex is a multi-subunit protein complex which plays a significant role in the regulation of eukaryotic gene transcription. It provides a platform for the interaction of transcriptional factors and RNA polymerase II, thus coupling external and internal stimuli with transcriptional programs. Molecular mechanisms underlying Mediator functioning are intensively studied, although most often using simple models such as tumor cell lines and yeast. Transgenic mouse models are required to study the role of Mediator components in physiological processes, disease, and development. As constitutive knockouts of most of the Mediator protein coding genes are embryonically lethal, conditional knockouts and corresponding activator strains are needed for these studies. Recently, they have become more easily available with the development of modern genetic engineering techniques. Here, we review existing mouse models for studying the Mediator, and data obtained in corresponding experiments.
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Affiliation(s)
- Leonid A Ilchuk
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Marina V Kubekina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Yulia D Okulova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Yulia Yu Silaeva
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
| | - Maxim A Filatov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Alexandra V Bruter
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Federal State Budgetary Institution "N.N. Blokhin National Medical Research Center of Oncology", Ministry of Health of the Russian Federation, Kashirskoe Sh. 24, 115478 Moscow, Russia
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4
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Zhi X, Pu L, Wu B, Cui Y, Yu C, Dong Y, Li D, Cai C. Identification of two aberrant transcripts by RNA sequencing for a novel variant c.3354 + 5 G > A of MED12 in a Chinese girl with non-syndromic intellectual disability. Clin Chim Acta 2022; 532:137-144. [PMID: 35690084 DOI: 10.1016/j.cca.2022.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Missense variants in MED12 are associated with MED12-related disorders. We aimed to clarify the molecular level changes and underlying pathogenic mechanism of a female patient in our study. METHODS We reported a Chinese girl with clinical characteristics similar to MED12-related disorders. Trio whole exome sequencing (WES) was performed to identify related pathogenic variant(s) and RNA sequencing (RNA-seq) was subsequently applied to evaluate the effect of identified variant(s) on mRNA splicing. Moreover, X-chromosome inactivation (XCI) assay based on AR and RP2 was performed to reveal the XCI pattern of the female patient. RESULTS The proband manifested mainly as mental retardation and language impairment. Trio WES revealed a novel heterozygous variant c.3354 + 5 G > A in intron 23 of MED12. RNA-seq identified two aberrant transcripts. XCI assay on AR revealed a homozygous result, while XCI based on RP2 showed random pattern in peripheral blood. CONCLUSION In conclusion, we identified a novel variant c.3354 + 5 G > A by WES combined with RNA-seq, which extends the spectrum of MED12 variants and provide a basis for further genetic counseling. According to the result of two aberrant transcripts by RNA-seq, we speculate that our patient's milder clinical feature may be the consequence of multiple different transcripts.
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Affiliation(s)
- Xiufang Zhi
- Graduate College of Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin 300070, China; Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin 300134, China
| | - Linjie Pu
- Graduate College of Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin 300070, China; Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin 300134, China
| | - Bo Wu
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin 300134, China; Department of Neurology, Tianjin Children's Hospital, No. 238 Longyan Road, eichen District, Tianjin 300134, China
| | - Yaqiong Cui
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin 300134, China; Tianjin Pediatric Research Institute, No. 238 Longyan Road, Beichen District, Tianjin 300134, China; Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No. 238 Longyan Road, Beichen District, Tianjin 300134, China
| | - Changshun Yu
- Tianjin Kingmed Center for Clinical Laboratory Co. Ltd, Haitai Huake 5th Rd, Huayuan Industrial Park, High Tech Zone, Xiqing District, Tianjin 300392, China
| | - Yan Dong
- Graduate College of Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin 300070, China; Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin 300134, China
| | - Dong Li
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin 300134, China; Department of Neurology, Tianjin Children's Hospital, No. 238 Longyan Road, eichen District, Tianjin 300134, China.
| | - Chunquan Cai
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin 300134, China; Tianjin Pediatric Research Institute, No. 238 Longyan Road, Beichen District, Tianjin 300134, China; Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No. 238 Longyan Road, Beichen District, Tianjin 300134, China.
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Diagnostic yield of patients with undiagnosed intellectual disability, global developmental delay and multiples congenital anomalies using karyotype, microarray analysis, whole exome sequencing from Central Brazil. PLoS One 2022; 17:e0266493. [PMID: 35390071 PMCID: PMC8989190 DOI: 10.1371/journal.pone.0266493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/21/2022] [Indexed: 11/19/2022] Open
Abstract
Intellectual Disability (ID) is a neurodevelopmental disorder that affects approximately 3% of children and adolescents worldwide. It is a heterogeneous and multifactorial clinical condition. Several methodologies have been used to identify the genetic causes of ID and in recent years new generation sequencing techniques, such as exome sequencing, have enabled an increase in the detection of new pathogenic variants and new genes associated with ID. The aim of this study was to evaluate exome sequencing with analysis of the ID gene panel as a tool to increase the diagnostic yield of patients with ID/GDD/MCA in Central Brazil, together with karyotype and CMA tests. A retrospective cohort study was carried out with 369 patients encompassing both sexes. Karyotype analysis was performed for all patients. CMA was performed for patients who did not present structural and or numerical alterations in the karyotype. Cases that were not diagnosed after performing karyotyping and CMA were referred for exome sequencing using a gene panel for ID that included 1,252 genes. The karyotype identified chromosomal alterations in 34.7% (128/369). CMA was performed in 83 patients who had normal karyotype results resulting in a diagnostic yield of 21.7% (18/83). Exome sequencing with analysis of the ID gene panel was performed in 19 trios of families that had negative results with previous methodologies. With the ID gene panel analysis, we identified mutations in 63.1% (12/19) of the cases of which 75% (9/12) were pathogenic variants,8.3% (1/12) likely pathogenic and in 16.7% (2/12) it concerned a Variant of Uncertain Significance. With the three methodologies applied, it was possible to identify the genetic cause of ID in 42.3% (156/369) of the patients. In conclusion, our studies show the different methodologies that can be useful in diagnosing ID/GDD/MCA and that whole exome sequencing followed by gene panel analysis, when combined with clinical and laboratory screening, is an efficient diagnostic strategy.
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Munabi NCO, Mikhail S, Toubat O, Webb M, Auslander A, Sanchez-Lara PA, Manojlovic Z, Schmidt RJ, Craig D, Magee WP, Kumar SR. High prevalence of deleterious mutations in concomitant nonsyndromic cleft and outflow tract heart defects. Am J Med Genet A 2022; 188:2082-2095. [PMID: 35385219 PMCID: PMC9197864 DOI: 10.1002/ajmg.a.62748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 02/26/2022] [Accepted: 03/18/2022] [Indexed: 11/18/2022]
Abstract
Our previous work demonstrating enrichment of outflow tract (OFT) congenital heart disease (CHD) in children with cleft lip and/or palate (CL/P) suggests derangements in common underlying developmental pathways. The current pilot study examines the underlying genetics of concomitant nonsyndromic CL/P and OFT CHD phenotype. Of 575 patients who underwent CL/P surgery at Children's Hospital Los Angeles, seven with OFT CHD, negative chromosomal microarray analysis, and no recognizable syndromic association were recruited with their parents (as available). Whole genome sequencing of blood samples paired with whole‐blood‐based RNA sequencing for probands was performed. A pathogenic or potentially pathogenic variant was identified in 6/7 (85.7%) probands. A total of seven candidate genes were mutated (CHD7, SMARCA4, MED12, APOB, RNF213, SETX, and JAG1). Gene ontology analysis of variants predicted involvement in binding (100%), regulation of transcription (42.9%), and helicase activity (42.9%). Four patients (57.1%) expressed gene variants (CHD7, SMARCA4, MED12, and RNF213) previously involved in the Wnt signaling pathway. Our pilot analysis of a small cohort of patients with combined CL/P and OFT CHD phenotype suggests a potentially significant prevalence of deleterious mutations. In our cohort, an overrepresentation of mutations in molecules associated with Wnt‐signaling was found. These variants may represent an expanded phenotypic heterogeneity within known monogenic disease genes or provide novel evidence of shared developmental pathways. The mechanistic implications of these mutations and subsequent developmental derangements resulting in the CL/P and OFT CHD phenotype require further analysis in a larger cohort of patients.
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Affiliation(s)
- Naikhoba C O Munabi
- Division of Plastic and Reconstructive Surgery, Keck School of Medicine of USC, Los Angeles, California, USA
| | | | - Omar Toubat
- Division of Cardiac Surgery, Department of Surgery, Keck School of Medicine of USC, Los Angeles, California, USA
| | - Michelle Webb
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, California, USA
| | | | - Pedro A Sanchez-Lara
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Zarko Manojlovic
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, California, USA
| | - Ryan J Schmidt
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA.,Department of Pathology, Keck School of Medicine of USC, Los Angeles, California, USA
| | - David Craig
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, California, USA
| | - William P Magee
- Division of Plastic and Reconstructive Surgery, Keck School of Medicine of USC, Los Angeles, California, USA.,Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, California, USA.,Department of Plastic Surgery, Shriners Hospital for Children, Los Angeles, California, USA
| | - Subramanyan Ram Kumar
- Division of Cardiac Surgery, Department of Surgery, Keck School of Medicine of USC, Los Angeles, California, USA.,Heart Institute, Children's Hospital Los Angeles, Los Angeles, California, USA
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7
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Rocchetti L, Evangelista E, De Falco L, Savarese G, Savarese P, Ruggiero R, D’Amore L, Sensi A, Fico A. MED12 Mutation in Two Families with X-Linked Ohdo Syndrome. Genes (Basel) 2021; 12:1328. [PMID: 34573309 PMCID: PMC8471817 DOI: 10.3390/genes12091328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/12/2021] [Accepted: 08/26/2021] [Indexed: 12/04/2022] Open
Abstract
X-linked intellectual deficiency (XLID) is a widely heterogeneous group of genetic disorders that involves more than 100 genes. The mediator of RNA polymerase II subunit 12 (MED12) is involved in the regulation of the majority of RNA polymerase II-dependent genes and has been shown to cause several forms of XLID, including Opitz-Kaveggia syndrome also known as FG syndrome (MIM #305450), Lujan-Fryns syndrome (MIM #309520) and the X-linked Ohdo syndrome (MIM #300895). Here, we report on two first cousins with X-linked Ohdo syndrome with a missense mutation in MED12 gene, identified through whole exome sequencing. The probands had facial features typical of X-linked Ohdo syndrome, including blepharophimosis, ptosis, a round face with a characteristic nose and a narrow mouth. Nextera DNA Exome kit (Illumina Inc., San Diego, CA, USA) was used for exome capture. The variant identified was a c.887G > A substitution in exon 7 of the MED12 gene leading to the substitution of a glutamine for a highly conserved arginine (p. Arg296Gln). Although the variant described has been previously reported in the literature, our study contributes to the expanding phenotypic spectrum of MED12-related disorders and above all, it demonstrates the phenotypic variability among different affected patients despite harboring identical mutations.
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Affiliation(s)
- Luca Rocchetti
- U.O. Genetica Medica della Romagna, Dipartimento di Patologia Clinica AUSL, 47522 Cesena, Italy; (L.R.); (A.S.)
| | - Eloisa Evangelista
- AMES-Centro Polidiagnostico Strumentale, Srl, 80013 Naples, Italy; (E.E.); (G.S.); (P.S.); (R.R.); (L.D.); (A.F.)
- Fondazione Genetica per la Vita Onlus, 80013 Naples, Italy
| | - Luigia De Falco
- AMES-Centro Polidiagnostico Strumentale, Srl, 80013 Naples, Italy; (E.E.); (G.S.); (P.S.); (R.R.); (L.D.); (A.F.)
- Fondazione Genetica per la Vita Onlus, 80013 Naples, Italy
| | - Giovanni Savarese
- AMES-Centro Polidiagnostico Strumentale, Srl, 80013 Naples, Italy; (E.E.); (G.S.); (P.S.); (R.R.); (L.D.); (A.F.)
- Fondazione Genetica per la Vita Onlus, 80013 Naples, Italy
| | - Pasquale Savarese
- AMES-Centro Polidiagnostico Strumentale, Srl, 80013 Naples, Italy; (E.E.); (G.S.); (P.S.); (R.R.); (L.D.); (A.F.)
- Fondazione Genetica per la Vita Onlus, 80013 Naples, Italy
| | - Raffaella Ruggiero
- AMES-Centro Polidiagnostico Strumentale, Srl, 80013 Naples, Italy; (E.E.); (G.S.); (P.S.); (R.R.); (L.D.); (A.F.)
- Fondazione Genetica per la Vita Onlus, 80013 Naples, Italy
| | - Luigi D’Amore
- AMES-Centro Polidiagnostico Strumentale, Srl, 80013 Naples, Italy; (E.E.); (G.S.); (P.S.); (R.R.); (L.D.); (A.F.)
- Fondazione Genetica per la Vita Onlus, 80013 Naples, Italy
| | - Alberto Sensi
- U.O. Genetica Medica della Romagna, Dipartimento di Patologia Clinica AUSL, 47522 Cesena, Italy; (L.R.); (A.S.)
| | - Antonio Fico
- AMES-Centro Polidiagnostico Strumentale, Srl, 80013 Naples, Italy; (E.E.); (G.S.); (P.S.); (R.R.); (L.D.); (A.F.)
- Fondazione Genetica per la Vita Onlus, 80013 Naples, Italy
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8
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Gonzalez A, Kapur S, Walsh M, Vengoechea J. Two females with distinct de novo missense pathogenic variants in MED12 and vastly differing phenotypes. Am J Med Genet A 2021; 185:2582-2585. [PMID: 33913598 DOI: 10.1002/ajmg.a.62233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/08/2021] [Accepted: 04/07/2021] [Indexed: 11/07/2022]
Affiliation(s)
- Aixa Gonzalez
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Sunaina Kapur
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Matthew Walsh
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Jaime Vengoechea
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA.,Department of Medicine, Emory University, Atlanta, Georgia, USA
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9
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van de Plassche SR, de Brouwer APM. MED12-Related (Neuro)Developmental Disorders: A Question of Causality. Genes (Basel) 2021; 12:663. [PMID: 33925166 PMCID: PMC8146938 DOI: 10.3390/genes12050663] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022] Open
Abstract
MED12 is a member of the Mediator complex that is involved in the regulation of transcription. Missense variants in MED12 cause FG syndrome, Lujan-Fryns syndrome, and Ohdo syndrome, as well as non-syndromic intellectual disability (ID) in hemizygous males. Recently, female patients with de novo missense variants and de novo protein truncating variants in MED12 were described, resulting in a clinical spectrum centered around ID and Hardikar syndrome without ID. The missense variants are found throughout MED12, whether they are inherited in hemizygous males or de novo in females. They can result in syndromic or nonsyndromic ID. The de novo nonsense variants resulting in Hardikar syndrome that is characterized by facial clefting, pigmentary retinopathy, biliary anomalies, and intestinal malrotation, are found more N-terminally, whereas the more C-terminally positioned variants are de novo protein truncating variants that cause a severe, syndromic phenotype consisting of ID, facial dysmorphism, short stature, skeletal abnormalities, feeding difficulties, and variable other abnormalities. This broad range of distinct phenotypes calls for a method to distinguish between pathogenic and non-pathogenic variants in MED12. We propose an isogenic iNeuron model to establish the unique gene expression patterns that are associated with the specific MED12 variants. The discovery of these patterns would help in future diagnostics and determine the causality of the MED12 variants.
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Affiliation(s)
| | - Arjan P. M. de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
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10
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Martin HC, Gardner EJ, Samocha KE, Kaplanis J, Akawi N, Sifrim A, Eberhardt RY, Tavares ALT, Neville MDC, Niemi MEK, Gallone G, McRae J, Wright CF, FitzPatrick DR, Firth HV, Hurles ME. The contribution of X-linked coding variation to severe developmental disorders. Nat Commun 2021; 12:627. [PMID: 33504798 PMCID: PMC7840967 DOI: 10.1038/s41467-020-20852-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022] Open
Abstract
Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders.
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Affiliation(s)
- Hilary C Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | | | | | - Joanna Kaplanis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nadia Akawi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Alejandro Sifrim
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | | | - Ana Lisa Taylor Tavares
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Genomics England, Queen Mary University of London, London, EC1M 6BQ, UK
| | | | - Mari E K Niemi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Institute for Molecular Medicine Finland, University of Helsinki, Tukholmankatu 8, Helsinki, FI-00014, Finland
| | - Giuseppe Gallone
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Max Planck Institute for Molecular Genetics, Ihnestraße 63, 14195, Berlin, Germany
| | - Jeremy McRae
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Caroline F Wright
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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Rubin Z, Grange DK, Cooper MA. Siblings with a novel MED12 variant and Odho syndrome with immune defects. Clin Genet 2020; 98:308-310. [PMID: 32715471 DOI: 10.1111/cge.13806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/22/2020] [Accepted: 07/01/2020] [Indexed: 02/03/2023]
Affiliation(s)
- Zachary Rubin
- Department of Pediatrics, Division of Allergy, Immunology and Pulmonary Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dorothy K Grange
- Department of Pediatrics, Division of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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Tejada MI, Ibarluzea N. Non-syndromic X linked intellectual disability: Current knowledge in light of the recent advances in molecular and functional studies. Clin Genet 2020; 97:677-687. [PMID: 31898314 DOI: 10.1111/cge.13698] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/09/2019] [Accepted: 12/24/2019] [Indexed: 12/23/2022]
Abstract
Since the discovery of the FMR1 gene and the clinical and molecular characterization of Fragile X Syndrome in 1991, more than 141 genes have been identified in the X-chromosome in these 28 years thanks to applying continuously evolving molecular techniques to X-linked intellectual disability (XLID) families. In the past decade, array comparative genomic hybridization and next generation sequencing technologies have accelerated gene discovery exponentially. Classically, XLID has been subdivided in syndromic intellectual disability (S-XLID)-where intellectual disability (ID) is always associated with other recognizable physical and/or neurological features-and non-specific or non-syndromic intellectual disability (NS-XLID) where the only common feature is ID. Nevertheless, new advances on the study of these entities have showed that this classification is not always clear-cut because distinct variants in several of these XLID genes can result in S-XLID as well as in NS-XLID. This review focuses on the current knowledge on the XLID genes involved in non-syndromic forms, with the emphasis on their pathogenic mechanism, thus allowing the possibility to elucidate why some of them can give both syndromic and non-syndromic phenotypes.
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Affiliation(s)
- María Isabel Tejada
- Genetics Service, Cruces University Hospital, Osakidetza Basque Health Service, Barakaldo, Spain.,Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain.,Clinical Group, Centre for Biomedical Research on Rare Diseases (CIBERER), Valencia, Spain
| | - Nekane Ibarluzea
- Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain.,Clinical Group, Centre for Biomedical Research on Rare Diseases (CIBERER), Valencia, Spain
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