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Smol T, Frénois F, Manouvrier-Hanu S, Petit F, Ghoumid J. Performance of meta-predictors for the classification of MED13L missense variations, implication of raw parameters. Eur J Med Genet 2021; 65:104398. [PMID: 34798324 DOI: 10.1016/j.ejmg.2021.104398] [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: 06/23/2021] [Revised: 09/14/2021] [Accepted: 11/13/2021] [Indexed: 11/26/2022]
Abstract
MED13L syndrome is a rare congenital disorder comprising moderate intellectual disability, hypotonia and facial dysmorphism. Whole exome or genome sequencing in patients with non-specific neurodevelopmental disorders leads to identification of an increasing number of MED13L missense variations of unknown signification. The aim of our study was to identify relevant annotation parameters enhancing discrimination between candidate pathogenic or neutral missense variations, and to assess the performance of seven meta-predictor algorithms: BayesDel, CADD, DANN, FATHMM-XF, M-CAP, MISTIC and REVEL for the classification of MED13L missense variants. Significant differences were identified for five parameters: global conservation through verPhyloP and verPhCons scores; physico-chemical difference between amino acids estimated by Grantham scores; conservation of residues between MED13L and MED13 protein; proximity to phosphorylation sites for pathogenic variations. Among the seven selected in-silico tools, BayesDel, REVEL, and MISTIC provided the most interesting performances to discriminate pathogenic from neutral missense variations. Individual gene parameter studies with MED13L have provided expertise on elements of annotation improving meta-predictor choices. The in-silico approach allows us to make valuable hypotheses to predict the involvement of these amino acids in MED13L pathogenic missense variations.
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Affiliation(s)
- Thomas Smol
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Institut de Génétique Médicale, F-59000, Lille, France
| | - Frédéric Frénois
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France
| | - Sylvie Manouvrier-Hanu
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France
| | - Florence Petit
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France
| | - Jamal Ghoumid
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France.
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Yi Z, Zhang Y, Song Z, Pan H, Yang C, Li F, Xue J, Qu Z. Report of a de novo c.2605C > T (p.Pro869Ser) change in the MED13L gene and review of the literature for MED13L-related intellectual disability. Ital J Pediatr 2020; 46:95. [PMID: 32646507 PMCID: PMC7350599 DOI: 10.1186/s13052-020-00847-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/08/2020] [Indexed: 11/25/2022] Open
Abstract
Background MED13L-related intellectual disability is a new syndrome that is characterized by intellectual disability (ID), motor developmental delay, speech impairment, hypotonia and facial dysmorphism. Both the MED13L haploinsufficiency mutation and missense mutation were reported to be causative. It has also been reported that patients carrying missense mutations have more frequent epilepsy and show a more severe phenotype. Case presentation We report a child with ID, speech impairment, severe motor developmental delay, facial deformity, hypotonia, muscular atrophy, scoliosis, odontoprisis, abnormal electroencephalogram (EEG), and congenital ureteropelvic junction obstruction (UPJO) combined with high ureter attachment. We used whole-exome sequencing (WES) to detect the genetic aberration of the child and found a de novo mutation, c.2605C > T (p.Pro869Ser), in the MED13L gene. Neither of her parents carried the mutation. Additionally, we review the literature and summarize the phenotypes and features of reported missense mutations. After reviewing the literature, approximately 17 missense mutations in 20 patients have been reported thus far. For 18 patients (including our case) whose clinical manifestations were provided, 100% of the patients had ID or developmental delay (DD). A total of 88.9, 83.3 and 66.7% of the patients had speech impairment, delayed milestones and hypotonia, respectively. A total of 83.3% of the patients exhibited craniofacial deformity or other dysmorphic features. Behavioral difficulties and autistic features were observed in 55.6% of the patients. Cardiac anomalies were seen in only 27.8% of the patients. Of these patients, 44.4% had epileptic seizures. Of the 17 mutations, 2 were located in the N-terminal domain, 8 were located in the C-terminal domain, and 1 was located in an α-helical sequence stretch. One of them was located in the MID domain of the MedPIWI module. Conclusions We report a new patient with a reported missense mutation, c.2605C > T (p.Pro869Ser), who exhibited some infrequent manifestations except common phenotypes, which may broaden the known clinical spectrum. Additionally, by reviewing the literature, we also found that patients with missense mutations have a higher incidence of seizures, MRI abnormalities, autistic features and cardiac anomalies. They also have more severe ID and hypotonia. Our case further demonstrates that Pro869Ser is a hotspot mutation of the MED13L gene.
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Affiliation(s)
- Zhi Yi
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Ying Zhang
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Zhenfeng Song
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Hong Pan
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Chengqing Yang
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Fei Li
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Jiao Xue
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Zhenghai Qu
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China.
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Tørring PM, Larsen MJ, Brasch-Andersen C, Krogh LN, Kibæk M, Laulund L, Illum N, Dunkhase-Heinl U, Wiesener A, Popp B, Marangi G, Hjortshøj TD, Ek J, Vogel I, Becher N, Roos L, Zollino M, Fagerberg CR. Is MED13L-related intellectual disability a recognizable syndrome? Eur J Med Genet 2018; 62:129-136. [PMID: 29959045 DOI: 10.1016/j.ejmg.2018.06.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 05/22/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
Abstract
INTRODUCTION MED13L-related intellectual disability is characterized by moderate intellectual disability (ID), speech impairment, and dysmorphic facial features. We present 8 patients with MED13L-related intellectual disability and review the literature for phenotypical and genetic aspects of previously described patients. MATERIALS AND METHODS In the search for genetic aberrations in individuals with ID, two of the patients were identified by chromosomal microarray analysis, and five by exome sequencing. One of the individuals, suspected of MED13L-related intellectual disability, based on clinical features, was identified by Sanger sequencing. RESULTS All 8 individuals had de novo MED13L aberrations, including two intragenic microdeletions, two frameshift, three nonsense variants, and one missense variant. Phenotypically, they all had intellectual disability, speech and motor delay, and features of the mouth (open mouth appearance, macroglossia, and/or macrostomia). Two individuals were diagnosed with autism, and one had autistic features. One had complex congenital heart defect, and one had persistent foramen ovale. The literature was reviewed with respect to clinical and dysmorphic features, and genetic aberrations. CONCLUSIONS Even if most clinical features of MED13L-related intellectual disability are rather non-specific, the syndrome may be suspected in some individuals based on the association of developmental delay, speech impairment, bulbous nasal tip, and macroglossia, macrostomia, or open mouth appearance.
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Affiliation(s)
| | - Martin Jakob Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | | | - Maria Kibæk
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | - Lone Laulund
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | - Niels Illum
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | | | - Antje Wiesener
- Institute of Human Genetics, University of Erlangen-Nürnberg, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Erlangen-Nürnberg, Germany
| | - Giuseppe Marangi
- Institute of Genomic Medicine, Catholic University, Hospital A. Gemelli Foundation, Rome, Italy
| | | | - Jakob Ek
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Ida Vogel
- Department of Clinical Genetics, Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark
| | - Naja Becher
- Department of Clinical Genetics, Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark
| | - Laura Roos
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Marcella Zollino
- Institute of Genomic Medicine, Catholic University, Hospital A. Gemelli Foundation, Rome, Italy
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5
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Smol T, Petit F, Piton A, Keren B, Sanlaville D, Afenjar A, Baker S, Bedoukian EC, Bhoj EJ, Bonneau D, Boudry-Labis E, Bouquillon S, Boute-Benejean O, Caumes R, Chatron N, Colson C, Coubes C, Coutton C, Devillard F, Dieux-Coeslier A, Doco-Fenzy M, Ewans LJ, Faivre L, Fassi E, Field M, Fournier C, Francannet C, Genevieve D, Giurgea I, Goldenberg A, Green AK, Guerrot AM, Heron D, Isidor B, Keena BA, Krock BL, Kuentz P, Lapi E, Le Meur N, Lesca G, Li D, Marey I, Mignot C, Nava C, Nesbitt A, Nicolas G, Roche-Lestienne C, Roscioli T, Satre V, Santani A, Stefanova M, Steinwall Larsen S, Saugier-Veber P, Picker-Minh S, Thuillier C, Verloes A, Vieville G, Wenzel M, Willems M, Whalen S, Zarate YA, Ziegler A, Manouvrier-Hanu S, Kalscheuer VM, Gerard B, Ghoumid J. MED13L-related intellectual disability: involvement of missense variants and delineation of the phenotype. Neurogenetics 2018; 19:93-103. [PMID: 29511999 DOI: 10.1007/s10048-018-0541-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/17/2018] [Indexed: 12/30/2022]
Abstract
Molecular anomalies in MED13L, leading to haploinsufficiency, have been reported in patients with moderate to severe intellectual disability (ID) and distinct facial features, with or without congenital heart defects. Phenotype of the patients was referred to "MED13L haploinsufficiency syndrome." Missense variants in MED13L were already previously described to cause the MED13L-related syndrome, but only in a limited number of patients. Here we report 36 patients with MED13L molecular anomaly, recruited through an international collaboration between centers of expertise for developmental anomalies. All patients presented with intellectual disability and severe language impairment. Hypotonia, ataxia, and recognizable facial gestalt were frequent findings, but not congenital heart defects. We identified seven de novo missense variations, in addition to protein-truncating variants and intragenic deletions. Missense variants clustered in two mutation hot-spots, i.e., exons 15-17 and 25-31. We found that patients carrying missense mutations had more frequently epilepsy and showed a more severe phenotype. This study ascertains missense variations in MED13L as a cause for MED13L-related intellectual disability and improves the clinical delineation of the condition.
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Affiliation(s)
- T Smol
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France.,University of Lille, EA 7364-RADEME, Lille, France
| | - F Petit
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - A Piton
- Laboratoire de diagnostic génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - B Keren
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - D Sanlaville
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - A Afenjar
- Service de Génétique, Hôpital d'Enfants Armand-Trousseau, AP-HP, Paris, France
| | - S Baker
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - E C Bedoukian
- Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - E J Bhoj
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - D Bonneau
- Service de Génétique, CHU d'Angers, Angers, France
| | - E Boudry-Labis
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - S Bouquillon
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - O Boute-Benejean
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - R Caumes
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - N Chatron
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - C Colson
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - C Coubes
- Département de Génétique Médicale, CHU Montpellier, Montpellier, France
| | - C Coutton
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - F Devillard
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - A Dieux-Coeslier
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - M Doco-Fenzy
- Service de Génétique, EA3801, SFR-CAP Santé, CHU de Reims, Reims, France
| | - L J Ewans
- St Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia
| | - L Faivre
- Centre de Génétique et Centre de Référence Maladies Rares 'Anomalies du Développement, CHU Dijon, Dijon, France.,Equipe GAD, UMR INSERM 1231, Université de Bourgogne, Dijon, France
| | - E Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - M Field
- The Genetics of Learning Disability Service, Waratah, New South Wales, Australia
| | - C Fournier
- Laboratoire de diagnostic génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - C Francannet
- Service de Génétique Médicale, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - D Genevieve
- Département de Génétique Médicale, CHU Montpellier, Montpellier, France
| | - I Giurgea
- Service de Génétique, Hôpital Trousseau, AP-HP, Paris, France
| | - A Goldenberg
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - A K Green
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - A M Guerrot
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - D Heron
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - B Isidor
- Service de Génétique Médicale, Unité de Génétique Clinique, CHU de Nantes, Nantes, France
| | - B A Keena
- Clinical Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - B L Krock
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - P Kuentz
- Equipe GAD, UMR INSERM 1231, Université de Bourgogne, Dijon, France
| | - E Lapi
- Medical Genetics Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | - N Le Meur
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - G Lesca
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - D Li
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - I Marey
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - C Mignot
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - C Nava
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - A Nesbitt
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - G Nicolas
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - C Roche-Lestienne
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - T Roscioli
- St Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia
| | - V Satre
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - A Santani
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - M Stefanova
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - S Steinwall Larsen
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - P Saugier-Veber
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - S Picker-Minh
- Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - C Thuillier
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - A Verloes
- Unité Fonctionnelle de Génétique Clinique, Hôpital Robert Debré, AP-HP, Paris, France
| | - G Vieville
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - M Wenzel
- Clinical Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - M Willems
- Département de Génétique Médicale, CHU Montpellier, Montpellier, France
| | - S Whalen
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - Y A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - A Ziegler
- Service de Génétique, CHU d'Angers, Angers, France
| | - S Manouvrier-Hanu
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - V M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - B Gerard
- Laboratoire de diagnostic génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jamal Ghoumid
- University of Lille, EA 7364-RADEME, Lille, France. .,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France.
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