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van den Akker WMR, Brummelman I, Martis LM, Timmermans RN, Pfundt R, Kleefstra T, Willemsen MH, Gerkes EH, Herkert JC, van Essen AJ, Rump P, Vansenne F, Terhal PA, van Haelst MM, Cristian I, Turner CE, Cho MT, Begtrup A, Willaert R, Fassi E, van Gassen KLI, Stegmann APA, de Vries BBA, Schuurs-Hoeijmakers JHM. De novo variants in CDK13 associated with syndromic ID/DD: Molecular and clinical delineation of 15 individuals and a further review. Clin Genet 2019; 93:1000-1007. [PMID: 29393965 DOI: 10.1111/cge.13225] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/03/2018] [Accepted: 01/24/2018] [Indexed: 01/06/2023]
Abstract
De novo variants in the gene encoding cyclin-dependent kinase 13 (CDK13) have been associated with congenital heart defects and intellectual disability (ID). Here, we present the clinical assessment of 15 individuals and report novel de novo missense variants within the kinase domain of CDK13. Furthermore, we describe 2 nonsense variants and a recurrent frame-shift variant. We demonstrate the synthesis of 2 aberrant CDK13 transcripts in lymphoblastoid cells from an individual with a splice-site variant. Clinical characteristics of the individuals include mild to severe ID, developmental delay, behavioral problems, (neonatal) hypotonia and a variety of facial dysmorphism. Congenital heart defects were present in 2 individuals of the current cohort, but in at least 42% of all known individuals. An overview of all published cases is provided and does not demonstrate an obvious genotype-phenotype correlation, although 2 individuals harboring a stop codons at the end of the kinase domain might have a milder phenotype. Overall, there seems not to be a clinically recognizable facial appearance. The variability in the phenotypes impedes an à vue diagnosis of this syndrome and therefore genome-wide or gene-panel driven genetic testing is needed. Based on this overview, we provide suggestions for clinical work-up and management of this recently described ID syndrome.
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Affiliation(s)
- W M R van den Akker
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - I Brummelman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L M Martis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R N Timmermans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - T Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - E H Gerkes
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J C Herkert
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - A J van Essen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - P Rump
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - F Vansenne
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - P A Terhal
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - M M van Haelst
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands.,Department of Clinical Genetics, AMC/VUmc, Amsterdam, The Netherlands
| | - I Cristian
- Division of Genetics and Metabolism, Department of Pediatrics, Nemours Children's Hospital Orlando, Orlando, Florida
| | - C E Turner
- Department of Genetics, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - M T Cho
- GeneDx, Gaithersburg, Maryland
| | | | | | - E Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri
| | - K L I van Gassen
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A P A Stegmann
- Department of Human Genetics, Maastricht University Hospital, Maastricht, The Netherlands
| | - B B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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Reijnders MRF, Kousi M, van Woerden GM, Klein M, Bralten J, Mancini GMS, van Essen T, Proietti-Onori M, Smeets EEJ, van Gastel M, Stegmann APA, Stevens SJC, Lelieveld SH, Gilissen C, Pfundt R, Tan PL, Kleefstra T, Franke B, Elgersma Y, Katsanis N, Brunner HG. Variation in a range of mTOR-related genes associates with intracranial volume and intellectual disability. Nat Commun 2017; 8:1052. [PMID: 29051493 PMCID: PMC5648772 DOI: 10.1038/s41467-017-00933-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/08/2017] [Indexed: 11/09/2022] Open
Abstract
De novo mutations in specific mTOR pathway genes cause brain overgrowth in the context of intellectual disability (ID). By analyzing 101 mMTOR-related genes in a large ID patient cohort and two independent population cohorts, we show that these genes modulate brain growth in health and disease. We report the mTOR activator gene RHEB as an ID gene that is associated with megalencephaly when mutated. Functional testing of mutant RHEB in vertebrate animal models indicates pathway hyperactivation with a concomitant increase in cell and head size, aberrant neuronal migration, and induction of seizures, concordant with the human phenotype. This study reveals that tight control of brain volume is exerted through a large community of mTOR-related genes. Human brain volume can be altered, by either rare disruptive events causing hyperactivation of the pathway, or through the collective effects of common alleles.
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Affiliation(s)
- M R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - M Kousi
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - G M van Woerden
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - M Klein
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - J Bralten
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - G M S Mancini
- Department of Clinical Genetics, Erasmus MC, Sophia Children's Hospital, 3000 CA, Rotterdam, The Netherlands
| | - T van Essen
- Department of Genetics, University of Groningen, University Medical Center of Groningen, 9700 RB, Groningen, The Netherlands
| | - M Proietti-Onori
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - E E J Smeets
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - M van Gastel
- Department of Medical Care, SWZ zorg, 5691 AG, Son, The Netherlands
| | - A P A Stegmann
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - S J C Stevens
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - S H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 GA, Nijmegen, The Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - R Pfundt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - P L Tan
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - T Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - B Franke
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands.,Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 GA, Nijmegen, The Netherlands
| | - Y Elgersma
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - N Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - H G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands. .,Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands.
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Vreeburg M, Sallevelt SCEH, Stegmann APA, van Geel M, Detisch YJHA, Schrander-Stumpel CTRM, van Steensel MAM, Marcus-Soekarman D. Cutaneous clues for diagnosing X-chromosomal disorders. Clin Genet 2013; 85:328-35. [PMID: 23578112 DOI: 10.1111/cge.12162] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 04/05/2013] [Accepted: 04/05/2013] [Indexed: 11/28/2022]
Abstract
In a multidisciplinary outpatient clinic for hereditary skin diseases and/or syndromes involving the skin, 7% (30 of 409) of patients were found to have an abnormality involving the X chromosome, a mutation in a gene located on the X chromosome or a clinical diagnosis of an X-linked monogenetic condition. The collaboration of a dermatologist and a clinical geneticist proves to be very valuable in recognizing and diagnosing these conditions. By combining their specific expertize in counselling an individual patient, X-linked diagnoses were recognized and could be confirmed by molecular and/or cytogenetic studies in 24 of 30 cases. Mosaicism plays an important role in many X-linked hereditary skin disorders. From our experience, we extracted clinical clues for specialists working in the field of genetics and/or dermatology for considering X-linked disorders involving the skin.
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van Steensel MAM, Vreeburg M, Engelen J, Ghesquiere S, Stegmann APA, Herbergs J, van Lent J, Smeets B, Vles JH. Contiguous gene syndrome due to a maternally inherited 8.41 Mb distal deletion of chromosome band Xp22.3 in a boy with short stature, ichthyosis, epilepsy, mental retardation, cerebral cortical heterotopias and Dandy-Walker malformation. Am J Med Genet A 2008; 146A:2944-9. [PMID: 18925676 DOI: 10.1002/ajmg.a.32473] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Microdeletions of Xp22.3 are associated with contiguous gene syndromes, the extent and nature of which depend on the genes encompassed by the deletion. Common symptoms include ichthyosis, mental retardation and hypogonadism. We report on a boy with short stature, ichthyosis, severe mental retardation, cortical heterotopias and Dandy-Walker malformation. The latter two abnormalities have so far not been reported in terminal Xp deletions. MLPA showed deletion of SHOX and subsequent analysis using FISH and SNP-arrays revealed that the patient had an 8.41 Mb distal deletion of chromosome region Xp22.31 --> Xpter. This interval contains several genes whose deletion can partly explain our patient's phenotype. His cortical heterotopias and DWM suggest that a gene involved in brain development may be in the deleted interval, but we found no immediately obvious candidates. Interestingly, further analysis of the family revealed that the patient had inherited his deletion from his mother, who has a mos 46,X,del(X)(p22)/45,X/46, XX karyotype.
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Affiliation(s)
- M A M van Steensel
- Department of Dermatology, University Hospital Maastricht, Maastricht, The Netherlands.
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