Evidence map›Paper›PMID 31928709›Full record

ArticleAmerican journal of human genetics2020

Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency.

David B Beck, Ana Petracovici, Chongsheng He, Hannah W Moore, Raymond J Louie, Muhammad Ansar, Sofia Douzgou, Sivagamy Sithambaram, Trudie Cottrell, Regie Lyn P Santos-Cortez and 22 more

Open access · bronzeAbstract read
In one paragraph

Article in American journal of human genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.

0numbers the graph read from it
0cells of the map it votes in
58citing papers in PubMed
5.5field-weighted citation impact, top 3% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

58 citing papers in PubMed, 112 citations in OpenAlex.

  1. Nonlinearities and Switch-Like Behavior in Gene Expression: From Genetics to Biochemistry and Back.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026
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  11. Chromatin modifiers in neurodevelopment.Frontiers in molecular neuroscience · 2025
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  16. A New De Novo Missense Variant of theInternational journal of molecular sciences · 2024
    Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

32 authors at 17 institutions in 6 countries.

David B BeckNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Ana PetracoviciGraduate Group in Genetics and Epigenetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
Chongsheng HeDepartment of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Current address: Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082 Hunan, P.R. China.
Hannah W MooreGreenwood Genetic Center, Greenwood, SC 29646, USA.
Raymond J LouieGreenwood Genetic Center, Greenwood, SC 29646, USA.
Muhammad AnsarDepartment of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan.
Sofia DouzgouDivision of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK.
Sivagamy SithambaramManchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK.
Trudie CottrellManchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK.
Regie Lyn P Santos-CortezDepartment of Otolaryngology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Eloise J PrijolesGreenwood Genetic Center, Greenwood, SC 29646, USA.
Renee BendGreenwood Genetic Center, Greenwood, SC 29646, USA.
Boris KerenAssistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France.
Cyril MignotAssistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris 75013, France.
Marie-Christine NouguesAssistance Publique-Hôpitaux de Paris, Armand Trousseau Hospital, Department of Neuropediatrics, Paris 75012, France.
Katrin ÕunapDepartment of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia.
Tiia ReimandDepartment of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50406, Estonia.
Sander PajusaluDepartment of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Yale University School of Medicine, Department of Genetics, New Haven, CT 06510, USA.
Muhammad ZahidDepartment of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan.
Muhammad Arif Nadeem SaqibPakistan Health Research Council, 45320 Islamabad, Pakistan.
Julien BurattiAssistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France.
Eleanor G SeabyProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
Kirsty McWalterGeneDx, Gaithersburg, MD 20877, USA.
Aida TelegrafiGeneDx, Gaithersburg, MD 20877, USA.
Dustin BaldridgeDepartment of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
Marwan ShinawiDepartment of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
Suzanne M LealCenter for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's D disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY 10032, USA.
G Bradley SchaeferUniversity of Arkansas for Medical Sciences, Lowell, AK 72745, USA.
Roger E StevensonGreenwood Genetic Center, Greenwood, SC 29646, USA.
Siddharth BankaDivision of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK.
Roberto BonasioDepartment of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
Jill A FahrnerDepartment of Pediatrics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA. Electronic address: jfahrne1@jhmi.edu.
Greenwood Genetic Center · USAssistance Publique – Hôpitaux de Paris · FRUniversity of Pennsylvania · USQuaid-i-Azam University · PKSt Mary's Hospital · GBTartu University Hospital · EEWashington University in St. Louis · USBroad Institute · USColumbia University Irving Medical Center · USJohns Hopkins University · USManchester University NHS Foundation Trust · GBNational Human Genome Research Institute · USPakistan Health Research Council · PKSt. Mary's Hospital · GBUniversity of Arkansas for Medical Sciences · USUniversity of Colorado Denver · USUniversity of Tartu · EE

Funding

Joint Center for Mendelian GenomicsUM1HG008900 · NHGRI · BROAD INSTITUTE, INC. · PI O'DONNELL-LURIA, ANNE, REHM, HEIDI L · 2016 to 2020
$16.5M
Baylor-Johns Hopkins Center for Mendelian GeneticsUM1HG006542 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI VALLE, DAVID · 2016 to 2020
$14.5M
Sleep and Circadian Dysfunction, Brain and Neurobehavioral Development in AutismP50HD103538 · NICHD · HUGO W. MOSER RES INST KENNEDY KRIEGER · PI Stewart H Mostofsky · 2020 to 2026
$9.9M
Graduate Training in Developmental BiologyT32HD083185 · NICHD · UNIVERSITY OF PENNSYLVANIA · PI Michael Granato, Foteini Mourkioti · 2015 to 2026
$4.0M
Studying epigenetic pathways in brain function and social behavior using antsDP2MH107055 · NIMH · UNIVERSITY OF PENNSYLVANIA · PI BONASIO, ROBERTO · 2014 to 2014
$2.4M
Function and RNA-mediated regulation of SCMH1 in Polycomb repressionR01GM127408 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI BONASIO, ROBERTO · 2018 to 2021
$1.3M
Exploring Disrupted H3K27me3 in Mendelian Disorders of the Epigenetic Machinery and Restoring Its Balance as a Therapeutic Approach to Treat Abnormal GrowthK08HD086250 · NICHD · JOHNS HOPKINS UNIVERSITY · PI FAHRNER, JILL A · 2018 to 2023
$966k
NHGRI NIH HHS UM1 HG006542NHGRI NIH HHS UM1 HG008900NICHD NIH HHS K08 HD086250NICHD NIH HHS P50 HD103538NICHD NIH HHS T32 HD083185NIGMS NIH HHS R01 GM127408NIMH NIH HHS DP2 MH107055Wellcome Trust
6 · The paper itself

Abstract

Germline pathogenic variants in chromatin-modifying enzymes are a common cause of pediatric developmental disorders. These enzymes catalyze reactions that regulate epigenetic inheritance via histone post-translational modifications and DNA methylation. Cytosine methylation (5-methylcytosine [5mC]) of DNA is the quintessential epigenetic mark, yet no human Mendelian disorder of DNA demethylation has yet been delineated. Here, we describe in detail a Mendelian disorder caused by the disruption of DNA demethylation. TET3 is a methylcytosine dioxygenase that initiates DNA demethylation during early zygote formation, embryogenesis, and neuronal differentiation and is intolerant to haploinsufficiency in mice and humans. We identify and characterize 11 cases of human TET3 deficiency in eight families with the common phenotypic features of intellectual disability and/or global developmental delay; hypotonia; autistic traits; movement disorders; growth abnormalities; and facial dysmorphism. Mono-allelic frameshift and nonsense variants in TET3 occur throughout the coding region. Mono-allelic and bi-allelic missense variants localize to conserved residues; all but one such variant occur within the catalytic domain, and most display hypomorphic function in an assay of catalytic activity. TET3 deficiency and other Mendelian disorders of the epigenetic machinery show substantial phenotypic overlap, including features of intellectual disability and abnormal growth, underscoring shared disease mechanisms.

Indexed as

DNA DemethylationAdultAmino Acid SequenceAutistic DisorderChildChild, PreschoolDevelopmental DisabilitiesDioxygenasesEmbryonic DevelopmentFemaleGene Expression Regulation, DevelopmentalGrowth DisordersHumansInfantMaleMiddle AgedDioxygenasesTET3 protein, human5-hydroxymethylcytosine5-methylcytosineDNA methylationepigeneticgeneticintellectual disabilityTET

Identifiers

PMID31928709
PMCPMC7010978
OpenAlexW3000483332

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.