Delineation of the first 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, Eloise J. Prijoles, Renee Bend, Boris Keren, Cyril Mignot, Marie Christine Nougues, Katrin Õunap, Tiia Reimand, Sander Pajusalu, Muhammad Zahid, Muhammad Arif Nadeem SaqibJulien Buratti, Eleanor G. Seaby, Kirsty McWalter, Aida Telegrafi, Dustin Baldridge, Marwan Shinawi, Suzanne M. Leal, G. Bradley Schaefer, Roger E. Stevenson, Siddharth Banka, Roberto Bonasio, Jill A. Fahrner

Research output: Contribution to journalArticlepeer-review


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 of DNA (5mC) is the quintessential epigenetic mark, yet no human Mendelian disorder of DNA demethylation has been delineated. Here, we describe in detail the first Mendelian disorder caused by 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. Here we identify and characterize 11 cases of human TET3 deficiency in 8 families with the common phenotypic features of intellectual disability/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 with all but one occurring within the catalytic domain and most displaying hypomorphic function in a catalytic activity assay. TET3 deficiency shows substantial phenotypic overlap with other Mendelian disorders of the epigenetic machinery, including intellectual disability and growth abnormalities, underscoring shared disease mechanisms.

Original languageEnglish (US)
JournalUnknown Journal
StatePublished - Jul 31 2019

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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