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Li, V. EHMT1 Gene. Encyclopedia. Available online: (accessed on 03 March 2024).
Li V. EHMT1 Gene. Encyclopedia. Available at: Accessed March 03, 2024.
Li, Vivi. "EHMT1 Gene" Encyclopedia, (accessed March 03, 2024).
Li, V. (2020, December 24). EHMT1 Gene. In Encyclopedia.
Li, Vivi. "EHMT1 Gene." Encyclopedia. Web. 24 December, 2020.
EHMT1 Gene

Euchromatic histone lysine methyltransferase 1: The EHMT1 gene provides instructions for making an enzyme called euchromatic histone methyltransferase 1. 


1. Normal Function

Histone methyltransferases are enzymes that modify proteins called histones. Histones are structural proteins that attach (bind) to DNA and give chromosomes their shape. By adding a molecule called a methyl group to histones, histone methyltransferases can turn off (suppress) the activity of certain genes, which is essential for normal development and function.

2. Health Conditions Related to Genetic Changes

2.1 Kleefstra Syndrome

Kleefstra syndrome, a disorder affecting many parts of the body, is caused by the loss of the EHMT1 gene or by mutations that disable its function.

Most people with Kleefstra syndrome are missing a sequence of about 1 million DNA building blocks (base pairs) on one copy of chromosome 9 in each cell. The deletion occurs near the end of the long (q) arm of the chromosome at a location designated q34.3, a region containing the EHMT1 gene. Some affected individuals have shorter or longer deletions in the same region.

The loss of the EHMT1 gene from one copy of chromosome 9 in each cell is believed to be responsible for the characteristic features of Kleefstra syndrome in people with the 9q34.3 deletion. However, the loss of other genes in the same region may lead to additional health problems in some affected individuals.

About 25 percent of individuals with Kleefstra syndrome do not have a deletion of genetic material from chromosome 9; instead, these individuals have mutations in the EHMT1 gene. Some of these mutations change single protein building blocks (amino acids) in euchromatic histone methyltransferase 1. Others create a premature stop signal in the instructions for making the enzyme or alter the way the gene's instructions are pieced together to produce the enzyme. These changes generally result in an enzyme that is unstable and decays rapidly, or that is disabled and cannot function properly.

Either a deletion or a mutation affecting the EHMT1 gene results in a lack of functional euchromatic histone methyltransferase 1 enzyme. A lack of this enzyme impairs proper control of the activity of certain genes in many of the body's organs and tissues, resulting in the abnormalities of development and function characteristic of Kleefstra syndrome.

3. Other Names for This Gene

  • bA188C12.1

  • DEL9q34

  • DKFZp667M072


  • Eu-HMTase1

  • euchromatic histone-lysine N-methyltransferase 1


  • FLJ12879

  • FP13812

  • G9a like protein

  • G9a-like protein 1

  • GLP

  • GLP1

  • H3-K9-HMTase 5

  • histone H3-K9 methyltransferase 5

  • histone-lysine N-methyltransferase, H3 lysine-9 specific 5

  • KIAA1876

  • KMT1D

  • lysine N-methyltransferase 1D

  • RP11-188C12.1


  1. Kleefstra T, Brunner HG, Amiel J, Oudakker AR, Nillesen WM, Magee A, GenevièveD, Cormier-Daire V, van Esch H, Fryns JP, Hamel BC, Sistermans EA, de Vries BB,van Bokhoven H. Loss-of-function mutations in euchromatin histone methyltransferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome. Am J HumGenet. 2006 Aug;79(2):370-7.
  2. Kleefstra T, Smidt M, Banning MJ, Oudakker AR, Van Esch H, de Brouwer AP,Nillesen W, Sistermans EA, Hamel BC, de Bruijn D, Fryns JP, Yntema HG, BrunnerHG, de Vries BB, van Bokhoven H. Disruption of the gene Euchromatin HistoneMethyl Transferase1 (Eu-HMTase1) is associated with the 9q34 subtelomericdeletion syndrome. J Med Genet. 2005 Apr;42(4):299-306.
  3. Kleefstra T, van Zelst-Stams WA, Nillesen WM, Cormier-Daire V, Houge G, FouldsN, van Dooren M, Willemsen MH, Pfundt R, Turner A, Wilson M, McGaughran J, Rauch A, Zenker M, Adam MP, Innes M, Davies C, López AG, Casalone R, Weber A, BruetonLA, Navarro AD, Bralo MP, Venselaar H, Stegmann SP, Yntema HG, van Bokhoven H,Brunner HG. Further clinical and molecular delineation of the 9q subtelomericdeletion syndrome supports a major contribution of EHMT1 haploinsufficiency tothe core phenotype. J Med Genet. 2009 Sep;46(9):598-606. doi:10.1136/jmg.2008.062950.
  4. Stewart DR, Kleefstra T. The chromosome 9q subtelomere deletion syndrome. Am JMed Genet C Semin Med Genet. 2007 Nov 15;145C(4):383-92. Review.
  5. Willemsen MH, Beunders G, Callaghan M, de Leeuw N, Nillesen WM, Yntema HG, vanHagen JM, Nieuwint AW, Morrison N, Keijzers-Vloet ST, Hoischen A, Brunner HG,Tolmie J, Kleefstra T. Familial Kleefstra syndrome due to maternal somaticmosaicism for interstitial 9q34.3 microdeletions. Clin Genet. 2011Jul;80(1):31-8. doi: 10.1111/j.1399-0004.2010.01607.x.
  6. Yatsenko SA, Brundage EK, Roney EK, Cheung SW, Chinault AC, Lupski JR.Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3microdeletion syndrome. Hum Mol Genet. 2009 Jun 1;18(11):1924-36. doi:10.1093/hmg/ddp114.
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