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Genetics Home Reference: your guide to understanding genetic conditions     A service of the U.S. National Library of Medicine®

Kleefstra syndrome

Reviewed January 2016

What is Kleefstra syndrome?

Kleefstra syndrome is a disorder that involves many parts of the body. Characteristic features of Kleefstra syndrome include developmental delay and intellectual disability, severely limited or absent speech, and weak muscle tone (hypotonia). Affected individuals also have an unusually small head size (microcephaly) and a wide, short skull (brachycephaly). Distinctive facial features include eyebrows that grow together in the middle (synophrys), widely spaced eyes (hypertelorism), a sunken appearance of the middle of the face (midface hypoplasia), nostrils that open to the front rather than downward (anteverted nares), a protruding jaw (prognathism), rolled out (everted) lips, and a large tongue (macroglossia). Affected individuals may have a high birth weight and childhood obesity.

People with Kleefstra syndrome may also have structural brain abnormalities, congenital heart defects, genitourinary abnormalities, seizures, and a tendency to develop severe respiratory infections. During childhood they may exhibit features of autism or related developmental disorders affecting communication and social interaction. In adolescence, they may develop a general loss of interest and enthusiasm (apathy) or unresponsiveness (catatonia).

How common is Kleefstra syndrome?

The prevalence of Kleefstra syndrome is unknown. Only recently has testing become available to distinguish it from other disorders with similar features.

What are the genetic changes related to Kleefstra syndrome?

Kleefstra syndrome is caused by the loss of the EHMT1 gene or by mutations that disable its function. The EHMT1 gene provides instructions for making an enzyme called euchromatic histone methyltransferase 1. 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.

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.

Related Chromosome(s)

Changes involving this chromosome are associated with Kleefstra syndrome.

  • chromosome 9

Related Gene(s)

Changes in this gene are associated with Kleefstra syndrome.

  • EHMT1

Can Kleefstra syndrome be inherited?

The inheritance of Kleefstra syndrome is considered to be autosomal dominant because a deletion in one copy of chromosome 9 in each cell or a mutation in one copy of the EHMT1 gene is sufficient to cause the condition. Most cases of Kleefstra syndrome are not inherited, however. The genetic change occurs most often as a random event during the formation of reproductive cells (eggs or sperm) or in early fetal development. Affected people typically have no history of the disorder in their family, though they can pass the disorder on to their children. Only a few people with Kleefstra syndrome have been known to reproduce.

Rarely, affected individuals inherit a chromosome 9 with a deleted segment from an unaffected parent. In these cases, the parent carries a chromosomal rearrangement called a balanced translocation, in which no genetic material is gained or lost. Balanced translocations usually do not cause any health problems; however, they can become unbalanced as they are passed to the next generation. Children who inherit an unbalanced translocation can have a chromosomal rearrangement with extra or missing genetic material. Individuals with Kleefstra syndrome who inherit an unbalanced translocation are missing genetic material from the long arm of chromosome 9.

A few individuals with Kleefstra syndrome have inherited the chromosome 9q34.3 deletion from an unaffected parent who is mosaic for the deletion. Mosaic means that an individual has the deletion in some cells (including some sperm or egg cells), but not in others.

Where can I find information about diagnosis or management of Kleefstra syndrome?

These resources address the diagnosis or management of Kleefstra syndrome and may include treatment providers.

  • Gene Review: Kleefstra Syndrome (
  • Genetic Testing Registry: Chromosome 9q deletion syndrome (

You might also find information on the diagnosis or management of Kleefstra syndrome in Educational resources and Patient support.

General information about the diagnosis ( and management ( of genetic conditions is available in the Handbook. Read more about genetic testing (, particularly the difference between clinical tests and research tests (

To locate a healthcare provider, see How can I find a genetics professional in my area? ( in the Handbook.

Where can I find additional information about Kleefstra syndrome?

You may find the following resources about Kleefstra syndrome helpful. These materials are written for the general public.

You may also be interested in these resources, which are designed for healthcare professionals and researchers.

What other names do people use for Kleefstra syndrome?

  • 9q34.3 deletion syndrome
  • 9q34.3 microdeletion syndrome
  • 9q subtelomeric deletion syndrome
  • 9q- syndrome
  • chromosome 9q deletion syndrome

For more information about naming genetic conditions, see the Genetics Home Reference Condition Naming Guidelines ( and How are genetic conditions and genes named? ( in the Handbook.

What if I still have specific questions about Kleefstra syndrome?

Ask the Genetic and Rare Diseases Information Center (

What glossary definitions help with understanding Kleefstra syndrome?

acids ; autism ; autosomal ; autosomal dominant ; brachycephaly ; cell ; chromosome ; congenital ; deletion ; developmental delay ; disability ; DNA ; egg ; enzyme ; gene ; histone ; hypertelorism ; hypoplasia ; hypotonia ; inherit ; inheritance ; inherited ; macroglossia ; methyl ; methyltransferase ; microcephaly ; microdeletion syndrome ; molecule ; mosaic ; muscle tone ; mutation ; prevalence ; prognathism ; protein ; rearrangement ; reproductive cells ; respiratory ; sperm ; syndrome ; translocation

You may find definitions for these and many other terms in the Genetics Home Reference Glossary.


  • Gene Review: Kleefstra Syndrome (
  • Iwakoshi M, Okamoto N, Harada N, Nakamura T, Yamamori S, Fujita H, Niikawa N, Matsumoto N. 9q34.3 deletion syndrome in three unrelated children. Am J Med Genet A. 2004 Apr 30;126A(3):278-83. Review. (
  • Kleefstra T, Brunner HG, Amiel J, Oudakker AR, Nillesen WM, Magee A, Geneviève D, 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 methyl transferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome. Am J Hum Genet. 2006 Aug;79(2):370-7. Epub 2006 Jun 13. (
  • 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, Brunner HG, de Vries BB, van Bokhoven H. Disruption of the gene Euchromatin Histone Methyl Transferase1 (Eu-HMTase1) is associated with the 9q34 subtelomeric deletion syndrome. J Med Genet. 2005 Apr;42(4):299-306. (
  • Kleefstra T, van Zelst-Stams WA, Nillesen WM, Cormier-Daire V, Houge G, Foulds N, 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, Brueton LA, Navarro AD, Bralo MP, Venselaar H, Stegmann SP, Yntema HG, van Bokhoven H, Brunner HG. Further clinical and molecular delineation of the 9q subtelomeric deletion syndrome supports a major contribution of EHMT1 haploinsufficiency to the core phenotype. J Med Genet. 2009 Sep;46(9):598-606. doi: 10.1136/jmg.2008.062950. Epub 2009 Mar 4. (
  • Neas KR, Smith JM, Chia N, Huseyin S, St Heaps L, Peters G, Sholler G, Tzioumi D, Sillence DO, Mowat D. Three patients with terminal deletions within the subtelomeric region of chromosome 9q. Am J Med Genet A. 2005 Feb 1;132A(4):425-30. Review. (
  • Stewart DR, Kleefstra T. The chromosome 9q subtelomere deletion syndrome. Am J Med Genet C Semin Med Genet. 2007 Nov 15;145C(4):383-92. Review. (
  • Verhoeven WM, Egger JI, Vermeulen K, van de Warrenburg BP, Kleefstra T. Kleefstra syndrome in three adult patients: further delineation of the behavioral and neurological phenotype shows aspects of a neurodegenerative course. Am J Med Genet A. 2011 Oct;155A(10):2409-15. doi: 10.1002/ajmg.a.34186. Epub 2011 Sep 9. (
  • Willemsen MH, Beunders G, Callaghan M, de Leeuw N, Nillesen WM, Yntema HG, van Hagen JM, Nieuwint AW, Morrison N, Keijzers-Vloet ST, Hoischen A, Brunner HG, Tolmie J, Kleefstra T. Familial Kleefstra syndrome due to maternal somatic mosaicism for interstitial 9q34.3 microdeletions. Clin Genet. 2011 Jul;80(1):31-8. doi: 10.1111/j.1399-0004.2010.01607.x. Epub 2011 Jan 10. (


The resources on this site should not be used as a substitute for professional medical care or advice. Users seeking information about a personal genetic disease, syndrome, or condition should consult with a qualified healthcare professional. See How can I find a genetics professional in my area? ( in the Handbook.

Reviewed: January 2016
Published: February 1, 2016