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


Reviewed January 2009

What is the official name of the MSX1 gene?

The official name of this gene is “msh homeobox 1.”

MSX1 is the gene's official symbol. The MSX1 gene is also known by other names, listed below.

What is the normal function of the MSX1 gene?

The MSX1 gene provides instructions for making a protein that regulates the activity of other genes. The MSX1 gene is part of a larger family of homeobox genes, which act during early development to control the formation of many body structures. Specifically, this gene is critical for the normal development of the teeth and other structures in the mouth. It may also be important for development of the fingernails and toenails.

Does the MSX1 gene share characteristics with other genes?

The MSX1 gene belongs to a family of genes called homeobox (homeoboxes).

A gene family is a group of genes that share important characteristics. Classifying individual genes into families helps researchers describe how genes are related to each other. For more information, see What are gene families? ( in the Handbook.

How are changes in the MSX1 gene related to health conditions?

Wolf-Hirschhorn syndrome - associated with the MSX1 gene

The MSX1 gene is often deleted in people with Wolf-Hirschhorn syndrome, even though it is located outside the region of chromosome 4 that is typically deleted in people with this condition. A loss of the MSX1 gene probably disrupts the regulation of several other genes, particularly genes involved in the development of the mouth and teeth. Researchers believe that a deletion of the MSX1 gene disrupts the formation of oral structures in early development, leading to missing teeth and other dental abnormalities. A loss of the MSX1 gene probably also causes an opening in the roof of the mouth (cleft palate) and/or a split in the upper lip (cleft lip) in some people with Wolf-Hirschhorn syndrome.

other disorders - associated with the MSX1 gene

Changes in the MSX1 gene are also associated with other abnormalities of mouth and tooth development. For example, changes in this gene contribute to some cases of cleft lip and/or cleft palate in people who do not have Wolf-Hirschhorn syndrome. These genetic variations (polymorphisms) have been associated with isolated cleft lip and cleft palate in several different populations worldwide. MSX1 polymorphisms appear to be one of many genetic and environmental factors that play a role in oral clefting.

At least six MSX1 mutations are responsible for oligodontia, a condition in which multiple teeth fail to develop. Some individuals with MSX1 mutations have a combination of oligodontia and cleft lip and/or cleft palate. Mutations in the MSX1 gene likely reduce the amount of functional MSX1 protein within cells, which disrupts the early development of structures in the mouth.

Another mutation in the MSX1 gene has been found to cause Witkop syndrome (also known as tooth-and-nail syndrome) in one large family. This rare condition is characterized by a variable number of missing teeth and abnormalities of the fingernails and toenails. The MSX1 mutation responsible for Witkop syndrome, written as Ser202Ter or S202X, leads to the production of an abnormally short, nonfunctional version of the MSX1 protein. A loss of this protein disrupts the formation of the teeth and nails during early development.

Where is the MSX1 gene located?

Cytogenetic Location: 4p16.2

Molecular Location on chromosome 4: base pairs 4,859,665 to 4,863,936

(Homo sapiens Annotation Release 107, GRCh38.p2) (NCBI (

The MSX1 gene is located on the short (p) arm of chromosome 4 at position 16.2.

The MSX1 gene is located on the short (p) arm of chromosome 4 at position 16.2.

More precisely, the MSX1 gene is located from base pair 4,859,665 to base pair 4,863,936 on chromosome 4.

See How do geneticists indicate the location of a gene? ( in the Handbook.

Where can I find additional information about MSX1?

You and your healthcare professional may find the following resources about MSX1 helpful.

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

What other names do people use for the MSX1 gene or gene products?

  • homeobox 7
  • homeobox protein MSX-1
  • HOX7
  • HYD1
  • msh homeo box 1
  • msh homeobox homolog 1
  • MSH Homeo Box Homolog 1 (Drosophila) Gene
  • OFC5

See How are genetic conditions and genes named? ( in the Handbook.

What glossary definitions help with understanding MSX1?

agenesis ; chromosome ; cleft palate ; deletion ; gene ; homeobox ; hypodontia ; mutation ; oligodontia ; palate ; protein ; syndrome ; transcription ; transcription factor

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


  • Hu G, Vastardis H, Bendall AJ, Wang Z, Logan M, Zhang H, Nelson C, Stein S, Greenfield N, Seidman CE, Seidman JG, Abate-Shen C. Haploinsufficiency of MSX1: a mechanism for selective tooth agenesis. Mol Cell Biol. 1998 Oct;18(10):6044-51. (
  • Jezewski PA, Vieira AR, Nishimura C, Ludwig B, Johnson M, O'Brien SE, Daack-Hirsch S, Schultz RE, Weber A, Nepomucena B, Romitti PA, Christensen K, Orioli IM, Castilla EE, Machida J, Natsume N, Murray JC. Complete sequencing shows a role for MSX1 in non-syndromic cleft lip and palate. J Med Genet. 2003 Jun;40(6):399-407. (
  • Jumlongras D, Bei M, Stimson JM, Wang WF, DePalma SR, Seidman CE, Felbor U, Maas R, Seidman JG, Olsen BR. A nonsense mutation in MSX1 causes Witkop syndrome. Am J Hum Genet. 2001 Jul;69(1):67-74. Epub 2001 May 16. (
  • Kim JW, Simmer JP, Lin BP, Hu JC. Novel MSX1 frameshift causes autosomal-dominant oligodontia. J Dent Res. 2006 Mar;85(3):267-71. (
  • Lidral AC, Reising BC. The role of MSX1 in human tooth agenesis. J Dent Res. 2002 Apr;81(4):274-8. (
  • Modesto A, Moreno LM, Krahn K, King S, Lidral AC. MSX1 and orofacial clefting with and without tooth agenesis. J Dent Res. 2006 Jun;85(6):542-6. (
  • Mostowska A, Kobielak A, Trzeciak WH. Molecular basis of non-syndromic tooth agenesis: mutations of MSX1 and PAX9 reflect their role in patterning human dentition. Eur J Oral Sci. 2003 Oct;111(5):365-70. Review. (
  • NCBI Gene (
  • Nieminen P, Kotilainen J, Aalto Y, Knuutila S, Pirinen S, Thesleff I. MSX1 gene is deleted in Wolf-Hirschhorn syndrome patients with oligodontia. J Dent Res. 2003 Dec;82(12):1013-7. (
  • van den Boogaard MJ, Dorland M, Beemer FA, van Amstel HK. MSX1 mutation is associated with orofacial clefting and tooth agenesis in humans. Nat Genet. 2000 Apr;24(4):342-3. Erratum in: Nat Genet 2000 May;25(1):125. (
  • Vastardis H, Karimbux N, Guthua SW, Seidman JG, Seidman CE. A human MSX1 homeodomain missense mutation causes selective tooth agenesis. Nat Genet. 1996 Aug;13(4):417-21. (


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 2009
Published: February 1, 2016