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HOXA13 gene

homeobox A13

Normal Function

The HOXA13 gene provides instructions for producing a type of protein called a transcription factor. These proteins attach (bind) to specific regions of DNA and helps control the activity of other genes. The HOXA13 gene is part of a larger family genes  called homeobox genes, which  provide instructions for making transcription factors that act during early embryonic development to control the formation of many body structures. Specifically, the HOXA13 protein appears to be critical for the formation and development of the limbs (particularly the hands and feet), urinary tract, and reproductive system.

The HOXA13 protein contains three areas where a protein building block (amino acid) called alanine is repeated multiple times. These stretches of alanines are known as polyalanine tracts or poly(A) tracts. The role these polyalanine tracts play in the normal function of this protein is unknown.

Health Conditions Related to Genetic Changes

Hand-foot-genital syndrome

Variants (also called mutations) in the HOXA13 gene have been found to cause hand-foot-genital syndrome. As its name suggests, this condition affects the development of the hands and feet, the urinary tract, and the reproductive system. More than half of the variants affect one of the polyalanine tracts in the HOXA13 protein.  These variants add extra alanines to these tracts, making them abnormally long and unstable.  The resulting altered protein is degraded by the cell, so it cannot regulate the activity of other genes during early development.  

Other HOXA13 gene variants result in the production of an abnormally short, nonfunctional version of the HOXA13 protein or change single amino acids in the protein. Variants that substitute one amino acid for another amino acid may change the way the HOXA13 protein folds. The altered protein may or may not function or bind to DNA normally. Variants that result in an altered but functional HOXA13 protein may cause more severe signs and symptoms of hand-foot-genital syndrome than variants that lead to a nonfunctional version of this protein.

More About This Health Condition


Chromosomal rearrangements (translocations) involving the short (p) arm of chromosome 7 have been associated with leukemia, a cancer of blood-forming cells. These translocations disrupt the region of chromosome 7 that contains several similar homeobox genes, including HOXA13.

Within cancer cells, researchers have found translocations between chromosome 7 and chromosome 11 in several people with leukemia. These rearrangements abnormally fuse part of the HOXA13 gene or a similar gene on chromosome 7 to part of the NUP98 gene on chromosome 11. The protein produced from the fused gene probably signals abnormal cells to continue dividing without control or order, which likely contributes to the development of cancer.

Other Names for This Gene

  • homeo box 1J
  • homeo box A13
  • Homeobox protein Hox-A13
  • homeobox protein HOXA13
  • Hox-1J
  • HOX1
  • HOX1J
  • transcription factor HOXA13

Additional Information & Resources

Tests Listed in the Genetic Testing Registry

Scientific Articles on PubMed

Catalog of Genes and Diseases from OMIM

Gene and Variant Databases


  • Fujino T, Suzuki A, Ito Y, Ohyashiki K, Hatano Y, Miura I, Nakamura T. Single-translocation and double-chimeric transcripts: detection of NUP98-HOXA9 in myeloid leukemias with HOXA11 or HOXA13 breaks of the chromosomal translocation t(7;11)(p15;p15). Blood. 2002 Feb 15;99(4):1428-33. doi: 10.1182/blood.v99.4.1428. Citation on PubMed
  • Goodman FR, Bacchelli C, Brady AF, Brueton LA, Fryns JP, Mortlock DP, Innis JW, Holmes LB, Donnenfeld AE, Feingold M, Beemer FA, Hennekam RC, Scambler PJ. Novel HOXA13 mutations and the phenotypic spectrum of hand-foot-genital syndrome. Am J Hum Genet. 2000 Jul;67(1):197-202. doi: 10.1086/302961. Epub 2000 Jun 5. Citation on PubMed or Free article on PubMed Central
  • Goodman FR. Limb malformations and the human HOX genes. Am J Med Genet. 2002 Oct 15;112(3):256-65. doi: 10.1002/ajmg.10776. Citation on PubMed
  • Innis JW, Mortlock D, Chen Z, Ludwig M, Williams ME, Williams TM, Doyle CD, Shao Z, Glynn M, Mikulic D, Lehmann K, Mundlos S, Utsch B. Polyalanine expansion in HOXA13: three new affected families and the molecular consequences in a mouse model. Hum Mol Genet. 2004 Nov 15;13(22):2841-51. doi: 10.1093/hmg/ddh306. Epub 2004 Sep 22. Citation on PubMed
  • Innis JW. Hand-Foot-Genital Syndrome. 2006 Jul 11 [updated 2019 Aug 8]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews(R) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024. Available from Citation on PubMed
  • Mortlock DP, Innis JW. Mutation of HOXA13 in hand-foot-genital syndrome. Nat Genet. 1997 Feb;15(2):179-80. doi: 10.1038/ng0297-179. Citation on PubMed
  • Quinonez SC, Innis JW. Human HOX gene disorders. Mol Genet Metab. 2014 Jan;111(1):4-15. doi: 10.1016/j.ymgme.2013.10.012. Epub 2013 Oct 29. Citation on PubMed
  • Taketani T, Taki T, Ono R, Kobayashi Y, Ida K, Hayashi Y. The chromosome translocation t(7;11)(p15;p15) in acute myeloid leukemia results in fusion of the NUP98 gene with a HOXA cluster gene, HOXA13, but not HOXA9. Genes Chromosomes Cancer. 2002 Aug;34(4):437-43. doi: 10.1002/gcc.10077. Citation on PubMed
  • Utsch B, Becker K, Brock D, Lentze MJ, Bidlingmaier F, Ludwig M. A novel stable polyalanine [poly(A)] expansion in the HOXA13 gene associated with hand-foot-genital syndrome: proper function of poly(A)-harbouring transcription factors depends on a critical repeat length? Hum Genet. 2002 May;110(5):488-94. doi: 10.1007/s00439-002-0712-8. Epub 2002 Apr 4. Citation on PubMed
  • Utsch B, McCabe CD, Galbraith K, Gonzalez R, Born M, Dotsch J, Ludwig M, Reutter H, Innis JW. Molecular characterization of HOXA13 polyalanine expansion proteins in hand-foot-genital syndrome. Am J Med Genet A. 2007 Dec 15;143A(24):3161-8. doi: 10.1002/ajmg.a.31967. Citation on PubMed

The information on this site should not be used as a substitute for professional medical care or advice. Contact a health care provider if you have questions about your health.