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HOXA13 gene
Reviewed by Medicinsk Expert•Last updated: 2026-10-22•Gene

HOXA13 gene

The HOXA13 gene encodes a transcription factor essential for the development of limbs, the urinary tract, and the reproductive system, with variants linked to hand-foot-genital syndrome and certain cancers.

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 help control the activity of other genes. The HOXA13 gene is part of a larger family of 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.

Cancers

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
  • HXA13_HUMAN
  • transcription factor HOXA13

Frequently Asked Questions

Yes. If a pathogenic HOXA13 variant has been identified in a family, targeted DNA testing can be performed on chorionic villus sampling (CVS) at 10–12 weeks or on amniocentesis at 15–20 weeks. Whole‑exome sequencing or a specific gene panel may also reveal a de novo mutation. Early detection allows parents to discuss potential interventions and prepare for the care of a child with hand‑foot‑genital syndrome.
Newborns may have abnormal hand and foot development such as missing digits, fused fingers or toes, or broad thumbs and toes. Urinary tract anomalies can include vesicoureteral reflux, duplex kidneys, or bladder exstrophy. Reproductive tract malformations may be present in females (e.g., vaginal agenesis) and can affect fertility. Early evaluation by a pediatric geneticist, urologist, and orthopedic surgeon is recommended to plan appropriate monitoring and interventions.
Hand‑foot‑genital syndrome is inherited in an autosomal dominant manner. This means that a child has a 50 % chance of inheriting the mutated gene if one parent carries it. Because many cases arise from new (de novo) mutations, a family history is not always present. Genetic counseling and testing can confirm whether a parent carries the mutation and help assess recurrence risk for future pregnancies.
Some studies have linked HOXA13 variants to a higher incidence of certain cancers, such as colorectal and endometrial cancers, although the evidence is still emerging. Individuals with HOXA13 mutations should follow standard cancer screening guidelines for their age and sex, and clinicians may consider earlier or more frequent surveillance if family history or additional risk factors are present. Regular check‑ups with a primary care provider and, if indicated, a specialist can help detect early signs of malignancy.
Source: MedlinePlus, National Library of Medicine

MedlinePlus brings together authoritative health information from the National Library of Medicine (NLM), the National Institutes of Health (NIH), and other government agencies and health-related organizations.

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