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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 2008

What is the official name of the SIX1 gene?

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

SIX1 is the gene's official symbol. The SIX1 gene is also known by other names, listed below.

What is the normal function of the SIX1 gene?

The SIX1 gene is part of a group of similar genes known as the SIX gene family. Genes in this family provide instructions for making proteins that bind to DNA and control the activity of other genes. Based on this role, SIX proteins are called transcription factors.

The SIX1 protein interacts with several other proteins, including the EYA1 protein, to regulate the activity of genes that are important for normal development. Before birth, these protein interactions appear to be essential for the normal formation of many tissues, including the second branchial arch (a structure that gives rise to tissues in the front and side of the neck), the ears, the kidneys, the nose, an immune system gland called the thymus, and muscles used for movement (skeletal muscles).

Does the SIX1 gene share characteristics with other genes?

The SIX1 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 SIX1 gene related to health conditions?

branchiootorenal syndrome - caused by mutations in the SIX1 gene

At least four mutations in the SIX1 gene are known to cause the features of branchiootorenal (BOR) syndrome. In some families with SIX1 mutations, researchers have identified the condition as branchiooto (BO) syndrome. Branchiooto syndrome includes many of the same features as branchiootorenal syndrome, but affected individuals do not have kidney (renal) malformations. The two conditions are otherwise so similar that researchers often consider them together (BOR/BO syndrome).

Each of the known SIX1 mutations changes a single protein building block (amino acid) in the SIX1 protein. Some of these mutations prevent the SIX1 protein from interacting with other proteins, such as EYA1. Other mutations also affect the ability of SIX1 protein to bind to DNA. Both of these functions are needed for the SIX1 protein to regulate gene activity during embryonic development. When the SIX1 protein is faulty, it disrupts the normal development of many tissues before birth. The major signs and symptoms of branchiootorenal syndrome result from abnormal development of the second branchial arch, ears, and kidneys.

Where is the SIX1 gene located?

Cytogenetic Location: 14q23.1

Molecular Location on chromosome 14: base pairs 60,644,699 to 60,649,437

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

The SIX1 gene is located on the long (q) arm of chromosome 14 at position 23.1.

The SIX1 gene is located on the long (q) arm of chromosome 14 at position 23.1.

More precisely, the SIX1 gene is located from base pair 60,644,699 to base pair 60,649,437 on chromosome 14.

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

Where can I find additional information about SIX1?

You and your healthcare professional may find the following resources about SIX1 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 SIX1 gene or gene products?

  • BOS3
  • Homeobox protein SIX1
  • sine oculis homeobox (Drosophila) homolog 1
  • sine oculis homeobox homolog 1
  • sine oculis homeobox homolog 1 (Drosophila)
  • TIP39

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

What glossary definitions help with understanding SIX1?

amino acid ; branchial arch ; DNA ; embryonic ; gene ; homeobox ; homeodomain ; immune system ; kidney ; protein ; renal ; syndrome ; thymus ; transcription

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


  • Gene Review: Branchiootorenal Spectrum Disorders (
  • Kochhar A, Fischer SM, Kimberling WJ, Smith RJ. Branchio-oto-renal syndrome. Am J Med Genet A. 2007 Jul 15;143A(14):1671-8. Review. (
  • Li X, Oghi KA, Zhang J, Krones A, Bush KT, Glass CK, Nigam SK, Aggarwal AK, Maas R, Rose DW, Rosenfeld MG. Eya protein phosphatase activity regulates Six1-Dach-Eya transcriptional effects in mammalian organogenesis. Nature. 2003 Nov 20;426(6964):247-54. Erratum in: Nature. 2004 Jan 15;427(6971):265. (
  • NCBI Gene (
  • Ruf RG, Xu PX, Silvius D, Otto EA, Beekmann F, Muerb UT, Kumar S, Neuhaus TJ, Kemper MJ, Raymond RM Jr, Brophy PD, Berkman J, Gattas M, Hyland V, Ruf EM, Schwartz C, Chang EH, Smith RJ, Stratakis CA, Weil D, Petit C, Hildebrandt F. SIX1 mutations cause branchio-oto-renal syndrome by disruption of EYA1-SIX1-DNA complexes. Proc Natl Acad Sci U S A. 2004 May 25;101(21):8090-5. Epub 2004 May 12. (
  • Sanggaard KM, Rendtorff ND, Kjaer KW, Eiberg H, Johnsen T, Gimsing S, Dyrmose J, Nielsen KO, Lage K, Tranebjaerg L. Branchio-oto-renal syndrome: detection of EYA1 and SIX1 mutations in five out of six Danish families by combining linkage, MLPA and sequencing analyses. Eur J Hum Genet. 2007 Nov;15(11):1121-31. Epub 2007 Jul 18. (


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 2008
Published: February 8, 2016