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Reviewed September 2010

What is the official name of the SIX3 gene?

The official name of this gene is “SIX homeobox 3.”

SIX3 is the gene's official symbol. The SIX3 gene is also known by other names, listed below.

Read more about gene names and symbols on the About page.

What is the normal function of the SIX3 gene?

The SIX3 gene provides instructions for making a protein that plays an important role in the development of the eyes and front part of the brain (forebrain). This protein is a transcription factor, which means that it attaches (binds) to specific regions of DNA and helps control the activity of certain genes. The SIX3 protein regulates genes involved in several signaling pathways that are important for embryonic development. Some of these genes are turned on (activated) by the SIX3 protein and others are turned off (repressed).

One gene that is activated by the SIX3 protein is the SHH gene, which provides instructions for making a protein called Sonic Hedgehog. Among its many functions, Sonic Hedgehog helps establish the right and left halves (hemispheres) of the forebrain. The SIX3 protein also regulates genes involved in the formation of the lens of the eye and the specialized tissue at the back of the eye that detects light and color (the retina).

Does the SIX3 gene share characteristics with other genes?

The SIX3 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 SIX3 gene related to health conditions?

nonsyndromic holoprosencephaly - caused by mutations in the SIX3 gene

At least 60 mutations in the SIX3 gene have been found to cause nonsyndromic holoprosencephaly. This condition occurs when the brain fails to divide into two hemispheres during early development. SIX3 gene mutations are the third most common cause of nonsyndromic holoprosencephaly. Although mutations in this gene can cause mild to severe forms of the condition, they tend to result in more severe signs and symptoms than mutations in other genes that cause nonsyndromic holoprosencephaly

SIX3 gene mutations change the structure of the SIX3 protein in different ways; however, all of them disrupt the protein's ability to bind with DNA. As a result, the genes involved in normal eye and forebrain development are not properly activated or repressed. Without the correct activity of these genes, the eyes will not form normally and the brain does not separate into two hemispheres. The signs and symptoms of nonsyndromic holoprosencephaly are caused by abnormal development of the brain and face.

Where is the SIX3 gene located?

Cytogenetic Location: 2p21

Molecular Location on chromosome 2: base pairs 44,941,729 to 44,966,751

(Homo sapiens Annotation Release 107, GRCh38.p2) (NCBIThis link leads to a site outside Genetics Home Reference.)

The SIX3 gene is located on the short (p) arm of chromosome 2 at position 21.

The SIX3 gene is located on the short (p) arm of chromosome 2 at position 21.

More precisely, the SIX3 gene is located from base pair 44,941,729 to base pair 44,966,751 on chromosome 2.

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

Where can I find additional information about SIX3?

You and your healthcare professional may find the following resources about SIX3 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 SIX3 gene or gene products?

  • homeobox protein SIX3
  • HPE2
  • sine oculis homeobox homolog 3

Where can I find general information about genes?

The Handbook provides basic information about genetics in clear language.

These links provide additional genetics resources that may be useful.

What glossary definitions help with understanding SIX3?

DNA ; embryonic ; gene ; holoprosencephaly ; homeobox ; protein ; retina ; tissue ; transcription ; transcription factor

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

See also Understanding Medical Terminology.

References (13 links)


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: September 2010
Published: February 8, 2016