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


Reviewed September 2010

What is the official name of the SHH gene?

The official name of this gene is “sonic hedgehog.”

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

What is the normal function of the SHH gene?

The SHH gene provides instructions for making a protein called Sonic Hedgehog. This protein functions as a chemical signal that is essential for embryonic development. Sonic Hedgehog plays a role in cell growth, cell specialization, and the normal shaping (patterning) of the body. This protein is important for development of the brain and spinal cord (central nervous system), eyes, limbs, and many other parts of the body.

Sonic Hedgehog is necessary for the development of the front part of the brain (forebrain). This signaling protein helps establish the line that separates the right and left sides of the forebrain (the midline). Specifically, Sonic Hedgehog establishes the midline for the underside (ventral surface) of the forebrain. Sonic Hedgehog and other signaling proteins are needed to form the right and left halves (hemispheres) of the brain.

Sonic Hedgehog also has an important role in the formation of the eyes. During early development, the cells that develop into the eyes form a single structure called the eye field. This structure is located in the center of the developing face. Sonic hedgehog signaling causes the eye field to separate into two distinct eyes.

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

nonsyndromic holoprosencephaly - caused by mutations in the SHH gene

More than 100 mutations in the SHH gene have been found to cause nonsyndromic holoprosencephaly. This condition occurs when the brain fails to divide into two hemispheres during early development. SHH gene mutations are the most common cause of nonsyndromic holoprosencephaly. These mutations reduce or eliminate the activity of Sonic Hedgehog. Without the correct activity of this protein, the eyes will not form normally and the brain does not separate into two hemispheres. The development of other parts of the face is affected if the eyes do not move to their proper position. The signs and symptoms of nonsyndromic holoprosencephaly are caused by abnormal development of the brain and face.

Where is the SHH gene located?

Cytogenetic Location: 7q36

Molecular Location on chromosome 7: base pairs 155,802,864 to 155,812,273

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

The SHH gene is located on the long (q) arm of chromosome 7 at position 36.

The SHH gene is located on the long (q) arm of chromosome 7 at position 36.

More precisely, the SHH gene is located from base pair 155,802,864 to base pair 155,812,273 on chromosome 7.

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

Where can I find additional information about SHH?

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

  • HPE3
  • sonic hedgehog homolog (Drosophila)
  • sonic hedgehog protein
  • sonic hedgehog protein preproprotein

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

What glossary definitions help with understanding SHH?

cell ; central nervous system ; embryonic ; gene ; holoprosencephaly ; nervous system ; protein

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


  • Dubourg C, Bendavid C, Pasquier L, Henry C, Odent S, David V. Holoprosencephaly. Orphanet J Rare Dis. 2007 Feb 2;2:8. Review. (
  • Gene Review: Holoprosencephaly Overview (
  • Monuki ES. The morphogen signaling network in forebrain development and holoprosencephaly. J Neuropathol Exp Neurol. 2007 Jul;66(7):566-75. Review. (
  • Nanni L, Ming JE, Bocian M, Steinhaus K, Bianchi DW, Die-Smulders C, Giannotti A, Imaizumi K, Jones KL, Campo MD, Martin RA, Meinecke P, Pierpont ME, Robin NH, Young ID, Roessler E, Muenke M. The mutational spectrum of the sonic hedgehog gene in holoprosencephaly: SHH mutations cause a significant proportion of autosomal dominant holoprosencephaly. Hum Mol Genet. 1999 Dec;8(13):2479-88. (
  • Nanni L, Ming JE, Du Y, Hall RK, Aldred M, Bankier A, Muenke M. SHH mutation is associated with solitary median maxillary central incisor: a study of 13 patients and review of the literature. Am J Med Genet. 2001 Jul 22;102(1):1-10. Review. (
  • NCBI Gene (
  • Roessler E, El-Jaick KB, Dubourg C, Vélez JI, Solomon BD, Pineda-Alvarez DE, Lacbawan F, Zhou N, Ouspenskaia M, Paulussen A, Smeets HJ, Hehr U, Bendavid C, Bale S, Odent S, David V, Muenke M. The mutational spectrum of holoprosencephaly-associated changes within the SHH gene in humans predicts loss-of-function through either key structural alterations of the ligand or its altered synthesis. Hum Mutat. 2009 Oct;30(10):E921-35. doi: 10.1002/humu.21090. (
  • Roessler E, Muenke M. The molecular genetics of holoprosencephaly. Am J Med Genet C Semin Med Genet. 2010 Feb 15;154C(1):52-61. doi: 10.1002/ajmg.c.30236. Review. (
  • Solomon BD, Mercier S, Vélez JI, Pineda-Alvarez DE, Wyllie A, Zhou N, Dubourg C, David V, Odent S, Roessler E, Muenke M. Analysis of genotype-phenotype correlations in human holoprosencephaly. Am J Med Genet C Semin Med Genet. 2010 Feb 15;154C(1):133-41. doi: 10.1002/ajmg.c.30240. Review. (


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 1, 2016