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SOX9 gene

SRY-box transcription factor 9

Normal Function

The SOX9 gene provides instructions for making a protein that plays a critical role during embryonic development. The SOX9 protein is especially important for development of the skeleton and plays a key role in the determination of sex before birth. The SOX9 protein attaches (binds) to specific regions of DNA and regulates the activity of other genes, particularly those that control skeletal development and sex determination. On the basis of this action, the SOX9 protein is called a transcription factor.

Health Conditions Related to Genetic Changes

Campomelic dysplasia

More than 70 mutations involving the SOX9 gene have been found to cause campomelic dysplasia, a disorder that affects skeletal development, sex determination, and other processes in the body and is often life-threatening in the newborn period. Most cases of campomelic dysplasia are caused by mutations within the SOX9 gene. These mutations prevent the production of the SOX9 protein or result in a protein with impaired ability to function as a transcription factor. About 5 percent of cases are caused by chromosome abnormalities that occur near the SOX9 gene. These chromosome abnormalities disrupt regions of DNA called enhancers that normally regulate the activity of the SOX9 gene. All of these genetic changes prevent the SOX9 protein from properly controlling the genes essential for normal development of the skeleton, reproductive organs, and other parts of the body. Abnormal development of these structures causes the signs and symptoms of campomelic dysplasia.

Individuals with milder forms of campomelic dysplasia are more likely to have chromosome abnormalities near the SOX9 gene rather than mutations within the gene.

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Isolated Pierre Robin sequence

Genetic changes that occur near the SOX9 gene cause some cases of isolated Pierre Robin sequence. Individuals with this condition have a small lower jaw (micrognathia) and a tongue that is placed further back than normal (glossoptosis), which can block the airways. Most affected individuals are also born with an opening in the roof of the mouth (a cleft palate). These cases of Pierre Robin sequence are described as isolated because they occur without other signs and symptoms.

The genetic changes associated with isolated Pierre Robin sequence are thought to disrupt enhancer regions that normally regulate the activity of the SOX9 gene during development of the lower jaw, which reduces SOX9 gene activity. As a result, the SOX9 protein cannot properly control the genes essential for normal jaw development, causing micrognathia. Underdevelopment of the lower jaw affects placement of the tongue and formation of the palate, leading to glossoptosis and, often, cleft palate.

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46,XX testicular difference of sex development

MedlinePlus Genetics provides information about 46,XX testicular difference of sex development

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Swyer syndrome

MedlinePlus Genetics provides information about Swyer syndrome

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Other Names for This Gene

  • SRA1
  • SRY (sex determining region Y)-box 9
  • SRY (sex-determining region Y)-box 9 protein
  • SRY box 9
  • transcription factor SOX9

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


  • Alankarage D, Lavery R, Svingen T, Kelly S, Ludbrook L, Bagheri-Fam S, Koopman P, Harley V. SOX9 regulates expression of the male fertility gene Ets variant factor 5 (ETV5) during mammalian sex development. Int J Biochem Cell Biol. 2016 Oct;79:41-51. doi: 10.1016/j.biocel.2016.08.005. Epub 2016 Aug 4. Citation on PubMed
  • Amarillo IE, Dipple KM, Quintero-Rivera F. Familial microdeletion of 17q24.3 upstream of SOX9 is associated with isolated Pierre Robin sequence due to position effect. Am J Med Genet A. 2013 May;161A(5):1167-72. doi: 10.1002/ajmg.a.35847. Epub 2013 Mar 26. Citation on PubMed
  • Benko S, Fantes JA, Amiel J, Kleinjan DJ, Thomas S, Ramsay J, Jamshidi N, Essafi A, Heaney S, Gordon CT, McBride D, Golzio C, Fisher M, Perry P, Abadie V, Ayuso C, Holder-Espinasse M, Kilpatrick N, Lees MM, Picard A, Temple IK, Thomas P, Vazquez MP, Vekemans M, Roest Crollius H, Hastie ND, Munnich A, Etchevers HC, Pelet A, Farlie PG, Fitzpatrick DR, Lyonnet S. Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat Genet. 2009 Mar;41(3):359-64. doi: 10.1038/ng.329. Epub 2009 Feb 22. Citation on PubMed
  • Bien-Willner GA, Stankiewicz P, Lupski JR. SOX9cre1, a cis-acting regulatory element located 1.1 Mb upstream of SOX9, mediates its enhancement through the SHH pathway. Hum Mol Genet. 2007 May 15;16(10):1143-56. doi: 10.1093/hmg/ddm061. Epub 2007 Apr 4. Citation on PubMed
  • Fonseca AC, Bonaldi A, Bertola DR, Kim CA, Otto PA, Vianna-Morgante AM. The clinical impact of chromosomal rearrangements with breakpoints upstream of the SOX9 gene: two novel de novo balanced translocations associated with acampomelic campomelic dysplasia. BMC Med Genet. 2013 May 7;14:50. doi: 10.1186/1471-2350-14-50. Citation on PubMed or Free article on PubMed Central
  • Gordon CT, Attanasio C, Bhatia S, Benko S, Ansari M, Tan TY, Munnich A, Pennacchio LA, Abadie V, Temple IK, Goldenberg A, van Heyningen V, Amiel J, FitzPatrick D, Kleinjan DA, Visel A, Lyonnet S. Identification of novel craniofacial regulatory domains located far upstream of SOX9 and disrupted in Pierre Robin sequence. Hum Mutat. 2014 Aug;35(8):1011-20. doi: 10.1002/humu.22606. Citation on PubMed or Free article on PubMed Central
  • Hill-Harfe KL, Kaplan L, Stalker HJ, Zori RT, Pop R, Scherer G, Wallace MR. Fine mapping of chromosome 17 translocation breakpoints > or = 900 Kb upstream of SOX9 in acampomelic campomelic dysplasia and a mild, familial skeletal dysplasia. Am J Hum Genet. 2005 Apr;76(4):663-71. doi: 10.1086/429254. Citation on PubMed or Free article on PubMed Central
  • Kobayashi A, Chang H, Chaboissier MC, Schedl A, Behringer RR. Sox9 in testis determination. Ann N Y Acad Sci. 2005 Dec;1061:9-17. doi: 10.1196/annals.1336.003. Citation on PubMed
  • Leipoldt M, Erdel M, Bien-Willner GA, Smyk M, Theurl M, Yatsenko SA, Lupski JR, Lane AH, Shanske AL, Stankiewicz P, Scherer G. Two novel translocation breakpoints upstream of SOX9 define borders of the proximal and distal breakpoint cluster region in campomelic dysplasia. Clin Genet. 2007 Jan;71(1):67-75. doi: 10.1111/j.1399-0004.2007.00736.x. Citation on PubMed
  • Mead TJ, Wang Q, Bhattaram P, Dy P, Afelik S, Jensen J, Lefebvre V. A far-upstream (-70 kb) enhancer mediates Sox9 auto-regulation in somatic tissues during development and adult regeneration. Nucleic Acids Res. 2013 Apr;41(8):4459-69. doi: 10.1093/nar/gkt140. Epub 2013 Feb 28. Citation on PubMed or Free article on PubMed Central
  • Velagaleti GV, Bien-Willner GA, Northup JK, Lockhart LH, Hawkins JC, Jalal SM, Withers M, Lupski JR, Stankiewicz P. Position effects due to chromosome breakpoints that map approximately 900 Kb upstream and approximately 1.3 Mb downstream of SOX9 in two patients with campomelic dysplasia. Am J Hum Genet. 2005 Apr;76(4):652-62. doi: 10.1086/429252. Epub 2005 Feb 22. Citation on PubMed or Free article on PubMed Central

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.