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COL9A3 gene

collagen type IX alpha 3 chain

Normal Function

The COL9A3 gene provides instructions for making part of a large molecule called type IX collagen. Collagens are a family of proteins that strengthen and support connective tissues, such as skin, bone, cartilage, tendons, and ligaments. In particular, type IX collagen is an important component of cartilage.

Type IX collagen is made up of three proteins that are produced from three distinct genes: one α1(IX) chain, which is produced from the COL9A1 gene, one α2(IX) chain, which is produced from the COL9A2 gene, and one α3(IX) chain, which is produced from the COL9A3 gene. Type IX collagen is more flexible than other types of collagen molecules and is closely associated with type II collagen. Researchers believe that the flexible nature of type IX collagen allows it to act as a bridge that connects type II collagen with other cartilage components. Studies have shown that type IX collagen also interacts with the proteins produced from the MATN3 and COMP genes.

Health Conditions Related to Genetic Changes

Multiple epiphyseal dysplasia

At least three mutations in the COL9A3 gene have been shown to cause dominant multiple epiphyseal dysplasia. All of these mutations disrupt how genetic information is spliced together to make the blueprint for producing the α3(IX) chain. These mutations, called splice-site mutations, change one DNA building block (nucleotide) near an area of the gene called exon 3. These mutations in the COL9A3 gene result in the deletion of 12 protein building blocks (amino acids) from the α3(IX) chain. It is not known how mutations in COL9A3 cause the signs and symptoms of dominant multiple epiphyseal dysplasia.

All identified mutations in type IX collagen delete a portion of the COL3 domain, which suggests that this region has an important function. Mutations may affect the ability of type IX collagen to fold correctly or interact with other cartilage components.

More About This Health Condition

Intervertebral disc disease

MedlinePlus Genetics provides information about Intervertebral disc disease

More About This Health Condition

Stickler syndrome

MedlinePlus Genetics provides information about Stickler syndrome

More About This Health Condition

Other Names for This Gene

  • alpha 3 type IX collagen
  • collagen type IX alpha 3
  • collagen, type IX, alpha 3
  • DJ885L7.4.1
  • EDM3
  • FLJ90759
  • IDD

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


  • Briggs MD, Chapman KL. Pseudoachondroplasia and multiple epiphyseal dysplasia: mutation review, molecular interactions, and genotype to phenotype correlations. Hum Mutat. 2002 May;19(5):465-78. doi: 10.1002/humu.10066. Citation on PubMed
  • Briggs MD, Wright MJ, Mortier GR. Multiple Epiphyseal Dysplasia, Autosomal Dominant. 2003 Jan 8 [updated 2019 Apr 25]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews(R) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024. Available from Citation on PubMed
  • Faletra F, D'Adamo AP, Bruno I, Athanasakis E, Biskup S, Esposito L, Gasparini P. Autosomal recessive Stickler syndrome due to a loss of function mutation in the COL9A3 gene. Am J Med Genet A. 2014 Jan;164A(1):42-7. doi: 10.1002/ajmg.a.36165. Epub 2013 Nov 22. Citation on PubMed
  • Higashino K, Matsui Y, Yagi S, Takata Y, Goto T, Sakai T, Katoh S, Yasui N. The alpha2 type IX collagen tryptophan polymorphism is associated with the severity of disc degeneration in younger patients with herniated nucleus pulposus of the lumbar spine. Int Orthop. 2007 Feb;31(1):107-11. doi: 10.1007/s00264-006-0117-8. Epub 2006 Apr 4. Citation on PubMed or Free article on PubMed Central
  • Jim JJ, Noponen-Hietala N, Cheung KM, Ott J, Karppinen J, Sahraravand A, Luk KD, Yip SP, Sham PC, Song YQ, Leong JC, Cheah KS, Ala-Kokko L, Chan D. The TRP2 allele of COL9A2 is an age-dependent risk factor for the development and severity of intervertebral disc degeneration. Spine (Phila Pa 1976). 2005 Dec 15;30(24):2735-42. doi: 10.1097/01.brs.0000190828.85331.ef. Citation on PubMed

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