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


Reviewed February 2008

What is the official name of the COL9A3 gene?

The official name of this gene is “collagen, type IX, alpha 3.”

COL9A3 is the gene's official symbol. The COL9A3 gene is also known by other names, listed below.

What is the normal function of the COL9A3 gene?

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.

Does the COL9A3 gene share characteristics with other genes?

The COL9A3 gene belongs to a family of genes called COL (collagens). It also belongs to a family of genes called collagen proteoglycans (collagen proteoglycans). It also belongs to a family of genes called proteoglycans (proteoglycans).

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 COL9A3 gene related to health conditions?

multiple epiphyseal dysplasia - caused by mutations in the COL9A3 gene

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.

other disorders - increased risk from variations of the COL9A3 gene

At least one mutation in the COL9A3 gene increases an individual's risk for intervertebral disc disease, one of the most common sources of lower back pain. This mutation substitutes the amino acid tryptophan for the amino acid arginine at position 103 in the α3(IX) chain. The mutation is commonly known as the Trp3 allele and is sometimes written as Arg103Trp. A person with at least one Trp3 allele has three times the risk of developing intervertebral disc disease compared with someone without the Trp3 allele. The amino acid tryptophan is rarely found in collagen molecules, and it likely alters the structure or function of type IX collagen.

Where is the COL9A3 gene located?

Cytogenetic Location: 20q13.3

Molecular Location on chromosome 20: base pairs 62,817,061 to 62,841,158

The COL9A3 gene is located on the long (q) arm of chromosome 20 at position 13.3.

The COL9A3 gene is located on the long (q) arm of chromosome 20 at position 13.3.

More precisely, the COL9A3 gene is located from base pair 62,817,061 to base pair 62,841,158 on chromosome 20.

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

Where can I find additional information about COL9A3?

You and your healthcare professional may find the following resources about COL9A3 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 COL9A3 gene or gene products?

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

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

What glossary definitions help with understanding COL9A3?

acids ; allele ; amino acid ; arginine ; cartilage ; collagen ; deletion ; DNA ; domain ; dysplasia ; exon ; gene ; molecule ; mutation ; nucleotide ; protein ; tryptophan

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


  • 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. Review. (
  • Gene Review: Multiple Epiphyseal Dysplasia, Dominant (
  • 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. Epub 2006 Apr 4. (
  • 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. (
  • NCBI Gene (


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: February 2008
Published: March 23, 2015