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COL9A3 gene
Reviewed by Medicinsk Expert•Last updated: 2026-10-22•Gene

COL9A3 gene

The COL9A3 gene provides instructions for creating a protein chain that is a key component of type IX collagen, which supports the structure of cartilage.

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.

Intervertebral disc disease

MedlinePlus Genetics provides information about Intervertebral disc disease.

Stickler syndrome

MedlinePlus Genetics provides information about Stickler syndrome.

Other Names for This Gene

  • alpha 3 type IX collagen
  • CO9A3_HUMAN
  • collagen type IX alpha 3
  • collagen, type IX, alpha 3
  • DJ885L7.4.1
  • EDM3
  • FLJ90759
  • IDD

Frequently Asked Questions

Management mirrors other forms of MED but emphasizes early joint preservation. Low‑impact aerobic exercise (swimming, water aerobics) and core strengthening reduce joint loading. Vitamin D and calcium supplementation support bone health, especially during rapid growth phases. Some clinicians use disease‑modifying osteoarthritis drugs (e.g., glucosamine/chondroitin) although evidence is limited; they can be trialed for symptom relief. In selected cases, prophylactic osteotomy or guided growth surgery may correct angular deformities before they become severe. Regular weight monitoring is crucial to keep joint stress low.
Baseline assessment should include a full musculoskeletal exam, standing radiographs of the hips, knees, and ankles, and a gait analysis. Follow‑up imaging is usually recommended every 1–2 years during growth, then every 2–3 years in adulthood, or sooner if new pain or functional limitation arises. Annual physical therapy reviews help detect early loss of range of motion. Early referral to an orthopedic surgeon is advised if deformities progress or if pain interferes with daily activities.
Splice‑site mutations in COL9A3 typically remove a short stretch of 12 amino acids from the α3(IX) chain. Clinical experience suggests that COL9A3‑related MED often presents with a milder phenotype than COL9A2 or COL9A1 mutations, but there is overlap. Some patients have only mild joint pain and minimal radiographic changes, while others develop early osteoarthritis. The exact severity is unpredictable and depends on additional genetic and environmental factors.
targeted next‑generation sequencing panel that includes COL9A3 exon‑3 coverage is the standard test. Whole‑exome sequencing can also identify the mutation but may be more costly. A peripheral blood draw (5–10 mL) in an EDTA tube is sufficient; saliva kits are an alternative if venipuncture is difficult. The laboratory will verify that the assay captures the splice‑site region; ask the ordering clinician to confirm this before sampling.
Source: MedlinePlus, National Library of Medicine

MedlinePlus brings together authoritative health information from the National Library of Medicine (NLM), the National Institutes of Health (NIH), and other government agencies and health-related organizations.

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