GENE REFERENCE / HGNC:2200

COL2A1

collagen type II alpha 1 chain

protein-coding gene12q13.11Gene information

What does this gene do?

The COL2A1 gene provides instructions for making the basic component of type II collagen, called the alpha-1(II) chain. Type II collagen adds structure and strength to connective tissues and plays an important role in the normal development of joints, eyes, and the inner ear.

Type II collagen is found primarily in cartilage, a tough, flexible tissue that makes up much of the skeleton during early development. Most cartilage is later replaced by bone, except for the cartilage that covers and protects the ends of bones and the cartilage that is present in the nose and external ears. Type II collagen is particularly abundant in a form of cartilage known as hyaline cartilage, which is found in the developing skeleton, joints, and at the end of the long bones of the arms and legs where new bone is produced (growth plates). Type II collagen is also part of the inner ear, the clear gel that fills the eyeball (the vitreous), and the center portion (nucleus pulposus) of the discs between the bones of the spine (vertebrae).

To construct type II collagen, three alpha-1(II) chains twist together to form a procollagen molecule. Procollagen molecules are then processed by enzymes in the cell. Once processed, the modified collagen molecules leave the cell and arrange themselves into long, thin fibrils that attach (bind) to one another in a lattice pattern (cross-link) in the spaces around cells. The cross-linkages result in the formation of very strong, mature type II collagen fibers.

Source: MedlinePlus, National Library of Medicine. Source publication: 2024-12-20. Source review: 2024-12.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
achondrogenesis type IIMONDO:0008702 · Evaluated 2020-10-05	Autosomal dominant	DefinitiveSkeletal Disorders Gene Curation Expert Panel
Kniest dysplasiaMONDO:0007987 · Evaluated 2021-12-15	Autosomal dominant	DefinitiveSkeletal Disorders Gene Curation Expert Panel
Stickler syndrome type 1MONDO:0007160 · Evaluated 2023-09-28	Autosomal dominant	DefinitiveSkeletal Disorders Gene Curation Expert Panel
dysplasia of the proximal femoral epiphysesMONDO:1030002 · Evaluated 2024-08-06	Autosomal dominant	DefinitiveSkeletal Disorders Gene Curation Expert Panel
platyspondylic dysplasia, Torrance typeMONDO:0007895 · Evaluated 2021-02-01	Autosomal dominant	DefinitiveSkeletal Disorders Gene Curation Expert Panel
COL2A1-related spondyloepiphyseal dysplasiaMONDO:0100602 · Evaluated 2021-12-06	Autosomal dominant	DefinitiveSkeletal Disorders Gene Curation Expert Panel
spondyloperipheral dysplasiaMONDO:0010078 · Evaluated 2023-09-28	Autosomal dominant	DefinitiveSkeletal Disorders Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 3,750
Submissions for variants in or overlapping this gene: 6,504
Submissions explicitly reporting this gene: 6,285
Alleles reported pathogenic / likely pathogenic: 1,216
VariationIDs with uncertain significance: 920
VariationIDs with conflicting classifications: 301

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about COL2A1?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 1,216 alleles in COL2A1 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in COL2A1.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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