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Gene

COL9A2

collagen type IX alpha 2 chain

Summary

Cytogenetic location
1p34.2
Coordinates
Chromosome 1: 40,300,489–40,317,286 (GRCh38)
Exons
32 exons across 16.8 kb
Protein
689 amino acids
Also known as
MED
Previous symbols
EDM2
MANE Select transcript
ENST00000372748.8NM_001852.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Epiphyseal and Spondyloepiphyseal Dysplasias

    • Multiple epiphyseal dysplasia

      A group of conditions affecting the ends of the long bones, causing joint pain and stiffness and early osteoarthritis, caused by genes including COMP, MATN3, COL9A1, COL9A2, COL9A3 and SLC26A2.

      • 2 GenCC submitters rate it definitive or strong

  • Vitreoretinopathy

    • Vitreoretinal Degeneration
      • 4 GenCC submitters rate it definitive or strong

How COL9A2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where COL9A2 sits. COL9A2 and 16 genes near it on chromosome 1, from 39,808,888 to 40,808,887.Chromosome 11p34.2p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q4440 Mb40.2 Mb40.4 Mb40.6 Mb40.8 MbTRIT1: 39,838,110–39,883,511, reverse strandTRIT1MYCL: 39,893,597–39,902,256, reverse strandMYCLMFSD2A: 39,955,112–39,972,134, forward strandMFSD2ACAP1: 40,039,735–40,072,767, forward strandCAP1PPT1: 40,072,710–40,097,267, reverse strandPPT1RLF: 40,161,357–40,240,923, forward strandRLFTMCO2: 40,245,947–40,251,684, forward strandTMCO2ZMPSTE24: 40,258,041–40,294,199, forward strandZMPSTE24COL9A2: 40,300,489–40,317,286, reverse strandCOL9A2SMAP2: 40,344,850–40,423,326, forward strandSMAP2ZFP69B: 40,450,053–40,464,142, forward strandZFP69BZFP69: 40,477,233–40,497,331, forward strandZFP69EXO5: 40,508,441–40,518,869, forward strandEXO5ZNF684: 40,531,557–40,593,265, forward strandZNF684RIMS3: 40,620,679–40,665,728, reverse strandRIMS3NFYC: 40,691,570–40,771,606, forward strandNFYCKCNQ4: 40,783,675–40,840,457, forward strandKCNQ4Diagram of COL9A2: 32 exons on the reverse strand of chromosome 1Exon 28: 3 known disease-causing sitesExon 24: 1 known disease-causing siteExon 23: 1 known disease-causing siteExon 21: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 32: 40,300,489–40,301,381, 893 basesExon 31: 40,301,812–40,301,889, 78 basesExon 30: 40,302,621–40,302,809, 189 basesExon 29: 40,303,131–40,303,185, 55 basesExon 28: 40,303,530–40,303,676, 147 basesExon 27: 40,303,807–40,303,839, 33 basesExon 26: 40,303,928–40,303,972, 45 basesExon 25: 40,304,064–40,304,099, 36 basesExon 24: 40,304,320–40,304,391, 72 basesExon 23: 40,304,476–40,304,529, 54 basesExon 22: 40,304,794–40,304,847, 54 basesExon 21: 40,305,715–40,305,768, 54 basesExon 20: 40,306,143–40,306,187, 45 basesExon 19: 40,307,446–40,307,499, 54 basesExon 18: 40,307,703–40,307,756, 54 basesExon 17: 40,308,192–40,308,245, 54 basesExon 16: 40,309,938–40,309,991, 54 basesExon 15: 40,310,111–40,310,164, 54 basesExon 14: 40,310,264–40,310,317, 54 basesExon 13: 40,310,714–40,310,767, 54 basesExon 12: 40,311,093–40,311,146, 54 basesExon 11: 40,311,230–40,311,286, 57 basesExon 10: 40,311,500–40,311,547, 48 basesExon 9: 40,311,662–40,311,715, 54 basesExon 8: 40,312,059–40,312,112, 54 basesExon 7: 40,312,456–40,312,479, 24 basesExon 6: 40,312,574–40,312,609, 36 basesExon 5: 40,312,731–40,312,784, 54 basesExon 4: 40,314,205–40,314,267, 63 basesExon 3: 40,314,352–40,314,387, 36 basesExon 2: 40,315,590–40,315,664, 75 basesExon 1: 40,317,123–40,317,286, 164 bases323025201510515′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 2.9 kb of the gene's 16.8 kb; 2,070 of those bases code for the protein.

How a genome test reads COL9A2

14

positions in COL9A2 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 16.8 kb of COL9A2, introns included, not only the 2.9 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). COL9A2 gene: collagen type IX alpha 2 chain. Retrieved 17 October 2026, from https://dantelabs.com/genes/col9a2

Vancouver

Dante Labs. COL9A2 gene: collagen type IX alpha 2 chain [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/col9a2

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