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Gene

COL9A3

collagen type IX alpha 3 chain

Summary

Cytogenetic location
20q13.33
Coordinates
Chromosome 20: 62,817,050–62,841,159 (GRCh38)
Exons
32 exons across 24.1 kb
Protein
684 amino acids
Also known as
IDD, MED, EDM3, FLJ90759, DJ885L7.4.1
MANE Select transcript
ENST00000649368.1NM_001853.4
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
      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong

How COL9A3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 20, with a bracket where COL9A3 sits. COL9A3 and 19 genes near it on chromosome 20, from 62,329,105 to 63,329,104.Chromosome 2020q13.33p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.3362.4 Mb62.6 Mb62.8 Mb63 Mb63.2 MbLAMA5: 62,307,955–62,367,333, reverse strandLAMA5RPS21: 62,365,598–62,388,680, forward strandRPS21CABLES2: 62,388,630–62,407,319, reverse strandCABLES2RBBP8NL: 62,410,143–62,427,548, reverse strandRBBP8NLGATA5: 62,463,481–62,476,094, reverse strandGATA5SLCO4A1: 62,642,440–62,685,785, forward strandSLCO4A1NTSR1: 62,708,427–62,762,771, forward strandNTSR1MRGBP: 62,796,452–62,801,729, forward strandMRGBPOGFR: 62,804,178–62,814,000, forward strandOGFRCOL9A3: 62,817,050–62,841,159, forward strandCOL9A3TCFL5: 62,840,997–62,861,840, reverse strandTCFL5DIDO1: 62,877,738–62,937,992, reverse strandDIDO1GID8: 62,937,060–62,948,589, forward strandGID8SLC17A9: 62,952,645–62,969,588, forward strandSLC17A9BHLHE23: 63,005,927–63,007,035, reverse strandBHLHE23YTHDF1: 63,195,429–63,216,149, reverse strandYTHDF1BIRC7: 63,235,435–63,240,497, forward strandBIRC7NKAIN4: 63,240,784–63,272,694, reverse strandNKAIN4ARFGAP1: 63,272,785–63,289,791, forward strandARFGAP1COL20A1: 63,293,186–63,334,851, forward strandCOL20A1Diagram of COL9A3: 32 exons on the forward strand of chromosome 20Exon 1: 1 known disease-causing siteExon 2: 2 known disease-causing sitesExon 5: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 11: 1 known disease-causing siteExon 13: 1 known disease-causing siteExon 14: 1 known disease-causing siteExon 28: 1 known disease-causing siteExon 30: 2 known disease-causing sitesExon 1: 62,817,050–62,817,142, 93 basesExon 2: 62,817,567–62,817,635, 69 basesExon 3: 62,818,518–62,818,553, 36 basesExon 4: 62,819,222–62,819,293, 72 basesExon 5: 62,819,929–62,819,982, 54 basesExon 6: 62,821,181–62,821,216, 36 basesExon 7: 62,821,507–62,821,530, 24 basesExon 8: 62,821,757–62,821,810, 54 basesExon 9: 62,822,111–62,822,164, 54 basesExon 10: 62,822,591–62,822,632, 42 basesExon 11: 62,824,445–62,824,501, 57 basesExon 12: 62,824,968–62,825,021, 54 basesExon 13: 62,825,817–62,825,870, 54 basesExon 14: 62,826,204–62,826,257, 54 basesExon 15: 62,826,767–62,826,820, 54 basesExon 16: 62,827,241–62,827,294, 54 basesExon 17: 62,827,923–62,827,976, 54 basesExon 18: 62,828,764–62,828,817, 54 basesExon 19: 62,828,923–62,828,976, 54 basesExon 20: 62,829,455–62,829,499, 45 basesExon 21: 62,829,628–62,829,681, 54 basesExon 22: 62,829,766–62,829,819, 54 basesExon 23: 62,830,360–62,830,413, 54 basesExon 24: 62,830,517–62,830,588, 72 basesExon 25: 62,832,154–62,832,189, 36 basesExon 26: 62,833,020–62,833,064, 45 basesExon 27: 62,835,921–62,835,953, 33 basesExon 28: 62,836,187–62,836,333, 147 basesExon 29: 62,836,478–62,836,532, 55 basesExon 30: 62,837,083–62,837,265, 183 basesExon 31: 62,838,684–62,838,761, 78 basesExon 32: 62,840,542–62,841,159, 618 bases151015202530325′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 2.5 kb of the gene's 24.1 kb; 2,055 of those bases code for the protein.

How a genome test reads COL9A3

16

positions in COL9A3 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 24.1 kb of COL9A3, introns included, not only the 2.5 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.). COL9A3 gene: collagen type IX alpha 3 chain. Retrieved 17 October 2026, from https://dantelabs.com/genes/col9a3

Vancouver

Dante Labs. COL9A3 gene: collagen type IX alpha 3 chain [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/col9a3

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