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Gene

COL9A1

collagen type IX alpha 1 chain

Summary

Cytogenetic location
6q13
Coordinates
Chromosome 6: 70,216,126–70,303,084 (GRCh38)
Exons
38 exons across 87 kb
Protein
921 amino acids
MANE Select transcript
ENST00000357250.11NM_001851.6
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.

      • 1 GenCC submitter rates it definitive or strong

  • Vitreoretinopathy

    • Vitreoretinal Degeneration
      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong

How COL9A1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 6, with a bracket where COL9A1 sits. COL9A1 and 5 genes near it on chromosome 6, from 69,759,605 to 70,759,604.Chromosome 66q13p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q2769.8 Mb70 Mb70.2 Mb70.4 Mb70.6 MbLMBRD1: 69,672,757–69,867,236, reverse strandLMBRD1COL19A1: 69,866,428–70,215,059, forward strandCOL19A1COL9A1: 70,216,126–70,303,084, reverse strandCOL9A1FAM135A: 70,412,941–70,561,610, forward strandFAM135ASDHAF4: 70,566,909–70,598,427, forward strandSDHAF4SMAP1: 70,667,646–70,862,015, forward strandSMAP1Diagram of COL9A1: 38 exons on the reverse strand of chromosome 6Exon 38: 2 known disease-causing sitesExon 22: 1 known disease-causing siteExon 12: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 1: 2 known disease-causing sitesExon 38: 70,216,126–70,217,081, 956 basesExon 37: 70,225,932–70,226,009, 78 basesExon 36: 70,232,583–70,232,771, 189 basesExon 35: 70,234,539–70,234,593, 55 basesExon 34: 70,234,794–70,234,940, 147 basesExon 33: 70,239,254–70,239,286, 33 basesExon 32: 70,240,689–70,240,733, 45 basesExon 31: 70,241,419–70,241,454, 36 basesExon 30: 70,241,964–70,242,035, 72 basesExon 29: 70,242,662–70,242,715, 54 basesExon 28: 70,252,120–70,252,173, 54 basesExon 27: 70,252,262–70,252,315, 54 basesExon 26: 70,253,385–70,253,429, 45 basesExon 25: 70,254,476–70,254,529, 54 basesExon 24: 70,254,963–70,255,016, 54 basesExon 23: 70,255,150–70,255,203, 54 basesExon 22: 70,255,337–70,255,390, 54 basesExon 21: 70,256,768–70,256,821, 54 basesExon 20: 70,260,657–70,260,710, 54 basesExon 19: 70,263,244–70,263,297, 54 basesExon 18: 70,266,717–70,266,770, 54 basesExon 17: 70,268,804–70,268,860, 57 basesExon 16: 70,269,633–70,269,665, 33 basesExon 15: 70,270,314–70,270,367, 54 basesExon 14: 70,271,655–70,271,708, 54 basesExon 13: 70,272,065–70,272,088, 24 basesExon 12: 70,274,047–70,274,082, 36 basesExon 11: 70,274,719–70,274,772, 54 basesExon 10: 70,280,812–70,280,874, 63 basesExon 9: 70,281,004–70,281,039, 36 basesExon 8: 70,281,390–70,281,464, 75 basesExon 7: 70,282,898–70,282,918, 21 basesExon 6: 70,283,737–70,283,820, 84 basesExon 5: 70,294,167–70,294,563, 397 basesExon 4: 70,300,043–70,300,175, 133 basesExon 3: 70,300,309–70,300,386, 78 basesExon 2: 70,302,001–70,302,074, 74 basesExon 1: 70,302,911–70,303,084, 174 bases38353025201510515′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 3.7 kb of the gene's 87 kb; 2,766 of those bases code for the protein.

How a genome test reads COL9A1

11

positions in COL9A1 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 87 kb of COL9A1, introns included, not only the 3.7 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.). COL9A1 gene: collagen type IX alpha 1 chain. Retrieved 17 October 2026, from https://dantelabs.com/genes/col9a1

Vancouver

Dante Labs. COL9A1 gene: collagen type IX alpha 1 chain [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/col9a1

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