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Gene

COL2A1

collagen type II alpha 1 chain

Summary

Cytogenetic location
12q13.11
Coordinates
Chromosome 12: 47,972,967–48,004,476 (GRCh38)
Exons
54 exons across 31.5 kb
Protein
1,487 amino acids
Inheritance
Autosomal dominant
Also known as
STL1
Previous symbols
SEDC, AOM
MANE Select transcript
ENST00000380518.8NM_001844.5
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

  • Achondrogenesis panel

    • Achondrogenesis

      Achondrogenesis describes a rare group of lethal skeletal dysplasias characterized by an endochondral ossification deficiency that leads to dwarfism with extreme micromelia, a small thorax, a prominent abdomen, anasarca and polyhydramnios. There are three types of achondrogenesis that exist and that differ clinically, radiologically, histologically and genetically: achondrogensis type 1a, type 1b and type 2.

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

  • Epiphyseal and Spondyloepiphyseal Dysplasias

    • COL2A1-related spondyloepiphyseal dysplasiaAutosomal dominant

      Skeletal dysplasias caused by COL2A1 variants that affect the spine and the ends of the long bones, often with nearsightedness and a risk of retinal detachment.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong
    • Kniest dysplasiaAutosomal dominant

      COL2A1 dysplasia with short trunk, enlarged joints, cleft palate, myopia and hearing loss.

      • ClinGen rates the link definitive
      • 3 GenCC submitters rate it definitive or strong
    • Platyspondylic dysplasia, Torrance typeAutosomal dominant

      Severe COL2A1 skeletal dysplasia with flattened vertebrae and short limbs.

      • ClinGen rates the link definitive
      • 1 GenCC submitter rates it definitive or strong
    • Spondyloepimetaphyseal dysplasia, Strudwick typeAutosomal dominant

      COL2A1 dysplasia with short stature, spinal curvature and irregular bone ends.

      • 1 GenCC submitter rates it definitive or strong
    • Legg-Calve-Perthes disease (COL2A1-related)Autosomal dominant

      Childhood loss of blood supply to the hip ball, in familial cases linked to COL2A1.

      • 1 GenCC submitter rates it definitive or strong
    • Avascular necrosis of the femoral head, primary, 1Autosomal dominant

      Adult-onset hip bone death in families carrying COL2A1 variants.

      • 1 GenCC submitter rates it definitive or strong
    • Dysplasia of the proximal femoral epiphysesAutosomal dominant

      COL2A1-related malformation of the hip ball causing early hip arthritis.

      • ClinGen rates the link definitive
      • 2 GenCC submitters rate it definitive or strong

  • Vitreoretinopathy

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

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How COL2A1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 12, with a bracket where COL2A1 sits. COL2A1 and 16 genes near it on chromosome 12, from 47,488,722 to 48,488,721.Chromosome 1212q13.11p13.33p13.32p13.31p13.2p13.1p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11q12q13.11q13.12q13.13q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.11q24.12q24.13q24.21q24.22q24.23q24.31q24.32q24.3347.6 Mb47.8 Mb48 Mb48.2 Mb48.4 MbRPAP3: 47,660,814–47,706,038, reverse strandRPAP3ENDOU: 47,709,734–47,725,567, reverse strandENDOURAPGEF3: 47,734,180–47,771,040, reverse strandRAPGEF3SLC48A1: 47,753,916–47,782,751, forward strandSLC48A1HDAC7: 47,782,722–47,833,132, reverse strandHDAC7VDR: 47,841,537–47,943,048, reverse strandVDRTMEM106C: 47,963,543–47,970,504, forward strandTMEM106CCOL2A1: 47,972,967–48,004,476, reverse strandCOL2A1SENP1: 48,039,784–48,106,316, reverse strandSENP1PFKM: 48,105,139–48,152,487, forward strandPFKMASB8: 48,147,789–48,181,213, reverse strandASB8CCDC184: 48,183,644–48,185,926, forward strandCCDC184OR10AD1: 48,202,339–48,203,292, reverse strandOR10AD1H1-7: 48,328,980–48,330,279, forward strandH1-7ZNF641: 48,337,180–48,351,414, reverse strandZNF641ANP32D: 48,472,559–48,473,622, forward strandANP32DLYLDT1: 48,482,498–48,496,524, forward strandLYLDT1Diagram of COL2A1: 54 exons on the reverse strand of chromosome 12Exon 54: 4 known disease-causing sitesExon 53: 7 known disease-causing sitesExon 52: 3 known disease-causing sitesExon 51: 8 known disease-causing sitesExon 50: 8 known disease-causing sitesExon 49: 8 known disease-causing sitesExon 48: 3 known disease-causing sitesExon 47: 6 known disease-causing sitesExon 46: 3 known disease-causing sitesExon 45: 5 known disease-causing sitesExon 44: 11 known disease-causing sitesExon 43: 10 known disease-causing sitesExon 42: 14 known disease-causing sitesExon 41: 3 known disease-causing sitesExon 40: 5 known disease-causing sitesExon 39: 8 known disease-causing sitesExon 38: 3 known disease-causing sitesExon 36: 6 known disease-causing sitesExon 35: 4 known disease-causing sitesExon 34: 4 known disease-causing sitesExon 33: 8 known disease-causing sitesExon 32: 2 known disease-causing sitesExon 31: 6 known disease-causing sitesExon 30: 8 known disease-causing sitesExon 29: 4 known disease-causing sitesExon 28: 3 known disease-causing sitesExon 27: 3 known disease-causing sitesExon 26: 2 known disease-causing sitesExon 25: 6 known disease-causing sitesExon 24: 6 known disease-causing sitesExon 23: 13 known disease-causing sitesExon 22: 1 known disease-causing siteExon 21: 7 known disease-causing sitesExon 20: 4 known disease-causing sitesExon 19: 5 known disease-causing sitesExon 18: 4 known disease-causing sitesExon 17: 6 known disease-causing sitesExon 16: 3 known disease-causing sitesExon 15: 1 known disease-causing siteExon 14: 6 known disease-causing sitesExon 13: 2 known disease-causing sitesExon 12: 1 known disease-causing siteExon 11: 2 known disease-causing sitesExon 10: 3 known disease-causing sitesExon 9: 4 known disease-causing sitesExon 8: 5 known disease-causing sitesExon 7: 7 known disease-causing sitesExon 6: 1 known disease-causing siteExon 2: 5 known disease-causing sitesExon 1: 2 known disease-causing sitesExon 54: 47,972,967–47,973,553, 587 basesExon 53: 47,974,089–47,974,331, 243 basesExon 52: 47,974,675–47,974,862, 188 basesExon 51: 47,975,317–47,975,605, 289 basesExon 50: 47,975,963–47,976,070, 108 basesExon 49: 47,976,514–47,976,567, 54 basesExon 48: 47,976,812–47,976,919, 108 basesExon 47: 47,977,102–47,977,155, 54 basesExon 46: 47,977,320–47,977,427, 108 basesExon 45: 47,977,600–47,977,653, 54 basesExon 44: 47,978,010–47,978,117, 108 basesExon 43: 47,978,291–47,978,398, 108 basesExon 42: 47,978,597–47,978,758, 162 basesExon 41: 47,979,511–47,979,564, 54 basesExon 40: 47,980,009–47,980,062, 54 basesExon 39: 47,980,554–47,980,661, 108 basesExon 38: 47,980,915–47,980,968, 54 basesExon 37: 47,981,343–47,981,396, 54 basesExon 36: 47,981,776–47,981,829, 54 basesExon 35: 47,982,107–47,982,160, 54 basesExon 34: 47,982,502–47,982,609, 108 basesExon 33: 47,982,848–47,982,946, 99 basesExon 32: 47,983,093–47,983,137, 45 basesExon 31: 47,983,385–47,983,438, 54 basesExon 30: 47,983,683–47,983,736, 54 basesExon 29: 47,984,087–47,984,140, 54 basesExon 28: 47,984,546–47,984,599, 54 basesExon 27: 47,984,995–47,985,093, 99 basesExon 26: 47,985,534–47,985,587, 54 basesExon 25: 47,985,728–47,985,826, 99 basesExon 24: 47,985,912–47,985,965, 54 basesExon 23: 47,986,336–47,986,443, 108 basesExon 22: 47,986,835–47,986,888, 54 basesExon 21: 47,987,078–47,987,176, 99 basesExon 20: 47,987,269–47,987,313, 45 basesExon 19: 47,987,611–47,987,709, 99 basesExon 18: 47,989,228–47,989,281, 54 basesExon 17: 47,989,761–47,989,805, 45 basesExon 16: 47,992,878–47,992,931, 54 basesExon 15: 47,993,458–47,993,502, 45 basesExon 14: 47,993,809–47,993,862, 54 basesExon 13: 47,993,994–47,994,047, 54 basesExon 12: 47,994,424–47,994,477, 54 basesExon 11: 47,995,255–47,995,308, 54 basesExon 10: 47,995,710–47,995,763, 54 basesExon 9: 47,995,875–47,995,919, 45 basesExon 8: 47,996,548–47,996,625, 78 basesExon 7: 47,997,606–47,997,707, 102 basesExon 6: 47,997,871–47,997,924, 54 basesExon 5: 47,998,032–47,998,064, 33 basesExon 4: 47,998,169–47,998,201, 33 basesExon 3: 47,998,415–47,998,431, 17 basesExon 2: 47,999,919–48,000,125, 207 basesExon 1: 48,004,237–48,004,476, 240 bases54504540353025201510515′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 5.1 kb of the gene's 31.5 kb; 4,464 of those bases code for the protein.

How a genome test reads COL2A1

321

positions in COL2A1 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 31.5 kb of COL2A1, introns included, not only the 5.1 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.). COL2A1 gene: collagen type II alpha 1 chain. Retrieved 17 October 2026, from https://dantelabs.com/genes/col2a1

Vancouver

Dante Labs. COL2A1 gene: collagen type II alpha 1 chain [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/col2a1

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