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Gene Review

COL9A1  -  collagen, type IX, alpha 1

Homo sapiens

Synonyms: Collagen alpha-1(IX) chain, DJ149L1.1.2, EDM6, MED, STL4
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Disease relevance of COL9A1


High impact information on COL9A1

  • We considered the COL9A1 gene, located on chromosome 6q13, to be a candidate gene on the basis of the structural association with collagen types II and XI and because of the high expression in the human inner ear indicated by cDNA microarray [5].
  • The analysis resulted in identification of three mutations in COMP and one in COL9A1, but none in the other two collagen IX genes [1].
  • Screening of COL9A1 for mutations in the two probands from the families in which this gene was not involved in the recombinations failed to identify any disease-causing mutations [1].
  • CONCLUSION: Our data suggest that susceptibility for hip OA is conferred within or close to the COL9A1 gene in linkage disequilibrium with the COL9A1 509-8B2 marker [2].
  • Regulation of human COL9A1 gene expression. Activation of the proximal promoter region by SOX9 [3].

Biological context of COL9A1

  • The COL9A1 gene is about 90 kb and consists of 38 exons [6].
  • The COL9A1 gene contains two promoter regions, one driving expression of a long alpha1(IX) chain in cartilage (upstream) and one driving expression of a shorter chain in the cornea and vitreous (downstream) [3].
  • A general drop of methylation in COL9A1 was apparent in tumors, when compared with blood and healthy breast tissue [7].
  • Previously, COL19A1 was mapped to human chromosome 6q12-q14, where COL9A1 is also located [8].
  • We identified and then genotyped twenty common single nucleotide polymorphisms (SNPs) from within COL9A1 in the 146 probands from our female THR-families and in 215 age-matched female controls [9].

Anatomical context of COL9A1

  • The sequence encoded by exon 7, predicted from human COL9A1, is absent from both short and long forms of alpha1(IX) from bovine nucleus pulposus and articular cartilage [10].
  • RT-PCR analysis using primers specific to COL9A1 isoforms 1 and 2 detected expression of both isoforms in human fetal cochlea [11].

Other interactions of COL9A1

  • Here we report the complete structure for the human COL9A1 and the complete sequence for the human COL9A2 genes [6].
  • Type IX collagen is composed of three polypeptides derived from the human genes COL9A1, COL9A2, and COL9A3 that assemble to form a mature collagen molecule with the structure alpha 1(IX)alpha 2(IX)alpha 3(IX) [12].
  • Association of COL1A2, COL2A1 and COL9A1 and primary osteoarthritis in a founder population [13].
  • The COL9A1 locus shows no recombination with the marker D6Z1 (Z = 27.61 at theta = O) and identifies the most likely locus order of KRAS1P-[D6Z1-COL9A1]-D6S30 [4].

Analytical, diagnostic and therapeutic context of COL9A1


  1. A mutation in COL9A1 causes multiple epiphyseal dysplasia: further evidence for locus heterogeneity. Czarny-Ratajczak, M., Lohiniva, J., Rogala, P., Kozlowski, K., Perälä, M., Carter, L., Spector, T.D., Kolodziej, L., Seppänen, U., Glazar, R., Królewski, J., Latos-Bielenska, A., Ala-Kokko, L. Am. J. Hum. Genet. (2001) [Pubmed]
  2. Evidence for a role of the genomic region of the gene encoding for the alpha1 chain of type IX collagen (COL9A1) in hip osteoarthritis: A population-based study. Alizadeh, B.Z., Njajou, O.T., Bijkerk, C., Meulenbelt, I., Wildt, S.C., Hofman, A., Pols, H.A., Slagboom, P.E., Duijn, C.M. Arthritis Rheum. (2005) [Pubmed]
  3. Regulation of human COL9A1 gene expression. Activation of the proximal promoter region by SOX9. Zhang, P., Jimenez, S.A., Stokes, D.G. J. Biol. Chem. (2003) [Pubmed]
  4. Physical and linkage mapping of the human and murine genes for the alpha 1 chain of type IX collagen (COL9A1). Warman, M.L., Tiller, G.E., Polumbo, P.A., Seldin, M.F., Rochelle, J.M., Knoll, J.H., Cheng, S.D., Olsen, B.R. Genomics (1993) [Pubmed]
  5. A new autosomal recessive form of Stickler syndrome is caused by a mutation in the COL9A1 gene. Van Camp, G., Snoeckx, R.L., Hilgert, N., van den Ende, J., Fukuoka, H., Wagatsuma, M., Suzuki, H., Smets, R.M., Vanhoenacker, F., Declau, F., Van de Heyning, P., Usami, S. Am. J. Hum. Genet. (2006) [Pubmed]
  6. Human COL9A1 and COL9A2 genes. Two genes of 90 and 15 kb code for similar polypeptides of the same collagen molecule. Pihlajamaa, T., Vuoristo, M.M., Annunen, S., Perälä, M., Prockop, D.J., Ala-Kokko, L. Matrix Biol. (1998) [Pubmed]
  7. Microarray-based survey of CpG islands identifies concurrent hyper- and hypomethylation patterns in tissues derived from patients with breast cancer. Piotrowski, A., Benetkiewicz, M., Menzel, U., de Ståhl, T.D., Mantripragada, K., Grigelionis, G., Buckley, P.G., Jankowski, M., Hoffman, J., Bała, D., Srutek, E., Laskowski, R., Zegarski, W., Dumanski, J.P. Genes Chromosomes Cancer (2006) [Pubmed]
  8. Structure of the human type XIX collagen (COL19A1) gene, which suggests it has arisen from an ancestor gene of the FACIT family. Khaleduzzaman, M., Sumiyoshi, H., Ueki, Y., Inoguchi, K., Ninomiya, Y., Yoshioka, H. Genomics (1997) [Pubmed]
  9. Finer linkage mapping of a primary hip osteoarthritis susceptibility locus on chromosome 6. Loughlin, J., Mustafa, Z., Dowling, B., Southam, L., Marcelline, L., Räinä, S.S., Ala-Kokko, L., Chapman, K. Eur. J. Hum. Genet. (2002) [Pubmed]
  10. Intervertebral disc collagen. Usage of the short form of the alpha1(IX) chain in bovine nucleus pulposus. Wu, J.J., Eyre, D.R. J. Biol. Chem. (2003) [Pubmed]
  11. Characterization of an abundant COL9A1 transcript in the cochlea with a novel 3' UTR: Expression studies and detection of miRNA target sequence. Sivakumaran, T.A., Resendes, B.L., Robertson, N.G., Giersch, A.B., Morton, C.C. J. Assoc. Res. Otolaryngol. (2006) [Pubmed]
  12. Molecular cloning of the alpha 3 chain of human type IX collagen: linkage of the gene COL9A3 to chromosome 20q13.3. Brewton, R.G., Wood, B.M., Ren, Z.X., Gong, Y., Tiller, G.E., Warman, M.L., Lee, B., Horton, W.A., Olsen, B.R., Baker, J.R. Genomics (1995) [Pubmed]
  13. Association of COL1A2, COL2A1 and COL9A1 and primary osteoarthritis in a founder population. Snelgrove, T.A., Peddle, L.J., Stone, C., Nofball, F., Peddle, D., Squire, D., Rockwood, P., Martin, R., Tobin, Y., Gladney, N., Rahman, P. Clin. Genet. (2005) [Pubmed]
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