U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

COL9A2 collagen type IX alpha 2 chain [ Homo sapiens (human) ]

Gene ID: 1298, updated on 5-Mar-2024

Summary

Go to the top of the page Help
Official Symbol
COL9A2provided by HGNC
Official Full Name
collagen type IX alpha 2 chainprovided by HGNC
Primary source
HGNC:HGNC:2218
See related
Ensembl:ENSG00000049089 MIM:120260; AllianceGenome:HGNC:2218
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MED; EDM2; STL5; DJ39G22.4
Summary
This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]
Expression
Broad expression in prostate (RPKM 5.8), brain (RPKM 5.5) and 20 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See COL9A2 in Genome Data Viewer
Location:
1p34.2
Exon count:
35
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (40300489..40317286, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (40169995..40187371, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40766161..40782958, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 837 Neighboring gene transmembrane and coiled-coil domains 2 Neighboring gene zinc metallopeptidase STE24 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 723 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 724 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:40781816-40782452 and GRCh37_chr1:40782453-40783089 Neighboring gene ribosomal protein L21 pseudogene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 844 Neighboring gene small ArfGAP2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 727 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:40839657-40840156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 845

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Autosomal recessive Stickler syndrome associated with homozygous mutations in the COL9A2 gene. Kjellström U, et al. Ophthalmic Genet, 2021 Apr. PMID 33356723
  2. Association between COL9A2 Gln326Arg mutations and the development of intervertebral disc disease in a Chinese population. Meng T, et al. Genet Mol Res, 2016 Dec 19. PMID 28002589
  3. Meta-analysis of the association between COL9A2 genetic polymorphisms and lumbar disc disease susceptibility. Zhang Z, et al. Spine (Phila Pa 1976), 2014 Sep 15. PMID 24983932
  4. [Analysis of COL9A2 gene mutations in a Chinese Han population with pathological myopia]. Chen R, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2014 Apr. PMID 24711017
  5. A loss of function mutation in the COL9A2 gene causes autosomal recessive Stickler syndrome. Baker S, et al. Am J Med Genet A, 2011 Jul. PMID 21671392

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Autosomal recessive Stickler syndrome associated with homozygous mutations in the COL9A2 gene.
    Title: Autosomal recessive Stickler syndrome associated with homozygous mutations in the COL9A2 gene.
  2. Lack of association between COL1A1 and COL9A2 single nucleotide polymorphisms and intervertebral disc degeneration.
    Title: Lack of association between COL1A1 and COL9A2 single nucleotide polymorphisms and intervertebral disc degeneration.
  3. Homozygous type IX collagen variants, COL9A1, COL9A2, and COL9A3, causing recessive Stickler syndrome, expand the disease phenotype.
    Title: Homozygous Type IX collagen variants (COL9A1, COL9A2, and COL9A3) causing recessive Stickler syndrome-Expanding the phenotype.
  4. No significant association was found between COL9A2 polymorphism rs7533552 and the risk of lumbar disc degeneration.
    Title: Association of CILP, COL9A2 and MMP3 Gene Polymorphisms with Lumbar Disc Degeneration in an Indian Population.
  5. rs12077871, rs12722877, and rs7533552 variants in COL9A2 were not significantly associated with a predisposition to lumbar disc degeneration.
    Title: Collagen IX gene polymorphisms and lumbar disc degeneration: a systematic review and meta-analysis.
  6. Study provides evidence that the COL9A2 Gln326Arg polymorphism contributes to the development of intervertebral disc disease in the Chinese population.
    Title: Association between COL9A2 Gln326Arg mutations and the development of intervertebral disc disease in a Chinese population.
  7. Meta-analysis. Our results suggest that the COL9A2 rs12077871, rs12722877, and rs7533552 polymorphisms may not be associated with lumbar disc disease.
    Title: Meta-analysis of the association between COL9A2 genetic polymorphisms and lumbar disc disease susceptibility.
  8. Two novel mutations, c.143G>C in exon 2 and c.884G>A in exon 17 of the COL9A2 gene, may contribute to the development of pathological myopia.
    Title: [Analysis of COL9A2 gene mutations in a Chinese Han population with pathological myopia].
  9. The allelic variants in the collagen IX genes - COL9A2 and COL9A3 have been identified as genetic risk factors for intervertebral disc disease--{review}
    Title: The role of polymorphisms of genes encoding collagen IX and XI in lumbar disc disease.
  10. The NC2 domain of type IX collagen determines the chain composition but also the chain register of the triple helix.
    Title: The NC2 domain of type IX collagen determines the chain register of the triple helix.
Submit: New GeneRIF Correction See all GeneRIFs (27)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated 2013-10-09)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated 2013-10-09)

ClinGen Genome Curation Page

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables extracellular matrix structural constituent conferring tensile strength IBA
Inferred from Biological aspect of Ancestor
more info
  
enables extracellular matrix structural constituent conferring tensile strength IC
Inferred by Curator
more info
 PubMed 
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in skeletal system development TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of collagen type IX trimer IDA
Inferred from Direct Assay
more info
 PubMed 
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
located_in extracellular region TAS
Traceable Author Statement
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

Go to the top of the page Help
Preferred Names
collagen alpha-2(IX) chain
Names
alpha 2 type IX collagen
collagen IX, alpha-2 polypeptide
collagen, type IX, alpha 2

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008031.1 RefSeqGene

    Range
    4982..21779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001852.4 → NP_001843.1  collagen alpha-2(IX) chain precursor

    See identical proteins and their annotated locations for NP_001843.1

    Status: REVIEWED

    Source sequence(s)
    BC136326, CB305733, CD722372
    Consensus CDS
    CCDS450.1
    UniProtKB/Swiss-Prot
    B2RMP9, Q14055
    Related
    ENSP00000361834.3, ENST00000372748.8
    Conserved Domains (1) summary
    pfam01391
    Location:259 → 316
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    40300489..40317286 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000332.2 → XP_016855821.1  collagen alpha-2(IX) chain isoform X1

    Conserved Domains (1) summary
    pfam01391
    Location:263 → 320
    Collagen; Collagen triple helix repeat (20 copies)

  2. XM_011540715.3 → XP_011539017.1  collagen alpha-2(IX) chain isoform X2

    See identical proteins and their annotated locations for XP_011539017.1

    Conserved Domains (1) summary
    pfam01391
    Location:169 → 226
    Collagen; Collagen triple helix repeat (20 copies)

  3. XM_017000333.2 → XP_016855822.1  collagen alpha-2(IX) chain isoform X3

    Conserved Domains (1) summary
    pfam01391
    Location:165 → 222
    Collagen; Collagen triple helix repeat (20 copies)

  4. XM_011540716.3 → XP_011539018.1  collagen alpha-2(IX) chain isoform X2

    See identical proteins and their annotated locations for XP_011539018.1

    Conserved Domains (1) summary
    pfam01391
    Location:169 → 226
    Collagen; Collagen triple helix repeat (20 copies)

  5. XM_047446392.1 → XP_047302348.1  collagen alpha-2(IX) chain isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    40169995..40187371 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334467.1 → XP_054190442.1  collagen alpha-2(IX) chain isoform X5

  2. XM_054334466.1 → XP_054190441.1  collagen alpha-2(IX) chain isoform X1

  3. XM_054334469.1 → XP_054190444.1  collagen alpha-2(IX) chain isoform X2

  4. XM_054334468.1 → XP_054190443.1  collagen alpha-2(IX) chain isoform X2

  5. XM_054334470.1 → XP_054190445.1  collagen alpha-2(IX) chain isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q14055.2 GenPept UniProtKB/Swiss-Prot:Q14055

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Medical
Molecular Biology Databases
Research Materials
Tools
Miscellaneous