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

    Gene ID: 1298, updated on 10-Dec-2024

    Summary

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    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
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    Genomic context

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    See COL9A2 in Genome Data Viewer
    Location:
    1p34.2
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (40300489..40317286, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (40169995..40187371, complement)
    RS_2024_09 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. 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
    2. Identification of novel pro-alpha2(IX) collagen gene mutations in two families with distinctive oligo-epiphyseal forms of multiple epiphyseal dysplasia. Holden P, et al. Am J Hum Genet, 1999 Jul. PMID 10364514, Free PMC Article
    3. An allele of COL9A2 associated with intervertebral disc disease. Annunen S, et al. Science, 1999 Jul 16. PMID 10411504
    4. Expression of the Trp2 allele of COL9A2 is associated with alterations in the mechanical properties of human intervertebral discs. Aladin DM, et al. Spine (Phila Pa 1976), 2007 Dec 1. PMID 18246003
    5. Candidate gene association study of magnetic resonance imaging-based hip osteoarthritis (OA): evidence for COL9A2 gene as a common predisposing factor for hip OA and lumbar disc degeneration. Näkki A, et al. J Rheumatol, 2011 Apr. PMID 21159828

    See all (67) 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

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

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Epiphyseal dysplasia, multiple, 2
    MedGen: C1838429 OMIM: 600204 GeneReviews: Multiple Epiphyseal Dysplasia, Dominant
    		not available
    Stickler syndrome, type 5
    MedGen: C3280342 OMIM: 614284 GeneReviews: Stickler Syndrome
    		not available

    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

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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 
    part_of collagen type IX trimer IPI
    Inferred from Physical Interaction
    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

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    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)

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    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_2024_08

    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.

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