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    COL9A1 collagen type IX alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1297, updated on 9-Dec-2024

    Summary

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    Official Symbol
    COL9A1provided by HGNC
    Official Full Name
    collagen type IX alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2217
    See related
    Ensembl:ENSG00000112280 MIM:120210; AllianceGenome:HGNC:2217
    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; EDM6; STL4; DJ149L1.1.2
    Summary
    This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in prostate (RPKM 6.1), testis (RPKM 1.3) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See COL9A1 in Genome Data Viewer
    Location:
    6q13
    Exon count:
    43
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (70215061..70303084, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (71395620..71483638, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (70924764..71012787, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene LMBR1 domain containing 1 Neighboring gene uncharacterized LOC124901337 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 42 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70505853-70506409 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70506410-70506965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17316 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:70597939-70598122 Neighboring gene NANOG hESC enhancer GRCh37_chr6:70623798-70624319 Neighboring gene collagen type XIX alpha 1 chain Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:70627263-70628462 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:70845103-70845604 Neighboring gene ribosomal protein L37 pseudogene 15 Neighboring gene MPRA-validated peak5887 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24730 Neighboring gene uncharacterized LOC105377848 Neighboring gene Sharpr-MPRA regulatory region 4194 Neighboring gene uncharacterized LOC105377847 Neighboring gene long intergenic non-protein coding RNA 1610

    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. Crystal structure of the N-terminal NC4 domain of collagen IX, a zinc binding member of the laminin-neurexin-sex hormone binding globulin (LNS) domain family. Leppänen VM, et al. J Biol Chem, 2007 Aug 10. PMID 17553797
    2. [Expression of COL9A1 gene and its polymorphism in children with idiopathic congenital talipes equinovarus]. Liu LY, et al. Zhongguo Dang Dai Er Ke Za Zhi, 2011 Jun. PMID 21672422
    3. Association of reduced type IX collagen gene expression in human osteoarthritic chondrocytes with epigenetic silencing by DNA hypermethylation. Imagawa K, et al. Arthritis Rheumatol, 2014 Nov. PMID 25048791, Free PMC Article
    4. COL9A1 gene polymorphism is associated with Kashin-Beck disease in a northwest Chinese Han population. Shi X, et al. PLoS One, 2015. PMID 25774918, Free PMC Article
    5. Regulation of human COL9A1 gene expression. Activation of the proximal promoter region by SOX9. Zhang P, et al. J Biol Chem, 2003 Jan 3. PMID 12399468

    See all (64) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Relationship of COL9A1 and SOX9 Genes with Genetic Susceptibility of Postmenopausal Osteoporosis.
      Title: Relationship of COL9A1 and SOX9 Genes with Genetic Susceptibility of Postmenopausal Osteoporosis.
    2. Gene Environment Interactions Between the COL9A1 Gene and Maternal Drinking of Alcohol Contribute to the Risk of Congenital Talipes Equinovarus.
      Title: Gene Environment Interactions Between the COL9A1 Gene and Maternal Drinking of Alcohol Contribute to the Risk of Congenital Talipes Equinovarus.
    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. The present study emphasizes the importance of exome-wide copy number variation analysis in molecular diagnosis and provides supporting evidence to associate COL9A1 with autosomal recessive non-syndromic HL.
      Title: Exome-wide copy number variation analysis identifies a COL9A1 in frame deletion that is associated with hearing loss.
    5. Two tagSNPs, rs28647489 in FAT1 gene and rs550675 in COL9A1 gene, were significantly associated with the risk of oral malignancy.
      Title: Variants in FAT1 and COL9A1 genes in male population with or without substance use to assess the risk factors for oral malignancy.
    6. Whole-genome sequencing reveals possible role of deleterious mutation of COL9A1 in ossification of the posterior longitudinal ligament of the thoracic spine in the Chinese population.
      Title: Whole-genome sequencing reveals novel genes in ossification of the posterior longitudinal ligament of the thoracic spine in the Chinese population.
    7. the COL9A1 rs35470562 variant may contribute to congenital talipes equinovarus susceptibility in the Chinese population examined.
      Title: Role of COL9A1 genetic polymorphisms in development of congenital talipes equinovarus in a Chinese population.
    8. We observed a significant association between rs6910140 of COL9A1 and KBD, suggesting a role of COL9A1 in the development of KBD.
      Title: COL9A1 gene polymorphism is associated with Kashin-Beck disease in a northwest Chinese Han population.
    9. The study demonstrated that hypermethylation is associated with down-regulation of COL9A1 expression in osteoarthritic (OA) cartilage and highlights the pivotal role of epigenetics in OA.
      Title: Association of reduced type IX collagen gene expression in human osteoarthritic chondrocytes with epigenetic silencing by DNA hypermethylation.
    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

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2013-11-06)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2013-11-06)

    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

    Clone Names

    • FLJ40263

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables carbohydrate binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables carbohydrate binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 animal organ morphogenesis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen type IX trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 
    part_of collagen type IX trimer TAS
    Traceable Author Statement
    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-1(IX) chain
    Names
    alpha-1(IX) collagen chain
    cartilage-specific short collagen
    collagen IX, alpha-1 polypeptide
    collagen, type IX, alpha 1

    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_011654.1 RefSeqGene

      Range
      5000..91958
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001377289.1 → NP_001364218.1  collagen alpha-1(IX) chain isoform 3 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080275, AL160262
      Consensus CDS
      CCDS93940.1
      UniProtKB/TrEMBL
      A0A804HIB6
      Related
      ENSP00000506990.1, ENST00000683980.2
      Conserved Domains (1) summary
      pfam01391
      Location:253 → 309
      Collagen; Collagen triple helix repeat (20 copies)

    2. NM_001377290.1 → NP_001364219.1  collagen alpha-1(IX) chain isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080275, AL160262
      Related
      ENSP00000508147.1, ENST00000683758.1
      Conserved Domains (1) summary
      pfam01391
      Location:244 → 298
      Collagen; Collagen triple helix repeat (20 copies)

    3. NM_001377291.1 → NP_001364220.1  collagen alpha-1(IX) chain isoform 5 precursor

      Status: REVIEWED

      Source sequence(s)
      AL080275
      Consensus CDS
      CCDS93941.1
      Related
      ENSP00000359527.3, ENST00000370496.3
      Conserved Domains (1) summary
      smart00210
      Location:50 → 244
      TSPN; Thrombospondin N-terminal -like domains

    4. NM_001851.6 → NP_001842.3  collagen alpha-1(IX) chain isoform 1 precursor

      See identical proteins and their annotated locations for NP_001842.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1, also known as the long form).
      Source sequence(s)
      AL080275, AL160262
      Consensus CDS
      CCDS4971.1
      UniProtKB/Swiss-Prot
      P20849, Q13699, Q13700, Q5TF52, Q6P467, Q96BM8, Q99225, Q9H151, Q9H152, Q9Y6P2, Q9Y6P3
      Related
      ENSP00000349790.6, ENST00000357250.11
      Conserved Domains (2) summary
      pfam01391
      Location:493 → 552
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50 → 244
      TSPN; Thrombospondin N-terminal -like domains

    5. NM_078485.4 → NP_511040.2  collagen alpha-1(IX) chain isoform 2 precursor

      See identical proteins and their annotated locations for NP_511040.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks several exons in the 5' coding region, compared to variant 1. These differences cause translation initiation at a unique AUG and an isoform (2, also known as the short form) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AL160262, AW021120, BC063646, BF196880, CA392556, X54412
      Consensus CDS
      CCDS47447.1
      UniProtKB/Swiss-Prot
      P20849
      Related
      ENSP00000315252.7, ENST00000320755.12
      Conserved Domains (1) summary
      pfam01391
      Location:250 → 309
      Collagen; Collagen triple helix repeat (20 copies)

    RNA

    1. NR_165185.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080275, AL160262

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      70215061..70303084 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011535429.4 → XP_011533731.1  collagen alpha-1(IX) chain isoform X1

      Conserved Domains (2) summary
      pfam01391
      Location:493 → 552
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50 → 244
      TSPN; Thrombospondin N-terminal -like domains

    2. XM_017010246.3 → XP_016865735.1  collagen alpha-1(IX) chain isoform X2

    3. XM_047418180.1 → XP_047274136.1  collagen alpha-1(IX) chain isoform X4

    4. XM_047418179.1 → XP_047274135.1  collagen alpha-1(IX) chain isoform X3

    5. XM_017010247.3 → XP_016865736.1  collagen alpha-1(IX) chain isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      71395620..71483638 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354214.1 → XP_054210189.1  collagen alpha-1(IX) chain isoform X1

    2. XM_054354215.1 → XP_054210190.1  collagen alpha-1(IX) chain isoform X2

    3. XM_054354217.1 → XP_054210192.1  collagen alpha-1(IX) chain isoform X4

    4. XM_054354216.1 → XP_054210191.1  collagen alpha-1(IX) chain isoform X3

    5. XM_054354218.1 → XP_054210193.1  collagen alpha-1(IX) chain isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P20849.3 GenPept UniProtKB/Swiss-Prot:P20849

    Gene LinkOut

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

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