Format

Send to:

Choose Destination

Links from PubMed

    • Showing Current items.

    COL2A1 collagen type II alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1280, updated on 22-Jul-2017
    Official Symbol
    COL2A1provided by HGNC
    Official Full Name
    collagen type II alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2200
    See related
    Ensembl:ENSG00000139219 MIM:120140; Vega:OTTHUMG00000149896
    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
    AOM; ANFH; SEDC; STL1; COL11A3
    Summary
    This gene encodes the alpha-1 chain of type II collagen, a fibrillar collagen found in cartilage and the vitreous humor of the eye. Mutations in this gene are associated with achondrogenesis, chondrodysplasia, early onset familial osteoarthritis, SED congenita, Langer-Saldino achondrogenesis, Kniest dysplasia, Stickler syndrome type I, and spondyloepimetaphyseal dysplasia Strudwick type. In addition, defects in processing chondrocalcin, a calcium binding protein that is the C-propeptide of this collagen molecule, are also associated with chondrodysplasia. There are two transcripts identified for this gene. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    12q13.11
    Exon count:
    57
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 12 NC_000012.12 (47972965..48006212, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (48366748..48398285, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene vitamin D receptor Neighboring gene transmembrane protein 106C Neighboring gene uncharacterized LOC105369752 Neighboring gene uncharacterized LOC105369750 Neighboring gene SUMO1/sentrin specific peptidase 1 Neighboring gene ribosomal protein L37 pseudogene 19

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Achondrogenesis, type II
    MedGen: C0220685 OMIM: 200610 GeneReviews: Not available
    Compare labs
    Avascular necrosis of the head of femur
    MedGen: C0410480 OMIM: 608805 GeneReviews: Not available
    Compare labs
    Coxa plana
    MedGen: C0023234 OMIM: 150600 GeneReviews: Not available
    Compare labs
    Czech dysplasia metatarsal type
    MedGen: C1836683 OMIM: 609162 GeneReviews: Not available
    Compare labs
    Epiphyseal dysplasia, multiple, with myopia and conductive deafness
    MedGen: C1851536 OMIM: 132450 GeneReviews: Not available
    Compare labs
    Kniest dysplasia
    MedGen: C0265279 OMIM: 156550 GeneReviews: Not available
    Compare labs
    not provided
    MedGen: C1836080 OMIM: 609508 GeneReviews: Not available
    not available
    Osteoarthritis with mild chondrodysplasia
    MedGen: C1858079 OMIM: 604864 GeneReviews: Not available
    Compare labs
    Otospondylomegaepiphyseal dysplasia
    MedGen: C0432210 OMIM: 215150 GeneReviews: Not available
    Compare labs
    Platyspondylic lethal skeletal dysplasia Torrance type
    MedGen: C1835437 OMIM: 151210 GeneReviews: Not available
    Compare labs
    Spondyloepimetaphyseal dysplasia Strudwick type
    MedGen: C0700635 OMIM: 184250 GeneReviews: Not available
    Compare labs
    Spondyloepiphyseal dysplasia congenita
    MedGen: C0038015 OMIM: 183900 GeneReviews: Not available
    Compare labs
    Spondyloepiphyseal dysplasia, stanescu type
    MedGen: C4225273 OMIM: 616583 GeneReviews: Not available
    Compare labs
    Spondyloperipheral dysplasia
    MedGen: C0796173 OMIM: 271700 GeneReviews: Not available
    Compare labs
    Stickler syndrome type 1
    MedGen: C2020284 OMIM: 108300 GeneReviews: Stickler Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2012-02-23)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2012-02-23)

    ClinGen Genome Curation PagePubMed
    • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
      Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
    • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
      Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
    • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
      Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
    • Collagen formation, organism-specific biosystem (from REACTOME)
      Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
    • ECM-receptor interaction, organism-specific biosystem (from KEGG)
      ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • ECM-receptor interaction, conserved biosystem (from KEGG)
      ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • Endochondral Ossification, organism-specific biosystem (from WikiPathways)
      Endochondral Ossification, organism-specific biosystemEndochondral ossification is the process by which the embryonic cartilaginous model of most bones contributes to longitudinal growth and is gradually replaced by bone. During endochondral ossificatio...
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
      Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
    • Focal Adhesion, organism-specific biosystem (from WikiPathways)
      Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • Focal adhesion, organism-specific biosystem (from KEGG)
      Focal adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • Focal adhesion, conserved biosystem (from KEGG)
      Focal adhesion, conserved biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • Neural Crest Differentiation, organism-specific biosystem (from WikiPathways)
      Neural Crest Differentiation, organism-specific biosystemGene regulatory network model of cranial neural crest cell (CNCC) development, adaped from PMID: 19575671. Most interactions in the model are proposed to regulate transcription of core factors involv...
    • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
      PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
      PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • Protein digestion and absorption, organism-specific biosystem (from KEGG)
      Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • Protein digestion and absorption, conserved biosystem (from KEGG)
      Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • Simplified Interaction Map Between LOXL4 and Oxidative Stress Pathway, organism-specific biosystem (from WikiPathways)
      Simplified Interaction Map Between LOXL4 and Oxidative Stress Pathway, organism-specific biosystemThis pathway Involved in chemo-resistance of cells in bladder cancer begins with LOXL2 activation of CDC37 and COL2A1. COL2A1 activates the complex NRF1/2 and two other complexes that trigger RTK/MAP...
    • Spinal Cord Injury, organism-specific biosystem (from WikiPathways)
      Spinal Cord Injury, organism-specific biosystemThis pathway provides an overview of cell types, therapeutic targets, drugs, new proposed targets and pathways implicated in spinal cord injury. Spinal cord injury is a complex multistep process that...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC131516

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    MHC class II protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    extracellular matrix structural constituent conferring tensile strength IC
    Inferred by Curator
    more info
    PubMed 
    identical protein binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    platelet-derived growth factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    cartilage condensation IEA
    Inferred from Electronic Annotation
    more info
     
    cartilage development TAS
    Traceable Author Statement
    more info
    PubMed 
    cartilage development involved in endochondral bone morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to BMP stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    central nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    chondrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    collagen catabolic process TAS
    Traceable Author Statement
    more info
     
    collagen fibril organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    embryonic skeletal joint morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    endochondral ossification IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
     
    heart morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    inner ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    limb bud formation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IEA
    Inferred from Electronic Annotation
    more info
     
    notochord development IEA
    Inferred from Electronic Annotation
    more info
     
    otic vesicle development IEA
    Inferred from Electronic Annotation
    more info
     
    palate development IEA
    Inferred from Electronic Annotation
    more info
     
    proteoglycan metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of immune response TAS
    Traceable Author Statement
    more info
     
    sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    tissue homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    visual perception IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    basement membrane IEA
    Inferred from Electronic Annotation
    more info
     
    collagen type II trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular region TAS
    Traceable Author Statement
    more info
     
    extracellular space IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    collagen alpha-1(II) chain
    Names
    alpha-1 type II collagen
    arthroophthalmopathy, progressive (Stickler syndrome)
    cartilage collagen
    chondrocalcin
    collagen II, alpha-1 polypeptide
    collagen, type II, alpha 1

    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_008072.1 RefSeqGene

      Range
      5001..36538
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001844.4NP_001835.3  collagen alpha-1(II) chain isoform 1 precursor

      See identical proteins and their annotated locations for NP_001835.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      AC004801
      Consensus CDS
      CCDS41778.1
      UniProtKB/Swiss-Prot
      P02458
      Related
      ENSP00000369889.3, OTTHUMP00000195063, ENST00000380518.7, OTTHUMT00000313810
      Conserved Domains (3) summary
      pfam01391
      Location:801860
      Collagen; Collagen triple helix repeat (20 copies)
      pfam00093
      Location:3489
      VWC; von Willebrand factor type C domain
      pfam01410
      Location:12541486
      COLFI; Fibrillar collagen C-terminal domain
    2. NM_033150.2NP_149162.2  collagen alpha-1(II) chain isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in a shorter protein. The resulting protein (isoform 2) lacks the von Willebrand factor type C (VWC) domain, compared to isoform 1.
      Source sequence(s)
      AC004801
      Consensus CDS
      CCDS8759.1
      UniProtKB/Swiss-Prot
      P02458
      Related
      ENSP00000338213.6, OTTHUMP00000195071, ENST00000337299.6, OTTHUMT00000313827
      Conserved Domains (2) summary
      pfam01391
      Location:732791
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:11851417
      COLFI; Fibrillar collagen C-terminal domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p7 Primary Assembly

      Range
      47972965..48006212 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017018830.1XP_016874319.1  collagen alpha-1(II) chain isoform X3

    2. XM_017018829.1XP_016874318.1  collagen alpha-1(II) chain isoform X2

      Conserved Domains (3) summary
      pfam01391
      Location:848907
      Collagen; Collagen triple helix repeat (20 copies)
      pfam00093
      Location:81136
      VWC; von Willebrand factor type C domain
      pfam01410
      Location:13011533
      COLFI; Fibrillar collagen C-terminal domain
    3. XM_017018828.1XP_016874317.1  collagen alpha-1(II) chain isoform X1

      Conserved Domains (3) summary
      pfam01391
      Location:849908
      Collagen; Collagen triple helix repeat (20 copies)
      pfam00093
      Location:81136
      VWC; von Willebrand factor type C domain
      pfam01410
      Location:13021534
      COLFI; Fibrillar collagen C-terminal domain
    4. XM_017018831.1XP_016874320.1  collagen alpha-1(II) chain isoform X4

    Alternate CHM1_1.1

    Genomic

    1. NC_018923.2 Alternate CHM1_1.1

      Range
      48332620..48364163 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center