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

    Gene ID: 1280, updated on 16-Aug-2015
    Official Symbol
    COL2A1provided by HGNC
    Official Full Name
    collagen, type II, alpha 1provided by HGNC
    Primary source
    HGNC:HGNC:2200
    See related
    Ensembl:ENSG00000139219; HPRD:00361; 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
    See COL2A1 in Epigenomics, MapViewer
    Location:
    12q13.11
    Exon count:
    67
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) 12 NC_000012.12 (47972965..48025286, 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 uncharacterized LOC105369749 Neighboring gene vitamin D (1,25- dihydroxyvitamin D3) receptor Neighboring gene transmembrane protein 106C Neighboring gene uncharacterized LOC105369752 Neighboring gene uncharacterized LOC105369751 Neighboring gene uncharacterized LOC105369750 Neighboring gene SUMO1/sentrin specific peptidase 1 Neighboring gene ribosomal protein L37 pseudogene 19 Neighboring gene V-type proton ATPase subunit F pseudogene

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Achondrogenesis type 2
    MedGen: C0220685 OMIM: 200610 GeneReviews: Not available
    Compare labs
    Avascular necrosis of the head of femur
    MedGen: C0410480 OMIM: 608805 GeneReviews: Not available
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    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
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    Kniest dysplasia
    MedGen: C0265279 OMIM: 156550 GeneReviews: Not available
    Compare labs
    Osteoarthritis with mild chondrodysplasia
    MedGen: C1858079 OMIM: 604864 GeneReviews: Not available
    Compare labs
    Otospondylomegaepiphyseal dysplasia
    MedGen: C0432210 OMIM: 215150 GeneReviews: Not available
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    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
    Spondyloperipheral dysplasia
    MedGen: C0796173 OMIM: 271700 GeneReviews: Not available
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    Stickler syndrome type 1
    MedGen: C2020284 OMIM: 108300 GeneReviews: Stickler Syndrome
    Compare labs
    STICKLER SYNDROME, TYPE I, NONSYNDROMIC OCULAR
    MedGen: C1836080 OMIM: 609508 GeneReviews: Not available
    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
    • Amoebiasis, organism-specific biosystem (from KEGG)
      Amoebiasis, organism-specific biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
    • Amoebiasis, conserved biosystem (from KEGG)
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      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...
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      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 biosystem
      Endochondral Ossification
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
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    • Focal adhesion, organism-specific biosystem (from KEGG)
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    • Focal adhesion, conserved biosystem (from KEGG)
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    • 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...
    • Platelet activation, organism-specific biosystem (from KEGG)
      Platelet activation, organism-specific biosystemPlatelets play a key and beneficial role for primary hemostasis on the disruption of the integrity of vessel wall. Platelet adhesion and activation at sites of vascular wall injury is initiated by ad...
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    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC131516

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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
    axon guidance TAS
    Traceable Author Statement
    more info
     
    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 disassembly TAS
    Traceable Author Statement
    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
     
    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

    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, OTTHUMP00000195063, ENST00000380518, OTTHUMT00000313810
      Conserved Domains (3) summary
      pfam01391
      Location:801860
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:12521487
      COLFI; Fibrillar collagens C-terminal domain
      pfam00093
      Location:3489
      VWC; von Willebrand factor type C 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, OTTHUMP00000195071, ENST00000337299, OTTHUMT00000313827
      Conserved Domains (2) summary
      pfam01391
      Location:732791
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:11831418
      COLFI; Fibrillar collagens C-terminal domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p2 Primary Assembly

      Range
      47972965..48025286
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006719242.2XP_006719305.2  

      See identical proteins and their annotated locations for XP_006719305.2

      Conserved Domains (3) summary
      pfam01391
      Location:849908
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:13001535
      COLFI; Fibrillar collagens C-terminal domain
      pfam00093
      Location:81136
      VWC; von Willebrand factor type C domain
    2. XM_011537932.1XP_011536234.1  

      See identical proteins and their annotated locations for XP_011536234.1

      Conserved Domains (3) summary
      pfam01391
      Location:849908
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:13001535
      COLFI; Fibrillar collagens C-terminal domain
      pfam00093
      Location:81136
      VWC; von Willebrand factor type C domain
    3. XM_011537931.1XP_011536233.1  

      See identical proteins and their annotated locations for XP_011536233.1

      Conserved Domains (3) summary
      pfam01391
      Location:849908
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:13001535
      COLFI; Fibrillar collagens C-terminal domain
      pfam00093
      Location:81136
      VWC; von Willebrand factor type C domain
    4. XM_011537929.1XP_011536231.1  

      See identical proteins and their annotated locations for XP_011536231.1

      Conserved Domains (3) summary
      pfam01391
      Location:849908
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:13001535
      COLFI; Fibrillar collagens C-terminal domain
      pfam00093
      Location:81136
      VWC; von Willebrand factor type C domain
    5. XM_011537930.1XP_011536232.1  

      See identical proteins and their annotated locations for XP_011536232.1

      Conserved Domains (3) summary
      pfam01391
      Location:849908
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:13001535
      COLFI; Fibrillar collagens C-terminal domain
      pfam00093
      Location:81136
      VWC; von Willebrand factor type C domain
    6. XM_011537934.1XP_011536236.1  

      Conserved Domains (3) summary
      pfam01391
      Location:848907
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:12991534
      COLFI; Fibrillar collagens C-terminal domain
      pfam00093
      Location:81136
      VWC; von Willebrand factor type C domain
    7. XM_011537928.1XP_011536230.1  

      See identical proteins and their annotated locations for XP_011536230.1

      Conserved Domains (3) summary
      pfam01391
      Location:849908
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:13001535
      COLFI; Fibrillar collagens C-terminal domain
      pfam00093
      Location:81136
      VWC; von Willebrand factor type C domain
    8. XM_011537933.1XP_011536235.1  

      See identical proteins and their annotated locations for XP_011536235.1

      Conserved Domains (3) summary
      pfam01391
      Location:849908
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:13001535
      COLFI; Fibrillar collagens C-terminal domain
      pfam00093
      Location:81136
      VWC; von Willebrand factor type C domain
    9. XM_011537935.1XP_011536237.1  

      Conserved Domains (2) summary
      pfam01391
      Location:497556
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:9481183
      COLFI; Fibrillar collagens C-terminal domain

    Alternate CHM1_1.1

    Genomic

    1. NC_018923.2 Alternate CHM1_1.1

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