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

    Gene ID: 1280, updated on 1-Mar-2024

    Summary

    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; AllianceGenome:HGNC:2200
    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]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL2A1 in Genome Data Viewer
    Location:
    12q13.11
    Exon count:
    57
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (47972967..48006212, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (47934691..47967944, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (48366750..48398259, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48236992-48237565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48237566-48238138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48239663-48240164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48262276-48262776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6272 Neighboring gene vitamin D receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48276324-48276836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6273 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48329073-48329573 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:48353651-48354181 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:48367908-48368120 Neighboring gene transmembrane protein 106C Neighboring gene uncharacterized LOC105369752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48375074-48375619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6277 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48404129-48404630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48404631-48405130 Neighboring gene uncharacterized LOC105369750 Neighboring gene uncharacterized LOC124902927 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr12:48415301-48416292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48431351-48432291 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:48439137-48440336 Neighboring gene SUMO specific peptidase 1 Neighboring gene ribosomal protein L37 pseudogene 19

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Achondrogenesis type II Compare labs
    Avascular necrosis of femoral head, primary, 1 Compare labs
    Czech dysplasia, metatarsal type
    MedGen: C1836683 OMIM: 609162 GeneReviews: Not available
    Compare labs
    Kniest dysplasia Compare labs
    Legg-Calve-Perthes disease
    MedGen: C0023234 OMIM: 150600 GeneReviews: Not available
    Compare labs
    Multiple epiphyseal dysplasia, Beighton type
    MedGen: C1851536 OMIM: 132450 GeneReviews: Not available
    Compare labs
    Namaqualand hip dysplasia Compare labs
    Platyspondylic dysplasia, Torrance type Compare labs
    Spondyloepimetaphyseal dysplasia, Strudwick type Compare labs
    Spondyloepiphyseal dysplasia congenita Compare labs
    Spondyloepiphyseal dysplasia, Stanescu type
    MedGen: C4225273 OMIM: 616583 GeneReviews: Not available
    Compare labs
    Spondylometaphyseal dysplasia - Sutcliffe type Compare labs
    Spondyloperipheral dysplasia Compare labs
    Stickler syndrome type 1 Compare labs
    Stickler syndrome, type I, nonsyndromic ocular
    MedGen: C1836080 OMIM: 609508 GeneReviews: Not available
    Compare labs
    Vitreoretinopathy with phalangeal epiphyseal dysplasia
    MedGen: C1852989 OMIM: 619248 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-07-29)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-07-29)

    ClinGen Genome Curation PagePubMed

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC131516

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in anterior head development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cartilage condensation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cartilage development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cartilage development involved in endochondral bone morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to BMP stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in central nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chondrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in collagen fibril organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in embryonic skeletal joint morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endochondral ossification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in extrinsic apoptotic signaling pathway in absence of ligand IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in heart morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inner ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in limb bud formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in notochord development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in otic vesicle development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in proteoglycan metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in roof of mouth development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in tissue homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in visual perception IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in basement membrane IEA
    Inferred from Electronic Annotation
    more info
     
    part_of collagen type II trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of collagen type II trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of collagen type XI trimer NAS
    Non-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 collagen-containing extracellular matrix NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region HDA PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    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

    NCBI Reference Sequences (RefSeq)

    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_008072.1 RefSeqGene

      Range
      5027..36536
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001844.5NP_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
      A6NGA0, P02458, Q12985, Q14009, Q14044, Q14045, Q14046, Q14047, Q14056, Q14058, Q16672, Q1JQ82, Q2V4X7, Q6LBY1, Q6LBY2, Q6LBY3, Q96IT5, Q99227, Q9UE38, Q9UE39, Q9UE40, Q9UE41, Q9UE42, Q9UE43
      Related
      ENSP00000369889.3, ENST00000380518.8
      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_033150.3NP_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, ENST00000337299.7
      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: 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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      47972967..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_047428315.1XP_047284271.1  collagen alpha-1(II) chain isoform X4

    5. XM_017018831.3XP_016874320.1  collagen alpha-1(II) chain isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      47934691..47967944 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371138.1XP_054227113.1  collagen alpha-1(II) chain isoform X3

    2. XM_054371137.1XP_054227112.1  collagen alpha-1(II) chain isoform X2

    3. XM_054371136.1XP_054227111.1  collagen alpha-1(II) chain isoform X1

    4. XM_054371140.1XP_054227115.1  collagen alpha-1(II) chain isoform X4

    5. XM_054371139.1XP_054227114.1  collagen alpha-1(II) chain isoform X4