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

Gene ID: 1280, updated on 6-Jul-2014
Official Symbol
COL2A1provided by HGNC
Official Full Name
collagen, type II, alpha 1provided by HGNC
Primary source
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]
See COL2A1 in Epigenomics, MapViewer
Location:
12q13.11
Exon count :
54
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 12 NC_000012.12 (47972965..48004554, 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 (1,25- dihydroxyvitamin D3) receptor Neighboring gene transmembrane protein 106C Neighboring gene uncharacterized LOC728114 Neighboring gene SUMO1/sentrin specific peptidase 1 Neighboring gene ribosomal protein L37 pseudogene 19

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Achondrogenesis type 2
MedGen: C0220685 OMIM: 200610 GeneReviews: Not available
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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
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Czech dysplasia metatarsal type
MedGen: C1836683 OMIM: 609162 GeneReviews: Not available
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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
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Osteoarthritis with mild chondrodysplasia
MedGen: C1858079 OMIM: 604864 GeneReviews: Not available
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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
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Spondyloepimetaphyseal dysplasia Strudwick type
MedGen: C0700635 OMIM: 184250 GeneReviews: Not available
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Spondyloepiphyseal dysplasia congenita
MedGen: C0038015 OMIM: 183900 GeneReviews: Not available
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Spondyloperipheral dysplasia
MedGen: C0796173 OMIM: 271700 GeneReviews: Not available
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Stickler syndrome type 1
MedGen: CN032634 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)

ISCA Genome Curation Page
Haploinsufficency

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

ISCA 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)
    Amoebiasis, conserved 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...
  • 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 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 biosystem
    Endochondral Ossification
  • 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...
  • 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...
  • 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...
  • 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

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 region TAS
Traceable Author Statement
more info
 
extracellular space IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
collagen alpha-1(II) chain
Names
collagen alpha-1(II) chain
chondrocalcin
cartilage collagen
alpha-1 type II collagen
collagen II, alpha-1 polypeptide
arthroophthalmopathy, progressive (Stickler syndrome)

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 

    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 proteins identical to 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
    Blast Score: 132
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:12521487
    Blast Score: 1184
    COLFI; Fibrillar collagens C-terminal domain
    pfam00093
    Location:3489
    Blast Score: 233
    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
    Blast Score: 132
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:11831418
    Blast Score: 1188
    COLFI; Fibrillar collagens C-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000012.12 

    Range
    47972965..48004554
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006719242.1XP_006719305.1  

    Conserved Domains (3) summary
    pfam01391
    Location:802861
    Blast Score: 132
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:12531488
    Blast Score: 1184
    COLFI; Fibrillar collagens C-terminal domain
    pfam00093
    Location:3489
    Blast Score: 233
    VWC; von Willebrand factor type C domain

Alternate HuRef

Genomic

  1. AC_000144.1 

    Range
    45398588..45430128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018923.2 

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

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