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

Gene ID: 1280, updated on 5-Apr-2020

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
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

Genomic context

See COL2A1 in Genome Data Viewer
Location:
12q13.11
Exon count:
57
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (47972967..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 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 the head of femur 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 Compare labs
Osteoarthritis with mild chondrodysplasia Compare labs
Platyspondylic lethal skeletal dysplasia Torrance type Compare labs
Spondyloepiphyseal dysplasia Compare labs
Spondyloepiphyseal dysplasia, stanescu type
MedGen: C4225273 OMIM: 616583 GeneReviews: Not available
Compare labs
Spondylometaphyseal dysplasia 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

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC131516

Gene Ontology Provided by GOA

Process Evidence Code Pubs
anterior head development IEA
Inferred from Electronic Annotation
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 fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
otic vesicle 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
 
roof of mouth development IEA
Inferred from Electronic Annotation
more info
 
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
skeletal system development IBA
Inferred from Biological aspect of Ancestor
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 trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type II trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type II trimer IDA
Inferred from Direct Assay
more info
PubMed 
collagen-containing extracellular matrix HDA PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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
    P02458
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 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_017018831.2XP_016874320.1  collagen alpha-1(II) chain isoform X4

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