• Gene id: 1280

Gene Summary

• Gene Symbol: COL2A1   Gene   UCSC   Ensembl
• Aliases: ANFH, AOM, COL11A3, SEDC, STL1
• Gene name: collagen type II alpha 1 chain
• Alternate names: collagen alpha-1(II) chain, alpha-1 type II collagen, arthroophthalmopathy, progressive (Stickler syndrome), cartilage collagen, chondrocalcin, collagen II, alpha-1 polypeptide, collagen, type II, alpha 1,
• Gene location: 12q13.11 (56907899: 56935846)     Exons: 5     NC_000004.12
• Gene summary(Entrez): 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 cong
• OMIM: 120140

Protein Summary

• Protein general information: P02458  
  • Name: Collagen alpha 1(II) chain (Alpha 1 type II collagen) [Cleaved into: Collagen alpha 1(II) chain; Chondrocalcin]
  • Length: 1487  
  • Mass: 141785
  • Tissue specificity: Isoform 2 is highly expressed in juvenile chondrocyte and low in fetal chondrocyte. {ECO
• Sequence:

  MIRLGAPQTLVLLTLLVAAVLRCQGQDVQEAGSCVQDGQRYNDKDVWKPEPCRICVCDTGTVLCDDIICEDVKDC
  LSPEIPFGECCPICPTDLATASGQPGPKGQKGEPGDIKDIVGPKGPPGPQGPAGEQGPRGDRGDKGEKGAPGPRG
  RDGEPGTPGNPGPPGPPGPPGPPGLGGNFAAQMAGGFDEKAGGAQLGVMQGPMGPMGPRGPPGPAGAPGPQGFQG
  NPGEPGEPGVSGPMGPRGPPGPPGKPGDDGEAGKPGKAGERGPPGPQGARGFPGTPGLPGVKGHRGYPGLDGAKG
  EAGAPGVKGESGSPGENGSPGPMGPRGLPGERGRTGPAGAAGARGNDGQPGPAGPPGPVGPAGGPGFPGAPGAKG
  EAGPTGARGPEGAQGPRGEPGTPGSPGPAGASGNPGTDGIPGAKGSAGAPGIAGAPGFPGPRGPPGPQGATGPLG
  PKGQTGEPGIAGFKGEQGPKGEPGPAGPQGAPGPAGEEGKRGARGEPGGVGPIGPPGERGAPGNRGFPGQDGLAG
  PKGAPGERGPSGLAGPKGANGDPGRPGEPGLPGARGLTGRPGDAGPQGKVGPSGAPGEDGRPGPPGPQGARGQPG
  VMGFPGPKGANGEPGKAGEKGLPGAPGLRGLPGKDGETGAAGPPGPAGPAGERGEQGAPGPSGFQGLPGPPGPPG
  EGGKPGDQGVPGEAGAPGLVGPRGERGFPGERGSPGAQGLQGPRGLPGTPGTDGPKGASGPAGPPGAQGPPGLQG
  MPGERGAAGIAGPKGDRGDVGEKGPEGAPGKDGGRGLTGPIGPPGPAGANGEKGEVGPPGPAGSAGARGAPGERG
  ETGPPGPAGFAGPPGADGQPGAKGEQGEAGQKGDAGAPGPQGPSGAPGPQGPTGVTGPKGARGAQGPPGATGFPG
  AAGRVGPPGSNGNPGPPGPPGPSGKDGPKGARGDSGPPGRAGEPGLQGPAGPPGEKGEPGDDGPSGAEGPPGPQG
  LAGQRGIVGLPGQRGERGFPGLPGPSGEPGKQGAPGASGDRGPPGPVGPPGLTGPAGEPGREGSPGADGPPGRDG
  AAGVKGDRGETGAVGAPGAPGPPGSPGPAGPTGKQGDRGEAGAQGPMGPSGPAGARGIQGPQGPRGDKGEAGEPG
  ERGLKGHRGFTGLQGLPGPPGPSGDQGASGPAGPSGPRGPPGPVGPSGKDGANGIPGPIGPPGPRGRSGETGPAG
  PPGNPGPPGPPGPPGPGIDMSAFAGLGPREKGPDPLQYMRADQAAGGLRQHDAEVDATLKSLNNQIESIRSPEGS
  RKNPARTCRDLKLCHPEWKSGDYWIDPNQGCTLDAMKVFCNMETGETCVYPNPANVPKKNWWSSKSKEKKHIWFG
  ETINGGFHFSYGDDNLAPNTANVQMTFLRLLSTEGSQNITYHCKNSIAYLDEAAGNLKKALLIQGSNDVEIRAEG
  NSRFTYTALKDGCTKHTGKWGKTVIEYRSQKTSRLPIIDIAPMDIGGPEQEFGVDIGPVCFL

• Structural information:
  • Protein Domains: (32..9-)
    (/note="VWFC-)
    (/evidence="ECO:0000255|PROSITE-ProRule:PRU00220-)
    (1253..148-)
    NC1 (/note="Fibrillar-collagen)
    (/evidence="ECO:0000255|PROSITE-ProRule:PRU00793"-)
  • Interpro: IPR008160  IPR000885  IPR001007  
  • Prosite: PS51461 PS01208 PS50184
  • PDB: 1U5M 2FSE 2SEB 5NIR 5OCX 5OCY 6BIN
  • PDBsum: 1U5M 2FSE 2SEB 5NIR 5OCX 5OCY 6BIN
  • STRING: ENSP00000369889
• Other Databases: GeneCards:  COL2A1  Malacards:  COL2A1

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0031012	extracellular matrix	IBA	cellular component
GO:0030903	notochord development	IBA	biological process
GO:0005615	extracellular space	IBA	cellular component
GO:0005585	collagen type II trimer	IBA	cellular component
GO:0005201	extracellular matrix structural constituent	IBA	molecular function
GO:0001501	skeletal system development	IBA	biological process
GO:0030199	collagen fibril organization	IBA	biological process
GO:0030198	extracellular matrix organization	IBA	biological process
GO:0005581	collagen trimer	IBA	cellular component
GO:0005201	extracellular matrix structural constituent	IEA	molecular function
GO:0046872	metal ion binding	IEA	molecular function
GO:0005576	extracellular region	IEA	cellular component
GO:0005581	collagen trimer	IEA	cellular component
GO:0048407	platelet-derived growth factor binding	IDA	molecular function
GO:0043394	proteoglycan binding	IDA	molecular function
GO:0030198	extracellular matrix organization	TAS	biological process
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005576	extracellular region	TAS	cellular component
GO:0005788	endoplasmic reticulum lumen	TAS	cellular component
GO:0005788	endoplasmic reticulum lumen	TAS	cellular component
GO:0005788	endoplasmic reticulum lumen	TAS	cellular component
GO:0005788	endoplasmic reticulum lumen	TAS	cellular component
GO:0050776	regulation of immune response	TAS	biological process
GO:0001503	ossification	IEA	biological process
GO:0001958	endochondral ossification	IEA	biological process
GO:0005585	collagen type II trimer	IEA	cellular component
GO:0005604	basement membrane	IEA	cellular component
GO:0005615	extracellular space	IEA	cellular component
GO:0007417	central nervous system development	IEA	biological process
GO:0030903	notochord development	IEA	biological process
GO:0031012	extracellular matrix	IEA	cellular component
GO:0042472	inner ear morphogenesis	IEA	biological process
GO:0048705	skeletal system morphogenesis	IEA	biological process
GO:0051216	cartilage development	IEA	biological process
GO:0060174	limb bud formation	IEA	biological process
GO:0060351	cartilage development involved in endochondral bone morphogenesis	IEA	biological process
GO:0071773	cellular response to BMP stimulus	IEA	biological process
GO:0001502	cartilage condensation	IEA	biological process
GO:0001894	tissue homeostasis	IEA	biological process
GO:0002062	chondrocyte differentiation	IEA	biological process
GO:0003007	heart morphogenesis	IEA	biological process
GO:0005581	collagen trimer	IEA	cellular component
GO:0005737	cytoplasm	IEA	cellular component
GO:0006029	proteoglycan metabolic process	IEA	biological process
GO:0010468	regulation of gene expression	IEA	biological process
GO:0030199	collagen fibril organization	IEA	biological process
GO:0035108	limb morphogenesis	IEA	biological process
GO:0042802	identical protein binding	IEA	molecular function
GO:0048839	inner ear development	IEA	biological process
GO:0060021	roof of mouth development	IEA	biological process
GO:0060348	bone development	IEA	biological process
GO:0071599	otic vesicle development	IEA	biological process
GO:0097065	anterior head development	IEA	biological process
GO:2001240	negative regulation of extrinsic apoptotic signaling pathway in absence of ligand	IEA	biological process
GO:0030020	extracellular matrix structural constituent conferring tensile strength	IC	molecular function
GO:0042802	identical protein binding	NAS	molecular function
GO:0005585	collagen type II trimer	IDA	cellular component
GO:0001501	skeletal system development	IMP	biological process
GO:0007601	visual perception	IMP	biological process
GO:0051216	cartilage development	TAS	biological process
GO:0030020	extracellular matrix structural constituent conferring tensile strength	RCA	molecular function
GO:0030020	extracellular matrix structural constituent conferring tensile strength	RCA	molecular function
GO:0030020	extracellular matrix structural constituent conferring tensile strength	HDA	molecular function
GO:0030020	extracellular matrix structural constituent conferring tensile strength	RCA	molecular function
GO:0007605	sensory perception of sound	IMP	biological process
GO:0030199	collagen fibril organization	IMP	biological process
GO:0060272	embryonic skeletal joint morphogenesis	IMP	biological process
GO:0062023	collagen-containing extracellular matrix	HDA	cellular component
GO:0062023	collagen-containing extracellular matrix	HDA	cellular component
GO:0062023	collagen-containing extracellular matrix	HDA	cellular component
GO:0062023	collagen-containing extracellular matrix	HDA	cellular component
GO:0005576	extracellular region	HDA	cellular component
GO:0042289	MHC class II protein binding	IPI	molecular function
GO:0062023	collagen-containing extracellular matrix	HDA	cellular component
GO:0007601	visual perception	IMP	biological process
GO:0005615	extracellular space	IMP	cellular component

KEGG pathways

Pathway id	Pathway name
hsa04151	PI3K-Akt signaling pathway
hsa05165	Human papillomavirus infection
hsa04510	Focal adhesion
hsa04974	Protein digestion and absorption
hsa04512	ECM-receptor interaction

Diseases

Associated diseases	References
Spondyloepimetaphyseal dysplasia	KEGG:H02187
Multiple epiphyseal dysplasia	KEGG:H00476
Stickler syndrome	KEGG:H02072
Vitreoretinal degeneration	KEGG:H00805
Glucocorticoid-induced osteonecrosis	KEGG:H01709
Osteoarthritis with mild chondrodysplasia	KEGG:H00445
Spondyloepiphyseal dysplasia congenita	KEGG:H00519
Type II collagenopathies	KEGG:H00520
Legg-Calve-Perthes Disease	KEGG:H01526
Avascular necrosis of femoral head	KEGG:H01529
Achondrogenesis type II	KEGG:H02066
Kniest dysplasia	KEGG:H02070
Czech dysplasia	KEGG:H02071
Spondyloepimetaphyseal dysplasia	KEGG:H02187
Multiple epiphyseal dysplasia	KEGG:H00476
Stickler syndrome	KEGG:H02072
Vitreoretinal degeneration	KEGG:H00805
Glucocorticoid-induced osteonecrosis	KEGG:H01709
Osteoarthritis with mild chondrodysplasia	KEGG:H00445
Spondyloepiphyseal dysplasia congenita	KEGG:H00519
Type II collagenopathies	KEGG:H00520
Legg-Calve-Perthes Disease	KEGG:H01526
Avascular necrosis of femoral head	KEGG:H01529
Achondrogenesis type II	KEGG:H02066
Kniest dysplasia	KEGG:H02070
Czech dysplasia	KEGG:H02071
Stickler syndrome	PMID:18276201
Stickler syndrome	PMID:8737653
Stickler syndrome	PMID:20179744
Stickler syndrome	PMID:7487609
Stickler syndrome	PMID:12511349
Stickler syndrome	PMID:1677770
Stickler syndrome	PMID:23592912
Stickler syndrome	PMID:9800905
Stickler syndrome	PMID:12204008
Spondyloarthropathy	PMID:7866404
Myopia	PMID:18276201
Myopia	PMID:17653045
Spondyloepiphyseal dysplasia congenita	PMID:21204228
Osteochondrodysplasia	PMID:15476249
chondrosarcoma	PMID:23770606
Retinal detachment	PMID:22574936
Eye disease	PMID:19430638
cleft palate	PMID:20672350
Osteoarthritis	PMID:16755660
Chorioretinitis	PMID:18523590
Aberrant CpGs in Low Motility Sperm	MIK: 21674046
Spermatogenic defects	MIK: 31037746
Teratozoospermia	MIK: 17327269

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes
17327269	Teratozoospermia			13 (5 controls, 8 cases)	Male infertility	GSE6967 analyzed by GEO2R (cutoff 1.5 fold)
21674046	Aberrant CpGs in Low Motility Sperm			18	Male infertility	GSE26881
31037746	Spermatogenic defects			28 men with azoospermia	Male infertility	Microarray