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COL2A1 Gene

protein-coding GIFtS: 61

GC12M048266

collagen, type II, alpha 1
(Previous names: collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital) )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: SEDC)

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
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Aliases & Descriptions
collagen, type II, alpha 1¹ ²		SEDC²
Alpha-1 type II collagen² ³		MGC131516²
collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)¹		collagen II, alpha-1 polypeptide²
cartilage collagen²		collagen alpha-1(II) chain²
ANFH²		chondrocalcin²
COL11A3²		AOM²

External Ids:	HGNC: 2200¹	Entrez Gene: 1280²	Ensembl: ENSG00000139219⁷	UniProtKB: P02458³

Search outside databases for aliases for COL2A1 gene

Previous GC identifers: GC12M048379 GC12M048083 GC12M046653

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for COL2A1:

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)

UniProtKB/Swiss-Prot: CO2A1_HUMAN, P02458

Function: Type II collagen is specific for cartilaginous tissues. It is essential for the normal embryonic development

of the skeleton, for linear growth and for the ability of cartilage to resist compressive forces

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC and Ensembl (release 56), Regulatory elements and Epigenetics data according to SABiosciences)
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Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the COL2A1 gene upstream (promoter) region

:
STAT1beta STAT1 STAT1alpha Sp1 ATF6 SRF CUTL1 POU3F2 LCR-F1 Nkx6-1

Epigenetics:

SABiosciences Methyl-Profiler DNA Methylation qPCR Primer Assays for COL2A1:

MePH16497-1A MePH16495-1A MePH16499-1A

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12q13.11 Ensembl cytogenetic band: 12q13.11 HGNC cytogenetic band: 12q12-q13.2

COL2A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 12 GeneLoc Exon Structure

GeneLoc location for GC12M048266: view genomic region (about GC identifiers)

Start:	48,366,748 bp from pter
End:	48,398,285 bp from pter
Size:	31,538 bases
Orientation:	minus strand

RefSeq DNA sequence:

NC_000012.11 NT_029419.12

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene, Novus Biologicals, and/or Sino Biological,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 May 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abnova, OriGene, Novus Biologicals, and/or Epitomics)
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UniProtKB/Swiss-Prot: CO2A1_HUMAN, P02458 (See protein sequence)

Recommended Name: Collagen alpha-1(II) chain precursor

Size: 1487 amino acids; 141785 Da

Subunit: Homotrimers of alpha 1(II) chains

Subcellular location: Secreted, extracellular space, extracellular matrix (By similarity)

Sequence caution: Sequence=AAH07252.1; Type=Frameshift; Positions=1198;

PDB structures from and Proteopedia :

1U5M (3D)

2FSE (3D)

2SEB (3D)

Secondary accessions: A6NGA0 Q12985 Q14009 Q14044 Q14045 Q14046 Q14047 Q14056 Q14058 Q16672 Q1JQ82

Q2V4X7 Q6LBY1 Q6LBY2 Q6LBY3 Q96IT5 Q99227 Q9UE38 Q9UE39 Q9UE40 Q9UE41 Q9UE42 Q9UE43

Alternative splicing: 3 isoforms: P02458-2 P02458-1 P02458-3

Post-translational modifications:

Proline residues at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the

chains. Proline residues at the second position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some of

the chains¹

The N-telopeptide is covalently linked to the helical COL2 region of alpha 1(IX), alpha 2(IX) and alpha 3(IX) chain.

The C-telopeptide is covalently linked to an another site in the helical region of alpha 3(IX) COL2¹

REFSEQ proteins (2 alternative transcripts):

NP_001835.3 NP_149162.2

ENSEMBL proteins:

ENSP00000378696 ENSP00000338213 ENSP00000369889

Human Recombinant Proteins

	Millipore Purified and/or Recombinant COL2A1 Protein
	Browse Human Recombinant Proteins at Sigma-Aldrich
	Browse R&D Systems for human recombinant proteins
	Enzo Life Sciences proteins for COL2A1
	HuPro® and/or Recombinant Proteins from Abnova for COL2A1
	Browse Origene full length recombinant human proteins expressed in human HEK293 cells
	Novus Biologicals Protein for COL2A1
	Browse Sino Biological Recombinant Proteins

5/6 Gene Ontology (GO) cellular component terms (GO ID links to tree view) (see all 6 ):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	EXP	15713743
GO:0005581	collagen	IEA	--
GO:0005585	collagen type II	IDA	8660302
GO:0005604	basement membrane	IEA	--
GO:0005615	extracellular space	IEA	--

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COL2A1 for ontologies About GeneDecksing

Antibodies for COL2A1:

	Millipore Mono- and Polyclonal Antibodies for the study of COL2A1
	Sigma-Aldrich Antibodies for COL2A1
	R&D Systems Antibodies for COL2A1 (Collagen II)
	Monoclonal and Polyclonal Antibodies from Abnova (COL2A1)
	Browse Origene Antibodies
	Novus Biologicals Antibodies for COL2A1
	Browse antibodies at Epitomics

Assays for COL2A1:

	Millipore Kits and Assays for the Analysis of COL2A1
	Browse ELISAs at Sigma-Aldrich
	Browse R&D Systems for biochemical assays
	Enzo Life Sciences assays for COL2A1

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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COL2A1 for domains About GeneDecksing

3 InterPro domains/families:

IPR000885 Fib_collagen_C

IPR001007 VWF_C

IPR008160 Collagen

Graphical View of Domain Structure for InterPro Entry P02458

ProtoNet protein and cluster: P02458

3 Blocks protein families:

IPB000885 Fibrillar collagen

IPB008160 Collagen triple helix repeat

IPB008161 Collagen helix repeat

UniProtKB/Swiss-Prot: CO2A1_HUMAN, P02458

Similarity: Belongs to the fibrillar collagen family

Similarity: Contains 1 fibrillar collagen NC1 domain

Similarity: Contains 1 VWFC domain

(According to MGI May 08 2010, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, Abnova, siRNAs from Applied Biosystems, Sigma-Aldrich, Clones from Millipore, Sigma-Aldrich, OriGene, Sino Biological, Ontologies according to Gene Ontology Consortium 01 May 2010 via Entrez Gene.)
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Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (COL2A1)
		Origene 29mer shRNA kits in GFP-retroviral vector (see all 3): COL2A1 Origene shRNA RFP (see all 3): COL2A1 Origene basic RS shRNA (see all 3): COL2A1
		Applied Biosystems Silencer® siRNAs for COL2A1
		Sigma-Aldrich siRNA for COL2A1 Sigma-Aldrich shRNA Panels and shRNA for COL2A1 Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Browse Clones for the Expression of Recombinant Proteins Available from Millipore
		Browse iPSC Reprogramming Factors at Sigma-Aldrich
		Origene GFP tagged cDNA clones in CMV expression vector (see all 2): COL2A1 Origene Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): COL2A1 Origene untagged cDNA clones in CMV expression vector (see all 3): COL2A1
		Browse Sino Biological Human cDNA Clones

UniProtKB/Swiss-Prot: CO2A1_HUMAN, P02458

Function: Type II collagen is specific for cartilaginous tissues. It is essential for the normal embryonic development

of the skeleton, for linear growth and for the ability of cartilage to resist compressive forces

Genatlas biochemistry entry for COL2A1:

collagen type II,alpha 1,fibril forming,chondrocalcin included,expressed in hyaline cartilage,in the ocular vitreous,

in the nucleus pulposus of the intervertebral disc and in the inner ear

5 Gene Ontology (GO) molecular function terms (GO ID links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005102	receptor binding	--	--
GO:0005201	extracellular matrix structural constituent	--	--
GO:0030020	extracellular matrix structural constituent conferring tensile strength	IC	8660302
GO:0042802	identical protein binding	NAS	2587267
GO:0048407	platelet-derived growth factor binding	IDA	8900172

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COL2A1 for ontologies About GeneDecksing

Animal Models: 15/17 MGI mutant phenotypes (inferred from 6 alleles) (MGI details for Col2a1) (see all 17 ):

behavior/neurological	cardiovascular system	craniofacial	digestive/alimentary	embryogenesis
growth/size	hearing/vestibular/ear	immune system	lethality-postnatal	lethality-prenatal/perinatal
limbs/digits/tail	liver/biliary system	nervous system	renal/urinary system	respiratory system

COL2A1 for phenotypes About GeneDecksing

(Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, Applied Biosystems GeneAssist, KEGG and/or UniProtKB, (map by GeneGo),
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 May 2010 via Entrez Gene).
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COL2A1 for pathways About GeneDecksing

5/6 Millipore Pathways for COL2A1 (see all 6 )

	Cell adhesion Integrin-mediated cell adhesion and migration
	Development Hedgehog and PTH signaling pathways in bone and cartilage development
	Cytoskeleton remodeling Integrin outside-in signaling
	Cell adhesion Integrin inside-out signaling
	Cell adhesion ECM remodeling

2 Sigma-Aldrich "Your Favorite Gene" Pathways for COL2A1 (Your Favorite Gene powered by Ingenuity)

	Atherosclerosis Signaling
	Dendritic Cell Maturation

5/16 GeneAssist Pathways for COL2A1 (see all 16 )

	Blood Coagulation Cascade
	Inhibition of Angiogenesis by TSP1
	Phospholipase-C Pathway
	ERK Signaling
	MAPK Signaling

2 Kegg Pathways (Kegg details for COL2A1):

	hsa04510 Focal adhesion
	hsa04512 ECM-receptor interaction

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for COL2A1

1 Interacting protein for COL2A1 (P02458²) via UniProtKB, MINT, and/or STRING

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
COCH	O43405²	MINT-6796062

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5/20 Gene Ontology (GO) biological process terms (GO ID links to tree view) (see all 20 ):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001501	skeletal system development	IMP	1429602
GO:0001502	cartilage condensation	IEA	--
GO:0001894	tissue homeostasis	IEA	--
GO:0001958	endochondral ossification	IEA	--
GO:0002062	chondrocyte differentiation	IEA	--

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COL2A1 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
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COL2A1 for compounds About GeneDecksing

Enzo Life Sciences drugs & compounds for COL2A1

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for COL2A1
10/87 Novoseek chemical compound relationships for COL2A1 gene (see all 87 )

Compound	Score	Articles	PubMed IDs for Articles with Shared Sentences (# sentences)
procollagen	7.98	8	1637314 (2), 15593085 (2), 8244341 (1), 19287128 (1) (see all 6)
pyridinoline	7.92	7	9675702 (2), 7951150 (1), 7931731 (1), 7633791 (1) (see all 6)
cnbr	4.43	4	6770846 (1), 4270660 (1), 1985108 (1), 1481841 (1)
cyanogen bromide	4.25	5	5550793 (1), 5126920 (1), 4732855 (1), 4334341 (1) (see all 5)
rhein	4.07	3	16912429 (1), 15299286 (1), 14527176 (1)
hind iii	3.34	4	8019561 (1), 2902229 (1), 1675622 (1), 10735581 (1)
hydroxylysine	2.46	2	6458288 (1), 10947951 (1)
pentosidine	2.00	2	10947951 (2)
sb 216763	1.85	1	19795391 (1)
n-chlorosuccinimide	1.73	1	8973556 (1)

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(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 223 Homo sapiens; Apr 2 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Millipore and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene, microRNA from SABiosciences,
Tagged/untagged cDNA clones from OriGene, Primers from OriGene and/or SABiosciences,
Expression Assays from Applied Biosystems)
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Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (COL2A1)
		Applied Biosystems Silencer® siRNAs: NM_001844 NM_033150
		Origene 29mer shRNA kits in GFP-retroviral vector (see all 3): COL2A1 Origene shRNA RFP (see all 3): COL2A1 Origene basic RS shRNA (see all 3): COL2A1
		Sigma-Aldrich siRNA for COL2A1 Sigma-Aldrich shRNA Panels and shRNA for COL2A1 Explore Sigma-Aldrich super-pooled esiRNAs

microRNA:		10 SABiosciences microRNAs that regulate COL2A1:
		hsa-miR-148b hsa-miR-134 hsa-miR-29c hsa-miR-29a hsa-miR-346 hsa-miR-7 hsa-miR-342-3p hsa-miR-152 hsa-miR-29b hsa-miR-148a

Assays:

Applied Biosystems TaqMan® Gene Expression Assays:

NM_001844 NM_033150

Clones:

Origene GFP tagged cDNA clones in CMV expression vector (see all 2): COL2A1
Origene Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): COL2A1
Origene untagged cDNA clones in CMV expression vector (see all 3): COL2A1

Primers:		Origene genome-wide validated SYBR primer pairs: COL2A1
		SABiosciences RT2 qPCR Primer Assay for COL2A1: PPH02134A

REFSEQ mRNAs for COL2A1 gene (2 alternative transcripts):

NM_001844.4 NM_033150.2

Additional cDNA sequence:

BC007252.1 BC116449.1 BT007205.1 CR603203.1 X06268.1 X13783.1 X16468.1 X16711.1

18 DOTS entries:

DT.95179525 DT.100782871 DT.95263999 DT.100038174 DT.100038169 DT.40132444 DT.102833022 DT.102833021

DT.102833024 DT.91785734 DT.92423549 DT.100038168 DT.100038175 DT.102833019 DT.121158231 DT.95263995

DT.95263998 DT.121630198

24/326 AceView cDNA sequences (see all 326 ):

CA414770 CA411736 BQ181744 BQ182793 CA447226 CN480116 BQ182210 BQ182892

CA425342 BQ182505 CN480206 BQ183639 BQ183373 CN479923 BQ181889 BE672454

BM711337 BQ044938 CN479626 BQ180866 BQ183023 BQ183392 BQ181470 CD655403

highest scoring ESTs for COL2A1:

AA102672 AA327682 AA332092 AA332273 AA332322 AA332398 AA332659 AA333341 AA334901 AA587678

Unigene Cluster for COL2A1:

Collagen, type II, alpha 1

Hs.408182 [show with all ESTs]

Unigene Representative Sequence: NM_001844

GeneLoc Exon Structure

5 Alternative Splicing Database (ASD) splice patterns (SP) for COL2A1

ExUns:	1a	·	1b	^	2	^	3	^	4	^	5	^	6	^	7	^	8	^	9	^	10	^	11	^	12	^	13	^	14	^	15	^	16	^	17	^	18	^	19	^	20	^	21	^	22	^	23a	·	23b	^	24	^
SP1:
SP2:																																																	-
SP3:
SP4:
SP5:					-

ExUns:	25	^	26	^	27a	·	27b	^	28	^	29	^	30	^	31	^	32	^	33	^	34	^	35	^	36	^	37	^	38	^	39	^	40	^	41	^	42	^	43	^	44	^	45	^	46	^	47	^	48	^	49	^
SP1:					-
SP2:
SP3:
SP4:
SP5:

ExUns:	50	^	51
SP1:
SP2:
SP3:
SP4:
SP5:

About this scheme

ECgene alternative splicing isoforms for COL2A1

9 Ensembl transcripts including schematic representations:

ENST00000395281 ENST00000493991 ENST00000337299 ENST00000483376 ENST00000465743 ENST00000466884

ENST00000490609 ENST00000474996 ENST00000380518

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 223 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems, Primers from OriGene and/or SABiosciences )
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COL2A1 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for COL2A1

¹ / ² / ³

7 probe-sets matching COL2A1 gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
37605_at²^{, 3}	U95-A	1	1.00	1.00	0.68	0.30	L10347	0.20	1.00	0.72	1
598_at²^{, 3}	U95-A	1	0.81	1.00	0.17	0.93	M60299	0.20	1.00	0.72	1
85915_at²^{, 3}	U95-D	1	0.69	1.00	0.89	1.07	AI038847	0.60	1.00	0.82	1
217404_s_at²^{, 3}	U133-A	1	1.00	1.00	--	--	X16468	0.60	1.00	0.82	1
213492_at²^{, 3}	U133-A	1	1.00	1.00	--	--	X06268	0.60	1.00	0.82	1
217404_s_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
213492_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--

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COL2A1 for expression About GeneDecksing

Data from Genenote (Publications) and GNF BioGPS
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About these images

CGAP SAGE TAG: GACATAGGAG

SOURCE GeneReport for Unigene cluster: Hs.408182

Expression variation in blood from EXPOLDB for COL2A1

UniProtKB/Swiss-Prot: CO2A1_HUMAN, P02458

Tissue specificity: Isoform 2 is highly expressed in juvenile chondrocyte and low in fetal chondrocyte

Primers:		Origene genome-wide validated SYBR primer pairs: COL2A1
		SABiosciences RT2 qPCR Primer Assay for COL2A1: PPH02134A

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI May 08 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
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Orthologs for COL2A1 gene from 5/8 species (see all 8 )

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	COL2A1¹	--	collagen, type II, alpha 1	92.58(n) 98.32(a)	403826 NM_001006951.1 NP_001006952.1
chimpanzee (Pan troglodytes)	COL2A1¹	--	collagen, type II, alpha 1	99.62(n) 99.93(a)	451860 XM_509026.2 XP_509026.2
rat (Rattus norvegicus)	Col2a1¹	--	collagen, type II, alpha 1	89.62(n) 96.47(a)	25412 NM_012929.1 NP_037061.1
mouse (Mus musculus)	Col2a1^{1, 5}	15 (54.50 cM)⁵	collagen, type II, alpha 1^{1, 5}	89.08(n)¹ 95.21(a)¹	12824¹ NM_031163.2¹ NP_112440.1¹ AK028295⁵ AK053784⁵ (see all 20)
chicken (Gallus gallus)	COL2A1¹	--	collagen, type II, alpha 1	79.82(n) 92.58(a)	395069 NM_204426.1 NP_989757.1

About this table Species with no ortholog for COL2A1

ENSEMBL Gene Tree for COL2A1

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
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Paralogs for COL2A1 gene

COL4A6² COL11A2² COL4A5² COL24A1² COL4A4² COL5A3² COL4A2² COL1A1²

COL5A2² COL5A1² COL4A3² COL7A1² COL1A2² COL3A1² COL27A1² COL4A1²

COL11A1²

COL2A1 for paralogs About GeneDecksing

(SNPs according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Genotyping Reagents from Applied Biosystems)
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10/432 NCBI SNPs in COL2A1 are shown (see all 432 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 209)

AB	SNP ID	Valid	Chr 12 pos	Sequence	Recs	AA Chg	Type	More	Recs	Pop	Total sample	More
AB	Genomic Data				Transcription Related Data				Allele Frequencies
				--	--	--		--	--			--
	rs1859444^1,2	C,F,O,A,H	45431246(-)	`CTGGGG/AAGAAG`	2	--	ng5¹ trp³		12	MN NS EA NA WA	820
	rs2071357^1,2	C,F,O,A,H	45398387(-)	`ACCCAC/TTGTTG`	2	--	ng3¹		5	NS NA EA WA	332
	rs2070739^1,2	C,F,O,A,H	48367976(-)	`CAGCTA/GGCAAC`	4	S G	mis¹ ref¹ ese³		23	MN NS NA EA	2272
	rs3803182^1,2	C,F,A,H	48398223(-)	`CTTCCT/CCCTCC`	2	--	ut5¹ trp³		5	MN NA	202
	rs2071356^1,2	C,F,A,H	45398390(-)	`GGAACC/TCACTG`	2	--	ng3¹		3	NA EA	164
	rs3803183^1,2	C,F,A,H	48398080(-)	`CCCAGT/ACGCTG`	4	/T /S	ref¹ mis¹ ese³		8	EA NS NA MN	502
--	rs10783226^1,2	C,F,A,H	45430193(+)	`CCCCCA/CGCTGG`	2	--	ng5¹		5	MN NA	202
	rs1859443^1,2	C,F,A	45431455(-)	`GCTCTC/TAGCTT`	2	--	ng5¹		8	MN NS EA NA WA	778
--	rs11611924^1,2	C,F,H	45430195(+)	`CCCAGC/ATGGGC`	2	--	ng5¹		1	NA	4
	rs3825404^1,2	C,F,A	45431774(-)	`CCAGCC/TTTCTT`	2	--	ng5¹		13	NS EA NA WA	766

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HapMap Linkage Disequilibrium images for COL2A1 (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for COL2A1: --

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
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COL2A1 for disorders About GeneDecksing

OMIM: 120140

UniProtKB/Swiss-Prot: CO2A1_HUMAN, P02458

Defects in COL2A1 are the cause of spondyloepiphyseal dysplasia congenital type (SEDC) [MIM:183900]. This

disorder is characterized by disproportionate short stature and pleiotropic involvement of the skeletal and ocular

systems

Defects in COL2A1 are the cause of spondyloepimetaphyseal dysplasia Strudwick type (SEMD-STR) [MIM:184250]. A

bone disease characterized by disproportionate short stature from birth, with a very short trunk and shortened limbs,

and skeletal abnormalities including lordosis, scoliosis, flattened vertebrae, pectus carinatum, coxa vara, clubfoot,

and abnormal epiphyses or metaphyses. A distinctive radiographic feature is irregular sclerotic changes, described as

dappled in the metaphyses of the long bones

Defects in COL2A1 are the cause of achondrogenesis type 2 (ACG2) [MIM:200610]; also known as

achondrogenesis-hypochondrogenesis type II. ACG2 is a disease characterized by the absence of ossification in the

vertebral column, sacrum and pubic bones

Defects in COL2A1 are the cause of Legg-Calve-Perthes disease (LCPD) [MIM:150600]; also known as Legg-Perthes

disease or Perthes disease. LCPD is characterized by loss of circulation to the femoral head, resulting in avascular

necrosis in a growing child. Clinical pictures of the disease vary, depending on the phase of disease progression

through ischemia, revascularization, fracture and collapse, and repair and remodeling of the bone

Defects in COL2A1 are the cause of Kniest syndrome (KS) [MIM:156550]; also known as Kniest dysplasia or

metatropic dwarfism type II. KS is a moderately severe chondrodysplasia phenotype that results from mutations in the

COL2A1 gene. Characteristics of the disorder include a short trunk and extremities, mid-face hypoplasia, cleft palate,

myopia, retinal detachment, and hearing loss

Defects in COL2A1 are a cause of primary avascular necrosis of femoral head (ANFH) [MIM:608805]; also known as

ischemic necrosis of the femoral head or osteonecrosis of the femoral head. ANFH causes disability that often requires

surgical intervention. Most cases are sporadic, but families in which there is an autosomal dominant inheritance of

the disease have been identified. It has been estimated that 300,000 to 600,000 people in the United States have ANFH.

Approximately 15,000 new cases of this common and disabling disorder are reported annually. The age at the onset is

earlier than that for osteoarthritis. The diagnosis is typically made when patients are between the ages of 30 and 60

years. The clinical manifestations, such as pain on exertion, a limping gait, and a discrepancy in leg length, cause

considerable disability. Moreover, nearly 10 percent of the 500,000 total-hip arthroplasties performed each year in

the United States involve patients with ANFH. As a result, this disease creates a substantial socioeconomic cost as

well as a burden for patients and their families

Defects in COL2A1 are the cause of osteoarthritis with mild chondrodysplasia [MIM:604864]. Osteoarthritis is a

common disease that produces joint pain and stiffness together with radiologic evidence of progressive degeneration of

joint cartilage. Some forms of osteoarthritis are secondary to events such as trauma, infections, metabolic disorders,

or congenital or heritable conditions that deform the epiphyses or related structures. In most patients, however,

there is no readily identifiable cause of osteoarthritis. Inheritance in a Mendelian dominant manner has been

demonstrated in some families with primary generalized osteoarthritis. Reports demonstrate coinheritance of primary

generalized osteoarthritis with specific alleles of the gene COL2A1, the precursor of the major protein of cartilage

Defects in COL2A1 are the cause of platyspondylic lethal skeletal dysplasia Torrance type (PLSD-T)

[MIM:151210]. Platyspondylic lethal skeletal dysplasias (PLSDs) are a heterogeneous group of chondrodysplasias

characterized by severe platyspondyly and limb shortening. PLSD-T is characterized by varying platyspondyly, short

ribs with anterior cupping, hypoplasia of the lower ilia with broad ischial and pubic bones, and shortening of the

tubular bones with splayed and cupped metaphyses. Histology of the growth plate typically shows focal hypercellularity

with slightly enlarged chondrocytes in the resting cartilage and relatively well-preserved columnar formation and

ossification at the chondro-osseous junction. PLSD-T is generally a perinatally lethal disease, but a few long-term

survivors have been reported

Defects in COL2A1 are the cause of multiple epiphyseal dysplasia with myopia and conductive deafness (EDMMD)

[MIM:132450]. Multiple epiphyseal dysplasia is a generalized skeletal dysplasia associated with significant morbidity.

Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. EDMMD is an

autosomal dominant disorder characterized by epiphyseal dysplasia associated with progressive myopia, retinal

thinning, crenated cataracts, conductive deafness

Defects in COL2A1 are the cause of spondyloperipheral dysplasia (SPD) [MIM:271700]. SPD patients manifest

short stature, midface hypoplasia, sensorineural hearing loss, spondyloepiphyseal dysplasia, platyspondyly and

brachydactyly

Defects in COL2A1 are the cause of Wagner syndrome type 2 (WGN2). WGN2 is characterized by early-onset

cataracts, lattice degeneration of the retina, and retinal detachment without involvement of monocular tissues

Defects in COL2A1 are the cause of Stickler syndrome type 1 (STL1) [MIM:108300]; also known as vitreous type

1, or membranous vitreous type. STL1 is an autosomal dominant form of Stickler syndrome, an inherited disorder that

associates ocular signs with more or less complete forms of Pierre Robin sequence, bone disorders and sensorineural

deafness. Ocular disorders may include juvenile cataract, myopia, strabismus, vitreoretinal or chorioretinal

degeneration, retinal detachment, and chronic uveitis. Robin sequence includes an opening in the roof of the mouth (a

cleft palate), a large tongue (macroglossia), and a small lower jaw (micrognathia). Bones are affected by slight

platyspondylisis and large, often defective epiphyses. Juvenile joint laxity is followed by early signs of arthrosis.

The degree of hearing loss varies among affected individuals and may become more severe over time. Syndrome

expressivity is variable

Defects in COL2A1 are the cause of Stickler syndrome type 1 non-syndromic ocular (STL1O) [MIM:609508]. STL1O

is an autosomal dominant form of Stickler syndrome characterized by the ocular signs typically seen in STL1 such as

cataract, myopia, retinal detachment. STL1 systemic features of premature osteoarthritis, cleft palate, hearing

impairment, and craniofacial abnormalities are either absent or very mild in STL1O patients

Defects in COL2A1 are a cause of rhegmatogenous retinal detachment autosomal dominant (DRRD) [MIM:609508].

Rhegmatogenous retinal detachment most frequently results from a break or tear in the retina that allows fluid from

the vitreous humor to enter the potential space beneath the retina. It is often associated with pathologic myopia and

in most cases leads to visual impairment or blindness if untreated

10/144 Novoseek disease relationships for COL2A1 gene (see all 144 )

Disease	Score	Articles	PubMed IDs for Articles with Shared Sentences (# sentences)
dysplasia; spondyloepiphyseal	100.00	42	12968670 (4), 8893763 (2), 8423604 (2), 8325895 (2) (see all 33)
stickler syndrome	100.00	77	2573273 (5), 9805127 (3), 10982970 (3), 10706362 (3) (see all 47)
col2a1	100.00	1220	9264261 (14), 12223098 (9), 10729292 (8), 8626777 (7) (see all 100)
chondrodysplasia	79.83	35	7612049 (3), 7989046 (2), 7752131 (2), 7550321 (2) (see all 28)
osteoarthritis	54.80	75	19019890 (4), 7612049 (3), 11824954 (3), 11237662 (3) (see all 57)
kniest dysplasia	52.89	19	10406661 (3), 9675039 (2), 9269170 (2), 8863156 (2) (see all 14)
hypochondrogenesis	31.80	11	10797431 (3), 8175802 (2), 9022054 (1), 8723098 (1) (see all 8)
type 1 stickler syndrome	28.16	9	10706362 (2), 8872475 (1), 18309338 (1), 16752401 (1) (see all 8)
type ii achondrogenesis	24.41	9	10797431 (3), 7829510 (2), 17994563 (2), 3195588 (1) (see all 5)
wagner syndrome	21.48	8	14644728 (2), 8317498 (1), 12939326 (1), 12511349 (1) (see all 7)

About this table

GeneTests: COL2A1

Stickler Syndrome

Human Gene Mutation Database: COL2A1
Genetic Association Database: COL2A1
Human Genome Epidemiology Navigator: COL2A1 (19 documents)

(Possibly Related Articles in Doctor's Guide)
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(in PubMed. Associations of this gene to articles via ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
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10/448 PubMed articles for COL2A1 gene (see all 448 ):

Insulin-like growth factor I gene promoter polymorphism, collagen type II alpha1 (COL2A1) gene, and the prevalence of radiographic osteoarthritis: the Rotterdam Study. (PubMed id 15082485)^{1, 3, 6} Zhai G....van Duijn C.M. (2004)
A novel mutation of COL2A1 resulting in dominantly inherited rhegmatogenous retinal detachment. (PubMed id 15671297)^{1, 3, 4} Richards A.J.... Snead M.P. (2005)
Autosomal dominant rhegmatogenous retinal detachment associated with an Arg453Ter mutation in the COL2A1 gene. (PubMed id 12939326)^{1, 3, 6} Go S.L....Hoyng C.B. (2003)
Widely distributed mutations in the COL2A1 gene produce achondrogenesis type II/hypochondrogenesis. (PubMed id 10797431)^{1, 3, 4} Koerkkoe J.... Prockop D.J. (2000)
Variation in the vitreous phenotype of Stickler syndrome can be caused by different amino acid substitutions in the X position of the type II collagen Gly-X-Y triple helix. (PubMed id 11007540)^{1, 3, 4} Richards A.J.... Snead M.P. (2000)
High efficiency of mutation detection in type 1 stickler syndrome using a two-stage approach: vitreoretinal assessment coupled with exon sequencing for screening COL2A1. (PubMed id 16752401)^{1, 3, 4} Richards A.J....Snead M.P. (2006)
Dominant negative mutations in the C-propeptide of COL2A1 cause platyspondylic lethal skeletal dysplasia, torrance type, and define a novel subfamily within the type 2 collagenopathies. (PubMed id 15643621)^{1, 3, 4} Zankl A.... Superti-Furga A. (2005)
Type II collagen gene variants and inherited osteonecrosis of the femoral head. (PubMed id 15930420)^{1, 3, 4} Liu Y.-F.... Tsai S.-F. (2005)
Spondyloperipheral dysplasia is caused by truncating mutations in the C-propeptide of COL2A1. (PubMed id 15316962)^{1, 3, 4} Zankl A.... Superti-Furga A. (2004)
The deletion of six amino acids at the C-terminus of the alpha 1 (II) chain causes overmodification of type II and type XI collagen: further evidence for the association between small deletions in COL2A1 and Kniest dysplasia. (PubMed id 8863156)^{1, 3, 4} Winterpacht A.... Zabel B. (1996)

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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 1280	HGNC: 2200	AceView: COL2A1	Ensembl:ENSG00000139219	euGenes: HUgn1280
ECgene: COL2A1	Kegg: 1280	H-InvDB: COL2A1

(According to HUGE)
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(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Name	Description
GeneReviews	http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL2A1

Intellectual Property for COL2A1 gene
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Patent Information for COL2A1 gene:

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