COL2A1 Gene (Protein Coding)

Collagen Type II Alpha 1 Chain

GC12M047972
GIFtS:
49
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 Strud... See more...

Aliases for COL2A1 Gene

Aliases for COL2A1 Gene

  • Collagen Type II Alpha 1 Chain 2 3 5
  • Arthroophthalmopathy, Progressive (Stickler Syndrome) 2 3
  • Collagen, Type II, Alpha 1 2 3
  • Collagen Alpha-1(II) Chain 3 4
  • Alpha-1 Type II Collagen 3 4
  • STL1 2 3
  • Collagen, Type II, Alpha 1 (Primary Osteoarthritis, Spondyloepiphyseal Dysplasia, Congenital) 2
  • Collagen II, Alpha-1 Polypeptide 3
  • Collagen Type II Alpha 1 2
  • Cartilage Collagen 3
  • Chondrocalcin 3
  • COL11A3 3
  • COL2A1 5
  • ANFH 3
  • SEDC 3
  • AOM 3

External Ids for COL2A1 Gene

Previous HGNC Symbols for COL2A1 Gene

  • SEDC
  • AOM

Previous GeneCards Identifiers for COL2A1 Gene

  • GC12M048379
  • GC12M048266
  • GC12M048083
  • GC12M046653
  • GC12M045398
  • GC12M048366

Summaries for COL2A1 Gene

Entrez Gene Summary for COL2A1 Gene

  • 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]

GeneCards Summary for COL2A1 Gene

COL2A1 (Collagen Type II Alpha 1 Chain) is a Protein Coding gene. Diseases associated with COL2A1 include Kniest Dysplasia and Epiphyseal Dysplasia, Multiple, With Myopia And Conductive Deafness. Among its related pathways are Collagen chain trimerization and Integrin Pathway. Gene Ontology (GO) annotations related to this gene include identical protein binding and platelet-derived growth factor binding. An important paralog of this gene is COL1A1.

UniProtKB/Swiss-Prot Summary for COL2A1 Gene

  • 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.

Additional gene information for COL2A1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COL2A1 Gene

Genomics for COL2A1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for COL2A1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL2A1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COL2A1

Top Transcription factor binding sites by QIAGEN in the COL2A1 gene promoter:
  • FOXI1
  • HFH-3
  • Lmo2
  • Pax-3
  • PPAR-alpha
  • SRF
  • SRF (504 AA)
  • STAT1
  • TBP

Genomic Locations for COL2A1 Gene

Latest Assembly
chr12:47,972,967-48,006,212
(GRCh38/hg38)
Size:
33,246 bases
Orientation:
Minus strand

Previous Assembly
chr12:48,366,750-48,398,259
(GRCh37/hg19 by Entrez Gene)
Size:
31,510 bases
Orientation:
Minus strand

chr12:48,366,748-48,398,269
(GRCh37/hg19 by Ensembl)
Size:
31,522 bases
Orientation:
Minus strand

Genomic View for COL2A1 Gene

Genes around COL2A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL2A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL2A1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for COL2A1 Gene

Proteins for COL2A1 Gene

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  • Protein details for COL2A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P02458-CO2A1_HUMAN
    Recommended name:
    Collagen alpha-1(II) chain
    Protein Accession:
    P02458
    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

    Protein attributes for COL2A1 Gene

    Size:
    1487 amino acids
    Molecular mass:
    141785 Da
    Quaternary structure:
    • Homotrimers of alpha 1(II) chains.
    SequenceCaution:
    • Sequence=AAH07252.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for COL2A1 Gene

    Alternative splice isoforms for COL2A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL2A1 Gene

Protein Expression for COL2A1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for COL2A1 Gene

  • 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) COL2.
  • Contains mostly 4-hydroxyproline. Prolines at the third position of the tripeptide repeating unit (G-X-P) are 4-hydroxylated in some or all of the chains.
  • Contains 3-hydroxyproline at a few sites. This modification occurs on the first proline residue in the sequence motif Gly-Pro-Hyp, where Hyp is 4-hydroxyproline.
  • Lysine residues at the third position of the tripeptide repeating unit (G-X-Y) are 5-hydroxylated in some or all of the chains.
  • O-glycosylated on hydroxylated lysine residues. The O-linked glycan consists of a Glc-Gal disaccharide.
  • Glycosylation at Lys190, Asn1388, Lys287, Lys299, Lys308, Lys374, Lys608, Lys620, and Lys1130
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • CO2A1_HUMAN (1126)

Other Protein References for COL2A1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

No data available for DME Specific Peptides for COL2A1 Gene

Domains & Families for COL2A1 Gene

Gene Families for COL2A1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted secreted proteins

Protein Domains for COL2A1 Gene

InterPro:
Blocks:
  • Collagen triple helix repeat
  • Collagen helix repeat
  • Fibrillar collagen, C-terminal

Suggested Antigen Peptide Sequences for COL2A1 Gene

GenScript: Design optimal peptide antigens:
  • Alpha-1 type II collagen (CO2A1_HUMAN)
  • Pro-alpha 1(II) collagen (Q16561_HUMAN)
  • Alpha-1 collagen type II (Q2V4X9_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P02458

UniProtKB/Swiss-Prot:

CO2A1_HUMAN :
  • The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function (By similarity).
  • Belongs to the fibrillar collagen family.
Domain:
  • The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function (By similarity).
Family:
  • Belongs to the fibrillar collagen family.
genes like me logo Genes that share domains with COL2A1: view

Function for COL2A1 Gene

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Molecular function for COL2A1 Gene

UniProtKB/Swiss-Prot 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:
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

Phenotypes From GWAS Catalog for COL2A1 Gene

Gene Ontology (GO) - Molecular Function for COL2A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent IBA 21873635
GO:0005515 protein binding IPI --
GO:0030020 extracellular matrix structural constituent conferring tensile strength RCA 27559042
GO:0042289 MHC class II protein binding IPI 9354468
GO:0042802 identical protein binding NAS 2587267
genes like me logo Genes that share ontologies with COL2A1: view
genes like me logo Genes that share phenotypes with COL2A1: view

Human Phenotype Ontology for COL2A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for COL2A1 Gene

MGI Knock Outs for COL2A1:

Animal Models for research

miRNA for COL2A1 Gene

miRTarBase miRNAs that target COL2A1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL2A1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for COL2A1 Gene

Localization for COL2A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL2A1 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL2A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
nucleus 3
plasma membrane 2
cytoskeleton 2
mitochondrion 2
cytosol 2
lysosome 2
peroxisome 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for COL2A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region HDA,TAS --
GO:0005581 collagen trimer IBA 21873635
GO:0005585 collagen type II trimer IDA 8660302
GO:0005604 basement membrane IEA --
GO:0005615 extracellular space IBA,IMP 20603131
genes like me logo Genes that share ontologies with COL2A1: view

Pathways & Interactions for COL2A1 Gene

PathCards logo

SuperPathways for COL2A1 Gene

SuperPathway Contained pathways
1 Collagen chain trimerization
Collagen biosynthesis and modifying enzymes
.75
Collagen formation
.75
Collagen chain trimerization
.67
Assembly of collagen fibrils and other multimeric structures
.65
Intrinsic Prothrombin Activation Pathway
.48
Blood Coagulation Cascade
.46
Protein digestion and absorption
.42
2 Integrin Pathway
FAK1 Signaling
.67
Integrin Pathway
.67
GnRH Signaling
.56
UPA-UPAR Pathway
.56
Inhibition of Angiogenesis by TSP1
.50
Transendothelial Migration of Leukocytes
.38
3 ERK Signaling
ERK Signaling
.61
Rho Family GTPases
.61
MAPK Signaling
.58
Molecular Mechanisms of Cancer
.51
ILK Signaling
.49
4 Focal Adhesion
Focal adhesion
.61
Focal Adhesion
.61
5 PI3K-Akt signaling pathway
Human papillomavirus infection
.30
PI3K-Akt signaling pathway
.30
genes like me logo Genes that share pathways with COL2A1: view

Pathways by source for COL2A1 Gene

4 GeneGo (Thomson Reuters) pathways for COL2A1 Gene
  • Cell adhesion Integrin inside-out signaling
  • Cell adhesion Integrin-mediated cell adhesion and migration
  • Cell adhesion_ECM remodeling
  • Cytoskeleton remodeling Integrin outside-in signaling
15 Qiagen pathways for COL2A1 Gene
  • Blood Coagulation Cascade
  • ERK Signaling
  • FAK1 Signaling
  • GnRH Signaling
  • ILK Signaling

SIGNOR curated interactions for COL2A1 Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for COL2A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IMP 1429602
GO:0001502 cartilage condensation IEA --
GO:0001503 ossification IEA --
GO:0001894 tissue homeostasis IEA --
GO:0001958 endochondral ossification IEA --
genes like me logo Genes that share ontologies with COL2A1: view

Drugs & Compounds for COL2A1 Gene

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(18) Drugs for COL2A1 Gene - From: DrugBank, DGIdb, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Collagenase Approved, Investigational Pharma Target, binder 0

(16) Additional Compounds for COL2A1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with COL2A1: view

Transcripts for COL2A1 Gene

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mRNA/cDNA for COL2A1 Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL2A1

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

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:

Relevant External Links for COL2A1 Gene

GeneLoc Exon Structure for
COL2A1

Expression for COL2A1 Gene

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  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for COL2A1 Gene

mRNA expression in normal human tissues for COL2A1 Gene
mRNA expression by GTEx for COL2A1 GenemRNA expression by BioGPS for COL2A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL2A1 Gene

This gene is overexpressed in Stomach (x20.7), Pituitary (x15.8), and Testis (x5.9).

Protein differential expression in normal tissues from HIPED for COL2A1 Gene

This gene is overexpressed in Vitreous humor (25.0), Breast (11.1), Plasma (9.5), and Fetal Liver (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for COL2A1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for COL2A1

SOURCE GeneReport for Unigene cluster for COL2A1 Gene:

Hs.408182

mRNA Expression by UniProt/SwissProt for COL2A1 Gene:

P02458-CO2A1_HUMAN
Tissue specificity: Isoform 2 is highly expressed in juvenile chondrocyte and low in fetal chondrocyte.

Evidence on tissue expression from TISSUES for COL2A1 Gene

  • Bone(4.8)
  • Blood(4.4)
  • Muscle(4.4)
  • Skin(2.2)
  • Heart(2.2)
  • Nervous system(2.1)
  • Bone marrow(2.1)
  • Eye(2)
  • Liver(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL2A1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • inner ear
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • skull
  • tongue
  • tooth
Thorax:
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • trachea
Abdomen:
  • abdominal wall
  • intestine
  • kidney
  • liver
Pelvis:
  • pelvis
  • placenta
  • uterus
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • lymph vessel
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with COL2A1: view

Primer products for research

No data available for Protein tissue co-expression partners for COL2A1 Gene

Orthologs for COL2A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL2A1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia COL2A1 29 30
  • 99.62 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia COL2A1 30
  • 93 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia COL2A1 29 30
  • 92.58 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia COL2A1 29 30
  • 92.31 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Col2a1 29
  • 89.55 (n)
Mouse
(Mus musculus)
 Mammalia Col2a1 29 16 30
  • 89.08 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia COL2A1 30
  • 81 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves COL2A1 29 30
  • 79.82 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia COL2A1 30
  • 91 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia col2a1 29
  • 80.06 (n)
Zebrafish
(Danio rerio)
 Actinopterygii col2a1b 30
  • 83 (a)
 OneToMany
col2a1a 29 30
  • 75.78 (n)
 OneToMany
Dr.27172 29
Fruit Fly
(Drosophila melanogaster)
 Insecta Cg25C 30
  • 28 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.7880 30
  • 57 (a)
 OneToMany
Species where no ortholog for COL2A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for COL2A1 Gene

ENSEMBL:
Gene Tree for COL2A1 (if available)
TreeFam:
Gene Tree for COL2A1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for COL2A1: view image
Alliance of Genome Resources:
Additional Orthologs for COL2A1

Paralogs for COL2A1 Gene

Paralogs for COL2A1 Gene

(13) SIMAP similar genes for COL2A1 Gene using alignment to 4 proteins:

  • CO2A1_HUMAN
  • L8EBB9_HUMAN
  • Q16561_HUMAN
  • Q2V4X9_HUMAN
genes like me logo Genes that share paralogs with COL2A1: view

Variants for COL2A1 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COL2A1 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
1000286 Uncertain Significance: not provided 47,993,468(-) G/A
NM_001844.5(COL2A1):c.959C>T (p.Pro320Leu) 		MISSENSE
1001920 Uncertain Significance: not provided 47,975,360(-) G/A
NM_001844.5(COL2A1):c.3843C>T (p.Arg1281=) 		SYNONYMOUS
1002508 Uncertain Significance: not provided 47,973,474(-) G/T
NM_001844.5(COL2A1):c.4397C>A (p.Ala1466Glu) 		MISSENSE
1002732 Uncertain Significance: not provided 47,980,609(-) T/C
NM_001844.5(COL2A1):c.2570A>G (p.Lys857Arg) 		MISSENSE
1003699 Uncertain Significance: Achondrogenesis type II; not provided 47,977,605(-) C/T
NM_001844.5(COL2A1):c.3160G>A (p.Val1054Ile) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for COL2A1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for COL2A1 Gene

Variant ID Type Subtype PubMed ID
esv3580262 CNV loss 25503493
nsv519659 CNV loss 19592680
nsv525456 CNV gain 19592680
nsv558789 CNV loss 21841781
nsv832401 CNV loss 17160897

Variation tolerance for COL2A1 Gene

Residual Variation Intolerance Score: 2.21% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.95; 87.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COL2A1 Gene

Human Gene Mutation Database (HGMD)
COL2A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL2A1
Leiden Open Variation Database (LOVD)
COL2A1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL2A1 Gene

Disorders for COL2A1 Gene

MalaCards: The human disease database

(112) MalaCards diseases for COL2A1 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CO2A1_HUMAN
  • Spondyloepiphyseal dysplasia congenital type (SEDC) [MIM:183900]: Disorder characterized by disproportionate short stature and pleiotropic involvement of the skeletal and ocular systems. {ECO:0000269 PubMed:10678662, ECO:0000269 PubMed:11746045, ECO:0000269 PubMed:2339128, ECO:0000269 PubMed:2543071, ECO:0000269 PubMed:7757086, ECO:0000269 PubMed:8019561, ECO:0000269 PubMed:8325895, ECO:0000269 PubMed:8423604}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Spondyloepiphyseal dysplasia, Stanescu type (SEDSTN) [MIM:616583]: An autosomal dominant spondyloepiphyseal dysplasia characterized by glycoproteins accumulation in chondrocytes. Clinical features include progressive joint contractures, premature degenerative joint disease particularly in the knee, hip and finger joints, and osseous distention of the metaphyseal ends of the phalanges causing swolling of interphalangeal joints of the hands. Radiological features include generalized platyspondyly, hypoplastic pelvis, epiphyseal flattening with metaphyseal splaying of the long bones, and enlarged phalangeal epimetaphyses of the hands. {ECO:0000269 PubMed:26183434}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Spondyloepimetaphyseal dysplasia, Strudwick type (SEMDSTWK) [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. {ECO:0000269 PubMed:16088915, ECO:0000269 PubMed:7550321, ECO:0000269 Ref.39}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Achondrogenesis 2 (ACG2) [MIM:200610]: An autosomal dominant disease characterized by the absence of ossification in the vertebral column, sacrum and pubic bones. {ECO:0000269 PubMed:10745044, ECO:0000269 PubMed:10797431, ECO:0000269 PubMed:15054848, ECO:0000269 PubMed:17994563, ECO:0000269 PubMed:2572591, ECO:0000269 PubMed:7757081, ECO:0000269 PubMed:7757086, ECO:0000269 PubMed:7829510}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Legg-Calve-Perthes disease (LCPD) [MIM:150600]: 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. {ECO:0000269 PubMed:17394019}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Kniest dysplasia (KD) [MIM:156550]: 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. {ECO:0000269 PubMed:7874117, ECO:0000269 PubMed:8863156}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Avascular necrosis of femoral head, primary, 1 (ANFH1) [MIM:608805]: A disease characterized by mechanical failure of the subchondral bone, and degeneration of the hip joint. It usually leads to destruction of the hip joint in the third to fifth decade of life. The clinical manifestations, such as pain on exertion, a limping gait, and a discrepancy in leg length, cause considerable disability. ANFH1 inheritance is autosomal dominant. {ECO:0000269 PubMed:15930420, ECO:0000269 PubMed:21671384}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Osteoarthritis with mild chondrodysplasia (OSCDP) [MIM:604864]: Osteoarthritis is a common disease that produces joint pain and stiffness together with radiologic evidence of progressive degeneration of joint cartilage. {ECO:0000269 PubMed:1975693, ECO:0000269 PubMed:1985108, ECO:0000269 PubMed:7757086, ECO:0000269 PubMed:8507190}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • 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. {ECO:0000269 PubMed:10745044, ECO:0000269 PubMed:14729840, ECO:0000269 PubMed:15643621}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Multiple epiphyseal dysplasia with myopia and conductive deafness (EDMMD) [MIM:132450]: 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. {ECO:0000269 PubMed:9800905}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Spondyloperipheral dysplasia (SPD) [MIM:271700]: SPD patients manifest short stature, midface hypoplasia, sensorineural hearing loss, spondyloepiphyseal dysplasia, platyspondyly and brachydactyly. {ECO:0000269 PubMed:15316962}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Stickler syndrome 1 (STL1) [MIM:108300]: 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. Pierre 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. {ECO:0000269 PubMed:11007540, ECO:0000269 PubMed:20513134, ECO:0000269 PubMed:7977371}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Stickler syndrome 1 non-syndromic ocular (STL1O) [MIM:609508]: An autosomal dominant form of Stickler syndrome characterized by the ocular signs typically seen in Stickler syndrome type 1 such as cataract, myopia, retinal detachment. Systemic features of premature osteoarthritis, cleft palate, hearing impairment, and craniofacial abnormalities are either absent or very mild. {ECO:0000269 PubMed:16752401, ECO:0000269 PubMed:17721977, ECO:0000269 PubMed:8317498}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Rhegmatogenous retinal detachment autosomal dominant (DRRD) [MIM:609508]: A eye disease that 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. {ECO:0000269 PubMed:11007540, ECO:0000269 PubMed:15671297}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • Czech dysplasia (CZECHD) [MIM:609162]: A skeletal dysplasia characterized by early-onset, progressive pseudorheumatoid arthritis, platyspondyly, and short third and fourth toes. {ECO:0000269 PubMed:18553548, ECO:0000269 PubMed:19764028, ECO:0000269 PubMed:7757086, ECO:0000269 PubMed:8244341}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for COL2A1

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Publications for COL2A1 Gene

  1. 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. (PMID: 15643621) Zankl A ā€¦ Superti-Furga A (American journal of medical genetics. Part A 2005) 3 4 22 72
  2. A novel mutation of COL2A1 resulting in dominantly inherited rhegmatogenous retinal detachment. (PMID: 15671297) Richards AJ ā€¦ Snead MP (Investigative ophthalmology & visual science 2005) 3 4 22 72
  3. Type II collagen gene variants and inherited osteonecrosis of the femoral head. (PMID: 15930420) Liu YF ā€¦ Tsai SF (The New England journal of medicine 2005) 3 4 22 72
  4. Spondyloperipheral dysplasia is caused by truncating mutations in the C-propeptide of COL2A1. (PMID: 15316962) Zankl A ā€¦ Superti-Furga A (American journal of medical genetics. Part A 2004) 3 4 22 72
  5. Widely distributed mutations in the COL2A1 gene produce achondrogenesis type II/hypochondrogenesis. (PMID: 10797431) Körkkö J ā€¦ Prockop DJ (American journal of medical genetics 2000) 3 4 22 72

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