Free for academic non-profit institutions. Other users need a Commercial license

Aliases for COL9A2 Gene

Aliases for COL9A2 Gene

  • Collagen Type IX Alpha 2 Chain 2 3 5
  • Collagen, Type IX, Alpha 2 2 3
  • Collagen IX, Alpha-2 Polypeptide 3
  • Collagen Alpha-2(IX) Chain 3
  • Alpha 2 Type IX Collagen 3
  • DJ39G22.4 3
  • STL5 3
  • EDM2 3
  • MED 3

External Ids for COL9A2 Gene

Previous HGNC Symbols for COL9A2 Gene

  • EDM2

Previous GeneCards Identifiers for COL9A2 Gene

  • GC01M040801
  • GC01M039769
  • GC01M040228
  • GC01M040179
  • GC01M040435
  • GC01M040538
  • GC01M040766
  • GC01M038884

Summaries for COL9A2 Gene

Entrez Gene Summary for COL9A2 Gene

  • This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]

GeneCards Summary for COL9A2 Gene

COL9A2 (Collagen Type IX Alpha 2 Chain) is a Protein Coding gene. Diseases associated with COL9A2 include Stickler Syndrome, Type V and Epiphyseal Dysplasia, Multiple, 2. Among its related pathways are ECM proteoglycans and Focal Adhesion. GO annotations related to this gene include extracellular matrix structural constituent conferring tensile strength. An important paralog of this gene is COL9A1.

UniProtKB/Swiss-Prot for COL9A2 Gene

  • Structural component of hyaline cartilage and vitreous of the eye.

Gene Wiki entry for COL9A2 Gene

Additional gene information for COL9A2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL9A2 Gene

Genomics for COL9A2 Gene

Regulatory Elements for COL9A2 Gene

Enhancers for COL9A2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H040338 1.8 FANTOM5 Ensembl ENCODE dbSUPER 12.6 -21.7 -21685 1.8 HDGF PKNOX1 MLX ARNT ARID4B SIN3A ZNF2 TCF12 SLC30A9 ZNF143 PPIE COL9A2 ENSG00000231296 ZMPSTE24 TMCO2 EXO5 SMAP2 PPT1 RLF RPL21P20
GH01H040256 1.2 ENCODE 14.2 +60.1 60108 3 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 ZC3H11A ZFP41 PPIE PPIEL EXO5 TRIT1 ENSG00000259943 RLF NFYC-AS1 LOC105378672 ENSG00000182109 COL9A2
GH01H040266 0.9 Ensembl ENCODE 15.4 +50.4 50361 2.7 FOXA2 MAX REST ATF2 FOXA1 GABPA YY1 ZNF664 JUND ATF3 COL9A2 ZMPSTE24 ENSG00000231296
GH01H040311 1.6 Ensembl ENCODE dbSUPER 7.4 +3.3 3310 5.4 HDGF PKNOX1 ARID4B DMAP1 CBX5 ZNF143 ZNF207 SP5 REST ZNF592 COL9A2 PPT1 ENSG00000231296
GH01H040413 0.9 ENCODE dbSUPER 11.5 -96.5 -96455 1.7 SOX5 SOX13 FOXA2 ZNF644 RARA NFIL3 RERE CEBPA TCF7 HNF4A SMAP2 ZFP69B COL9A2 LOC105378672 EXO5 ENSG00000231296 ZMPSTE24 ZFP69 RLF HEYL
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COL9A2 on UCSC Golden Path with GeneCards custom track

Genomic Locations for COL9A2 Gene

Genomic Locations for COL9A2 Gene
17,330 bases
Minus strand

Genomic View for COL9A2 Gene

Genes around COL9A2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL9A2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL9A2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL9A2 Gene

Proteins for COL9A2 Gene

  • Protein details for COL9A2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Collagen alpha-2(IX) chain
    Protein Accession:
    Secondary Accessions:
    • B2RMP9

    Protein attributes for COL9A2 Gene

    689 amino acids
    Molecular mass:
    65131 Da
    Quaternary structure:
    • Heterotrimer of an alpha 1(IX), an alpha 2(IX) and an alpha 3(IX) chain.

    Three dimensional structures from OCA and Proteopedia for COL9A2 Gene

neXtProt entry for COL9A2 Gene

Post-translational modifications for COL9A2 Gene

  • Covalently linked to the telopeptides of type II collagen by lysine-derived cross-links.
  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
  • Glycosylation at posLast=169169
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COL9A2 Gene

Domains & Families for COL9A2 Gene

Gene Families for COL9A2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for COL9A2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
genes like me logo Genes that share domains with COL9A2: view

Function for COL9A2 Gene

Molecular function for COL9A2 Gene

GENATLAS Biochemistry:
collagen,type IX,alpha 2,fibril associated collagen with interrupted triple helices (FACIT),expressed in cartilage
UniProtKB/Swiss-Prot Function:
Structural component of hyaline cartilage and vitreous of the eye.

Gene Ontology (GO) - Molecular Function for COL9A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030020 extracellular matrix structural constituent conferring tensile strength IC 8660302
genes like me logo Genes that share ontologies with COL9A2: view
genes like me logo Genes that share phenotypes with COL9A2: view

Human Phenotype Ontology for COL9A2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for COL9A2 Gene

MGI Knock Outs for COL9A2:

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for COL9A2 Gene

Localization for COL9A2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL9A2 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

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 COL9A2 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
plasma membrane 1
golgi apparatus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for COL9A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005581 collagen trimer IEA --
GO:0005594 collagen type IX trimer IDA,TAS 8660302
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL9A2: view

Pathways & Interactions for COL9A2 Gene

genes like me logo Genes that share pathways with COL9A2: view

Gene Ontology (GO) - Biological Process for COL9A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 10364514
GO:0030198 extracellular matrix organization TAS --
genes like me logo Genes that share ontologies with COL9A2: view

No data available for SIGNOR curated interactions for COL9A2 Gene

Drugs & Compounds for COL9A2 Gene

(1) Drugs for COL9A2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for COL9A2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with COL9A2: view

Transcripts for COL9A2 Gene

Unigene Clusters for COL9A2 Gene

Collagen, type IX, alpha 2:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL9A2 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^
SP3: - - - - -
SP4: -
SP8: - - - - - - - - - -
SP10: -

ExUns: 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31

Relevant External Links for COL9A2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for COL9A2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COL9A2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL9A2 Gene

This gene is overexpressed in Pituitary (x7.4), Brain - Spinal cord (cervical c-1) (x6.3), and Brain - Substantia nigra (x4.7).

Protein differential expression in normal tissues from HIPED for COL9A2 Gene

This gene is overexpressed in Vitreous humor (58.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL9A2 Gene

Protein tissue co-expression partners for COL9A2 Gene

NURSA nuclear receptor signaling pathways regulating expression of COL9A2 Gene:


SOURCE GeneReport for Unigene cluster for COL9A2 Gene:


Evidence on tissue expression from TISSUES for COL9A2 Gene

  • Nervous system(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL9A2 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cranial nerve
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • skull
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • peripheral nerve
  • peripheral nervous system
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with COL9A2: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for COL9A2 Gene

Orthologs for COL9A2 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL9A2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia COL9A2 33
  • 96.6 (n)
(Canis familiaris)
Mammalia COL9A2 33 34
  • 88.77 (n)
(Mus musculus)
Mammalia Col9a2 33 16 34
  • 87.27 (n)
(Rattus norvegicus)
Mammalia Col9a2 33
  • 87.16 (n)
(Bos Taurus)
Mammalia COL9A2 33 34
  • 86.38 (n)
(Monodelphis domestica)
Mammalia COL9A2 34
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia COL9A2 34
  • 75 (a)
(Gallus gallus)
Aves COL9A2 33 34
  • 71.95 (n)
(Anolis carolinensis)
Reptilia COL9A2 34
  • 79 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia col9a2 33
  • 66.46 (n)
(Danio rerio)
Actinopterygii col9a2 33 34
  • 62.42 (n)
(Caenorhabditis elegans)
Secernentea col-135 34
  • 37 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 22 (a)
Species where no ortholog for COL9A2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • fruit fly (Drosophila melanogaster)
  • 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 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)

Evolution for COL9A2 Gene

Gene Tree for COL9A2 (if available)
Gene Tree for COL9A2 (if available)

Paralogs for COL9A2 Gene

Paralogs for COL9A2 Gene

(9) SIMAP similar genes for COL9A2 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with COL9A2: view

Variants for COL9A2 Gene

Sequence variations from dbSNP and Humsavar for COL9A2 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs137853213 Intervertebral disc disease (IDD) [MIM:603932]
rs606231376 Pathogenic 40,309,934(-) GGTGA(-/CGAGGTGA)GTCCT intron-variant
rs11207843 Likely benign 40,312,120(+) GGGGA(A/G)CAGAG intron-variant, utr-variant-5-prime
rs112370406 Likely benign 40,303,916(+) CTAGG(C/T)CGCGC intron-variant
rs113549021 Likely benign 40,311,262(+) TTTCA(C/T)TCCGG reference, missense

Structural Variations from Database of Genomic Variants (DGV) for COL9A2 Gene

Variant ID Type Subtype PubMed ID
nsv950687 CNV deletion 24416366

Variation tolerance for COL9A2 Gene

Residual Variation Intolerance Score: 95.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.92; 94.90% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL9A2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL9A2 Gene

Disorders for COL9A2 Gene

MalaCards: The human disease database

(20) MalaCards diseases for COL9A2 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
stickler syndrome, type v
  • stickler syndrome 5
epiphyseal dysplasia, multiple, 2
  • multiple epiphyseal dysplasia 2
col9a2-related multiple epiphyseal dysplasia
  • epiphyseal dysplasia, multiple, 2
col9a2-related stickler syndrome
  • stickler syndrome type v
autosomal recessive stickler syndrome
- elite association - COSMIC cancer census association via MalaCards


  • Intervertebral disc disease (IDD) [MIM:603932]: A common musculo-skeletal disorder caused by degeneration of intervertebral disks of the lumbar spine. It results in low-back pain and unilateral leg pain. {ECO:0000269 PubMed:10411504}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Multiple epiphyseal dysplasia 2 (EDM2) [MIM:600204]: A generalized skeletal dysplasia associated with significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. Radiological examination of the skeleton shows delayed, irregular mineralization of the epiphyseal ossification centers and of the centers of the carpal and tarsal bones. Multiple epiphyseal dysplasia is broadly categorized into the more severe Fairbank and the milder Ribbing types. The Fairbank type is characterized by shortness of stature, short and stubby fingers, small epiphyses in several joints, including the knee, ankle, hand, and hip. The Ribbing type is confined predominantly to the hip joints and is characterized by hands that are normal and stature that is normal or near-normal. {ECO:0000269 PubMed:10364514}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Stickler syndrome 5 (STL5) [MIM:614284]: An autosomal recessive 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. STL5 is characterized by high myopia, vitreoretinal degeneration, retinal detachment, mild to moderate sensorineural hearing loss, short stature in childhood, and absence of cleft palate and Pierre Robin sequence. {ECO:0000269 PubMed:21671392}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COL9A2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with COL9A2: view

No data available for Genatlas for COL9A2 Gene

Publications for COL9A2 Gene

  1. An allele of COL9A2 associated with intervertebral disc disease. (PMID: 10411504) Annunen S … Ala-Kokko L (Science (New York, N.Y.) 1999) 3 4 22 45 60
  2. Molecular cloning of the human alpha 2(IX) collagen cDNA and assignment of the human COL9A2 gene to chromosome 1. (PMID: 8454052) Perälä M … Vuorio E (FEBS letters 1993) 2 3 4 22 60
  3. A loss of function mutation in the COL9A2 gene causes autosomal recessive Stickler syndrome. (PMID: 21671392) Baker S … Ala-Kokko L (American journal of medical genetics. Part A 2011) 2 3 4 60
  4. Absence of the mutated Trp2 allele but a common polymorphism of the COL9A2 collagen gene is associated with early recurrence after lumbar discectomy in a German population. (PMID: 18080148) Knoeringer M … Schlegel J (European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society 2008) 3 22 45 60
  5. Genetic factors are associated with modic changes in endplates of lumbar vertebral bodies. (PMID: 18469698) Karppinen J … Männikkö M (Spine 2008) 3 22 45 60

Products for COL9A2 Gene

Sources for COL9A2 Gene

Loading form....