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. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010] See more...

Aliases for COL9A3 Gene

Aliases for COL9A3 Gene

  • Collagen Type IX Alpha 3 Chain 2 3 5
  • Collagen Type IX Proteoglycan 2 3
  • Collagen, Type IX, Alpha 3 2 3
  • Collagen Alpha-3(IX) Chain 3 4
  • DJ885L7.4.1 2 3
  • EDM3 2 3
  • IDD 2 3
  • MED 2 3
  • Collagen IX, Alpha-3 Polypeptide 3
  • FLJ90759 2
  • COL9A3 5

External Ids for COL9A3 Gene

Previous GeneCards Identifiers for COL9A3 Gene

  • GC20P061325
  • GC20P062127
  • GC20P062174
  • GC20P060918
  • GC20P061447
  • GC20P058166

Summaries for COL9A3 Gene

Entrez Gene Summary for COL9A3 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. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]

GeneCards Summary for COL9A3 Gene

COL9A3 (Collagen Type IX Alpha 3 Chain) is a Protein Coding gene. Diseases associated with COL9A3 include Epiphyseal Dysplasia, Multiple, 3 and Intervertebral Disc Disease. Among its related pathways are Collagen chain trimerization and Integrin Pathway. Gene Ontology (GO) annotations related to this gene include extracellular matrix structural constituent conferring tensile strength. An important paralog of this gene is COL4A3.

UniProtKB/Swiss-Prot Summary for COL9A3 Gene

Gene Wiki entry for COL9A3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COL9A3 Gene

Genomics for COL9A3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for COL9A3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J062814 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 281.2 +1.5 1542 5.7 EZH2 ZNF600 ZMYM3 ZNF10 NFIC POLR2A ZIC2 ZBTB10 CHD4 KLF11 COL9A3 HSALNG0131568 TCFL5 ENSG00000223669 OGFR piR-36262
GH20J062836 Promoter/Enhancer 1.2 EPDnew Ensembl dbSUPER 255.4 +20.2 20157 0.4 ELF1 MAZ EGR1 BHLHE40 CREM HNRNPL MTA1 ZBTB33 RBFOX2 ELK1 COL9A3 HSALNG0131570 lnc-TCFL5-5 TCFL5
GH20J062816 Promoter/Enhancer 0.8 Ensembl dbSUPER 256.2 -1.7 -1743 0.2 RBM22 POLR2A PAF1 GLIS2 RBFOX2 SCRT2 COL9A3 lnc-TCFL5-6 TCFL5 ENSG00000223669 OGFR
GH20J062831 Promoter/Enhancer 1.5 Ensembl ENCODE CraniofacialAtlas dbSUPER 53.5 +16.3 16337 2.6 MYC ZNF600 CTCF CEBPB ZNF341 ZNF217 MBD2 CTBP1 KLF9 SP2 COL9A3 TCFL5 lnc-TCFL5-5 piR-36262
GH20J062821 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas dbSUPER 25.5 +7.8 7750 3.2 NCOR1 ZNF654 MYC ZNF600 SSRP1 ZNF580 ZMYM3 KLF9 CEBPA BRCA1 COL9A3 DIDO1 GMEB2 TAF4 MRGBP OGFR GID8 RTEL1 piR-36262 HSALNG0131568
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL9A3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COL9A3

Top Transcription factor binding sites by QIAGEN in the COL9A3 gene promoter:
  • AhR
  • CP2
  • HNF-4alpha1
  • HNF-4alpha2
  • Ik-3
  • MAZR
  • Pax-4a
  • POU2F1
  • POU2F1a
  • Zic3

Genomic Locations for COL9A3 Gene

Latest Assembly
24,916 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
24,110 bases
Plus strand

(GRCh37/hg19 by Ensembl)
24,916 bases
Plus strand

Genomic View for COL9A3 Gene

Genes around COL9A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL9A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL9A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL9A3 Gene

Proteins for COL9A3 Gene

  • Protein details for COL9A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Collagen alpha-3(IX) chain
    Protein Accession:
    Secondary Accessions:
    • Q13681
    • Q9H4G9
    • Q9UPE2

    Protein attributes for COL9A3 Gene

    684 amino acids
    Molecular mass:
    63616 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 COL9A3 Gene

neXtProt entry for COL9A3 Gene

Post-translational modifications for COL9A3 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 Asn483
  • Modification sites at PhosphoSitePlus

Other Protein References for COL9A3 Gene

No data available for DME Specific Peptides for COL9A3 Gene

Domains & Families for COL9A3 Gene

Gene Families for COL9A3 Gene

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

Protein Domains for COL9A3 Gene

  • Collagen triple helix repeat
  • Collagen helix repeat

Suggested Antigen Peptide Sequences for COL9A3 Gene

GenScript: Design optimal peptide antigens:
  • Collagen alpha-3(IX) chain (CO9A3_HUMAN)

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 COL9A3: view

Function for COL9A3 Gene

Molecular function for COL9A3 Gene

UniProtKB/Swiss-Prot Function:
Structural component of hyaline cartilage and vitreous of the eye.
GENATLAS Biochemistry:
collagen,type IX,alpha 3,fibril associated collagen with interrupted triple helices (FACIT),expressed in cartilage

Phenotypes From GWAS Catalog for COL9A3 Gene

Gene Ontology (GO) - Molecular Function for COL9A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent IBA 21873635
GO:0030020 extracellular matrix structural constituent conferring tensile strength RCA 25037231
genes like me logo Genes that share ontologies with COL9A3: view
genes like me logo Genes that share phenotypes with COL9A3: view

Human Phenotype Ontology for COL9A3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for COL9A3 Gene

miRTarBase miRNAs that target COL9A3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL9A3

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for COL9A3 Gene

Localization for COL9A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL9A3 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 COL9A3 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
nucleus 3
plasma membrane 2
cytoskeleton 2
mitochondrion 1
peroxisome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for COL9A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005581 collagen trimer IEA --
GO:0005594 collagen type IX trimer TAS,IDA 8660302
GO:0005604 basement membrane IBA 21873635
GO:0005615 extracellular space IBA 21873635
genes like me logo Genes that share ontologies with COL9A3: view

Pathways & Interactions for COL9A3 Gene

PathCards logo

SuperPathways for COL9A3 Gene

SuperPathway Contained pathways
1 Collagen chain trimerization
2 Integrin Pathway
3 ERK Signaling
4 Degradation of the extracellular matrix
5 ECM-receptor interaction
genes like me logo Genes that share pathways with COL9A3: view

Pathways by source for COL9A3 Gene

15 Qiagen pathways for COL9A3 Gene
  • Blood Coagulation Cascade
  • ERK Signaling
  • FAK1 Signaling
  • GnRH Signaling
  • ILK Signaling

Interacting Proteins for COL9A3 Gene

SIGNOR curated interactions for COL9A3 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for COL9A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008584 male gonad development IBA 21873635
GO:0008585 female gonad development IBA 21873635
GO:0030198 extracellular matrix organization TAS --
genes like me logo Genes that share ontologies with COL9A3: view

Drugs & Compounds for COL9A3 Gene

No Compound Related Data Available

Transcripts for COL9A3 Gene

mRNA/cDNA for COL9A3 Gene

7 NCBI additional mRNA sequence :
14 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 COL9A3

Alternative Splicing Database (ASD) splice patterns (SP) for COL9A3 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9
SP1: -
SP2: -

Relevant External Links for COL9A3 Gene

GeneLoc Exon Structure for

Expression for COL9A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for COL9A3 Gene

mRNA differential expression in normal tissues according to GTEx for COL9A3 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x6.8) and Brain - Substantia nigra (x4.7).

Protein differential expression in normal tissues from HIPED for COL9A3 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for COL9A3 Gene

Protein tissue co-expression partners for COL9A3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for COL9A3

SOURCE GeneReport for Unigene cluster for COL9A3 Gene:


Evidence on tissue expression from TISSUES for COL9A3 Gene

  • Skin(4.6)
  • Nervous system(2.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL9A3 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 COL9A3: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt for COL9A3 Gene

Orthologs for COL9A3 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL9A3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia COL9A3 29 30
  • 98.98 (n)
(Monodelphis domestica)
Mammalia COL9A3 30
  • 87 (a)
(Canis familiaris)
Mammalia COL9A3 29 30
  • 85.37 (n)
(Bos Taurus)
Mammalia COL9A3 29 30
  • 84.69 (n)
(Mus musculus)
Mammalia Col9a3 29 16 30
  • 84.04 (n)
(Rattus norvegicus)
Mammalia Col9a3 29
  • 83.83 (n)
(Ornithorhynchus anatinus)
Mammalia COL9A3 30
  • 81 (a)
(Gallus gallus)
Aves COL9A3 29 30
  • 69.97 (n)
(Anolis carolinensis)
Reptilia COL9A3 30
  • 75 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia col9a3 29
  • 67.93 (n)
Str.11870 29
(Danio rerio)
Actinopterygii col9a3 29 30
  • 63.59 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG42342 30
  • 27 (a)
(Caenorhabditis elegans)
Secernentea col-99 30
  • 30 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 48 (a)
Species where no ortholog for COL9A3 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)

Evolution for COL9A3 Gene

Gene Tree for COL9A3 (if available)
Gene Tree for COL9A3 (if available)
Evolutionary constrained regions (ECRs) for COL9A3: view image
Alliance of Genome Resources:
Additional Orthologs for COL9A3

Paralogs for COL9A3 Gene

(4) SIMAP similar genes for COL9A3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with COL9A3: view

Variants for COL9A3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COL9A3 Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
1003519 Uncertain Significance: not provided 62,836,515(+) G/C
NM_001853.4(COL9A3):c.1586G>C (p.Cys529Ser)
1004563 Uncertain Significance: not provided 62,830,540(+) C/A
NM_001853.4(COL9A3):c.1239C>A (p.Asp413Glu)
1004731 Uncertain Significance: not provided 62,837,168(+) GCCCCCAGGA/G
NM_001853.4(COL9A3):c.1698_1706del (p.561PPG[2])
1005993 Uncertain Significance: not provided 62,840,552(+) C/T
NM_001853.4(COL9A3):c.1875C>T (p.Gly625=)
1007050 Uncertain Significance: not provided 62,838,712(+) C/T
NM_001853.4(COL9A3):c.1815C>T (p.Gly605=)

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for COL9A3 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 COL9A3 Gene

Variant ID Type Subtype PubMed ID
esv1317287 CNV deletion 17803354
esv2259099 CNV deletion 18987734
esv2722838 CNV deletion 23290073
esv2722839 CNV deletion 23290073
nsv1131599 CNV deletion 24896259
nsv428380 CNV loss 18775914
nsv470558 CNV loss 18288195
nsv828794 CNV loss 20364138
nsv834027 CNV loss 17160897
nsv953302 CNV deletion 24416366
nsv9825 CNV gain 18304495

Variation tolerance for COL9A3 Gene

Residual Variation Intolerance Score: 96.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.65; 89.16% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COL9A3 Gene

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

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL9A3 Gene

Disorders for COL9A3 Gene

MalaCards: The human disease database

(42) MalaCards diseases for COL9A3 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD


  • Multiple epiphyseal dysplasia 3 (EDM3) [MIM:600969]: 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:10090888, ECO:0000269 PubMed:25381065}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • 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:11308397, ECO:0000269 PubMed:25381065}. Note=Disease susceptibility is associated with variants affecting the gene represented in this entry. Susceptibility to intervertebral disk disease is conferred by variant p.Arg103Trp (PubMed:11308397). {ECO:0000269 PubMed:11308397}.

Additional Disease Information for COL9A3

Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with COL9A3: view

No data available for Genatlas for COL9A3 Gene

Publications for COL9A3 Gene

  1. Identification of a novel common genetic risk factor for lumbar disk disease. (PMID: 11308397) Paassilta P … Ala-Kokko L (JAMA 2001) 3 4 22 72
  2. COL9A3: A third locus for multiple epiphyseal dysplasia. (PMID: 10090888) Paassilta P … Ala-Kokko L (American journal of human genetics 1999) 3 4 22 72
  3. Molecular cloning of the alpha 3 chain of human type IX collagen: linkage of the gene COL9A3 to chromosome 20q13.3. (PMID: 8586434) Brewton RG … Baker JR (Genomics 1995) 2 3 4 22
  4. Autosomal recessive Stickler syndrome due to a loss of function mutation in the COL9A3 gene. (PMID: 24273071) Faletra F … Gasparini P (American journal of medical genetics. Part A 2014) 2 3 72
  5. Occupational and genetic risk factors associated with intervertebral disc disease. (PMID: 17471097) Virtanen IM … Ala-Kokko L (Spine 2007) 3 22 40

Products for COL9A3 Gene

Sources for COL9A3 Gene