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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 IX, Alpha-3 Polypeptide 3
  • Collagen Alpha-3(IX) Chain 3
  • DJ885L7.4.1 3
  • EDM3 3
  • IDD 3
  • MED 3

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 ERK Signaling and Collagen chain trimerization. Gene Ontology (GO) annotations related to this gene include extracellular matrix structural constituent conferring tensile strength. An important paralog of this gene is COL9A2.

UniProtKB/Swiss-Prot for COL9A3 Gene

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

Gene Wiki entry for COL9A3 Gene

Additional gene information for COL9A3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL9A3 Gene

Genomics for COL9A3 Gene

GeneHancer (GH) Regulatory Elements for COL9A3 Gene

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 dbSUPER 681.3 +1.4 1423 5.9 PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF48 ZNF121 GLIS2 FOS COL9A3 MRGBP TCFL5 ENSG00000223669 OGFR GMEB2 DPH3P1
GH20J062836 Promoter 0.8 EPDnew 650.3 +20.1 20138 0.1 MAZ MTA1 ELK1 EGR1 ZBTB33 ELF1 CREM COL9A3 DPH3P1
GH20J062831 Enhancer 1.2 Ensembl ENCODE dbSUPER 53.5 +16.3 16337 2.6 PKNOX1 FOXA2 NFIB SIN3A RAD21 YY1 RCOR1 RXRA CEBPB GATAD2B COL9A3 TCFL5 DPH3P1
GH20J062922 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4.8 +110.2 110221 8.5 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 E2F8 ZNF207 DIDO1 TCFL5 GMEB2 TAF4 RTEL1 GID8 ARFRP1 MRGBP TNFRSF6B YTHDF1
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for COL9A3 Gene

Genomic Locations for COL9A3 Gene
24,916 bases
Plus strand
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 posLast=483483
  • 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

Suggested Antigen Peptide Sequences for COL9A3 Gene

GenScript: Design optimal peptide antigens:

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

Gene Ontology (GO) - Molecular Function for COL9A3 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 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

Animal Model Products

miRNA for COL9A3 Gene

miRTarBase miRNAs that target COL9A3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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 5
cytoskeleton 2
nucleus 2
plasma membrane 1
lysosome 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 IDA,TAS 8660302
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL9A3: view

Pathways & Interactions for COL9A3 Gene

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

Gene Ontology (GO) - Biological Process for COL9A3 Gene

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

No data available for SIGNOR curated interactions for COL9A3 Gene

Drugs & Compounds for COL9A3 Gene

No Compound Related Data Available

Transcripts for COL9A3 Gene

mRNA/cDNA for COL9A3 Gene

Unigene Clusters for COL9A3 Gene

Collagen, type IX, alpha 3:
Representative Sequences:

Clone Products

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
ECgene alternative splicing isoforms for

Expression for COL9A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of COL9A3 Gene:


SOURCE GeneReport for Unigene cluster for COL9A3 Gene:


Evidence on tissue expression from TISSUES for COL9A3 Gene

  • Skin(4.5)

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

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 34 33
  • 98.98 (n)
(Monodelphis domestica)
Mammalia COL9A3 34
  • 87 (a)
(Canis familiaris)
Mammalia COL9A3 34 33
  • 85.37 (n)
(Bos Taurus)
Mammalia COL9A3 34 33
  • 84.69 (n)
(Mus musculus)
Mammalia Col9a3 16 34 33
  • 84.04 (n)
(Rattus norvegicus)
Mammalia Col9a3 33
  • 83.83 (n)
(Ornithorhynchus anatinus)
Mammalia COL9A3 34
  • 81 (a)
(Gallus gallus)
Aves COL9A3 34 33
  • 69.97 (n)
(Anolis carolinensis)
Reptilia COL9A3 34
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia col9a3 33
  • 67.93 (n)
Str.11870 33
(Danio rerio)
Actinopterygii col9a3 34 33
  • 63.59 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG42342 34
  • 27 (a)
(Caenorhabditis elegans)
Secernentea col-99 34
  • 30 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 48 (a)
Species where no ortholog for COL9A3 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)
  • 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 COL9A3 Gene

Gene Tree for COL9A3 (if available)
Gene Tree for COL9A3 (if available)
Evolutionary constrained regions (ECRs) for COL9A3: view image

Paralogs for COL9A3 Gene

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 from dbSNP and Humsavar for COL9A3 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1011451878 uncertain-significance, Multiple Epiphyseal Dysplasia, Dominant 62,841,008(+) G/A/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1048100 benign, not specified, Multiple Epiphyseal Dysplasia, Dominant 62,840,721(+) C/A/G/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, stop_gained, synonymous_variant
rs1048132 benign, Multiple Epiphyseal Dysplasia, Dominant 62,841,088(+) C/G/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1055327177 uncertain-significance, Multiple Epiphyseal Dysplasia, Dominant 62,840,850(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1057518693 pathogenic, Multiple epiphyseal dysplasia 3 62,821,532(+) T/C splice_donor_variant

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

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

Disorders for COL9A3 Gene

MalaCards: The human disease database

(14) MalaCards diseases for COL9A3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • 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 mutations 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 variations 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

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

No data available for Genatlas for COL9A3 Gene

Publications for COL9A3 Gene

  1. 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 58
  2. Occupational and genetic risk factors associated with intervertebral disc disease. (PMID: 17471097) Virtanen IM … Ala-Kokko L (Spine 2007) 3 22 44 58
  3. Intervertebral disc degeneration in relation to the COL9A3 and the IL-1ss gene polymorphisms. (PMID: 16133074) Solovieva S … Riihimäki H (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 2006) 3 22 44 58
  4. Mutations in the known genes are not the major cause of MED; distinctive phenotypic entities among patients with no identified mutations. (PMID: 15523498) Jakkula E … Ala-Kokko L (European journal of human genetics : EJHG 2005) 3 22 44 58
  5. The role of sequence variations within the genes encoding collagen II, IX and XI in non-syndromic, early-onset osteoarthritis. (PMID: 15922184) Jakkula E … Ala-Kokko L (Osteoarthritis and cartilage 2005) 3 22 44 58

Products for COL9A3 Gene

Sources for COL9A3 Gene

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