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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

COL9A1 Gene

protein-coding   GIFtS: 63
GCID: GC06M070924

collagen, type IX, alpha 1
 Explore 25 diseases affiliated with
COL9A1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for COL9A1    

Aliases
for COL9A1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Collagen, Type IX, Alpha 11 2     Alpha-1(IX) Collagen Chain2
EDM62 5     Cartilage-Specific Short Collagen2
DJ149L1.1.22     Collagen Alpha-1(IX) Chain2
MED2     Collagen IX, Alpha-1 Polypeptide2
STL42     

External Ids:    HGNC: 22171   Entrez Gene: 12972   Ensembl: ENSG000001122807   OMIM: 1202105   UniProtKB: P208493   

Export aliases for COL9A1 gene to outside databases

Previous GC identifers: GC06M070884 GC06M070921 GC06M070982 GC06M068124


Summaries
for COL9A1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for COL9A1:
This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of
hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen.
Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen
molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis.
Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of
chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and
auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. (provided
by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: CO9A1_HUMAN, P20849
Function: Structural component of hyaline cartilage and vitreous of the eye

Gene Wiki entry for COL9A1 (Collagen, type IX, alpha 1)


Genomic Views
for COL9A1 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  NT_007299.13  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the COL9A1 gene promoter:
         IRF-2   Nkx2-2   FOXD3   AP-4   IRF-1   Pax-4a   C/EBPalpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): COL9A1 promoter sequence
   Search SABiosciences Chromatin IP Primers for COL9A1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat COL9A1


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

Entrez Gene cytogenetic band: 6q12-q14   Ensembl cytogenetic band:  6q13   HGNC cytogenetic band: 6q12-q14

COL9A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL9A1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M070924:  view genomic region     (about GC identifiers)

Start:
 70,924,764 bp from pter      End:
 71,012,786 bp from pter
Size:
 88,023 bases      Orientation:
 minus strand

Proteins
for COL9A1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: CO9A1_HUMAN, P20849 (See protein sequence)
Recommended Name: Collagen alpha-1(IX) chain precursor  
Size: 921 amino acids; 91869 Da
Subunit: Heterotrimer of an alpha 1(IX), an alpha 2(IX) and an alpha 3(IX) chain
Subcellular location: Secreted, extracellular space, extracellular matrix (By similarity)
1 PDB 3D structure from and Proteopedia for COL9A1:
2UUR (3D)    
Secondary accessions: Q13699 Q13700 Q5TF52 Q6P467 Q96BM8 Q99225 Q9H151 Q9H152 Q9Y6P2 Q9Y6P3
Alternative splicing: 3 isoforms:  P20849-1   P20849-2   P20849-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for COL9A1: NX_P20849

Post-translational modifications:

  • Covalently linked to the telopeptides of type II collagen by lysine-derived cross-links1
  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P20849

    • COL9A1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001842.3  NP_511040.2  

    ENSEMBL proteins: 
     ENSP00000349790   ENSP00000315252   ENSP00000359527   ENSP00000359530  
    Reactome Protein details: P20849
    Human Recombinant Protein Products: 
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    Novus Biologicals COL9A1 Proteins
    Novus Biologicals COL9A1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Uscn

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005594collagen type IX TAS9707347
    GO:0005788endoplasmic reticulum lumen TAS--


    COL9A1 for ontologies           About GeneDecksing



    COL9A1 Antibody Products: 
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    Browse ELISAs and CLIAs at Uscn

    Protein Domains /
    Families
    for COL9A1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    COL9A1 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR013320 ConA-like_subgrp
     IPR001791 Laminin_G
     IPR008160 Collagen
     IPR008985 ConA-like_lec_gl_sf

    Graphical View of Domain Structure for InterPro Entry P20849

    ProtoNet protein and cluster: P20849

    3 Blocks protein families:
    IPB003129 Thrombospondin
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat


    UniProtKB/Swiss-Prot: CO9A1_HUMAN, P20849
    Domain: Each subunit is composed of three triple-helical domains interspersed with non-collagenous domains. The
    globular domain at the N-terminus of type IX collagen molecules represents the NC4 domain which may participate in
    electrostatic interactions with polyanionic glycosaminoglycans in cartilage
    Similarity: Belongs to the fibril-associated collagens with interrupted helices (FACIT) family
    Similarity: Contains 10 collagen-like domains
    Similarity: Contains 1 laminin G-like domain


    Function
    for COL9A1 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: CO9A1_HUMAN, P20849
    Function: Structural component of hyaline cartilage and vitreous of the eye

         Genatlas biochemistry entry for COL9A1:
    collagen,type IX,alpha 1,fibril associated collagen with interrupted triple helices (FACIT),expressed in cartilage

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat COL9A1
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    Inhib. RNA
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    Gene Editing
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    Clone
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    Cell Line
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    LifeMap BioReagents: cell lines associated with COL9A1: Chondrogenic Package 7PEND24,
    Chondrogenic Package E15, Chondrogenic Package SM30, PureStem 7PEND24, NCr-fac & Meso-prx Progenitor

    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL9A1

    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030020extracellular matrix structural constituent conferring tensile strength IC8660302
    GO:0046872metal ion binding IEA--


    COL9A1 for ontologies           About GeneDecksing


    3 GenomeRNAi human phenotypes for COL9A1:
     Decreased nuclei size in G2M  Elongated cells  Increased gamma-H2AX phosphory 

    Animal Models:
         Mouse knock-out Col9a1tm1Jae for COL9A1
         6 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Col9a1):
     hearing/vestibular/ear  homeostasis/metabolism  immune system  limbs/digits/tail  skeleton 
     vision/eye 

    COL9A1 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for COL9A1 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways - 5/11 super-pathways (see all 11) About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Integrin Pathway
    		Integrin Pathway1.00
    		UPA-UPAR Pathway0.51
    		FAK1 Signaling0.67
    		Transendothelial Migration of Leukocytes0.38
    		GnRH Signaling0.56
    		Inhibition of Angiogenesis by TSP10.37
    2Rho Family GTPases
    		Rho Family GTPases1.00
    		MAPK Signaling0.51
    		ERK Signaling0.61
    		ILK Signaling0.45
    		Molecular Mechanisms of Cancer0.51
    3Collagen formation
    		Collagen formation1.00
    		Extracellular matrix organization0.54
    		Collagen biosynthesis and modifying enzymes0.74
    		Secretion of collagens0.49
    4NCAM signaling for neurite out-growth
    		NCAM signaling for neurite out-growth1.00
    		NCAM1 interactions0.62
    5Degradation of the extracellular matrix
    		Degradation of the extracellular matrix1.00
    		Degradation of collagen0.79

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    5/15 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for COL9A1 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    5/12        Reactome Pathways for COL9A1 (see all 12)
        Developmental Biology
    Secretion of collagens
    NCAM1 interactions
    NCAM signaling for neurite out-growth
    Collagen formation


    1         Kegg Pathway  (Kegg details for COL9A1):
        Protein digestion and absorption


    COL9A1 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for COL9A1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/43 Interacting proteins for COL9A1 (P208493 ENSP000003497904) via UniProtKB, MINT, STRING, and/or I2D (see all 43)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    COL9A2Q140553, ENSP000003618344I2D: score=1 STRING: ENSP00000361834
    COMPP497473, ENSP000002222714I2D: score=1 STRING: ENSP00000222271
    COL9A3Q140503, ENSP000003416404I2D: score=1 STRING: ENSP00000341640
    COL2A1P024583, ENSP000003698894I2D: score=1 STRING: ENSP00000369889
    MAGP209163I2D: score=3 
    About this table

    Gene Ontology (GO): 5/7 biological process terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001894tissue homeostasis IEA--
    GO:0002062chondrocyte differentiation ----
    GO:0003417growth plate cartilage development IEA--
    GO:0007411axon guidance TAS--
    GO:0009887organ morphogenesis TAS3473493


    COL9A1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for COL9A1 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for COL9A1
    Search CenterWatch for drugs/clinical trials and news about COL9A1 / CO9A1 

    Transcripts
    for COL9A1 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for COL9A1 gene (2 alternative transcripts): 
    NM_001851.4  NM_078485.3  

    Unigene Cluster for COL9A1:

    Collagen, type IX, alpha 1
    Hs.590892  [show with all ESTs]
    Unigene Representative Sequence: NM_001851
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000357250(uc003pfg.4) ENST00000320755(uc003pfe.4 uc003pff.4)
    ENST00000486080 ENST00000489611 ENST00000447041 ENST00000493682 ENST00000360859
    ENST00000489861 ENST00000470652 ENST00000370496 ENST00000370499

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat COL9A1
    1 QIAGEN miScript miRNA Assays for microRNA that regulate COL9A1:
    hsa-miR-9
    SwitchGear 3'UTR luciferase reporter plasmid: COL9A1 3' UTR sequence
    Inhib. RNA
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    OriGene shRNA RFP: COL9A1
    OriGene siRNA: COL9A1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat COL9A1
    Clone
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    Primer
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    Additional cDNA sequence: 

    AK097582.1 AK125738.1 BC008620.1 BC015409.1 BC063646.1 X54412.1 X54413.1 

    9 DOTS entries:

    DT.91850102  DT.209488  DT.100024648  DT.95185541  DT.99931581  DT.100024649  DT.121344198  DT.99935914 
    DT.121344211 

    24/93 AceView cDNA sequences (see all 93):

    H89286 CB215908 AI986458 BQ007752 BQ573750 BC015409 AI273829 CA415443 
    N67231 AI277812 AL044696 BG030514 AU119275 AI270780 AW950082 N63235 
    CA412796 BI492246 BI492066 BQ573748 BE221644 BQ772356 AK125738 N66382 

    GeneLoc Exon Structure


    Expression
    for COL9A1 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    COL9A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TTCAATGAAA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    COL9A1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    10/18 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 18) 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BoneAutopod Epiphyseal EndPrechondrocytesBone, Cartilage
    BoneStylopod Epiphyseal EndPrechondrocytesBone, Cartilage
    BoneZeugopod Epiphyseal EndPrechondrocytesBone, Cartilage
    LimbStylopod Synovial JointCentral Intermediate Lamina CellsCartilage
    LimbZeugopod Synovial JointCentral Intermediate Lamina CellsCartilage
    HeartAtrioventricular NodeAtrioventricular Node CellsMyocardium
    HeartEndocardiumCushion Mesenchymal CellsEndocardium
    BoneAutopod Long BoneBone
    BoneCaudal Endochondral BonesBone
    BoneEndochondral Facial BonesBone
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 9 LifeMap Cells 
    NameCategory
    HyStem+TGF?3+GDF5-induced SK11 cells (HyStem+TGF?3+GDF5 in...)Bone, Cartilage
    HyStem+TGF?3+GDF5-induced SM30 cells (HyStem+TGF?3+GDF5 in...)Bone, Cartilage
    Micromass-induced chondrocytes (Micromass chondrogen...)Bone, Cartilage
    Micromass-induced chondrocytes (Micromass chondrogen...)Bone, Cartilage
    HyStem+TGF?3+GDF5-induced 7PEND24 cells (HyStem+TGF?3+GDF5 in...)Bone
    HyStem+TGF?3+GDF5-induced 4D20.8 cells (HyStem+TGF?3+GDF5 in...)Bone, Cartilage
    Micromass-induced chondrocytes (Micromass chondrogen...)Bone, Cartilage
    HyStem+BMP4-induced 4D20.8 cells (Chondrogenic inducti...)Bone, Cartilage
    TGF?3+BMP7-induced chondrocytes (Chondrogenic HyStem+...)

    See COL9A1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for COL9A1

    SOURCE GeneReport for Unigene cluster: Hs.590892
        SABiosciences Expression via Pathway-Focused PCR Array including COL9A1: 
              Stem Cells in human mouse rat

    Primer
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    In Situ
    Assay Products:     
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    Orthologs
    for COL9A1 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of chordates.

    Orthologs for COL9A1 gene from 4/12 species (see all 12)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves COL9A11 collagen, type IX, alpha 1 73.41(n)
    74.43(a)    		   771873  NM_001100911.1  NP_001094381.1 
    lizard
    (Anolis carolinensis)    		 Reptilia --
    		 --
    		 71(a)
    		 1 ↔ 1
    		 1(167454638-167518315)
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.160422 Xenopus laevis, Similar to collagen, type IX, alpha more 71.66(n)    BC045244.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii CD778000.12   -- 73.63(n)   335031  CD778000.1 


    ENSEMBL Gene Tree for COL9A1 (if available)
    TreeFam Gene Tree for COL9A1 (if available) 

    Paralogs
    for COL9A1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for COL9A1 gene
    VWA12  MATN42  COL14A12  MATN32  MATN22  COL12A12  VIT2  COL9A32  
    COCH2  COL9A22  COL20A12  VWA22  MATN12  COL21A12  
    9 SIMAP similar genes for COL9A1 using alignment to 2 protein entries:     CO9A1_HUMAN (see all proteins):
    FCN2    COL9A2    COL9A3    C1QTNF9    MARCO    C1QTNF9B
    SFTPD    COL7A1    DKFZp434L081

    COL9A1 for paralogs           About GeneDecksing



    Genomic Variants
    for COL9A1 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1852 NCBI SNPs in COL9A1 are shown (see all 1852)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 6 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1837718661,2
    		--70925262(+) AGTAGA/GTGTTA 2 -- ds50010--------
    rs4776801,2
    		C,F,O,H,--70925287(-) TAATCA/GTATTG 2 -- ds500118Minor allele frequency- G:0.12NS EA NA WA 1876
    rs1884474631,2
    		--70925485(+) AGCAAC/GGCTAG 2 -- ds50010--------
    rs1817669991,2
    		--70925512(+) GAAATA/CTCTGA 2 -- ds50010--------
    rs1864993531,2
    		--70925545(+) GCGCAC/TGCAGC 2 -- ds50010--------
    rs1485207571,2
    		C,--70925615(+) CTAAA-/ACAC  
      ACACAC    ACACA     		2 -- ds50010--------
    rs1914329581,2
    		--70926059(+) ATTTCA/GGGAGA 2 -- ut310--------
    rs557097761,2
    		C,--70926062(+) TCGGGT/AGATGT 2 -- ut311Minor allele frequency- A:0.50WA 2
    rs1868828981,2
    		--70926188(+) AATAAC/TCTGAG 2 -- ut310--------
    rs1914069211,2
    		--70926235(+) GTAAAC/GCAAAC 2 -- ut310--------

    HapMap Linkage Disequilibrium report for COL9A1 (70924764 - 71012786 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for COL9A1: --
    Human Gene Mutation Database (HGMD): COL9A1

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing COL9A1
    DNA2.0 Custom Variant and Variant Library Synthesis for COL9A1

    Disorders / Diseases
    for COL9A1 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    COL9A1 for disorders           About GeneDecksing

    OMIM gene information: 120210    OMIM disorders: --

    UniProtKB/Swiss-Prot: CO9A1_HUMAN, P20849
  • Defects in COL9A1 are the cause of multiple epiphyseal dysplasia type 6 (EDM6) [MIM:614135]. 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
  • Defects in COL9A1 are the cause of Stickler syndrome type 4 (STL4) [MIM:614134]. 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. 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

    20/25 diseases for COL9A1 (see all 25):    About MalaCards
    multiple epiphyseal dysplasia    epiphyseal dysplasia    stickler syndrome    osteoarthritis
    multiple epiphyseal dysplasia, dominant    pierre robin sequence    chondrodysplasia    osteochondritis dissecans
    spinal stenosis    talipes equinovarus    lipoid proteinosis    interstitial keratitis
    short stature    macroglossia    retinal detachment    pseudoachondroplasia
    keratitis    chorioretinitis    strabismus    myopia

    6 diseases from the University of Copenhagen DISEASES database for COL9A1:
    Multiple epiphyseal dysplasia     Clubfoot     Stickler syndrome     Osteoarthritis
    Pseudoachondroplasia     Osteochondritis dissecans

    4 Novoseek disease relationships for COL9A1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    multiple epiphyseal dysplasia 93 1 11565064 (1)
    psach 73 1 11968079 (1)
    osteoarthritis 55.9 3 8244386 (1), 15733274 (1)
    collagen fibril 53.6 2 15869539 (1), 2007255 (1)

    GeneTests: COL9A1
    Stickler Syndrome
    Multiple Epiphyseal Dysplasia, Dominant

    Genetic Association Database (GAD): COL9A1
    Human Genome Epidemiology (HuGE) Navigator: COL9A1 (10 documents)

    Export disorders for COL9A1 gene to outside databases

    Publications
    for COL9A1 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for COL9A1 gene, integrated from 9 sources (see all 77):
    (articles sorted by number of sources associating them with COL9A1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. A mutation in COL9A1 causes multiple epiphyseal dysplasia: further evidence for locus heterogeneity. (PubMed id 11565064)1, 2, 9 Czarny-Ratajczak M.... Ala-Kokko L. (2001)
    2. A new autosomal recessive form of Stickler syndrome is caused by a mutation in the COL9A1 gene. (PubMed id 16909383)1, 2, 9 Van Camp G.... Usami S. (2006)
    3. Human COL9A1 and COL9A2 genes. Two genes of 90 and 15 kb code for similar polypeptides of the same collagen molecule. (PubMed id 9707347)1, 2, 9 Pihlajamaa T....Ala-Kokko L. (1998)
    4. Evidence for a role of the genomic region of the gene encoding for the alpha1 chain of type IX collagen (COL9A1) in hip osteoarthritis: A population-based study. (PubMed id 15880806)1, 4, 9 Alizadeh B.Z....Duijn C.M. (2005)
    5. Mutations in the known genes are not the major cause of MED; distinctive phenotypic entities among patients with no identified mutations. (PubMed id 15523498)1, 4, 9 Jakkula E....Ala-Kokko L. (2005)
    6. The role of sequence variations within the genes encoding collagen II, IX and XI in non-syndromic, early-onset osteoarthritis. (PubMed id 15922184)1, 4, 9 Jakkula E....Ala-Kokko L. (2005)
    7. Crystal structure of the N-terminal NC4 domain of collagen IX, a zinc binding member of the laminin-neurexin-sex hormone binding globulin (LNS) domain family. (PubMed id 17553797)1, 2 Leppanen V.M.... Pihlajamaa T. (2007)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    9. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    10. Collagen type IX from human cartilage: a structural profile of intermolecular cross-linking sites. (PubMed id 8660302)1, 2 Diab M.... Eyre D.R. (1996)

    External Searches for COL9A1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
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    Genome Databases showing COL9A1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 1297 HGNC: 2217 AceView: COL9A1 Ensembl:ENSG00000112280 euGenes: HUgn1297
    ECgene: COL9A1 Kegg: 1297 H-InvDB: COL9A1

    Other Databases showing COL9A1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing COL9A1 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for COL9A1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL9A1

    Intellectual Property
    for COL9A1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for COL9A1 gene:
    Search GeneIP for patents involving COL9A1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
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