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

COL9A1 Gene

protein-coding   GIFtS: 64
GCID: GC06M070924

Collagen, Type IX, Alpha 1

Microbiology & Infectious Diseases Congress
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at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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


(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 Gene:
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)

GeneCards Summary for COL9A1 Gene: 
COL9A1 (collagen, type IX, alpha 1) is a protein-coding gene. Diseases associated with COL9A1 include interstitial keratitis, and autosomal recessive stickler syndrome, and among its related super-pathways are Collagen biosynthesis and modifying enzymes and FAK1 Signaling. GO annotations related to this gene include extracellular matrix structural constituent conferring tensile strength and metal ion binding. An important paralog of this gene is COL25A1.

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) 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NT_007299.13  NC_018917.2  
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: 6q13   Ensembl cytogenetic band:  6q13   HGNC cytogenetic band: 6q13

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

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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

Explore proteomics data for COL9A1 at MOPED 

Post-translational modifications:

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

  • COL9A1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    COL9A1 Protein Expression
    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 for COL9A1: 
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    Sino Biological Cell Lysate for COL9A1 
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    Browse Proteins at Cloud-Clone Corp. 

    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



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    COLPG: Proteoglycans / Extracellular Matrix : Collagen proteoglycans
    COLLAGEN: Collagens

    4 InterPro protein domains:
     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 domains:
    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


    COL9A1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: 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

         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


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

         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

    Animal Models:
         MGI mouse knock-out Col9a1tm1Jae for COL9A1

       inGenious Targeting Laboratory - Custom generated mouse model solutions for COL9A1 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for COL9A1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for COL9A1 
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    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL9A1


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for COL9A1 About   (see all 12)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Collagen biosynthesis and modifying enzymes
    Collagen biosynthesis and modifying enzymes0.74
    Extracellular matrix organization0.39
    Collagen formation0.74
    Blood Coagulation Cascade0.39
    Intrinsic Prothrombin Activation Pathway0.40
    2Integrin Pathway
    Integrin Pathway0.67
    UPA-UPAR Pathway0.56
    FAK1 Signaling0.67
    Inhibition of Angiogenesis by TSP10.50
    GnRH Signaling0.56
    Transendothelial Migration of Leukocytes0.38
    3Rho Family GTPases
    Rho Family GTPases0.61
    Molecular Mechanisms of Cancer0.51
    ERK Signaling0.61
    ILK Signaling0.49
    MAPK Signaling0.58
    4Degradation of the extracellular matrix
    Degradation of the extracellular matrix0.79
    Degradation of collagen0.79
    5Axon guidance
    Axon guidance0.69
    Developmental Biology0.69

    Pathways by source                                                                                                                                                                 See SuperPaths
    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

    1 BioSystems Pathway for COL9A1
        Gastric cancer network 2


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


    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): 5/8 biological process terms (GO ID links to tree view) (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001894tissue homeostasis IEA--
    GO:0003417growth plate cartilage development IEA--
    GO:0007411axon guidance TAS--
    GO:0009887organ morphogenesis TAS3473493
    GO:0022617extracellular matrix disassembly TAS--

    COL9A1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 (CO9A1)

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

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, 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, Sirion Biotech, 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
    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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    1 QIAGEN miScript miRNA Assays for microRNA that regulate COL9A1:
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    Additional mRNA 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):

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

    GeneLoc Exon Structure


    (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)      COL9A1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTCAATGAAA
    COL9A1 Expression
    About this image


    COL9A1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/21 selected tissues (see all 21) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 24 entries
             Prechondrocytes Autopod Epiphyseal End
             Zeugopod Long Bone
             HyStem+TGFbeta3+GDF5-induced SK11 cells
             skeleton/pectoral girdle and thoracic body wall/sternum   
     
     Cartilage (Muscoskeletal System)    fully expand to see all 19 entries
             Prechondrocytes Autopod Epiphyseal End
             Juvenile neocartilage (RevaFlex)
             HyStem+TGFbeta3+GDF5-induced SK11 cells
             sensory organ/nose/nasal septum   
     
     Limb (Muscoskeletal System)    fully expand to see all 3 entries
             Central Intermediate Lamina Cells Zeugopod Synovial Joint
             Pelvic Girdle
     
     Nose (Sensory Organs)    fully expand to see all 2 entries
             sensory organ/nose/naris   
     
     Neural Crest (Gastrulation Derivatives)    fully expand to see all 2 entries
             skeleton/cranium/viscerocranium   

    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

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

    (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 animals.

    Orthologs for COL9A1 gene from 6/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col9a11 , 5 collagen, type IX, alpha 11, 5 86.78(n)1
    90.11(a)1
      1 (9.95 cM)5
    128391  NM_007740.31  NP_031766.31 
     241776105 
    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 --
    --
    --
    73(a)
    71(a)
    1 ↔ many
    1 ↔ many
    1(167420281-167433580)
    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 
    worm
    (Caenorhabditis elegans)
    Secernentea mec-56
    Protein MEC-5
    32(a)
    1 → many
    X(15944009-15948951)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for COL9A1 gene
    COL25A12  COL19A12  COL22A12  COL13A12  COL9A32  COL9A22  COL16A12  COL23A12  
    COL21A12  
    6 SIMAP similar genes for COL9A1 using alignment to 2 protein entries:     CO9A1_HUMAN (see all proteins):
    FCN2    COL9A2    COL9A3    C1QTNF9    MARCO    C1QTNF9B

    COL9A1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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

    10/2237 SNPs in COL9A1 are shown (see all 2237)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs717496911,2
    C--70930093(+) GCAGG-/GTGT  
            
    GTGTG
    2 -- int10--------
    rs721550961,2
    C--70930093(+) GCAGG-/GTGTGT
            
    GTGTG
    2 -- int10--------
    rs593969981,2
    C--70930116(+) GTGTG-/TGTGTG
            
    GTCAT
    2 -- int11Minor allele frequency- TGTGTG:0.00NA 2
    rs582072131,2
    C--70930802(+) TTTTT-/TAAACA 2 -- int10--------
    rs38404081,2
    C--70932442(+) TTTTTT/-ATTCA 2 -- int11Minor allele frequency- -:0.00NA 2
    rs38426091,2
    C--70934598(+) TCATG-/TTTTTT 2 -- int10--------
    rs38426101,2
    C--70941266(+) AAAAA-/ATGTAA 2 -- int10--------
    rs360548521,2
    C--70941418(+) AAAAAA/-CAACC 2 -- int12Minor allele frequency- -:0.25NA 4
    rs358948051,2
    C--70941767(+) AAAAAA/-TCCAT 2 -- int11Minor allele frequency- -:0.00NA 2
    rs1487883351,2
    C--70942870(+) TATGT-/GGAAGC 2 -- int10--------

    HapMap Linkage Disequilibrium report for COL9A1 (70924764 - 71012786 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for COL9A1:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv271252CNV Insertion20981092
    nsv830683CNV Gain17160897
    nsv886143CNV Gain21882294
    nsv524328CNV Gain19592680
    nsv886142CNV Gain21882294


    Human Gene Mutation Database (HGMD): COL9A1
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing COL9A1
    DNA2.0 Custom Variant and Variant Library Synthesis for COL9A1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 120210    OMIM disorders: --

    UniProtKB/Swiss-Prot: CO9A1_HUMAN, P20849
  • Multiple epiphyseal dysplasia 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. Note=The disease is caused by mutations affecting the gene
    represented in this entry
  • Stickler syndrome 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. Note=The disease is caused by mutations affecting the gene
    represented in this entry

  • 20/31 diseases for COL9A1 (see all 31):    About MalaCards
    interstitial keratitis    autosomal recessive stickler syndrome    col9a1-related multiple epiphyseal dysplasia    col9a1-related stickler syndrome
    osteoarthritis    lipoid proteinosis    multiple epiphyseal dysplasia    stickler syndrome
    talipes equinovarus    multiple epiphyseal dysplasia, dominant    osteochondritis dissecans    pierre robin sequence
    macroglossia    pseudoachondroplasia    keratitis    spinal stenosis
    chondrodysplasia    chorioretinitis    retinal detachment    strabismus

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

    COL9A1 for disorders           About GeneDecksing

    4 Novoseek inferred 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
    GeneReviews: COL9A1
    Genetic Association Database (GAD): COL9A1
    Human Genome Epidemiology (HuGE) Navigator: COL9A1 (10 documents)

    Export disorders for COL9A1 gene to outside databases

    (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 79):
    (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. [Analysis of association between COL9A1 gene and idiopathic congenital talipes equinovarus] (PubMed id 17548304)1, 4, 9 Liu L.Y....Sun K.L. (2007)
    3. 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)
    4. 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)
    5. 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)
    6. 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)
    7. 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)
    8. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (2010)
    9. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (2010)
    10. Associations of 25 structural, degradative, and inflammatory candidate genes with lumbar disc desiccation, bulging, and height narrowing. (PubMed id 19180518)1, 4 Videman T....BattiAc M.C. (2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (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

    (According to HUGE)
    About This Section
      --

    (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

    (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



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    About This Section

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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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