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COL10A1 Gene

protein-coding   GIFtS: 59
GCID: GC06M116440

Collagen, Type X, Alpha 1

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Collagen, Type X, Alpha 11 2
Schmid Metaphyseal Chondrodysplasia1 2
Collagen Alpha-1(X) Chain2
Collagen X, Alpha-1 Polypeptide2

External Ids:    HGNC: 21851   Entrez Gene: 13002   Ensembl: ENSG000001235007   OMIM: 1201105   UniProtKB: Q036923   

Export aliases for COL10A1 gene to outside databases

Previous GC identifers: GC06M116275 GC06M116462 GC06M116485 GC06M116546 GC06M114020


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for COL10A1 Gene:
This gene encodes the alpha chain of type X collagen, a short chain collagen expressed by hypertrophic
chondrocytes during endochondral ossification. Unlike type VIII collagen, the other short chain collagen, type X
collagen is a homotrimer. Mutations in this gene are associated with Schmid type metaphyseal chondrodysplasia
(SMCD) and Japanese type spondylometaphyseal dysplasia (SMD). (provided by RefSeq, Jul 2008)

GeneCards Summary for COL10A1 Gene:
COL10A1 (collagen, type X, alpha 1) is a protein-coding gene. Diseases associated with COL10A1 include cartilage disease, and schmid metaphyseal chondrodysplasia. An important paralog of this gene is C1QTNF6.

UniProtKB/Swiss-Prot: COAA1_HUMAN, Q03692
Function: Type X collagen is a product of hypertrophic chondrocytes and has been localized to presumptive
mineralization zones of hyaline cartilage

Gene Wiki entry for COL10A1 (Collagen, type X, 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000006.12  NT_025741.16  NC_018917.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the COL10A1 gene promoter:
         TBP   ISGF-3   AML1a   STAT5A   NF-kappaB   TFIID   NF-kappaB2   ARP-1   Sox9   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOL10A1 promoter sequence
   Search Chromatin IP Primers for COL10A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL10A1


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

Entrez Gene cytogenetic band: 6q21-q22   Ensembl cytogenetic band:  6q22.1   HGNC cytogenetic band: 6q21-q22

COL10A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL10A1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M116440:  view genomic region     (about GC identifiers)

Start:
116,440,085 bp from pter      End:
116,479,910 bp from pter
Size:
39,826 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: COAA1_HUMAN, Q03692 (See protein sequence)
Recommended Name: Collagen alpha-1(X) chain precursor  
Size: 680 amino acids; 66158 Da
Subunit: Homotrimer
1 PDB 3D structure from and Proteopedia for COL10A1:
1GR3 (3D)    
Secondary accessions: A1L4P2

Explore the universe of human proteins at neXtProt for COL10A1: NX_Q03692

Explore proteomics data for COL10A1 at MOPED

Post-translational modifications: 

  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the
    chains1
  • Modification sites at neXtProt

  • See COL10A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_000484.2  
    ENSEMBL proteins: 
     ENSP00000327368   ENSP00000411285   ENSP00000392712   ENSP00000243222  
    Reactome Protein details: Q03692

    COL10A1 Human Recombinant Protein Products:

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    OriGene MassSpec for COL10A1
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    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
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    Browse Proteins at Cloud-Clone Corp.

    COL10A1 Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
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    Novus Biologicals COL10A1 Antibody
    Abcam antibodies for COL10A1 (Q03692, A1L4P2)
    Browse Antibodies at Cloud-Clone Corp.
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    LSBio Antibodies in human, mouse, rat for COL10A1

    COL10A1 Assay Products:

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    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    COLLAGEN: Collagens

    3 InterPro protein domains:
     IPR008983 Tumour_necrosis_fac-like_dom
     IPR008160 Collagen
     IPR001073 C1q

    Graphical View of Domain Structure for InterPro Entry Q03692

    ProtoNet protein and cluster: Q03692

    3 Blocks protein domains:
    IPB001073 Complement C1q protein
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat


    UniProtKB/Swiss-Prot: COAA1_HUMAN, Q03692
    Similarity: Contains 1 C1q domain


    COL10A1 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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: COAA1_HUMAN, Q03692
    Function: Type X collagen is a product of hypertrophic chondrocytes and has been localized to presumptive
    mineralization zones of hyaline cartilage

         Genatlas biochemistry entry for COL10A1:
    collagen,type X,alpha 1,short chain,expressed by chondrocytes in the hypertrophic region of the growth plate
    cartilage

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0046872metal ion binding IEA--
         
    COL10A1 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for COL10A1:
     Cell cycle / mitosis defect  Increased S DNA content 

         10 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Col10a1):
     behavior/neurological  cellular  craniofacial  growth/size/body  hematopoietic system 
     immune system  limbs/digits/tail  mortality/aging  nervous system  skeleton 

    COL10A1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for COL10A1: Col10a1tm1Ksec Col10a1tm1Bhr

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for COL10A1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for COL10A1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for COL10A1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for COL10A1

    miRNA
    Products:
        
    miRTarBase miRNAs that target COL10A1:
    hsa-mir-335-5p (MIRT017342)

    Block miRNA regulation of human, mouse, rat COL10A1 using miScript Target Protectors
    8 qRT-PCR Assays for microRNAs that regulate COL10A1:
    hsa-miR-501-3p hsa-miR-502-3p hsa-miR-1297 hsa-miR-144 hsa-miR-26a hsa-miR-101 hsa-miR-26b hsa-miR-548c-3p
    SwitchGear 3'UTR luciferase reporter plasmidCOL10A1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for COL10A1
    Predesigned siRNA for gene silencing in human, mouse, rat COL10A1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for COL10A1

    Clone
    Products:
         
    OriGene clones in human, mouse for COL10A1 (see all 6)
    OriGene ORF clones in mouse, rat for COL10A1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: COL10A1 (NM_000493)
    Sino Biological Human cDNA Clone for COL10A1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL10A1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL10A1

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for COL10A1
    ESI BIO PureStem Progenitor for COL10A1: 
    PureStem 7PEND24, NCr-fac & Meso-prx Progenitor
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL10A1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    COAA1_HUMAN, Q03692: Secreted, extracellular space, extracellular matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum4
    extracellular4
    lysosome1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005578proteinaceous extracellular matrix ----
    GO:0005581collagen IEA--
    GO:0005788endoplasmic reticulum lumen TAS--
    GO:0005938cell cortex IEA--

    COL10A1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for COL10A1 About   (see all 7)  
    See pathways by source

    SuperPathContained pathways About
    1Collagen biosynthesis and modifying enzymes
    Collagen biosynthesis and modifying enzymes0.75
    Intrinsic Prothrombin Activation Pathway0.39
    Collagen formation0.75
    Blood Coagulation Cascade0.38
    Assembly of collagen fibrils and other multimeric structures0.62
    2Integrin Pathway
    FAK1 Signaling0.67
    UPA-UPAR Pathway0.56
    Integrin Pathway0.67
    Inhibition of Angiogenesis by TSP10.50
    GnRH Signaling0.56
    Transendothelial Migration of Leukocytes0.38
    3ERK Signaling
    Rho Family GTPases0.61
    Molecular Mechanisms of Cancer0.51
    ERK Signaling0.61
    ILK Signaling0.49
    MAPK Signaling0.58
    4Phospholipase-C Pathway
    Phospholipase-C Pathway0.56
    PTEN Pathway0.56
    5Degradation of the extracellular matrix
    Extracellular matrix organization0.34

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL10A1 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    2 BioSystems Pathways for COL10A1
        Senescence and Autophagy
    Endochondral Ossification


    5 Reactome Pathways for COL10A1
        Integrin cell surface interactions
    Collagen biosynthesis and modifying enzymes
    Assembly of collagen fibrils and other multimeric structures
    Non-integrin membrane-ECM interactions
    Collagen degradation



    COL10A1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL10A1: 
              Osteogenesis in human mouse rat
              Lung Cancer in human mouse rat
              Cell Lineage Identification in human mouse rat
              Terminal Differentiation Markers in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for COL10A1

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

    Selected Interacting proteins for COL10A1 (Q036922, 3 ENSP000002432224) via UniProtKB, MINT, STRING, and/or I2D (see all 45)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    P4HBP072372, 3, ENSP000003278014MINT-13883 I2D: score=3 STRING: ENSP00000327801
    ANXA5P087583, ENSP000002965114I2D: score=3 STRING: ENSP00000296511
    COL11A1ENSP000003511634STRING: ENSP00000351163
    COL12A1ENSP000003251464STRING: ENSP00000325146
    COL13A1ENSP000003486954STRING: ENSP00000348695
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001501skeletal system development TAS8554571
    GO:0001958endochondral ossification IEA--
    GO:0022617extracellular matrix disassembly TAS--
    GO:0030198extracellular matrix organization TAS--
    GO:0030574collagen catabolic process TAS--

    COL10A1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for COL10A1 (COAA1)



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for COL10A1 gene: 
    NM_000493.3  

    Unigene Cluster for COL10A1:

    Collagen, type X, alpha 1
    Hs.520339  [show with all ESTs]
    Unigene Representative Sequence: NM_000493
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000327673 ENST00000452729 ENST00000418500 ENST00000243222(uc003pwm.3)

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat COL10A1 using miScript Target Protectors
    8 qRT-PCR Assays for microRNAs that regulate COL10A1:
    hsa-miR-501-3p hsa-miR-502-3p hsa-miR-1297 hsa-miR-144 hsa-miR-26a hsa-miR-101 hsa-miR-26b hsa-miR-548c-3p
    SwitchGear 3'UTR luciferase reporter plasmidCOL10A1 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for COL10A1
    Predesigned siRNA for gene silencing in human, mouse, rat COL10A1
    Clone
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    OriGene ORF clones in mouse, rat for COL10A1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: COL10A1 (NM_000493)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL10A1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL10A1
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for COL10A1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL10A1
      QuantiTect SYBR Green Assays in human, mouse, rat COL10A1
      QuantiFast Probe-based Assays in human, mouse, rat COL10A1

    Additional mRNA sequence: 

    BC130621.1 BC130623.1 S68531.1 

    2 DOTS entries:

    DT.310407  DT.95276608 

    Selected AceView cDNA sequences (see all 30):

    BQ005242 BM728321 BQ026891 CA447328 BF001577 AI623760 AA513722 BU742857 
    BQ771621 AW130440 NM_000493 BQ575261 CA420684 AI376003 AA627427 CD608626 
    BI521533 AI814157 AI858106 AI866828 AI815220 AI752114 AW385820 AA907109 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    COL10A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TACCTTGTGC
    COL10A1 Expression
    About this image


    COL10A1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 45 entries
             Hypertrophic Chondrocytes Stylopod Growth Plate
             Endochondral Facial Bones
             HyStem+TGFbeta3+GDF5-induced MEL2 cells
     
     Cartilage (Muscoskeletal System)    fully expand to see all 38 entries
             Hypertrophic Chondrocytes Temporomandibular Joint
             HyStem+TGFbeta3+GDF5-induced MEL2 cells
     
     Limb (Muscoskeletal System)    fully expand to see all 4 entries
             Mesenchymal Condensate Cells Stylopod
             Pelvic Girdle
     
     NULL (Uncategorized)
             Connective tissue progenitor cells
    COL10A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COL10A1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.520339
        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL10A1: 
              Osteogenesis in human mouse rat
              Lung Cancer in human mouse rat
              Cell Lineage Identification in human mouse rat
              Terminal Differentiation Markers in human mouse rat

    Primer
    Products:
    OriGene qSTAR qPCR primer pairs in human, mouse for COL10A1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL10A1
    QuantiTect SYBR Green Assays in human, mouse, rat COL10A1
    QuantiFast Probe-based Assays in human, mouse, rat COL10A1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL10A1

    (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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for COL10A1 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col10a11 , 5 collagen, type X, alpha 11, 5 85.69(n)1
    87.35(a)1
      10 (18.85 cM)5
    128131  NM_009925.41  NP_034055.11 
     343899815 
    chicken
    (Gallus gallus)
    Aves LOC1008589791 collagen alpha-1(X) chain-like 70.93(n)
    74.89(a)
      100858979  XM_004940291.1  XP_004940348.1 
    lizard
    (Anolis carolinensis)
    Reptilia COL10A16
    collagen, type X, alpha 1
    74(a)
    1 ↔ 1
    1(186425305-186427176)
    zebrafish
    (Danio rerio)
    Actinopterygii col10a1a1 collagen, type X, alpha 1a 59.22(n)
    56.43(a)
      558919  NM_001083827.1  NP_001077296.1 


    ENSEMBL Gene Tree for COL10A1 (if available)
    TreeFam Gene Tree for COL10A1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section

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    Paralogs for COL10A1 gene
    C1QTNF62  C1QB2  C1QTNF12  C1QTNF9B2  C1QA2  C1QTNF42  COL8A22  C1QTNF92  
    C1QTNF52  COL8A12  OTOL12  C1QTNF82  C1QTNF72  C1QC2  C1QTNF22  ADIPOQ2  
    10 SIMAP similar genes for COL10A1 using alignment to 3 protein entries:     COAA1_HUMAN (see all proteins):
    COL8A2    COL8A1    COL14A1    SFTPD    ADIPOQ    C1QB
    COL11A1    COL11A2    COL28A1    COL6A2

    COL10A1 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for COL10A1 (see all 23)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0080394
    Schmid type metaphyseal chondrodysplasia (SMCD)4--see VAR_0080392 Y C mis40--------
    VAR_0231914
    Schmid type metaphyseal chondrodysplasia (SMCD)4--see VAR_0231912 W R mis40--------
    VAR_0231924
    Schmid type metaphyseal chondrodysplasia (SMCD)4--see VAR_0231922 Q P mis40--------
    VAR_0018504
    Schmid type metaphyseal chondrodysplasia (SMCD)4--see VAR_0018502 D G mis40--------
    VAR_0231894
    Schmid type metaphyseal chondrodysplasia (SMCD)4--see VAR_0231892 G R mis40--------
    VAR_0018394
    Schmid type metaphyseal chondrodysplasia (SMCD)4--see VAR_0018392 G R mis40--------
    VAR_0231934
    Schmid type metaphyseal chondrodysplasia (SMCD)4--see VAR_0231932 S P mis40--------
    VAR_0231884
    Schmid type metaphyseal chondrodysplasia (SMCD)4--see VAR_0231882 Y D mis40--------
    VAR_0018454
    Schmid type metaphyseal chondrodysplasia (SMCD)4--see VAR_0018452 S P mis40--------
    VAR_0018424
    Schmid type metaphyseal chondrodysplasia (SMCD)4--see VAR_0018422 G E mis40--------

    HapMap Linkage Disequilibrium report for COL10A1 (116440085 - 116479910 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for COL10A1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv523972CNV Gain19592680

    Human Gene Mutation Database (HGMD): COL10A1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COL10A1
    DNA2.0 Custom Variant and Variant Library Synthesis for COL10A1

    (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.)
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    OMIM gene information: 120110   
    OMIM disorders: 156500  
    UniProtKB/Swiss-Prot: COAA1_HUMAN, Q03692
  • Schmid type metaphyseal chondrodysplasia (SMCD) [MIM:156500]: Dominantly inherited disorder of the
    osseous skeleton. The cardinal features of the phenotype are mild short stature, coxa vara and a waddling gait.
    Radiography usually shows sclerosis of the ribs, flaring of the metaphyses, and a wide irregular growth plate,
    especially of the knees. A variant form of SMCD is spondylometaphyseal dysplasia Japanese type. It is
    characterized by spinal involvement comprising mild platyspondyly, vertebral body abnormalities, and end-plate
    irregularity. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 20 diseases for COL10A1:    
    About MalaCards
    cartilage disease    schmid metaphyseal chondrodysplasia    cartilage-hair hypoplasia    chondrodysplasia
    metaphyseal dysplasia    cleidocranial dysplasia    pseudoachondroplasia    hyperostosis
    age related macular degeneration    short stature    skeletal dysplasias    chondrosarcoma
    osteoarthritis    lung adenocarcinoma    adenocarcinoma    lung cancer
    multiple myeloma    cervicitis    myeloma    breast cancer

    3 diseases from the University of Copenhagen DISEASES database for COL10A1:
    Metaphyseal dysplasia     Osteoarthritis     cartilage-hair hypoplasia

    COL10A1 for disorders           About GeneDecksing

    Selected Novoseek inferred disease relationships for COL10A1 gene (see all 13)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    metaphyseal chondrodysplasia, schmid type 96.6 7 8782043 (2), 17403716 (2), 10991694 (1), 9920912 (1) (see all 5)
    spondylometaphyseal dysplasia 87.7 4 11214689 (1), 8361538 (1), 9837818 (1)
    metaphyseal dysplasia 80 4 11214689 (1), 7607655 (1)
    cartilage-hair hypoplasia 79.5 1 14569119 (1)
    skeletal dysplasia 72.2 4 16845471 (3)
    cartilage diseases 67.3 3 15880705 (1), 16845471 (1)
    hypertrophy 59.9 8 18759285 (2), 17683641 (2), 19062577 (1), 20495570 (1) (see all 6)
    skeletal disorder 58.1 1 19113928 (1)
    short stature 56.5 4 16845471 (2), 15578582 (1)
    osteoarthritis 46.6 1 20495570 (1)

    Genetic Association Database (GAD): COL10A1
    Human Genome Epidemiology (HuGE) Navigator: COL10A1 (2 documents)

    Export disorders for COL10A1 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)
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    PubMed articles for COL10A1 gene, integrated from 10 sources (see all 109):
    (articles sorted by number of sources associating them with COL10A1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning of human alpha 1(X) collagen DNA and localization of the COL10A1 gene to the q21-q22 region of human chromosome 6. (PubMed id 2037056)1, 2, 3, 9 Apte S.... Olsen B.R. (FEBS Lett. 1991)
    2. Mutations within the gene encoding the alpha 1 (X) chain of type X collagen (COL10A1) cause metaphyseal chondrodysplasia type Schmid but not several other forms of metaphyseal chondrodysplasia. (PubMed id 8782043)1, 2, 9 Wallis G.A.... Boot-Handford R.P. (J. Med. Genet. 1996)
    3. Mutations of COL10A1 in Schmid metaphyseal chondrodysplasia. (PubMed id 15880705)1, 2, 9 Bateman J.F.... Savarirayan R. (Hum. Mutat. 2005)
    4. Mutation of the type X collagen gene 'COL10A1' causes spondylometaphyseal dysplasia. (PubMed id 9837818)1, 2, 9 Ikegawa S....Nakamura Y. (Am. J. Hum. Genet. 1998)
    5. Mutations in the N-terminal globular domain of the type X collagen gene (COL10A1) in patients with schmid metaphyseal chondrodysplasia. (PubMed id 9067753)1, 2, 9 Ikegawa S.... Nakamura Y. (Hum. Mutat. 1997)
    6. Cloning of the human and mouse type X collagen genes and mapping of the mouse type X collagen gene to chromosome 10. (PubMed id 1587271)1, 2, 9 Apte S.S.... Olsen B.R. (Eur. J. Biochem. 1992)
    7. Type X collagen multimer assembly in vitro is prevented by a Gly618 to Val mutation in the alpha 1(X) NC1 domain resulting in Schmid metaphyseal chondrodysplasia. (PubMed id 7876225)1, 2, 9 Chan D.... Bateman J.F. (J. Biol. Chem. 1995)
    8. Additional mutations of type X collagen confirm COL10A1 as the Schmid metaphyseal chondrodysplasia locus. (PubMed id 8004099)1, 2, 9 McIntosh I.... Francomano C.A. (Hum. Mol. Genet. 1994)
    9. Amino acid substitutions of conserved residues in the carboxyl- terminal domain of the alpha 1(X) chain of type X collagen occur in two unrelated families with metaphyseal chondrodysplasia type Schmid. (PubMed id 8304336)1, 2, 9 Wallis G.A.... Boot-Handford R.P. (Am. J. Hum. Genet. 1994)
    10. Novel missense mutation resulting in the substitution of tyrosine by cysteine at codon 597 of the type X collagen gene associated with Schmid metaphyseal chondrodysplasia. (PubMed id 9852679)1, 2, 9 Sawai H.... Koyama K. (J. Hum. Genet. 1998)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 1300 HGNC: 2185 AceView: COL10A1 Ensembl:ENSG00000123500 euGenes: HUgn1300
    ECgene: COL10A1 H-InvDB: COL10A1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for COL10A1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=COL10A1[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for COL10A1 gene:
    Search GeneIP for patents involving COL10A1

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



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