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

COL11A1 Gene

protein-coding   GIFtS: 62
GCID: GC01M103342

collagen, type XI, alpha 1


(Previous symbol: COLL6)
 Explore 45 diseases affiliated with
COL11A1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for COL11A1    

Aliases
for COL11A1 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 XI, Alpha 11 2
COLL61 2 3
STL21 2 5
CO11A11 2
Collagen Alpha-1(XI) Chain2
Collagen XI, Alpha-1 Polypeptide2

External Ids:    HGNC: 21861   Entrez Gene: 13012   Ensembl: ENSG000000607187   OMIM: 1202805   UniProtKB: P121073   

Export aliases for COL11A1 gene to outside databases

Previous GC identifers: GC01M104172 GC01M102524 GC01M102633 GC01M102805 GC01M103055 GC01M101474


Summaries
for COL11A1 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 COL11A1:
This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. Type XI collagen is a
heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Mutations in this
gene are associated with type II Stickler syndrome and with Marshall syndrome. A single-nucleotide polymorphism in
this gene is also associated with susceptibility to lumbar disc herniation. Multiple transcript variants have been
identified for this gene. (provided by RefSeq, Nov 2009)

UniProtKB/Swiss-Prot: COBA1_HUMAN, P12107
Function: May play an important role in fibrillogenesis by controlling lateral growth of collagen II fibrils

Gene Wiki entry for COL11A1 (Collagen, type XI, alpha 1)


Genomic Views
for COL11A1 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_000001.10  NC_018912.1  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the COL11A1 gene promoter:
         Spz1   GCNF   Nkx2-5   PPAR-gamma1   POU2F1   GCNF-1   HSF2   POU2F1a   PPAR-gamma2   GCNF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: COL11A1 promoter sequence
   Search SABiosciences Chromatin IP Primers for COL11A1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat COL11A1


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

Entrez Gene cytogenetic band: 1p21   Ensembl cytogenetic band:  1p21.1   HGNC cytogenetic band: 1p21

COL11A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL11A1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M103342:  view genomic region     (about GC identifiers)

Start:
 103,342,023 bp from pter      End:
 103,574,052 bp from pter
Size:
 232,030 bases      Orientation:
 minus strand

Proteins
for COL11A1 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: COBA1_HUMAN, P12107 (See protein sequence)
Recommended Name: Collagen alpha-1(XI) chain precursor  
Size: 1806 amino acids; 181065 Da
Subunit: Trimers composed of three different chains: alpha 1(XI), alpha 2(XI), and alpha 3(XI). Alpha 3(XI) is a
post-translational modification of alpha 1(II). Alpha 1(V) can also be found instead of alpha 3(XI)=1(II)
Subcellular location: Secreted, extracellular space, extracellular matrix (By similarity)
Secondary accessions: B1ASK7 D3DT73 E9PCU0 Q14034 Q149N0 Q9UIT4 Q9UIT5 Q9UIT6
Alternative splicing: 4 isoforms:  P12107-1   P12107-2   P12107-3   P12107-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for COL11A1: NX_P12107

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
  • N-glycosylated (By similarity)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P12107

    • COL11A1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (4 alternative transcripts): 
    NP_001177638.1  NP_001845.3  NP_542196.2  NP_542197.3  

    ENSEMBL proteins: 
     ENSP00000359114   ENSP00000426533   ENSP00000408640   ENSP00000410177   ENSP00000351163  
     ENSP00000302551  
    Reactome Protein details: P12107
    Human Recombinant Protein Products: 
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    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005581collagen ----
    GO:0005592collagen type XI NAS10486316
    GO:0005788endoplasmic reticulum lumen TAS--
    GO:0031012extracellular matrix ----


    COL11A1 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for COL11A1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    COL11A1 for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR013320 ConA-like_subgrp
     IPR001791 Laminin_G
     IPR000885 Fib_collagen_C
     IPR008160 Collagen
     IPR008985 ConA-like_lec_gl_sf

    Graphical View of Domain Structure for InterPro Entry P12107

    ProtoNet protein and cluster: P12107

    5 Blocks protein families:
    IPB000885 Fibrillar collagen
    IPB001791 Laminin G
    IPB003129 Thrombospondin
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat


    UniProtKB/Swiss-Prot: COBA1_HUMAN, P12107
    Domain: The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by
    controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen
    fibrils. It binds a calcium ion which is essential for its function (By similarity)
    Similarity: Belongs to the fibrillar collagen family
    Similarity: Contains 8 collagen-like domains
    Similarity: Contains 1 fibrillar collagen NC1 domain
    Similarity: Contains 1 laminin G-like domain


    Function
    for COL11A1 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: COBA1_HUMAN, P12107
    Function: May play an important role in fibrillogenesis by controlling lateral growth of collagen II fibrils

         Genatlas biochemistry entry for COL11A1:
    collagen type XI,alpha 1,fibril forming,expressed in hyaline cartilage,in the ocular vitreous, in the nucleus pulposus
    of the intervertebral disc and in the inner ear,playing an essential role in skeletal morphogenesis and in maitaining
    the interfibrillar spacing and fibril diameter of type II collagen

    miRNA
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    hsa-let-7d hsa-miR-300 hsa-miR-29a hsa-miR-550a* hsa-let-7g hsa-let-7a hsa-miR-98 hsa-miR-200c*
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    Inhib. RNA
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    Gene Editing
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    Clone
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    In Situ Assay
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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005201extracellular matrix structural constituent NAS10486316
    GO:0030674protein binding, bridging NAS10486316
    GO:0046872metal ion binding IEA--
    GO:0050840extracellular matrix binding NAS3182841


    COL11A1 for ontologies           About GeneDecksing


    5 GenomeRNAi human phenotypes for COL11A1:
     Decreased NANOG protein expres  Decreased OCT4 protein express  Decreased POU5F1-GFP protein e  Increased gamma-H2AX phosphory 
     Synthetic lethal with Ras 

    Animal Models:
         9 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Col11a1):
     craniofacial  digestive/alimentary  hearing/vestibular/ear  immune system  limbs/digits/tail 
     mortality/aging  nervous system  respiratory system  skeleton 

    COL11A1 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for COL11A1 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 - 5/12 super-pathways (see all 12) 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
    2Collagen formation
    		Collagen formation1.00
    		Extracellular matrix organization0.54
    		Collagen biosynthesis and modifying enzymes0.74
    		Secretion of collagens0.49
    		Assembly of collagen fibrils and other multimeric structures0.65
    3Rho Family GTPases
    		Rho Family GTPases1.00
    		MAPK Signaling0.51
    		ERK Signaling0.61
    		ILK Signaling0.45
    		Molecular Mechanisms of Cancer0.51
    4Formation of collagen fibres
    		Formation of collagen fibrils1.00
    		Type XII and XIV collagens associate with type I and type II fibrils.0.45
    		Formation of collagen fibres1.00
    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 COL11A1 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    1 BioSystems Pathway for COL11A1 
        Focal Adhesion

    5/12        Reactome Pathways for COL11A1 (see all 12)
        Formation of collagen fibrils
    Secretion of collagens
    Assembly of collagen fibrils and other multimeric structures
    Type XII and XIV collagens associate with type I and type II fibrils.
    Collagen formation


    4         Kegg Pathways  (Kegg details for COL11A1):
        Focal adhesion
    ECM-receptor interaction
    Protein digestion and absorption
    Amoebiasis


    COL11A1 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for COL11A1

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

    5/92 Interacting proteins for COL11A1 (P121073 ENSP000003511634) via UniProtKB, MINT, STRING, and/or I2D (see all 92)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    COL2A1P024583, ENSP000003698894I2D: score=1 STRING: ENSP00000369889
    COL5A1P209083, ENSP000003608824I2D: score=1 STRING: ENSP00000360882
    COL5A2P059973, ENSP000003640004I2D: score=1 STRING: ENSP00000364000
    DDR1Q083453, ENSP000004060914I2D: score=1 STRING: ENSP00000406091
    COL10A1ENSP000002432224STRING: ENSP00000243222
    About this table

    Gene Ontology (GO): 5/15 biological process terms (GO ID links to tree view) (see all 15):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001502cartilage condensation IEA--
    GO:0001503ossification ----
    GO:0002063chondrocyte development IEA--
    GO:0003007heart morphogenesis ----
    GO:0006029proteoglycan metabolic process IEA--


    COL11A1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for COL11A1 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

    COL11A1 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for COL11A1
    1 Novoseek chemical compound relationship for COL11A1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    oligonucleotide 24.7 1 17016581 (1)

    Search CenterWatch for drugs/clinical trials and news about COL11A1 / COBA1 

    Transcripts
    for COL11A1 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,
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    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 COL11A1 gene (4 alternative transcripts): 
    NM_001190709.1  NM_001854.3  NM_080629.2  NM_080630.3  

    Unigene Cluster for COL11A1:

    Collagen, type XI, alpha 1
    Hs.523446  [show with all ESTs]
    Unigene Representative Sequence: NM_080629
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000370096(uc001duk.3 uc001dul.3 uc009weh.3) ENST00000470170
    ENST00000512756 ENST00000465209 ENST00000461720 ENST00000475980 ENST00000427239
    ENST00000447608 ENST00000358392(uc001dum.3) ENST00000353414(uc001dun.3)


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    Inhib. RNA
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    Additional cDNA sequence: 

    AB208844.1 AK299025.1 BC117697.1 J04177.1 

    10 DOTS entries:

    DT.315738  DT.92423416  DT.100752223  DT.100029041  DT.75103415  DT.97831784  DT.315740  DT.92423418 
    DT.97812254  DT.91740538 

    24/186 AceView cDNA sequences (see all 186):

    CA448616 BQ677134 BU753538 CA411719 AI306727 CA412510 CA413902 CF529910 
    CA392383 CA414536 CA415617 BQ008905 CA447834 AA330510 BU170754 BQ009532 
    AA328825 N66519 BU839402 AA622554 BI491893 BF970469 CN479608 CA412517 

    GeneLoc Exon Structure


    Expression
    for COL11A1 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

    COL11A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GCAAAAGCTT

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

    COL11A1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    10/16 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 16) 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BoneAutopod Epiphyseal EndPrechondrocytesBone, Cartilage
    BoneStylopod Epiphyseal EndPrechondrocytesBone, Cartilage
    BoneZeugopod Epiphyseal EndPrechondrocytesBone, Cartilage
    CartilageSynchondrosesChondrocytesBone, Cartilage
    EyeCiliary Marginal ZoneCiliary Marginal Zone CellsNeural Ectoderm
    Head MesenchymeBranchial Arch 2ChondrocytesBone, Cartilage
    LimbAutopodMesenchymal Condensate CellsBone, Cartilage
    LimbStylopodMesenchymal Condensate CellsBone, Cartilage
    LimbZeugopodMesenchymal Condensate CellsBone, Cartilage
    Tendons & LigamentsAxial Tendons and LigamnetsTenocytesTendons & Ligaments
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 10/26 LifeMap Cells (see all 26) 
    NameCategory
    PureStem™ myogenic progenitor Z11 (Embryonic Progenitor Cell)Heart, Myocardium, Smooth Muscle
    PureStem™ progenitor E68 (Embryonic Progenitor Cell)
    PureStem™ mesenchymal Progenitor SK11 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor SM30 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor MEL2 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor 4D20.8 (Embryonic Progenitor Cell)Lateral Plate Mesoderm, Neural Crest
    PureStem™ progenitor E69 (Embryonic Progenitor Cell)
    PureStem™ progenitor EN13 (Embryonic Progenitor Cell)
    PureStem™ progenitor EN7 (Embryonic Progenitor Cell)
    PureStem™ progenitor SK17 (Embryonic Progenitor Cell)

    See COL11A1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for COL11A1

    SOURCE GeneReport for Unigene cluster: Hs.523446

    UniProtKB/Swiss-Prot: COBA1_HUMAN, P12107
    Tissue specificity: Cartilage, placenta and some tumor or virally transformed cell lines. Isoforms using exon IIA or
    IIB are found in the cartilage while isoforms using only exon IIB are found in the tendon

        SABiosciences Expression via Pathway-Focused PCR Arrays including COL11A1: 
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    Orthologs
    for COL11A1 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 animals.

    Orthologs for COL11A1 gene from 5/15 species (see all 15)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves COL11A11 collagen, type XI, alpha 1 81.8(n)
    89.15(a)    		   374046  XM_001231623.2  XP_001231624.2 
    lizard
    (Anolis carolinensis)    		 Reptilia COL11A16
    		 --
    		 88(a)
    		 1 ↔ 1
    		 4(85947317-86223442)
    tropical clawed frog
    (Xenopus tropicalis)    		 Amphibia Str.138512 Transcribed sequence with moderate similarity to protein more 79.65(n)    BX714579.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii col11a1a1 collagen, type XI, alpha 1a 71.41(n)
    80.43(a)    		   565402  NM_001083844.1  NP_001077313.1 
    worm
    (Caenorhabditis elegans)    		 Secernentea mec-56
    		 MEChanosensory abnormality family member (mec-5)
    		 32(a)
    		 1 → many
    		 X(15943939-15948881)


    ENSEMBL Gene Tree for COL11A1 (if available)
    TreeFam Gene Tree for COL11A1 (if available) 

    Paralogs
    for COL11A1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for COL11A1 gene
    COL4A62  COL19A12  COL11A22  COL4A52  COL24A12  COL4A42  COL5A32  COL1A12  
    COL16A12  COL4A22  COL5A22  COL5A12  COL4A32  COL22A12  COL7A12  COL1A22  
    COL27A12  COL3A12  COL2A12  COL4A12  
    13 SIMAP similar genes for COL11A1 using alignment to 10 protein entries:     COBA1_HUMAN (see all proteins):
    COL5A1    COL11A2    COL5A3    C1QTNF9    COL2A1    C1QTNF9B
    COL5A2    COL1A1    COL10A1    COL23A1    SFTPD    COL1A2
    COL3A1

    COL11A1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for COL11A1
    PGOHUM00000262881


    Genomic Variants
    for COL11A1 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

    10/4595 NCBI SNPs in COL11A1 are shown (see all 4595)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 1 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs562003151,2
    		C,--101473767(+) AAAAAA/TGTCTG 4 -- ds50012Minor allele frequency- T:0.12WA 120
    rs747764451,2
    		F,--101473975(+) AAATAT/CCTCTT 4 -- ds50011Minor allele frequency- C:0.05WA 118
    rs618139001,2
    		--101474160(+) TGAAAC/TTGAGA 4 -- ds50011Minor allele frequency- T:0.50NA 2
    rs96590241,2
    		H--101474480(+) TTTAAT/ATTTTA 4 -- ut312Minor allele frequency- A:0.00NS 214
    rs120736191,2
    		C,--101474649(+) TGAAAG/AGAAAA 4 -- ut31 trp32Minor allele frequency- A:0.24WA 120
    rs741080281,2
    		C,--101475050(+) GCTGAA/GATTCA 4 -- ut312Minor allele frequency- G:0.04WA 120
    rs741080291,2
    		C,--101475122(+) TTTGCC/TCTCTG 4 -- ut312Minor allele frequency- T:0.05WA 120
    rs111646261,2
    		C,H--101475600(+) ATTCTG/ACCCCC 4 -- ut314Minor allele frequency- A:0.00NS EA 420
    rs19759161,2
    		H--101475762(+) GCCAAG/AAAAAC 8 /L /F mis1 ese36Minor allele frequency- A:0.31MN NS EA NA 592
    rs121332881,2
    		H,--101476195(+) TGATGT/ATGGTA 4 -- int14Minor allele frequency- A:0.00NS EA 400

    HapMap Linkage Disequilibrium report for COL11A1 (103342023 - 103574052 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for COL11A1
         1 CNV: 53079
         2 Indels: 44425 69217
    Human Gene Mutation Database (HGMD): COL11A1

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    Disorders / Diseases
    for COL11A1 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
    COL11A1 for disorders           About GeneDecksing

    OMIM gene information: 120280   
    OMIM disorders: 604841  154780  603932  
    UniProtKB/Swiss-Prot: COBA1_HUMAN, P12107
  • Defects in COL11A1 are the cause of Stickler syndrome type 2 (STL2) [MIM:604841]; also known as Stickler
    • syndrome vitreous type 2. STL2 is an autosomal dominant 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
  • Defects in COL11A1 are the cause of Marshall syndrome (MRSHS) [MIM:154780]. It is an autosomal dominant
    • disorder characterized by ocular abnormalities, deafness, craniofacial anomalies, and anhidrotic ectodermal dysplasia.
    Clinical features include short stature; flat or retruded midface with short, depressed nose, flat nasal bridge and
    anteverted nares; cleft palate with or without the Pierre Robin sequence; appearance of large eyes with ocular
    hypertelorism; cataracts, either congenital or juvenile; esotropia; high myopia; sensorineural hearing loss;
    spondyloepiphyseal abnormalities; calcification of the falx cerebri; ectodermal abnormalities, including defects in
    sweating and dental structures
  • Defects in COL11A1 are the cause of fibrochondrogenesis type 1 (FBCG1) [MIM:228520]. A severe short-limbed
    • skeletal dysplasia characterized by broad long-bone metaphyses, pear-shaped vertebral bodies, and characteristic
    morphology of the growth plate, in which the chondrocytes have a fibroblastic appearance and there are regions of
    fibrous cartilage extracellular matrix. Clinical features include a flat midface with a small nose and anteverted
    nares, significant shortening of all limb segments but relatively normal hands and feet, and a small bell-shaped
    thorax with a protuberant abdomen

    20/45 diseases for COL11A1 (see all 45):    About MalaCards
    lumbar disc herniation    stickler syndrome    marshall syndrome    pierre robin sequence
    snowflake vitreoretinal degeneration    dihydropyrimidine dehydrogenase deficiency    mitral valve prolapse    vitreoretinal degeneration
    spinal stenosis    stickler syndrome, type 2    stickler syndrome type 1    epiphyseal dysplasia
    hearing loss    multiple epiphyseal dysplasia    abdominal aortic aneurysm    back pain
    fibrochondrogenesis    vitreoretinal dystrophy    cleft palate    aortic aneurysm

    6 diseases from the University of Copenhagen DISEASES database for COL11A1:
    Stickler syndrome     Myopia     Vitreoretinal dystrophy     Vitreous syneresis
    Retinal detachment     Sensorineural hearing loss

    10/12 Novoseek disease relationships for COL11A1 gene (see all 12)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    myopia 71.4 2 10889003 (1), 18280717 (1)
    collagen fibril 53.5 2 17062562 (1), 16752401 (1)
    hearing loss sensorineural 48.6 1 10889003 (1)
    micrognathia 46.9 2 12673280 (2)
    cleft palate 37.3 1 12673280 (1)
    cataract 33.7 1 10889003 (1)
    colorectal carcinoma 13.9 2 11707154 (2)
    metastasis 8.45 3 17123152 (1), 16159426 (1), 17016581 (1)
    nsclc 3.15 2 17016581 (2)
    colorectal cancer 2.93 2 11707154 (1), 11375892 (1)

    GeneTests: COL11A1
    Stickler Syndrome

    Genetic Association Database (GAD): COL11A1
    Human Genome Epidemiology (HuGE) Navigator: COL11A1 (11 documents)

    Export disorders for COL11A1 gene to outside databases

    Publications
    for COL11A1 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 COL11A1 gene, integrated from 9 sources (see all 105):
    (articles sorted by number of sources associating them with COL11A1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and sequencing of pro-alpha 1 (XI) collagen cDNA demonstrates that type XI belongs to the fibrillar class of collagens and reveals that the expression of the gene is not restricted to cartilagenous tissue. (PubMed id 3182841)1, 2, 3 Bernard M.... Ramirez F. (1988)
    2. Stickler syndrome and the vitreous phenotype: mutatio ns in COL2A1 and COL11A1. (PubMed id 20513134)1, 2, 9 Richards A.J....Snead M.P. (2010)
    3. Splicing mutations of 54-bp exons in the COL11A1 gene cause Marshall syndrome, but other mutations cause overlapping Marshall/Stickler phenotypes. (PubMed id 10486316)1, 2, 9 Annunen S.... Ala-Kokko L. (1999)
    4. A family with Stickler syndrome type 2 has a mutation in the COL11A1 gene resulting in the substitution of glycine 97 by valine in alpha- 1(XI) collagen. (PubMed id 8872475)1, 2, 9 Richards A.J.... Snead M.P. (1996)
    5. 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)
    6. Fibrochondrogenesis results from mutations in the COL 11A1 type XI collagen gene. (PubMed id 21035103)1, 2 Tompson S.W....Cohn D.H. (2010)
    7. Alternative mRNA processing occurs in the variable region of the pro- alpha 1(XI) and pro-alpha 2(XI) collagen chains. (PubMed id 7721876)1, 2 Zhidkova N.I.... Mayne R. (1995)
    8. Pro-alpha 1(XI) collagen. Structure of the amino-terminal propeptide and expression of the gene in tumor cell lines. (PubMed id 1690726)1, 2 Yoshioka H. and Ramirez F. (1990)
    9. Collagen 11a1 is indirectly activated by lymphocyte enhancer-binding factor 1 (Lef1) and negatively regulates osteoblast maturation. (PubMed id 18280717)1, 9 Kahler R.A....Westendorf J.J. (2008)
    10. COL11A1 in FAP polyps and in sporadic colorectal tumors. (PubMed id 11707154)1, 9 Fischer H....Lindblom A. (2001)

    External Searches for COL11A1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
    OMIM
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      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing COL11A1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 1301 HGNC: 2186 AceView: COL11A1 Ensembl:ENSG00000060718 euGenes: HUgn1301
    ECgene: COL11A1 Kegg: 1301 H-InvDB: COL11A1

    Other Databases showing COL11A1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing COL11A1 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 COL11A1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL11A1

    Intellectual Property
    for COL11A1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for COL11A1 gene:
    Search GeneIP for patents involving COL11A1

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



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