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    COL5A1 collagen, type V, alpha 1 [ Homo sapiens (human) ]

    Gene ID: 1289, updated on 22-May-2013
    Official Symbol
    COL5A1provided by HGNC
    Official Full Name
    collagen, type V, alpha 1provided by HGNC
    Primary source
    HGNC:2209
    Locus tag
    RP11-263F14.1
    See related
    Ensembl:ENSG00000130635; HPRD:00368; MIM:120215; Vega:OTTHUMG00000020891
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. The encoded procollagen protein occurs commonly as the heterotrimer pro-alpha1(V)-pro-alpha1(V)-pro-alpha2(V). Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]
    Location :
    9q34.2-q34.3
    Sequence :
    Chromosome: 9; NC_000009.11 (137533652..137736689)
    See COL5A1 in Epigenomics, MapViewer

    Chromosome 9 - NC_000009.11Genomic Context describing neighboring genes Neighboring gene retinoid X receptor, alpha Neighboring gene microRNA 4669 Neighboring gene uncharacterized LOC100506532 Neighboring gene microRNA 3689c Neighboring gene microRNA 3689a

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    Ehlers-Danlos syndrome, type 1

    Summary from GeneReviews: Ehlers-Danlos Syndrome, Classic Type Go to GeneReviews

    Disease Characteristics
    Ehlers-Danlos syndrome (EDS), classic type is a connective tissue disorder characterized by skin hyperextensibility, abnormal wound healing, and joint hypermobility. It includes two previously designated subtypes (EDS type I and EDS type II) that are now recognized to form a continuum of clinical findings. The skin is smooth, velvety to the touch, and hyperelastic; i.e., it extends easily and snaps back after release (unlike lax, redundant skin, as in cutis laxa). The skin is fragile, as manifested by splitting of the dermis following relatively minor trauma, especially over pressure points (knees, elbows) and areas prone to trauma (shins, forehead, chin). Wound healing is delayed, and stretching of scars after apparently successful primary wound healing is characteristic. Complications of joint hypermobility, such as dislocations of the shoulder, patella, digits, hip, radius, and clavicle, usually resolve spontaneously or are easily managed by the affected individual. Other features include hypotonia with delayed motor development, fatigue and muscle cramps, and easy bruising. Less common findings include mitral and tricuspid valve prolapse, aortic root dilatation, and spontaneous rupture of large arteries.
    Diagnosis Testing
    The diagnosis of EDS, classic type is established by family history and clinical examination. Quantitative and qualitative studies of type V collagen chains are usually not useful in confirming a diagnosis. At least 50% of individuals with classic EDS have an identifiable mutation in COL5A1 or COL5A2, the genes encoding type V collagen; however, this number may be an underestimate, since no prospective molecular studies of COL5A1 and COL5A2 have been performed in a clinically well-defined group. Molecular genetic testing for these two genes is available on a clinical basis.
    Genetic Counseling
    EDS, classic type is inherited in an autosomal dominant manner. It is estimated that approximately 50% of affected individuals have inherited the disease-causing mutation from an affected parent, and approximately 50% of affected individuals have a de novo disease-causing mutation. Each child of an affected individual has a 50% chance of inheriting the mutation. Prenatal testing for pregnancies at increased risk may be possible for families in which the disease-causing mutation has been identified in an affected family member.
    References

    Ehlers-Danlos syndrome, type 2

    Summary from GeneReviews: Ehlers-Danlos Syndrome, Classic Type Go to GeneReviews

    Disease Characteristics
    Ehlers-Danlos syndrome (EDS), classic type is a connective tissue disorder characterized by skin hyperextensibility, abnormal wound healing, and joint hypermobility. It includes two previously designated subtypes (EDS type I and EDS type II) that are now recognized to form a continuum of clinical findings. The skin is smooth, velvety to the touch, and hyperelastic; i.e., it extends easily and snaps back after release (unlike lax, redundant skin, as in cutis laxa). The skin is fragile, as manifested by splitting of the dermis following relatively minor trauma, especially over pressure points (knees, elbows) and areas prone to trauma (shins, forehead, chin). Wound healing is delayed, and stretching of scars after apparently successful primary wound healing is characteristic. Complications of joint hypermobility, such as dislocations of the shoulder, patella, digits, hip, radius, and clavicle, usually resolve spontaneously or are easily managed by the affected individual. Other features include hypotonia with delayed motor development, fatigue and muscle cramps, and easy bruising. Less common findings include mitral and tricuspid valve prolapse, aortic root dilatation, and spontaneous rupture of large arteries.
    Diagnosis Testing
    The diagnosis of EDS, classic type is established by family history and clinical examination. Quantitative and qualitative studies of type V collagen chains are usually not useful in confirming a diagnosis. At least 50% of individuals with classic EDS have an identifiable mutation in COL5A1 or COL5A2, the genes encoding type V collagen; however, this number may be an underestimate, since no prospective molecular studies of COL5A1 and COL5A2 have been performed in a clinically well-defined group. Molecular genetic testing for these two genes is available on a clinical basis.
    Genetic Counseling
    EDS, classic type is inherited in an autosomal dominant manner. It is estimated that approximately 50% of affected individuals have inherited the disease-causing mutation from an affected parent, and approximately 50% of affected individuals have a de novo disease-causing mutation. Each child of an affected individual has a 50% chance of inheriting the mutation. Prenatal testing for pregnancies at increased risk may be possible for families in which the disease-causing mutation has been identified in an affected family member.
    References
    Products Interactant Other Gene Complex Source Pubs Description
    P20908 P13497 BMP1    HPRD  PubMed  
    P20908 P25940 COL5A3    HPRD  PubMed  
    P20908 P07585 DCN    HPRD  PubMed  
    P20908 Q08380 LGALS3BP    HPRD  PubMed  
    P20908 O75056 SDC3    HPRD  PubMed  
    P20908 P07996 THBS1    HPRD  PubMed  
    BioGRID:107686 BioGRID:205897 Igfbp7    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:107686 BioGRID:110273 MAG    BioGRID  PubMed Reconstituted Complex 
    BioGRID:107686 BioGRID:119602 SIRT7    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107686 BioGRID:112560 SPARC    BioGRID  PubMed Reconstituted Complex 
    BioGRID:107686 BioGRID:112915 THBS1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:107686 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS 
    • Amoebiasis, organism-specific biosystem (from KEGG)
      Amoebiasis, organism-specific biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
    • Amoebiasis, conserved biosystem (from KEGG)
      Amoebiasis, conserved biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
    • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
      Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
    • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
      Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
    • Collagen formation, organism-specific biosystem (from REACTOME)
      Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
    • ECM-receptor interaction, organism-specific biosystem (from KEGG)
      ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • ECM-receptor interaction, conserved biosystem (from KEGG)
      ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
      Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin, fibronectin and laminin embedded in a viscoelastic gel of ani...
    • Focal Adhesion, organism-specific biosystem (from WikiPathways)
      Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • Focal adhesion, organism-specific biosystem (from KEGG)
      Focal adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • Focal adhesion, conserved biosystem (from KEGG)
      Focal adhesion, conserved biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
      PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
      PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • Protein digestion and absorption, organism-specific biosystem (from KEGG)
      Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • Protein digestion and absorption, conserved biosystem (from KEGG)
      Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...

    Markers

    Homology

    Clone Names

    • FLJ45760

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    extracellular matrix structural constituent IEA
    Inferred from Electronic Annotation
    more info
     
    heparin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integrin binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    platelet-derived growth factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    proteoglycan binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    axon guidance TAS
    Traceable Author Statement
    more info
     
    blood vessel development IEA
    Inferred from Electronic Annotation
    more info
     
    cell adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    collagen biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    collagen catabolic process TAS
    Traceable Author Statement
    more info
     
    collagen fibril organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    collagen fibril organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    extracellular fibril organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    extracellular matrix disassembly TAS
    Traceable Author Statement
    more info
     
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
     
    eye morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    heart morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    integrin biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cellular component organization IEA
    Inferred from Electronic Annotation
    more info
     
    skin development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    wound healing, spreading of epidermal cells IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    basement membrane IEA
    Inferred from Electronic Annotation
    more info
     
    collagen type V IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    colocalizes_with extracellular matrix IDA
    Inferred from Direct Assay
    more info
     
    extracellular matrix IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    extracellular region TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    collagen alpha-1(V) chain
    Names
    collagen alpha-1(V) chain

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008030.1 RefSeqGene

      Range
      5000..208038
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000093.4NP_000084.3  collagen alpha-1(V) chain isoform 1 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AB209864, AB371583, AI190929, AL591890, BC032405, BM051019, CA446007, CB152831, CN399221, CN399265, CN484933, ES314363
      Consensus CDS
      CCDS6982.1
      UniProtKB/Swiss-Prot
      P20908
      UniProtKB/TrEMBL
      Q59EE7
      Related
      ENSP00000360882, OTTHUMP00000022513, ENST00000371817, OTTHUMT00000054954
      Conserved Domains (3) summary
      cd00110
      Location:89226
      Blast Score: 103
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam01391
      Location:10361076
      Blast Score: 89
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:16081837
      Blast Score: 950
      COLFI; Fibrillar collagens C-terminal domain
    2. NM_001278074.1NP_001265003.1  collagen alpha-1(V) chain isoform 2 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate in-frame exon in the 3' coding region compared to variant 1. It encodes isoform 2 which is of the same length but contains an alternate segment, compared to isoform 1. This variant is based on experimental data in PMID 22149965 and is supported by partial transcripts and RNA-seq data.
      Source sequence(s)
      AB209864, AB371583, AI190929, AL591890, BC032405, BM051019, CA446007, CB152831, CN399198, CN399221, CN399265, CN484933, ES314363
      Conserved Domains (3) summary
      pfam01391
      Location:10361076
      Blast Score: 89
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:16081837
      Blast Score: 928
      COLFI; Fibrillar collagens C-terminal domain
      smart00210
      Location:39230
      Blast Score: 538
      TSPN; Thrombospondin N-terminal -like domains

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000009.11 Reference GRCh37.p10 Primary Assembly

      Range
      137533652..137736689
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000141.1 Alternate HuRef

      Range
      106996263..107200594
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018920.1 Alternate CHM1_1.0

      Range
      137568598..137771403
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

      Supplemental Content

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