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    COL5A2 collagen type V alpha 2 chain [ Homo sapiens (human) ]

    Gene ID: 1290, updated on 27-Nov-2024

    Summary

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    Official Symbol
    COL5A2provided by HGNC
    Official Full Name
    collagen type V alpha 2 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2210
    See related
    Ensembl:ENSG00000204262 MIM:120190; AllianceGenome:HGNC:2210
    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
    Also known as
    EDSC; EDSCL2
    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. Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in gall bladder (RPKM 57.0), placenta (RPKM 54.1) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See COL5A2 in Genome Data Viewer
    Location:
    2q32.2
    Exon count:
    61
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (189031898..189441111, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (189520729..189930392, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (189896624..190044487, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373791 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:189866210-189867409 Neighboring gene microRNA 1245a Neighboring gene microRNA 1245b Neighboring gene collagen type III alpha 1 chain Neighboring gene microRNA 3606 Neighboring gene microRNA 3129 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:190081672-190082544 Neighboring gene keratin 18 pseudogene 19 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:190243866-190244425 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:190291422-190292024 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:190305066-190305764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16847 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16850 Neighboring gene WD repeat domain 75 Neighboring gene KDM3A pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Genetic distance of two fibrillar collagen loci, COL3A1 and COL5A2, located on the long arm of human chromosome 2. Tsipouras P, et al. Genomics, 1988 Oct. PMID 3224983
    2. Cell-specific regulation of alpha1(III) and alpha2(V) collagen by TGF-beta1 in tubulointerstitial cell models. Bertelli R, et al. Nephrol Dial Transplant, 1998 Mar. PMID 9550630
    3. Association of two loci on chromosome 2q with nodal osteoarthritis. Wright GD, et al. Ann Rheum Dis, 1996 May. PMID 8660106, Free PMC Article
    4. The clinical significance of COL5A2 in patients with bladder cancer: A retrospective analysis of bladder cancer gene expression data. Zeng XT, et al. Medicine (Baltimore), 2018 Mar. PMID 29517678, Free PMC Article
    5. Sequence analysis of the COL5A2 gene in patients with spontaneous cervical artery dissections. Grond-Ginsbach C, et al. Neurology, 2002 Apr 9. PMID 11940702

    See all (80) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Collagen type V alpha 2 promotes the development of gastric cancer via M2 macrophage polarization.
      Title: Collagen type V alpha 2 promotes the development of gastric cancer via M2 macrophage polarization.
    2. Phenotype of COL3A1/COL5A2 deletion patients.
      Title: Phenotype of COL3A1/COL5A2 deletion patients.
    3. lncRNA BZRAP1-AS1 alleviates rheumatoid arthritis by regulating miR-1286/COL5A2 axis.
      Title: lncRNA BZRAP1-AS1 alleviates rheumatoid arthritis by regulating miR-1286/COL5A2 axis.
    4. High expression of COL5A2, a member of COL5 family, indicates the poor survival and facilitates cell migration in gastric cancer.
      Title: High expression of COL5A2, a member of COL5 family, indicates the poor survival and facilitates cell migration in gastric cancer.
    5. Rare functional genetic variants in COL7A1, COL6A5, COL1A2 and COL5A2 frequently occur in Chiari Malformation Type 1.
      Title: Rare functional genetic variants in COL7A1, COL6A5, COL1A2 and COL5A2 frequently occur in Chiari Malformation Type 1.
    6. Arterial complications in classical Ehlers-Danlos syndrome: a case series.
      Title: Arterial complications in classical Ehlers-Danlos syndrome: a case series.
    7. Foxf2 and Smad6 co-regulation of collagen 5A2 transcription is involved in the pathogenesis of intrauterine adhesion.
      Title: Foxf2 and Smad6 co-regulation of collagen 5A2 transcription is involved in the pathogenesis of intrauterine adhesion.
    8. COL5A2 as a potential clinical biomarker for gastric cancer and renal metastasis.
      Title: COL5A2 as a potential clinical biomarker for gastric cancer and renal metastasis.
    9. COL5A1 is an unfavorable factor for tumorigenesis, clinicopathological outcomes, and prognosis, whereas COL5A2 is only a favorable factor for prognosis in tongue squamous cell carcinoma
      Title: Differential clinical significance of COL5A1 and COL5A2 in tongue squamous cell carcinoma.
    10. Mutations affecting COL5A1 or COL5A2 are responsible for spectrum of mucocutaneous, ocular and facial features in 62 classical Ehlers-Danlos syndrome patients.
      Title: Spectrum of mucocutaneous, ocular and facial features and delineation of novel presentations in 62 classical Ehlers-Danlos syndrome patients.
    Submit: New GeneRIF Correction See all GeneRIFs (27)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Ehlers-Danlos syndrome, classic type, 2
    MedGen: C0268336 OMIM: 130010 GeneReviews: Classic Ehlers-Danlos Syndrome
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC105115

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SMAD binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables extracellular matrix structural constituent conferring tensile strength HDA PubMed 
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cellular response to amino acid stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in collagen fibril organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in collagen fibril organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in collagen fibril organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in eye morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of endodermal cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ossification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in skeletal system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in skin development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in skin development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in skin development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen type V trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of collagen type V trimer IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    part_of collagen type V trimer NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of collagen type XI trimer NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in collagen-containing extracellular matrix NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular matrix NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    collagen alpha-2(V) chain
    Names
    AB collagen
    collagen, fetal membrane, A polypeptide
    type V preprocollagen alpha 2 chain

    NCBI Reference Sequences (RefSeq)

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    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_011799.3 RefSeqGene

      Range
      50541..198404
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_738

    mRNA and Protein(s)

    1. NM_000393.5 → NP_000384.2  collagen alpha-2(V) chain preproprotein

      See identical proteins and their annotated locations for NP_000384.2

      Status: REVIEWED

      Source sequence(s)
      AB209045, AC133106, AL552427, J04478
      Consensus CDS
      CCDS33350.1
      UniProtKB/Swiss-Prot
      P05997, P78440, Q13908, Q53WR4, Q59GR4, Q6LDJ5, Q7KZ55, Q86XF6, Q96QB0, Q96QB3
      Related
      ENSP00000364000.3, ENST00000374866.9
      Conserved Domains (4) summary
      pfam01391
      Location:495 → 553
      Collagen; Collagen triple helix repeat (20 copies)
      PRK07764
      Location:346 → 553
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam00093
      Location:41 → 96
      VWC; von Willebrand factor type C domain
      pfam01410
      Location:1265 → 1498
      COLFI; Fibrillar collagen C-terminal domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      189031898..189441111 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047443252.1 → XP_047299208.1  collagen alpha-2(V) chain isoform X1

    2. XM_011510573.4 → XP_011508875.1  collagen alpha-2(V) chain isoform X1

      Conserved Domains (4) summary
      pfam01391
      Location:449 → 507
      Collagen; Collagen triple helix repeat (20 copies)
      PRK07764
      Location:300 → 507
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam00093
      Location:1 → 50
      VWC; von Willebrand factor type C domain
      pfam01410
      Location:1219 → 1452
      COLFI; Fibrillar collagen C-terminal domain

    3. XM_047443251.1 → XP_047299207.1  collagen alpha-2(V) chain isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      189520729..189930392 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340460.1 → XP_054196435.1  collagen alpha-2(V) chain isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P05997.3 GenPept UniProtKB/Swiss-Prot:P05997

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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