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

Gene ID: 1290, updated on 7-Apr-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
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Genomic context

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Location:
2q32.2
Exon count:
61
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (189031898..189441111, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (189520729..189930392, complement)
105.20220307 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. Collagen type V alpha 2 promotes the development of gastric cancer via M2 macrophage polarization. Guo X, et al. Chin J Physiol, 2023 Mar-Apr. PMID 37082997
  2. High expression of COL5A2, a member of COL5 family, indicates the poor survival and facilitates cell migration in gastric cancer. Tan Y, et al. Biosci Rep, 2021 Apr 30. PMID 33739392, Free PMC Article
  3. COL5A2 as a potential clinical biomarker for gastric cancer and renal metastasis. Ding YL, et al. Medicine (Baltimore), 2021 Feb 19. PMID 33607786, 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. Analysis of a gene co-expression network establishes robust association between Col5a2 and ischemic heart disease. Azuaje F, et al. BMC Med Genomics, 2013 Apr 10. PMID 23574622, Free PMC Article

See all (73) 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)

Genotypes

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_2023_10

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

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