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COL4A1 collagen type IV alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 1282, updated on 26-Apr-2020

Summary

Official Symbol
COL4A1provided by HGNC
Official Full Name
collagen type IV alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:2202
See related
Ensembl:ENSG00000187498 MIM:120130
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
BSVD; BSVD1; RATOR; PADMAL; COL4A1s
Summary
This gene encodes a type IV collagen alpha protein. Type IV collagen proteins are integral components of basement membranes. This gene shares a bidirectional promoter with a paralogous gene on the opposite strand. The protein consists of an amino-terminal 7S domain, a triple-helix forming collagenous domain, and a carboxy-terminal non-collagenous domain. It functions as part of a heterotrimer and interacts with other extracellular matrix components such as perlecans, proteoglycans, and laminins. In addition, proteolytic cleavage of the non-collagenous carboxy-terminal domain results in a biologically active fragment known as arresten, which has anti-angiogenic and tumor suppressor properties. Mutations in this gene cause porencephaly, cerebrovascular disease, and renal and muscular defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Expression
Biased expression in placenta (RPKM 204.1), fat (RPKM 72.2) and 9 other tissues See more
Orthologs

Genomic context

See COL4A1 in Genome Data Viewer
Location:
13q34
Exon count:
54
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (110148963..110307157, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (110801310..110959496, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370361 Neighboring gene uncharacterized LOC101927712 Neighboring gene collagen type IV alpha 2 chain Neighboring gene microRNA 8073 Neighboring gene COL4A2 antisense 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps
MedGen: C2673195 OMIM: 611773 GeneReviews: COL4A1-Related Disorders
Compare labs
Brain small vessel disease 1 with or without ocular anomalies
MedGen: C4551998 OMIM: 175780 GeneReviews: COL4A1-Related Disorders
Compare labs
Brain small vessel disease with hemorrhage
MedGen: C4013035 GeneReviews: COL4A1-Related Disorders
Compare labs
Hemorrhage, intracerebral, susceptibility to
MedGen: C3281105 OMIM: 614519 GeneReviews: Not available
Compare labs
MICROANGIOPATHY AND LEUKOENCEPHALOPATHY, PONTINE, AUTOSOMAL DOMINANT
MedGen: CN262231 OMIM: 618564 GeneReviews: Not available
Compare labs
Retinal arteries, tortuosity of
MedGen: C1867327 OMIM: 180000 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
COL4A1 is associated with arterial stiffness by genome-wide association scan.
NHGRI GWA Catalog
Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction.
NHGRI GWA Catalog
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies in multiethnic Asians identifies two loci for age-related nuclear cataract.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 and serum-free macrophage supernatant (MSP) enhance synthesis of type IV collagen by mesangial cells; anti-TGF-beta antibodies attenuate this gp160/MSP-induced collagen synthesis PubMed
Tat tat Treatment with cannabinoids inhibits HIV-1 Tat-enhanced attachment of U937 cells to collagen IV, laminin, or ECM1 proteins, which is linked to the cannabinoid receptor type 2 and the modulation of beta1-integrin and actin distribution PubMed
tat HIV-1 Tat enhances adhesion of human U937 monocyte-like cells to proteins of the extracellular matrix, such as collagen IV, laminin, and ECM1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10041, FLJ25428

Gene Ontology Provided by GOA

Process Evidence Code Pubs
basement membrane organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
blood vessel morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
brain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
branching involved in blood vessel morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
 
collagen-activated tyrosine kinase receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
epithelial cell differentiation IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
neuromuscular junction development IEA
Inferred from Electronic Annotation
more info
 
renal tubule morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
retinal blood vessel morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
basement membrane IC
Inferred by Curator
more info
PubMed 
collagen type IV trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type IV trimer IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen-containing extracellular matrix HDA PubMed 
colocalizes_with collagen-containing extracellular matrix ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region NAS
Non-traceable Author Statement
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
collagen alpha-1(IV) chain
Names
COL4A1 NC1 domain
arresten
collagen IV, alpha-1 polypeptide
collagen of basement membrane, alpha-1 chain

NCBI Reference Sequences (RefSeq)

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_011544.2 RefSeqGene

    Range
    4993..163187
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001303110.2NP_001290039.1  collagen alpha-1(IV) chain isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks alternate exons in the 3' region and contains an alternate 3' terminal exon, resulting in a distinct 3' coding region and 3' UTR compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus compared to isoform 1.
    Source sequence(s)
    AL161773, AL390755, BC142626, X05561
    Consensus CDS
    CCDS76649.1
    UniProtKB/Swiss-Prot
    P02462
    UniProtKB/TrEMBL
    A5PKV2, F5H5K0
    Related
    ENSP00000443348.1, ENST00000543140.6
    Conserved Domains (2) summary
    pfam01391
    Location:275325
    Collagen; Collagen triple helix repeat (20 copies)
    cl25751
    Location:231310
    DUF4045; Domain of unknown function (DUF4045)
  2. NM_001845.6NP_001836.3  collagen alpha-1(IV) chain isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_001836.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AA678474, AL161773, AL390755, BC047305, BC151220, X05561, Y00706
    Consensus CDS
    CCDS9511.1
    UniProtKB/Swiss-Prot
    P02462
    Related
    ENSP00000364979.4, ENST00000375820.10
    Conserved Domains (2) summary
    pfam01391
    Location:9751033
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:15561666
    C4; C-terminal tandem repeated domain in type 4 procollagen

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    110148963..110307157 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521048.2XP_011519350.1  collagen alpha-1(IV) chain isoform X1

    Conserved Domains (2) summary
    pfam01391
    Location:911969
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14921602
    C4; C-terminal tandem repeated domain in type 4 procollagen
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