COL4A2 collagen type IV alpha 2 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL4A2provided by HGNC
Official Full Name: collagen type IV alpha 2 chainprovided by HGNC
Primary source: HGNC:HGNC:2203
See related: Ensembl:ENSG00000134871 MIM:120090; AllianceGenome:HGNC:2203
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: ICH; BSVD2; POREN2
Summary: This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. The C-terminal portion of the protein, known as canstatin, is an inhibitor of angiogenesis and tumor growth. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. [provided by RefSeq, Jul 2008]
Expression: Biased expression in placenta (RPKM 373.6), fat (RPKM 158.9) and 13 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q34

Exon count:: 48

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (110307284..110513209)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (109536748..109743647)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (110959631..111165556)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Venous Tortuosity in COL4A2-Associated Gould Syndrome.
Title: Venous Tortuosity in COL4A2-Associated Gould Syndrome.
Secretome analysis reveals reduced expression of COL4A2 in hypoxic cancer-associated fibroblasts with a tumor-promoting function in gastric cancer.
Title: Secretome analysis reveals reduced expression of COL4A2 in hypoxic cancer-associated fibroblasts with a tumor-promoting function in gastric cancer.
Lysyl hydroxylase 3-mediated post-translational modifications are required for proper biosynthesis of collagen alpha1alpha1alpha2(IV).
Title: Lysyl hydroxylase 3-mediated post-translational modifications are required for proper biosynthesis of collagen α1α1α2(IV).
Next-generation sequencing in a large pedigree segregating visceral artery aneurysms suggests potential role of COL4A1/COL4A2 in disease etiology.
Title: Next-generation sequencing in a large pedigree segregating visceral artery aneurysms suggests potential role of COL4A1/COL4A2 in disease etiology.
The ETS1-LINC00278 negative feedback loop plays a role in COL4A1/COL4A2 regulation in laryngeal squamous cell carcinoma.
Title: The ETS1-LINC00278 negative feedback loop plays a role in COL4A1/COL4A2 regulation in laryngeal squamous cell carcinoma.
Deletion in COL4A2 is associated with a three-generation variable phenotype: from fetal to adult manifestations.
Title: Deletion in COL4A2 is associated with a three-generation variable phenotype: from fetal to adult manifestations.
Prenatal clinical manifestations in individuals with COL4A1/2 variants.
Title: Prenatal clinical manifestations in individuals with COL4A1/2 variants.
Whole-exome sequencing of Finnish patients with vascular cognitive impairment.
Title: Whole-exome sequencing of Finnish patients with vascular cognitive impairment.
Epilepsy and related challenges in children with COL4A1 and COL4A2 mutations: A Gould syndrome patient registry.
Title: Epilepsy and related challenges in children with COL4A1 and COL4A2 mutations: A Gould syndrome patient registry.
Prevalence of COL4A1 and COL4A2 mutations in severe fetal multifocal hemorrhagic and/or ischemic cerebral lesions.
Title: Prevalence of COL4A1 and COL4A2 mutations in severe fetal multifocal hemorrhagic and/or ischemic cerebral lesions.

Submit: New GeneRIF Correction See all GeneRIFs (59)

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
Hemorrhage, intracerebral, susceptibility to MedGen: C3281105 OMIM: 614519 GeneReviews: Not available	Compare labs
Porencephaly 2 MedGen: C3280970 OMIM: 614483 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G19261 (e-PCR)
- UniSTS:58400

RH46595 (e-PCR)
- UniSTS:49953

COL4A2_2599 (e-PCR)
- UniSTS:280618

SHGC-146027 (e-PCR)
- UniSTS:174947

STS-W87433 (e-PCR)
- UniSTS:50315

RH78290 (e-PCR)
- UniSTS:37266

RH1614 (e-PCR)
- UniSTS:56227

G20580 (e-PCR)
- UniSTS:59864

A005X39 (e-PCR)
- UniSTS:59865

SHGC-79998 (e-PCR)
- UniSTS:101622

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	TAS Traceable Author Statement more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	HDA more info	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	ISS Inferred from Sequence or Structural Similarity more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables molecular adaptor activity	EXP Inferred from Experiment more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in cellular response to transforming growth factor beta stimulus	IEA Inferred from Electronic Annotation more info
involved_in collagen-activated tyrosine kinase receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in endodermal cell differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in extracellular matrix organization	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of angiogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in response to activity	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type IV trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type IV trimer	TAS Traceable Author Statement more info	PubMed
colocalizes_with collagen-containing extracellular matrix	HDA more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
colocalizes_with collagen-containing extracellular matrix	ISS Inferred from Sequence or Structural Similarity more info	PubMed
colocalizes_with collagen-containing extracellular matrix	TAS Traceable Author Statement more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA 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(IV) chain

Names: canstatin

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

NG_032137.2 RefSeqGene

Range

5002..210927

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001846.4 → NP_001837.2 collagen alpha-2(IV) chain preproprotein

See identical proteins and their annotated locations for NP_001837.2

Status: REVIEWED

Source sequence(s)

AL139385, AL159153, AL161773

Consensus CDS

CCDS41907.1

UniProtKB/Swiss-Prot

P08572, Q14052, Q548C3, Q5VZA9, Q66K23

Related

ENSP00000353654.5, ENST00000360467.7

Conserved Domains (2) summary

pfam01391
Location:791 → 849

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1598 → 1709

C4; C-terminal tandem repeated domain in type 4 procollagen