VCAN versican [Homo sapiens (human)] - Gene

Summary

Official Symbol: VCANprovided by HGNC
Official Full Name: versicanprovided by HGNC
Primary source: HGNC:HGNC:2464
See related: Ensembl:ENSG00000038427 MIM:118661; AllianceGenome:HGNC:2464
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: WGN; ERVR; GHAP; PG-M; WGN1; CSPG2
Summary: This gene is a member of the aggrecan/versican proteoglycan family. The protein encoded is a large chondroitin sulfate proteoglycan and is a major component of the extracellular matrix. This protein is involved in cell adhesion, proliferation, proliferation, migration and angiogenesis and plays a central role in tissue morphogenesis and maintenance. Mutations in this gene are the cause of Wagner syndrome type 1. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]
Expression: Broad expression in appendix (RPKM 45.0), placenta (RPKM 35.3) and 15 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q14.2-q14.3

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (83471744..83582302)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (83960520..84071053)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (82767563..82878121)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

The oncogenic ADAMTS1-VCAN-EGFR cyclic axis drives anoikis resistance and invasion in renal cell carcinoma.
Title: The oncogenic ADAMTS1-VCAN-EGFR cyclic axis drives anoikis resistance and invasion in renal cell carcinoma.
CircVCAN promotes glioma progression through the miR-488-3p/MEF2C-JAGGED1 axis.
Title: CircVCAN promotes glioma progression through the miR-488-3p/MEF2C-JAGGED1 axis.
Expression of versican isoforms V0/V1 by pancreatic cancer associated fibroblasts increases fibroblast proliferation.
Title: Expression of versican isoforms V0/V1 by pancreatic cancer associated fibroblasts increases fibroblast proliferation.
Versican Associates with Tumor Immune Phenotype and Limits T-cell Trafficking via Chondroitin Sulfate.
Title: Versican Associates with Tumor Immune Phenotype and Limits T-cell Trafficking via Chondroitin Sulfate.
Versican Promotes Cardiomyocyte Proliferation and Cardiac Repair.
Title: Versican Promotes Cardiomyocyte Proliferation and Cardiac Repair.
Identification of mutation gene prognostic biomarker in multiple myeloma through gene panel exome sequencing and transcriptome analysis in Chinese population.
Title: Identification of mutation gene prognostic biomarker in multiple myeloma through gene panel exome sequencing and transcriptome analysis in Chinese population.
V3: an enigmatic isoform of the proteoglycan versican.
Title: V3: an enigmatic isoform of the proteoglycan versican.
Knockdown of versican 1 in lung fibroblasts aggravates Lipopolysaccharide-induced acute inflammation through up-regulation of the SP1-Toll-like Receptor 2-NF-kappaB Axis: a potential barrier to promising Versican-targeted therapy.
Title: Knockdown of versican 1 in lung fibroblasts aggravates Lipopolysaccharide-induced acute inflammation through up-regulation of the SP1-Toll-like Receptor 2-NF-κB Axis: a potential barrier to promising Versican-targeted therapy.
TGF-beta1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells.
Title: TGF-β1 dominates stromal fibroblast-mediated EMT via the FAP/VCAN axis in bladder cancer cells.
VCAN Hypomethylation and Expression as Predictive Biomarkers of Drug Sensitivity in Upper Urinary Tract Urothelial Carcinoma.
Title: VCAN Hypomethylation and Expression as Predictive Biomarkers of Drug Sensitivity in Upper Urinary Tract Urothelial Carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (160)

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
Wagner syndrome MedGen: C1840452 OMIM: 143200 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study identifies three susceptibility loci for laryngeal squamous cell carcinoma in the Chinese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of major recurrent depression in the U.K. population. 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 transmembrane glycoprotein gp41	env	A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 upregulates the expression of versican (VCAN) in peptide-treated PBMCs	PubMed

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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

RH17573 (e-PCR)
- UniSTS:22275

RH45290 (e-PCR)
- UniSTS:6404

SHGC-82303 (e-PCR)
- UniSTS:104244

L28255 (e-PCR)
- UniSTS:80695

RH69411 (e-PCR)
- UniSTS:33638

CSPG2 (e-PCR)
- UniSTS:504954

RH35859 (e-PCR)
- UniSTS:1679

SHGC-68433 (e-PCR)
- UniSTS:95423

SHGC-148767 (e-PCR)
- UniSTS:176596

STS-W72577 (e-PCR)
- UniSTS:60398

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent conferring compression resistance	ISS Inferred from Sequence or Structural Similarity more info
enables extracellular matrix structural constituent conferring compression resistance	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables glycosaminoglycan binding	TAS Traceable Author Statement more info	PubMed
enables hyaluronic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein tyrosine phosphatase activator activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell recognition	TAS Traceable Author Statement more info	PubMed
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in glial cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in osteoblast differentiation	HDA more info	PubMed
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi lumen	TAS Traceable Author Statement more info
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
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular matrix	TAS Traceable Author Statement more info	PubMed
located_in extracellular region	HDA more info	PubMed
located_in extracellular region	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in interphotoreceptor matrix	IEA Inferred from Electronic Annotation more info
located_in lysosomal lumen	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
is_active_in perineuronal net	IBA Inferred from Biological aspect of Ancestor more info
located_in photoreceptor outer segment	IEA Inferred from Electronic Annotation more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: versican core protein

Names: chondroitin sulfate proteoglycan core protein 2; glial hyaluronate-binding protein; large fibroblast proteoglycan; versican proteoglycan

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_012682.1 RefSeqGene

Range

5034..115592

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001126336.3 → NP_001119808.1 versican core protein isoform 2 precursor

See identical proteins and their annotated locations for NP_001119808.1

Status: REVIEWED

Description

Transcript Variant: This variant (2), also known as PG-M(V3), omits two coding exons, compared to variant 1. This results in a shorter protein (isoform 2) with no chondroitin sulfate attachment domain.

Source sequence(s)

AC026696, BC050524, D32039, DA361670, DT217515

Consensus CDS

CCDS47242.1

UniProtKB/Swiss-Prot

P13611

UniProtKB/TrEMBL

Q86W61

Related

ENSP00000421362.2, ENST00000502527.2

Conserved Domains (7) summary

cd05901
Location:36 → 151

Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican

cd00033
Location:555 → 611

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

smart00410
Location:29 → 147

IG_like; Immunoglobulin like

cd00054
Location:386 → 422

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd03517
Location:150 → 244

Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...

cd03520
Location:251 → 346

Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...

cl02432
Location:428 → 551

CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
NM_001164097.2 → NP_001157569.1 versican core protein isoform 3 precursor

See identical proteins and their annotated locations for NP_001157569.1

Status: REVIEWED

Description

Transcript Variant: This variant (3), also known as PG-M(V1), lacks an exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.

Source sequence(s)

AA320958, AC026696, BX641036, DA361670, X15998

Consensus CDS

CCDS54876.1

UniProtKB/TrEMBL

Q6MZK8

Related

ENSP00000340062.5, ENST00000343200.9

Conserved Domains (7) summary

cd05901
Location:36 → 151

Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican

cd00033
Location:2309 → 2365

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

cd03588
Location:2182 → 2305

CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins

smart00410
Location:29 → 147

IG_like; Immunoglobulin like

cd00054
Location:2140 → 2176

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd03517
Location:150 → 244

Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...

cd03520
Location:251 → 346

Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...
NM_001164098.2 → NP_001157570.1 versican core protein isoform 4 precursor

See identical proteins and their annotated locations for NP_001157570.1

Status: REVIEWED

Description

Transcript Variant: This variant (4), also known as PG-M(V2), lacks an exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 4), compared to isoform 1.

Source sequence(s)

AA320958, AC026696, DA361670, U26555

Consensus CDS

CCDS54875.1

UniProtKB/TrEMBL

E9PF17

Related

ENSP00000342768.4, ENST00000342785.8

Conserved Domains (7) summary

cd05901
Location:36 → 151

Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican

cd00033
Location:1542 → 1598

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

cd03588
Location:1415 → 1538

CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins

smart00410
Location:29 → 147

IG_like; Immunoglobulin like

cd00054
Location:1373 → 1409

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd03517
Location:150 → 244

Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...

cd03520
Location:251 → 346

Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...
NM_004385.5 → NP_004376.2 versican core protein isoform 1 precursor

See identical proteins and their annotated locations for NP_004376.2

Status: REVIEWED

Description

Transcript Variant: This variant (1), also known as PG-M(V0), encodes the longest isoform (1).

Source sequence(s)

AB209491, AC026696, DA361670, DT217515, U16306

Consensus CDS

CCDS4060.1

UniProtKB/Swiss-Prot

P13611, P20754, Q13010, Q13189, Q15123, Q9UCL9, Q9UNW5

UniProtKB/TrEMBL

Q59FG9

Related

ENSP00000265077.3, ENST00000265077.8

Conserved Domains (7) summary

cd05901
Location:36 → 151

Ig_Versican; Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican

cd00033
Location:3296 → 3352

CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

cd03588
Location:3169 → 3292

CLECT_CSPGs; C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins

smart00410
Location:29 → 147

IG_like; Immunoglobulin like

cd00054
Location:3127 → 3163

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd03517
Location:150 → 244

Link_domain_CSPGs_modules_1_3; Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: ...

cd03520
Location:251 → 346

Link_domain_CSPGs_modules_2_4; Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The ...