VCL vinculin [Homo sapiens (human)] - Gene

Summary

Official Symbol: VCLprovided by HGNC
Official Full Name: vinculinprovided by HGNC
Primary source: HGNC:HGNC:12665
See related: Ensembl:ENSG00000035403 MIM:193065; AllianceGenome:HGNC:12665
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: MV; MVCL; VINC; CMD1W; CMH15; HEL114
Summary: Vinculin is a cytoskeletal protein associated with cell-cell and cell-matrix junctions, where it is thought to function as one of several interacting proteins involved in anchoring F-actin to the membrane. Defects in VCL are the cause of cardiomyopathy dilated type 1W. Dilated cardiomyopathy is a disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in endometrium (RPKM 87.7), prostate (RPKM 70.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q22.2

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (73998116..74121363)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (74869505..74992765)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (75757874..75881121)

Chromosome 10 - NC_000010.11 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
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?

Effect of Focal Adhesion Kinase and Vinculin Expression on Migration Parameters of Normal and Tumor Epitheliocytes.
Title: Effect of Focal Adhesion Kinase and Vinculin Expression on Migration Parameters of Normal and Tumor Epitheliocytes.
Heart Failure with Recovered Ejection Fraction in Patients with Vinculin Loss-of-function Variants.
Title: Heart Failure with Recovered Ejection Fraction in Patients with Vinculin Loss-of-function Variants.
Serum claudin-5, claudin-11, occludin, vinculin, paxillin, and beta-catenin levels in preschool children with autism spectrum disorder.
Title: Serum claudin-5, claudin-11, occludin, vinculin, paxillin, and beta-catenin levels in preschool children with autism spectrum disorder.
Vinculin Y822 is an important determinant of ligand binding.
Title: Vinculin Y822 is an important determinant of ligand binding.
[No Effect of the p.Arg230His Variant Of The VCL Protein on the Course of the Hypertrophic Cardiomyopathy In Russian Family Carrying The p.Gln1233Ter Pathogenic Variant In The MYBPC3 Gene].
Title: [No Effect of the p.Arg230His Variant Of The VCL Protein on the Course of the Hypertrophic Cardiomyopathy In Russian Family Carrying The p.Gln1233Ter Pathogenic Variant In The MYBPC3 Gene].
Expression of the phagocytic receptors alphaMbeta2 and alphaXbeta2 is controlled by RIAM, VASP and Vinculin in neutrophil-differentiated HL-60 cells.
Title: Expression of the phagocytic receptors α(M)β(2) and α(X)β(2) is controlled by RIAM, VASP and Vinculin in neutrophil-differentiated HL-60 cells.
Study of Antibodies to Cytolethal Distending Toxin B (CdtB) and Antibodies to Vinculin in Patients with Irritable Bowel Syndrome.
Title: Study of Antibodies to Cytolethal Distending Toxin B (CdtB) and Antibodies to Vinculin in Patients with Irritable Bowel Syndrome.
An assessment of the role of vinculin loss of function variants in inherited cardiomyopathy.
Title: An assessment of the role of vinculin loss of function variants in inherited cardiomyopathy.
Vinculin orchestrates prostate cancer progression by regulating tumor cell invasion, migration, and proliferation.
Title: Vinculin orchestrates prostate cancer progression by regulating tumor cell invasion, migration, and proliferation.
High expression of vinculin predicts poor prognosis and distant metastasis and associates with influencing tumor-associated NK cell infiltration and epithelial-mesenchymal transition in gastric cancer.
Title: High expression of vinculin predicts poor prognosis and distant metastasis and associates with influencing tumor-associated NK cell infiltration and epithelial-mesenchymal transition in gastric cancer.

Submit: New GeneRIF Correction See all GeneRIFs (106)

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
Dilated cardiomyopathy 1W MedGen: C1969639 OMIM: 611407 GeneReviews: Dilated Cardiomyopathy Overview	not available
Hypertrophic cardiomyopathy 15 MedGen: C2750459 OMIM: 613255 GeneReviews: Not available	not available
Primary dilated cardiomyopathy MedGen: C0007193 GeneReviews: Dilated Cardiomyopathy Overview	not available

EBI GWAS Catalog

Description
Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances. 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
Nef	nef	HIV-1 Nef co-localizes with vinvulin inside podosomes in human monocyte-derived macrophages	PubMed
	nef	HIV-1 Nef induces polarization of vinculin, a molecule important for dendritic cell (DC) adhesion, motility, and maturation, at one pole of DCs corresponding to the substrate-adhering portion or leading edge of the cell	PubMed
matrix	gag	HIV-1 MA co-localizes with beta2 integrin, alphaM and alphaX integrins in the intracellular thick electron-dense membrane compartments, which contain talin, vinculin and paxillin that connect the integrin complexes to the actin cytoskeleton	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

D10S2208 (e-PCR)
- UniSTS:23560

D10S2342 (e-PCR)
- UniSTS:57376

D10S2142 (e-PCR)
- UniSTS:7474

STS-M33308 (e-PCR)
- UniSTS:3639

VCL (e-PCR)
- UniSTS:266571

Vcl (e-PCR), detects polymorphism
- UniSTS:144747

GDB:193875 (e-PCR)
- UniSTS:155783

SHGC-77943 (e-PCR)
- UniSTS:101357

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
NOT enables actin binding	IDA Inferred from Direct Assay more info	PubMed
enables actin binding	IDA Inferred from Direct Assay more info	PubMed
enables alpha-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables alpha-catenin binding	IPI Inferred from Physical Interaction more info	PubMed
enables beta-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables beta-catenin binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables cadherin binding	HDA more info	PubMed
enables cadherin binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables dystroglycan binding	IPI Inferred from Physical Interaction 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
enables structural molecule activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in adherens junction assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in apical junction assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axon extension	IEA Inferred from Electronic Annotation more info
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell adhesion	TAS Traceable Author Statement more info	PubMed
involved_in cell-matrix adhesion	TAS Traceable Author Statement more info	PubMed
involved_in epithelial cell-cell adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lamellipodium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in maintenance of blood-brain barrier	NAS Non-traceable Author Statement more info	PubMed
involved_in morphogenesis of an epithelium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell migration	TAS Traceable Author Statement more info	PubMed
involved_in platelet aggregation	HMP more info	PubMed
involved_in protein localization to cell surface	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of establishment of endothelial barrier	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of focal adhesion assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of focal adhesion assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of protein localization to adherens junction	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in adherens junction	IDA Inferred from Direct Assay more info	PubMed
located_in adherens junction	ISS Inferred from Sequence or Structural Similarity more info
located_in brush border	ISS Inferred from Sequence or Structural Similarity more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in cell-cell contact zone	IBA Inferred from Biological aspect of Ancestor more info
located_in cell-cell contact zone	IMP Inferred from Mutant Phenotype more info	PubMed
located_in cell-cell junction	IMP Inferred from Mutant Phenotype more info	PubMed
located_in cell-cell junction	ISS Inferred from Sequence or Structural Similarity more info
located_in cell-substrate junction	NAS Non-traceable Author Statement more info	PubMed
located_in costamere	IDA Inferred from Direct Assay more info	PubMed
located_in costamere	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoskeleton	TAS Traceable Author Statement more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular vesicle	HDA more info	PubMed
located_in fascia adherens	IEA Inferred from Electronic Annotation more info
located_in ficolin-1-rich granule lumen	TAS Traceable Author Statement more info
located_in focal adhesion	HDA more info	PubMed
is_active_in focal adhesion	IBA Inferred from Biological aspect of Ancestor more info
located_in focal adhesion	IDA Inferred from Direct Assay more info	PubMed
located_in focal adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
located_in focal adhesion	ISS Inferred from Sequence or Structural Similarity more info
located_in inner dense plaque of desmosome	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane raft	IDA Inferred from Direct Assay more info	PubMed
located_in outer dense plaque of desmosome	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in podosome ring	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
located_in sarcolemma	ISS Inferred from Sequence or Structural Similarity more info
located_in secretory granule lumen	TAS Traceable Author Statement more info
located_in specific granule lumen	TAS Traceable Author Statement more info
located_in terminal web	ISS Inferred from Sequence or Structural Similarity more info
located_in zonula adherens	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: vinculin

Names: epididymis luminal protein 114; epididymis secretory sperm binding protein; meta-vinculin; metavinculin

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_008868.1 RefSeqGene

Range

5001..127047

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_383

mRNA and Protein(s)

NM_003373.4 → NP_003364.1 vinculin isoform VCL

See identical proteins and their annotated locations for NP_003364.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks a 3' coding exon, as compared to variant 1. It encodes a shorter isoform (VCL), which is the major talin-binding protein in platelets.

Source sequence(s)

AI290052, AK126978, AL708715, AL731576, AL832130, BC013847, BC039174, BX537994

Consensus CDS

CCDS7340.1

UniProtKB/TrEMBL

A0A384NYN5

Related

ENSP00000361841.3, ENST00000372755.7

Conserved Domains (1) summary

pfam01044
Location:66 → 1066

Vinculin; Vinculin family
NM_014000.3 → NP_054706.1 vinculin isoform meta-VCL

See identical proteins and their annotated locations for NP_054706.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) differs from variant 2 in having an additional exon in the 3' coding region. It thus encodes a longer isoform (meta-VCL).

Source sequence(s)

AA368699, AI290052, AK126978, AL700886, AL708715, AL731576, AL832130, BC013847, BC039174

Consensus CDS

CCDS7341.1

UniProtKB/Swiss-Prot

P18206, Q16450, Q5SWX2, Q7Z3B8, Q8IXU7

UniProtKB/TrEMBL

A0A384NYN5, V9HWK2

Related

ENSP00000211998.5, ENST00000211998.10

Conserved Domains (1) summary

pfam01044
Location:66 → 1134

Vinculin; Vinculin family