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VCL vinculin [ Homo sapiens (human) ]

Gene ID: 7414, updated on 10-May-2020

Summary

Official Symbol
VCLprovided by HGNC
Official Full Name
vinculinprovided by HGNC
Primary source
HGNC:HGNC:12665
See related
Ensembl:ENSG00000035403 MIM:193065
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; 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

Genomic context

See VCL in Genome Data Viewer
Location:
10q22.2
Exon count:
22
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (73998116..74121363)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (75757836..75879918)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr10.2661 Neighboring gene CRISPRi-validated cis-regulatory element chr10.2662 Neighboring gene uncharacterized LOC107984244 Neighboring gene adaptor related protein complex 3 subunit mu 1 Neighboring gene adenosine kinase Neighboring gene TIMM9 pseudogene 1 Neighboring gene ribosomal protein SA pseudogene 6

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
Dilated cardiomyopathy 1W
MedGen: C1969639 OMIM: 611407
Compare labs
Familial hypertrophic cardiomyopathy 15
MedGen: C2750459 OMIM: 613255 GeneReviews: Not available
Compare labs
Primary dilated cardiomyopathy
MedGen: C0007193
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances.
NHGRI GWA Catalog

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin binding IDA
Inferred from Direct Assay
more info
PubMed 
NOT actin binding IDA
Inferred from Direct Assay
more info
PubMed 
alpha-catenin binding IPI
Inferred from Physical Interaction
more info
PubMed 
beta-catenin binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cadherin binding HDA PubMed 
cadherin binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
dystroglycan binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
structural molecule activity IEA
Inferred from Electronic Annotation
more info
 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
adherens junction assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
apical junction assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
axon extension IEA
Inferred from Electronic Annotation
more info
 
cell adhesion TAS
Traceable Author Statement
more info
PubMed 
cell-matrix adhesion TAS
Traceable Author Statement
more info
PubMed 
epithelial cell-cell adhesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
lamellipodium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
morphogenesis of an epithelium IMP
Inferred from Mutant Phenotype
more info
PubMed 
muscle contraction TAS
Traceable Author Statement
more info
 
negative regulation of cell migration TAS
Traceable Author Statement
more info
PubMed 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
platelet aggregation HMP PubMed 
platelet degranulation TAS
Traceable Author Statement
more info
 
protein localization to cell surface IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of establishment of endothelial barrier IDA
Inferred from Direct Assay
more info
PubMed 
regulation of focal adhesion assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein localization to cell-cell adherens junction IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
adherens junction IDA
Inferred from Direct Assay
more info
PubMed 
adherens junction ISS
Inferred from Sequence or Structural Similarity
more info
 
cell-cell contact zone IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell-cell junction IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell-cell junction ISS
Inferred from Sequence or Structural Similarity
more info
 
cell-substrate junction NAS
Non-traceable Author Statement
more info
PubMed 
costamere IDA
Inferred from Direct Assay
more info
PubMed 
costamere ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoskeleton TAS
Traceable Author Statement
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular vesicle HDA PubMed 
fascia adherens IEA
Inferred from Electronic Annotation
more info
 
ficolin-1-rich granule lumen TAS
Traceable Author Statement
more info
 
focal adhesion HDA PubMed 
focal adhesion IDA
Inferred from Direct Assay
more info
PubMed 
focal adhesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
focal adhesion ISS
Inferred from Sequence or Structural Similarity
more info
 
podosome IEA
Inferred from Electronic Annotation
more info
 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
sarcolemma ISS
Inferred from Sequence or Structural Similarity
more info
 
secretory granule lumen TAS
Traceable Author Statement
more info
 
specific granule lumen TAS
Traceable Author Statement
more info
 

General protein information

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

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_008868.1 RefSeqGene

    Range
    5001..127047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_383

mRNA and Protein(s)

  1. NM_003373.4NP_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/Swiss-Prot
    P18206
    UniProtKB/TrEMBL
    A0A024QZN4, B3KXA2
    Related
    ENSP00000361841.3, ENST00000372755.7
    Conserved Domains (1) summary
    pfam01044
    Location:661066
    Vinculin; Vinculin family
  2. NM_014000.3NP_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
    UniProtKB/TrEMBL
    B3KXA2, V9HWK2
    Related
    ENSP00000211998.4, ENST00000211998.9
    Conserved Domains (1) summary
    pfam01044
    Location:661134
    Vinculin; Vinculin family

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_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    73998116..74121363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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