VIM vimentin [Homo sapiens (human)] - Gene

Summary

Official Symbol: VIMprovided by HGNC
Official Full Name: vimentinprovided by HGNC
Primary source: HGNC:HGNC:12692
See related: Ensembl:ENSG00000026025 MIM:193060; AllianceGenome:HGNC:12692
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
Summary: This gene encodes a type III intermediate filament protein. Intermediate filaments, along with microtubules and actin microfilaments, make up the cytoskeleton. The encoded protein is responsible for maintaining cell shape and integrity of the cytoplasm, and stabilizing cytoskeletal interactions. This protein is involved in neuritogenesis and cholesterol transport and functions as an organizer of a number of other critical proteins involved in cell attachment, migration, and signaling. Bacterial and viral pathogens have been shown to attach to this protein on the host cell surface. Mutations in this gene are associated with congenital cataracts in human patients. [provided by RefSeq, Aug 2017]
Expression: Ubiquitous expression in ovary (RPKM 1051.1), fat (RPKM 720.1) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10p13

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (17228241..17237593)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (17246786..17256137)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (17270240..17279592)

Chromosome 10 - NC_000010.11 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?

Vimentin at the core of wound healing.
Title: Vimentin at the core of wound healing.
CircGLIS3 promotes gastric cancer progression by regulating the miR-1343-3p/PGK1 pathway and inhibiting vimentin phosphorylation.
Title: CircGLIS3 promotes gastric cancer progression by regulating the miR-1343-3p/PGK1 pathway and inhibiting vimentin phosphorylation.
Salivary IgA and vimentin differentiate in vitro SARS-CoV-2 infection: A study of 290 convalescent COVID-19 patients.
Title: Salivary IgA and vimentin differentiate in vitro SARS-CoV-2 infection: A study of 290 convalescent COVID-19 patients.
A tumor suppressor protein encoded by circKEAP1 inhibits osteosarcoma cell stemness and metastasis by promoting vimentin proteasome degradation and activating anti-tumor immunity.
Title: A tumor suppressor protein encoded by circKEAP1 inhibits osteosarcoma cell stemness and metastasis by promoting vimentin proteasome degradation and activating anti-tumor immunity.
Phosphorylated vimentin at Ser72 is associated with epithelial-mesenchymal transition in lupus nephritis.
Title: Phosphorylated vimentin at Ser72 is associated with epithelial-mesenchymal transition in lupus nephritis.
Circular RNA cVIM promotes hepatic stellate cell activation in liver fibrosis via miR-122-5p/miR-9-5p-mediated TGF-beta signaling cascade.
Title: Circular RNA cVIM promotes hepatic stellate cell activation in liver fibrosis via miR-122-5p/miR-9-5p-mediated TGF-β signaling cascade.
Caspase-9-mediated cleavage of vimentin attenuates the aggressiveness of leukemic NB4 cells.
Title: Caspase-9-mediated cleavage of vimentin attenuates the aggressiveness of leukemic NB4 cells.
Expression of Wilms' Tumor 1 Antigen, Vimentin, and Corticotropin-Releasing Factor in the Human Kidney with Focal Segmental Glomerulosclerosis and Effect of Oxidative Stress on These Markers in HEK 293 Cells.
Title: Expression of Wilms' Tumor 1 Antigen, Vimentin, and Corticotropin-Releasing Factor in the Human Kidney with Focal Segmental Glomerulosclerosis and Effect of Oxidative Stress on These Markers in HEK 293 Cells.
ENAH-202 promotes cancer progression in oral squamous cell carcinoma by regulating ZNF502/VIM axis.
Title: ENAH-202 promotes cancer progression in oral squamous cell carcinoma by regulating ZNF502/VIM axis.
Interaction of species A rotavirus VP4 with the cellular proteins vimentin and actin related protein 2 discovered by a proximity interactome assay.
Title: Interaction of species A rotavirus VP4 with the cellular proteins vimentin and actin related protein 2 discovered by a proximity interactome assay.

Submit: New GeneRIF Correction See all GeneRIFs (438)

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
Cataract 30 MedGen: C3805411 OMIM: 116300 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Discovery and refinement of loci associated with lipid levels. 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 gp120	env	Tandem affinity purification and mass spectrometry analysis identify vimentin (VIM), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
	env	The phosphorylation of the two major cytoskeletal proteins, vimentin and GFAP, which is normally stimulated by isoproterenol, is partially prevented by HIV-1 gp120 in astrocytes	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify vimentin (VIM), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify vimentin (VIM), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	HIV-1 Gag trafficking to the plasma membrane is inhibited by LGALS3BP (M2BP) and the inhibition by LGALS3BP is dependent upon vimentin	PubMed
	gag	Tandem affinity purification and mass spectrometry analysis identify vimentin (VIM), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Vif	vif	Vif has been reported to colocalize with vimentin filaments in the cytoplasm and cause the collapse of the intermediate filament network into a perinuclear aggregate, however in other reports this co-localization was not observed	PubMed
Vpr	vpr	A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of vimentin (VIM) expression by HIV-1 Vpr in Vpr transduced macrophages	PubMed
	vpr	The proteomic assay from Vpr-expressing HTLV-1 transformed cells reveals apoptosis related protein changes, such as CASP3 activity indicator proteins (vimentin and Rho GDP-dissociation inhibitor 2)	PubMed
matrix	gag	Treatment of human stellate cells with HIV-1 MA upregulates the expression of CXCR2, syndecan-2, collagen-I, alpha-SMA, vimentin, and endothelin-1	PubMed
retropepsin	gag-pol	HIV-1 protease cleaves three secondary sites of vimentin at positions 51-52, 60-61, and 92-93.	PubMed
	gag-pol	HIV-1 protease cleaves the intermediate filament proteins vimentin (both human and murine vimentin are cleaved between leucine-422 and arginine-423), desmin, and glial fibrillary acidic protein in vitro	PubMed
	gag-pol	Two regions of the vimentin head domain, residues 17-60 and 68-92, are released as a result of vimentin cleavage by HIV-1 protease, leading to altered chromatin distribution	PubMed
	gag-pol	Exposure of human skin fibroblasts to HIV-1 protease induces the degradation of the vimentin filament network and the disappearance of the tropomyosin isoforms microfilament network	PubMed
	gag-pol	Phosphorylation of human recombinant vimentin by PKC inhibits the cleavage of the vimentin head domain by HIV-1 protease	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

VIM (e-PCR)
- UniSTS:253717

RH11024 (e-PCR)
- UniSTS:32309

GDB:193876 (e-PCR)
- UniSTS:155784

VIM (e-PCR)
- UniSTS:527007

Vim (e-PCR), detects polymorphism
- UniSTS:527007

Vim (e-PCR), detects polymorphism
- UniSTS:507308

G43223 (e-PCR)
- UniSTS:94898

VIM_2538 (e-PCR)
- UniSTS:281077

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables double-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables keratin filament 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 protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables scaffold protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural constituent of cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
enables structural constituent of eye lens	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in Bergmann glial cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in astrocyte development	IEA Inferred from Electronic Annotation more info
involved_in cellular response to lipopolysaccharide	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to muramyl dipeptide	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to type II interferon	IEA Inferred from Electronic Annotation more info
involved_in intermediate filament organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in intermediate filament organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in lens fiber cell development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neuron projection development	IEA Inferred from Electronic Annotation more info
involved_in neuron projection development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of collagen biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in regulation of mRNA stability	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in cell leading edge	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
located_in cytoskeleton	TAS Traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in focal adhesion	HDA more info	PubMed
is_active_in intermediate filament	IBA Inferred from Biological aspect of Ancestor more info
located_in intermediate filament	IDA Inferred from Direct Assay more info	PubMed
located_in intermediate filament cytoskeleton	IDA Inferred from Direct Assay more info
located_in microtubule organizing center	TAS Traceable Author Statement more info
located_in nuclear matrix	IEA Inferred from Electronic Annotation more info
located_in peroxisome	IDA Inferred from Direct Assay more info	PubMed
located_in phagocytic vesicle	IEA Inferred from Electronic Annotation 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

General protein information

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Preferred Names: vimentin

Names: epididymis secretory sperm binding protein

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.