VPS4B vacuolar protein sorting 4 homolog B [Homo sapiens (human)] - Gene

Summary

Official Symbol: VPS4Bprovided by HGNC
Official Full Name: vacuolar protein sorting 4 homolog Bprovided by HGNC
Primary source: HGNC:HGNC:10895
See related: Ensembl:ENSG00000119541 MIM:609983; AllianceGenome:HGNC:10895
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: MIG1; SKD1; SKD1B; VPS4-2
Summary: The protein encoded by this gene is a member of the AAA protein family (ATPases associated with diverse cellular activities), and is the homolog of the yeast Vps4 protein. In humans, two paralogs of the yeast protein have been identified. The former share a high degree of aa sequence similarity with each other, and also with yeast Vps4 and mouse Skd1 proteins. Mouse Skd1 (suppressor of K+ transport defect 1) has been shown to be a yeast Vps4 ortholog. Functional studies indicate that both human paralogs associate with the endosomal compartments, and are involved in intracellular protein trafficking, similar to Vps4 protein in yeast. The gene encoding this paralog has been mapped to chromosome 18; the gene for the other resides on chromosome 16. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in esophagus (RPKM 35.7), colon (RPKM 23.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 18q21.33

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	18	NC_000018.10 (63389190..63422476, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	18	NC_060942.1 (63594233..63627515, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	18	NC_000018.9 (61056423..61089709, complement)

Chromosome 18 - NC_000018.10 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?

p-AKT/VPS4B regulates the small extracellular vesicle size in venous malformation endothelial cells.
Title: p-AKT/VPS4B regulates the small extracellular vesicle size in venous malformation endothelial cells.
Analysis of individual HIV-1 budding event using fast AFM reveals a multiplexed role for VPS4.
Title: Analysis of individual HIV-1 budding event using fast AFM reveals a multiplexed role for VPS4.
Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q.
Title: Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q.
Synthetic lethality between VPS4A and VPS4B triggers an inflammatory response in colorectal cancer.
Title: Synthetic lethality between VPS4A and VPS4B triggers an inflammatory response in colorectal cancer.
VPS4B mutation impairs the osteogenic differentiation of dental follicle cells derived from a patient with dentin dysplasia type I.
Title: VPS4B mutation impairs the osteogenic differentiation of dental follicle cells derived from a patient with dentin dysplasia type I.
VPS4B, via Wnt-beta-catenin signalling, acts as a regulator of the proliferation and differentiation of hDPSCs
Title: Vacuolar protein sorting 4B regulates the proliferation and odontoblastic differentiation of human dental pulp stem cells through the Wnt-β-catenin signalling pathway.
VPS4B might facilitate chondrocyte apoptosis in Osteoarthritis via p38 MAPK signaling pathway.
Title: Vacuolar Protein Sorting 4B (VPS4B) Regulates Apoptosis of Chondrocytes via p38 Mitogen-Activated Protein Kinases (MAPK) in Osteoarthritis.
Knockdown of vps4b in zebrafish recapitulated the reduction of tooth size.
Title: A splicing mutation in VPS4B causes dentin dysplasia I.
Our findings support a role for VPS4B in MM cell proliferation, adhesion, and drug resistance, and pave the way for a novel therapeutic approach targeting this molecule.
Title: Cell adhesion down-regulates the expression of vacuolar protein sorting 4B (VPS4B) and contributes to drug resistance in multiple myeloma cells.
Lack of ALG-2, ALIX or Vps4B each prevents shedding, and repair of the injured cell membrane
Title: Mechanism of Ca²⁺-triggered ESCRT assembly and regulation of cell membrane repair.

Submit: New GeneRIF Correction See all GeneRIFs (29)

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

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 targets CD4 to CD63-containing lysosomes for Nef-induced degradation of CD4, which requires the VPS4-mediated ESCRT machinery	PubMed
Pr55(Gag)	gag	ALIX, CHMP2A/B, CHMP4A/B, and VPS4A/B proteins are required for the budding of HIV-1 Gag and the HIV-1 infectivity	PubMed
	gag	VPS4A/B proteins are recruited to assist with membrane fission after full assembly of HIV-1 Gag into the VLP	PubMed
	gag	ISG15 inhibits budding of HIV-1 by disrupting the association between Vps4 and the Gag budding complex	PubMed
	gag	The budding defect of p6-deficient HIV-1 Gag is caused primarily by C-terminal exposure of p1. The p1 domain of p6-deficient Gag acts as an inhibitory budding signal by blocking the interaction of Gag with CD63 and VPS4B	PubMed
Vpu	vpu	The v-ATPase VPS4 is required for Vpu-induced cell surface downregulation of BST-2. VPS4 E223/Q mutant impairs the ability of Vpu to downregulate BST-2 from the cell surface	PubMed
p1	gag	The budding defect of p6-deficient HIV-1 Gag is caused primarily by C-terminal exposure of p1, which activates a cis-acting inhibitory budding signal (IBS) and impairs exosomes and microvesicles (EMV) cargo-VPS4 interaction	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

D8S2279 (e-PCR)
- UniSTS:473907

SHGC-78169 (e-PCR)
- UniSTS:101198

SHGC-106325 (e-PCR)
- UniSTS:169816

RH99091 (e-PCR)
- UniSTS:84644

D18S934E (e-PCR)
- UniSTS:150526

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP hydrolysis activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in ESCRT III complex disassembly	IDA Inferred from Direct Assay more info	PubMed
involved_in ESCRT III complex disassembly	NAS Non-traceable Author Statement more info	PubMed
involved_in angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in autophagosome maturation	NAS Non-traceable Author Statement more info	PubMed
involved_in autophagy	NAS Non-traceable Author Statement more info	PubMed
involved_in canonical Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in cholesterol transport	IEA Inferred from Electronic Annotation more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in endosomal transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within endosomal transport	IDA Inferred from Direct Assay more info	PubMed
involved_in endosome to lysosome transport via multivesicular body sorting pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment of blood-brain barrier	IEA Inferred from Electronic Annotation more info
involved_in late endosomal microautophagy	IEA Inferred from Electronic Annotation more info
involved_in late endosome to lysosome transport via multivesicular body sorting pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in macroautophagy	NAS Non-traceable Author Statement more info	PubMed
involved_in membrane fission	NAS Non-traceable Author Statement more info	PubMed
involved_in midbody abscission	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in midbody abscission	NAS Non-traceable Author Statement more info	PubMed
involved_in mitotic metaphase chromosome alignment	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in multivesicular body assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in multivesicular body sorting pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of exosomal secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear membrane reassembly	NAS Non-traceable Author Statement more info	PubMed
involved_in nucleus organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleus organization	NAS Non-traceable Author Statement more info	PubMed
involved_in plasma membrane repair	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of G2/M transition of mitotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of centriole elongation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of exosomal secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in potassium ion transport	IEA Inferred from Electronic Annotation more info
involved_in protein depolymerization	IDA Inferred from Direct Assay more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of centrosome duplication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mitotic spindle assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to lipid	IDA Inferred from Direct Assay more info	PubMed
involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vacuole organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in viral budding from plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in viral budding via host ESCRT complex	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
part_of ATPase complex	NAS Non-traceable Author Statement more info	PubMed
located_in Flemming body	IDA Inferred from Direct Assay more info	PubMed
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in midbody	NAS Non-traceable Author Statement more info	PubMed
part_of nuclear pore	NAS Non-traceable Author Statement more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in spindle pole	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 4B

Names: cell migration-inducing 1; cell migration-inducing gene 1 protein; suppressor of K(+) transport growth defect 1; suppressor of K+ transport defect 1; vacuolar protein sorting 4B

NP_004860.2

EC 3.6.4.6

XP_047293905.1

EC 3.6.4.6

XP_054175353.1

EC 3.6.4.6

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.

mRNA and Protein(s)

NM_004869.4 → NP_004860.2 vacuolar protein sorting-associated protein 4B

See identical proteins and their annotated locations for NP_004860.2

Status: REVIEWED

Source sequence(s)

AF195514, DA306069

Consensus CDS

CCDS11983.1

UniProtKB/Swiss-Prot

O75351, Q69HW4, Q9GZS7

UniProtKB/TrEMBL

A8K4G7

Related

ENSP00000238497.4, ENST00000238497.10

Conserved Domains (3) summary

COG0464
Location:124 → 355

SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]

cd02678
Location:6 → 81

MIT_VPS4; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.

pfam09336
Location:381 → 441

Vps4_C; Vps4 C terminal oligomerization domain