U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

VBP1 VHL binding protein 1 [ Homo sapiens (human) ]

Gene ID: 7411, updated on 7-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
VBP1provided by HGNC
Official Full Name
VHL binding protein 1provided by HGNC
Primary source
HGNC:HGNC:12662
See related
Ensembl:ENSG00000155959 MIM:300133; AllianceGenome:HGNC:12662
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
PFD3; PFDN3; VBP-1; HIBBJ46
Summary
The protein encoded by this gene interacts with the Von Hippel-Lindau protein to form an intracellular complex. The encoded protein functions as a chaperone protein, and may play a role in the transport of the Von Hippel-Lindau protein from the perinuclear granules to the nucleus or cytoplasm. Alternative splicing and the use of alternate transcription start sites results in multiple transcript variants encoding different protein isoforms. [provided by RefSeq, Jan 2015]
Expression
Ubiquitous expression in brain (RPKM 27.3), heart (RPKM 18.7) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
Xq28
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (155197007..155239841)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (153433306..153476144)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (154425284..154468122)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30074 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:154299323-154300044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:154300045-154300766 Neighboring gene mature T cell proliferation 1 Neighboring gene C-X9-C motif containing 4 Neighboring gene BRCA1/BRCA2-containing complex subunit 3 Neighboring gene int1h-2 recombination region Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:154425831-154426332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:154426333-154426832 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:154444390-154445178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21125 Neighboring gene RAB39B, member RAS oncogene family Neighboring gene chloride intracellular channel 2 Neighboring gene twinfilin 1 pseudogene 2

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. [Identification of a factor, which binds to HIF-1 alpha and regulates the function of HIF-1 alpha]. Horiuchi I. Hokkaido Igaku Zasshi, 2003 Jan. PMID 12613020
  2. Genomic organization and chromosomal localization of the human CUL2 gene and the role of von Hippel-Lindau tumor suppressor-binding protein (CUL2 and VBP1) mutation and loss in renal-cell carcinoma development. Clifford SC, et al. Genes Chromosomes Cancer, 1999 Sep. PMID 10441001
  3. Characterization of the gene (VBP1) and transcript for the von Hippel-Lindau binding protein and isolation of the highly conserved murine homologue. Brinke A, et al. Genomics, 1997 Oct 1. PMID 9339366
  4. Human MutS homologue MSH4 physically interacts with von Hippel-Lindau tumor suppressor-binding protein 1. Her C, et al. Cancer Res, 2003 Feb 15. PMID 12591739
  5. Expression of the von Hippel-Lindau-binding protein-1 (Vbp1) in fetal and adult mouse tissues. Hemberger M, et al. Hum Mol Genet, 1999 Feb. PMID 9931330

See all (90) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. VBP1 modulates Wnt/beta-catenin signaling by mediating the stability of the transcription factors TCF/LEFs.
    Title: VBP1 modulates Wnt/β-catenin signaling by mediating the stability of the transcription factors TCF/LEFs.
  2. The prefoldin complex stabilizes the von Hippel-Lindau protein against aggregation and degradation.
    Title: The prefoldin complex stabilizes the von Hippel-Lindau protein against aggregation and degradation.
  3. Data show that von Hippel-Lindau-binding protein 1 (VBP1) enhances the stability of von Hippel-Lindau tumor suppressor protein (pVHL) and facilitates pVHL-mediated ubiquitination of hypoxia-inducible factor 1, alpha subunit (HIF-1alpha).
    Title: VBP1 represses cancer metastasis by enhancing HIF-1α degradation induced by pVHL.
  4. VBP1 acts together with p97 to regulate hMSH4 degradation.
    Title: VBP1 facilitates proteasome and autophagy-mediated degradation of MutS homologue hMSH4.
  5. VBP1 and cullin2/von Hippel-Lindau are required for proper HIV-1 expression at a step between integrase-dependent proviral integration into the host genome and transcription of viral genes
    Title: von Hippel Lindau binding protein 1-mediated degradation of integrase affects HIV-1 gene expression at a postintegration step.
  6. binds to HIF-1 alpha and regulates the function of HIF-1 alpha
    Title: [Identification of a factor, which binds to HIF-1 alpha and regulates the function of HIF-1 alpha].
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

Go to the top of the page Help

Protein interactions

Protein Gene Interaction Pubs
integrase gag-pol Systematic yeast two-hybrid screenings identify von Hippel-Lindau binding protein 1 (VBP1) as cellular binding partners of HIV-1 integrase PubMed
retropepsin gag-pol HIV-1 PR is identified to have a physical interaction with von Hippel-Lindau binding protein 1 (VBP1; PFD3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables amyloid-beta binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables tubulin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables unfolded protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in chaperone-mediated protein folding NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in microtubule-based process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of amyloid fibril formation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein folding IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in tubulin complex assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
part_of prefoldin complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of prefoldin complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of prefoldin complex NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
prefoldin subunit 3
Names
von Hippel-Lindau binding protein 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_013269.2 RefSeqGene

    Range
    24454..47835
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001303543.1 → NP_001290472.1  prefoldin subunit 3 isoform 2

    See identical proteins and their annotated locations for NP_001290472.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) initiates transcription at an alternate position and has a longer 5' terminal exon than variant 1. It initiates translation at an alternate start codon and the encoded isoform (2) has a longer N-terminus than isoform 1.
    Source sequence(s)
    AA626259, BC009570, BX682237, U96759
    Conserved Domains (1) summary
    pfam02996
    Location:96 → 216
    Prefoldin; Prefoldin subunit

  2. NM_001303544.1 → NP_001290473.1  prefoldin subunit 3 isoform 3

    See identical proteins and their annotated locations for NP_001290473.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AA626259, AK301646, BC009570
    Consensus CDS
    CCDS78525.1
    UniProtKB/TrEMBL
    B4DWR3
    Related
    ENSP00000438694.1, ENST00000535916.5
    Conserved Domains (1) summary
    cd00584
    Location:45 → 176
    Prefoldin_alpha; Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta ...

  3. NM_001303545.1 → NP_001290474.1  prefoldin subunit 3 isoform 4

    See identical proteins and their annotated locations for NP_001290474.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 5' region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AA626259, BC009570, BC040002, DA610631
    UniProtKB/TrEMBL
    Q6FH24
    Conserved Domains (1) summary
    pfam02996
    Location:23 → 143
    Prefoldin; Prefoldin subunit

  4. NM_003372.7 → NP_003363.1  prefoldin subunit 3 isoform 1

    See identical proteins and their annotated locations for NP_003363.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AA626259, BC009570, BC046094, DA610631
    Consensus CDS
    CCDS14765.1
    UniProtKB/Swiss-Prot
    B2R8L5, B4DWR3, F5H2A7, O55228, P61758, Q15765, Q5JT81, Q86X96
    Related
    ENSP00000286428.5, ENST00000286428.7
    Conserved Domains (1) summary
    pfam02996
    Location:60 → 180
    Prefoldin; Prefoldin subunit

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    155197007..155239841
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    153433306..153476144
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P61758.4 GenPept UniProtKB/Swiss-Prot:P61758

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous