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

    Gene ID: 7411, updated on 3-Nov-2024

    Summary

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    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
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    Genomic context

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    See VBP1 in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (155197007..155239841)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (153433306..153476144)
    RS_2024_09 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. VBP1 promotes tumor proliferation as a part of the hypoxia-related signature in esophageal squamous cell carcinoma. Miao H, et al. Hum Cell, 2024 Jul. PMID 38700744, Free PMC Article
    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. [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
    4. 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
    5. USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle. Song N, et al. Mol Carcinog, 2023 Oct. PMID 37314216

    See all (109) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. VBP1 promotes tumor proliferation as a part of the hypoxia-related signature in esophageal squamous cell carcinoma.
      Title: VBP1 promotes tumor proliferation as a part of the hypoxia-related signature in esophageal squamous cell carcinoma.
    2. 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.
    3. 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.
    4. 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.
    5. VBP1 acts together with p97 to regulate hMSH4 degradation.
      Title: VBP1 facilitates proteasome and autophagy-mediated degradation of MutS homologue hMSH4.
    6. 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.
    7. 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

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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)

    Genotypes

    HIV-1 interactions

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    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

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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

    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

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    Preferred Names
    prefoldin subunit 3
    Names
    von Hippel-Lindau binding protein 1

    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

    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

      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

      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

      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

      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_2024_08

    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

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