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Aliases for VBP1 Gene

Aliases for VBP1 Gene

  • VHL Binding Protein 1 2 3 5
  • Von Hippel-Lindau Binding Protein 1 2 3
  • HIBBJ46 3 4
  • PFDN3 3 4
  • VBP-1 3 4
  • Von Hippel-Lindau-Binding Protein 1 4
  • VHL-Binding Protein 1 4
  • Prefoldin Subunit 3 3
  • Prefoldin 3 2
  • PFD3 3

External Ids for VBP1 Gene

Previous GeneCards Identifiers for VBP1 Gene

  • GC0XM148650
  • GC0XM150967
  • GC0XP151961
  • GC0XP152866
  • GC0XP154008
  • GC0XP154097
  • GC0XP154444
  • GC0XP142988

Summaries for VBP1 Gene

Entrez Gene Summary for VBP1 Gene

  • 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]

GeneCards Summary for VBP1 Gene

VBP1 (VHL Binding Protein 1) is a Protein Coding gene. Diseases associated with VBP1 include Renal Cell Carcinoma. Among its related pathways are Chaperonin-mediated protein folding and Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding. GO annotations related to this gene include unfolded protein binding.

UniProtKB/Swiss-Prot for VBP1 Gene

  • Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Additional gene information for VBP1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VBP1 Gene

Genomics for VBP1 Gene

Regulatory Elements for VBP1 Gene

Enhancers for VBP1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XH155215 1 ENCODE 4 +19.9 19861 3.1 PKNOX1 ATF1 ARNT DMAP1 YY1 GLIS2 ZNF143 FOS ATF7 SP3 F8A1 DKC1 WASH6P SNORA70 VBP1 ENSG00000224978 RAB39B
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VBP1 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the VBP1 gene promoter:

Genomic Locations for VBP1 Gene

Genomic Locations for VBP1 Gene
chrX:155,197,007-155,239,841
(GRCh38/hg38)
Size:
42,835 bases
Orientation:
Plus strand
chrX:154,425,284-154,468,098
(GRCh37/hg19)

Genomic View for VBP1 Gene

Genes around VBP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VBP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VBP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VBP1 Gene

Proteins for VBP1 Gene

  • Protein details for VBP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P61758-PFD3_HUMAN
    Recommended name:
    Prefoldin subunit 3
    Protein Accession:
    P61758
    Secondary Accessions:
    • B2R8L5
    • O55228
    • Q15765
    • Q5JT81
    • Q86X96

    Protein attributes for VBP1 Gene

    Size:
    197 amino acids
    Molecular mass:
    22658 Da
    Quaternary structure:
    • Heterohexamer of two PFD-alpha type and four PFD-beta type subunits. Binds to the C-terminal part of VHL.
    SequenceCaution:
    • Sequence=AAC23907.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for VBP1 Gene

Post-translational modifications for VBP1 Gene

  • Ubiquitination at posLast=55, posLast=5959, posLast=6161, Lys82, and Lys89
  • Modification sites at PhosphoSitePlus

Other Protein References for VBP1 Gene

No data available for DME Specific Peptides for VBP1 Gene

Domains & Families for VBP1 Gene

Gene Families for VBP1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VBP1 Gene

Graphical View of Domain Structure for InterPro Entry

P61758

UniProtKB/Swiss-Prot:

PFD3_HUMAN :
  • Belongs to the prefoldin subunit alpha family.
Family:
  • Belongs to the prefoldin subunit alpha family.
genes like me logo Genes that share domains with VBP1: view

Function for VBP1 Gene

Molecular function for VBP1 Gene

GENATLAS Biochemistry:
von Hippel-Lindau binding protein 1,unlikely to oinvolved in renal cell carcinoma
UniProtKB/Swiss-Prot Function:
Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Gene Ontology (GO) - Molecular Function for VBP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 22190034
GO:0015631 tubulin binding IBA --
genes like me logo Genes that share ontologies with VBP1: view

Phenotypes for VBP1 Gene

genes like me logo Genes that share phenotypes with VBP1: view

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VBP1 Gene

Localization for VBP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VBP1 Gene

Cytoplasm. Nucleus. Note=In complex with VHL can translocate to the nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VBP1 gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Vesicles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VBP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm TAS,IBA --
GO:0005829 cytosol IDA --
GO:0005844 polysome IBA --
GO:0016272 prefoldin complex IBA,IEA --
genes like me logo Genes that share ontologies with VBP1: view

Pathways & Interactions for VBP1 Gene

genes like me logo Genes that share pathways with VBP1: view

Gene Ontology (GO) - Biological Process for VBP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006457 protein folding IEA --
GO:0007017 microtubule-based process IBA --
GO:0007021 tubulin complex assembly IBA --
genes like me logo Genes that share ontologies with VBP1: view

No data available for SIGNOR curated interactions for VBP1 Gene

Drugs & Compounds for VBP1 Gene

No Compound Related Data Available

Transcripts for VBP1 Gene

Unigene Clusters for VBP1 Gene

Von Hippel-Lindau binding protein 1:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for VBP1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7
SP1: - -
SP2: - -
SP3: - -
SP4:
SP5: -

Relevant External Links for VBP1 Gene

GeneLoc Exon Structure for
VBP1
ECgene alternative splicing isoforms for
VBP1

Expression for VBP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VBP1 Gene

Protein differential expression in normal tissues from HIPED for VBP1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (21.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VBP1 Gene



Protein tissue co-expression partners for VBP1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VBP1 Gene:

VBP1

SOURCE GeneReport for Unigene cluster for VBP1 Gene:

Hs.436803

mRNA Expression by UniProt/SwissProt for VBP1 Gene:

P61758-PFD3_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for VBP1 Gene

  • Nervous system(4.9)
  • Lung(4.5)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with VBP1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for VBP1 Gene

Orthologs for VBP1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VBP1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VBP1 33 34
  • 100 (n)
dog
(Canis familiaris)
Mammalia VBP1 33 34
  • 94.42 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VBP1 34
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vbp1 33 16 34
  • 91.84 (n)
cow
(Bos Taurus)
Mammalia VBP1 33 34
  • 91.37 (n)
chicken
(Gallus gallus)
Aves VBP1 33 34
  • 81.73 (n)
lizard
(Anolis carolinensis)
Reptilia VBP1 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vbp1 33
  • 77.43 (n)
Str.6377 33
African clawed frog
(Xenopus laevis)
Amphibia vbp1-prov 33
zebrafish
(Danio rerio)
Actinopterygii vbp1 33 34
  • 71.38 (n)
Dr.29111 33
fruit fly
(Drosophila melanogaster)
Insecta CG6719 35
  • 57 (a)
mgr 34 33
  • 55.86 (n)
OneToMany
CG15676 34
  • 24 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011165 33
  • 56.85 (n)
worm
(Caenorhabditis elegans)
Secernentea pfd-3 33 34
  • 50.88 (n)
T06G6.9 35
  • 40 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C04510g 33
  • 56.1 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER210C 33
  • 52.26 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PAC10 33 34 36
  • 50.62 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons PFD3 33
  • 51.36 (n)
rice
(Oryza sativa)
Liliopsida Os12g0562900 33
  • 50.17 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02264 33
  • 53.88 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes pac10 33
  • 50.4 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5790 33
Species where no ortholog for VBP1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VBP1 Gene

ENSEMBL:
Gene Tree for VBP1 (if available)
TreeFam:
Gene Tree for VBP1 (if available)

Paralogs for VBP1 Gene

Pseudogenes.org Pseudogenes for VBP1 Gene

genes like me logo Genes that share paralogs with VBP1: view

No data available for Paralogs for VBP1 Gene

Variants for VBP1 Gene

Sequence variations from dbSNP and Humsavar for VBP1 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs1000251998 -- 155,218,009(+) ATTGA(A/T)TTTCC intron-variant
rs1000557317 -- 155,237,998(+) AGCTA(C/T)GAGAT intron-variant
rs1000583890 -- 155,206,688(+) AGGGT(C/T)GTCTG intron-variant
rs1000702418 -- 155,217,700(+) AATTT(A/G)TTGAG intron-variant
rs1000821034 -- 155,228,429(+) ATAAC(C/G)TGTAT reference, missense

Structural Variations from Database of Genomic Variants (DGV) for VBP1 Gene

Variant ID Type Subtype PubMed ID
nsv528909 CNV gain 19592680
esv3575068 CNV loss 25503493
esv33784 CNV gain+loss 17666407
esv29972 CNV gain 17803354
esv29815 CNV gain 19812545

Variation tolerance for VBP1 Gene

Residual Variation Intolerance Score: 41.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.14; 3.18% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VBP1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VBP1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VBP1 Gene

Disorders for VBP1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for VBP1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
renal cell carcinoma
  • renal cell carcinoma, clear cell, somatic
- elite association - COSMIC cancer census association via MalaCards
Search VBP1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for VBP1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VBP1
genes like me logo Genes that share disorders with VBP1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VBP1 Gene

Publications for VBP1 Gene

  1. Identification of a novel protein (VBP-1) binding to the von Hippel-Lindau (VHL) tumor suppressor gene product. (PMID: 8674032) Tsuchiya H … Hino O (Cancer research 1996) 2 3 4 22 60
  2. Characterization of the gene (VBP1) and transcript for the von Hippel-Lindau binding protein and isolation of the highly conserved murine homologue. (PMID: 9339366) Brinke A … Giannelli F (Genomics 1997) 2 3 4 60
  3. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 60
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  5. Expression of the von Hippel-Lindau-binding protein-1 (Vbp1) in fetal and adult mouse tissues. (PMID: 9931330) Hemberger M … Fundele R (Human molecular genetics 1999) 3 22 60

Products for VBP1 Gene

Sources for VBP1 Gene

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