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

Summary

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

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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
VBP1 acts together with p97 to regulate hMSH4 degradation.
Title: VBP1 facilitates proteasome and autophagy-mediated degradation of MutS homologue hMSH4.
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.
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)

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

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

WIAF-2536 (e-PCR)
- UniSTS:5919

Vbp1 (e-PCR), detects polymorphism
- UniSTS:516727

RH35912 (e-PCR)
- UniSTS:37064

G59503 (e-PCR)
- UniSTS:136667

WI-15153 (e-PCR)
- UniSTS:21483

RH36657 (e-PCR)
- UniSTS:86509

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

NG_013269.2 RefSeqGene

Range

24454..47835

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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 ...
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
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