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VHL von Hippel-Lindau tumor suppressor [ Homo sapiens (human) ]

Gene ID: 7428, updated on 11-Jul-2021

Summary

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Official Symbol
VHLprovided by HGNC
Official Full Name
von Hippel-Lindau tumor suppressorprovided by HGNC
Primary source
HGNC:HGNC:12687
See related
Ensembl:ENSG00000134086 MIM:608537
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
RCA1; VHL1; pVHL; HRCA1
Summary
Von Hippel-Lindau syndrome (VHL) is a dominantly inherited familial cancer syndrome predisposing to a variety of malignant and benign tumors. A germline mutation of this gene is the basis of familial inheritance of VHL syndrome. The protein encoded by this gene is a component of the protein complex that includes elongin B, elongin C, and cullin-2, and possesses ubiquitin ligase E3 activity. This protein is involved in the ubiquitination and degradation of hypoxia-inducible-factor (HIF), which is a transcription factor that plays a central role in the regulation of gene expression by oxygen. RNA polymerase II subunit POLR2G/RPB7 is also reported to be a target of this protein. Alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lymph node (RPKM 12.2), spleen (RPKM 10.0) and 25 other tissues See more
Orthologs
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Genomic context

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See VHL in Genome Data Viewer
Location:
3p25.3
Exon count:
4
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (10141778..10153667)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (10183462..10195351)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene FA complementation group D2 Neighboring gene FANCD2 opposite strand Neighboring gene 3p25 BRK1 Alu-mediated recombination region Neighboring gene 3p25 von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase Alu-mediated recombination region Neighboring gene BRICK1 subunit of SCAR/WAVE actin nucleating complex Neighboring gene 3p25 IRAK2 Alu-mediated recombination region Neighboring gene interleukin 1 receptor associated kinase 2 Neighboring gene 3p25 TatD DNase domain containing 2 Alu-mediated recombination region Neighboring gene TatD DNase domain containing 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
  • 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. Clinicopathological comparison of VHL expression as a prognostic tumor marker in renal cell carcinoma: A single center experience. Sekar H, et al. Niger J Clin Pract, 2021 Apr. PMID 33851686
  2. Intravitreal Triamcinolone Acetonide in Von Hippel-Lindau Patient with Novel Mutation. Bunajem M, et al. Middle East Afr J Ophthalmol, 2020 Jul-Sep. PMID 33488018, Free PMC Article
  3. Algorithmic assessment of missense mutation severity in the Von-Hippel Lindau protein. Fields FR, et al. PLoS One, 2020. PMID 33151962, Free PMC Article
  4. 8q24 clear cell renal cell carcinoma germline variant is associated with VHL mutation status and clinical aggressiveness. Eckel-Passow JE, et al. BMC Urol, 2020 Oct 29. PMID 33121461, Free PMC Article
  5. Intronic mutation of the VHL gene associated with central nervous system hemangioblastomas in two Chinese families with Von Hippel-Lindau disease: case report. Liu Z, et al. BMC Med Genet, 2020 Oct 1. PMID 33004005, Free PMC Article

See all (814) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Germline mutations in the new E1' cryptic exon of the VHL gene in patients with tumours of von Hippel-Lindau disease spectrum or with paraganglioma.
    Title: Germline mutations in the new E1' cryptic exon of the <i>VHL</i> gene in patients with tumours of von Hippel-Lindau disease spectrum or with paraganglioma.
  2. High nuclear expression of HIF1alpha, synergizing with inactivation of LIMD1 and VHL, portray worst prognosis among the bladder cancer patients: association with arsenic prevalence.
    Title: High nuclear expression of HIF1α, synergizing with inactivation of LIMD1 and VHL, portray worst prognosis among the bladder cancer patients: association with arsenic prevalence.
  3. TBK1 Is a Synthetic Lethal Target in Cancer with VHL Loss.
    Title: TBK1 Is a Synthetic Lethal Target in Cancer with <i>VHL</i> Loss.
  4. 8q24 clear cell renal cell carcinoma germline variant is associated with VHL mutation status and clinical aggressiveness.
    Title: 8q24 clear cell renal cell carcinoma germline variant is associated with VHL mutation status and clinical aggressiveness.
  5. Novel mutations in the EPO-R, VHL and EPAS1 genes in the Congenital Erythrocytosis patients.
    Title: Novel mutations in the EPO-R, VHL and EPAS1 genes in the Congenital Erythrocytosis patients.
  6. Prolyl Hydroxylase 3 Knockdown Accelerates VHL-Mutant Kidney Cancer Growth In Vivo.
    Title: Prolyl Hydroxylase 3 Knockdown Accelerates <i>VHL</i>-Mutant Kidney Cancer Growth In Vivo.
  7. Relationship between visceral adipose tissue and genetic mutations (VHL and KDM5C) in clear cell renal cell carcinoma.
    Title: Relationship between visceral adipose tissue and genetic mutations (VHL and KDM5C) in clear cell renal cell carcinoma.
  8. Identification of anti-tumoral feedback loop between VHLalpha and hnRNPA2B1 in renal cancer.
    Title: Identification of anti-tumoral feedback loop between VHLα and hnRNPA2B1 in renal cancer.
  9. Clinicopathological comparison of VHL expression as a prognostic tumor marker in renal cell carcinoma: A single center experience.
    Title: Clinicopathological comparison of VHL expression as a prognostic tumor marker in renal cell carcinoma: A single center experience.
  10. Control of Angiogenesis via a VHL/miR-212/132 Axis.
    Title: Control of Angiogenesis via a VHL/miR-212/132 Axis.
Submit: New GeneRIF Correction See all GeneRIFs (543)

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

Professional guidelines

Description
Professional guideline
ACMG 2013

The ACMG recommends that laboratories performing clinical sequencing seek and report mutations in VHL that are pathogenic or expected to be pathogenic.

GuidelinePubMed

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2017-06-28)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2017-06-28)

ClinGen Genome Curation PagePubMed

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

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 enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin ligase-substrate adaptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin-protein transferase activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in cell morphogenesis NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of apoptotic process NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of receptor signaling pathway via JAK-STAT IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of transcription from RNA polymerase II promoter in response to hypoxia IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cell differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein stabilization NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
involved_in protein ubiquitination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in proteolysis TAS
Traceable Author Statement
more info
 PubMed 
involved_in regulation of transcription from RNA polymerase II promoter in response to hypoxia TAS
Traceable Author Statement
more info
  
involved_in regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum NAS
Non-traceable Author Statement
more info
 PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
von Hippel-Lindau disease tumor suppressor
Names
elongin binding protein
protein G7
von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase

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_008212.3 RefSeqGene

    Range
    5001..17036
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_322

mRNA and Protein(s)

  1. NM_000551.4 → NP_000542.1  von Hippel-Lindau disease tumor suppressor isoform 1

    See identical proteins and their annotated locations for NP_000542.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC034193
    Consensus CDS
    CCDS2597.1
    UniProtKB/Swiss-Prot
    P40337
    UniProtKB/TrEMBL
    A0A024R2F2
    Related
    ENSP00000256474.3, ENST00000256474.3
    Conserved Domains (2) summary
    cd05468
    Location:64 → 203
    pVHL; von Hippel-Landau (pVHL) tumor suppressor protein
    cl25865
    Location:7 → 86
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)

  2. NM_001354723.2 → NP_001341652.1  von Hippel-Lindau disease tumor suppressor isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon and contains another alternate exon compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to variant 1.
    Source sequence(s)
    AC034193
    Conserved Domains (2) summary
    cl03381
    Location:63 → 113
    pVHL; von Hippel-Landau (pVHL) tumor suppressor protein
    cl25865
    Location:7 → 86
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)

  3. NM_198156.3 → NP_937799.1  von Hippel-Lindau disease tumor suppressor isoform 2

    See identical proteins and their annotated locations for NP_937799.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame coding exon compared to variant 1. The resulting isoform (2) lacks an internal region, as compared to isoform 1.
    Source sequence(s)
    AC034193
    Consensus CDS
    CCDS2598.1
    UniProtKB/Swiss-Prot
    P40337
    UniProtKB/TrEMBL
    A0A0S2Z4K1
    Related
    ENSP00000344757.2, ENST00000345392.2
    Conserved Domains (3) summary
    pfam17211
    Location:114 → 163
    VHL_C; VHL box domain
    cl03381
    Location:63 → 113
    pVHL; von Hippel-Landau (pVHL) tumor suppressor protein
    cl25865
    Location:7 → 86
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    10141778..10153667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P40337.2 GenPept UniProtKB/Swiss-Prot:P40337

Gene LinkOut

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