Aliases for VPS8 Gene

Aliases for VPS8 Gene

  • VPS8 Subunit Of CORVET Complex 2 3 5
  • KIAA0804 2 3 4
  • Vacuolar Protein Sorting-Associated Protein 8 Homolog 3 4
  • VPS8, CORVET Complex Subunit 2 3
  • Vacuolar Protein Sorting 8 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 8 Homolog 3

External Ids for VPS8 Gene

Previous HGNC Symbols for VPS8 Gene

  • KIAA0804

Previous GeneCards Identifiers for VPS8 Gene

  • GC03P186012
  • GC03P184529
  • GC03P181939

Summaries for VPS8 Gene

GeneCards Summary for VPS8 Gene

VPS8 (VPS8 Subunit Of CORVET Complex) is a Protein Coding gene. Diseases associated with VPS8 include Arthrogryposis, Renal Dysfunction, And Cholestasis 1. Gene Ontology (GO) annotations related to this gene include binding. An important paralog of this gene is WDR72.

UniProtKB/Swiss-Prot Summary for VPS8 Gene

  • Plays a role in vesicle-mediated protein trafficking of the endocytic membrane transport pathway. Believed to act as a component of the putative CORVET endosomal tethering complexes which is proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The CORVET complex is proposed to function as a Rab5 effector to mediate early endosome fusion probably in specific endosome subpopulations (PubMed:25266290). Functions predominantly in APPL1-containing endosomes (PubMed:25266290).

Additional gene information for VPS8 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VPS8 Gene

Genomics for VPS8 Gene

GeneHancer (GH) Regulatory Elements for VPS8 Gene

Promoters and enhancers for VPS8 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J184811 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 514.6 +0.6 620 2.5 ZNF217 CTCF SIN3A NRF1 POLR2G USF1 SP1 PHF8 ZFX POLR2A VPS8 lnc-EPHB3-5 EPHB3 LINC01840 HSALNG0031276
GH03J184804 Enhancer 0.9 FANTOM5 ENCODE 51.6 -6.1 -6099 2.3 CTBP1 FOXA2 OSR2 NFIC ZBTB17 TCF7L2 GATA3 CEBPB SPI1 NR2F1 VPS8 EPHB3 LINC01840 C3orf70 LOC105374253
GH03J185253 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 16.8 +441.9 441864 1.6 POLR2G NCOR1 GTF2E2 PHF8 ZIC2 POLR2A ZBTB11 TCF7 ZNF423 ZBTB26 MIR5588 EHHADH VPS8 MAP3K13 piR-31951-020 lnc-EHHADH-1
GH03J185068 Enhancer 0.9 Ensembl ENCODE 35 +258.0 257963 2.6 CTCF USF1 SMC3 RAD21 NCOR1 ZNF205 GABPB1 ELF1 TAL1 SMAD4 VPS8 C3orf70 piR-53774 FJ601684-333
GH03J185151 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 14.4 +339.7 339664 4.4 POLR2G ZFX ZIC2 GABPA ZBTB26 RFX1 CTBP1 ZNF341 EZH2 HDAC2 C3orf70 TRA2B VPS8 POLR2H RF00017-4195
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS8 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VPS8

Top Transcription factor binding sites by QIAGEN in the VPS8 gene promoter:
  • AML1a
  • AREB6
  • ER-alpha
  • Evi-1
  • HSF1 (long)
  • HSF1short
  • NF-1
  • NF-1/L
  • USF-1
  • USF1

Genomic Locations for VPS8 Gene

Genomic Locations for VPS8 Gene
chr3:184,812,137-185,052,614
(GRCh38/hg38)
Size:
240,478 bases
Orientation:
Plus strand
chr3:184,529,931-184,770,402
(GRCh37/hg19)
Size:
240,472 bases
Orientation:
Plus strand

Genomic View for VPS8 Gene

Genes around VPS8 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS8 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS8 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS8 Gene

Proteins for VPS8 Gene

  • Protein details for VPS8 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N3P4-VPS8_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 8 homolog
    Protein Accession:
    Q8N3P4
    Secondary Accessions:
    • A8K8Q8
    • B9EIQ1
    • C9JB61
    • O94896
    • Q63HP2
    • Q9BVP9
    • Q9H9B0

    Protein attributes for VPS8 Gene

    Size:
    1428 amino acids
    Molecular mass:
    161754 Da
    Quaternary structure:
    • Interacts with RAB5C (By similarity). Interacts with TGFBRAP1 (PubMed:25266290). Component of the putative class C core vacuole/endosome tethering (CORVET) complex; the core of which composed of the class C Vps proteins VPS11, VPS16, VPS18 and VPS33A, is associated with VPS8 and TGFBRAP1 (PubMed:25266290).
    SequenceCaution:
    • Sequence=BAB14322.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAH56195.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS8 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS8 Gene

Post-translational modifications for VPS8 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for VPS8 Gene

Domains & Families for VPS8 Gene

Gene Families for VPS8 Gene

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

Suggested Antigen Peptide Sequences for VPS8 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ78757 (A8K8Q8_HUMAN)
  • Vacuolar protein sorting-associated protein 8 homolog (VPS8_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N3P4

UniProtKB/Swiss-Prot:

VPS8_HUMAN :
  • Belongs to the VPS8 family.
Family:
  • Belongs to the VPS8 family.
genes like me logo Genes that share domains with VPS8: view

Function for VPS8 Gene

Molecular function for VPS8 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in vesicle-mediated protein trafficking of the endocytic membrane transport pathway. Believed to act as a component of the putative CORVET endosomal tethering complexes which is proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The CORVET complex is proposed to function as a Rab5 effector to mediate early endosome fusion probably in specific endosome subpopulations (PubMed:25266290). Functions predominantly in APPL1-containing endosomes (PubMed:25266290).

Phenotypes From GWAS Catalog for VPS8 Gene

Gene Ontology (GO) - Molecular Function for VPS8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25266290
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with VPS8: view
genes like me logo Genes that share phenotypes with VPS8: view

miRNA for VPS8 Gene

miRTarBase miRNAs that target VPS8

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS8 Gene

Localization for VPS8 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS8 Gene

Early endosome.

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 VPS8 gene
Compartment Confidence
endosome 5
plasma membrane 3
cytosol 3
nucleus 2
lysosome 2
golgi apparatus 2
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VPS8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IEA --
GO:0005769 early endosome IDA,IBA 25266290
GO:0033263 CORVET complex IBA 21873635
genes like me logo Genes that share ontologies with VPS8: view

Pathways & Interactions for VPS8 Gene

PathCards logo

SuperPathways for VPS8 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015031 protein transport IEA --
GO:0034058 endosomal vesicle fusion IMP,IBA 25266290
genes like me logo Genes that share ontologies with VPS8: view

No data available for Pathways by source and SIGNOR curated interactions for VPS8 Gene

Drugs & Compounds for VPS8 Gene

No Compound Related Data Available

Transcripts for VPS8 Gene

mRNA/cDNA for VPS8 Gene

9 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
28 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS8 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^
SP1: - - -
SP2:
SP3: - -
SP4: - -
SP5: -
SP6:
SP7:
SP8:
SP9: -
SP10:

ExUns: 20a · 20b ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27a · 27b ^ 28a · 28b ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^
SP1: - - -
SP2: -
SP3:
SP4:
SP5: - -
SP6:
SP7:
SP8: - -
SP9:
SP10:

ExUns: 43 ^ 44 ^ 45 ^ 46 ^ 47
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for VPS8 Gene

GeneLoc Exon Structure for
VPS8

Expression for VPS8 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VPS8 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for VPS8 Gene

This gene is overexpressed in Lymph node (12.2), Frontal cortex (7.0), and Placenta (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VPS8 Gene



Protein tissue co-expression partners for VPS8 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VPS8

SOURCE GeneReport for Unigene cluster for VPS8 Gene:

Hs.269263

Evidence on tissue expression from TISSUES for VPS8 Gene

  • Nervous system(4.7)
  • Intestine(4.2)
genes like me logo Genes that share expression patterns with VPS8: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS8 Gene

Orthologs for VPS8 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS8 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS8 31 30
  • 98.9 (n)
OneToOne
dog
(Canis familiaris)
Mammalia VPS8 31 30
  • 93.6 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VPS8 31 30
  • 92.85 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 92 (a)
OneToMany
-- 31
  • 90 (a)
OneToMany
-- 31
  • 90 (a)
OneToMany
-- 31
  • 90 (a)
OneToMany
-- 31
  • 80 (a)
OneToMany
-- 31
  • 76 (a)
OneToMany
-- 31
  • 71 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia VPS8 31
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vps8 17 31 30
  • 85.86 (n)
rat
(Rattus norvegicus)
Mammalia Vps8 30
  • 85.67 (n)
chicken
(Gallus gallus)
Aves VPS8 31 30
  • 76.92 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS8 31
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps8 30
  • 70.75 (n)
Str.17234 30
zebrafish
(Danio rerio)
Actinopterygii vps8 31 30
  • 67.52 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG10144 31 30
  • 46.85 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007578 30
  • 44.2 (n)
worm
(Caenorhabditis elegans)
Secernentea C42C1.4 31 30
  • 42.4 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS8 33 31
  • 18 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G00800 30
  • 44.71 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 43 (a)
OneToOne
Species where no ortholog for VPS8 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • 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 VPS8 Gene

ENSEMBL:
Gene Tree for VPS8 (if available)
TreeFam:
Gene Tree for VPS8 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VPS8: view image

Paralogs for VPS8 Gene

Paralogs for VPS8 Gene

genes like me logo Genes that share paralogs with VPS8: view

Variants for VPS8 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VPS8 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
712529 Benign: not provided 184,930,527(+) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
719032 Likely Benign: not provided 184,886,122(+) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR_VARIANT
720260 Benign: not provided 184,920,156(+) A/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
732575 Likely Benign: not provided 184,834,639(+) T/C INTRON_VARIANT
737672 Likely Benign: not provided 184,852,505(+) A/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT

Additional dbSNP identifiers (rs#s) for VPS8 Gene

Structural Variations from Database of Genomic Variants (DGV) for VPS8 Gene

Variant ID Type Subtype PubMed ID
esv26122 CNV gain 19812545
esv2643797 CNV insertion 19546169
esv2661930 CNV deletion 23128226
esv2726320 CNV deletion 23290073
esv3422145 CNV insertion 20981092
esv3598946 CNV gain 21293372
esv3598957 CNV gain 21293372
esv3598958 CNV gain 21293372
esv3598959 CNV loss 21293372
nsv1011155 CNV gain 25217958
nsv1119514 CNV insertion 24896259
nsv473754 CNV novel sequence insertion 20440878
nsv520816 CNV gain 19592680

Variation tolerance for VPS8 Gene

Residual Variation Intolerance Score: 72% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.84; 91.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS8 Gene

Human Gene Mutation Database (HGMD)
VPS8
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS8

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS8 Gene

Disorders for VPS8 Gene

MalaCards: The human disease database

(1) MalaCards diseases for VPS8 Gene - From: DISEASES

Disorder Aliases PubMed IDs
arthrogryposis, renal dysfunction, and cholestasis 1
  • arcs1
- elite association - COSMIC cancer census association via MalaCards
Search VPS8 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VPS8

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VPS8: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VPS8 Gene

Publications for VPS8 Gene

  1. Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9872452) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 54
  2. VPS18 recruits VPS41 to the human HOPS complex via a RING-RING interaction. (PMID: 28931724) Hunter MR … Graham SC (The Biochemical journal 2017) 2 3 54
  3. Mammalian CORVET is required for fusion and conversion of distinct early endosome subpopulations. (PMID: 25266290) Perini ED … Zerial M (Traffic (Copenhagen, Denmark) 2014) 3 4 54
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  5. 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 54

Products for VPS8 Gene

Sources for VPS8 Gene