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Aliases for VPS16 Gene

Aliases for VPS16 Gene

  • VPS16, CORVET/HOPS Core Subunit 2 3 5
  • HVPS16 3 4
  • Vacuolar Protein Sorting 16 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 16 Homolog 3
  • Vacuolar Protein Sorting Protein 16 3
  • VPS16 CORVET/HOPS Core Subunit 3

External Ids for VPS16 Gene

Previous GeneCards Identifiers for VPS16 Gene

  • GC20U990060
  • GC20P002769
  • GC20P002817
  • GC20P002818
  • GC20P002821

Summaries for VPS16 Gene

Entrez Gene Summary for VPS16 Gene

  • Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps16 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]

GeneCards Summary for VPS16 Gene

VPS16 (VPS16, CORVET/HOPS Core Subunit) is a Protein Coding gene. GO annotations related to this gene include actin binding and actin filament binding.

UniProtKB/Swiss-Prot for VPS16 Gene

  • Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act as a core component of the putative HOPS and CORVET endosomal tethering complexes which are 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 HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes. The CORVET complex is proposed to function as a Rab5 effector to mediate early endosome fusion probably in specific endosome subpopulations (PubMed:11382755, PubMed:23351085, PubMed:24554770, PubMed:25266290, PubMed:25783203). Required for recruitment of VPS33A to the HOPS complex (PubMed:23901104). Required for fusion of endosomes and autophagosomes with lysosomes; the function is dependent on its association with VPS33A but not VPS33B (PubMed:25783203). The function in autophagosome-lysosome fusion implicates STX17 but not UVRAG (PubMed:24554770).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS16 Gene

Genomics for VPS16 Gene

Regulatory Elements for VPS16 Gene

Enhancers for VPS16 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around VPS16 on UCSC Golden Path with GeneCards custom track

Promoters for VPS16 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around VPS16 on UCSC Golden Path with GeneCards custom track

Genomic Location for VPS16 Gene

Chromosome:
20
Start:
2,840,697 bp from pter
End:
2,866,732 bp from pter
Size:
26,036 bases
Orientation:
Plus strand

Genomic View for VPS16 Gene

Genes around VPS16 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS16 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS16 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS16 Gene

Proteins for VPS16 Gene

  • Protein details for VPS16 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H269-VPS16_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 16 homolog
    Protein Accession:
    Q9H269
    Secondary Accessions:
    • Q5JUB1
    • Q8WU31
    • Q96EE7
    • Q96N92
    • Q9H1Q4
    • Q9H1Q5

    Protein attributes for VPS16 Gene

    Size:
    839 amino acids
    Molecular mass:
    94694 Da
    Quaternary structure:
    • Core component of at least two putative endosomal tethering complexes, the homotypic fusion and vacuole protein sorting (HOPS) complex and the class C core vacuaole/endosome tethering (CORVET) complex. Their common core is composed of the class C Vps proteins VPS11, VPS16, VPS18 and VPS33A, which in HOPS further associates with VPS39 and VPS41 and in CORVET with VPS8 and TGFBRAP1 (PubMed:11382755, PubMed:25783203, PubMed:23901104, PubMed:25266290). Interacts with RAB5C (By similarity). Interacts with STX17, MON1B (PubMed:20434987, PubMed:24554770). Associates with adaptor protein complex 3 (AP-3) and clathrin:AP-3 complexes (By similarity).

    Three dimensional structures from OCA and Proteopedia for VPS16 Gene

    Alternative splice isoforms for VPS16 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS16 Gene

Proteomics data for VPS16 Gene at MOPED

Post-translational modifications for VPS16 Gene

  • Ubiquitination at Lys 58, Lys 163, Lys 496, Lys 510, Lys 537, and Lys 660
  • Modification sites at PhosphoSitePlus

Other Protein References for VPS16 Gene

Antibody Products

No data available for DME Specific Peptides for VPS16 Gene

Domains & Families for VPS16 Gene

Protein Domains for VPS16 Gene

InterPro:
Blocks:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q9H269

UniProtKB/Swiss-Prot:

VPS16_HUMAN :
  • Belongs to the VPS16 family.
Family:
  • Belongs to the VPS16 family.
genes like me logo Genes that share domains with VPS16: view

No data available for Gene Families for VPS16 Gene

Function for VPS16 Gene

Molecular function for VPS16 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act as a core component of the putative HOPS and CORVET endosomal tethering complexes which are 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 HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes. The CORVET complex is proposed to function as a Rab5 effector to mediate early endosome fusion probably in specific endosome subpopulations (PubMed:11382755, PubMed:23351085, PubMed:24554770, PubMed:25266290, PubMed:25783203). Required for recruitment of VPS33A to the HOPS complex (PubMed:23901104). Required for fusion of endosomes and autophagosomes with lysosomes; the function is dependent on its association with VPS33A but not VPS33B (PubMed:25783203). The function in autophagosome-lysosome fusion implicates STX17 but not UVRAG (PubMed:24554770).

Gene Ontology (GO) - Molecular Function for VPS16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0051015 actin filament binding IEA --
genes like me logo Genes that share ontologies with VPS16: view
genes like me logo Genes that share phenotypes with VPS16: view

Animal Model Products

miRNA for VPS16 Gene

miRTarBase miRNAs that target VPS16

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS16 Gene

Localization for VPS16 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS16 Gene

Late endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane; Peripheral membrane protein; Cytoplasmic side. Early endosome. Cytoplasmic vesicle, clathrin-coated vesicle. Cytoplasmic vesicle, autophagosome. Note=Colocalizes with AP-3, clathrin, Rab5 and Rab7b (By similarity). Cytoplasmic, peripheral membrane protein associated with early endosomes and late endosomes/lysosomes. {ECO:0000250 UniProtKB:Q920Q4, ECO:0000305}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VPS16 Gene COMPARTMENTS Subcellular localization image for VPS16 gene
Compartment Confidence
endosome 5
lysosome 5
vacuole 5
cytoskeleton 2
nucleus 2
cytosol 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for VPS16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005765 lysosomal membrane IDA 17897319
GO:0005769 early endosome IDA 19109425
GO:0005770 late endosome IDA 11382755
GO:0030136 clathrin-coated vesicle IEA --
genes like me logo Genes that share ontologies with VPS16: view

Pathways & Interactions for VPS16 Gene

SuperPathways for VPS16 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS16 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for VPS16 Gene

Drugs & Compounds for VPS16 Gene

No Compound Related Data Available

Transcripts for VPS16 Gene

Alternative Splicing Database (ASD) splice patterns (SP) for VPS16 Gene

No ASD Table

Relevant External Links for VPS16 Gene

GeneLoc Exon Structure for
VPS16
ECgene alternative splicing isoforms for
VPS16

Expression for VPS16 Gene

mRNA expression in normal human tissues for VPS16 Gene

Protein differential expression in normal tissues from HIPED for VPS16 Gene

This gene is overexpressed in Lymph node (8.4) and Peripheral blood mononuclear cells (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for VPS16 Gene



mRNA Expression by UniProt/SwissProt for VPS16 Gene

Q9H269-VPS16_HUMAN
Tissue specificity: Ubiquitous.
genes like me logo Genes that share expression patterns with VPS16: view

Protein tissue co-expression partners for VPS16 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for VPS16 Gene

Orthologs for VPS16 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS16 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia VPS16 35
  • 91.97 (n)
  • 98.09 (a)
VPS16 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS16 35
  • 91.93 (n)
  • 97.85 (a)
VPS16 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vps16 35
  • 89.67 (n)
  • 97.02 (a)
Vps16 16
Vps16 36
  • 97 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps16 35
  • 89.39 (n)
  • 96.66 (a)
oppossum
(Monodelphis domestica)
Mammalia VPS16 36
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS16 36
  • 79 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia VPS16 36
  • 100 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS16 35
  • 75.86 (n)
  • 77.45 (a)
lizard
(Anolis carolinensis)
Reptilia VPS16 36
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps16 35
  • 67.47 (n)
  • 67.03 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.25398 35
zebrafish
(Danio rerio)
Actinopterygii vps16 35
  • 66.71 (n)
  • 67.9 (a)
vps16 36
  • 68 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5648 35
fruit fly
(Drosophila melanogaster)
Insecta CG8454 37
  • 35 (a)
Vps16A 35
  • 48.79 (n)
  • 36.53 (a)
Vps16A 36
  • 36 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000529 35
  • 50.63 (n)
  • 40.05 (a)
worm
(Caenorhabditis elegans)
Secernentea C05D11.2 37
  • 25 (a)
vps-16 36
  • 23 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS16 36
  • 23 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons VCL1 35
  • 46.57 (n)
  • 36.93 (a)
rice
(Oryza sativa)
Liliopsida Os01g0666800 35
  • 44.12 (n)
  • 33.2 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU06268 35
  • 48.67 (n)
  • 38.43 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vps16 35
  • 43 (n)
  • 32.82 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 42 (a)
OneToOne
Species with no ortholog for VPS16:
  • A. gosspyii yeast (Ashbya gossypii)
  • 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)
  • 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)
  • 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 VPS16 Gene

ENSEMBL:
Gene Tree for VPS16 (if available)
TreeFam:
Gene Tree for VPS16 (if available)

Paralogs for VPS16 Gene

No data available for Paralogs for VPS16 Gene

Variants for VPS16 Gene

Sequence variations from dbSNP and Humsavar for VPS16 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
VAR_053776 -
rs1854474 -- 2,855,110(+) CGCAC(G/T)CCACC intron-variant
rs1854475 -- 2,855,118(+) ACCAT(C/G)CCCGG intron-variant
rs873711 -- 2,846,822(+) TCACT(A/G)TTTCC intron-variant
rs2297048 -- 2,860,283(+) GAGGA(A/G)GAGCT reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for VPS16 Gene

Variant ID Type Subtype PubMed ID
nsv833895 CNV Loss 17160897
nsv522009 CNV Gain 19592680
nsv3261 CNV Loss 18451855
esv1548519 CNV Insertion 17803354
nsv518708 CNV Loss 19592680

Variation tolerance for VPS16 Gene

Residual Variation Intolerance Score: 32.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.91; 48.82% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VPS16 Gene

HapMap Linkage Disequilibrium report
VPS16

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS16 Gene

Disorders for VPS16 Gene

Relevant External Links for VPS16

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS16

No disorders were found for VPS16 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VPS16 Gene

Publications for VPS16 Gene

  1. Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes. (PMID: 25783203) Wartosch L. … Luzio J.P. (Traffic 2015) 2 3 4 67
  2. Characterization of the Mammalian CORVET and HOPS Complexes and Their Modular Restructuring for Endosome Specificity. (PMID: 26463206) van der Kant R. … Neefjes J. (J. Biol. Chem. 2015) 2 3
  3. Molecular characterization of mammalian homologues of class C Vps proteins that interact with syntaxin-7. (PMID: 11382755) Kim B.Y. … Akazawa C. (J. Biol. Chem. 2001) 3 23
  4. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3

Products for VPS16 Gene

Sources for VPS16 Gene

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