Free for academic non-profit institutions. Other users need a Commercial license

Aliases for VPS16 Gene

Aliases for VPS16 Gene

  • VPS16, CORVET/HOPS Core Subunit 2 3 5
  • HVPS16 3 4
  • Vacuolar Protein Sorting-Associated Protein 16 Homolog 3
  • Vacuolar Protein Sorting 16 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 16 Homolog 3
  • Vacuolar Protein Sorting Protein 16 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. Diseases associated with VPS16 include Arthrogryposis, Renal Dysfunction, And Cholestasis 1 and Leukodystrophy, Hypomyelinating, 6. 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 CIViC summary , 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 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
GH20G002870 1.1 ENCODE 32.3 +31.9 31922 4.7 HNRNPUL1 PKNOX1 FOXA2 MLX CREB3L1 SIN3A ARID4B DMAP1 ZNF2 YY1 VPS16 PCED1A TMEM239 ENSG00000241690 C20orf141 ITPA PTPRA GC20M002886
GH20G002946 1.3 Ensembl ENCODE 19.3 +107.0 106975 1.6 PKNOX1 FOXA2 ATF1 MLX ARNT ZFP64 ARID4B DMAP1 YY1 SLC30A9 VPS16 PTPRA PCED1A GC20M002886 GC20P003041
GH20G002983 1 Ensembl ENCODE 20.4 +144.6 144614 3.3 PKNOX1 NFIB BMI1 YY1 ZFHX2 EGR1 RELB FOS IKZF2 EGR2 VPS16 PTPRA EBF4 TMEM239 ENSG00000241690 C20orf141 GC20P003041 GC20M002886
GH20G002885 0.6 Ensembl 33 +44.4 44405 0.2 CTCF ZNF654 MAZ RAD21 IKZF1 SCRT2 NBN MLLT1 IKZF2 EGR2 VPS16 PTPRA TMEM239 ENSG00000241690 C20orf141 GC20M002886
GH20G003809 1.4 ENCODE dbSUPER 13.7 +971.3 971291 4.7 HDGF PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ENSG00000229539 VPS16 CDC25B ENSG00000274949 GC20M003810
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000133708 203 1401 HNRNPUL1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 ZNF207

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 vacuole/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

Post-translational modifications for VPS16 Gene

  • Ubiquitination at posLast=5858, posLast=163163, Lys496, posLast=510510, Lys537, and Lys660
  • Modification sites at PhosphoSitePlus

Other Protein References for VPS16 Gene

No data available for DME Specific Peptides for VPS16 Gene

Domains & Families for VPS16 Gene

Protein Domains for VPS16 Gene

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:0003779 actin binding IBA --
GO:0005515 protein binding IPI 11382755
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

CRISPR Products

miRNA for VPS16 Gene

miRTarBase miRNAs that target VPS16

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for 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
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 VPS16 gene
Compartment Confidence
lysosome 5
endosome 5
nucleus 2
mitochondrion 1
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for VPS16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005764 lysosome IDA,IEA 11382755
GO:0005765 lysosomal membrane IDA,IEA 17897319
GO:0005768 endosome IEA --
GO:0005769 early endosome IEA,IDA 19109425
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

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006886 intracellular protein transport IEA --
GO:0006914 autophagy IEA --
GO:0007033 vacuole organization IEA --
GO:0008333 endosome to lysosome transport IMP 25783203
genes like me logo Genes that share ontologies with VPS16: view

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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for VPS16

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for VPS16 Gene



Protein tissue co-expression partners for VPS16 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS16 Gene:

VPS16

mRNA Expression by UniProt/SwissProt for VPS16 Gene:

Q9H269-VPS16_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for VPS16 Gene

  • Intestine(4.2)
  • Kidney(4.2)
  • Lung(4.2)
  • Nervous system(4.2)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with VPS16: view

Primer Products

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 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
chimpanzee
(Pan troglodytes)
Mammalia VPS16 35
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS16 34 35
  • 91.97 (n)
dog
(Canis familiaris)
Mammalia VPS16 34 35
  • 91.93 (n)
mouse
(Mus musculus)
Mammalia Vps16 34 16 35
  • 89.67 (n)
rat
(Rattus norvegicus)
Mammalia Vps16 34
  • 89.39 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS16 35
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS16 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS16 34
  • 75.86 (n)
lizard
(Anolis carolinensis)
Reptilia VPS16 35
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps16 34
  • 67.47 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.25398 34
zebrafish
(Danio rerio)
Actinopterygii vps16 34 35
  • 66.71 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5648 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000529 34
  • 50.63 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vps16A 34 35
  • 48.79 (n)
CG8454 36
  • 35 (a)
worm
(Caenorhabditis elegans)
Secernentea C05D11.2 36
  • 25 (a)
vps-16 35
  • 23 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS16 35
  • 23 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons VCL1 34
  • 46.57 (n)
rice
(Oryza sativa)
Liliopsida Os01g0666800 34
  • 44.12 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06268 34
  • 48.67 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vps16 34
  • 43 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 42 (a)
OneToOne
Species where no ortholog for VPS16 was found in the sources mined by GeneCards:
  • 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
rs1000067326 -- 2,841,068(+) TTAGC(C/T)TCCGG intron-variant, upstream-variant-2KB, utr-variant-5-prime
rs1000133986 -- 2,840,141(+) GCGCG(A/G)CGCCG intron-variant, upstream-variant-2KB
rs1000206164 -- 2,846,150(+) CTCGC(C/T)CTGTC intron-variant
rs1000390265 -- 2,840,592(+) GGCGG(A/G)CGCGA intron-variant, nc-transcript-variant, upstream-variant-2KB, utr-variant-5-prime
rs1000403838 -- 2,862,357(+) TTACT(A/G)TTGGG intron-variant, upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
dgv2204n106 CNV tandem duplication 24896259
esv1548519 CNV insertion 17803354
esv2762056 CNV gain 21179565
esv3645020 CNV gain 21293372
nsv1057464 CNV gain 25217958
nsv1117278 CNV tandem duplication 24896259
nsv1132895 CNV insertion 24896259
nsv3261 CNV deletion 18451855
nsv518708 CNV loss 19592680
nsv522009 CNV gain 19592680
nsv833895 CNV loss 17160897
nsv952978 CNV deletion 24416366
nsv954274 CNV insertion 24416366

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

Human Gene Mutation Database (HGMD)
VPS16
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS16

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

Disorders for VPS16 Gene

MalaCards: The human disease database

(2) MalaCards diseases for VPS16 Gene - From: DISEASES and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search VPS16 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VPS16_HUMAN
  • Note=VSP16 mutation have been found in one familly with adolescent-onset primary dystonia. Dystonia is defined by the presence of sustained involuntary muscle contractions, often leading to abnormal postures. {ECO:0000269 PubMed:27174565}.

Relevant External Links for VPS16

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS16
genes like me logo Genes that share disorders with VPS16: view

No data available for 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 64
  2. 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 4 22 64
  3. 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 64
  4. The HOPS complex mediates autophagosome-lysosome fusion through interaction with syntaxin 17. (PMID: 24554770) Jiang P. … Mizushima N. (Mol. Biol. Cell 2014) 3 4 64
  5. Mammalian CORVET is required for fusion and conversion of distinct early endosome subpopulations. (PMID: 25266290) Perini E.D. … Zerial M. (Traffic 2014) 3 4 64

Products for VPS16 Gene

  • Addgene plasmids for VPS16

Sources for VPS16 Gene

Content
Loading form....