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VPS16 Gene

protein-coding   GIFtS: 47
GCID: GC20P002821

Vacuolar Protein Sorting 16 Homolog (S. Cerevisiae)

  Search for VPS16
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Vacuolar Protein Sorting 16 Homolog (S. Cerevisiae)1 2
hVPS162 3
Vacuolar Protein Sorting Protein 162
Vacuolar Protein Sorting-Associated Protein 16 Homolog2

External Ids:    HGNC: 145841   Entrez Gene: 646012   Ensembl: ENSG000002153057   OMIM: 6085505   UniProtKB: Q9H2693   

Export aliases for VPS16 gene to outside databases

Previous GC identifers: GC20U990060 GC20P002769 GC20P002817 GC20P002818


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 (vacuolar protein sorting 16 homolog (S. cerevisiae)) is a protein-coding gene. GO annotations related to this gene include actin filament binding.

UniProtKB/Swiss-Prot: VPS16_HUMAN, Q9H269
Function: May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membrane
docking/fusion reactions of late endosomes/lysosomes




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Search for regulatory transcription factor binding sites for VPS16
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVPS16 promoter sequence
   Search Chromatin IP Primers for VPS16

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VPS16


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 20p13   Ensembl cytogenetic band:  20p13   HGNC cytogenetic band: 20p13

VPS16 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VPS16 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P002821:  view genomic region     (about GC identifiers)

Start:
2,821,349 bp from pter      End:
2,847,378 bp from pter
Size:
26,030 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: VPS16_HUMAN, Q9H269 (See protein sequence)
Recommended Name: Vacuolar protein sorting-associated protein 16 homolog  
Size: 839 amino acids; 94694 Da
Subunit: Large hetero-oligomeric complex together with VPS11, VPS18 and VPS33A. Interacts with STX7
1 PDB 3D structure from and Proteopedia for VPS16:
4BX9 (3D)    
Secondary accessions: Q5JUB1 Q8WU31 Q96EE7 Q96N92 Q9H1Q4 Q9H1Q5
Alternative splicing: 2 isoforms:  Q9H269-1   Q9H269-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for VPS16: NX_Q9H269

Explore proteomics data for VPS16 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys58, Lys163, Lys496, Lys510, Lys537, Lys660
  • Modification sites at PhosphoSitePlus

  • See VPS16 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_072097.2  NP_536338.1  

    ENSEMBL proteins: 
     ENSP00000369810   ENSP00000369836   ENSP00000417031   ENSP00000409840   ENSP00000369808  

    VPS16 Human Recombinant Protein Products:

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    Search eBioscience for ELISAs for VPS16 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR016534 VPS16
     IPR006926 Vps16_N
     IPR006925 Vps16_C

    Graphical View of Domain Structure for InterPro Entry Q9H269

    ProtoNet protein and cluster: Q9H269

    1 Blocks protein domain: IPB006926 Vps16

    UniProtKB/Swiss-Prot: VPS16_HUMAN, Q9H269
    Similarity: Belongs to the VPS16 family


    Find genes that share domains with VPS16           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: VPS16_HUMAN, Q9H269
    Function: May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membrane
    docking/fusion reactions of late endosomes/lysosomes

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003779actin binding ----
    GO:0005515protein binding ----
    GO:0051015actin filament binding IEA--
         
    Find genes that share ontologies with VPS16           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for VPS16:
     Decreased nuclei size in G2M  Increased viability with TRAIL 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for VPS16
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    miRNA
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    miRTarBase miRNAs that target VPS16:
    hsa-mir-335-5p (MIRT019172)

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    VPS16_HUMAN, Q9H269: Late endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane;
    Peripheral membrane protein; Cytoplasmic side. Note=Cytoplasmic, peripheral membrane protein associated with late
    endosomes/lysosomes
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endosome5
    lysosome5
    vacuole5
    cytoskeleton2
    nucleus2
    cytosol1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm ----
    GO:0005765lysosomal membrane IDA17897319
    GO:0005768endosome ----
    GO:0005769early endosome IDA19109425
    GO:0005770late endosome IDA19109425

    Find genes that share ontologies with VPS16           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for VPS16
    Interactions:

        Search GeneGlobe Interaction Network for VPS16

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for VPS16 (Q9H2693 ENSP000003698104) via UniProtKB, MINT, STRING, and/or I2D (see all 117)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    VPS18Q9P2533, ENSP000002205094I2D: score=9 STRING: ENSP00000220509
    AKTIPQ9H8T03, ENSP000003002454I2D: score=1 STRING: ENSP00000300245
    AP3D1O146173, ENSP000003440554I2D: score=1 STRING: ENSP00000344055
    ATP5A1P257053, ENSP000002820504I2D: score=1 STRING: ENSP00000282050
    VPS33AQ96AX13, ENSP000002671994I2D: score=10 STRING: ENSP00000267199
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006886intracellular protein transport IEA--

    Find genes that share ontologies with VPS16           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for VPS16



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for VPS16 gene (3 alternative transcripts): 
    NM_022575.3  NM_080413.2  NM_080414.1  

    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000380445(uc002whe.3) ENST00000380469(uc002whf.3) ENST00000453689
    ENST00000417508 ENST00000481812 ENST00000380443(uc002whg.3) ENST00000487461
    ENST00000466415
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat VPS16

    Selected AceView cDNA sequences (see all 232):

    BQ070914 AA701899 BF038833 CB243563 AA879430 AI360263 BU845142 NM_080413 
    CA430967 AI568221 CD631486 BG701461 BQ068622 BU726865 BU153152 AA383943 
    BM457709 BM855623 AL530956 BG470488 CN480070 CN479639 NM_022575 AI282429 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    VPS16 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    VPS16 Expression
    About this image

    VPS16 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VPS16 Protein Expression

    UniProtKB/Swiss-Prot: VPS16_HUMAN, Q9H269
    Tissue specificity: Ubiquitous

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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for VPS16 gene from Selected species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vps161 , 5 vacuolar protein sorting 16 (yeast)1, 5 89.67(n)1
    97.02(a)1
      2 (63.22 cM)5
    807431  NM_030559.31  NP_085036.31 
     1304243395 
    chicken
    (Gallus gallus)
    Aves VPS161 vacuolar protein sorting 16 homolog (S. cerevisiae) 75.86(n)
    77.45(a)
      426571  NM_001271150.1  NP_001258079.1 
    lizard
    (Anolis carolinensis)
    Reptilia VPS166
    vacuolar protein sorting 16 homolog (S. cerevisiae...
    72(a)
    1 ↔ 1
    GL343838.1(14072-71800)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.253982 Xenopus laevis transcribed sequence with weak similarity more 73.78(n)    BJ612598.1 
    zebrafish
    (Danio rerio)
    Actinopterygii vps161 vacuolar protein sorting protein 16 66.71(n)
    67.9(a)
      798985  NM_001098189.1  NP_001091659.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG84543
    Vps16A1
    Vacuolar protein sorting 16A1 35(a)3
    48.79(n)1
    36.53(a)1
      85D73
    411071  NM_141620.21  NP_649877.11 
    worm
    (Caenorhabditis elegans)
    Secernentea C05D11.23   -- 25(a)   III(6505003-6508106)   --
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes VPS166
    Subunit of the vacuole fusion and protein sorting ...
    23(a)
    1 ↔ 1
    XVI(467260-469656) YPL045W
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons VCL11 VCL1 46.57(n)
    36.93(a)
      818380  NM_129359.3  NP_565879.1 
    rice
    (Oryza sativa)
    Liliopsida Os01g06668001 Os01g0666800 44.12(n)
    33.2(a)
      4326864  NM_001050339.2  NP_001043804.2 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for VPS16 (see all 504)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1448347101,2
    C--2823906(+) AACCCC/TGTCTC 2 -- int10--------
    rs1865589841,2
    --2823923(+) AAATAC/GAAAAA 2 -- int10--------
    rs1387639821,2
    --2824063(+) ACAGAG/TCAAGA 2 -- int10--------
    rs1170831261,2
    F--2824089(+) AAAAAA/GAAAAG 2 -- int11Minor allele frequency- G:0.02NA 120
    rs1427277441,2
    --2824109(+) ATGCCG/TGTGCA 2 -- int10--------
    rs1153699501,2
    C,F--2824146(+) TAAAAA/CTCCAT 2 -- int11Minor allele frequency- C:0.08WA 118
    rs1442451361,2
    --2824249(+) TAGTTA/GATACA 2 -- int10--------
    rs1483057521,2
    --2824454(+) AGACAA/CAATCT 2 -- int10--------
    rs169881301,2
    C,F,H--2824849(+) GCTTTA/GAGAGC 2 -- int119Minor allele frequency- G:0.27NA EA NS WA 1420
    rs1920072431,2
    --2824850(+) CTTTAA/GGAGCA 2 -- int10--------

    HapMap Linkage Disequilibrium report for VPS16 (2821349 - 2847378 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for VPS16:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1548519CNV Insertion17803354
    nsv518708CNV Loss19592680
    nsv833895CNV Loss17160897
    nsv3261CNV Loss18451855
    nsv522009CNV Gain19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing VPS16
    DNA2.0 Custom Variant and Variant Library Synthesis for VPS16

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 608550    OMIM disorders: --

    1 disease from the University of Copenhagen DISEASES database for VPS16:
    Hermansky-Pudlak syndrome

    Find genes that share disorders with VPS16           About GenesLikeMe


    Export disorders for VPS16 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for VPS16 gene, integrated from 10 sources (see all 24):
    (articles sorted by number of sources associating them with VPS16)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular characterization of mammalian homologues of class C Vps proteins that interact with syntaxin-7. (PubMed id 11382755)1, 2, 9 Kim B.Y....Akazawa C. (J. Biol. Chem. 2001)
    2. Integral and associated lysosomal membrane proteins. (PubMed id 17897319)1, 2 Schroeder B.... Hasilik A. (Traffic 2007)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)
    6. Molecular cloning and characterization of human VPS18, VPS11, VPS16, and VPS33. (PubMed id 11250079)1, 2 Huizing M.... Kraemer H. (Gene 2001)
    7. Structural basis of Vps33A recruitment to the human HOPS complex by Vps16. (PubMed id 23901104)1 Graham S.C....Owen D.J. (Proc. Natl. Acad. Sci. U.S.A. 2013)
    8. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    9. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    10. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 64601 HGNC: 14584 AceView: VPS16 Ensembl:ENSG00000215305 euGenes: HUgn64601
    ECgene: VPS16 H-InvDB: VPS16

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for VPS16 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for VPS16 gene:
    Search GeneIP for patents involving VPS16

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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