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    VPS16 VPS16 core subunit of CORVET and HOPS complexes [ Homo sapiens (human) ]

    Gene ID: 64601, updated on 10-Dec-2024

    Summary

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    Official Symbol
    VPS16provided by HGNC
    Official Full Name
    VPS16 core subunit of CORVET and HOPS complexesprovided by HGNC
    Primary source
    HGNC:HGNC:14584
    See related
    Ensembl:ENSG00000215305 MIM:608550; AllianceGenome:HGNC:14584
    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
    DYT30; hVPS16
    Summary
    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]
    Expression
    Ubiquitous expression in appendix (RPKM 12.2), thyroid (RPKM 11.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VPS16 in Genome Data Viewer
    Location:
    20p13
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (2840745..2866732)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (2871419..2897578)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (2821391..2847378)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2778855-2779842 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2779843-2780830 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2780831-2781816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12607 Neighboring gene carboxypeptidase X, M14 family member 1 Neighboring gene CRISPRi-validated cis-regulatory element chr20.196 Neighboring gene chromosome 20 open reading frame 141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2812614-2813114 Neighboring gene transmembrane protein 239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17472 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2820603-2821134 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:2821668-2822199 Neighboring gene PC-esterase domain containing 1A Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:2840338-2840838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2852243-2852874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2852875-2853504 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2853505-2854136 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:2854137-2854766 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60029 Neighboring gene protein tyrosine phosphatase receptor type A Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:2903375-2903875 Neighboring gene Sharpr-MPRA regulatory region 1396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17473 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:3007535-3008734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17475 Neighboring gene mitochondrial ribosomal protein S26 Neighboring gene gonadotropin releasing hormone 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Dominant VPS16 Pathogenic Variants: Not Only Isolated Dystonia. Monfrini E, et al. Mov Disord Clin Pract, 2024 Jan. PMID 38291845, Free PMC Article
    2. Bioinformatics Analysis of the Prognostic Significance of VPS16 in Hepatocellular Carcinoma and Its Role in Drug Screening. Gong X, et al. Biomed Res Int, 2023. PMID 37124933, Free PMC Article
    3. Mutation screening of VPS16 gene in patients with isolated dystonia. Li LX, et al. Parkinsonism Relat Disord, 2021 Feb. PMID 33482438
    4. Mutations in the VPS16 Gene in 56 Early-Onset Dystonia Patients. Li XY, et al. Mov Disord, 2021 Mar. PMID 33595841
    5. A Recurrent VPS16 p.Arg187* Nonsense Variant in Early-Onset Generalized Dystonia. Ostrozovicova M, et al. Mov Disord, 2021 Aug. PMID 33998058

    See all (83) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Dominant VPS16 Pathogenic Variants: Not Only Isolated Dystonia.
      Title: Dominant VPS16 Pathogenic Variants: Not Only Isolated Dystonia.
    2. Bioinformatics Analysis of the Prognostic Significance of VPS16 in Hepatocellular Carcinoma and Its Role in Drug Screening.
      Title: Bioinformatics Analysis of the Prognostic Significance of VPS16 in Hepatocellular Carcinoma and Its Role in Drug Screening.
    3. Overexpression of VPS16 correlates with tumor progression and chemoresistance in colorectal cancer.
      Title: Overexpression of VPS16 correlates with tumor progression and chemoresistance in colorectal cancer.
    4. Homozygous missense VPS16 variant is associated with a novel disease, resembling mucopolysaccharidosis-plus syndrome in two siblings.
      Title: Homozygous missense VPS16 variant is associated with a novel disease, resembling mucopolysaccharidosis-plus syndrome in two siblings.
    5. Mutation screening of VPS16 gene in patients with isolated dystonia.
      Title: Mutation screening of VPS16 gene in patients with isolated dystonia.
    6. A Recurrent VPS16 p.Arg187* Nonsense Variant in Early-Onset Generalized Dystonia.
      Title: A Recurrent VPS16 p.Arg187* Nonsense Variant in Early-Onset Generalized Dystonia.
    7. Bi-allelic VPS16 variants limit HOPS/CORVET levels and cause a mucopolysaccharidosis-like disease.
      Title: Bi-allelic VPS16 variants limit HOPS/CORVET levels and cause a mucopolysaccharidosis-like disease.
    8. Mutations in the VPS16 Gene in 56 Early-Onset Dystonia Patients.
      Title: Mutations in the VPS16 Gene in 56 Early-Onset Dystonia Patients.
    9. Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities.
      Title: Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities.
    10. VPS16 is a new causative gene for adolescent-onset primary dystonia.
      Title: Homozygous mutation of VPS16 gene is responsible for an autosomal recessive adolescent-onset primary dystonia.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    Associated conditions

    Description Tests
    Dystonia 30
    MedGen: C5543312 OMIM: 619291 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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 actin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables actin filament binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endosomal transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endosomal vesicle fusion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in endosome to lysosome transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of SNARE complex assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in vacuole fusion, non-autophagic IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of CORVET complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of HOPS complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of HOPS complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of HOPS complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in autophagosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in clathrin-coated vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosomal membrane HDA PubMed 
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in recycling endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 16 homolog
    Names
    VPS16, CORVET/HOPS core subunit
    vacuolar protein sorting 16 homolog
    vacuolar protein sorting protein 16

    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.

    mRNA and Protein(s)

    1. NM_022575.4 → NP_072097.2  vacuolar protein sorting-associated protein 16 homolog isoform 1

      See identical proteins and their annotated locations for NP_072097.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AF308801, BM468030, BU845142
      Consensus CDS
      CCDS13036.1
      UniProtKB/Swiss-Prot
      Q5JUB1, Q8WU31, Q96EE7, Q96N92, Q9H1Q4, Q9H1Q5, Q9H269
      Related
      ENSP00000369810.3, ENST00000380445.8
      Conserved Domains (2) summary
      pfam04841
      Location:4 → 420
      Vps16_N; Vps16, N-terminal region
      pfam04840
      Location:517 → 835
      Vps16_C; Vps16, C-terminal region

    2. NM_080413.3 → NP_536338.1  vacuolar protein sorting-associated protein 16 homolog isoform 3

      See identical proteins and their annotated locations for NP_536338.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an internal sequence segment compared to transcript variant 1. It thus encodes a shorter isoform (3) which is shorter than isoform 1.
      Source sequence(s)
      AK055787, BC021291, CN483115
      Consensus CDS
      CCDS13037.1
      UniProtKB/Swiss-Prot
      Q9H269
      Related
      ENSP00000369836.3, ENST00000380469.7
      Conserved Domains (2) summary
      pfam04841
      Location:4 → 301
      Vps16_N; Vps16, N-terminal region
      pfam04840
      Location:373 → 691
      Vps16_C; Vps16, C-terminal region

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      2840745..2866732
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      2871419..2897578
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_080414.1: Suppressed sequence

      Description
      NM_080414.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H269.2 GenPept UniProtKB/Swiss-Prot:Q9H269

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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