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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

    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
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    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (336 hits/1290 screens)

    Associated conditions

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

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin binding  
    enables actin filament binding  
    enables protein binding PubMed 
    Process Evidence Code Pubs
    involved_in autophagosome maturation PubMed 
    involved_in endosomal transport  
    involved_in endosomal vesicle fusion PubMed 
    involved_in endosome to lysosome transport PubMed 
    involved_in intracellular protein transport  
    involved_in regulation of SNARE complex assembly PubMed 
    involved_in vacuole fusion, non-autophagic  
    Component Evidence Code Pubs
    part_of CORVET complex PubMed 
    part_of HOPS complex  
    part_of HOPS complex PubMed 
    part_of HOPS complex PubMed 
    located_in autophagosome  
    located_in axon  
    located_in clathrin-coated vesicle  
    located_in early endosome PubMed 
    is_active_in endosome  
    located_in endosome membrane  
    located_in late endosome PubMed 
    located_in late endosome membrane  
    located_in lysosomal membrane PubMed 
    located_in lysosome PubMed 
    located_in neuronal cell body  
    located_in presynapse  
    located_in recycling endosome PubMed 

    General protein information

    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)

    NEW Try the new Transcript table

    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)

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