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

Gene ID: 64601, updated on 2-Nov-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
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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: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 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 (82) 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)

Genotypes

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 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 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 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

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