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VPS36 vacuolar protein sorting 36 homolog [ Homo sapiens (human) ]

Gene ID: 51028, updated on 7-Apr-2024

Summary

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Official Symbol
VPS36provided by HGNC
Official Full Name
vacuolar protein sorting 36 homologprovided by HGNC
Primary source
HGNC:HGNC:20312
See related
Ensembl:ENSG00000136100 MIM:610903; AllianceGenome:HGNC:20312
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
EAP45; C13orf9; CGI-145
Summary
This gene encodes a protein that is a subunit of the endosomal sorting complex required for transport II (ESCRT-II). This protein complex functions in sorting of ubiquitinated membrane proteins during endocytosis. A similar protein complex in rat is associated with RNA polymerase elongation factor II. [provided by RefSeq, Aug 2013]
Expression
Ubiquitous expression in skin (RPKM 25.0), thyroid (RPKM 15.1) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
13q14.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (52412606..52450634, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (51627427..51665457, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (52986741..53024769, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370207 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:52922389-52923588 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:52951563-52952064 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:52952065-52952564 Neighboring gene thrombospondin type 1 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5384 Neighboring gene RNY4 pseudogene 24 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:53024355-53024935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7791 Neighboring gene CKAP2 divergent transcript Neighboring gene cytoskeleton associated protein 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
  • 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. Porcine Epidemic Diarrhea Virus (PEDV) ORF3 Interactome Reveals Inhibition of Virus Replication by Cellular VPS36 Protein. Kaewborisuth C, et al. Viruses, 2019 Apr 24. PMID 31022991, Free PMC Article
  2. Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain. Alam SL, et al. Nat Struct Mol Biol, 2006 Nov. PMID 17057716
  3. RAB27A, RAB27B and VPS36 are downregulated in advanced prostate cancer and show functional relevance in prostate cancer cells. Worst TS, et al. Int J Oncol, 2017 Mar. PMID 28197629
  4. Structural insight into the ESCRT-I/-II link and its role in MVB trafficking. Gill DJ, et al. EMBO J, 2007 Jan 24. PMID 17215868, Free PMC Article
  5. Evidence that the endosomal sorting complex required for transport-II (ESCRT-II) is required for efficient human immunodeficiency virus-1 (HIV-1) production. Meng B, et al. Retrovirology, 2015 Aug 14. PMID 26268989, Free PMC Article

See all (48) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. As a result of VPS36-ORF3 interaction, Porcine Epidemic Diarrhea Virus replication was substantially suppressed in cells overexpressing VPS36.
    Title: Porcine Epidemic Diarrhea Virus (PEDV) ORF3 Interactome Reveals Inhibition of Virus Replication by Cellular VPS36 Protein.
  2. RAB27A, RAB27B and VPS36 are frequently underexpressed in advanced prostate cancer and are inversely correlated with prostate cancer outcome. There seems to be a close relationship in the expression of RAB27A, RAB27B and VPS36, with RAB27A and RAB27B being dependent on VPS36.
    Title: RAB27A, RAB27B and VPS36 are downregulated in advanced prostate cancer and show functional relevance in prostate cancer cells.
  3. mammalian ESCRTII is made up of hVps25p, hVps22p, and hVps36p and may be redundant, cargo-specific, or not required for protein sorting at the multivesicular body
    Title: Degradation of endocytosed epidermal growth factor and virally ubiquitinated major histocompatibility complex class I is independent of mammalian ESCRTII.
  4. Crystallographic and biochemical analyses reveal that the GLUE domain of the human ESCRT-II EAP45 (also called VPS36) subunit is a split pleckstrin-homology domain that binds ubiquitin along one edge of the beta-sandwich.
    Title: Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain.
Submit: New GeneRIF Correction

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

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

HIV-1 interactions

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Replication interactions

Interaction Pubs
shRNA knockdown of VPS36 (ESCRT-II component) decreases HIV-1 CA-p24 supernatant levels when using wild type (HIV-1 LAI) and VSV-pseudotyped virus; HIV replication is enhanced by VPS36 PubMed
CRISPR/Cas9 knockout of VPS36 (EAP45) reduces intracellular CA (p24) in, and reduces virion-associated CA (p24) release from, pHIV (BH10)-transfected HAP1 cells (Haplogen GmbH, Vienna, Austria); VPS36 enhances HIV-1 replication PubMed

Protein interactions

Protein Gene Interaction Pubs
capsid gag Knockdown of VPS36 (ESCRT-II component) decreases HIV-1 CA-p24 secretion when using wild type (HIV-1 LAI) and VSV-pseudotyped virus PubMed
gag Knockout of VPS36 (EAP45) reduces virion-associated CA (p24) release from HAP1 cells PubMed
gag Knockout of VPS36 (EAP45) reduces intracellular CA (p24) in HAP1 cells PubMed
gag The EAP45 mutant, IERK159-162AAAA, (that substantially reduces ESCRTII-ESCRTI interaction in vitro), impairs the production of extracellular CA-p24 PubMed
gag The EAP45 mutant, IERK159-162AAAA, (substantially reduces ESCRTII-ESCRTI interaction in vitro), impairs the production of intracellular CA-p24 PubMed
gag Overexpression of GLUE (GRAM-like ubiquitin-binding in EAP45) domain in isolation (amino acids 1-139, not sufficient to interact with ESCRT-I) decreases extracellular CA-p24 levels PubMed
gag Overexpression of GLUE (GRAM-like ubiquitin-binding in EAP45) domain in isolation (amino acids 1-139, not sufficient to interact with ESCRT-I) impairs the production of intracellular CA-p24 PubMed
gag Knockdown of VPS36 (ESCRT-II component) impairs HIV-1 CA-p24 production when using wild type (HIV-1 LAI) and VSV-pseudotyped virus PubMed

Go to the HIV-1, Human Interaction Database

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

Potential readthrough

Included gene: THSD1

Homology

Clone Names

  • DKFZp781E0871

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phosphatidylinositol-3-phosphate binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in macroautophagy TAS
Traceable Author Statement
more info
 PubMed 
involved_in membrane fission NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in multivesicular body assembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in multivesicular body assembly TAS
Traceable Author Statement
more info
 PubMed 
involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of ESCRT II complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of ESCRT II complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of ESCRT II complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of ESCRT II complex TAS
Traceable Author Statement
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
is_active_in late endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in late endosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lysosome IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
vacuolar protein-sorting-associated protein 36
Names
ELL-associated protein of 45 kDa
ESCRT-II complex subunit VPS36

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_001282168.2 → NP_001269097.1  vacuolar protein-sorting-associated protein 36 isoform 2

    See identical proteins and their annotated locations for NP_001269097.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' terminal exon compared to variant 1. This results in a shorter protein (isoform 2) compared to isoform 1.
    Source sequence(s)
    AI352102, AL359513, BX647847, CB959894, DA461148
    Conserved Domains (2) summary
    cd13226
    Location:1 → 119
    PH-GRAM-like_Eap45; Pleckstrin homology-like domain or GLUE (GRAM-like ubiquitin-binding in Eap45) domain of Eap45
    pfam04157
    Location:146 → 360
    EAP30; EAP30/Vps36 family

  2. NM_001282169.2 → NP_001269098.1  vacuolar protein-sorting-associated protein 36 isoform 3

    See identical proteins and their annotated locations for NP_001269098.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon, lacks a portion of the 5' coding region and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AI221133, AI352102, AL359513
    Consensus CDS
    CCDS73577.1
    UniProtKB/Swiss-Prot
    Q86VN1
    Related
    ENSP00000484968.1, ENST00000611132.4
    Conserved Domains (2) summary
    pfam04157
    Location:96 → 311
    EAP30; EAP30/Vps36 family
    cl17171
    Location:1 → 70
    PH-like; Pleckstrin homology-like domain

  3. NM_016075.4 → NP_057159.2  vacuolar protein-sorting-associated protein 36 isoform 1

    See identical proteins and their annotated locations for NP_057159.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AI352102, AK289740, BC037279, DA461148
    Consensus CDS
    CCDS9434.1
    UniProtKB/Swiss-Prot
    A8K125, Q3ZCV7, Q5H9S1, Q5VXB6, Q86VN1, Q9H8Z5, Q9Y3E3
    Related
    ENSP00000367299.3, ENST00000378060.9
    Conserved Domains (2) summary
    cd13226
    Location:1 → 128
    PH-GRAM-like_Eap45; Pleckstrin homology-like domain or GLUE (GRAM-like ubiquitin-binding in Eap45) domain of Eap45
    pfam04157
    Location:154 → 369
    EAP30; EAP30/Vps36 family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    52412606..52450634 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    51627427..51665457 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86VN1.1 GenPept UniProtKB/Swiss-Prot:Q86VN1

Gene LinkOut

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

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