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CHMP3 charged multivesicular body protein 3 [ Homo sapiens (human) ]

Gene ID: 51652, updated on 22-May-2022

Summary

Official Symbol
CHMP3provided by HGNC
Official Full Name
charged multivesicular body protein 3provided by HGNC
Primary source
HGNC:HGNC:29865
See related
Ensembl:ENSG00000115561 MIM:610052; AllianceGenome:HGNC:29865
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
NEDF; VPS24; CGI-149
Summary
This gene encodes a protein that sorts transmembrane proteins into lysosomes/vacuoles via the multivesicular body (MVB) pathway. This protein, along with other soluble coiled-coil containing proteins, forms part of the ESCRT-III protein complex that binds to the endosomal membrane and recruits additional cofactors for protein sorting into the MVB. This protein may also co-immunoprecipitate with a member of the IFG-binding protein superfamily. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the upstream ring finger protein 103 (RNF103) gene. [provided by RefSeq, Nov 2010]
Expression
Ubiquitous expression in esophagus (RPKM 41.6), thyroid (RPKM 40.0) and 25 other tissues See more
Orthologs
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Genomic context

See CHMP3 in Genome Data Viewer
Location:
2p11.2
Exon count:
6
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (86503430..86563443, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (86505444..86565457, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (86730553..86790566, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene U8 small nucleolar RNA Neighboring gene lysine demethylase 3A Neighboring gene RNF103-CHMP3 readthrough Neighboring gene RNA, U6 small nuclear 640, pseudogene Neighboring gene Sharpr-MPRA regulatory region 1991 Neighboring gene CHMP3 and RNF103 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 3990 Neighboring gene uncharacterized LOC124907853 Neighboring gene ring finger protein 103

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Downregulation of guanine nucleotide-releasing protein, CD151/PETA-3, neuronatin, neuroendocrine differentiation factor, mitochondria 16s rRNA, and signal recognition particle is observed in HIV-1 infected and HIV-1 gp120-treated astrocytes PubMed
Pr55(Gag) gag Recruitment of CHMP2A and CHMP3 by CHMP4B to HIV-1 Gag puncta is observed in in-vitro membrane model PubMed
gag Replacing the NC-p1-p6 region of HIV-1 Gag with the leucine zipper domain of yeast GCN4 overcomes inhibition of HIV-1 particle budding by dominant-negative ESCRT proteins such as CHMP3 and Vps4A PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Readthrough RNF103-CHMP3

Readthrough gene: RNF103-CHMP3, Included gene: RNF103

Homology

Clone Names

  • FLJ38114

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phosphatidylcholine binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables phosphatidylinositol-4,5-bisphosphate binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables ubiquitin-specific protease binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in autophagosome maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in autophagosome maturation TAS
Traceable Author Statement
more info
PubMed 
involved_in autophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in endosome transport via multivesicular body sorting pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in late endosome to lysosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in late endosome to vacuole transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in macroautophagy TAS
Traceable Author Statement
more info
PubMed 
involved_in membrane fission IC
Inferred by Curator
more info
PubMed 
involved_in midbody abscission IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT involved_in mitotic metaphase plate congression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in mitotic metaphase plate congression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in multivesicular body assembly IC
Inferred by Curator
more info
PubMed 
involved_in multivesicular body assembly TAS
Traceable Author Statement
more info
PubMed 
involved_in multivesicular body sorting pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in multivesicular body sorting pathway TAS
Traceable Author Statement
more info
PubMed 
involved_in multivesicular body-lysosome fusion IC
Inferred by Curator
more info
PubMed 
involved_in multivesicular body-lysosome fusion IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of cell death IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nuclear membrane reassembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT involved_in nucleus organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nucleus organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in plasma membrane repair IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of cytokinesis IEA
Inferred from Electronic Annotation
more info
 
involved_in protein polymerization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of centrosome duplication IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of early endosome to late endosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of endosome size IEA
Inferred from Electronic Annotation
more info
 
NOT involved_in regulation of exosomal secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT involved_in regulation of mitotic spindle assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of mitotic spindle assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in suppression of viral release by host IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in vesicle fusion with vacuole IC
Inferred by Curator
more info
PubMed 
involved_in viral budding from plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
involved_in viral budding from plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in viral budding via host ESCRT complex IDA
Inferred from Direct Assay
more info
PubMed 
involved_in viral budding via host ESCRT complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in viral budding via host ESCRT complex TAS
Traceable Author Statement
more info
PubMed 
involved_in viral release from host cell IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in viral release from host cell IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of ESCRT III complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of ESCRT III complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of ESCRT III complex TAS
Traceable Author Statement
more info
PubMed 
located_in amphisome membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in autophagosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in early endosome IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular exosome HDA PubMed 
located_in kinetochore IDA
Inferred from Direct Assay
more info
PubMed 
located_in kinetochore microtubule IDA
Inferred from Direct Assay
more info
PubMed 
located_in late endosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in midbody IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in multivesicular body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in multivesicular body membrane IDA
Inferred from Direct Assay
more info
PubMed 
part_of nuclear pore IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
charged multivesicular body protein 3
Names
25.1 protein
CHMP family, member 3
chromatin-modifying protein 3
neuroendocrine differentiation factor
vacuolar protein sorting 24 homolog
vacuolar protein sorting-associated protein 24

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_001005753.3NP_001005753.1  charged multivesicular body protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001005753.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region, compared to variant 1. This results in translation initiation from a downstream start codon and an isoform (2, also known as Vps24beta) that has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC068288, AF151907, AK290725, DA290886
    Consensus CDS
    CCDS42707.1
    UniProtKB/Swiss-Prot
    Q9Y3E7
    Related
    ENSP00000386590.2, ENST00000409225.2
    Conserved Domains (1) summary
    cl21588
    Location:1121
    Snf7; Snf7
  2. NM_001193517.2NP_001180446.1  charged multivesicular body protein 3 isoform 3

    See identical proteins and their annotated locations for NP_001180446.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
    Source sequence(s)
    AC068288, AF151907, AK129502, DA290886
    Consensus CDS
    CCDS54375.1
    UniProtKB/Swiss-Prot
    Q9Y3E7
    Related
    ENSP00000387045.1, ENST00000409727.5
    Conserved Domains (1) summary
    cl21588
    Location:18147
    Snf7; Snf7
  3. NM_016079.4NP_057163.1  charged multivesicular body protein 3 isoform 1

    See identical proteins and their annotated locations for NP_057163.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also known as Vps24alpha).
    Source sequence(s)
    AF151907, AK025046, AK312353, BC004419, BU192410, DA290886
    Consensus CDS
    CCDS33236.1
    UniProtKB/Swiss-Prot
    Q9Y3E7
    Related
    ENSP00000263856.4, ENST00000263856.9
    Conserved Domains (1) summary
    pfam03357
    Location:18187
    Snf7; Snf7

RNA

  1. NR_036454.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lack two internal exons in the 5' region, compared to variant 1. This variant is represented as non-coding because it lacks a significant portion of the coding region, as found in variant 1. Translation from the upstream start codon, as found in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC068288, AF151907, DA046087, DA290886

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    86503430..86563443 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    86505444..86565457 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)