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

    Gene ID: 51652, updated on 28-Oct-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CHMP3 in Genome Data Viewer
    Location:
    2p11.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (86503430..86563443, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (86505444..86565457, complement)
    RS_2024_09 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 OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:86667563-86668106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11713 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16161 Neighboring gene lysine demethylase 3A Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:86708929-86710128 Neighboring gene MPRA-validated peak3779 silencer Neighboring gene RNF103-CHMP3 readthrough Neighboring gene RNA, U6 small nuclear 640, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_59439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16163 Neighboring gene Sharpr-MPRA regulatory region 1991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16164 Neighboring gene CHMP3 and RNF103 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11717 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 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

    Clone Names

    • FLJ38114

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables molecular function inhibitor activity EXP
    Inferred from Experiment
    more info
    PubMed 
    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
     
    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
     
    involved_in macroautophagy TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in membrane fission NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in midbody abscission IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT involved_in mitotic metaphase chromosome alignment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mitotic metaphase chromosome alignment IMP
    Inferred from Mutant Phenotype
    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 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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in multivesicular body-lysosome fusion NAS
    Non-traceable Author Statement
    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
     
    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 NAS
    Non-traceable Author Statement
    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
     
    part_of ESCRT III complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of ESCRT III complex NAS
    Non-traceable Author Statement
    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
     
    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
      A8K3W0, B4DG34, B8ZZM0, B8ZZX5, Q3ZTS9, Q53S71, Q53SU5, Q9NZ51, 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: 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_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)