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

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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CHMP3 promotes the progression of hepatocellular carcinoma by inhibiting caspase-1-dependent pyroptosis.
Title: CHMP3 promotes the progression of hepatocellular carcinoma by inhibiting caspase‑1‑dependent pyroptosis.
A homozygous variant in CHMP3 is associated with complex hereditary spastic paraplegia.
Title: A homozygous variant in CHMP3 is associated with complex hereditary spastic paraplegia.
RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis.
Title: RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis.
miR-122-5p promotes aggression and epithelial-mesenchymal transition in triple-negative breast cancer by suppressing charged multivesicular body protein 3 through mitogen-activated protein kinase signaling.
Title: miR-122-5p promotes aggression and epithelial-mesenchymal transition in triple-negative breast cancer by suppressing charged multivesicular body protein 3 through mitogen-activated protein kinase signaling.
Protein kinase CK2 alpha is involved in the phosphorylation of the ESCRT-III subunits CHMP3 and CHMP2B, as well as of VPS4B/SKD1, an ATPase that mediates ESCRT-III disassembly.
Title: CK2 involvement in ESCRT-III complex phosphorylation.
tight coupling of ESCRT-III CHMP3 and AMSH functions and provide insight into the regulation of ESCRT-III
Title: Structural basis for ESCRT-III CHMP3 recruitment of AMSH.
Data show that the N-terminal core domains of increased sodium tolerance-1 (IST1) and charged multivesicular body protein-3 (CHMP3) form equivalent four-helix bundles, revealing that IST1 is a previously unrecognized ESCRT-III family member.
Title: Structural basis for ESCRT-III protein autoinhibition.
study found the ESCRT-III proteins CHMP2A & CHMP3 could assemble in vitro into helical tubular structures that expose their membrane interaction sites on the outside of the tubule; VPS4 could bind on the inside of the tubule & disassemble the tubes
Title: Helical structures of ESCRT-III are disassembled by VPS4.
expression of dominant negative forms of Vps4 and Vps24, two components of the MVB pathway, rresult in an impairment in infectious herpes simplex virus assembly/egress
Title: Intracellular trafficking and maturation of herpes simplex virus type 1 gB and virus egress require functional biogenesis of multivesicular bodies.
UBPY MIT domain and another ubiquitin isopeptidase, AMSH, reveals common interactions with CHMP1A and CHMP1B but a distinct selectivity of AMSH for CHMP3/VPS24, a core subunit of the ESCRT-III complex, and UBPY for CHMP7.
Title: The MIT domain of UBPY constitutes a CHMP binding and endosomal localization signal required for efficient epidermal growth factor receptor degradation.

Submit: New GeneRIF Correction See all GeneRIFs (16)

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)

HIV-1 interactions

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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

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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

RH69455 (e-PCR)
- UniSTS:30984

RH78340 (e-PCR)
- UniSTS:66228

SGC31339 (e-PCR)
- UniSTS:40133

D2S1879 (e-PCR)
- UniSTS:153571

Readthrough RNF103-CHMP3

Readthrough gene: RNF103-CHMP3, Included gene: RNF103

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 more info	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

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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)

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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)

NM_001005753.3 → NP_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:1 → 121

Snf7; Snf7
NM_001193517.2 → NP_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:18 → 147

Snf7; Snf7
NM_016079.4 → NP_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:18 → 187

Snf7; Snf7

RNA

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