CHMP2A charged multivesicular body protein 2A [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHMP2Aprovided by HGNC
Official Full Name: charged multivesicular body protein 2Aprovided by HGNC
Primary source: HGNC:HGNC:30216
See related: Ensembl:ENSG00000130724 MIM:610893; AllianceGenome:HGNC:30216
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: BC2; BC-2; VPS2; CHMP2; VPS2A
Summary: CHMP2A belongs to the chromatin-modifying protein/charged multivesicular body protein (CHMP) family. These proteins are components of ESCRT-III (endosomal sorting complex required for transport III), a complex involved in degradation of surface receptor proteins and formation of endocytic multivesicular bodies (MVBs). Some CHMPs have both nuclear and cytoplasmic/vesicular distributions, and one such CHMP, CHMP1A (MIM 164010), is required for both MVB formation and regulation of cell cycle progression (Tsang et al., 2006 [PubMed 16730941]).[supplied by OMIM, Mar 2008]
Expression: Ubiquitous expression in colon (RPKM 34.2), kidney (RPKM 32.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.43

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (58551566..58555105, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (61649242..61652782, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (59062933..59066472, complement)

Chromosome 19 - NC_000019.10 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
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?

PTEN alleviates maladaptive repair of renal tubular epithelial cells by restoring CHMP2A-mediated phagosome closure.
Title: PTEN alleviates maladaptive repair of renal tubular epithelial cells by restoring CHMP2A-mediated phagosome closure.
Targeting the ESCRT-III component CHMP2A for noncanonical Caspase-8 activation on autophagosomal membranes.
Title: Targeting the ESCRT-III component CHMP2A for noncanonical Caspase-8 activation on autophagosomal membranes.
The ESCRT-III isoforms CHMP2A and CHMP2B display different effects on membranes upon polymerization.
Title: The ESCRT-III isoforms CHMP2A and CHMP2B display different effects on membranes upon polymerization.
CHMP2A is the ESCRT-III component that regulates phagophore closure
Title: An autophagy assay reveals the ESCRT-III component CHMP2A as a regulator of phagophore closure.
Data show that gamma2-adaptin in MVB sorting specifically interacts with the ESCRT subunits Vps28 and CHMP2A.
Title: γ2-Adaptin is functioning in the late endosomal sorting pathway and interacts with ESCRT-I and -III subunits.
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.

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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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Replication interactions

Interaction	Pubs
Knockdown of charged multivesicular body protein 2A (CHMP2A) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Three-dimensional superresolution microscopy and correlative electron microscopy demonstrate that the ESCRT proteins TSG101, CHMP2A, and CHMP4B co-cluster with membrane-localized HIV-1 Gag at assembly sites	PubMed
	gag	ALIX, CHMP2A/B, CHMP4A/B, and VPS4A/B proteins are required for the budding of HIV-1 Gag and the HIV-1 infectivity	PubMed
	gag	Released Gag VLPs contain TSG101 and CHMP4B, but reduced levels of CHMP2A relative to CHMP4B	PubMed
	gag	Recruitment of CHMP2A and CHMP3 by CHMP4B to HIV-1 Gag puncta is observed in in-vitro membrane model	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

L17705 (e-PCR)
- UniSTS:66091

D11S3114 (e-PCR)
- UniSTS:152207

L17877 (e-PCR)
- UniSTS:61334

L17809 (e-PCR)
- UniSTS:39087

MARC_7283-7284:996687724:1 (e-PCR)
- UniSTS:269759

STS-N23430 (e-PCR)
- UniSTS:79810

NoName (e-PCR)
- UniSTS:490192

SHGC-30173 (e-PCR)
- UniSTS:54518

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables phosphatidylcholine binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in ESCRT III complex disassembly	NAS Non-traceable Author Statement more info	PubMed
involved_in autophagosome maturation	IMP Inferred from Mutant Phenotype 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 establishment of protein localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in exit from mitosis	IMP Inferred from Mutant Phenotype 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
involved_in macroautophagy	TAS Traceable Author Statement more info	PubMed
involved_in membrane fission	NAS Non-traceable Author Statement more info	PubMed
involved_in membrane invagination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in midbody abscission	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-lysosome fusion	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of centriole elongation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear membrane reassembly	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 exosomal secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein homooligomerization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein polymerization	IMP Inferred from Mutant Phenotype 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 mitotic spindle assembly	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	IGI Inferred from Genetic Interaction 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
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement 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 lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
part_of membrane coat	IMP Inferred from Mutant Phenotype 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
located_in nuclear envelope	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 2a

Names: VPS2 homolog A; chromatin modifying protein 2A; putative breast adenocarcinoma marker (32kD); putative breast adenocarcinoma marker BC-2; vacuolar protein sorting-associated protein 2-1; vps2-1

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_014453.4 → NP_055268.1 charged multivesicular body protein 2a

See identical proteins and their annotated locations for NP_055268.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.

Source sequence(s)

BC002502, BP315111

Consensus CDS

CCDS12986.1

UniProtKB/Swiss-Prot

B2R4W6, O43633, Q3ZTT0

Related

ENSP00000310440.1, ENST00000312547.7

Conserved Domains (1) summary

pfam03357
Location:17 → 185

Snf7
NM_198426.3 → NP_940818.1 charged multivesicular body protein 2a

See identical proteins and their annotated locations for NP_940818.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

AC016630, BC002502, CN305066

Consensus CDS

CCDS12986.1

UniProtKB/Swiss-Prot

B2R4W6, O43633, Q3ZTT0

Related

ENSP00000472680.1, ENST00000601220.5

Conserved Domains (1) summary

pfam03357
Location:17 → 185

Snf7

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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

58551566..58555105 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005258746.3 → XP_005258803.1 charged multivesicular body protein 2a isoform X1

See identical proteins and their annotated locations for XP_005258803.1

UniProtKB/TrEMBL

M0R1T5

Related

ENSP00000472097.2, ENST00000600006.6

Conserved Domains (1) summary

pfam03357
Location:17 → 181

Snf7; Snf7
XM_005258747.4 → XP_005258804.1 charged multivesicular body protein 2a isoform X1

See identical proteins and their annotated locations for XP_005258804.1

UniProtKB/TrEMBL

M0R1T5

Conserved Domains (1) summary

pfam03357
Location:17 → 181

Snf7; Snf7

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

61649242..61652782 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054320574.1 → XP_054176549.1 charged multivesicular body protein 2a isoform X1

UniProtKB/TrEMBL

M0R1T5
XM_054320575.1 → XP_054176550.1 charged multivesicular body protein 2a isoform X1

UniProtKB/TrEMBL

M0R1T5