CHMP1A charged multivesicular body protein 1A [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHMP1Aprovided by HGNC
Official Full Name: charged multivesicular body protein 1Aprovided by HGNC
Primary source: HGNC:HGNC:8740
See related: Ensembl:ENSG00000131165 MIM:164010; AllianceGenome:HGNC:8740
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: PCH8; CHMP1; PRSM1; PCOLN3; VPS46A; VPS46-1
Summary: This gene encodes a member of the CHMP/Chmp family of proteins which are involved in multivesicular body sorting of proteins to the interiors of lysosomes. The initial prediction of the protein sequence encoded by this gene suggested that the encoded protein was a metallopeptidase. The nomenclature has been updated recently to reflect the correct biological function of this encoded protein. Several transcripts encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
Expression: Ubiquitous expression in small intestine (RPKM 17.5), colon (RPKM 16.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q24.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (89644435..89657708, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (95728224..95742519, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (89710843..89724116, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

A single genetic locus controls both expression of DPEP1/CHMP1A and kidney disease development via ferroptosis.
Title: A single genetic locus controls both expression of DPEP1/CHMP1A and kidney disease development via ferroptosis.
Findings show CHMP1A loss impairs secretion of SHH on ART-EVs, providing molecular mechanistic insights into the role of ESCRT proteins and EVs in the brain.
Title: The ESCRT-III Protein CHMP1A Mediates Secretion of Sonic Hedgehog on a Distinctive Subtype of Extracellular Vesicles.
Letter: rs6860 polymorphism of the CHMP1A gene, is associated with fibromyalgia susceptibility in southern Spanish women.
Title: The TT genotype of the rs6860 polymorphism of the charged multivesicular body protein 1A gene is associated with susceptibility to fibromyalgia in southern Spanish women.
we identified Ser(179) and Ser(182) located in the C-terminal region of the CHMP1A as major phosphorylation sites that cause a mobility shift.
Title: Identification of phosphorylation sites in the C-terminal region of charged multivesicular body protein 1A (CHMP1A).
Study reports the discovery of a chimeric RNA between ZC3HAV1L and CHMP1A in human, located on chromosome 7 and 16, respectively. The fusion occurs at an exon-exon boundary, and was detected both computationally and experimentally from different cells or tissue types.
Title: Detection of a common chimeric transcript between human chromosomes 7 and 16.
Our results suggest that CHMP1A serves as a critical link between cytoplasmic signals and BMI1-mediated chromatin modifications that regulate proliferation of central nervous system progenitor cells.
Title: CHMP1A encodes an essential regulator of BMI1-INK4A in cerebellar development.
our results demonstrate that Chmp1A functions as a tumor suppressor gene in renal cells
Title: Chmp1A acts as a tumor suppressor gene that inhibits proliferation of renal cell carcinoma.
Chmp1A regulates tumor growth through ATM sugnaling and that neclear locaization of Chmp1A is reqired for the growth inhibition and ATM activation.
Title: Chromatin modifying protein 1A (Chmp1A) of the endosomal sorting complex required for transport (ESCRT)-III family activates ataxia telangiectasia mutated (ATM) for PanC-1 cell growth inhibition.
Both Vps4A and CHMP1A localized in the vicinity of viral cytoplasmic assembly compartments, sites of viral maturation that develop in Cytomegalovirus-infected cells. Thus, ESCRT machinery is involved in the final steps of HCMV replication.
Title: Human cytomegalovirus exploits ESCRT machinery in the process of virion maturation.
Chmp1A is a novel tumor suppressor, especially in pancreas and that Chmp1A regulates tumor growth potentially through p53 signaling pathway.
Title: Chmp1A functions as a novel tumor suppressor gene in human embryonic kidney and ductal pancreatic tumor cells.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

Associated conditions

Description	Tests
Pontocerebellar hypoplasia type 8 MedGen: C3554209 OMIM: 614961 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study in Han Chinese identifies three novel loci for human height. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH17441 (e-PCR)
- UniSTS:71478

SHGC-61043 (e-PCR)
- UniSTS:78404

RH66573 (e-PCR)
- UniSTS:67204

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables metallopeptidase activity	TAS Traceable Author Statement 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
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	TAS Traceable Author Statement 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 cell division	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 membrane fission	NAS Non-traceable Author Statement more info	PubMed
involved_in midbody abscission	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mitotic chromosome condensation	IDA Inferred from Direct Assay 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 sorting pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in multivesicular body-lysosome fusion	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression	IDA Inferred from Direct Assay 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 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 vesicle-mediated transport	IDA Inferred from Direct Assay more info	PubMed
involved_in viral budding from plasma membrane	IDA Inferred from Direct Assay 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	NAS Non-traceable Author Statement 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	NAS Non-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 condensed nuclear chromosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endomembrane system	IDA Inferred from Direct Assay more info	PubMed
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 microtubule organizing center	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
located_in nuclear matrix	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 1a

Names: VPS46 homolog A; charged multivesicular body protein 1/chromatin modifying protein 1; chromatin modifying protein 1A; procollagen (type III) N-endopeptidase; protease, metallo, 1, 33kD; vacuolar protein sorting-associated protein 46-1

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.

Genomic

NG_033005.2 RefSeqGene

Range

5078..18351

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001083314.4 → NP_001076783.1 charged multivesicular body protein 1a isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) lacks an alternate exon in the 5' coding region that results in a frameshift in subsequent regions of the CDS, compared to variant 2. The encoded isoform (1) shares the first two residues but is otherwise distinct and longer than isoform 2. Translation of this isoform is assumed due to use of the expected start codon, which has a strong Kozak signal.

Source sequence(s)

BC007527, HY089525

UniProtKB/TrEMBL

A0A6Q8PFF8

Related

ENSP00000442120.3, ENST00000535997.7
NM_002768.5 → NP_002759.2 charged multivesicular body protein 1a isoform 2

See identical proteins and their annotated locations for NP_002759.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) encodes the functionally supported isoform (2).

Source sequence(s)

BC007527, HY008690

Consensus CDS

CCDS45552.1

UniProtKB/Swiss-Prot

A2RU09, Q14468, Q15779, Q96G31, Q9HD42

UniProtKB/TrEMBL

A0A6Q8PG85

Related

ENSP00000380998.3, ENST00000397901.8

Conserved Domains (1) summary

cl21588
Location:12 → 195

Snf7

RNA

NR_046418.3 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 3' region, compared to variant 2. This variant is represented as non-coding because use of the supported start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BC007527, BX363674, HY008690

Related

ENST00000549328.2

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

89644435..89657708 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047434195.1 → XP_047290151.1 charged multivesicular body protein 1a isoform X2

UniProtKB/TrEMBL

A0A6Q8PFX8

Related

ENSP00000502267.1, ENST00000674799.1
XM_011523098.2 → XP_011521400.1 charged multivesicular body protein 1a isoform X1

Related

ENSP00000501794.1, ENST00000676402.1

Conserved Domains (1) summary

PHA03269
Location:153 → 267

PHA03269; envelope glycoprotein C; Provisional

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

95728224..95742519 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054380436.1 → XP_054236411.1 charged multivesicular body protein 1a isoform X2

UniProtKB/TrEMBL

A0A6Q8PFX8
XM_054380435.1 → XP_054236410.1 charged multivesicular body protein 1a isoform X1