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

Gene ID: 5119, updated on 17-Jun-2019

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
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

Genomic context

See CHMP1A in Genome Data Viewer
Location:
16q24.3
Exon count:
8
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (89644431..89657785, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (89710839..89724193, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene copine 7 Neighboring gene dipeptidase 1 Neighboring gene spermatogenesis associated 33 Neighboring gene long intergenic non-protein coding RNA 2166 Neighboring gene cyclin dependent kinase 10 Neighboring gene spermatogenesis associated 2 like

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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

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

NHGRI GWAS Catalog

Description
Genome-wide association study in Han Chinese identifies three novel loci for human height.
NHGRI GWA Catalog

Pathways from BioSystems

  • ESCRT-III complex, organism-specific biosystem (from KEGG)
    ESCRT-III complex, organism-specific biosystemStructural complex; Genetic information processing; Protein processing
  • ESCRT-III complex, conserved biosystem (from KEGG)
    ESCRT-III complex, conserved biosystemStructural complex; Genetic information processing; Protein processing
  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0047

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
metallopeptidase activity TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
ESCRT III complex disassembly NAS
Non-traceable Author Statement
more info
PubMed 
cell division IMP
Inferred from Mutant Phenotype
more info
PubMed 
endosome transport via multivesicular body sorting pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
gene silencing IDA
Inferred from Direct Assay
more info
PubMed 
late endosome to vacuole transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
midbody abscission IMP
Inferred from Mutant Phenotype
more info
PubMed 
mitotic chromosome condensation IDA
Inferred from Direct Assay
more info
PubMed 
mitotic metaphase plate congression IMP
Inferred from Mutant Phenotype
more info
PubMed 
multivesicular body assembly NAS
Non-traceable Author Statement
more info
PubMed 
negative regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
nucleus organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proteolysis IEA
Inferred from Electronic Annotation
more info
 
regulation of centrosome duplication IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of mitotic spindle assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
vesicle-mediated transport IDA
Inferred from Direct Assay
more info
PubMed 
viral budding via host ESCRT complex NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
ESCRT III complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
condensed nuclear chromosome IDA
Inferred from Direct Assay
more info
PubMed 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
endomembrane system IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
microtubule organizing center IDA
Inferred from Direct Assay
more info
PubMed 
multivesicular body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
charged multivesicular body protein 1a
Names
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)

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

  1. NG_033005.2 RefSeqGene

    Range
    5001..18355
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001083314.4NP_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
  2. NM_002768.5NP_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
    Q9HD42
    Related
    ENSP00000380998.3, ENST00000397901.8
    Conserved Domains (1) summary
    cl21588
    Location:12195
    Snf7; Snf7

RNA

  1. NR_046418.2 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)
    AI362697, BC007527, BX363674, HY008690
    Related
    ENST00000535997.6

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    89644431..89657785 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011523098.1XP_011521400.1  charged multivesicular body protein 1a isoform X1

    Conserved Domains (1) summary
    PHA03269
    Location:153267
    PHA03269; envelope glycoprotein C; Provisional
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