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

    Gene ID: 5119, updated on 5-May-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CHMP1A in Genome Data Viewer
    Location:
    16q24.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (89644435..89657708, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (95728224..95742519, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (89710843..89724116, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene copine 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89665942-89666855 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:89679650-89679808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89681214-89681918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89681919-89682621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89689900-89690772 Neighboring gene dipeptidase 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89698470-89699324 Neighboring gene uncharacterized LOC124903758 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_46628 and experimental_46635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7918 Neighboring gene spermatogenesis associated 33 Neighboring gene MPRA-validated peak2666 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7919 Neighboring gene long intergenic non-protein coding RNA 2166 Neighboring gene cyclin dependent kinase 10

    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 Functions

    What's a GeneRIF?

    Phenotypes

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0047

    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 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

    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)

    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.

    Genomic

    1. NG_033005.2 RefSeqGene

      Range
      5078..18351
      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
      UniProtKB/TrEMBL
      A0A6Q8PFF8
      Related
      ENSP00000442120.3, ENST00000535997.7
    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
      A2RU09, Q14468, Q15779, Q96G31, Q9HD42
      UniProtKB/TrEMBL
      A0A6Q8PG85
      Related
      ENSP00000380998.3, ENST00000397901.8
      Conserved Domains (1) summary
      cl21588
      Location:12195
      Snf7

    RNA

    1. 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_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      89644435..89657708 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      UniProtKB/TrEMBL
      A0A6Q8PFX8
      Related
      ENSP00000502267.1, ENST00000674799.1
    2. XM_011523098.2XP_011521400.1  charged multivesicular body protein 1a isoform X1

      Related
      ENSP00000501794.1, ENST00000676402.1
      Conserved Domains (1) summary
      PHA03269
      Location:153267
      PHA03269; envelope glycoprotein C; Provisional

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      95728224..95742519 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      UniProtKB/TrEMBL
      A0A6Q8PFX8
    2. XM_054380435.1XP_054236410.1  charged multivesicular body protein 1a isoform X1