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Aliases for CHMP1A Gene

Aliases for CHMP1A Gene

  • Charged Multivesicular Body Protein 1A 2 3 5
  • Vacuolar Protein Sorting-Associated Protein 46-1 3 4
  • Procollagen (Type III) N-Endopeptidase 2 3
  • Chromatin Modifying Protein 1A 2 3
  • VPS46-1 3 4
  • PCOLN3 3 4
  • PRSM1 3 4
  • CHMP1 3 4
  • Charged Multivesicular Body Protein 1/Chromatin Modifying Protein 1 3
  • Chromatin-Modifying Protein 1a 4
  • Protease, Metallo, 1, 33kD 3
  • KIAA0047 4
  • HVps46-1 4
  • VPS46A 3
  • CHMP1a 4
  • PCH8 3

External Ids for CHMP1A Gene

Previous HGNC Symbols for CHMP1A Gene

  • PRSM1
  • PCOLN3

Previous GeneCards Identifiers for CHMP1A Gene

  • GC16M088239
  • GC16M089710
  • GC16M075406

Summaries for CHMP1A Gene

Entrez Gene Summary for CHMP1A Gene

  • 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]

GeneCards Summary for CHMP1A Gene

CHMP1A (Charged Multivesicular Body Protein 1A) is a Protein Coding gene. Diseases associated with CHMP1A include Pontocerebellar Hypoplasia, Type 8 and Borna Disease. Among its related pathways are Endocytosis. GO annotations related to this gene include protein homodimerization activity and metallopeptidase activity. An important paralog of this gene is CHMP1B.

UniProtKB/Swiss-Prot for CHMP1A Gene

  • Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. Involved in cytokinesis. Involved in recruiting VPS4A and/or VPS4B to the midbody of dividing cells. May also be involved in chromosome condensation. Targets the Polycomb group (PcG) protein BMI1/PCGF4 to regions of condensed chromatin. May play a role in stable cell cycle progression and in PcG gene silencing.

Gene Wiki entry for CHMP1A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CHMP1A Gene

Genomics for CHMP1A Gene

Regulatory Elements for CHMP1A Gene

Enhancers for CHMP1A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16F089630 1.4 Ensembl ENCODE 12 +25.5 25528 3.0 HDGF PKNOX1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 CDK10 CHMP1A TUBB3 RPL13 GALNS PIR44959 DPEP1
GH16F089639 1.2 Ensembl ENCODE 12.2 +16.7 16737 2.4 ATF1 PKNOX1 DMAP1 ZNF2 ZNF48 YY1 ZNF143 ZNF207 REST KAT8 CDK10 SPIRE2 GAS8-AS1 CHMP1A DPEP1 RPL13 PIR44959
GH16F089615 1 Ensembl ENCODE 14.3 +42.0 42008 0.3 CTCF KLF6 FOXA3 ARID4B ZBTB7A RAD21 ZNF316 ZGPAT GABPB1 MXD3 CHMP1A DBNDD1 CDK10 SPIRE2 DPEP1 PIR44959
GH16F089612 0.8 Ensembl ENCODE 10.1 +44.4 44357 2.1 BCOR ZNF146 ZNF580 ZMYM3 PRDM10 KDM1A CHMP1A CDK10 SPIRE2 GAS8-AS1 DPEP1 PIR44959
GH16F089656 1.1 ENCODE 6.6 +0.1 81 2.6 PKNOX1 CREB3L1 WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF143 CDK10 ENSG00000259877 GAS8-AS1 DBNDD1 CTU2 AFG3L1P MC1R CHMP1A SPIRE2 SPATA33
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CHMP1A on UCSC Golden Path with GeneCards custom track

Promoters for CHMP1A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001507554 45 2001 CREB3L1 WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF143 KLF13
ENSR00001804083 -1255 201

Genomic Location for CHMP1A Gene

Chromosome:
16
Start:
89,644,431 bp from pter
End:
89,657,845 bp from pter
Size:
13,415 bases
Orientation:
Minus strand

Genomic View for CHMP1A Gene

Genes around CHMP1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHMP1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHMP1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHMP1A Gene

Proteins for CHMP1A Gene

  • Protein details for CHMP1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HD42-CHM1A_HUMAN
    Recommended name:
    Charged multivesicular body protein 1a
    Protein Accession:
    Q9HD42
    Secondary Accessions:
    • A2RU09
    • Q14468
    • Q15779
    • Q96G31

    Protein attributes for CHMP1A Gene

    Size:
    196 amino acids
    Molecular mass:
    21703 Da
    Quaternary structure:
    • Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III). ESCRT-III components are thought to multimerize to form a flat lattice on the perimeter membrane of the endosome. Several assembly forms of ESCRT-III may exist that interact and act sequentally. Self-associates. Interacts with CHMP1B. Interacts with VPS4A. Interacts with VPS4B. Interacts with PHF1. Interacts with IST1. Interacts with MITD1.
    SequenceCaution:
    • Sequence=AAC50775.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305}; Sequence=BAA07557.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CHMP1A Gene

    Alternative splice isoforms for CHMP1A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CHMP1A Gene

Post-translational modifications for CHMP1A Gene

  • Ubiquitination at Lys 56 and Lys 98
  • Modification sites at PhosphoSitePlus

Other Protein References for CHMP1A Gene

Antibody Products

  • Abcam antibodies for CHMP1A
  • Santa Cruz Biotechnology (SCBT) Antibodies for CHMP1A

No data available for DME Specific Peptides for CHMP1A Gene

Domains & Families for CHMP1A Gene

Protein Domains for CHMP1A Gene

Suggested Antigen Peptide Sequences for CHMP1A Gene

Graphical View of Domain Structure for InterPro Entry

Q9HD42

UniProtKB/Swiss-Prot:

CHM1A_HUMAN :
  • Belongs to the SNF7 family.
Family:
  • Belongs to the SNF7 family.
genes like me logo Genes that share domains with CHMP1A: view

Function for CHMP1A Gene

Molecular function for CHMP1A Gene

UniProtKB/Swiss-Prot Function:
Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. Involved in cytokinesis. Involved in recruiting VPS4A and/or VPS4B to the midbody of dividing cells. May also be involved in chromosome condensation. Targets the Polycomb group (PcG) protein BMI1/PCGF4 to regions of condensed chromatin. May play a role in stable cell cycle progression and in PcG gene silencing.
UniProtKB/Swiss-Prot Induction:
By muristerone.

Gene Ontology (GO) - Molecular Function for CHMP1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11559748
GO:0008237 metallopeptidase activity TAS 8863740
GO:0008270 zinc ion binding TAS 8863740
GO:0019904 protein domain specific binding IPI 17928862
GO:0042802 identical protein binding IPI 16730941
genes like me logo Genes that share ontologies with CHMP1A: view
genes like me logo Genes that share phenotypes with CHMP1A: view

Human Phenotype Ontology for CHMP1A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CHMP1A Gene

Localization for CHMP1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHMP1A Gene

Cytoplasm. Endosome membrane; Peripheral membrane protein. Nucleus matrix. Note=The cytoplasmic form is partially membrane-associated and localizes to early endosomes. The nuclear form remains associated with the chromosome scaffold during mitosis. On overexpression, it localizes to nuclear bodies characterized by nuclease-resistant condensed chromatin.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CHMP1A gene
Compartment Confidence
extracellular 5
cytoskeleton 5
nucleus 5
endosome 5
cytosol 2
lysosome 1

Gene Ontology (GO) - Cellular Components for CHMP1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000794 condensed nuclear chromosome IDA 11559747
GO:0000815 ESCRT III complex IEA --
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0005768 endosome IEA --
genes like me logo Genes that share ontologies with CHMP1A: view

Pathways & Interactions for CHMP1A Gene

SuperPathways for CHMP1A Gene

SuperPathway Contained pathways
1 Endocytosis
genes like me logo Genes that share pathways with CHMP1A: view

Pathways by source for CHMP1A Gene

1 KEGG pathway for CHMP1A Gene

Gene Ontology (GO) - Biological Process for CHMP1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000920 cell separation after cytokinesis IMP 20616062
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006508 proteolysis IEA --
GO:0006810 transport IEA --
genes like me logo Genes that share ontologies with CHMP1A: view

No data available for SIGNOR curated interactions for CHMP1A Gene

Transcripts for CHMP1A Gene

Unigene Clusters for CHMP1A Gene

Charged multivesicular body protein 1A:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CHMP1A Gene

No ASD Table

Relevant External Links for CHMP1A Gene

GeneLoc Exon Structure for
CHMP1A
ECgene alternative splicing isoforms for
CHMP1A

Expression for CHMP1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CHMP1A Gene

Protein differential expression in normal tissues from HIPED for CHMP1A Gene

This gene is overexpressed in Peripheral blood mononuclear cells (7.7) and Heart (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CHMP1A Gene



Protein tissue co-expression partners for CHMP1A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CHMP1A Gene:

CHMP1A

SOURCE GeneReport for Unigene cluster for CHMP1A Gene:

Hs.589427

mRNA Expression by UniProt/SwissProt for CHMP1A Gene:

Q9HD42-CHM1A_HUMAN
Tissue specificity: Expressed in placenta, cultured skin fibroblasts and in osteoblast cell line MG-63.
genes like me logo Genes that share expression patterns with CHMP1A: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for CHMP1A Gene

Orthologs for CHMP1A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CHMP1A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CHMP1A 35
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CHMP1A 34 35
  • 92.69 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CHMP1A 35
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CHMP1A 34 35
  • 91.16 (n)
mouse
(Mus musculus)
Mammalia Chmp1a 34 16 35
  • 90.82 (n)
rat
(Rattus norvegicus)
Mammalia Chmp1a 34
  • 90.31 (n)
oppossum
(Monodelphis domestica)
Mammalia CHMP1A 35
  • 90 (a)
OneToOne
chicken
(Gallus gallus)
Aves CHMP1A 34 35
  • 85.2 (n)
lizard
(Anolis carolinensis)
Reptilia CHMP1A 35
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia chmp1a 34
  • 79.59 (n)
Str.8453 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.25584 34
zebrafish
(Danio rerio)
Actinopterygii chmp1a 34 35
  • 82.82 (n)
zgc65914 34
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DID2 35
  • 45 (a)
OneToMany
soybean
(Glycine max)
eudicotyledons Gma.15489 34
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.8778 34
barley
(Hordeum vulgare)
Liliopsida Hv.5716 34
wheat
(Triticum aestivum)
Liliopsida Ta.6651 34
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3436 34
Species where no ortholog for CHMP1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • worm (Caenorhabditis elegans)

Evolution for CHMP1A Gene

ENSEMBL:
Gene Tree for CHMP1A (if available)
TreeFam:
Gene Tree for CHMP1A (if available)

Paralogs for CHMP1A Gene

Paralogs for CHMP1A Gene

(3) SIMAP similar genes for CHMP1A Gene using alignment to 5 proteins:

Pseudogenes.org Pseudogenes for CHMP1A Gene

genes like me logo Genes that share paralogs with CHMP1A: view

Variants for CHMP1A Gene

Sequence variations from dbSNP and Humsavar for CHMP1A Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs397515426 Pathogenic 89,651,586(-) CGGAG(C/T)AGGCC nc-transcript-variant, reference, missense, stop-gained
rs398122918 Pathogenic 89,651,659(-) ATTCC(A/G/T)GCTTC intron-variant
rs116634240 Likely benign 89,646,722(+) GGGGG(A/C)AGGGG intron-variant
rs114931496 Uncertain significance 89,649,393(+) ACTGC(A/G)TCTAC nc-transcript-variant, reference, synonymous-codon, missense
rs201479143 Uncertain significance 89,649,405(+) CGGGA(C/T)GCCAT nc-transcript-variant, reference, synonymous-codon, missense

Structural Variations from Database of Genomic Variants (DGV) for CHMP1A Gene

Variant ID Type Subtype PubMed ID
nsv573739 CNV gain 21841781
nsv509639 CNV insertion 20534489
nsv482951 CNV loss 15286789
nsv428331 CNV gain+loss 18775914
nsv1151881 CNV deletion 26484159
nsv1071316 CNV deletion 25765185
nsv1070369 CNV deletion 25765185
nsv1066382 CNV gain 25217958
nsv1063483 CNV gain 25217958
nsv1057351 CNV loss 25217958
nsv102951 CNV deletion 16902084
esv992091 CNV deletion 20482838
esv3553909 CNV deletion 23714750
esv2762221 CNV gain+loss 21179565
esv2715194 CNV deletion 23290073
esv2715193 CNV deletion 23290073
esv2715192 CNV deletion 23290073
esv2715191 CNV deletion 23290073
esv2715190 CNV deletion 23290073
esv2715189 CNV deletion 23290073
esv2665924 CNV deletion 23128226
esv2657571 CNV deletion 23128226
esv26093 CNV gain+loss 19812545
esv1520837 CNV insertion 17803354
dgv5323n54 CNV loss 21841781

Variation tolerance for CHMP1A Gene

Residual Variation Intolerance Score: 79% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.46; 64.19% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CHMP1A Gene

Human Gene Mutation Database (HGMD)
CHMP1A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CHMP1A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHMP1A Gene

Disorders for CHMP1A Gene

MalaCards: The human disease database

(3) MalaCards diseases for CHMP1A Gene - From: OMIM, ClinVar, GeneTests, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
pontocerebellar hypoplasia, type 8
  • pontocerebellar hypoplasia type 8
borna disease
  • enzootic encephalomyelitis
distichiasis
  • isolated distichiasis
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CHM1A_HUMAN
  • Pontocerebellar hypoplasia 8 (PCH8) [MIM:614961]: An autosomal recessive neurodevelopmental disorder characterized by severe psychomotor retardation, abnormal movements, hypotonia, spasticity, and variable visual defects. Brain MRI shows pontocerebellar hypoplasia, decreased cerebral white matter, and a thin corpus callosum. {ECO:0000269 PubMed:23023333}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CHMP1A

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CHMP1A
genes like me logo Genes that share disorders with CHMP1A: view

No data available for Genatlas for CHMP1A Gene

Publications for CHMP1A Gene

  1. CHMP1 is a novel nuclear matrix protein affecting chromatin structure and cell-cycle progression. (PMID: 11559747) Stauffer D.R. … Hollenberg S.M. (J. Cell Sci. 2001) 2 3 4 22 64
  2. Biochemical analyses of human IST1 and its function in cytokinesis. (PMID: 19129479) Bajorek M. … Sundquist W.I. (Mol. Biol. Cell 2009) 3 4 22 64
  3. CHMP1 functions as a member of a newly defined family of vesicle trafficking proteins. (PMID: 11559748) Howard T.L. … Hollenberg S.M. (J. Cell Sci. 2001) 2 3 4 64
  4. Molecular cloning, expression and chromosomal localization of a human gene encoding a 33 kDa putative metallopeptidase (PRSM1). (PMID: 8863740) Scott I.C. … Kadler K.E. (Gene 1996) 3 4 22 64
  5. CHMP1A encodes an essential regulator of BMI1-INK4A in cerebellar development. (PMID: 23023333) Mochida G.H. … Walsh C.A. (Nat. Genet. 2012) 3 4 64

Products for CHMP1A Gene

Sources for CHMP1A Gene

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