Atlas of Genetics and Cytogenetics in Oncology and Haematology


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CHMP1A (charged multivesicular body protein 1A)

Identity

Alias_namesPRSM1
PCOLN3
procollagen (type III) N-endopeptidase
chromatin modifying protein 1A
Alias_symbol (synonym)KIAA0047
CHMP1
Vps46A
Other aliasPCH8
VPS46-1
VPS46A
HGNC (Hugo) CHMP1A
LocusID (NCBI) 5119
Atlas_Id 50500
Location 16q24.3  [Link to chromosome band 16q24]
Location_base_pair Starts at 89710839 and ends at 89724193 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
ABCA2 (9q34.3) / CHMP1A (16q24.3)CENPK (5q12.3) / CHMP1A (16q24.3)CHMP1A (16q24.3) / CHMP1A (16q24.3)
CHUK (10q24.31) / CHMP1A (16q24.3)CPSF6 (12q15) / CHMP1A (16q24.3)FUBP1 (1p31.1) / CHMP1A (16q24.3)
HMGA2 (12q14.3) / CHMP1A (16q24.3)HPS1 (10q24.2) / CHMP1A (16q24.3)ING3 (7q31.31) / CHMP1A (16q24.3)
LRBA (4q31.3) / CHMP1A (16q24.3)PCDH10 (4q28.3) / CHMP1A (16q24.3)PPP4R3B (2p16.1) / CHMP1A (16q24.3)
PTPRK (6q22.33) / CHMP1A (16q24.3)RAB3GAP1 (2q21.3) / CHMP1A (16q24.3)TTC12 (11q23.2) / CHMP1A (16q24.3)
ZC3H18 (16q24.2) / CHMP1A (16q24.3)ZC3HAV1L (7q34) / CHMP1A (16q24.3)ZNF736 (7q11.21) / CHMP1A (16q24.3)
CPSF6 12q15 / CHMP1A 16q24.3ZC3H18 16q24.2 / CHMP1A 16q24.3

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)CHMP1A   8740
Cards
Entrez_Gene (NCBI)CHMP1A  5119  charged multivesicular body protein 1A
AliasesCHMP1; PCH8; PCOLN3; PRSM1; 
VPS46-1; VPS46A
GeneCards (Weizmann)CHMP1A
Ensembl hg19 (Hinxton)ENSG00000131165 [Gene_View]  chr16:89710839-89724193 [Contig_View]  CHMP1A [Vega]
Ensembl hg38 (Hinxton)ENSG00000131165 [Gene_View]  chr16:89710839-89724193 [Contig_View]  CHMP1A [Vega]
ICGC DataPortalENSG00000131165
TCGA cBioPortalCHMP1A
AceView (NCBI)CHMP1A
Genatlas (Paris)CHMP1A
WikiGenes5119
SOURCE (Princeton)CHMP1A
Genetics Home Reference (NIH)CHMP1A
Genomic and cartography
GoldenPath hg19 (UCSC)CHMP1A  -     chr16:89710839-89724193 -  16q24.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)CHMP1A  -     16q24.3   [Description]    (hg38-Dec_2013)
EnsemblCHMP1A - 16q24.3 [CytoView hg19]  CHMP1A - 16q24.3 [CytoView hg38]
Mapping of homologs : NCBICHMP1A [Mapview hg19]  CHMP1A [Mapview hg38]
OMIM164010   614961   
Gene and transcription
Genbank (Entrez)AF281063 AI356110 AI362697 AK302055 BC007527
RefSeq transcript (Entrez)NM_001083314 NM_002768
RefSeq genomic (Entrez)NC_000016 NC_018927 NG_033005 NT_010498 NW_004929403
Consensus coding sequences : CCDS (NCBI)CHMP1A
Cluster EST : UnigeneHs.589427 [ NCBI ]
CGAP (NCI)Hs.589427
Alternative Splicing GalleryENSG00000131165
Gene ExpressionCHMP1A [ NCBI-GEO ]   CHMP1A [ EBI - ARRAY_EXPRESS ]   CHMP1A [ SEEK ]   CHMP1A [ MEM ]
Gene Expression Viewer (FireBrowse)CHMP1A [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5119
GTEX Portal (Tissue expression)CHMP1A
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9HD42   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9HD42  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9HD42
Splice isoforms : SwissVarQ9HD42
PhosPhoSitePlusQ9HD42
Domains : Interpro (EBI)CHMP1A    Snf7_fam   
Domain families : Pfam (Sanger)Snf7 (PF03357)   
Domain families : Pfam (NCBI)pfam03357   
Conserved Domain (NCBI)CHMP1A
DMDM Disease mutations5119
Blocks (Seattle)CHMP1A
PDB (SRS)2JQ9    2YMB    4A5X   
PDB (PDBSum)2JQ9    2YMB    4A5X   
PDB (IMB)2JQ9    2YMB    4A5X   
PDB (RSDB)2JQ9    2YMB    4A5X   
Structural Biology KnowledgeBase2JQ9    2YMB    4A5X   
SCOP (Structural Classification of Proteins)2JQ9    2YMB    4A5X   
CATH (Classification of proteins structures)2JQ9    2YMB    4A5X   
SuperfamilyQ9HD42
Human Protein AtlasENSG00000131165
Peptide AtlasQ9HD42
HPRD01237
IPIIPI00382452   IPI01015759   IPI01022903   IPI01022543   IPI00003169   
Protein Interaction databases
DIP (DOE-UCLA)Q9HD42
IntAct (EBI)Q9HD42
FunCoupENSG00000131165
BioGRIDCHMP1A
STRING (EMBL)CHMP1A
ZODIACCHMP1A
Ontologies - Pathways
QuickGOQ9HD42
Ontology : AmiGOcondensed nuclear chromosome  ESCRT III complex  cell separation after cytokinesis  protein binding  early endosome  microtubule organizing center  transcription, DNA-templated  proteolysis  nucleus organization  vacuolar transport  mitotic chromosome condensation  mitotic metaphase plate congression  metallopeptidase activity  zinc ion binding  regulation of centrosome duplication  endomembrane system  protein transport  vesicle-mediated transport  nuclear matrix  gene silencing  protein domain specific binding  multivesicular body assembly  viral budding via host ESCRT complex  identical protein binding  protein homodimerization activity  negative regulation of transcription by glucose  negative regulation of transcription, DNA-templated  cell division  extracellular exosome  regulation of mitotic spindle assembly  ESCRT III complex disassembly  
Ontology : EGO-EBIcondensed nuclear chromosome  ESCRT III complex  cell separation after cytokinesis  protein binding  early endosome  microtubule organizing center  transcription, DNA-templated  proteolysis  nucleus organization  vacuolar transport  mitotic chromosome condensation  mitotic metaphase plate congression  metallopeptidase activity  zinc ion binding  regulation of centrosome duplication  endomembrane system  protein transport  vesicle-mediated transport  nuclear matrix  gene silencing  protein domain specific binding  multivesicular body assembly  viral budding via host ESCRT complex  identical protein binding  protein homodimerization activity  negative regulation of transcription by glucose  negative regulation of transcription, DNA-templated  cell division  extracellular exosome  regulation of mitotic spindle assembly  ESCRT III complex disassembly  
NDEx NetworkCHMP1A
Atlas of Cancer Signalling NetworkCHMP1A
Wikipedia pathwaysCHMP1A
Orthology - Evolution
OrthoDB5119
GeneTree (enSembl)ENSG00000131165
Phylogenetic Trees/Animal Genes : TreeFamCHMP1A
HOVERGENQ9HD42
HOGENOMQ9HD42
Homologs : HomoloGeneCHMP1A
Homology/Alignments : Family Browser (UCSC)CHMP1A
Gene fusions - Rearrangements
Fusion : MitelmanCPSF6/CHMP1A [12q15/16q24.3]  [t(12;16)(q15;q24)]  
Fusion : MitelmanZC3H18/CHMP1A [16q24.2/16q24.3]  [t(16;16)(q24;q24)]  
Fusion : MitelmanZC3HAV1L/CHMP1A [7q34/16q24.3]  [t(7;16)(q34;q24)]  
Fusion: TCGACPSF6 12q15 CHMP1A 16q24.3 BLCA
Fusion: TCGAZC3H18 16q24.2 CHMP1A 16q24.3 GBM
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCHMP1A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CHMP1A
dbVarCHMP1A
ClinVarCHMP1A
1000_GenomesCHMP1A 
Exome Variant ServerCHMP1A
ExAC (Exome Aggregation Consortium)CHMP1A (select the gene name)
Genetic variants : HAPMAP5119
Genomic Variants (DGV)CHMP1A [DGVbeta]
DECIPHER (Syndromes)16:89710839-89724193  ENSG00000131165
CONAN: Copy Number AnalysisCHMP1A 
Mutations
ICGC Data PortalCHMP1A 
TCGA Data PortalCHMP1A 
Broad Tumor PortalCHMP1A
OASIS PortalCHMP1A [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCHMP1A  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCHMP1A
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch CHMP1A
DgiDB (Drug Gene Interaction Database)CHMP1A
DoCM (Curated mutations)CHMP1A (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CHMP1A (select a term)
intoGenCHMP1A
Cancer3DCHMP1A(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM164010    614961   
Orphanet21786   
MedgenCHMP1A
Genetic Testing Registry CHMP1A
NextProtQ9HD42 [Medical]
TSGene5119
GENETestsCHMP1A
Huge Navigator CHMP1A [HugePedia]
snp3D : Map Gene to Disease5119
BioCentury BCIQCHMP1A
ClinGenCHMP1A
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5119
Chemical/Pharm GKB GenePA33085
Clinical trialCHMP1A
Miscellaneous
canSAR (ICR)CHMP1A (select the gene name)
Probes
Litterature
PubMed42 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCHMP1A
EVEXCHMP1A
GoPubMedCHMP1A
iHOPCHMP1A
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Mar 14 13:00:23 CET 2017

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