Atlas of Genetics and Cytogenetics in Oncology and Haematology


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CALCOCO2 (calcium binding and coiled-coil domain 2)

Identity

Alias_symbol (synonym)MGC17318
NDP52
Other alias
HGNC (Hugo) CALCOCO2
LocusID (NCBI) 10241
Atlas_Id 61386
Location 17q21.32  [Link to chromosome band 17q21]
Location_base_pair Starts at 48830988 and ends at 48865245 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
ALDH18A1 (10q24.1) / CALCOCO2 (17q21.32)LRRFIP1 (2q37.3) / CALCOCO2 (17q21.32)PCTP (17q22) / CALCOCO2 (17q21.32)
RNF169 (11q13.4) / CALCOCO2 (17q21.32)SKAP1 (17q21.32) / CALCOCO2 (17q21.32)SLC12A8 (3q21.2) / CALCOCO2 (17q21.32)
PCTP CALCOCO2RNF169 CALCOCO2SKAP1 CALCOCO2

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)CALCOCO2   29912
Cards
Entrez_Gene (NCBI)CALCOCO2  10241  calcium binding and coiled-coil domain 2
AliasesNDP52
GeneCards (Weizmann)CALCOCO2
Ensembl hg19 (Hinxton)ENSG00000136436 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000136436 [Gene_View]  chr17:48830988-48865245 [Contig_View]  CALCOCO2 [Vega]
ICGC DataPortalENSG00000136436
TCGA cBioPortalCALCOCO2
AceView (NCBI)CALCOCO2
Genatlas (Paris)CALCOCO2
WikiGenes10241
SOURCE (Princeton)CALCOCO2
Genetics Home Reference (NIH)CALCOCO2
Genomic and cartography
GoldenPath hg38 (UCSC)CALCOCO2  -     chr17:48830988-48865245 +  17q21.32   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CALCOCO2  -     17q21.32   [Description]    (hg19-Feb_2009)
EnsemblCALCOCO2 - 17q21.32 [CytoView hg19]  CALCOCO2 - 17q21.32 [CytoView hg38]
Mapping of homologs : NCBICALCOCO2 [Mapview hg19]  CALCOCO2 [Mapview hg38]
OMIM604587   
Gene and transcription
Genbank (Entrez)AF085965 AK222666 AK223227 AK293137 AK293329
RefSeq transcript (Entrez)NM_001261390 NM_001261391 NM_001261393 NM_001261395 NM_005831
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CALCOCO2
Cluster EST : UnigeneHs.514920 [ NCBI ]
CGAP (NCI)Hs.514920
Alternative Splicing GalleryENSG00000136436
Gene ExpressionCALCOCO2 [ NCBI-GEO ]   CALCOCO2 [ EBI - ARRAY_EXPRESS ]   CALCOCO2 [ SEEK ]   CALCOCO2 [ MEM ]
Gene Expression Viewer (FireBrowse)CALCOCO2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10241
GTEX Portal (Tissue expression)CALCOCO2
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13137   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ13137  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ13137
Splice isoforms : SwissVarQ13137
PhosPhoSitePlusQ13137
Domains : Interpro (EBI)CALCOCO1-like   
Domain families : Pfam (Sanger)CALCOCO1 (PF07888)   
Domain families : Pfam (NCBI)pfam07888   
Conserved Domain (NCBI)CALCOCO2
DMDM Disease mutations10241
Blocks (Seattle)CALCOCO2
PDB (SRS)2MXP    3VVV    3VVW    4GXL    4HAN    4XKL    5AAQ   
PDB (PDBSum)2MXP    3VVV    3VVW    4GXL    4HAN    4XKL    5AAQ   
PDB (IMB)2MXP    3VVV    3VVW    4GXL    4HAN    4XKL    5AAQ   
PDB (RSDB)2MXP    3VVV    3VVW    4GXL    4HAN    4XKL    5AAQ   
Structural Biology KnowledgeBase2MXP    3VVV    3VVW    4GXL    4HAN    4XKL    5AAQ   
SCOP (Structural Classification of Proteins)2MXP    3VVV    3VVW    4GXL    4HAN    4XKL    5AAQ   
CATH (Classification of proteins structures)2MXP    3VVV    3VVW    4GXL    4HAN    4XKL    5AAQ   
SuperfamilyQ13137
Human Protein AtlasENSG00000136436
Peptide AtlasQ13137
HPRD06846
IPIIPI00965684   IPI00965451   IPI00908968   IPI00966998   IPI00910883   IPI00966690   IPI00965197   IPI00965209   IPI00966087   IPI00963985   IPI00965967   IPI00983528   
Protein Interaction databases
DIP (DOE-UCLA)Q13137
IntAct (EBI)Q13137
FunCoupENSG00000136436
BioGRIDCALCOCO2
STRING (EMBL)CALCOCO2
ZODIACCALCOCO2
Ontologies - Pathways
QuickGOQ13137
Ontology : AmiGOautophagosome membrane  protein binding  nucleus  cytoplasm  autophagosome  cytosol  cytoskeleton  membrane  viral process  cytoplasmic vesicle  response to interferon-gamma  protein homodimerization activity  intracellular membrane-bounded organelle  perinuclear region of cytoplasm  xenophagy  positive regulation of autophagosome maturation  
Ontology : EGO-EBIautophagosome membrane  protein binding  nucleus  cytoplasm  autophagosome  cytosol  cytoskeleton  membrane  viral process  cytoplasmic vesicle  response to interferon-gamma  protein homodimerization activity  intracellular membrane-bounded organelle  perinuclear region of cytoplasm  xenophagy  positive regulation of autophagosome maturation  
NDEx NetworkCALCOCO2
Atlas of Cancer Signalling NetworkCALCOCO2
Wikipedia pathwaysCALCOCO2
Orthology - Evolution
OrthoDB10241
GeneTree (enSembl)ENSG00000136436
Phylogenetic Trees/Animal Genes : TreeFamCALCOCO2
HOVERGENQ13137
HOGENOMQ13137
Homologs : HomoloGeneCALCOCO2
Homology/Alignments : Family Browser (UCSC)CALCOCO2
Gene fusions - Rearrangements
Fusion: TCGAPCTP CALCOCO2
Fusion: TCGARNF169 CALCOCO2
Fusion: TCGASKAP1 CALCOCO2
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCALCOCO2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CALCOCO2
dbVarCALCOCO2
ClinVarCALCOCO2
1000_GenomesCALCOCO2 
Exome Variant ServerCALCOCO2
ExAC (Exome Aggregation Consortium)CALCOCO2 (select the gene name)
Genetic variants : HAPMAP10241
Genomic Variants (DGV)CALCOCO2 [DGVbeta]
DECIPHERCALCOCO2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCALCOCO2 
Mutations
ICGC Data PortalCALCOCO2 
TCGA Data PortalCALCOCO2 
Broad Tumor PortalCALCOCO2
OASIS PortalCALCOCO2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCALCOCO2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCALCOCO2
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
BioMutasearch CALCOCO2
DgiDB (Drug Gene Interaction Database)CALCOCO2
DoCM (Curated mutations)CALCOCO2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CALCOCO2 (select a term)
intoGenCALCOCO2
Cancer3DCALCOCO2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604587   
Orphanet
MedgenCALCOCO2
Genetic Testing Registry CALCOCO2
NextProtQ13137 [Medical]
TSGene10241
GENETestsCALCOCO2
Target ValidationCALCOCO2
Huge Navigator CALCOCO2 [HugePedia]
snp3D : Map Gene to Disease10241
BioCentury BCIQCALCOCO2
ClinGenCALCOCO2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD10241
Chemical/Pharm GKB GenePA143485407
Clinical trialCALCOCO2
Miscellaneous
canSAR (ICR)CALCOCO2 (select the gene name)
Probes
Litterature
PubMed52 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCALCOCO2
EVEXCALCOCO2
GoPubMedCALCOCO2
iHOPCALCOCO2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Mon Sep 18 13:03:47 CEST 2017

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