Atlas of Genetics and Cytogenetics in Oncology and Haematology


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CALR (calreticulin)

Identity

Alias_symbol (synonym)RO
SSA
cC1qR
CRT
FLJ26680
Other aliasHEL-S-99n
HGNC (Hugo) CALR
LocusID (NCBI) 811
Atlas_Id 904
Location 19p13.13  [Link to chromosome band 19p13]
Location_base_pair Starts at 12938600 and ends at 12944490 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
ADGRF4 (6p12.3) / CALR (19p13.2)BRD2 (6p21.32) / CALR (19p13.2)CALR (19p13.2) / ACACA (17q12)
CALR (19p13.2) / AFP (4q13.3)CALR (19p13.2) / BRD2 (6p21.32)CALR (19p13.2) / CALR (19p13.2)
CALR (19p13.2) / EIF2B4 (2p23.3)CALR (19p13.2) / MCM3 (6p12.2)FAU (11q13.1) / CALR (19p13.2)
H19 (11p15.5) / CALR (19p13.2)KIF18B (17q21.31) / CALR (19p13.2)NDRG2 (14q11.2) / CALR (19p13.2)
NME4 (16p13.3) / CALR (19p13.2)OXSR1 (3p22.2) / CALR (19p13.2)RPLP2 (11p15.5) / CALR (19p13.2)
RYR2 (1q43) / CALR (19p13.2)TENM4 (11q14.1) / CALR (19p13.2)CALR 19p13.2 / BRD2 6p21.32

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

 


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  Myelodysplastic/myeloproliferative neoplasm with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T)


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Lung: Translocations in Adenocarcinoma


External links

Nomenclature
HGNC (Hugo)CALR   1455
LRG (Locus Reference Genomic)LRG_828
Cards
Entrez_Gene (NCBI)CALR  811  calreticulin
AliasesCRT; HEL-S-99n; RO; SSA; 
cC1qR
GeneCards (Weizmann)CALR
Ensembl hg19 (Hinxton)ENSG00000179218 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000179218 [Gene_View]  chr19:12938600-12944490 [Contig_View]  CALR [Vega]
ICGC DataPortalENSG00000179218
TCGA cBioPortalCALR
AceView (NCBI)CALR
Genatlas (Paris)CALR
WikiGenes811
SOURCE (Princeton)CALR
Genetics Home Reference (NIH)CALR
Genomic and cartography
GoldenPath hg38 (UCSC)CALR  -     chr19:12938600-12944490 +  19p13.13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CALR  -     19p13.13   [Description]    (hg19-Feb_2009)
EnsemblCALR - 19p13.13 [CytoView hg19]  CALR - 19p13.13 [CytoView hg38]
Mapping of homologs : NCBICALR [Mapview hg19]  CALR [Mapview hg38]
OMIM109091   187950   254450   
Gene and transcription
Genbank (Entrez)AB451408 AF087986 AK130190 AK223060 AK295230
RefSeq transcript (Entrez)NM_004343
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CALR
Cluster EST : UnigeneHs.515162 [ NCBI ]
CGAP (NCI)Hs.515162
Alternative Splicing GalleryENSG00000179218
Gene ExpressionCALR [ NCBI-GEO ]   CALR [ EBI - ARRAY_EXPRESS ]   CALR [ SEEK ]   CALR [ MEM ]
Gene Expression Viewer (FireBrowse)CALR [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)811
GTEX Portal (Tissue expression)CALR
Protein : pattern, domain, 3D structure
UniProt/SwissProtP27797   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP27797  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP27797
Splice isoforms : SwissVarP27797
PhosPhoSitePlusP27797
Domaine pattern : Prosite (Expaxy)CALRETICULIN_1 (PS00803)    CALRETICULIN_2 (PS00804)    CALRETICULIN_REPEAT (PS00805)    ER_TARGET (PS00014)   
Domains : Interpro (EBI)Calret/calnex    Calret/calnex_CS    Calreticulin    Calreticulin/calnexin_P_dom    ConA-like_dom   
Domain families : Pfam (Sanger)Calreticulin (PF00262)   
Domain families : Pfam (NCBI)pfam00262   
Conserved Domain (NCBI)CALR
DMDM Disease mutations811
Blocks (Seattle)CALR
PDB (SRS)2CLR    3DOW    3POS    3POW    5LK5   
PDB (PDBSum)2CLR    3DOW    3POS    3POW    5LK5   
PDB (IMB)2CLR    3DOW    3POS    3POW    5LK5   
PDB (RSDB)2CLR    3DOW    3POS    3POW    5LK5   
Structural Biology KnowledgeBase2CLR    3DOW    3POS    3POW    5LK5   
SCOP (Structural Classification of Proteins)2CLR    3DOW    3POS    3POW    5LK5   
CATH (Classification of proteins structures)2CLR    3DOW    3POS    3POW    5LK5   
SuperfamilyP27797
Human Protein AtlasENSG00000179218
Peptide AtlasP27797
HPRD00169
IPIIPI00020599   IPI01013746   
Protein Interaction databases
DIP (DOE-UCLA)P27797
IntAct (EBI)P27797
FunCoupENSG00000179218
BioGRIDCALR
STRING (EMBL)CALR
ZODIACCALR
Ontologies - Pathways
QuickGOP27797
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  acrosomal vesicle  complement component C1q binding  glycoprotein binding  antigen processing and presentation of peptide antigen via MHC class I  antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent  peptide antigen assembly with MHC class I protein complex  DNA binding  RNA binding  mRNA binding  integrin binding  iron ion binding  calcium ion binding  calcium ion binding  protein binding  extracellular region  proteinaceous extracellular matrix  extracellular space  extracellular space  intracellular  nucleus  cytoplasm  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum lumen  endoplasmic reticulum lumen  smooth endoplasmic reticulum  Golgi apparatus  cytosol  polysome  focal adhesion  regulation of transcription, DNA-templated  protein folding  protein export from nucleus  cellular calcium ion homeostasis  receptor-mediated endocytosis  spermatogenesis  zinc ion binding  positive regulation of cell proliferation  external side of plasma membrane  cell surface  positive regulation of endothelial cell migration  positive regulation of gene expression  membrane  negative regulation of translation  negative regulation of translation  protein maturation by protein folding  carbohydrate binding  phagocytic vesicle membrane  cortical actin cytoskeleton organization  ubiquitin protein ligase binding  response to estradiol  sarcoplasmic reticulum lumen  endoplasmic reticulum-Golgi intermediate compartment membrane  negative regulation of intracellular steroid hormone receptor signaling pathway  response to testosterone  protein localization to nucleus  protein folding in endoplasmic reticulum  ATF6-mediated unfolded protein response  regulation of meiotic nuclear division  peptide binding  response to drug  hormone binding  MHC class I peptide loading complex  glucocorticoid receptor signaling pathway  regulation of apoptotic process  protein binding involved in protein folding  negative regulation of neuron differentiation  positive regulation of DNA replication  positive regulation of cell cycle  negative regulation of transcription, DNA-templated  negative regulation of retinoic acid receptor signaling pathway  perinuclear region of cytoplasm  androgen receptor binding  positive regulation of phagocytosis  protein stabilization  protein stabilization  unfolded protein binding  chaperone binding  sequestering of calcium ion  cardiac muscle cell differentiation  chaperone-mediated protein folding  extracellular exosome  negative regulation of cell cycle arrest  cellular response to lithium ion  integral component of lumenal side of endoplasmic reticulum membrane  endocytic vesicle lumen  cellular senescence  positive regulation of substrate adhesion-dependent cell spreading  negative regulation of trophoblast cell migration  positive regulation of NIK/NF-kappaB signaling  vesicle fusion with endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane  positive regulation of dendritic cell chemotaxis  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  acrosomal vesicle  complement component C1q binding  glycoprotein binding  antigen processing and presentation of peptide antigen via MHC class I  antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent  peptide antigen assembly with MHC class I protein complex  DNA binding  RNA binding  mRNA binding  integrin binding  iron ion binding  calcium ion binding  calcium ion binding  protein binding  extracellular region  proteinaceous extracellular matrix  extracellular space  extracellular space  intracellular  nucleus  cytoplasm  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum lumen  endoplasmic reticulum lumen  smooth endoplasmic reticulum  Golgi apparatus  cytosol  polysome  focal adhesion  regulation of transcription, DNA-templated  protein folding  protein export from nucleus  cellular calcium ion homeostasis  receptor-mediated endocytosis  spermatogenesis  zinc ion binding  positive regulation of cell proliferation  external side of plasma membrane  cell surface  positive regulation of endothelial cell migration  positive regulation of gene expression  membrane  negative regulation of translation  negative regulation of translation  protein maturation by protein folding  carbohydrate binding  phagocytic vesicle membrane  cortical actin cytoskeleton organization  ubiquitin protein ligase binding  response to estradiol  sarcoplasmic reticulum lumen  endoplasmic reticulum-Golgi intermediate compartment membrane  negative regulation of intracellular steroid hormone receptor signaling pathway  response to testosterone  protein localization to nucleus  protein folding in endoplasmic reticulum  ATF6-mediated unfolded protein response  regulation of meiotic nuclear division  peptide binding  response to drug  hormone binding  MHC class I peptide loading complex  glucocorticoid receptor signaling pathway  regulation of apoptotic process  protein binding involved in protein folding  negative regulation of neuron differentiation  positive regulation of DNA replication  positive regulation of cell cycle  negative regulation of transcription, DNA-templated  negative regulation of retinoic acid receptor signaling pathway  perinuclear region of cytoplasm  androgen receptor binding  positive regulation of phagocytosis  protein stabilization  protein stabilization  unfolded protein binding  chaperone binding  sequestering of calcium ion  cardiac muscle cell differentiation  chaperone-mediated protein folding  extracellular exosome  negative regulation of cell cycle arrest  cellular response to lithium ion  integral component of lumenal side of endoplasmic reticulum membrane  endocytic vesicle lumen  cellular senescence  positive regulation of substrate adhesion-dependent cell spreading  negative regulation of trophoblast cell migration  positive regulation of NIK/NF-kappaB signaling  vesicle fusion with endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane  positive regulation of dendritic cell chemotaxis  
Pathways : BIOCARTANFAT and Hypertrophy of the heart (Transcription in the broken heart) [Genes]   
Pathways : KEGGProtein processing in endoplasmic reticulum    Phagosome    Antigen processing and presentation    Chagas disease (American trypanosomiasis)    HTLV-I infection   
NDEx NetworkCALR
Atlas of Cancer Signalling NetworkCALR
Wikipedia pathwaysCALR
Orthology - Evolution
OrthoDB811
GeneTree (enSembl)ENSG00000179218
Phylogenetic Trees/Animal Genes : TreeFamCALR
HOVERGENP27797
HOGENOMP27797
Homologs : HomoloGeneCALR
Homology/Alignments : Family Browser (UCSC)CALR
Gene fusions - Rearrangements
Fusion : MitelmanADGRF4/CALR [6p12.3/19p13.2]  [t(6;19)(p12;p13)]  
Fusion : MitelmanCALR/ACACA [19p13.2/17q12]  [t(17;19)(q12;p13)]  
Fusion : MitelmanCALR/BRD2 [19p13.2/6p21.32]  [t(6;19)(p21;p13)]  
Fusion : MitelmanH19/CALR [11p15.5/19p13.2]  [t(11;19)(p15;p13)]  
Fusion: TCGACALR 19p13.2 BRD2 6p21.32 PRAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCALR [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CALR
dbVarCALR
ClinVarCALR
1000_GenomesCALR 
Exome Variant ServerCALR
ExAC (Exome Aggregation Consortium)CALR (select the gene name)
Genetic variants : HAPMAP811
Genomic Variants (DGV)CALR [DGVbeta]
DECIPHERCALR [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCALR 
Mutations
ICGC Data PortalCALR 
TCGA Data PortalCALR 
Broad Tumor PortalCALR
OASIS PortalCALR [ Somatic mutations - Copy number]
Cancer Gene: CensusCALR 
Somatic Mutations in Cancer : COSMICCALR  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCALR
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch CALR
DgiDB (Drug Gene Interaction Database)CALR
DoCM (Curated mutations)CALR (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CALR (select a term)
intoGenCALR
Cancer3DCALR(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM109091    187950    254450   
Orphanet3599    8745   
MedgenCALR
Genetic Testing Registry CALR
NextProtP27797 [Medical]
TSGene811
GENETestsCALR
Target ValidationCALR
Huge Navigator CALR [HugePedia]
snp3D : Map Gene to Disease811
BioCentury BCIQCALR
ClinGenCALR
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD811
Chemical/Pharm GKB GenePA26046
Clinical trialCALR
Miscellaneous
canSAR (ICR)CALR (select the gene name)
Probes
Litterature
PubMed390 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCALR
EVEXCALR
GoPubMedCALR
iHOPCALR
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 25 19:00:19 CEST 2017

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