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PICALM (clathrin assembly lymphoid myeloid leukemia gene)

Written1998-01Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias (NCBI)CALM
HGNC (Hugo) PICALM
HGNC Alias symbCALM
CLTH
LocusID (NCBI) 8301
Atlas_Id 64
Location 11q14.2  [Link to chromosome band 11q14]
Location_base_pair Starts at 85957176 and ends at 86069084 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping PICALM.png]
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ARRB1 (11q13.4)::PICALM (11q14.2)CCDC83 (11q14.1)::PICALM (11q14.2)COL6A3 (2q37.3)::PICALM (11q14.2)
DLG2 (11q14.1)::PICALM (11q14.2)FAM21A (10q11.23)::PICALM (11q14.2)HIKESHI (11q14.2)::PICALM (11q14.2)
KMT2A (11q23.3)::PICALM (11q14.2)MLLT10 (10p12.31)::PICALM (11q14.2)PICALM (11q14.2)::ABRAXAS1 (4q21.23)
PICALM (11q14.2)::BRDT (1p22.1)PICALM (11q14.2)::CCDC81 (11q14.2)PICALM (11q14.2)::DIAPH1 (5q31.3)
PICALM (11q14.2)::KMT2A (11q23.3)PICALM (11q14.2)::MLLT10 (10p12.31)PICALM (11q14.2)::PICALM (11q14.2)
PICALM (11q14.2)::TF (3q22.1)RCC1 (1p35.3)::PICALM (11q14.2)SYTL2 (11q14.1)::PICALM (11q14.2)
TMEM123 (11q22.2)::PICALM (11q14.2)TMX2 (11q12.1)::PICALM (11q14.2)TYR (11q14.3)::PICALM (11q14.2)
Note Must not be confused with CALM1 (calmodulin 1, sitting in 14q24-31), or with neurofibromatosis type 6 (also called CALM, for: cafe au lait spots multiple); therefore the name is likely to change.

DNA/RNA

Transcription Major mRNA: 4 kb; other: 3 and 9 kb.

Protein

 
Description 652 amino acids.
Function Role in the integration of signals from different pathways (clathrin, phosphoinositols, receptor-mediated endocytosis).
Homology With AP3 (Adaptor Related Proteins), a clathrin assembly protein, and SNAP91 (AP180).

Implicated in

  
Entity PICALM / MLLT10
Disease T-cell acute lymphoblastic leukemia (ALL) mainly; at times acute myeloid leukemia (AML) and/or AML with T-cell markers (Dreyling et al., 1996; Kobayashi et al., 1997).
Prognosis uncertain (median survival 2 yrs?).
Cytogenetics may well be confused with the , where KMT2A in 11q23 is involved, instead of PICALM
Hybrid/Mutated Gene 5' PICALM - 3' MLLT10
Abnormal Protein Both PICALM-MLLT10 and the reciprocal MLLT10-PICALM are expressed.
  
  
Entity KMT2A / PICALM
Disease AML and B-cell ALL (Meyer et al., 2013; Wechsler et al., 2003).
Hybrid/Mutated Gene 5' KMT2A - 3' PICALM
Abnormal Protein The KMT2A/PICALM fusion protein was contained 1803 amino acids and included 1406 amino acids from KMT2A A-T hooks and repression domain, and a PICALM-derived clathrin-binding domain in Wechsler et al., 2003.
  

Breakpoints

 

Bibliography

The t(10;11)(p13;q14) in the U937 cell line results in the fusion of the AF10 gene and CALM, encoding a new member of the AP-3 clathrin assembly protein family.
Dreyling MH, Martinez-Climent JA, Zheng M, Mao J, Rowley JD, Bohlander SK.
Proc Natl Acad Sci U S A. 1996 May 14;93(10):4804-9.
PMID 8643484
 
Hematologic malignancies with the t(10;11) (p13;q21) have the same molecular event and a variety of morphologic or immunologic phenotypes.
Kobayashi H, Hosoda F, Maseki N, Sakurai M, Imashuku S, Ohki M, Kaneko Y.
Genes Chromosomes Cancer. 1997 Nov;20(3):253-9.
PMID 9365832
 
The MLL recombinome of acute leukemias in 2013.
Meyer C, Hofmann J, Burmeister T, Gröger D, Park TS, Emerenciano M, Pombo de Oliveira M, Renneville A, Villarese P, Macintyre E, Cavé H, Clappier E, Mass-Malo K, Zuna J, Trka J, De Braekeleer E, De Braekeleer M, Oh SH, Tsaur G, Fechina L, van der Velden VH, van Dongen JJ, Delabesse E, Binato R, Silva ML, Kustanovich A, Aleinikova O, Harris MH, Lund-Aho T, Juvonen V, Heidenreich O, Vormoor J, Choi WW, Jarosova M, Kolenova A, Bueno C, Menendez P, Wehner S, Eckert C, Talmant P, Tondeur S, Lippert E, Launay E, Henry C, Ballerini P, Lapillone H, Callanan MB, Cayuela JM, Herbaux C, Cazzaniga G, Kakadiya PM, Bohlander S, Ahlmann M, Choi JR, Gameiro P, Lee DS, Krauter J, Cornillet-Lefebvre P, Te Kronnie G, Schäfer BW, Kubetzko S, Alonso CN, zur Stadt U, Sutton R, Venn NC, Izraeli S, Trakhtenbrot L, Madsen HO, Archer P, Hancock J, Cerveira N, Teixeira MR, Lo Nigro L, Möricke A, Stanulla M, Schrappe M, Sedék L, Szczepa?ski T, Zwaan CM, Coenen EA, van den Heuvel-Eibrink MM, Strehl S, Dworzak M, Panzer-Grümayer R, Dingermann T, Klingebiel T, Marschalek R.
Leukemia. 2013 Nov;27(11):2165-76. doi: 10.1038/leu.2013.135.
PMID 23628958
 
A novel chromosomal inversion at 11q23 in infant acute myeloid leukemia fuses MLL to CALM, a gene that encodes a clathrin assembly protein.
Wechsler DS, Engstrom LD, Alexander BM, Motto DG, Roulston D.
Genes Chromosomes Cancer. 2003 Jan;36(1):26-36.
PMID 12461747
 

Citation

This paper should be referenced as such :
Jean-Loup Huret
PICALM (phosphatidylinositol binding clathrin assembly protein)
Atlas Genet Cytogenet Oncol Haematol. 1998;2(1):1-1.
Free journal version : [ pdf ]   [ DOI ]


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 8 ]
  Pediatric T-Cell Acute Lymphoblastic Leukemia
inv(7)(p15q34) TRB::HOXA10::t(7;7)(p15;q34) TRB::HOXA10
t(7;14)(p15;q11) TRD::HOXA10
t(10;11)(p12;q21) PICALM::MLLT10
t(10;11)(p11.2;q23) KMT2A::ABI1
t(11;11)(q14;q23) KMT2A::PICALM::inv(11)(q14q23) KMT2A::PICALM
T-lineage acute lymphoblastic leukemia (T-ALL)
t(1;11)(p35;q14) RCC1::PICALM


External links

 

Nomenclature
HGNC (Hugo)PICALM   15514
Cards
AtlasCALMID64
Atlas Explorer : (Salamanque)PICALM
Entrez_Gene (NCBI)PICALM    phosphatidylinositol binding clathrin assembly protein
AliasesCALM; CLTH; LAP
GeneCards (Weizmann)PICALM
Ensembl hg19 (Hinxton)ENSG00000073921 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000073921 [Gene_View]  ENSG00000073921 [Sequence]  chr11:85957176-86069084 [Contig_View]  PICALM [Vega]
ICGC DataPortalENSG00000073921
TCGA cBioPortalPICALM
AceView (NCBI)PICALM
Genatlas (Paris)PICALM
SOURCE (Princeton)PICALM
Genetics Home Reference (NIH)PICALM
Genomic and cartography
GoldenPath hg38 (UCSC)PICALM  -     chr11:85957176-86069084 -  11q14.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PICALM  -     11q14.2   [Description]    (hg19-Feb_2009)
GoldenPathPICALM - 11q14.2 [CytoView hg19]  PICALM - 11q14.2 [CytoView hg38]
ImmunoBaseENSG00000073921
Genome Data Viewer NCBIPICALM [Mapview hg19]  
OMIM601626   603025   
Gene and transcription
Genbank (Entrez)AB210017 AB451308 AF060939 AF060940 AK128786
RefSeq transcript (Entrez)NM_001008660 NM_001206946 NM_001206947 NM_007166
Consensus coding sequences : CCDS (NCBI)PICALM
Gene ExpressionPICALM [ NCBI-GEO ]   PICALM [ EBI - ARRAY_EXPRESS ]   PICALM [ SEEK ]   PICALM [ MEM ]
Gene Expression Viewer (FireBrowse)PICALM [ Firebrowse - Broad ]
GenevisibleExpression of PICALM in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8301
GTEX Portal (Tissue expression)PICALM
Human Protein AtlasENSG00000073921-PICALM [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13492   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ13492  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ13492
PhosPhoSitePlusQ13492
Domaine pattern : Prosite (Expaxy)ENTH (PS50942)   
Domains : Interpro (EBI)ANTH_dom    Clathrin_AP_dom2    ENTH    ENTH_VHS    PICALM   
Domain families : Pfam (Sanger)ANTH (PF07651)   
Domain families : Pfam (NCBI)pfam07651   
Domain families : Smart (EMBL)ENTH (SM00273)  
Conserved Domain (NCBI)PICALM
SuperfamilyQ13492
AlphaFold pdb e-kbQ13492   
Human Protein Atlas [tissue]ENSG00000073921-PICALM [tissue]
HPRD04320
Protein Interaction databases
DIP (DOE-UCLA)Q13492
IntAct (EBI)Q13492
BioGRIDPICALM
STRING (EMBL)PICALM
ZODIACPICALM
Ontologies - Pathways
QuickGOQ13492
Ontology : AmiGOSNARE binding  SNARE binding  amyloid-beta binding  protein binding  1-phosphatidylinositol binding  1-phosphatidylinositol binding  phosphatidylinositol-4,5-bisphosphate binding  phosphatidylinositol-4,5-bisphosphate binding  nucleus  early endosome  Golgi apparatus  cytosol  plasma membrane  clathrin-coated pit  clathrin-coated pit  clathrin-coated pit  endocytosis  receptor-mediated endocytosis  vesicle budding from membrane  vesicle budding from membrane  axonogenesis  learning or memory  synaptic vesicle  cell surface  negative regulation of gene expression  membrane  synaptic vesicle budding from presynaptic endocytic zone membrane  synaptic vesicle maturation  vesicle-mediated transport  endosomal transport  hemopoiesis  regulation of endocytosis  clathrin coat of coated pit  clathrin-coated vesicle  clathrin-coated vesicle  clathrin binding  intrinsic component of membrane  small GTPase binding  receptor internalization  vesicle  clathrin heavy chain binding  clathrin heavy chain binding  regulation of protein localization  vesicle cargo loading  presynaptic membrane  neuronal cell body  intracellular membrane-bounded organelle  positive regulation of GTPase activity  postsynaptic membrane  cadherin binding  clathrin-coated endocytic vesicle  positive regulation of transcription, DNA-templated  tau protein binding  negative regulation of receptor-mediated endocytosis  clathrin coat assembly  perinuclear region of cytoplasm  dendrite morphogenesis  low-density lipoprotein particle receptor binding  iron ion homeostasis  protein-containing complex assembly  endosome to plasma membrane transport vesicle  clathrin-dependent endocytosis  clathrin-dependent endocytosis  modulation of age-related behavioral decline  neurofibrillary tangle  regulation of vesicle size  membrane bending  extrinsic component of presynaptic endocytic zone membrane  amyloid-beta clearance by transcytosis  amyloid-beta clearance by transcytosis  positive regulation of neuron death  regulation of amyloid-beta formation  positive regulation of amyloid-beta formation  regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process  positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process  negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process  negative regulation of protein localization to plasma membrane  clathrin-coated pit assembly  negative regulation of protein localization to cell surface  
Ontology : EGO-EBISNARE binding  SNARE binding  amyloid-beta binding  protein binding  1-phosphatidylinositol binding  1-phosphatidylinositol binding  phosphatidylinositol-4,5-bisphosphate binding  phosphatidylinositol-4,5-bisphosphate binding  nucleus  early endosome  Golgi apparatus  cytosol  plasma membrane  clathrin-coated pit  clathrin-coated pit  clathrin-coated pit  endocytosis  receptor-mediated endocytosis  vesicle budding from membrane  vesicle budding from membrane  axonogenesis  learning or memory  synaptic vesicle  cell surface  negative regulation of gene expression  membrane  synaptic vesicle budding from presynaptic endocytic zone membrane  synaptic vesicle maturation  vesicle-mediated transport  endosomal transport  hemopoiesis  regulation of endocytosis  clathrin coat of coated pit  clathrin-coated vesicle  clathrin-coated vesicle  clathrin binding  intrinsic component of membrane  small GTPase binding  receptor internalization  vesicle  clathrin heavy chain binding  clathrin heavy chain binding  regulation of protein localization  vesicle cargo loading  presynaptic membrane  neuronal cell body  intracellular membrane-bounded organelle  positive regulation of GTPase activity  postsynaptic membrane  cadherin binding  clathrin-coated endocytic vesicle  positive regulation of transcription, DNA-templated  tau protein binding  negative regulation of receptor-mediated endocytosis  clathrin coat assembly  perinuclear region of cytoplasm  dendrite morphogenesis  low-density lipoprotein particle receptor binding  iron ion homeostasis  protein-containing complex assembly  endosome to plasma membrane transport vesicle  clathrin-dependent endocytosis  clathrin-dependent endocytosis  modulation of age-related behavioral decline  neurofibrillary tangle  regulation of vesicle size  membrane bending  extrinsic component of presynaptic endocytic zone membrane  amyloid-beta clearance by transcytosis  amyloid-beta clearance by transcytosis  positive regulation of neuron death  regulation of amyloid-beta formation  positive regulation of amyloid-beta formation  regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process  positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process  negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process  negative regulation of protein localization to plasma membrane  clathrin-coated pit assembly  negative regulation of protein localization to cell surface  
Pathways : BIOCARTABIOCARTA_NDKDYNAMINPATHWAY   
REACTOMEQ13492 [protein]
REACTOME PathwaysR-HSA-8856828 [pathway]   
NDEx NetworkPICALM
Atlas of Cancer Signalling NetworkPICALM
Wikipedia pathwaysPICALM
Orthology - Evolution
OrthoDB8301
GeneTree (enSembl)ENSG00000073921
Phylogenetic Trees/Animal Genes : TreeFamPICALM
Homologs : HomoloGenePICALM
Homology/Alignments : Family Browser (UCSC)PICALM
Gene fusions - Rearrangements
Fusion : MitelmanARRB1::PICALM [11q13.4/11q14.2]  
Fusion : MitelmanMLLT10::PICALM [10p12.31/11q14.2]  
Fusion : MitelmanPICALM::CCDC81 [11q14.2/11q14.2]  
Fusion : MitelmanPICALM::MLLT10 [11q14.2/10p12.31]  
Fusion : MitelmanRCC1::PICALM [1p35.3/11q14.2]  
Fusion : MitelmanSYTL2::PICALM [11q14.1/11q14.2]  
Fusion : COSMICKMT2A [11q23.3]  -  PICALM [11q14.2]  [fusion_1966]  [fusion_1967]  
Fusion Cancer (Beijing)cytochrome_b [PICALM]  -  11q14.2 [FUSC002836]
Fusion : FusionHubAAR2--PICALM    AC009403.2--PICALM    AF10--PICALM    AF1Q--PICALM    AKT3--PICALM    ALK--PICALM    APLP2--PICALM    ARHGAP24--PICALM    ARHGAP26--PICALM    ARRB1--PICALM   
ASPH--PICALM    ATG3--PICALM    ATP1A1--PICALM    ATP9A--PICALM    B2M--PICALM    BRAF--PICALM    C11ORF73--PICALM    C2ORF27A--PICALM    CALCOCO2--PICALM    CBL--PICALM   
CCDC3--PICALM    CCDC81--PICALM    CCDC82--PICALM    CCDC83--PICALM    CCDC90B--PICALM    CD44--PICALM    CDKAL1--PICALM    CHORDC1--PICALM    CLIP1--PICALM    CLNS1A--PICALM   
COL6A3--PICALM    CSNK1E--PICALM    CTNND1--PICALM    CTSC--PICALM    CYTOCHROME_B--PICALM    DACT3--PICALM    DDN--PICALM    DDX10--PICALM    DGAT2--PICALM    DHTKD1--PICALM   
DHX36--PICALM    DLG2--PICALM    DR1--PICALM    DTNA--PICALM    DYNC2H1--PICALM    DYSF--PICALM    ECHDC2--PICALM    EIF3E--PICALM    EIF3F--PICALM    EP400--PICALM   
EPS8--PICALM    ETV4--PICALM    FAM180B--PICALM    FAM35A--PICALM    FBXL22--PICALM    FBXL5--PICALM    FBXW2--PICALM    FNBP4--PICALM    FUCA2--PICALM    GAB2--PICALM   
GNPTG--PICALM    GPATCH2L--PICALM    HIST1H2BD--PICALM    HOXB6--PICALM    HSD17B7--PICALM    IGF2R--PICALM    IL15RA--PICALM    IL1R2--PICALM    JAM3--PICALM    KANSL3--PICALM   
KATNBL1--PICALM    KIAA1671--PICALM    KMT2A--PICALM    LANCL1--PICALM    LMCD1--PICALM    MEF2A--PICALM    MGAT4A--PICALM    MLL--PICALM    MLLT10--PICALM    MRAS--PICALM   
MTMR2--PICALM    MTX2--PICALM    MYL9--PICALM    NBPF24--PICALM    NCOR1--PICALM    NFRKB--PICALM    NME2--PICALM    NPTN--PICALM    NTRK2--PICALM    PCF11--PICALM   
PCNX--PICALM    PDE9A--PICALM    PDLIM5--PICALM    PHLDB1--PICALM    PICALM--ALOX5    PICALM--ARPP19    PICALM--BRDT    PICALM--C11ORF73    PICALM--CCAR2    PICALM--CCDC81   
PICALM--CD59    PICALM--CD82    PICALM--CHD2    PICALM--CHMP1A    PICALM--CSNK1D    PICALM--CYSTM1    PICALM--DDX10    PICALM--DDX21    PICALM--DIAPH1    PICALM--DYNLT1   
PICALM--EED    PICALM--FAM120B    PICALM--FAM192A    PICALM--FUS    PICALM--HSPA9    PICALM--MARK2    PICALM--MAX    PICALM--ME3    PICALM--MINOS1-NBL1    PICALM--MLL   
PICALM--MLLT10    PICALM--NNMT    PICALM--PICALM    PICALM--PIK3R4    PICALM--PNRC1    PICALM--PPME1    PICALM--PRB3    PICALM--PSMA5    PICALM--PTBP3    PICALM--RCC1   
PICALM--RP11-849H4.2    PICALM--SERGEF    PICALM--SLC38A1    PICALM--SYTL2    PICALM--TEX10    PICALM--TF    PICALM--THRAP3    PICALM--TMEM135    PICALM--TMEM57    PICALM--UBE2D3   
PICALM--YAP1    PILRB--PICALM    PJA2--PICALM    PNLIPRP1--PICALM    PRSS23--PICALM    PSPC1--PICALM    PTPRG--PICALM    RAB10--PICALM    RAB12--PICALM    RDH10--PICALM   
RDX--PICALM    RP11-1055B8.7--PICALM    RP2--PICALM    RPTOR--PICALM    RSF1--PICALM    SBF2--PICALM    SLC15A4--PICALM    SLC24A3--PICALM    SLC37A3--PICALM    SMCO4--PICALM   
SNAP91--PICALM    SOCS4--PICALM    SORCS2--PICALM    SSFA2--PICALM    STK17B--PICALM    STK38--PICALM    SYTL2--PICALM    SYTL3--PICALM    TBC1D1--PICALM    TBC1D25--PICALM   
TBCEL--PICALM    TCF4--PICALM    TGFBR2--PICALM    TMEM123--PICALM    TMEM126B--PICALM    TMEM131--PICALM    TMEM135--PICALM    TMEM59--PICALM    TMTC2--PICALM    TMX2--PICALM   
TYR--PICALM    U2AF1--PICALM    UBE2B--PICALM    UBE2D3--PICALM    UGT1A6--PICALM    UPF3A--PICALM    WNK1--PICALM    ZBED1--PICALM    ZKSCAN1--PICALM    ZNF286A--PICALM   
ZNF395--PICALM    ZWILCH--PICALM   
Fusion : QuiverPICALM
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPICALM [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PICALM
dbVarPICALM
ClinVarPICALM
MonarchPICALM
1000_GenomesPICALM 
Exome Variant ServerPICALM
GNOMAD BrowserENSG00000073921
Varsome BrowserPICALM
ACMGPICALM variants
VarityQ13492
Genomic Variants (DGV)PICALM [DGVbeta]
DECIPHERPICALM [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPICALM 
Mutations
ICGC Data PortalPICALM 
TCGA Data PortalPICALM 
Broad Tumor PortalPICALM
OASIS PortalPICALM [ Somatic mutations - Copy number]
Cancer Gene: CensusPICALM 
Somatic Mutations in Cancer : COSMICPICALM  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DPICALM
Mutations and Diseases : HGMDPICALM
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaPICALM
DgiDB (Drug Gene Interaction Database)PICALM
DoCM (Curated mutations)PICALM
CIViC (Clinical Interpretations of Variants in Cancer)PICALM
OncoKBPICALM
NCG (London)PICALM
Cancer3DPICALM
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601626    603025   
Orphanet14434   
DisGeNETPICALM
MedgenPICALM
Genetic Testing Registry PICALM
NextProtQ13492 [Medical]
GENETestsPICALM
Target ValidationPICALM
Huge Navigator PICALM [HugePedia]
ClinGenPICALM
Clinical trials, drugs, therapy
MyCancerGenomePICALM
Protein Interactions : CTDPICALM
Pharm GKB GenePA33287
PharosQ13492
Clinical trialPICALM
Miscellaneous
canSAR (ICR)PICALM
HarmonizomePICALM
ARCHS4PICALM
DataMed IndexPICALM
Probes
Litterature
PubMed177 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXPICALM
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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