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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_symbol (synonym)CALM
CLTH
Other alias
HGNC (Hugo) PICALM
LocusID (NCBI) 8301
Atlas_Id 64
Location 11q14.2  [Link to chromosome band 11q14]
Location_base_pair Starts at 85957171 and ends at 86069097 bp from pter ( according to hg19-Feb_2009)  [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 t(10;11)(p13;q14-21) 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 t(10;11)(p12;q23) , 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 t(11;11)(q14;q23) 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 ]
On line version : http://AtlasGeneticsOncology.org/Genes/CALMID64.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 6 ]
  inv(7)(p15q34) TRB/HOXA10::t(7;7)(p15;q34) TRB/HOXA10
t(7;14)(p15;q11) TRD/HOXA10
t(10;11)(p13;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)


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


External links

Nomenclature
HGNC (Hugo)PICALM   15514
Cards
AtlasCALMID64
Entrez_Gene (NCBI)PICALM  8301  phosphatidylinositol binding clathrin assembly protein
AliasesCALM; CLTH; LAP
GeneCards (Weizmann)PICALM
Ensembl hg19 (Hinxton)ENSG00000073921 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000073921 [Gene_View]  chr11:85957171-86069097 [Contig_View]  PICALM [Vega]
ICGC DataPortalENSG00000073921
TCGA cBioPortalPICALM
AceView (NCBI)PICALM
Genatlas (Paris)PICALM
WikiGenes8301
SOURCE (Princeton)PICALM
Genetics Home Reference (NIH)PICALM
Genomic and cartography
GoldenPath hg38 (UCSC)PICALM  -     chr11:85957171-86069097 -  11q14.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PICALM  -     11q14.2   [Description]    (hg19-Feb_2009)
EnsemblPICALM - 11q14.2 [CytoView hg19]  PICALM - 11q14.2 [CytoView hg38]
Mapping of homologs : NCBIPICALM [Mapview hg19]  PICALM [Mapview hg38]
OMIM603025   
Gene and transcription
Genbank (Entrez)AB210017 AB451308 AF060939 AF060940 AK128786
RefSeq transcript (Entrez)NM_001008660 NM_001206946 NM_001206947 NM_007166
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PICALM
Cluster EST : UnigeneHs.163893 [ NCBI ]
CGAP (NCI)Hs.163893
Alternative Splicing GalleryENSG00000073921
Gene ExpressionPICALM [ NCBI-GEO ]   PICALM [ EBI - ARRAY_EXPRESS ]   PICALM [ SEEK ]   PICALM [ MEM ]
Gene Expression Viewer (FireBrowse)PICALM [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression 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
Splice isoforms : SwissVarQ13492
PhosPhoSitePlusQ13492
Domaine pattern : Prosite (Expaxy)ENTH (PS50942)   
Domains : Interpro (EBI)ANTH_dom    Clathrin_AP_2    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
DMDM Disease mutations8301
Blocks (Seattle)PICALM
SuperfamilyQ13492
Human Protein Atlas [tissue]ENSG00000073921-PICALM [tissue]
Peptide AtlasQ13492
HPRD04320
IPIIPI00290738   IPI00216184   IPI00400849   IPI00981891   IPI00455611   IPI00984627   IPI00980570   IPI00980475   IPI00978502   IPI00977780   IPI00977120   IPI00975853   IPI00976441   IPI00983898   IPI00982453   IPI00983288   IPI00981984   
Protein Interaction databases
DIP (DOE-UCLA)Q13492
IntAct (EBI)Q13492
FunCoupENSG00000073921
BioGRIDPICALM
STRING (EMBL)PICALM
ZODIACPICALM
Ontologies - Pathways
QuickGOQ13492
Ontology : AmiGOprotein binding  1-phosphatidylinositol binding  nucleus  Golgi apparatus  cytosol  clathrin-coated pit  clathrin-coated pit  protein complex assembly  receptor-mediated endocytosis  receptor-mediated endocytosis  axonogenesis  cell proliferation  negative regulation of gene expression  membrane  synaptic vesicle maturation  vesicle-mediated transport  endosomal transport  hemopoiesis  regulation of endocytosis  AP-2 adaptor complex  clathrin coat of coated pit  clathrin-coated vesicle  clathrin binding  clathrin binding  clathrin binding  receptor internalization  vesicle  clathrin heavy chain binding  regulation of protein localization  cargo loading into vesicle  clathrin adaptor activity  presynaptic membrane  neuronal cell body  intracellular membrane-bounded organelle  postsynaptic membrane  cadherin binding  positive regulation of transcription, DNA-templated  negative regulation of receptor-mediated endocytosis  clathrin coat assembly  perinuclear region of cytoplasm  dendrite morphogenesis  iron ion homeostasis  membrane organization  clathrin-dependent endocytosis  neurofibrillary tangle  iron ion import across plasma membrane  positive regulation of neuron death  positive regulation of beta-amyloid 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  
Ontology : EGO-EBIprotein binding  1-phosphatidylinositol binding  nucleus  Golgi apparatus  cytosol  clathrin-coated pit  clathrin-coated pit  protein complex assembly  receptor-mediated endocytosis  receptor-mediated endocytosis  axonogenesis  cell proliferation  negative regulation of gene expression  membrane  synaptic vesicle maturation  vesicle-mediated transport  endosomal transport  hemopoiesis  regulation of endocytosis  AP-2 adaptor complex  clathrin coat of coated pit  clathrin-coated vesicle  clathrin binding  clathrin binding  clathrin binding  receptor internalization  vesicle  clathrin heavy chain binding  regulation of protein localization  cargo loading into vesicle  clathrin adaptor activity  presynaptic membrane  neuronal cell body  intracellular membrane-bounded organelle  postsynaptic membrane  cadherin binding  positive regulation of transcription, DNA-templated  negative regulation of receptor-mediated endocytosis  clathrin coat assembly  perinuclear region of cytoplasm  dendrite morphogenesis  iron ion homeostasis  membrane organization  clathrin-dependent endocytosis  neurofibrillary tangle  iron ion import across plasma membrane  positive regulation of neuron death  positive regulation of beta-amyloid 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  
Pathways : BIOCARTAEndocytotic role of NDK, Phosphins and Dynamin [Genes]   
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
HOVERGENQ13492
HOGENOMQ13492
Homologs : HomoloGenePICALM
Homology/Alignments : Family Browser (UCSC)PICALM
Gene fusions - Rearrangements
Fusion : MitelmanARRB1/PICALM [11q13.4/11q14.2]  [t(11;11)(q13;q14)]  
Fusion : MitelmanMLLT10/PICALM [10p12.31/11q14.2]  [t(10;11)(p12;q14)]  
Fusion : MitelmanPICALM/CCDC81 [11q14.2/11q14.2]  [t(11;11)(q14;q14)]  
Fusion : MitelmanPICALM/MLLT10 [11q14.2/10p12.31]  [t(10;11)(p12;q14)]  [t(10;11)(p12;q23)]  
[t(10;19;11)(p12;p13;q14)]  [t(9;11)(p12;q14)]  
Fusion : MitelmanRCC1/PICALM [1p35.3/11q14.2]  [t(1;11)(p35;q14)]  
Fusion : MitelmanSYTL2/PICALM [11q14.1/11q14.2]  [t(11;11)(q14;q14)]  
Fusion : COSMICKMT2A [11q23.3]  -  PICALM [11q14.2]  [fusion_1966]  [fusion_1967]  
Fusion: TCGA_MDACCARRB1 11q13.4 PICALM 11q14.2 BRCA
Fusion: TCGA_MDACCMLLT10 10p12.31 PICALM 11q14.2 LAML
Fusion: TCGA_MDACCPICALM 11q14.2 MLLT10 10p12.31 LAML
Fusion: TCGA_MDACCPICALM 11q14.2 RP11-849H4.2 BRCA
Tumor Fusion PortalPICALM
Fusion : TICdbKMT2A [11q23.3]  -  PICALM [11q14.2]
Fusion : TICdbPICALM [11q14.2]  -  MLLT10 [10p12.31]
Fusion Cancer (Beijing)cytochrome_b [PICALM]  -  11q14.2 [FUSC002836]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPICALM [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PICALM
dbVarPICALM
ClinVarPICALM
1000_GenomesPICALM 
Exome Variant ServerPICALM
ExAC (Exome Aggregation Consortium)ENSG00000073921
GNOMAD BrowserENSG00000073921
Genetic variants : HAPMAP8301
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]  
Mutations and Diseases : HGMDPICALM
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 PICALM
DgiDB (Drug Gene Interaction Database)PICALM
DoCM (Curated mutations)PICALM (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PICALM (select a term)
intoGenPICALM
NCG5 (London)PICALM
Cancer3DPICALM(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603025   
Orphanet14434   
DisGeNETPICALM
MedgenPICALM
Genetic Testing Registry PICALM
NextProtQ13492 [Medical]
TSGene8301
GENETestsPICALM
Target ValidationPICALM
Huge Navigator PICALM [HugePedia]
snp3D : Map Gene to Disease8301
BioCentury BCIQPICALM
ClinGenPICALM
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8301
Chemical/Pharm GKB GenePA33287
Clinical trialPICALM
Miscellaneous
canSAR (ICR)PICALM (select the gene name)
Probes
Litterature
PubMed108 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePICALM
EVEXPICALM
GoPubMedPICALM
iHOPPICALM
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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