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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
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-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  membrane organization  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-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  membrane organization  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 : 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
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 : 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
DataMed IndexPICALM
Probes
Litterature
PubMed163 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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