CALM (clathrin assembly lymphoid myeloid leukemia gene)

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CALM (clathrin assembly lymphoid myeloid leukemia gene)

Identity

HGNC (Hugo)	PICALM
LocusID (NCBI)	8301
Location	11q14-21
Location_base_pair	Starts at 85668214 and ends at 85780139 bp from pter ( according to hg19-Feb_2009) [Mapping]


	Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics

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 ap-3, a clathrin assembly protein (mouse)

Implicated in


Entity	t(10;11)(p13;q14-21) --> CALM-AF10 and/or AF10-CALM
Disease	yet to be well delineated; T-cell ALL
Prognosis	uncertain (median survival 2 yrs?)
Cytogenetics	may well be confused with the t(10;11)(p12;q23), where MLL on 11q23 is involved, instead of CALM
Hybrid/Mutated Gene	5' CALM - 3' AF10 and 5' AF10 - 3' CALM
Abnormal Protein	both CALM-AF10 and the reciprocal AF10-CALM are expressed

Breakpoints

External links

	Nomenclature
HGNC (Hugo)	PICALM 15514
Entrez_Gene (NCBI)	PICALM 8301 phosphatidylinositol binding clathrin assembly protein
	Cards
Atlas	CALM
GeneCards (Weizmann)	PICALM
Ensembl (Hinxton)	ENSG00000073921 [Gene_View] chr11:85668214-85780139 [Contig_View] PICALM [Vega]
AceView (NCBI)	PICALM
Genatlas (Paris)	PICALM
euGene (Indiana)	8301
SOURCE (Stanford)	NM_001008660 NM_001206946 NM_001206947 NM_007166
	Genomic and cartography
GoldenPath (UCSC)	PICALM - chr11:85668214-85780139 - 11q14 [Description] (hg19-Feb_2009)
Ensembl	PICALM - 11q14 [CytoView]
Mapping of homologs : NCBI	PICALM [Mapview]
OMIM	601626 603025
	Gene and transcription
Genbank (Entrez)	AB210017 AB451308 AF060939 AF060940 AK128786
RefSeq transcript (SRS)	NM_001008660 NM_001206946 NM_001206947 NM_007166
RefSeq transcript (Entrez)	NM_001008660 NM_001206946 NM_001206947 NM_007166
RefSeq genomic (SRS)	AC_000143 NC_000011 NG_028942 NT_167190 NW_001838028
RefSeq genomic (Entrez)	AC_000143 NC_000011 NG_028942 NT_167190 NW_001838028
Consensus coding sequences : CCDS (NCBI)	PICALM
Cluster EST : Unigene	Hs.163893 [ SRS ] Hs.163893 [ NCBI ]
Alternative Splicing : Fast-db (Paris)	12520
Alternative Splicing Gallery	ENSG00000073921
Gene Expression	PICALM [ NCBI-GEO ] PICALM [ EBI - ARRAY_EXPRESS ]
	Protein : pattern, domain, 3D structure
UniProt/SwissProt	Q13492 (SRS) Q13492 (Uniprot)
With graphics : InterPro	Q13492
Splice isoforms : SwissVar	Q13492(Swissvar)
Domaine pattern : Prosite (SRS)	ENTH (PS50942)
Domaine pattern : Prosite (Expaxy)	ENTH (PS50942)
Domains : Interpro (SRS)	ANTH Clathrin_Pinositid-bd_GAT-like ENTH_VHS Epsin-like_N
Domains : Interpro (EBI)	ANTH Clathrin_Pinositid-bd_GAT-like ENTH_VHS Epsin-like_N
Related proteins : CluSTr	Q13492
Domain families : Pfam (SRS)	ANTH (PF07651)
Domain families : Pfam (Sanger)	ANTH (PF07651)
Domain families : Pfam (NCBI)	pfam07651
Domain families : Smart (EMBL)	ENTH (SM00273)
Blocks (Seattle)	Q13492
Human Protein Atlas	ENSG00000073921
HPRD	04320
IPI	IPI00290738 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
FunCoup	ENSG00000073921
REACTOME	PICALM
BioGRID	PICALM
InParanoid	Q13492
Interologous Interaction database	Q13492
	Polymorphism : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)	PICALM
SNP (GeneSNP Utah)	PICALM
SNP : HGBase	PICALM
Genetic variants : HAPMAP	PICALM
Cancer Gene: Census	PICALM
Somatic Mutations in Cancer : COSMIC	PICALM
CONAN: Copy Number Analysis	PICALM
Mutations and Diseases : HGMD	PICALM
OMIM	601626 603025
GENETests	601626 603025
Disease Genetic Association	PICALM
Huge Navigator	PICALM [HugePedia] PICALM [HugeCancerGEM]
Genomic Variants	PICALM
snp3D : Map Gene to Disease	8301
	General knowledge
Homologs : HomoloGene	PICALM
Homology/Alignments : Family Browser (UCSC)	PICALM
Phylogenetic Trees/Animal Genes : TreeFam	PICALM
Chemical/Protein Interactions : CTD	8301
Chemical/Pharm GKB Gene	PA33287
Clinical trial	PICALM
Cancer Resource (Charite)	ENSG00000073921
Ontology : AmiGO	protein binding phospholipid binding 1-phosphatidylinositol binding intracellular nucleus Golgi apparatus coated pit protein complex assembly receptor-mediated endocytosis axonogenesis membrane vesicle-mediated transport endosome transport hemopoiesis regulation of endocytosis AP-2 adaptor complex clathrin coat of coated pit clathrin-coated vesicle clathrin binding cytoplasmic vesicle receptor internalization clathrin heavy chain binding regulation of protein localization presynaptic membrane intracellular membrane-bounded organelle postsynaptic membrane positive regulation of transcription, DNA-dependent negative regulation of receptor-mediated endocytosis clathrin coat assembly perinuclear region of cytoplasm dendrite morphogenesis
Ontology : EGO-EBI	protein binding phospholipid binding 1-phosphatidylinositol binding intracellular nucleus Golgi apparatus coated pit protein complex assembly receptor-mediated endocytosis axonogenesis membrane vesicle-mediated transport endosome transport hemopoiesis regulation of endocytosis AP-2 adaptor complex clathrin coat of coated pit clathrin-coated vesicle clathrin binding cytoplasmic vesicle receptor internalization clathrin heavy chain binding regulation of protein localization presynaptic membrane intracellular membrane-bounded organelle postsynaptic membrane positive regulation of transcription, DNA-dependent negative regulation of receptor-mediated endocytosis clathrin coat assembly perinuclear region of cytoplasm dendrite morphogenesis
Pathways : BIOCARTA	Endocytotic role of NDK, Phosphins and Dynamin [Genes]
	Other databases
	Probes
Probes : Imagenes	PICALM Related clones (RZPD - Berlin)
	Litterature
PubMed	52 Pubmed reference(s) in Entrez
PubGene	PICALM
iHOP	PICALM

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

REVIEW articles	automatic search in PubMed
Last year publications	automatic search in PubMed

Search in all EBI NCBI

Contributor(s)

Written	01-1998	Jean-Loup Huret

Citation
This paper should be referenced as such :
Huret JL . CALM (clathrin assembly lymphoid myeloid leukemia gene). Atlas Genet Cytogenet Oncol Haematol. January 1998 .
URL : http://AtlasGeneticsOncology.org/Genes/CALM.html

This paper is referenced by INIST as such :
http://documents.irevues.inist.fr/bitstream/handle/2042/32088/01-1998-CALM.pdf [ Bibliographic record ]

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Apr 28 15:11:15 CEST 2012

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