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LCP1 (lymphocyte cytosolic protein1)

Written1998-03Sylvie Galiègue-Zouitina
U.124 INSERM, I.R.C.L., Place de Verdun, 59045 LILLE Cedex, France

(Note : for Links provided by Atlas : click)

Identity

Other namesL-Plastine
HGNC (Hugo) LCP1
LocusID (NCBI) 3936
Atlas_Id 95
Location 13q14.13  [Link to chromosome band 13q14]
Location_base_pair Starts at 46700058 and ends at 46756459 bp from pter ( according to hg19-Feb_2009)  [Mapping LCP1.png]
Fusion genes
(updated 2016)
AP3D1 (19p13.3) / LCP1 (13q14.13)BCL6 (3q27.3) / LCP1 (13q14.13)GNB1 (1p36.33) / LCP1 (13q14.13)
LCP1 (13q14.13) / BCL6 (3q27.3)LCP1 (13q14.13) / LCP1 (13q14.13)LCP1 (13q14.13) / SLC43A1 (11q12.1)
LCP1 (13q14.13) / SLC4A10 (2q24.2)SH3KBP1 (Xp22.12) / LCP1 (13q14.13)

DNA/RNA

Description spans on a 90 kb genomic fragment; 16 exons, large first intron (20kb)
Transcription 3.7 kb mRNA; coding sequence from exon 2 to exon 16: 3500 bp

Protein

Description 570 amino acids
Expression restricted to the hematopoietic cells (leukocytes); expression induced in all tumor cells of all tissues
Localisation membrane
Homology belongs to an actin-binding protein family (T-Plastin, Fimbrin, I-Plastin)

Implicated in

Note
Entity t(3;13)(q27;q14)/ NHL --> LCP1 - BCL6
Disease non Hodgkin follicular as well as Burkitt lymphomas
Cytogenetics t(3;13) is observed as a secondary anomaly
Hybrid/Mutated Gene both 5' L-Plastin- 3' BCL6 and 5' BCL6 - 3' L-Plastin, leading to two fusion transcripts
Abnormal Protein no fusion protein, but promoter exchange between both partner genes
  

Bibliography

Cytogenetics in multiple myeloma: a multicenter study of 24 patients with t(11;14)(q13;q32) or its variant.
Laï JL, Michaux L, Dastugue N, Vasseur F, Daudignon A, Facon T, Bauters F, Zandecki M
Cancer genetics and cytogenetics. 1998 ; 104 (2) : 133-138.
PMID 9666807
 
Molecular cloning and characterization of plastin, a human leukocyte protein expressed in transformed human fibroblasts.
Lin CS, Aebersold RH, Kent SB, Varma M, Leavitt J
Molecular and cellular biology. 1988 ; 8 (11) : 4659-4668.
PMID 3211125
 
Human plastin genes. Comparative gene structure, chromosome location, and differential expression in normal and neoplastic cells.
Lin CS, Park T, Chen ZP, Leavitt J
The Journal of biological chemistry. 1993 ; 268 (4) : 2781-2792.
PMID 8428952
 
Activation of the leukocyte plastin gene occurs in most human cancer cells.
Park T, Chen ZP, Leavitt J
Cancer research. 1994 ; 54 (7) : 1775-1781.
PMID 8137292
 
Interaction of a Dictyostelium member of the plastin/fimbrin family with actin filaments and actin-myosin complexes.
Prassler J, Stocker S, Marriott G, Heidecker M, Kellermann J, Gerisch G
Molecular biology of the cell. 1997 ; 8 (1) : 83-95.
PMID 9017597
 

Citation

This paper should be referenced as such :
Gali&ögue-Zouitina, S
LCP1 (lymphocyte cytosolic protein1)
Atlas Genet Cytogenet Oncol Haematol. 1998;2(2):36-36.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/LCP1ID95.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
  3q27 rearrangements (BCL6) in non Hodgkin lymphoma;t(3;Var)(q27;Var) in non Hodgkin lymphoma
t(3;13)(q27;q14) LCP1/BCL6
t(3;14)(q27;q32) IGH/BCL6;t(2;3)(p12;q27) IGK/BCL6;t(3;22)(q27;q11) IGL/BCL6

External links

Nomenclature
HGNC (Hugo)LCP1   6528
Cards
AtlasLCP1ID95
Entrez_Gene (NCBI)LCP1  3936  lymphocyte cytosolic protein 1
AliasesCP64; HEL-S-37; L-PLASTIN; LC64P; 
LPL; PLS2
GeneCards (Weizmann)LCP1
Ensembl hg19 (Hinxton)ENSG00000136167 [Gene_View]  chr13:46700058-46756459 [Contig_View]  LCP1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000136167 [Gene_View]  chr13:46700058-46756459 [Contig_View]  LCP1 [Vega]
ICGC DataPortalENSG00000136167
TCGA cBioPortalLCP1
AceView (NCBI)LCP1
Genatlas (Paris)LCP1
WikiGenes3936
SOURCE (Princeton)LCP1
Genomic and cartography
GoldenPath hg19 (UCSC)LCP1  -     chr13:46700058-46756459 -  13q14.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)LCP1  -     13q14.3   [Description]    (hg38-Dec_2013)
EnsemblLCP1 - 13q14.3 [CytoView hg19]  LCP1 - 13q14.3 [CytoView hg38]
Mapping of homologs : NCBILCP1 [Mapview hg19]  LCP1 [Mapview hg38]
OMIM153430   
Gene and transcription
Genbank (Entrez)AB208984 AK058152 AK093568 AK097174 AK097275
RefSeq transcript (Entrez)NM_002298
RefSeq genomic (Entrez)NC_000013 NC_018924 NT_024524 NW_004929388
Consensus coding sequences : CCDS (NCBI)LCP1
Cluster EST : UnigeneHs.658408 [ NCBI ]
CGAP (NCI)Hs.658408
Alternative Splicing GalleryENSG00000136167
Gene ExpressionLCP1 [ NCBI-GEO ]   LCP1 [ EBI - ARRAY_EXPRESS ]   LCP1 [ SEEK ]   LCP1 [ MEM ]
Gene Expression Viewer (FireBrowse)LCP1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3936
GTEX Portal (Tissue expression)LCP1
Protein : pattern, domain, 3D structure
UniProt/SwissProtP13796 (Uniprot)
NextProtP13796  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP13796
Splice isoforms : SwissVarP13796 (Swissvar)
PhosPhoSitePlusP13796
Domaine pattern : Prosite (Expaxy)ACTININ_1 (PS00019)    ACTININ_2 (PS00020)    CH (PS50021)    EF_HAND_1 (PS00018)    EF_HAND_2 (PS50222)   
Domains : Interpro (EBI)Actinin_actin-bd_CS    CH-domain    EF-hand-dom_pair    EF_Hand_1_Ca_BS    EF_hand_dom   
Domain families : Pfam (Sanger)CH (PF00307)    EF-hand_7 (PF13499)   
Domain families : Pfam (NCBI)pfam00307    pfam13499   
Domain families : Smart (EMBL)CH (SM00033)  EFh (SM00054)  
DMDM Disease mutations3936
Blocks (Seattle)LCP1
PDB (SRS)2D85   
PDB (PDBSum)2D85   
PDB (IMB)2D85   
PDB (RSDB)2D85   
Structural Biology KnowledgeBase2D85   
SCOP (Structural Classification of Proteins)2D85   
CATH (Classification of proteins structures)2D85   
SuperfamilyP13796
Human Protein AtlasENSG00000136167
Peptide AtlasP13796
HPRD01082
IPIIPI00010471   IPI00909658   IPI00921552   IPI00646259   IPI00643270   
Protein Interaction databases
DIP (DOE-UCLA)P13796
IntAct (EBI)P13796
FunCoupENSG00000136167
BioGRIDLCP1
STRING (EMBL)LCP1
ZODIACLCP1
Ontologies - Pathways
QuickGOP13796
Ontology : AmiGOstress fiber  ruffle  phagocytic cup  podosome  T cell activation involved in immune response  actin binding  calcium ion binding  extracellular space  cytoplasm  cytoplasm  cytosol  actin filament  plasma membrane  focal adhesion  protein kinase A signaling  actin cytoskeleton  cell migration  extracellular matrix disassembly  filopodium  organ regeneration  actin filament bundle  ruffle membrane  regulation of intracellular protein transport  identical protein binding  wound healing, spreading of cells  actin filament binding  actin filament bundle assembly  GTPase binding  extracellular exosome  positive regulation of podosome assembly  
Ontology : EGO-EBIstress fiber  ruffle  phagocytic cup  podosome  T cell activation involved in immune response  actin binding  calcium ion binding  extracellular space  cytoplasm  cytoplasm  cytosol  actin filament  plasma membrane  focal adhesion  protein kinase A signaling  actin cytoskeleton  cell migration  extracellular matrix disassembly  filopodium  organ regeneration  actin filament bundle  ruffle membrane  regulation of intracellular protein transport  identical protein binding  wound healing, spreading of cells  actin filament binding  actin filament bundle assembly  GTPase binding  extracellular exosome  positive regulation of podosome assembly  
NDEx NetworkLCP1
Atlas of Cancer Signalling NetworkLCP1
Wikipedia pathwaysLCP1
Orthology - Evolution
OrthoDB3936
GeneTree (enSembl)ENSG00000136167
Phylogenetic Trees/Animal Genes : TreeFamLCP1
Homologs : HomoloGeneLCP1
Homology/Alignments : Family Browser (UCSC)LCP1
Gene fusions - Rearrangements
Fusion : MitelmanBCL6/LCP1 [3q27.3/13q14.13]  [t(3;13)(q27;q14)]  
Fusion : MitelmanLCP1/BCL6 [13q14.13/3q27.3]  [t(3;13)(q27;q14)]  
Fusion : TICdbLCP1 [13q14.13]  -  BCL6 [3q27.3]
Polymorphisms : SNP, variants
NCBI Variation ViewerLCP1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LCP1
dbVarLCP1
ClinVarLCP1
1000_GenomesLCP1 
Exome Variant ServerLCP1
ExAC (Exome Aggregation Consortium)LCP1 (select the gene name)
Genetic variants : HAPMAP3936
Genomic Variants (DGV)LCP1 [DGVbeta]
Mutations
ICGC Data PortalLCP1 
TCGA Data PortalLCP1 
Broad Tumor PortalLCP1
OASIS PortalLCP1 [ Somatic mutations - Copy number]
Cancer Gene: CensusLCP1 
Somatic Mutations in Cancer : COSMICLCP1 
intOGen PortalLCP1
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 LCP1
DgiDB (Drug Gene Interaction Database)LCP1
DoCM (Curated mutations)LCP1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LCP1 (select a term)
intoGenLCP1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)13:46700058-46756459  ENSG00000136167
CONAN: Copy Number AnalysisLCP1 
Mutations and Diseases : HGMDLCP1
OMIM153430   
MedgenLCP1
Genetic Testing Registry LCP1
NextProtP13796 [Medical]
TSGene3936
GENETestsLCP1
Huge Navigator LCP1 [HugePedia]
snp3D : Map Gene to Disease3936
BioCentury BCIQLCP1
ClinGenLCP1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3936
Chemical/Pharm GKB GenePA30312
Clinical trialLCP1
Miscellaneous
canSAR (ICR)LCP1 (select the gene name)
Probes
Litterature
PubMed72 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLCP1
EVEXLCP1
GoPubMedLCP1
iHOPLCP1
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 : Wed Sep 28 15:55:49 CEST 2016

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