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NPM1 (nucleophosmin)

Identity

Other namesNPM
B23
Numatrin
NO38
HGNC NPM1
Location 5q35
Location_base_pair Starts at 170747403 and ends at 170766338 bp from pter ( according to hg18-Mar_2006).
 
  NPM1 (5q35) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics. Laboratories willing to validate the probes are welcome : contact rocchi@biologia.uniba.it

DNA/RNA

Description 11 exons on 25 kb;
Transcription in a centromeric --> telomeric orientation; transcription is cell-cycle regulated, reaching peaks at G1/S transition and being baseline at S/G2 1.6 kb mRNA

Protein

 
  DNA Diagram
Description 294 amino acids, 32.5 kDa; contains in C-term an oligomerization domain (residues 1-83), a metal binding site (residues 104-115) , 2 domains rich in acidic amino acids (residues 120- 132 and 161-188) , and 2 nuclear localisation signals in C-term; forms homo-hexameres; binds to single and double strand nucleic acids
Expression wide
Localisation nuclear, mainly in the nucleolus
Function RNA binding nucleolar phosphoprotein involved in preribosomal assembly; transport ribonucleoproteins between cellular compartments
Homology with nucleoplasmin

Implicated in

Entity Anaplasic large cell lymphoma (ALCL) with t(2;5)(p23;q35) --> NPM1-ALK
Disease ALCL are high grade non Hodgkin lymphomas; ALK+ ALCL are ALCL where ALK is involved in a fusion gene; ALK+ ALCL represent 50 to 60 % of ALCL cases (they are CD30+, ALK+;); 80% of ALK+ ALCL cases bear a t(2;5)
Prognosis nonetheless, a 80% five yr survival may be associated with this anomaly
Cytogenetics additional anomalies are most often found
Hybrid/Mutated Gene 5' NPM1-3' ALK on der(5)
Abnormal Protein 680 amino acids, 80 kDa; N-term 116 amino acids from NPM1 fused to the 563 C-term aminoacids of ALK (i.e. composed of the oligomerization domain and the metal binding site of NPM1 ,and the entire cytoplasmic portion of ALK); no apparent expression of the ALK/NPM1 counterpart; Characteristic localisation both in the cytoplasm and in the nucleus, due to heterooligomerization of NPM-ALK and normal NPM whereas the normal NPM protein is confined to the nucleus; constitutive activation of the catalytic domain of ALK.
Oncogenesis via the kinase function activated by oligomerization of NPM1-ALK mediated by the NPM1 part
  
Entity t(3;5)(q25;q34)/in myeloid malignancies --> NPM - MLF1
Disease Acute non lymphocytic leukemia (ANLL), myelodysplasia (MDS), chronic myelogenous leukemia in blast crisis (BC-CML); trilineage involvement
Prognosis very poor
Cytogenetics location of breakpoints difficult to ascertain
Hybrid/Mutated Gene 5' NPM-3' MLF1 on der(5)
Abnormal Protein with the 175 N term amino acids of NPM1; nuclear protein
  
Entity t(5;17)(q34;q21)/M3-ANLL --> NPM1-RARa
Disease promyelocytic ANLL (M3-ANLL)
Cytogenetics variant translocation of the well known t(15;17)
Hybrid/Mutated Gene 5' NPM1-3' RARa on der(5)
Abnormal Protein with the 117 N term amino acids of NPM1
  

Breakpoints

 
 
Note within the 4th intron in the cases of t(2;5) or t(5;17), within the 6th intron in case of t(3;5)

External links

Nomenclature
HGNCNPM1   7910
Entrez_GeneNPM1  4869  nucleophosmin (nucleolar phosphoprotein B23, numatrin)
Cards
AtlasNPM1
GeneCardsNPM1
EnsemblENSG00000181163 [Gene_View]  NPM1 [Vega]
GenatlasNPM1
Genomic and cartography
GoldenPathNPM1  -  5q35   chr5:170747403-170766338 +  5q35   [Description]    (hg18-Mar_2006)
EnsemblNPM1 - 5q35 [CytoView]
NCBIMapview
OMIM164040 Disease map [OMIM]
OMIM601626 Disease map [OMIM]
HomoloGeneNPM1
Gene and transcription
GenbankAB042278 [ ENTREZ ]
GenbankAI687394 [ ENTREZ ]
GenbankAK000472 [ ENTREZ ]
GenbankAK290652 [ ENTREZ ]
GenbankAY347529 [ ENTREZ ]
RefSeqNM_001037738 [ SRS ]    NM_001037738 [ ENTREZ ]
RefSeqNM_002520 [ SRS ]    NM_002520 [ ENTREZ ]
RefSeqNM_199185 [ SRS ]    NM_199185 [ ENTREZ ]
RefSeqAC_000048 [ SRS ]    AC_000048 [ ENTREZ ]
RefSeqAC_000137 [ SRS ]    AC_000137 [ ENTREZ ]
RefSeqNC_000005 [ SRS ]    NC_000005 [ ENTREZ ]
RefSeqNT_023133 [ SRS ]    NT_023133 [ ENTREZ ]
RefSeqNW_001838954 [ SRS ]    NW_001838954 [ ENTREZ ]
RefSeqNW_922784 [ SRS ]    NW_922784 [ ENTREZ ]
CCDSNPM1 CCDS - NCBI
AceViewNPM1 AceView - NCBI
UnigeneHs.557550 [ SRS ]    Hs.557550 [ NCBI ]
Fast-db13008 (alternative variants)
Protein : pattern, domain, 3D structure
SwissProtP06748 [ SRS]    P06748 [ EXPASY ]     P06748 [ INTERPRO ]     P06748 [ UNIPROT ] P06748 [ VarSplice FASTA ]
InterproIPR004301 Nucleoplasmin [ SRS ]    IPR004301 Nucleoplasmin [ EBI ]
CluSTrP06748
PfamPF03066 Nucleoplasmin [ SRS ]    PF03066 Nucleoplasmin [ Sanger ]    pfam03066 [ NCBI-CDD ]
BlocksP06748
PDB2P1B [ SRS ]    2P1B [ PdbSum ],   2P1B [ IMB ]   2P1B [ RSDB ]
HPRD01246
Protein Interaction databases
DIPP06748
IntActP06748
Polymorphism : SNP, mutations, diseases
OMIM164040    [ map ]   
OMIM601626    [ map ]   
GENETests164040
GENETests601626
SNPNPM1 [dbSNP-NCBI]  
SNPNM_001037738 [SNP-NCI]  
SNPNM_002520 [SNP-NCI]  
SNPNM_199185 [SNP-NCI]  
SNPNPM1 [GeneSNPs - Utah]  NPM1] [HGBASE - SRS]
HAPMAPNPM1 [HAPMAP]  
COSMICNPM1 [Somatic mutation (COSMIC-CGP-Sanger)]  
TICdbNPM1 [Translocation breakpoints In Cancer]  
HGMDNPM1
Genetic AssociationNPM1
CDC HuGENPM1
General knowledge
Family BrowserNPM1 [UCSC Family Browser]
SOURCENM_001037738
SOURCENM_002520
SOURCENM_199185
SMDHs.557550
SAGEHs.557550
GOnucleic acid binding [Amigo]  nucleic acid binding
GOtranscription coactivator activity [Amigo]  transcription coactivator activity
GORNA binding [Amigo]  RNA binding
GOnucleus [Amigo]  nucleus
GOnucleus [Amigo]  nucleus
GOnucleus [Amigo]  nucleus
GOnucleolus [Amigo]  nucleolus
GOcytoplasm [Amigo]  cytoplasm
GOcytoplasm [Amigo]  cytoplasm
GOcytoplasm [Amigo]  cytoplasm
GOcentrosome [Amigo]  centrosome
GOcentrosome [Amigo]  centrosome
GOintracellular protein transport [Amigo]  intracellular protein transport
GOnucleocytoplasmic transport [Amigo]  nucleocytoplasmic transport
GOanti-apoptosis [Amigo]  anti-apoptosis
GOresponse to stress [Amigo]  response to stress
GOcentrosome cycle [Amigo]  centrosome cycle
GOcentrosome cycle [Amigo]  centrosome cycle
GOsignal transduction [Amigo]  signal transduction
GOcell aging [Amigo]  cell aging
GOcell aging [Amigo]  cell aging
GOnegative regulation of cell proliferation [Amigo]  negative regulation of cell proliferation
GOnegative regulation of cell proliferation [Amigo]  negative regulation of cell proliferation
GOTat protein binding [Amigo]  Tat protein binding
GOribosome assembly [Amigo]  ribosome assembly
GOprotein homodimerization activity [Amigo]  protein homodimerization activity
GOprotein heterodimerization activity [Amigo]  protein heterodimerization activity
GONF-kappaB binding [Amigo]  NF-kappaB binding
GONF-kappaB binding [Amigo]  NF-kappaB binding
GOunfolded protein binding [Amigo]  unfolded protein binding
GOunfolded protein binding [Amigo]  unfolded protein binding
GOpositive regulation of NF-kappaB transcription factor activity [Amigo]  positive regulation of NF-kappaB transcription factor activity
PubGeneNPM1
TreeFamNPM1
CTD4869 [Comparative ToxicoGenomics Database]
Other databases
Probes
ProbeCancer Cytogenetics (Bari)
ProbeNPM1 Related clones (RZPD - Berlin)
PubMed
PubMed178 Pubmed reference(s) in Entrez

Bibliography

Fusion of a kinase gene, ALK, to a nucleolar protein gene, NPM, in non-Hodgkin's lymphoma.
Morris SW, Kirstein MN, Valentine MB, Dittmer KG, Shapiro DN, Saltman DL, Look AT
Science (New York, N.Y.). 1994 ; 263 (5151) : 1281-1284.
PMID 8122112
 
The t(3;5)(q25.1;q34) of myelodysplastic syndrome and acute myeloid leukemia produces a novel fusion gene, NPM-MLF1.
Yoneda-Kato N, Look AT, Kirstein MN, Valentine MB, Raimondi SC, Cohen KJ, Carroll AJ, Morris SW
Oncogene. 1996 ; 12 (2) : 265-275.
PMID 8570204
 
The t(5;17) variant of acute promyelocytic leukemia expresses a nucleophosmin-retinoic acid receptor fusion.
Redner RL, Rush EA, Faas S, Rudert WA, Corey SJ
Blood. 1996 ; 87 (3) : 882-886.
PMID 8562957
 
The t(5;17) variant of acute promyelocytic leukemia expresses a nucleophosmin-retinoic acid receptor fusion.
Redner RL, Rush EA, Faas S, Rudert WA, Corey SJ
Blood. 1996 ; 87 (3) : 882-886.
PMID 8562957
 
Isolation and characterization of the human nucleophosmin/B23 (NPM) gene: identification of the YY1 binding site at the 5' enhancer region.
Chan PK, Chan FY, Morris SW, Xie Z
Nucleic acids research. 1997 ; 25 (6) : 1225-1232.
PMID 9092633
 
Role of the nucleophosmin (NPM) portion of the non-Hodgkin's lymphoma-associated NPM-anaplastic lymphoma kinase fusion protein in oncogenesis.
Bischof D, Pulford K, Mason DY, Morris SW
Molecular and cellular biology. 1997 ; 17 (4) : 2312-2325.
PMID 9121481
 
CD30(+) anaplastic large cell lymphoma: a review of its histopathologic, genetic, and clinical features.
Stein H, Foss HD, Dˆºrkop H, Marafioti T, Delsol G, Pulford K, Pileri S, Falini B
Blood. 2000 ; 96 (12) : 3681-3695.
PMID 11090048
 
Pathobiology of NPM-ALK and variant fusion genes in anaplastic large cell lymphoma and other lymphomas.
Drexler HG, Gignac SM, von Wasielewski R, Werner M, Dirks WG
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 2000 ; 14 (9) : 1533-1559.
PMID 10994999
 
Anaplastic large cell lymphomas, Primary systemic (T/Null cell type).
Delsol G, Ralfkiaer E, Stein H, Wright D, Jaffe E
World Health Organization (WHO) Classification of Tumors..
 
Alk+ CD30+ lymphomas: a distinct molecular genetic subtype of non-Hodgkin's lymphoma.
Morris SW, Xue L, Ma Z, Kinney MC
British journal of haematology. 2001 ; 113 (2) : 275-295.
PMID 11380391
 
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written12-1997Jean-Loup Huret
Updated08-2001Jean-Loup Huret

Citation

This paper should be referenced as such :
Huret JL . NPM1 (nucleophosmin). Atlas Genet Cytogenet Oncol Haematol. December 1997 .
URL : http://AtlasGeneticsOncology.org/Genes/NPM1.html
Huret JL . NPM1 (nucleophosmin). Atlas Genet Cytogenet Oncol Haematol. August 2001 .
URL : http://AtlasGeneticsOncology.org/Genes/NPM1.html

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Dec 6 17:57:55 2008


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