Atlas of Genetics and Cytogenetics in Oncology and Haematology

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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
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SETBP1 (SET binding protein 1)


Other namesSEB
LocusID (NCBI) 26040
Location 18q12.3
Location_base_pair Starts at 42260138 and ends at 42457379 bp from pter ( according to hg19-Feb_2009)  [Mapping]
Local_order From centromere to telomere: SETBP1, SMAD2, SMAD4, BCL2.


Description SETBP1 has two isoforms: transcript variant a spans 387,61 kb on the genomic DNA and has 6 exons; transcript variant b spans 197,24 kb on the genomic DNA and includes 4 exons.
Transcription 9899 bp mRNA (isoform a); 1804 bp mRNA (isoform b).


Description Two isoforms: variant a (1596 amino acids); variant b (242 amino acids).
Expression Expressed in numerous tissues.
Localisation Predominantly in the nucleus (Minakuchi et al., 2001; Cristóbal et al., 2010).
Function SETBP1 overexpression promotes leukemogenesis by enhancing full-length SET protein and then impairing the phosphatase activity of the tumor suppressor PP2A in acute myeloid leukaemia. In addition, defects in SETBP1 have been described as the cause of Schinzel-Giedion syndrome.
Homology The protein contains a region homologous to the dimerization domain of the SKI oncoprotein, six PEST sequences, three AT-hook DNA binding domains, a SET-binding domain and three nuclear localization signals.


Somatic De novo mutations have been decribed in patients with Schinzel-Giedion syndrome: I871T (5 unrelated patients), D868N (4 unrelated patients), D868A (one case), G870D (one case) and G870S (three unrelated patients) (Hoischen et al., 2010; Suphapeetiporn et al., 2011).

Implicated in

Entity Pediatric T-cell acute lymphoblastic leukemia (T-ALL) (Panagopoulos et al., 2007)
Cytogenetics t(11;18)(p15;q12); only one case decribed so far.
Hybrid/Mutated Gene 5' NUP98 - 3' SETBP1
Abnormal Protein The NUP98-SETBP1 fusion protein consists in the exon 12 of NUP98 fused in-frame with exon 5 of SETBP1.
Oncogenesis SETBP1/NUP98 expression was not detected, suggesting that the NUP98/SETBP1 transcript is pathogenetically important.
Entity Schinzel-Giedion syndrome
Prognosis Defects in SETBP1 caused by the presence of the novo mutations have been described as the cause of Schinzel-Giedion midface retraction syndrome.
Cytogenetics Normal karyotype.
Entity Acute myeloid leukemia (AML)
Prognosis SETBP1 overexpression associates with worse overall survival specially in the subgroup of elderly patients (older than 60 years).
Cytogenetics The presence of a t(12;18)(p13;q12) has been describe in one case with AML secondary to myelodysplastic syndrome (figure 1) (Cristóbal et al., 2010), and in one case with AML secondary to primary myelofibrosis (Albano et al., 2012).
Figure 1.
Oncogenesis SETBP1 overexpression promotes leukemogenesis by enhancing full-length SET protein and then impairing the phosphatase activity of the tumor suppressor PP2A through the formation of a SETBP1-SET-PP2A complex.

Other Leukemias implicated (Data extracted from papers in the Atlas)

Leukemias 11q23ChildAMLID1615 11q23ID1030 11q23secondLeukID1131

External links

HGNC (Hugo)SETBP1   15573
Entrez_Gene (NCBI)SETBP1  26040  SET binding protein 1
GeneCards (Weizmann)SETBP1
Ensembl hg19 (Hinxton)ENSG00000152217 [Gene_View]  chr18:42260138-42457379 [Contig_View]  SETBP1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000152217 [Gene_View]  chr18:42260138-42457379 [Contig_View]  SETBP1 [Vega]
ICGC DataPortalENSG00000152217
Genatlas (Paris)SETBP1
SOURCE (Princeton)SETBP1
Genomic and cartography
GoldenPath hg19 (UCSC)SETBP1  -     chr18:42260138-42457379 +  18q21.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SETBP1  -     18q21.1   [Description]    (hg38-Dec_2013)
EnsemblSETBP1 - 18q21.1 [CytoView hg19]  SETBP1 - 18q21.1 [CytoView hg38]
Mapping of homologs : NCBISETBP1 [Mapview hg19]  SETBP1 [Mapview hg38]
OMIM269150   611060   616078   
Gene and transcription
Genbank (Entrez)AB007897 AB022660 AK123972 AL832945 BC062338
RefSeq transcript (Entrez)NM_001130110 NM_015559
RefSeq genomic (Entrez)NC_000018 NC_018929 NG_027527 NT_010966 NW_004929410
Consensus coding sequences : CCDS (NCBI)SETBP1
Cluster EST : UnigeneHs.435458 [ NCBI ]
CGAP (NCI)Hs.435458
Alternative Splicing : Fast-db (Paris)GSHG0014019
Alternative Splicing GalleryENSG00000152217
Gene ExpressionSETBP1 [ NCBI-GEO ]     SETBP1 [ SEEK ]   SETBP1 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9Y6X0 (Uniprot)
NextProtQ9Y6X0  [Medical]
With graphics : InterProQ9Y6X0
Splice isoforms : SwissVarQ9Y6X0 (Swissvar)
Domains : Interpro (EBI)AT_hook_DNA-bd_motif   
Related proteins : CluSTrQ9Y6X0
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Domain families : Smart (EMBL)AT_hook (SM00384)  
DMDM Disease mutations26040
Blocks (Seattle)Q9Y6X0
Human Protein AtlasENSG00000152217
Peptide AtlasQ9Y6X0
IPIIPI00159049   IPI00441195   IPI01021397   
Protein Interaction databases
IntAct (EBI)Q9Y6X0
Ontologies - Pathways
Ontology : AmiGODNA binding  protein binding  nucleus  
Ontology : EGO-EBIDNA binding  protein binding  nucleus  
Protein Interaction DatabaseSETBP1
DoCM (Curated mutations)SETBP1
Wikipedia pathwaysSETBP1
Gene fusion - rearrangements
Rearrangement : TICdbNUP98 [11p15.4]  -  SETBP1 [3p25.2]
Polymorphisms : SNP, variants
NCBI Variation ViewerSETBP1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SETBP1
Exome Variant ServerSETBP1
Genetic variants : HAPMAPSETBP1
Genomic Variants (DGV)SETBP1 [DGVbeta]
ICGC Data PortalENSG00000152217 
Somatic Mutations in Cancer : COSMICSETBP1 
CONAN: Copy Number AnalysisSETBP1 
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
LOVD (Leiden Open Variation Database)Mendelian genes
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
DECIPHER (Syndromes)18:42260138-42457379
Mutations and Diseases : HGMDSETBP1
OMIM269150    611060    616078   
NextProtQ9Y6X0 [Medical]
Disease Genetic AssociationSETBP1
Huge Navigator SETBP1 [HugePedia]  SETBP1 [HugeCancerGEM]
snp3D : Map Gene to Disease26040
DGIdb (Drug Gene Interaction db)SETBP1
General knowledge
Homologs : HomoloGeneSETBP1
Homology/Alignments : Family Browser (UCSC)SETBP1
Phylogenetic Trees/Animal Genes : TreeFamSETBP1
Chemical/Protein Interactions : CTD26040
Chemical/Pharm GKB GenePA37982
Clinical trialSETBP1
Cancer Resource (Charite)ENSG00000152217
Other databases
PubMed35 Pubmed reference(s) in Entrez


Identification and characterization of SEB, a novel protein that binds to the acute undifferentiated leukemia-associated protein SET.
Minakuchi M, Kakazu N, Gorrin-Rivas MJ, Abe T, Copeland TD, Ueda K, Adachi Y.
Eur J Biochem. 2001 Mar;268(5):1340-51.
PMID 11231286
Fusion of NUP98 and the SET binding protein 1 (SETBP1) gene in a paediatric acute T cell lymphoblastic leukaemia with t(11;18)(p15;q12).
Panagopoulos I, Kerndrup G, Carlsen N, Strombeck B, Isaksson M, Johansson B.
Br J Haematol. 2007 Jan;136(2):294-6.
PMID 17233820
SETBP1 overexpression is a novel leukemogenic mechanism that predicts adverse outcome in elderly patients with acute myeloid leukemia.
Cristobal I, Blanco FJ, Garcia-Orti L, Marcotegui N, Vicente C, Rifon J, Novo FJ, Bandres E, Calasanz MJ, Bernabeu C, Odero MD.
Blood. 2010 Jan 21;115(3):615-25. Epub 2009 Nov 16.
PMID 19965692
De novo mutations of SETBP1 cause Schinzel-Giedion syndrome.
Hoischen A, van Bon BW, Gilissen C, Arts P, van Lier B, Steehouwer M, de Vries P, de Reuver R, Wieskamp N, Mortier G, Devriendt K, Amorim MZ, Revencu N, Kidd A, Barbosa M, Turner A, Smith J, Oley C, Henderson A, Hayes IM, Thompson EM, Brunner HG, de Vries BB, Veltman JA.
Nat Genet. 2010 Jun;42(6):483-5. Epub 2010 May 2.
PMID 20436468
SETBP1 mutations in two Thai patients with Schinzel-Giedion syndrome.
Suphapeetiporn K, Srichomthong C, Shotelersuk V.
Clin Genet. 2011 Apr;79(4):391-3. doi: 10.1111/j.1399-0004.2010.01552.x.
PMID 21371013
SETBP1 and miR_4319 dysregulation in primary myelofibrosis progression to acute myeloid leukemia.
Albano F, Anelli L, Zagaria A, Coccaro N, Casieri P, Minervini A, Specchia G.
J Hematol Oncol. 2012 Aug 8;5:48. doi: 10.1186/1756-8722-5-48.
PMID 22873195
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Written09-2012Ion Cristóbal, Laura García-Orti, María D Odero
Translational Oncology Division, Health Research Institute and Oncology Department, University Hospital "Fundacion Jimenez Diaz", Autonomous University of Madrid, E-28040 Madrid, Spain (IC); Division of Oncology, Center for Applied Medical Research (CIMA), University of Navarra, E-31008 Pamplona, Spain (LGO, MDO); Department of Genetics, School of Sciences, University of Navarra E-31008 Pamplona, Spain (MDO)


This paper should be referenced as such :
Cristòbal, I ; Garcia-Orti, L ; Odero, MD
SETBP1 (SET binding protein 1)
Atlas Genet Cytogenet Oncol Haematol. 2013;17(3):159-160.
Free journal version : [ pdf ]   [ DOI ]

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indexed on : Sat Mar 28 12:15:11 CET 2015

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