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SETBP1 (SET binding protein 1)

Written2012-09Ion Cristóbal, Laura García-Orti, María D Odero
Translational Oncology Division, Health Research Institute, 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)

(Note : for Links provided by Atlas : click)


HGNC Alias symbSEB
LocusID (NCBI) 26040
Atlas_Id 44031
Location 18q12.3  [Link to chromosome band 18q12]
Location_base_pair Starts at 44680888 and ends at 45068510 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping SETBP1.png]
Local_order From centromere to telomere: SETBP1, SMAD2, SMAD4, BCL2.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
HMGA2 (12q14.3) / SETBP1 (18q12.3)NUP98 (11p15.4) / SETBP1 (18q12.3)RNF165 (18q21.1) / SETBP1 (18q12.3)
SETBP1 (18q12.3) / FANCI (15q26.1)SETBP1 (18q12.3) / HNRNPM (19p13.2)SETBP1 (18q12.3) / NUP98 (11p15.4)
SETBP1 (18q12.3) / SMCO4 (11q21)SNRPE (1q32.1) / SETBP1 (18q12.3)


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.


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
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
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 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


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 ]

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 7 ]
  Chronic Eosinophilic Leukemia-Not Otherwise Specified (CEL-NOS)::Idiopathic Hypereosinophilic Syndrome (IHES)
Chronic Myelomonocytic Leukemia (CMML)
Juvenile myelomonocytic leukemia (JMML)
Myelodysplastic/myeloproliferative neoplasms
t(11;18)(p15;q12) NUP98/SETBP1
t(12;18)(p13;q12) ETV6/SETBP1
T-lineage acute lymphoblastic leukemia (T-ALL)

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(12;18)(q14;q12) HMGA2/SETBP1
t(18;18)(q12;q21) RNF165/SETBP1

Other Cancer prone implicated (Data extracted from papers in the Atlas) [ 1 ]
  Schinzel-Giedion midface retraction syndrome

External links

HGNC (Hugo)SETBP1   15573
LRG (Locus Reference Genomic)LRG_1150
Entrez_Gene (NCBI)SETBP1    SET binding protein 1
AliasesMRD29; SEB
GeneCards (Weizmann)SETBP1
Ensembl hg19 (Hinxton)ENSG00000152217 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000152217 [Gene_View]  ENSG00000152217 [Sequence]  chr18:44680888-45068510 [Contig_View]  SETBP1 [Vega]
ICGC DataPortalENSG00000152217
Genatlas (Paris)SETBP1
SOURCE (Princeton)SETBP1
Genetics Home Reference (NIH)SETBP1
Genomic and cartography
GoldenPath hg38 (UCSC)SETBP1  -     chr18:44680888-45068510 +  18q12.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SETBP1  -     18q12.3   [Description]    (hg19-Feb_2009)
GoldenPathSETBP1 - 18q12.3 [CytoView hg19]  SETBP1 - 18q12.3 [CytoView hg38]
genome Data Viewer NCBISETBP1 [Mapview hg19]  
OMIM269150   611060   616078   
Gene and transcription
Genbank (Entrez)AB007897 AB022660 AK123972 AL832945 BC062338
RefSeq transcript (Entrez)NM_001130110 NM_001379141 NM_001379142 NM_015559
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SETBP1
Alternative Splicing GalleryENSG00000152217
Gene ExpressionSETBP1 [ NCBI-GEO ]   SETBP1 [ EBI - ARRAY_EXPRESS ]   SETBP1 [ SEEK ]   SETBP1 [ MEM ]
Gene Expression Viewer (FireBrowse)SETBP1 [ Firebrowse - Broad ]
GenevisibleExpression of SETBP1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)26040
GTEX Portal (Tissue expression)SETBP1
Human Protein AtlasENSG00000152217-SETBP1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9Y6X0   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9Y6X0  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9Y6X0
Splice isoforms : SwissVarQ9Y6X0
Domains : Interpro (EBI)AT_hook_DNA-bd_motif   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Domain families : Smart (EMBL)AT_hook (SM00384)  
Conserved Domain (NCBI)SETBP1
Blocks (Seattle)SETBP1
Human Protein Atlas [tissue]ENSG00000152217-SETBP1 [tissue]
Peptide AtlasQ9Y6X0
IPIIPI00159049   IPI00441195   IPI01021397   
Protein Interaction databases
IntAct (EBI)Q9Y6X0
Ontologies - Pathways
Ontology : AmiGODNA binding  protein binding  nucleoplasm  cytosol  nuclear body  
Ontology : EGO-EBIDNA binding  protein binding  nucleoplasm  cytosol  nuclear body  
NDEx NetworkSETBP1
Atlas of Cancer Signalling NetworkSETBP1
Wikipedia pathwaysSETBP1
Orthology - Evolution
GeneTree (enSembl)ENSG00000152217
Phylogenetic Trees/Animal Genes : TreeFamSETBP1
Homologs : HomoloGeneSETBP1
Homology/Alignments : Family Browser (UCSC)SETBP1
Gene fusions - Rearrangements
Fusion : MitelmanNUP98/SETBP1 [11p15.4/18q12.3]  
Fusion : MitelmanRNF165/SETBP1 [18q21.1/18q12.3]  
Fusion PortalRNF165 18q21.1 SETBP1 18q12.3 BRCA
Fusion : TICdbNUP98 [11p15.4]  -  SETBP1 [18q12.3]
Fusion : Fusion_HubHMGA2--SETBP1    MPDZ--SETBP1    MSI2--SETBP1    NCR2--SETBP1    NFIX--SETBP1    NUP98--SETBP1    PLEKHB2--SETBP1    RNF165--SETBP1    SETBP1--ARNTL    SETBP1--ATP5A1    SETBP1--C11ORF75    SETBP1--DNAJB14    SETBP1--FANCI    SETBP1--FHOD3    SETBP1--HMGA2   
Fusion : QuiverSETBP1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSETBP1 [hg38]
Exome Variant ServerSETBP1
GNOMAD BrowserENSG00000152217
Varsome BrowserSETBP1
Genomic Variants (DGV)SETBP1 [DGVbeta]
DECIPHERSETBP1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSETBP1 
ICGC Data PortalSETBP1 
TCGA Data PortalSETBP1 
Broad Tumor PortalSETBP1
OASIS PortalSETBP1 [ Somatic mutations - Copy number]
Cancer Gene: CensusSETBP1 
Somatic Mutations in Cancer : COSMICSETBP1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSETBP1
Mutations and Diseases : HGMDSETBP1
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
BioMutasearch SETBP1
DgiDB (Drug Gene Interaction Database)SETBP1
DoCM (Curated mutations)SETBP1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SETBP1 (select a term)
NCG6 (London) select SETBP1
Cancer3DSETBP1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
OMIM269150    611060    616078   
Orphanet2807    23328   
Genetic Testing Registry SETBP1
NextProtQ9Y6X0 [Medical]
Target ValidationSETBP1
Huge Navigator SETBP1 [HugePedia]
ClinGenSETBP1 (curated)
Clinical trials, drugs, therapy
Protein Interactions : CTD
Pharm GKB GenePA37982
Clinical trialSETBP1
canSAR (ICR)SETBP1 (select the gene name)
DataMed IndexSETBP1
PubMed60 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Feb 19 18:00:06 CET 2021

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