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Aliases for SETBP1 Gene

Aliases for SETBP1 Gene

  • SET Binding Protein 1 2 3 5
  • SEB 3 4
  • SET-Binding Protein 3
  • KIAA0437 4
  • MRD29 3

External Ids for SETBP1 Gene

Previous GeneCards Identifiers for SETBP1 Gene

  • GC18P042594
  • GC18P042047
  • GC18P042148
  • GC18P040512
  • GC18P040535
  • GC18P042260
  • GC18P039118

Summaries for SETBP1 Gene

Entrez Gene Summary for SETBP1 Gene

  • This gene encodes a protein which contains a several motifs including a ski homology region and a SET-binding region in addition to three nuclear localization signals. The encoded protein has been shown to bind the SET nuclear oncogene which is involved in DNA replication. Mutations in this gene are associated with Schinzel-Giedion midface retraction syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

CIViC summary for SETBP1 Gene

GeneCards Summary for SETBP1 Gene

SETBP1 (SET Binding Protein 1) is a Protein Coding gene. Diseases associated with SETBP1 include Schinzel-Giedion Midface Retraction Syndrome and Mental Retardation, Autosomal Dominant 29. Among its related pathways are PKMTs methylate histone lysines. An important paralog of this gene is NSD1.

Additional gene information for SETBP1 Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SETBP1 Gene

Genomics for SETBP1 Gene

GeneHancer (GH) Regulatory Elements for SETBP1 Gene

Promoters and enhancers for SETBP1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18J044678 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 669.8 +1.2 1209 5.7 ARID4B FEZF1 IRF4 ZNF48 YY1 GLIS2 ZNF207 ZNF143 RUNX3 SP3 SETBP1 GC18M044677 GC18P044681 LOC101927943 GC18M044726
GH18J044686 Promoter/Enhancer 0.7 EPDnew dbSUPER 650.4 +6.0 6005 0.1 SETBP1 GC18P044681 GC18M044726
GH18J044741 Enhancer 1.8 VISTA FANTOM5 Ensembl ENCODE dbSUPER 14 +63.4 63381 5 CTCF ZSCAN18 ZNF792 ZIC2 RAD21 YY1 ZNF335 ZNF791 POLR2A ZNF366 SETBP1 LOC101927943 ENSG00000280365 GC18M044779
GH18J044699 Enhancer 1.1 Ensembl ENCODE dbSUPER 21.6 +20.5 20541 2.3 TAF1 BACH1 MAX FEZF1 RAD21 YY1 ZNF766 EGR1 ZSCAN5C ATF7 SETBP1 LOC101927943 GC18P044681 GC18M044726
GH18J044723 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 12.9 +45.1 45070 4.1 IRF4 TCF12 ATF7 RUNX3 RXRA JUNB MAFF SMARCA4 NBN STAT3 SETBP1 GC18M044726 GC18P044681
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SETBP1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SETBP1 gene promoter:
  • Lmo2
  • aMEF-2
  • MEF-2A
  • AP-2gamma
  • FOXO4

Genomic Locations for SETBP1 Gene

Genomic Locations for SETBP1 Gene
388,338 bases
Plus strand
388,338 bases
Plus strand

Genomic View for SETBP1 Gene

Genes around SETBP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETBP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETBP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETBP1 Gene

Proteins for SETBP1 Gene

  • Protein details for SETBP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    SET-binding protein
    Protein Accession:
    Secondary Accessions:
    • A6H8W5
    • Q6P6C3
    • Q9UEF3

    Protein attributes for SETBP1 Gene

    1596 amino acids
    Molecular mass:
    175008 Da
    Quaternary structure:
    • Interacts with SET.
    • Sequence=AAI46777.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA24826.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAA82444.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for SETBP1 Gene


neXtProt entry for SETBP1 Gene

Post-translational modifications for SETBP1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SETBP1 Gene

Domains & Families for SETBP1 Gene

Gene Families for SETBP1 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SETBP1 Gene


Suggested Antigen Peptide Sequences for SETBP1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SETBP1: view

No data available for UniProtKB/Swiss-Prot for SETBP1 Gene

Function for SETBP1 Gene

Phenotypes From GWAS Catalog for SETBP1 Gene

Gene Ontology (GO) - Molecular Function for SETBP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM 19274049
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with SETBP1: view
genes like me logo Genes that share phenotypes with SETBP1: view

Human Phenotype Ontology for SETBP1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SETBP1 Gene

MGI Knock Outs for SETBP1:
  • Setbp1 Setbp1<tm1b(EUCOMM)Wtsi>

Animal Model Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SETBP1 Gene

Localization for SETBP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETBP1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SETBP1 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
  • Nucleus (3)
  • Cytosol (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SETBP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005829 cytosol IDA --
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with SETBP1: view

Pathways & Interactions for SETBP1 Gene

SuperPathways for SETBP1 Gene

SuperPathway Contained pathways
1 PKMTs methylate histone lysines
genes like me logo Genes that share pathways with SETBP1: view

Pathways by source for SETBP1 Gene

1 BioSystems pathway for SETBP1 Gene

SIGNOR curated interactions for SETBP1 Gene


Gene Ontology (GO) - Biological Process for SETBP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006357 regulation of transcription by RNA polymerase II IEA --
genes like me logo Genes that share ontologies with SETBP1: view

Drugs & Compounds for SETBP1 Gene

No Compound Related Data Available

Transcripts for SETBP1 Gene

mRNA/cDNA for SETBP1 Gene

Unigene Clusters for SETBP1 Gene

SET binding protein 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SETBP1 Gene

No ASD Table

Relevant External Links for SETBP1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SETBP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SETBP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SETBP1 Gene

This gene is overexpressed in Cerebrospinal fluid (35.9), Heart (16.0), and Plasma (14.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SETBP1 Gene

Protein tissue co-expression partners for SETBP1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SETBP1 Gene:


SOURCE GeneReport for Unigene cluster for SETBP1 Gene:


mRNA Expression by UniProt/SwissProt for SETBP1 Gene:

Tissue specificity: Expressed in numerous tissues. Expressed at low levels in myeloid and monocytic cells as well as in CD34+ cells; expression levels are higher in myeloid malignancies.

Evidence on tissue expression from TISSUES for SETBP1 Gene

  • Nervous system(4.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SETBP1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • skull
  • tongue
  • tooth
  • breast
  • chest wall
  • clavicle
  • heart
  • heart valve
  • rib
  • rib cage
  • scapula
  • sternum
  • kidney
  • liver
  • ovary
  • pelvis
  • penis
  • testicle
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vulva
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SETBP1: view

No data available for mRNA differential expression in normal tissues for SETBP1 Gene

Orthologs for SETBP1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SETBP1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SETBP1 34 33
  • 99.69 (n)
(Canis familiaris)
Mammalia SETBP1 34 33
  • 91.9 (n)
(Bos Taurus)
Mammalia SETBP1 34 33
  • 91.7 (n)
(Rattus norvegicus)
Mammalia Setbp1 33
  • 87.51 (n)
(Mus musculus)
Mammalia Setbp1 16 34 33
  • 87.23 (n)
(Monodelphis domestica)
Mammalia SETBP1 34
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia SETBP1 34
  • 80 (a)
(Gallus gallus)
Aves SETBP1 34 33
  • 75.84 (n)
(Anolis carolinensis)
Reptilia SETBP1 34
  • 72 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.13769 33
(Danio rerio)
Actinopterygii setbp1 34 33
  • 57.28 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4565 34
  • 13 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 6 (a)
Species where no ortholog for SETBP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SETBP1 Gene

Gene Tree for SETBP1 (if available)
Gene Tree for SETBP1 (if available)
Evolutionary constrained regions (ECRs) for SETBP1: view image

Paralogs for SETBP1 Gene

(1) SIMAP similar genes for SETBP1 Gene using alignment to 2 proteins:

  • K7ES17_HUMAN
genes like me logo Genes that share paralogs with SETBP1: view

Variants for SETBP1 Gene

Sequence variations from dbSNP and Humsavar for SETBP1 Gene

SNP ID Clin Chr 18 pos Variation AA Info Type
rs1009609185 uncertain-significance, Schinzel-Giedion syndrome 45,065,075(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1014009326 uncertain-significance, Schinzel-Giedion syndrome 45,063,903(+) C/G 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1021752299 uncertain-significance, Schinzel-Giedion syndrome 45,067,902(+) A/G 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1026085062 uncertain-significance, Schinzel-Giedion syndrome 45,067,798(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1032938179 uncertain-significance, Schinzel-Giedion syndrome 45,065,036(+) C/A 3_prime_UTR_variant, genic_downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SETBP1 Gene

Variant ID Type Subtype PubMed ID
esv1005718 CNV deletion 20482838
esv1008653 CNV insertion 20482838
esv22280 CNV loss 19812545
esv2671518 CNV deletion 23128226
esv3330726 CNV insertion 20981092
esv3583035 CNV loss 25503493
esv3642401 CNV loss 21293372
esv3642402 CNV loss 21293372
nsv1059424 CNV gain 25217958
nsv1072796 CNV deletion 25765185
nsv1132882 CNV insertion 24896259
nsv2272 CNV deletion 18451855
nsv2273 CNV deletion 18451855
nsv2274 CNV insertion 18451855
nsv472338 CNV novel sequence insertion 20440878
nsv474017 CNV novel sequence insertion 20440878
nsv828220 CNV gain 20364138
nsv833637 CNV gain 17160897
nsv960274 CNV duplication 23825009

Variation tolerance for SETBP1 Gene

Residual Variation Intolerance Score: 9.62% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.16; 92.34% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SETBP1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETBP1 Gene

Disorders for SETBP1 Gene

MalaCards: The human disease database

(20) MalaCards diseases for SETBP1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • Schinzel-Giedion midface retraction syndrome (SGMFS) [MIM:269150]: A disorder characterized by severe mental retardation, distinctive facial features, and multiple congenital malformations including skeletal abnormalities, genitourinary and renal malformations, cardiac defects, as well as a higher-than-normal prevalence of tumors, notably neuroepithelial neoplasia. {ECO:0000269 PubMed:20436468}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=SETBP1 somatic mutations are frequently found in myeloid malignancies. They cause gain of function associated with myeloid leukemic transformation (PubMed:23832012). Myeloid malignancies are separated into three main categories: myeloproliferative neoplasms (MPN) characterized by cellular proliferation of one or more hematologic cell lines in the peripheral blood, myelodysplastic syndromes (MDS) and MDS/MPN. The MDS/MPN category shows overlapping characteristics of both MDS and MPN and includes chronic myelomonocytic leukemia (CMML), juvenile myelomonocytic leukemia, atypical chronic myeloid leukemia (ACML) and unclassified MDS/MPN (PubMed:23628959). {ECO:0000269 PubMed:23628959, ECO:0000269 PubMed:23832012}.
  • Myelodysplastic syndrome (MDS) [MIM:614286]: A heterogeneous group of closely related clonal hematopoietic disorders. All are characterized by a hypercellular or hypocellular bone marrow with impaired morphology and maturation, dysplasia of the myeloid, megakaryocytic and/or erythroid lineages, and peripheral blood cytopenias resulting from ineffective blood cell production. Included diseases are: refractory anemia (RA), refractory anemia with ringed sideroblasts (RARS), refractory anemia with excess blasts (RAEB), refractory cytopenia with multilineage dysplasia and ringed sideroblasts (RCMD-RS); chronic myelomonocytic leukemia (CMML) is a myelodysplastic/myeloproliferative disease. MDS is considered a premalignant condition in a subgroup of patients that often progresses to acute myeloid leukemia (AML). {ECO:0000269 PubMed:23648668, ECO:0000269 PubMed:23889083}. Note=The gene represented in this entry is involved in disease pathogenesis.
  • Mental retardation, autosomal dominant 29 (MRD29) [MIM:616078]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD29 patients manifest severe intellectual disability, behavioral difficulties, speech and motor delays, and dysmorphic facial features. {ECO:0000269 PubMed:25217958}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Leukemia, acute myelogenous (AML) [MIM:601626]: A subtype of acute leukemia, a cancer of the white blood cells. AML is a malignant disease of bone marrow characterized by maturational arrest of hematopoietic precursors at an early stage of development. Clonal expansion of myeloid blasts occurs in bone marrow, blood, and other tissue. Myelogenous leukemias develop from changes in cells that normally produce neutrophils, basophils, eosinophils and monocytes. {ECO:0000269 PubMed:23648668, ECO:0000269 PubMed:23889083}. Note=The gene represented in this entry is involved in disease pathogenesis.
  • Leukemia, chronic myeloid, atypical (ACML) [MIM:608232]: A myeloproliferative disorder that shares clinical and laboratory features with chronic myeloid leukemia but lacks the pathognomonic Philadelphia chromosome and the corresponding BCR/ABL1 fusion transcript. Features include myeloid predominance in the bone marrow, myeloid proliferation and low leukocyte alkaline phosphatase value, splenomegaly, hepatomegaly, elevated white blood cell count. Enlarged spleen may also be associated with a hypermetabolic state, fever, weight loss, and chronic fatigue. The enlarged liver may contribute to the patients weight loss. {ECO:0000269 PubMed:23222956}. Note=The gene represented in this entry is involved in disease pathogenesis.
  • Leukemia, juvenile myelomonocytic (JMML) [MIM:607785]: An aggressive pediatric myelodysplastic syndrome/myeloproliferative disorder characterized by malignant transformation in the hematopoietic stem cell compartment with proliferation of differentiated progeny. Patients have splenomegaly, enlarged lymph nodes, rashes, and hemorrhages. {ECO:0000269 PubMed:23832011}. Note=The gene represented in this entry is involved in disease pathogenesis.

Additional Disease Information for SETBP1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SETBP1: view

No data available for Genatlas for SETBP1 Gene

Publications for SETBP1 Gene

  1. Identification and characterization of SEB, a novel protein that binds to the acute undifferentiated leukemia-associated protein SET. (PMID: 11231286) Minakuchi M … Adachi Y (European journal of biochemistry 2001) 2 3 4 22 58
  2. Refining analyses of copy number variation identifies specific genes associated with developmental delay. (PMID: 25217958) Coe BP … Eichler EE (Nature genetics 2014) 3 4 58
  3. Recurrent SETBP1 mutations in atypical chronic myeloid leukemia. (PMID: 23222956) Piazza R … Gambacorti-Passerini C (Nature genetics 2013) 3 4 58
  4. Mutations in SETBP1 are recurrent in myelodysplastic syndromes and often coexist with cytogenetic markers associated with disease progression. (PMID: 23889083) Fernandez-Mercado M … Boultwood J (British journal of haematology 2013) 3 4 58
  5. Somatic SETBP1 mutations in myeloid malignancies. (PMID: 23832012) Makishima H … Maciejewski JP (Nature genetics 2013) 3 4 58

Products for SETBP1 Gene

Sources for SETBP1 Gene

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