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    SETBP1 SET binding protein 1 [ Homo sapiens (human) ]

    Gene ID: 26040, updated on 9-Jun-2013
    Official Symbol
    SETBP1provided by HGNC
    Official Full Name
    SET binding protein 1provided by HGNC
    Primary source
    HGNC:15573
    See related
    Ensembl:ENSG00000152217; HPRD:10224; MIM:611060; Vega:OTTHUMG00000132613
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SEB
    Summary
    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]
    Location :
    18q21.1
    Sequence :
    Chromosome: 18; NC_000018.9 (42260138..42648475)
    See SETBP1 in Epigenomics, MapViewer

    Chromosome 18 - NC_000018.9Genomic Context describing neighboring genes Neighboring gene IBTK pseudogene 1 Neighboring gene keratin 8 pseudogene 5 Neighboring gene uncharacterized LOC100131669 Neighboring gene microRNA 4319 Neighboring gene solute carrier family 14 (urea transporter), member 2 Neighboring gene uncharacterized LOC100652778 Neighboring gene solute carrier family 14 (urea transporter), member 1 (Kidd blood group)

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details

    Related articles in PubMed

    1. Recurrent SETBP1 mutations in atypical chronic myeloid leukemia. Piazza R, et al. Nat Genet, 2013 Jan. PMID 23222956.
    2. Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases. Li R, et al. PLoS Genet, 2012 May. PMID 22693459.
    3. 372 kb microdeletion in 18q12.3 causing SETBP1 haploinsufficiency associated with mild mental retardation and expressive speech impairment. Marseglia G, et al. Eur J Med Genet, 2012 Mar. PMID 22333924.
    4. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. Oláh J, et al. J Biol Chem, 2011 Sep 30. PMID 21832049.
    5. SETBP1 mutations in two Thai patients with Schinzel-Giedion syndrome. Suphapeetiporn K, et al. Clin Genet, 2011 Apr. PMID 21371013.

    See all (19) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. mutated SETBP1 represents a newly discovered oncogene present in Atypical chronic myeloid leukemia (aCML) and closely related diseases.
      Title: Recurrent SETBP1 mutations in atypical chronic myeloid leukemia.
    2. We describe a patient with a 18q12.3 microdeletion that causes the disruption of SETBP1 resulting in mild mental retardation and expressive speech impairment with striking discrepancy between expressive and receptive language skills.
      Title: 372 kb microdeletion in 18q12.3 causing SETBP1 haploinsufficiency associated with mild mental retardation and expressive speech impairment.
    3. study of 2 unrelated Thai patients with clinical manifestations fulfilling criteria of Schinzel-Giedion syndrome; demonstrate SETBP1 is gene responsible for SGS in Thai patients confirming previous report of this gene associated with SGS in Caucasians
      Title: SETBP1 mutations in two Thai patients with Schinzel-Giedion syndrome.
    4. Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel-Giedion syndrome.
      Title: Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel-Giedion syndrome.
    5. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    8. We sequenced the exomes of four affected individuals (cases) and found heterozygous de novo variants in SETBP1 in all four
      Title: De novo mutations of SETBP1 cause Schinzel-Giedion syndrome.
    9. Correction of X-linked chronic granulomatous disease by gene therapy was augmented by insertional activation of SETBP1.
      Title: Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1.
    Submit: New GeneRIF Correction

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Products Interactant Other Gene Complex Source Pubs Description
    Q9Y6X0 Q01105 SET    HPRD  PubMed  
    BioGRID:117506 BioGRID:106848 APP    BioGRID  PubMed Reconstituted Complex 
    BioGRID:117506 BioGRID:112316 SET    BioGRID  PubMed Affinity Capture-Western; Two-hybrid 
    BioGRID:117506 BioGRID:113188 SUMO1    BioGRID  PubMed Affinity Capture-MS 

    Markers

    Genotypes

    Homology

    Clone Names

    • KIAA0437, DKFZp666J1210

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    Preferred Names
    SET-binding protein
    Names
    SET-binding protein

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_027527.1 RefSeqGene

      Range
      5001..393338
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001130110.1 → NP_001123582.1  SET-binding protein isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, 3' UTR, and coding region compared to variant 1. The resulting isoform (b) has a shorter and distinct C-terminus compared to isoform a.
      Source sequence(s)
      BC062338, CF143191
      Consensus CDS
      CCDS45859.1
      UniProtKB/Swiss-Prot
      Q9Y6X0
      Related
      ENSP00000390687, OTTHUMP00000209757, ENST00000426838, OTTHUMT00000343906

    2. NM_015559.2 → NP_056374.2  SET-binding protein isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AC090376, AC105074, BC146776, BQ641251
      Consensus CDS
      CCDS11923.2
      UniProtKB/Swiss-Prot
      Q9Y6X0
      Related
      ENSP00000282030, OTTHUMP00000163447, ENST00000282030, OTTHUMT00000255854

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000018.9 Reference GRCh37.p10 Primary Assembly

      Range
      42260138..42648475
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000150.1 Alternate HuRef

      Range
      39118875..39506275
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018929.1 Alternate CHM1_1.0

      Range
      42239804..42628179
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    genomic ABBA01022341.1 (102330..330767) None
    genomic ABBA01022342.1 None
    genomic ABBA01022343.1 (378..15287) None
    genomic AC015954.9 (35172..180507) None
    genomic AC021766.6 (74394..151558) None
    genomic AC090376.6 (150444..204903) None
    genomic AC105074.5 None
    genomic AC120049.5 (106560..125488) None
    genomic AMYH01008967.1 None
    genomic AMYH01008968.1 None
    genomic AMYH01008969.1 None
    genomic CH471088.1 EAX01441.1
    mRNA AB007897.2 BAA24826.2
    mRNA AB022660.1 BAA82444.1
    mRNA AK123972.1 None
    mRNA AL832945.1 None
    mRNA BC062338.1 AAH62338.1
    mRNA BC146776.1 AAI46777.1
    mRNA BQ641251.1 None
    mRNA CF143191.1 None
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y6X0.3 GenPept UniProtKB/Swiss-Prot:Q9Y6X0

    Additional Links

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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      Supplemental Content

      Table of contents

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      • Order cDNA clone
        Order cDNA clone
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      • CCDS
        Links from Gene to CCDS are established if a gene encodes a protein sequence that is a member of a Consensus CDS (CCDS).
      • ClinVar
        Related medical variations
      • dbVar
        Link from Gene to dbVar
      • EST
        Link to related EST entry
      • Full text in PMC
        PMC links
      • Full text in PMC_nucleotide
        Full text in PubMedCentral identified from shared sequence links
      • GAP
        GAP Links
      • Genome
        Genome records having the gene annotated on corresponding genomic reference sequence.
      • GEO Profiles
        Related GEO
      • GTR
        GTR associated with a gene
      • HomoloGene
        Links between HomoloGene and Gene are provided by the HomoloGene group when a gene is included in a HomoloGene record.
      • Map Viewer
        These links are maintained by the Map Viewer group and are provided when a GeneID is annotated on a map for the same species.
      • MedGen
        Related information in MedGen
      • Nucleotide
        Link to related Nucleotide entry
      • OMIM
        Links between OMIM and Gene are calculated by Gene based on MIM numbers included in the summary and phenotype sections of the Gene record.
      • Probe
        Related Probe entry
      • Protein
        Link to related protein entry
      • PubChem Compound
        PubChem Compounds
      • PubChem Substance
        PubChem Substances
      • PubMed
        Links between Gene and PubMed are the result of the following: 1. Manual curation within NCBI. Part of the process of generating a REVIEWED RefSeq is an analysis of the current literature. Papers that are seminal in defining the gene, its sequence, and its function are added to the record at that time. Alert users point out gaps or errors in papers associated with a Gene record. These messages are reviewed and implemented as required. 2. Integration of information from other public databases. Gene integrates gene-citation from resources external to NCBI such as model organism-specific databases, Gene Ontology (GO), groups curating interactions, and sequence databases. The assumption in using these source is that they report citations specific to a gene in a known species. Gene does not process citations from OMIM automatically, because many of citations in OMIM refer to studies of genes in species other than human.
      • PubMed (GeneRIF)
        GeneRIF -- Gene Reference Into Function Staff of the Index Section in the National Library of Medicine review the current literature. When they find articles focused on the structure and function of a gene, they write a brief summary of the impact of the paper and make the connection between the citation (PubMed) and Gene. An interface exists for interested users to submit such data as well. http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html
      • PubMed (OMIM)
        Links are provided when Gene has a link to a record in OMIM, and OMIM explicitly cites these publications in PubMed.
      • PubMed(nucleotide/PMC)
        Citations in PubMed identified from shared sequence and PMC links.
      • RefSeq Proteins
        Link to Protein RefSeqs
      • RefSeq RNAs
        Link to Nucleotide RefSeq RNAs
      • RefSeqGene
        Link to Nucleotide RefSeqGenes
      • SNP
        Related SNP records
      • SNP: GeneView
        SNPs linked from GeneView
      • SNP: Genotype
        Gene Genotype Report
      • SNP: VarView
        Related Clinical SNP
      • Taxonomy
        Link to related taxonomy entry
      • UniGene
        Links are provided between Gene and UniGene when both databases calculate links to the same mRNA record (gi).
      • UniSTS
        Related UniSTS records

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