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

    Gene ID: 26040, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SETBP1provided by HGNC
    Official Full Name
    SET binding protein 1provided by HGNC
    Primary source
    HGNC:HGNC:15573
    See related
    Ensembl:ENSG00000152217 MIM:611060; AllianceGenome:HGNC:15573
    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; MRD29
    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]
    Expression
    Ubiquitous expression in endometrium (RPKM 3.9), prostate (RPKM 3.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SETBP1 in Genome Data Viewer
    Location:
    18q12.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (44680073..45068510)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (44871239..45259841)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (42260038..42648475)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372089 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9411 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9412 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13251 Neighboring gene VISTA enhancer hs2335 Neighboring gene SETBP1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13254 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:42313178-42314377 Neighboring gene VISTA enhancer hs1362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13255 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:42360675-42360877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13256 Neighboring gene skeletal muscle cis-regulatory module in SETBP1 intron Neighboring gene VISTA enhancer hs2336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13258 Neighboring gene Sharpr-MPRA regulatory region 15026 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:42523301-42523910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:42588617-42589118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:42589119-42589618 Neighboring gene microRNA 4319 Neighboring gene uncharacterized LOC105372091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13260 Neighboring gene uncharacterized LOC101927961 Neighboring gene solute carrier family 14 member 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. SETBP1 mutations in juvenile myelomonocytic leukaemia and myelodysplastic syndrome but not in paediatric acute myeloid leukaemia. Shiba N, et al. Br J Haematol, 2014 Jan. PMID 24117422
    2. A pathogenic variant in the SETBP1 hotspot results in a forme-fruste Schinzel-Giedion syndrome. Sullivan JA, et al. Am J Med Genet A, 2020 Aug. PMID 32445275
    3. SETBP1 mutations occur in 9% of MDS/MPN and in 4% of MPN cases and are strongly associated with atypical CML, monosomy 7, isochromosome i(17)(q10), ASXL1 and CBL mutations. Meggendorfer M, et al. Leukemia, 2013 Sep. PMID 23628959
    4. Common variation within the SETBP1 gene is associated with reading-related skills and patterns of functional neural activation. Perdue MV, et al. Neuropsychologia, 2019 Jul. PMID 30009840, Free PMC Article
    5. SETBP1 induces transcription of a network of development genes by acting as an epigenetic hub. Piazza R, et al. Nat Commun, 2018 Jun 6. PMID 29875417, Free PMC Article

    See all (85) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SETBP1 haploinsufficiency and related disorders clinical and neurobehavioral phenotype study.
      Title: SETBP1 haploinsufficiency and related disorders clinical and neurobehavioral phenotype study.
    2. First-hit SETBP1 mutations cause a myeloproliferative disorder with bone marrow fibrosis.
      Title: First-hit SETBP1 mutations cause a myeloproliferative disorder with bone marrow fibrosis.
    3. Structural rearrangements as a recurrent pathogenic mechanism for SETBP1 haploinsufficiency.
      Title: Structural rearrangements as a recurrent pathogenic mechanism for SETBP1 haploinsufficiency.
    4. The landscape of SETBP1 gene expression and transcription factor activity across human tissues.
      Title: The landscape of SETBP1 gene expression and transcription factor activity across human tissues.
    5. Novel SETBP1 mutation in a chinese family with intellectual disability.
      Title: Novel SETBP1 mutation in a chinese family with intellectual disability.
    6. The impact of SETBP1 mutations in neurological diseases and cancer.
      Title: The impact of SETBP1 mutations in neurological diseases and cancer.
    7. SETBP1 mutation determines sensitivity to immune checkpoint inhibitors in melanoma and NSCLC.
      Title: SETBP1 mutation determines sensitivity to immune checkpoint inhibitors in melanoma and NSCLC.
    8. Co-occurring mutations in ASXL1, SRSF2, and SETBP1 define a subset of myelodysplastic/ myeloproliferative neoplasm with neutrophilia.
      Title: Co-occurring mutations in ASXL1, SRSF2, and SETBP1 define a subset of myelodysplastic/ myeloproliferative neoplasm with neutrophilia.
    9. Identification of a novel de novo mutation of SETBP1 and new findings of SETBP1 in tumorgenesis.
      Title: Identification of a novel de novo mutation of SETBP1 and new findings of SETBP1 in tumorgenesis.
    10. Impaired neurogenesis and neural progenitor fate choice in a human stem cell model of SETBP1 disorder.
      Title: Impaired neurogenesis and neural progenitor fate choice in a human stem cell model of SETBP1 disorder.
    Submit: New GeneRIF Correction See all GeneRIFs (60)

    Phenotypes

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

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Intellectual disability, autosomal dominant 29
    MedGen: C4015141 OMIM: 616078 GeneReviews: SETBP1 Haploinsufficiency Disorder
    		not available
    Schinzel-Giedion syndrome
    MedGen: C0265227 OMIM: 269150 GeneReviews: Schinzel-Giedion Syndrome
    		not available

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2018-05-23)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2018-05-23)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
    EBI GWAS Catalog
    Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0437, DKFZp666J1210

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SET-binding protein

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_027527.2 RefSeqGene

      Range
      5716..393338
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1150

    mRNA and Protein(s)

    1. NM_001130110.2 → NP_001123582.1  SET-binding protein isoform b

      See identical proteins and their annotated locations for NP_001123582.1

      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)
      AC015954, AC120049, BC062338, CF143191
      Consensus CDS
      CCDS45859.1
      UniProtKB/Swiss-Prot
      Q9Y6X0
      Related
      ENSP00000390687.3, ENST00000426838.8

    2. NM_001379141.1 → NP_001366070.1  SET-binding protein isoform a

      Status: REVIEWED

      Description
      Transcript Variant: Variants 1, 3 and 4 all encode the same isoform (a).
      Source sequence(s)
      AC015954, AC090376, AC105074, AC120049
      Consensus CDS
      CCDS11923.2
      UniProtKB/Swiss-Prot
      A6H8W5, Q6P6C3, Q9UEF3, Q9Y6X0
      Related
      ENSP00000504398.1, ENST00000677068.1

    3. NM_001379142.1 → NP_001366071.1  SET-binding protein isoform a

      Status: REVIEWED

      Description
      Transcript Variant: Variants 1, 3 and 4 all encode the same isoform (a).
      Source sequence(s)
      AC015954, AC090376, AC105074, AC120049
      Consensus CDS
      CCDS11923.2
      UniProtKB/Swiss-Prot
      A6H8W5, Q6P6C3, Q9UEF3, Q9Y6X0
      Related
      ENSP00000503094.1, ENST00000677130.1

    4. NM_001410862.1 → NP_001397791.1  SET-binding protein isoform c

      Status: REVIEWED

      Source sequence(s)
      AC015954, AC090376, AC105074, AC120049
      Consensus CDS
      CCDS92452.1
      UniProtKB/TrEMBL
      A0A7I2V4X1
      Related
      ENSP00000503964.1, ENST00000677699.1

    5. NM_015559.3 → NP_056374.2  SET-binding protein isoform a

      See identical proteins and their annotated locations for NP_056374.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a). Variants 1, 3 and 4 all encode isoform a.
      Source sequence(s)
      AC090376, AC105074, BC146776, BG433843, BQ641251
      Consensus CDS
      CCDS11923.2
      UniProtKB/Swiss-Prot
      A6H8W5, Q6P6C3, Q9UEF3, Q9Y6X0
      Related
      ENSP00000497406.1, ENST00000649279.2

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      44680073..45068510
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024451149.2 → XP_024306917.1  SET-binding protein isoform X1

    2. XM_024451156.2 → XP_024306924.1  SET-binding protein isoform X3

    3. XM_047437477.1 → XP_047293433.1  SET-binding protein isoform X4

      UniProtKB/TrEMBL
      A0A7I2V4X1

    4. XM_024451158.2 → XP_024306926.1  SET-binding protein isoform X6

    5. XM_047437479.1 → XP_047293435.1  SET-binding protein isoform X5

    6. XM_047437480.1 → XP_047293436.1  SET-binding protein isoform X5

    7. XM_047437481.1 → XP_047293437.1  SET-binding protein isoform X7

    8. XM_024451157.2 → XP_024306925.1  SET-binding protein isoform X5

    9. XM_024451150.2 → XP_024306918.1  SET-binding protein isoform X1

    10. XM_024451154.2 → XP_024306922.1  SET-binding protein isoform X2

      UniProtKB/Swiss-Prot
      A6H8W5, Q6P6C3, Q9UEF3, Q9Y6X0
      Related
      ENSP00000502995.1, ENST00000678152.1

    11. XM_024451152.2 → XP_024306920.1  SET-binding protein isoform X1

    12. XM_024451151.2 → XP_024306919.1  SET-binding protein isoform X1

    13. XM_047437476.1 → XP_047293432.1  SET-binding protein isoform X2

      UniProtKB/Swiss-Prot
      A6H8W5, Q6P6C3, Q9UEF3, Q9Y6X0
      Related
      ENSP00000503656.1, ENST00000677077.1

    14. XM_047437475.1 → XP_047293431.1  SET-binding protein isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      44871239..45259841
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054318508.1 → XP_054174483.1  SET-binding protein isoform X1

    2. XM_054318515.1 → XP_054174490.1  SET-binding protein isoform X3

    3. XM_054318516.1 → XP_054174491.1  SET-binding protein isoform X4

      UniProtKB/TrEMBL
      A0A7I2V4X1

    4. XM_054318521.1 → XP_054174496.1  SET-binding protein isoform X6

    5. XM_054318517.1 → XP_054174492.1  SET-binding protein isoform X5

    6. XM_054318518.1 → XP_054174493.1  SET-binding protein isoform X5

    7. XM_054318522.1 → XP_054174497.1  SET-binding protein isoform X7

    8. XM_054318519.1 → XP_054174494.1  SET-binding protein isoform X5

    9. XM_054318510.1 → XP_054174485.1  SET-binding protein isoform X1

    10. XM_054318514.1 → XP_054174489.1  SET-binding protein isoform X2

      UniProtKB/Swiss-Prot
      A6H8W5, Q6P6C3, Q9UEF3, Q9Y6X0

    11. XM_054318511.1 → XP_054174486.1  SET-binding protein isoform X1

    12. XM_054318512.1 → XP_054174487.1  SET-binding protein isoform X1

    13. XM_054318513.1 → XP_054174488.1  SET-binding protein isoform X2

      UniProtKB/Swiss-Prot
      A6H8W5, Q6P6C3, Q9UEF3, Q9Y6X0

    14. XM_054318509.1 → XP_054174484.1  SET-binding protein isoform X1

    15. XM_054318520.1 → XP_054174495.1  SET-binding protein isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y6X0.3 GenPept UniProtKB/Swiss-Prot:Q9Y6X0

    Gene LinkOut

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

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