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

    Gene ID: 26040, updated on 5-Aug-2022

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SETBP1 in Genome Data Viewer
    Location:
    18q12.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    110 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (44680073..45068510)
    110 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (44871239..45259841)
    105.20220307 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 LOC124904290 Neighboring gene uncharacterized LOC105372089 Neighboring gene VISTA enhancer hs2335 Neighboring gene VISTA enhancer hs1362 Neighboring gene skeletal muscle cis-regulatory module in SETBP1 intron Neighboring gene VISTA enhancer hs2336 Neighboring gene microRNA 4319 Neighboring gene uncharacterized LOC105372091 Neighboring gene uncharacterized LOC101927961 Neighboring gene solute carrier family 14 member 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Intellectual disability, autosomal dominant 29 Compare labs
    Schinzel-Giedion syndrome
    MedGen: C0265227 OMIM: 269150 GeneReviews: Not available
    Compare labs

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    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 methyltransferase activity (H3-K4 specific) IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in histone H3-K36 dimethylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in histone H3-K4 methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     

    NCBI Reference Sequences (RefSeq)

    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_001130110.2NP_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_001379141.1NP_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
      UniProtKB/Swiss-Prot
      Q9UEF3
      Related
      ENSP00000504398.1, ENST00000677068.1
    3. NM_001379142.1NP_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
      UniProtKB/Swiss-Prot
      Q9UEF3
      Related
      ENSP00000503094.1, ENST00000677130.1
    4. NM_015559.3NP_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
      Q9UEF3, Q9Y6X0
      Related
      ENSP00000497406.1, ENST00000649279.2

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

    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_024451149.2XP_024306917.1  SET-binding protein isoform X1

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

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

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

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

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

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

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

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

    10. XM_047437478.1XP_047293434.1  SET-binding protein isoform X4

      Related
      ENSP00000503964.1, ENST00000677699.1
    11. XM_024451154.2XP_024306922.1  SET-binding protein isoform X2

      UniProtKB/Swiss-Prot
      Q9UEF3
      Related
      ENSP00000502995.1, ENST00000678152.1
    12. XM_024451152.2XP_024306920.1  SET-binding protein isoform X1

    13. XM_024451151.2XP_024306919.1  SET-binding protein isoform X1

    14. XM_047437476.1XP_047293432.1  SET-binding protein isoform X2

      UniProtKB/Swiss-Prot
      Q9UEF3
      Related
      ENSP00000503656.1, ENST00000677077.1
    15. XM_047437475.1XP_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)