U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 26040, updated on 16-Apr-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See SETBP1 in Genome Data Viewer
Location:
18q12.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (44680073..45068510)
RS_2023_10 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 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Identification of a novel de novo mutation of SETBP1 and new findings of SETBP1 in tumorgenesis. Wang H, et al. Orphanet J Rare Dis, 2023 May 7. PMID 37150818, Free PMC Article
  2. Impaired neurogenesis and neural progenitor fate choice in a human stem cell model of SETBP1 disorder. Cardo LF, et al. Mol Autism, 2023 Feb 20. PMID 36805818, Free PMC Article
  3. Prenatal diagnosis and molecular cytogenetic characterization of an inherited microdeletion of 18q12.3 encompassing SETBP1. Zhou Y, et al. J Int Med Res, 2022 Sep. PMID 36113068, Free PMC Article
  4. SETBP1 Haploinsufficiency Disorder. Adam MP, et al. , 1993. PMID 34807554
  5. Speech and language deficits are central to SETBP1 haploinsufficiency disorder. Morgan A, et al. Eur J Hum Genet, 2021 Aug. PMID 33907317, Free PMC Article

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Structural rearrangements as a recurrent pathogenic mechanism for SETBP1 haploinsufficiency.
    Title: Structural rearrangements as a recurrent pathogenic mechanism for SETBP1 haploinsufficiency.
  3. 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.
  4. Novel SETBP1 mutation in a chinese family with intellectual disability.
    Title: Novel SETBP1 mutation in a chinese family with intellectual disability.
  5. The impact of SETBP1 mutations in neurological diseases and cancer.
    Title: The impact of SETBP1 mutations in neurological diseases and cancer.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Prenatal diagnosis and molecular cytogenetic characterization of an inherited microdeletion of 18q12.3 encompassing SETBP1.
    Title: Prenatal diagnosis and molecular cytogenetic characterization of an inherited microdeletion of 18q12.3 encompassing SETBP1.
Submit: New GeneRIF Correction See all GeneRIFs (59)

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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
  

General protein information

Go to the top of the page Help
Preferred Names
SET-binding protein

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_2023_10

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.

Chemical Information
Medical
Molecular Biology Databases
Research Materials
Tools
Miscellaneous