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 4-Nov-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 H3K4 methyltransferase activity 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
    Consensus CDS
    CCDS11923.2
    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
    Consensus CDS
    CCDS11923.2
    UniProtKB/Swiss-Prot
    Q9UEF3
    Related
    ENSP00000503094.1, ENST00000677130.1
  4. NM_001410862.1NP_001397791.1  SET-binding protein isoform c

    Status: REVIEWED

    Source sequence(s)
    AC015954, AC090376, AC105074, AC120049
    Consensus CDS
    CCDS92452.1
    UniProtKB/TrEMBL
    A0A7I2V4X1
  5. 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

    UniProtKB/TrEMBL
    A0A7I2V4X1
  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)