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

Gene ID: 26040, updated on 16-Sep-2018

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; 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; 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

Genomic context

See SETBP1 in Genome Data Viewer
Location:
18q12.3
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 18 NC_000018.10 (44680072..45068510)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (42258849..42648475)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372089 Neighboring gene uncharacterized LOC101927943 Neighboring gene VISTA enhancer hs1362 Neighboring gene skeletal muscle cis-regulatory module in SETBP1 intron Neighboring gene microRNA 4319 Neighboring gene uncharacterized LOC105372091 Neighboring gene uncharacterized LOC101927961

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mental retardation, autosomal dominant 29
MedGen: C4015141 OMIM: 616078 GeneReviews: Not available
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

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Histone Modifications, organism-specific biosystem (from WikiPathways)
    Histone Modifications, organism-specific biosystemHistones can undergo many post-translational modifications that are involved in transcription regulation. This pathway provides an overview of various modifications for histones H3 and H4 and the en...

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
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
nuclear body IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 

NCBI Reference Sequences (RefSeq)

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_001130110.1NP_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)
    BC062338, CF143191
    Consensus CDS
    CCDS45859.1
    UniProtKB/Swiss-Prot
    Q9Y6X0
    Related
    ENSP00000390687.3, OTTHUMP00000209757, ENST00000426838.8, OTTHUMT00000343906
  2. 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).
    Source sequence(s)
    AC090376, AC105074, BC146776, BG433843, BQ641251
    Consensus CDS
    CCDS11923.2
    UniProtKB/Swiss-Prot
    Q9Y6X0
    Related
    ENSP00000282030.5, OTTHUMP00000163447, ENST00000282030.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p12 Primary Assembly

    Range
    44680072..45068510
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

  3. XM_024451153.1XP_024306921.1  SET-binding protein isoform X2

  4. XM_024451158.1XP_024306926.1  SET-binding protein isoform X5

  5. XM_024451150.1XP_024306918.1  SET-binding protein isoform X1

  6. XM_024451154.1XP_024306922.1  SET-binding protein isoform X2

  7. XM_024451151.1XP_024306919.1  SET-binding protein isoform X1

  8. XM_024451152.1XP_024306920.1  SET-binding protein isoform X1

  9. XM_024451155.1XP_024306923.1  SET-binding protein isoform X2

  10. XM_024451157.1XP_024306925.1  SET-binding protein isoform X4

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