This gene encodes a member of a family of proteins that contain a methyl-CpG-binding domain (MBD) and a SET domain and function as histone methyltransferases. This protein is recruited to heterochromatin and plays a role in the regulation of chromosome segregation. This region is commonly deleted in chronic lymphocytic leukemia. Naturally-occuring readthrough transcription occu... See more...

Aliases for SETDB2 Gene

Aliases for SETDB2 Gene

  • SET Domain Bifurcated Histone Lysine Methyltransferase 2 2 3 5
  • SET Domain Bifurcated 2 2 3 4
  • CLLD8 2 3 4
  • KMT1F 2 3 4
  • Chronic Lymphocytic Leukemia Deletion Region Gene 8 Protein 3 4
  • Histone-Lysine N-Methyltransferase SETDB2 3 4
  • Lysine N-Methyltransferase 1F 3 4
  • C13orf4 3 4
  • CLLL8 2 3
  • Chromosome 13 Open Reading Frame 4 2
  • SET Domain, Bifurcated 2 2
  • EC 2.1.1.- 4
  • SETDB2 5

External Ids for SETDB2 Gene

Previous HGNC Symbols for SETDB2 Gene

  • C13orf4

Previous GeneCards Identifiers for SETDB2 Gene

  • GC13P048954
  • GC13P047816
  • GC13P048916
  • GC13P050018
  • GC13P030812

Summaries for SETDB2 Gene

Entrez Gene Summary for SETDB2 Gene

  • This gene encodes a member of a family of proteins that contain a methyl-CpG-binding domain (MBD) and a SET domain and function as histone methyltransferases. This protein is recruited to heterochromatin and plays a role in the regulation of chromosome segregation. This region is commonly deleted in chronic lymphocytic leukemia. Naturally-occuring readthrough transcription occurs from this gene to the downstream PHF11 (PHD finger protein 11) gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

GeneCards Summary for SETDB2 Gene

SETDB2 (SET Domain Bifurcated Histone Lysine Methyltransferase 2) is a Protein Coding gene. Among its related pathways are Chromatin organization and Lysine degradation. Gene Ontology (GO) annotations related to this gene include histone-lysine N-methyltransferase activity and histone methyltransferase activity (H3-K9 specific). An important paralog of this gene is SETDB1.

UniProtKB/Swiss-Prot Summary for SETDB2 Gene

  • Histone methyltransferase involved in left-right axis specification in early development and mitosis. Specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). H3K9me3 is a specific tag for epigenetic transcriptional repression that recruits HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Contributes to H3K9me3 in both the interspersed repetitive elements and centromere-associated repeats. Plays a role in chromosome condensation and segregation during mitosis.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SETDB2 Gene

Genomics for SETDB2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SETDB2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SETDB2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SETDB2

Top Transcription factor binding sites by QIAGEN in the SETDB2 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Pax-4a
  • POU2F1
  • POU2F1a

Genomic Locations for SETDB2 Gene

Latest Assembly
chr13:49,444,274-49,495,003
(GRCh38/hg38)
Size:
50,730 bases
Orientation:
Plus strand

Previous Assembly
chr13:50,018,410-50,069,139
(GRCh37/hg19 by Entrez Gene)
Size:
50,730 bases
Orientation:
Plus strand

chr13:50,018,429-50,069,138
(GRCh37/hg19 by Ensembl)
Size:
50,710 bases
Orientation:
Plus strand

Genomic View for SETDB2 Gene

Genes around SETDB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETDB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETDB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETDB2 Gene

Proteins for SETDB2 Gene

  • Protein details for SETDB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96T68-SETB2_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase SETDB2
    Protein Accession:
    Q96T68
    Secondary Accessions:
    • Q5TC65
    • Q5TC66
    • Q5W0A7
    • Q659A7
    • Q86UD6
    • Q96AI6

    Protein attributes for SETDB2 Gene

    Size:
    719 amino acids
    Molecular mass:
    81894 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=CAH56265.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SETDB2 Gene

    Alternative splice isoforms for SETDB2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SETDB2 Gene

Post-translational modifications for SETDB2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SETDB2 Gene

Domains & Families for SETDB2 Gene

Gene Families for SETDB2 Gene

Protein Domains for SETDB2 Gene

InterPro:
Blocks:
  • Nuclear protein SET

Suggested Antigen Peptide Sequences for SETDB2 Gene

GenScript: Design optimal peptide antigens:
  • SET domain bifurcated 2 (SETB2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96T68

UniProtKB/Swiss-Prot:

SETB2_HUMAN :
  • In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Domain:
  • In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with SETDB2: view

Function for SETDB2 Gene

Molecular function for SETDB2 Gene

UniProtKB/Swiss-Prot Function:
Histone methyltransferase involved in left-right axis specification in early development and mitosis. Specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). H3K9me3 is a specific tag for epigenetic transcriptional repression that recruits HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Contributes to H3K9me3 in both the interspersed repetitive elements and centromere-associated repeats. Plays a role in chromosome condensation and segregation during mitosis.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine = H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60288, Rhea:RHEA-COMP:15538, Rhea:RHEA-COMP:15541, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961, ChEBI:CHEBI:61976;.

Enzyme Numbers (IUBMB) for SETDB2 Gene

Phenotypes From GWAS Catalog for SETDB2 Gene

Gene Ontology (GO) - Molecular Function for SETDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IEA,IPI 25416956
GO:0008168 methyltransferase activity IEA --
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with SETDB2: view
genes like me logo Genes that share phenotypes with SETDB2: view

Animal Models for SETDB2 Gene

MGI Knock Outs for SETDB2:
  • Setdb2 Setdb2<tm1a(KOMP)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SETDB2

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SETDB2 Gene

Localization for SETDB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETDB2 Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SETDB2 gene
Compartment Confidence
nucleus 5
cytosol 4
plasma membrane 2
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SETDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 20404330
GO:0005654 nucleoplasm IDA,TAS --
GO:0005694 chromosome IEA --
GO:0005829 cytosol IDA --
GO:0042025 host cell nucleus IEA --
genes like me logo Genes that share ontologies with SETDB2: view

Pathways & Interactions for SETDB2 Gene

genes like me logo Genes that share pathways with SETDB2: view

Pathways by source for SETDB2 Gene

1 BioSystems pathway for SETDB2 Gene
2 KEGG pathways for SETDB2 Gene

SIGNOR curated interactions for SETDB2 Gene

Activates:

Gene Ontology (GO) - Biological Process for SETDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 mitotic cell cycle IMP 20404330
GO:0001947 heart looping ISS --
GO:0006325 chromatin organization IEA --
GO:0007049 cell cycle IEA --
GO:0007059 chromosome segregation IMP 20404330
genes like me logo Genes that share ontologies with SETDB2: view

Drugs & Compounds for SETDB2 Gene

(1) Drugs for SETDB2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for SETDB2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-Amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with SETDB2: view

Transcripts for SETDB2 Gene

mRNA/cDNA for SETDB2 Gene

9 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SETDB2

Alternative Splicing Database (ASD) splice patterns (SP) for SETDB2 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c · 2d ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^
SP1:
SP2: -
SP3: - -
SP4:
SP5: -
SP6:
SP7: - - - -
SP8: - -
SP9:

ExUns: 17a · 17b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for SETDB2 Gene

GeneLoc Exon Structure for
SETDB2

Expression for SETDB2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SETDB2 Gene

Protein differential expression in normal tissues from HIPED for SETDB2 Gene

This gene is overexpressed in CD4 Tcells (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SETDB2 Gene



Protein tissue co-expression partners for SETDB2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SETDB2

SOURCE GeneReport for Unigene cluster for SETDB2 Gene:

Hs.631789

mRNA Expression by UniProt/SwissProt for SETDB2 Gene:

Q96T68-SETB2_HUMAN
Tissue specificity: Ubiquitous. Highest expression in heart, testis and ovary.

Evidence on tissue expression from TISSUES for SETDB2 Gene

  • Nervous system(4.4)
  • Intestine(4.4)
  • Skin(2)
genes like me logo Genes that share expression patterns with SETDB2: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SETDB2 Gene

Orthologs for SETDB2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SETDB2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SETDB2 29 30
  • 99.63 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SETDB2 29 30
  • 87.59 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SETDB2 29 30
  • 87.29 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Setdb2 29 16 30
  • 78.95 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SETDB2 30
  • 54 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SETDB2 30
  • 53 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SETDB2 29 30
  • 59.64 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SETDB2 30
  • 43 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia setdb2 29
  • 56.91 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC398711 29
Zebrafish
(Danio rerio)
Actinopterygii SETDB2 30
  • 29 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Set2 30
  • 4 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea set-11 30
  • 24 (a)
ManyToMany
met-2 30
  • 12 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET2 30
  • 9 (a)
OneToMany
Species where no ortholog for SETDB2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SETDB2 Gene

ENSEMBL:
Gene Tree for SETDB2 (if available)
TreeFam:
Gene Tree for SETDB2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SETDB2: view image
Alliance of Genome Resources:
Additional Orthologs for SETDB2

Paralogs for SETDB2 Gene

(2) SIMAP similar genes for SETDB2 Gene using alignment to 1 proteins:

  • SETB2_HUMAN
genes like me logo Genes that share paralogs with SETDB2: view

Variants for SETDB2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SETDB2 Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
rs111983452 Benign: not provided 49,482,790(+) G/A
NM_031915.3(SETDB2):c.1246G>A (p.Gly416Arg)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
rs189713465 Benign: not provided 49,490,916(+) A/C
NM_031915.3(SETDB2):c.2042+6A>C
INTRON
rs73491278 Benign: not provided 49,482,767(+) A/T
NM_031915.3(SETDB2):c.1223A>T (p.Lys408Ile)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
rs77248806 Benign: not provided 49,467,916(+) C/T
NM_031915.3(SETDB2):c.297C>T (p.Pro99=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs2057413 -- p.Val473Met

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SETDB2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SETDB2 Gene

Variant ID Type Subtype PubMed ID
dgv3139n54 CNV loss 21841781
esv2747394 CNV deletion 23290073
esv2747395 CNV deletion 23290073
esv3360364 CNV insertion 20981092
esv3374012 CNV insertion 20981092
esv3404 CNV loss 18987735
esv3632048 CNV loss 21293372
nsv523648 CNV gain 19592680
nsv561613 CNV loss 21841781

Variation tolerance for SETDB2 Gene

Residual Variation Intolerance Score: 32.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.70; 46.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SETDB2 Gene

Human Gene Mutation Database (HGMD)
SETDB2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SETDB2
Leiden Open Variation Database (LOVD)
SETDB2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETDB2 Gene

Disorders for SETDB2 Gene

Additional Disease Information for SETDB2

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for SETDB2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SETDB2 Gene

Publications for SETDB2 Gene

  1. Cloning and characterization of CLLD6, CLLD7, and CLLD8, novel candidate genes for leukemogenesis at chromosome 13q14, a region commonly deleted in B-cell chronic lymphocytic leukemia. (PMID: 11306461) Mabuchi H … Croce CM (Cancer research 2001) 2 3 4
  2. CLLD8/KMT1F is a lysine methyltransferase that is important for chromosome segregation. (PMID: 20404330) Falandry C … Magdinier F (The Journal of biological chemistry 2010) 3 4
  3. A multi-centre study of candidate genes for wheeze and allergy: the International Study of Asthma and Allergies in Childhood Phase 2. (PMID: 20085599) Genuneit J … ISAAC Phase 2 Study Group (Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology 2009) 3 40
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. The DNA sequence and analysis of human chromosome 13. (PMID: 15057823) Dunham A … Ross MT (Nature 2004) 3 4

Products for SETDB2 Gene

Sources for SETDB2 Gene