Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	83852
Gene name	SET domain bifurcated histone lysine methyltransferase 2
Gene symbol	SETDB2
Synonyms (NCBI Gene)	C13orf4CLLD8CLLL8KMT1F
Chromosome	13
Chromosome location	13q14.2
Summary	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 se

154

Show/Hide all (154)

miRTarBase ID	miRNA	Experiments	Reference
MIRT717908	hsa-miR-4293	HITS-CLIP	19536157
MIRT717907	hsa-miR-4719	HITS-CLIP	19536157
MIRT717906	hsa-miR-4735-5p	HITS-CLIP	19536157
MIRT717905	hsa-miR-513b-5p	HITS-CLIP	19536157
MIRT717904	hsa-miR-3157-5p	HITS-CLIP	19536157
MIRT717903	hsa-miR-3161	HITS-CLIP	19536157
MIRT717908	hsa-miR-4293	HITS-CLIP	19536157
MIRT717907	hsa-miR-4719	HITS-CLIP	19536157
MIRT717906	hsa-miR-4735-5p	HITS-CLIP	19536157
MIRT717905	hsa-miR-513b-5p	HITS-CLIP	19536157
MIRT717904	hsa-miR-3157-5p	HITS-CLIP	19536157
MIRT717903	hsa-miR-3161	HITS-CLIP	19536157
MIRT717908	hsa-miR-4293	HITS-CLIP	19536157
MIRT717907	hsa-miR-4719	HITS-CLIP	19536157
MIRT717906	hsa-miR-4735-5p	HITS-CLIP	19536157
MIRT717905	hsa-miR-513b-5p	HITS-CLIP	19536157
MIRT717904	hsa-miR-3157-5p	HITS-CLIP	19536157
MIRT717903	hsa-miR-3161	HITS-CLIP	19536157
MIRT717908	hsa-miR-4293	HITS-CLIP	19536157
MIRT717907	hsa-miR-4719	HITS-CLIP	19536157
MIRT717906	hsa-miR-4735-5p	HITS-CLIP	19536157
MIRT717905	hsa-miR-513b-5p	HITS-CLIP	19536157
MIRT717904	hsa-miR-3157-5p	HITS-CLIP	19536157
MIRT717903	hsa-miR-3161	HITS-CLIP	19536157
MIRT1340779	hsa-miR-198	CLIP-seq
MIRT1340780	hsa-miR-214	CLIP-seq
MIRT1340781	hsa-miR-338-5p	CLIP-seq
MIRT1340782	hsa-miR-3619-5p	CLIP-seq
MIRT1340783	hsa-miR-3652	CLIP-seq
MIRT1340784	hsa-miR-3672	CLIP-seq
MIRT1340785	hsa-miR-4291	CLIP-seq
MIRT1340786	hsa-miR-431	CLIP-seq
MIRT1340787	hsa-miR-4422	CLIP-seq
MIRT1340788	hsa-miR-4430	CLIP-seq
MIRT1340789	hsa-miR-4436b-5p	CLIP-seq
MIRT1340790	hsa-miR-4496	CLIP-seq
MIRT1340791	hsa-miR-4517	CLIP-seq
MIRT1340792	hsa-miR-455-3p	CLIP-seq
MIRT1340793	hsa-miR-4662a-3p	CLIP-seq
MIRT1340794	hsa-miR-4712-3p	CLIP-seq
MIRT1340795	hsa-miR-4766-5p	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT1340796	hsa-miR-657	CLIP-seq
MIRT1340797	hsa-miR-761	CLIP-seq
MIRT1340798	hsa-miR-922	CLIP-seq
MIRT1340799	hsa-miR-1276	CLIP-seq
MIRT1340800	hsa-miR-142-5p	CLIP-seq
MIRT1340801	hsa-miR-2052	CLIP-seq
MIRT1340802	hsa-miR-3160-3p	CLIP-seq
MIRT1340803	hsa-miR-340	CLIP-seq
MIRT1340804	hsa-miR-3646	CLIP-seq
MIRT1340805	hsa-miR-3662	CLIP-seq
MIRT1340806	hsa-miR-3685	CLIP-seq
MIRT1340807	hsa-miR-3689d	CLIP-seq
MIRT1340808	hsa-miR-384	CLIP-seq
MIRT1340809	hsa-miR-3915	CLIP-seq
MIRT1340810	hsa-miR-3928	CLIP-seq
MIRT1340811	hsa-miR-4268	CLIP-seq
MIRT1340812	hsa-miR-4307	CLIP-seq
MIRT1340813	hsa-miR-4311	CLIP-seq
MIRT1340814	hsa-miR-4423-5p	CLIP-seq
MIRT1340815	hsa-miR-4448	CLIP-seq
MIRT1340816	hsa-miR-451b	CLIP-seq
MIRT1340817	hsa-miR-4698	CLIP-seq
MIRT1340795	hsa-miR-4766-5p	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT1340818	hsa-miR-488	CLIP-seq
MIRT1340819	hsa-miR-489	CLIP-seq
MIRT1340820	hsa-miR-514	CLIP-seq
MIRT1340821	hsa-miR-514b-3p	CLIP-seq
MIRT1340822	hsa-miR-548a-3p	CLIP-seq
MIRT1340823	hsa-miR-548e	CLIP-seq
MIRT1340824	hsa-miR-548f	CLIP-seq
MIRT1340825	hsa-miR-583	CLIP-seq
MIRT1553607	hsa-miR-4428	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT2100822	hsa-miR-106a	CLIP-seq
MIRT2100823	hsa-miR-106b	CLIP-seq
MIRT2100824	hsa-miR-1234	CLIP-seq
MIRT2100825	hsa-miR-17	CLIP-seq
MIRT1340801	hsa-miR-2052	CLIP-seq
MIRT2100826	hsa-miR-20a	CLIP-seq
MIRT2100827	hsa-miR-20b	CLIP-seq
MIRT2100828	hsa-miR-302a	CLIP-seq
MIRT2100829	hsa-miR-302b	CLIP-seq
MIRT2100830	hsa-miR-302c	CLIP-seq
MIRT2100831	hsa-miR-302d	CLIP-seq
MIRT2100832	hsa-miR-302e	CLIP-seq
MIRT1340806	hsa-miR-3685	CLIP-seq
MIRT2100833	hsa-miR-371-5p	CLIP-seq
MIRT2100834	hsa-miR-371b-5p	CLIP-seq
MIRT2100835	hsa-miR-372	CLIP-seq
MIRT2100836	hsa-miR-373	CLIP-seq
MIRT1340808	hsa-miR-384	CLIP-seq
MIRT2100837	hsa-miR-3973	CLIP-seq
MIRT1340811	hsa-miR-4268	CLIP-seq
MIRT1340812	hsa-miR-4307	CLIP-seq
MIRT1340815	hsa-miR-4448	CLIP-seq
MIRT2100838	hsa-miR-4757-5p	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT2100839	hsa-miR-519d	CLIP-seq
MIRT2100840	hsa-miR-520a-3p	CLIP-seq
MIRT2100841	hsa-miR-520b	CLIP-seq
MIRT2100842	hsa-miR-520c-3p	CLIP-seq
MIRT2100843	hsa-miR-520d-3p	CLIP-seq
MIRT2100844	hsa-miR-520e	CLIP-seq
MIRT2100845	hsa-miR-520g	CLIP-seq
MIRT2100846	hsa-miR-520h	CLIP-seq
MIRT2100847	hsa-miR-93	CLIP-seq
MIRT2100822	hsa-miR-106a	CLIP-seq
MIRT2100823	hsa-miR-106b	CLIP-seq
MIRT2100824	hsa-miR-1234	CLIP-seq
MIRT2100825	hsa-miR-17	CLIP-seq
MIRT2100826	hsa-miR-20a	CLIP-seq
MIRT2100827	hsa-miR-20b	CLIP-seq
MIRT2100833	hsa-miR-371-5p	CLIP-seq
MIRT2100834	hsa-miR-371b-5p	CLIP-seq
MIRT2100837	hsa-miR-3973	CLIP-seq
MIRT2325357	hsa-miR-4276	CLIP-seq
MIRT2100838	hsa-miR-4757-5p	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT2325358	hsa-miR-4803	CLIP-seq
MIRT2100839	hsa-miR-519d	CLIP-seq
MIRT2100845	hsa-miR-520g	CLIP-seq
MIRT2100846	hsa-miR-520h	CLIP-seq
MIRT2100847	hsa-miR-93	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT1340783	hsa-miR-3652	CLIP-seq
MIRT1340786	hsa-miR-431	CLIP-seq
MIRT1340788	hsa-miR-4430	CLIP-seq
MIRT2459174	hsa-miR-924	CLIP-seq
MIRT1340783	hsa-miR-3652	CLIP-seq
MIRT1340786	hsa-miR-431	CLIP-seq
MIRT1340788	hsa-miR-4430	CLIP-seq
MIRT2459174	hsa-miR-924	CLIP-seq
MIRT2621024	hsa-miR-129-5p	CLIP-seq
MIRT2621025	hsa-miR-21	CLIP-seq
MIRT2621026	hsa-miR-3149	CLIP-seq
MIRT2621027	hsa-miR-3674	CLIP-seq
MIRT2621028	hsa-miR-4694-5p	CLIP-seq
MIRT2621029	hsa-miR-4755-3p	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT2621030	hsa-miR-590-3p	CLIP-seq
MIRT2621031	hsa-miR-590-5p	CLIP-seq
MIRT2621026	hsa-miR-3149	CLIP-seq
MIRT2621029	hsa-miR-4755-3p	CLIP-seq
MIRT739064	hsa-miR-4775	CLIP-seq
MIRT2621030	hsa-miR-590-3p	CLIP-seq

Show/Hide all (31)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000278	Process	Mitotic cell cycle	IMP	20404330
GO:0001947	Process	Heart looping	ISS
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	25416956, 28514442, 31515488, 32296183, 33961781
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	20404330
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IEA
GO:0007059	Process	Chromosome segregation	IMP	20404330
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0010629	Process	Negative regulation of gene expression	IBA
GO:0016740	Function	Transferase activity	IEA
GO:0032259	Process	Methylation	IEA
GO:0042054	Function	Histone methyltransferase activity	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	ISS
GO:0046872	Function	Metal ion binding	IEA
GO:0046974	Function	Histone H3K9 methyltransferase activity	IBA
GO:0046974	Function	Histone H3K9 methyltransferase activity	IDA	20404330
GO:0046974	Function	Histone H3K9 methyltransferase activity	IEA
GO:0051301	Process	Cell division	IEA
GO:0070828	Process	Heterochromatin organization	IBA
GO:0070986	Process	Left/right axis specification	ISS
GO:0140938	Function	Histone H3 methyltransferase activity	TAS
GO:0140948	Function	Histone H3K9 monomethyltransferase activity	IEA

MIM	HGNC	e!Ensembl
607865	20263	ENSG00000136169

Q96T68

Protein name

Histone-lysine N-methyltransferase SETDB2 (EC 2.1.1.366) (Chronic lymphocytic leukemia deletion region gene 8 protein) (Lysine N-methyltransferase 1F) (SET domain bifurcated 2)

Protein 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 H

PDB

5TFP , 8HFP

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01429	MBD	160 → 232	Methyl-CpG binding domain	Domain
PF05033	Pre-SET	246 → 359	Pre-SET motif	Family
PF00856	SET	378 → 694	SET domain	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous. Highest expression in heart, testis and ovary.

Sequence

MGEKNGDAKTFWMELEDDGKVDFIFEQVQNVLQSLKQKIKDGSATNKEYIQAMILVNEAT
IINSSTSIKGASQKEVNAQSSDPMPVTQKEQENKSNAFPSTSCENSFPEDCTFLTTENKE
ILSLEDKVVDFREKDSSSNLSYQSHDCSGACLMKMPLNLKGENPLQLPIKCHFQRRHAKT
NSHSSALHVSYKTPCGRSLRNVEEVFRYLLETECNFLFTDNFSFNTYVQLARNYPKQKEV
VSDVDISNGVESVPISFCNEIDSRKLPQFKYRKTVWPRAYNLTNFSSMFTDSCDCSEGCI
DITKCACLQLTARNAKTSPLSSDKITTGYKYKRLQRQIPTGIYECSLLCKCNRQLCQNRV
VQHGPQVRLQVFKTEQKGWGVRCLDDIDRGTFVCIYSGRLLSRANTEKSYGIDENGRDEN
TMKNIFSKKRKLEVACSDCEVEVLPLGLETHPRTAKTEKCPPKFSNNPKELTVETKYDNI
SRIQYHSVIRDPESKTAIFQHNGKKMEFVSSESVTPEDNDGFKPPREHLNSKTKGAQKDS
SSNHVDEFEDNLLIESDVIDITKYREETPPRSRCNQATTLDNQNIKKAIEVQIQKPQEGR
STACQRQQVFCDEELLSETKNTSSDSLTKFNKGNVFLLDATKEGNVGRFLNHSCCPNLLV
QNVFVETHNRNFPLVAFFTNRYVKARTELTWDYGYEAGTVPEKEIFCQCGVNKCRKKIL

Sequence length

719

Interactions

View interactions

	KEGG		Reactome
	Lysine degradation Metabolic pathways		PKMTs methylate histone lysines

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
DYSLEXIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (27)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Acute leukemia	Leukemia	BEFREE	29694893		★★★★★ ★☆☆☆☆ Found in Text Mining only
Acute lymphocytic leukemia	Lymphocytic Leukemia	BEFREE	29694893		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adult Acute Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	29694893		★★★★★ ★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	Pubtator	26378653, 29234167	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	Pubtator	23055267	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
B-CELL MALIGNANCY, LOW-GRADE	Lymphocytic Leukemia	BEFREE	11306461		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	32549764	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	29099276	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	29099276	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Childhood Acute Lymphoblastic Leukemia	Lymphoblastic Leukemia	BEFREE	29694893		★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	11306461		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	24925220		★★★★★ ★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	29099276		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	31350176		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	31350176		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	31433963	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	31433963		★★★★★ ★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	BEFREE	30670717		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hurthle Cell Tumor	Tumor	BEFREE	29099276		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypersensitivity Immediate	Hypersensitivity	Pubtator	29234167	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia	Leukemia	Pubtator	29694893	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	29694893, 32549764	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	30850015		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	29694893		★★★★★ ★☆☆☆☆ Found in Text Mining only
Papillary Renal Cell Carcinoma	Papillary Renal Carcinoma	BEFREE	29099276		★★★★★ ★☆☆☆☆ Found in Text Mining only
Renal Cell Carcinoma	Renal Carcinoma	BEFREE	29099276		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	27572307, 32549764	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

SETDB2 (SET domain bifurcated histone lysine methyltransferase 2)