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	56950
Gene name	SET and MYND domain containing 2
Gene symbol	SMYD2
Synonyms (NCBI Gene)	HSKM-BKMT3CZMYND14
Chromosome	1
Chromosome location	1q32.3
Summary	SET domain-containing proteins, such as SMYD2, catalyze lysine methylation (Brown et al., 2006 [PubMed 16805913]).[supplied by OMIM, Nov 2008]

Show/Hide all (78)

miRTarBase ID	miRNA	Experiments	Reference
MIRT020273	hsa-miR-130b-3p	Sequencing	20371350
MIRT029735	hsa-miR-26b-5p	Microarray	19088304
MIRT031254	hsa-miR-19b-3p	Sequencing	20371350
MIRT449759	hsa-miR-8087	PAR-CLIP	22100165
MIRT449758	hsa-miR-5588-3p	PAR-CLIP	22100165
MIRT449757	hsa-miR-4680-3p	PAR-CLIP	22100165
MIRT449756	hsa-miR-1253	PAR-CLIP	22100165
MIRT449755	hsa-miR-27b-5p	PAR-CLIP	22100165
MIRT449754	hsa-miR-4434	PAR-CLIP	22100165
MIRT449753	hsa-miR-4516	PAR-CLIP	22100165
MIRT449752	hsa-miR-5703	PAR-CLIP	22100165
MIRT449751	hsa-miR-183-3p	PAR-CLIP	22100165
MIRT449750	hsa-miR-628-5p	PAR-CLIP	22100165
MIRT449749	hsa-miR-4531	PAR-CLIP	22100165
MIRT737439	hsa-miR-125b-5p	MicroarrayImmunoprecipitaion (IP)Immunohistochemistry (IHC)qRT-PCRIn situ hybridization	31754403
MIRT449759	hsa-miR-8087	PAR-CLIP	22100165
MIRT449758	hsa-miR-5588-3p	PAR-CLIP	22100165
MIRT449757	hsa-miR-4680-3p	PAR-CLIP	22100165
MIRT449756	hsa-miR-1253	PAR-CLIP	22100165
MIRT449755	hsa-miR-27b-5p	PAR-CLIP	22100165
MIRT449754	hsa-miR-4434	PAR-CLIP	22100165
MIRT449753	hsa-miR-4516	PAR-CLIP	22100165
MIRT449752	hsa-miR-5703	PAR-CLIP	22100165
MIRT449751	hsa-miR-183-3p	PAR-CLIP	22100165
MIRT449750	hsa-miR-628-5p	PAR-CLIP	22100165
MIRT449749	hsa-miR-4531	PAR-CLIP	22100165
MIRT1374568	hsa-miR-122	CLIP-seq
MIRT1374569	hsa-miR-1287	CLIP-seq
MIRT1374570	hsa-miR-1297	CLIP-seq
MIRT1374571	hsa-miR-1298	CLIP-seq
MIRT1374572	hsa-miR-19a	CLIP-seq
MIRT1374573	hsa-miR-19b	CLIP-seq
MIRT1374574	hsa-miR-200b	CLIP-seq
MIRT1374575	hsa-miR-200c	CLIP-seq
MIRT1374576	hsa-miR-203	CLIP-seq
MIRT1374577	hsa-miR-26a	CLIP-seq
MIRT1374578	hsa-miR-26b	CLIP-seq
MIRT1374579	hsa-miR-3135b	CLIP-seq
MIRT1374580	hsa-miR-323-3p	CLIP-seq
MIRT1374581	hsa-miR-3675-3p	CLIP-seq
MIRT1374582	hsa-miR-374c	CLIP-seq
MIRT1374583	hsa-miR-375	CLIP-seq
MIRT1374584	hsa-miR-429	CLIP-seq
MIRT1374585	hsa-miR-4465	CLIP-seq
MIRT1374586	hsa-miR-4708-5p	CLIP-seq
MIRT1374587	hsa-miR-4753-3p	CLIP-seq
MIRT1374588	hsa-miR-4756-3p	CLIP-seq
MIRT1374589	hsa-miR-4797-5p	CLIP-seq
MIRT1374590	hsa-miR-655	CLIP-seq
MIRT1374591	hsa-miR-944	CLIP-seq
MIRT1374571	hsa-miR-1298	CLIP-seq
MIRT2111459	hsa-miR-3150a-5p	CLIP-seq
MIRT2111460	hsa-miR-3150b-5p	CLIP-seq
MIRT2111461	hsa-miR-3973	CLIP-seq
MIRT2111462	hsa-miR-4304	CLIP-seq
MIRT2111463	hsa-miR-4494	CLIP-seq
MIRT2111464	hsa-miR-499a-5p	CLIP-seq
MIRT2111465	hsa-miR-520g	CLIP-seq
MIRT2111466	hsa-miR-520h	CLIP-seq
MIRT2111467	hsa-miR-548al	CLIP-seq
MIRT2111468	hsa-miR-548k	CLIP-seq
MIRT1374568	hsa-miR-122	CLIP-seq
MIRT1374569	hsa-miR-1287	CLIP-seq
MIRT1374570	hsa-miR-1297	CLIP-seq
MIRT1374577	hsa-miR-26a	CLIP-seq
MIRT1374578	hsa-miR-26b	CLIP-seq
MIRT1374579	hsa-miR-3135b	CLIP-seq
MIRT1374580	hsa-miR-323-3p	CLIP-seq
MIRT1374583	hsa-miR-375	CLIP-seq
MIRT2111461	hsa-miR-3973	CLIP-seq
MIRT1374585	hsa-miR-4465	CLIP-seq
MIRT1374586	hsa-miR-4708-5p	CLIP-seq
MIRT1374588	hsa-miR-4756-3p	CLIP-seq
MIRT1374589	hsa-miR-4797-5p	CLIP-seq
MIRT2111468	hsa-miR-548k	CLIP-seq
MIRT1374591	hsa-miR-944	CLIP-seq
MIRT1374581	hsa-miR-3675-3p	CLIP-seq
MIRT2628607	hsa-miR-4496	CLIP-seq

Show/Hide all (36)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IMP	17108971
GO:0000993	Function	RNA polymerase II complex binding	IEA
GO:0000993	Function	RNA polymerase II complex binding	ISS
GO:0002039	Function	P53 binding	IPI	17108971
GO:0005515	Function	Protein binding	IPI	17805299, 20870719, 21782458, 24880080, 25609649, 27173435, 32296183, 32707033
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IDA	24880080
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	ISS
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	ISS
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IEA
GO:0007507	Process	Heart development	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0008285	Process	Negative regulation of cell population proliferation	IEA
GO:0008285	Process	Negative regulation of cell population proliferation	ISS
GO:0016278	Function	Lysine N-methyltransferase activity	TAS
GO:0016279	Function	Protein-lysine N-methyltransferase activity	IDA	17108971, 20870719
GO:0016279	Function	Protein-lysine N-methyltransferase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0018026	Process	Peptidyl-lysine monomethylation	IDA	17108971, 20870719
GO:0018027	Process	Peptidyl-lysine dimethylation	ISS
GO:0032259	Process	Methylation	IEA
GO:0042054	Function	Histone methyltransferase activity	IEA
GO:0043516	Process	Regulation of DNA damage response, signal transduction by p53 class mediator	IMP	17108971
GO:0046872	Function	Metal ion binding	IEA
GO:0046975	Function	Histone H3K36 methyltransferase activity	IEA
GO:0046975	Function	Histone H3K36 methyltransferase activity	ISS
GO:0140938	Function	Histone H3 methyltransferase activity	TAS
GO:0140999	Function	Histone H3K4 trimethyltransferase activity	IEA
GO:1901796	Process	Regulation of signal transduction by p53 class mediator	TAS

MIM	HGNC	e!Ensembl
610663	20982	ENSG00000143499

Q9NRG4

Protein name

N-lysine methyltransferase SMYD2 (EC 2.1.1.-) (HSKM-B) (Histone methyltransferase SMYD2) (EC 2.1.1.354) (Lysine N-methyltransferase 3C) (SET and MYND domain-containing protein 2)

Protein function

Protein-lysine N-methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. Specifically trimethylates histone H3 'Lys-4' (H3K4me3) in vivo. The activity requires interaction with HSP90alpha. Shows even

PDB

3RIB , 3S7B , 3S7D , 3S7F , 3S7J , 3TG4 , 3TG5 , 4O6F , 4WUY , 4YND , 5ARF , 5ARG , 5KJK , 5KJL , 5KJM , 5KJN , 5V3H , 5WCG , 6CBX , 6CBY , 6MON , 6N3G , 9CKC , 9CKF , 9CKG

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00856	SET	18 → 241	SET domain	Family
PF01753	zf-MYND	52 → 90	MYND finger	Domain

Sequence

MRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKE
GLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHP
ERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVN
CNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSY
IDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARN
VIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGAL
QYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDH
PYISEIKQEIESH

Sequence length

433

Interactions

View interactions

	KEGG		Reactome
	Lysine degradation Metabolic pathways		PKMTs methylate histone lysines Regulation of TP53 Activity through Methylation

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 (8)

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.
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIVERTICULAR DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ESOPHAGEAL NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROESOPHAGEAL REFLUX DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (28)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Achalasia Addisonianism Alacrimia syndrome	Associate	29507647	★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenoma Oxyphilic	Associate	26488939	★★★★★ ★☆☆☆☆ Found in Text Mining only
Aneurysm	Associate	29507647	★★★★★ ★☆☆☆☆ Found in Text Mining only
Aortic Aneurysm Abdominal	Associate	29507647	★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Associate	21103787, 25825497, 25925379	★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Stimulate	31693890	★★★★★ ★☆☆☆☆ Found in Text Mining only
Calcinosis Cutis	Associate	37121971	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Associate	21738746, 25825497, 30207284	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Associate	36411681, 36611819	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Non Small Cell Lung	Associate	28370702, 30207284	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Associate	26488939, 29099276	★★★★★ ★☆☆☆☆ Found in Text Mining only
COVID 19	Associate	35455942	★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Associate	25825497, 26750096	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Associate	33459509	★★★★★ ★☆☆☆☆ Found in Text Mining only
Inflammation	Associate	29507647	★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia	Associate	28187429	★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia Lymphocytic Chronic B Cell	Associate	26790435	★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Associate	28187429	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Stimulate	37121971	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Stimulate	25321194, 30319138	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasm Metastasis	Associate	37121971	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	21103787, 25825497, 25925379, 28370702, 36611819	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Stimulate	25321194, 30319138, 31693890	★★★★★ ★☆☆☆☆ Found in Text Mining only
Precancerous Conditions	Associate	30207284	★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinoblastoma	Associate	21738746	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Associate	25321194	★★★★★ ★☆☆☆☆ Found in Text Mining only
Thyroid Cancer Papillary	Associate	30319138	★★★★★ ★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Associate	30319138	★★★★★ ★☆☆☆☆ Found in Text Mining only

SMYD2 (SET and MYND domain containing 2)