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

Gene Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	56950
Gene name Gene Name - the full gene name approved by the HGNC.	SET and MYND domain containing 2
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SMYD2
Synonyms (NCBI Gene) Gene synonyms aliases	HSKM-B, KMT3C, ZMYND14
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1q32.3
Summary Summary of gene provided in NCBI Entrez Gene.	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	Microarray, Immunoprecipitaion (IP), Immunohistochemistry (IHC), qRT-PCR, In 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

Protein

UniProt ID

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

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Schizophrenia	Schizophrenia	N/A	N/A	GWAS

Show/Hide Text Mining Associations (28)

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

SMYD2 (SET and MYND domain containing 2)