SMYD2 (SET and MYND domain containing 2)

Gene

• Entrez ID: 56950
• Gene name: SET and MYND domain containing 2
• Gene symbol: SMYD2
• Synonyms (NCBI Gene): HSKM-B, KMT3C, ZMYND14
• 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]

miRNA

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

Gene ontology (GO)

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

Other IDs

• MIM: 610663
• HGNC: 20982
• e!Ensembl: 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

Pathways

KEGG:

Lysine degradation
Metabolic pathways

Reactome:

PKMTs methylate histone lysines
Regulation of TP53 Activity through Methylation

Associated diseases

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
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

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acute lymphocytic leukemia	Lymphocytic Leukemia	BEFREE	24631370, 31612757		★☆☆☆☆ Found in Text Mining only
Adult Acute Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	24631370		★☆☆☆☆ Found in Text Mining only
Aneurysm	Aneurysm	Pubtator	29507647	Associate	★☆☆☆☆ Found in Text Mining only
ANOPHTHALMIA AND PULMONARY HYPOPLASIA	Syndromic microphthalmia	BEFREE	26988419		★☆☆☆☆ Found in Text Mining only
Aortic Aneurysm Abdominal	Aortic aneurysm	Pubtator	29507647	Associate	★☆☆☆☆ Found in Text Mining only
Aortic Aneurysm, Abdominal	Aortic Aneurysm	BEFREE	27899403, 31680049		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	29487338, 30930987, 31693890		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	21103787, 25825497, 25925379	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	31693890	Stimulate	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	21738746, 25825497, 30207284	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	22787429, 26826421		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	36411681, 36611819	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of bladder	Bladder carcinoma	BEFREE	30319138		★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	26488939, 29099276	Associate	★☆☆☆☆ Found in Text Mining only
Cardiovascular Diseases	Cardiovascular Diseases	BEFREE	31370883		★☆☆☆☆ Found in Text Mining only
cervical cancer	Cervical Cancer	BEFREE	31548876		★☆☆☆☆ Found in Text Mining only
Cervix carcinoma	Cervix carcinoma	BEFREE	31548876		★☆☆☆☆ Found in Text Mining only
Childhood Acute Lymphoblastic Leukemia	Lymphoblastic Leukemia	BEFREE	24631370		★☆☆☆☆ Found in Text Mining only
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	26790435		★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	31040701		★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	26488939, 29099276, 31754403		★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophagus Neoplasm	CTD_human_DG	25825497		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	25825497, 26750096	Associate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	33459509	Associate	★☆☆☆☆ Found in Text Mining only
Hurthle Cell Tumor	Tumor	BEFREE	26488939		★☆☆☆☆ Found in Text Mining only
leukemia	Leukemia	BEFREE	28187429		★☆☆☆☆ Found in Text Mining only
Leukemia	Leukemia	Pubtator	28187429	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	28187429	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	28187429		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	29344279		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	37121971	Stimulate	★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	25321194, 30319138	Stimulate	★☆☆☆☆ Found in Text Mining only
Lymphoma	Lymphoma	BEFREE	31257681		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of brain	Brain Neoplasms	BEFREE	28494238		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	29487338, 31693890		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of esophagus	Esophagus Neoplasm	CTD_human_DG	25825497		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	26988419		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	25321194		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	22787429, 25321194, 26790435, 26826421, 31040701, 31370883, 31548876, 31612757		★☆☆☆☆ Found in Text Mining only
Malignant tumor of cervix	Cervical Tumor	BEFREE	31548876		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	31040701		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	29487338		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	25321194, 26488939, 26826421, 26988419, 28370702, 29344279, 29487338, 30319138, 30930987, 31106145, 31754403		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	28370702, 31106145		★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	26988419		★☆☆☆☆ Found in Text Mining only
Papillary thyroid carcinoma	Papillary thyroid carcinoma	BEFREE	30319138		★☆☆☆☆ Found in Text Mining only
POLYCYSTIC KIDNEY DISEASE 1	Polycystic kidney disease	BEFREE	28604386		★☆☆☆☆ Found in Text Mining only
Polycystic Kidney, Autosomal Dominant	Polycystic kidney disease	BEFREE	28604386		★☆☆☆☆ Found in Text Mining only
Precursor Cell Lymphoblastic Leukemia Lymphoma	Lymphoblastic Leukemia	BEFREE	31612757		★☆☆☆☆ Found in Text Mining only
Renal Cell Carcinoma	Renal Carcinoma	BEFREE	26488939, 31754403		★☆☆☆☆ Found in Text Mining only
Retinoblastoma	Retinoblastoma	Pubtator	21738746	Associate	★☆☆☆☆ Found in Text Mining only
Simple renal cyst	Renal cyst	BEFREE	28604386		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	26826421		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of the head and neck	Carcinoma Of The Head And Neck	BEFREE	26826421		★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	25321194		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	25321194	Associate	★☆☆☆☆ Found in Text Mining only
Thyroid Cancer Papillary	Papillary thyroid cancer	Pubtator	30319138	Associate	★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple Negative Breast Neoplasms	BEFREE	29487338		★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	30319138	Associate	★☆☆☆☆ Found in Text Mining only