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    SMYD2 SET and MYND domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 56950, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SMYD2provided by HGNC
    Official Full Name
    SET and MYND domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:20982
    See related
    Ensembl:ENSG00000143499 MIM:610663; AllianceGenome:HGNC:20982
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    KMT3C; HSKM-B; ZMYND14
    Summary
    SET domain-containing proteins, such as SMYD2, catalyze lysine methylation (Brown et al., 2006 [PubMed 16805913]).[supplied by OMIM, Nov 2008]
    Expression
    Broad expression in heart (RPKM 86.3), testis (RPKM 19.8) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMYD2 in Genome Data Viewer
    Location:
    1q32.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (214281159..214337131)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (213520680..213576627)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (214454502..214510474)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2775 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:214275569-214276768 Neighboring gene VISTA enhancer hs2357 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1810 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:214366166-214366732 Neighboring gene uncharacterized LOC124904509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1811 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:214453457-214454022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1814 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:214475531-214475666 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:214489845-214490348 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:214490349-214490852 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:214490853-214491356 Neighboring gene Sharpr-MPRA regulatory region 1006 Neighboring gene NANOG hESC enhancer GRCh37_chr1:214515875-214516376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:214543020-214543520 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:214553675-214554176 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:214554177-214554676 Neighboring gene protein tyrosine phosphatase non-receptor type 14 Neighboring gene uncharacterized LOC124904508 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:214592894-214593456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2532 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:214612491-214613462 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:214619781-214620467 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:214623549-214624048 Neighboring gene adaptor related protein complex 3 subunit sigma 1 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Discovery of substrates for a SET domain lysine methyltransferase predicted by multistate computational protein design. Lanouette S, et al. Structure, 2015 Jan 6. PMID 25533488
    2. SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells. Toghill BJ, et al. Clin Epigenetics, 2018. PMID 29507647, Free PMC Article
    3. Lysine methyltransferase SMYD2 promotes triple negative breast cancer progression. Li LX, et al. Cell Death Dis, 2018 Feb 27. PMID 29487338, Free PMC Article
    4. Genomic profiling in advanced stage non-small-cell lung cancer patients with platinum-based chemotherapy identifies germline variants with prognostic value in SMYD2. Galván-Femenía I, et al. Cancer Treat Res Commun, 2018. PMID 30207284
    5. Overexpression of SET and MYND Domain-Containing Protein 2 (SMYD2) Is Associated with Tumor Progression and Poor Prognosis in Patients with Papillary Thyroid Carcinoma. Xu W, et al. Med Sci Monit, 2018 Oct 15. PMID 30319138, Free PMC Article

    See all (90) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMYD2 Imparts Gemcitabine Resistance to Pancreatic Adenocarcinoma Cells by Upregulating EVI2A.
      Title: SMYD2 Imparts Gemcitabine Resistance to Pancreatic Adenocarcinoma Cells by Upregulating EVI2A.
    2. SMYD2 induced PGC1alpha methylation promotes stemness maintenance of glioblastoma stem cells.
      Title: SMYD2 induced PGC1α methylation promotes stemness maintenance of glioblastoma stem cells.
    3. Methylation of ESCRT-III components regulates the timing of cytokinetic abscission.
      Title: Methylation of ESCRT-III components regulates the timing of cytokinetic abscission.
    4. Lysine methyltransferase SMYD2 enhances androgen receptor signaling to modulate CRPC cell resistance to enzalutamide.
      Title: Lysine methyltransferase SMYD2 enhances androgen receptor signaling to modulate CRPC cell resistance to enzalutamide.
    5. Targeting SMYD2 inhibits prostate cancer cell growth by regulating c-Myc signaling.
      Title: Targeting SMYD2 inhibits prostate cancer cell growth by regulating c-Myc signaling.
    6. SMYD2 Expression: Its Relationship to Cytogenetic and Prognosis in a Newly Diagnosed Childhood B-Acute Lymphoblastic Leukemia.
      Title: SMYD2 Expression: Its Relationship to Cytogenetic and Prognosis in a Newly Diagnosed Childhood B-Acute Lymphoblastic Leukemia.
    7. SMYD2 Promotes Hepatocellular Carcinoma Progression by Reprogramming Glutamine Metabolism via c-Myc/GLS1 Axis.
      Title: SMYD2 Promotes Hepatocellular Carcinoma Progression by Reprogramming Glutamine Metabolism via c-Myc/GLS1 Axis.
    8. The lysine methyltransferases SET and MYND domain containing 2 (Smyd2) and Enhancer of Zeste 2 (Ezh2) co-regulate osteoblast proliferation and mineralization.
      Title: The lysine methyltransferases SET and MYND domain containing 2 (Smyd2) and Enhancer of Zeste 2 (Ezh2) co-regulate osteoblast proliferation and mineralization.
    9. Mechanistic and functional extrapolation of SET and MYND domain-containing protein 2 to pancreatic cancer.
      Title: Mechanistic and functional extrapolation of SET and MYND domain-containing protein 2 to pancreatic cancer.
    10. Overexpression of MCAM induced by SMYD2-H3K36me2 in breast cancer stem cell properties.
      Title: Overexpression of MCAM induced by SMYD2-H3K36me2 in breast cancer stem cell properties.
    Submit: New GeneRIF Correction See all GeneRIFs (61)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC119305

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase II complex binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables histone H3 methyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables histone H3K36 methyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables histone H3K4 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables lysine N-methyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables p53 binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-lysine N-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heart development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cell population proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in peptidyl-lysine dimethylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in peptidyl-lysine monomethylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA damage response, signal transduction by p53 class mediator IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of signal transduction by p53 class mediator TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    N-lysine methyltransferase SMYD2
    Names
    SET and MYND domain-containing protein 2
    histone methyltransferase SMYD2
    lysine N-methyltransferase 3C
    zinc finger, MYND domain containing 14
    NP_064582.2
    XP_047281656.1
    XP_047281658.1
    XP_054193731.1
    XP_054193732.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_020197.3 → NP_064582.2  N-lysine methyltransferase SMYD2

      See identical proteins and their annotated locations for NP_064582.2

      Status: VALIDATED

      Source sequence(s)
      AL929236, AW474469, BC098276, BG723585
      Consensus CDS
      CCDS31022.1
      UniProtKB/Swiss-Prot
      B2R9P9, I6L9H7, Q4V765, Q5VSH9, Q96AI4, Q9NRG4
      UniProtKB/TrEMBL
      I6L9D1
      Related
      ENSP00000355924.5, ENST00000366957.10
      Conserved Domains (2) summary
      cd19202
      Location:7 → 269
      SET_SMYD2; SET domain (including post-SET domain) found in SET and MYND domain-containing protein 2 (SMYD2) and similar proteins
      pfam01753
      Location:52 → 90
      zf-MYND; MYND finger

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      214281159..214337131
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425700.1 → XP_047281656.1  N-lysine methyltransferase SMYD2 isoform X1

      Related
      ENST00000460580.5

    2. XM_047425702.1 → XP_047281658.1  N-lysine methyltransferase SMYD2 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      213520680..213576627
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337756.1 → XP_054193731.1  N-lysine methyltransferase SMYD2 isoform X1

    2. XM_054337757.1 → XP_054193732.1  N-lysine methyltransferase SMYD2 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NRG4.2 GenPept UniProtKB/Swiss-Prot:Q9NRG4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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