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

Gene ID: 56950, updated on 3-Apr-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
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Genomic context

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Location:
1q32.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (214281159..214337131)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (213520680..213576627)
105.20220307 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
  • 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. Targeting SMYD2 inhibits prostate cancer cell growth by regulating c-Myc signaling. Li J, et al. Mol Carcinog, 2023 Jul. PMID 37036190
  2. SMYD2 Expression: Its Relationship to Cytogenetic and Prognosis in a Newly Diagnosed Childhood B-Acute Lymphoblastic Leukemia. Gawdat RM, et al. Clin Lab, 2023 Mar 1. PMID 36912291
  3. SMYD2 Promotes Hepatocellular Carcinoma Progression by Reprogramming Glutamine Metabolism via c-Myc/GLS1 Axis. Xu K, et al. Cells, 2022 Dec 21. PMID 36611819, Free PMC Article
  4. Mechanistic and functional extrapolation of SET and MYND domain-containing protein 2 to pancreatic cancer. Alshammari E, et al. World J Gastroenterol, 2022 Aug 7. PMID 36157542, Free PMC Article
  5. Overexpression of SET and MYND domain-containing protein 2 (SMYD2) is associated with poor prognosis in pediatric B lineage acute lymphoblastic leukemia. Zhang P, et al. Leuk Lymphoma, 2020 Feb. PMID 31612757

See all (85) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. SMYD2 facilitates cancer cell malignancy and xenograft tumor development through ERBB2-mediated FUT4 expression in colon cancer.
    Title: SMYD2 facilitates cancer cell malignancy and xenograft tumor development through ERBB2-mediated FUT4 expression in colon cancer.
  9. STUB1-SMYD2 Axis Regulates Drug Resistance in Glioma cells.
    Title: STUB1-SMYD2 Axis Regulates Drug Resistance in Glioma cells.
  10. SMYD2 epigenetically activates MEX3A and suppresses CDX2 in colorectal cancer cells to augment cancer growth.
    Title: SMYD2 epigenetically activates MEX3A and suppresses CDX2 in colorectal cancer cells to augment cancer growth.
Submit: New GeneRIF Correction See all GeneRIFs (58)

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_2023_10

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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