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SMYD1 SET and MYND domain containing 1 [ Homo sapiens (human) ]

Gene ID: 150572, updated on 10-Mar-2024

Summary

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Official Symbol
SMYD1provided by HGNC
Official Full Name
SET and MYND domain containing 1provided by HGNC
Primary source
HGNC:HGNC:20986
See related
Ensembl:ENSG00000115593 MIM:606846; AllianceGenome:HGNC:20986
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
BOP; KMT3D; ZMYND18; ZMYND22
Summary
Predicted to enable histone-lysine N-methyltransferase activity. Involved in positive regulation of myoblast differentiation and positive regulation of myotube differentiation. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward heart (RPKM 63.9) See more
Orthologs
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Genomic context

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Location:
2p11.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (88067825..88113384)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (88079089..88124637)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (88367344..88412903)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16166 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:88318573-88319088 Neighboring gene lysine rich coiled-coil 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16167 Neighboring gene CRISPRi-validated cis-regulatory element chr2.3248 Neighboring gene skeletal muscle cis-regulatory module upstream of SMYD1 Neighboring gene Sharpr-MPRA regulatory region 1533 Neighboring gene microRNA 4780 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:88406623-88407124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:88407125-88407624 Neighboring gene Sharpr-MPRA regulatory region 11659 Neighboring gene fatty acid binding protein 1 Neighboring gene uncharacterized LOC101928347

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. A de novo mutation of SMYD1 (p.F272L) is responsible for hypertrophic cardiomyopathy in a Chinese patient. Fan LL, et al. Clin Chem Lab Med, 2019 Mar 26. PMID 30205637
  2. SMYD1 is the underlying gene for the AnWj-negative blood group phenotype. Yahalom V, et al. Eur J Haematol, 2018 Oct. PMID 29956848
  3. SMYD1, an SRF-Interacting Partner, Is Involved in Angiogenesis. Ye X, et al. PLoS One, 2016. PMID 26799706, Free PMC Article
  4. The Methyltransferase Smyd1 Mediates LPS-Triggered Up-Regulation of IL-6 in Endothelial Cells. Shamloul A, et al. Cells, 2021 Dec 13. PMID 34944023, Free PMC Article
  5. Stability of Smyd1 in endothelial cells is controlled by PML-dependent SUMOylation upon cytokine stimulation. Becker S, et al. Biochem J, 2021 Jan 15. PMID 33241844

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Lysine Methyltransferase SMYD1 Regulates Myogenesis via skNAC Methylation.
    Title: Lysine Methyltransferase SMYD1 Regulates Myogenesis via skNAC Methylation.
  2. The Methyltransferase Smyd1 Mediates LPS-Triggered Up-Regulation of IL-6 in Endothelial Cells.
    Title: The Methyltransferase Smyd1 Mediates LPS-Triggered Up-Regulation of IL-6 in Endothelial Cells.
  3. Stability of Smyd1 in endothelial cells is controlled by PML-dependent SUMOylation upon cytokine stimulation.
    Title: Stability of Smyd1 in endothelial cells is controlled by PML-dependent SUMOylation upon cytokine stimulation.
  4. Modulation of chromatin remodeling proteins SMYD1 and SMARCD1 promotes contractile function of human pluripotent stem cell-derived ventricular cardiomyocyte in 3D-engineered cardiac tissues.
    Title: Modulation of chromatin remodeling proteins SMYD1 and SMARCD1 promotes contractile function of human pluripotent stem cell-derived ventricular cardiomyocyte in 3D-engineered cardiac tissues.
  5. This novel mutation (c.814T>C/p.F272L) may be the first identified disease-causing mutation of SMYD1 in Hypertrophic cardiomyopathy (HCM) patients worldwide.
    Title: A de novo mutation of SMYD1 (p.F272L) is responsible for hypertrophic cardiomyopathy in a Chinese patient.
  6. We present genetic and statistical evidence that the R320Q substitution in SMYD1 underlies an inherited form of the AnWj-negative blood group phenotype. The mechanism by which the mutation leads to this phenotype remains to be determined.
    Title: SMYD1 is the underlying gene for the AnWj-negative blood group phenotype.
  7. SMYD1 serves as an Serum Response Factor-interacting protein, enhances Serum Response Factor DNA binding activity, and is required for endothelial cell migration and tube formation to regulate angiogenesis.
    Title: SMYD1, an SRF-Interacting Partner, Is Involved in Angiogenesis.
  8. SMYD1 and G6PD modulation are critical events for miR-206-mediated differentiation of rhabdomyosarcoma.
    Title: SMYD1 and G6PD modulation are critical events for miR-206-mediated differentiation of rhabdomyosarcoma.
  9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  10. HDGF functions as a transcriptional repressor of the SMYD1 gene through interaction with the transcriptional corepressor CtBP.
    Title: Hepatoma-derived growth factor represses SET and MYND domain containing 1 gene expression through interaction with C-terminal binding protein.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K4 trimethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription corepressor activity IEA
Inferred from Electronic Annotation
more info
  
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 methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of myoblast differentiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of myotube differentiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in skeletal muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
histone-lysine N-methyltransferase SMYD1
Names
CD8 beta opposite
SET and MYND domain-containing protein 1
zinc finger, MYND domain containing 18
NP_001317293.1
NP_938015.1

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_001330364.2 → NP_001317293.1  histone-lysine N-methyltransferase SMYD1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2)
    Source sequence(s)
    AC092836
    Consensus CDS
    CCDS82480.1
    UniProtKB/TrEMBL
    E9PHG3, Q5HYE8
    Related
    ENSP00000407888.2, ENST00000444564.2
    Conserved Domains (2) summary
    smart00317
    Location:194 → 244
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam01753
    Location:52 → 90
    zf-MYND; MYND finger

  2. NM_198274.4 → NP_938015.1  histone-lysine N-methyltransferase SMYD1 isoform 1

    See identical proteins and their annotated locations for NP_938015.1

    Status: VALIDATED

    Source sequence(s)
    AC092836, AL832035, BC126191, BX647878
    Consensus CDS
    CCDS33240.1
    UniProtKB/Swiss-Prot
    A0AV30, A6NE13, Q8NB12
    UniProtKB/TrEMBL
    Q5HYE8
    Related
    ENSP00000393453.2, ENST00000419482.7
    Conserved Domains (2) summary
    smart00317
    Location:194 → 257
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    88067825..88113384
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    88079089..88124637
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NB12.1 GenPept UniProtKB/Swiss-Prot:Q8NB12

Gene LinkOut

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