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

    Gene ID: 150572, updated on 28-Oct-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 several functions, including histone H3K4 trimethyltransferase activity; metal ion binding activity; and transcription corepressor 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, Oct 2024]
    Expression
    Restricted expression toward heart (RPKM 63.9) See more
    Orthologs
    mouse all
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    Genomic context

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    See SMYD1 in Genome Data Viewer
    Location:
    2p11.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (88067825..88113384)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (88079089..88124637)
    RS_2024_09 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 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. Lysine Methyltransferase SMYD1 Regulates Myogenesis via skNAC Methylation. Zhu L, et al. Cells, 2023 Jun 22. PMID 37443729, Free PMC Article
    2. SMYD1, an SRF-Interacting Partner, Is Involved in Angiogenesis. Ye X, et al. PLoS One, 2016. PMID 26799706, Free PMC Article
    3. SMYD1 is the underlying gene for the AnWj-negative blood group phenotype. Yahalom V, et al. Eur J Haematol, 2018 Oct. PMID 29956848
    4. 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
    5. Binding Behavior of Human Hepatoma-Derived Growth Factor on SMYD1. Wu JK, et al. J Phys Chem B, 2024 Aug 15. PMID 39091133, Free PMC Article

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Binding Behavior of Human Hepatoma-Derived Growth Factor on SMYD1.
      Title: Binding Behavior of Human Hepatoma-Derived Growth Factor on SMYD1.
    2. Lysine Methyltransferase SMYD1 Regulates Myogenesis via skNAC Methylation.
      Title: Lysine Methyltransferase SMYD1 Regulates Myogenesis via skNAC Methylation.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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_2024_08

    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

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

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