Aliases for SMYD1 Gene

Aliases for SMYD1 Gene

  • SET And MYND Domain Containing 1 2 3 5
  • Histone-Lysine N-Methyltransferase SMYD1 3 4
  • SET And MYND Domain-Containing Protein 1 3 4
  • ZMYND22 2 3
  • KMT3D 2 3
  • BOP 2 3
  • Zinc Finger, MYND Domain Containing 18 3
  • CD8 Beta Opposite 3
  • EC 2.1.1.354 4
  • ZMYND18 3
  • SMYD1 5

External Ids for SMYD1 Gene

Previous GeneCards Identifiers for SMYD1 Gene

  • GC02P088252
  • GC02P088269
  • GC02P088206
  • GC02P088367
  • GC02P087289

Summaries for SMYD1 Gene

GeneCards Summary for SMYD1 Gene

SMYD1 (SET And MYND Domain Containing 1) is a Protein Coding gene. Diseases associated with SMYD1 include Hypertrophic Cardiomyopathy. Among its related pathways are Lysine degradation and Heart Development. Gene Ontology (GO) annotations related to this gene include transcription corepressor activity and histone-lysine N-methyltransferase activity. An important paralog of this gene is SMYD2.

UniProtKB/Swiss-Prot Summary for SMYD1 Gene

  • Methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. Acts as a transcriptional repressor. Essential for cardiomyocyte differentiation and cardiac morphogenesis.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMYD1 Gene

Genomics for SMYD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SMYD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J088066 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 256.8 +1.3 1290 5.8 MAFF MAFK NR2F6 L3MBTL2 GATA2 MLLT1 PKNOX1 SMYD1 FABP1 THNSL2 MIR4780
GH02J088067 Enhancer 0.2 Ensembl 250.7 -1.7 -1724 0.2 KRCC1 SMYD1
GH02J088074 Enhancer 1 FANTOM5 Ensembl ENCODE 4.4 +7.3 7275 1.8 CEBPA CEBPB TAL1 JUND TCF12 RAD21 POLR2A HLF KDM1A CBFA2T2 FABP1 THNSL2 SMYD1 MIR4780
GH02J088081 Enhancer 0.4 Ensembl 5.8 +15.0 14976 1.6 SOX5 SOX13 MNT MIR4780 FABP1 THNSL2 SMYD1 HSALNG0016673
GH02J088076 Enhancer 0.2 Ensembl 4.4 +9.8 9776 1.6 FABP1 THNSL2 SMYD1 MIR4780
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMYD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMYD1

Top Transcription factor binding sites by QIAGEN in the SMYD1 gene promoter:
  • aMEF-2
  • Elk-1
  • GATA-1
  • HOXA5
  • HOXA9
  • HOXA9B
  • MEF-2A
  • Meis-1
  • Meis-1a
  • POU6F1 (c2)

Genomic Locations for SMYD1 Gene

Latest Assembly
chr2:88,067,825-88,113,384
(GRCh38/hg38)
Size:
45,560 bases
Orientation:
Plus strand

Previous Assembly
chr2:88,367,344-88,412,903
(GRCh37/hg19 by Entrez Gene)
Size:
45,560 bases
Orientation:
Plus strand

chr2:88,367,299-88,412,906
(GRCh37/hg19 by Ensembl)
Size:
45,608 bases
Orientation:
Plus strand

Genomic View for SMYD1 Gene

Genes around SMYD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMYD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMYD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMYD1 Gene

Proteins for SMYD1 Gene

  • Protein details for SMYD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NB12-SMYD1_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase SMYD1
    Protein Accession:
    Q8NB12
    Secondary Accessions:
    • A0AV30
    • A6NE13

    Protein attributes for SMYD1 Gene

    Size:
    490 amino acids
    Molecular mass:
    56617 Da
    Quaternary structure:
    • Interacts with HDAC1, HDAC2 and HDAC3. Interacts (via MYND-type zinc finger) with NACA isoform skNAC.

neXtProt entry for SMYD1 Gene

Post-translational modifications for SMYD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SMYD1 Gene

No data available for DME Specific Peptides for SMYD1 Gene

Domains & Families for SMYD1 Gene

Gene Families for SMYD1 Gene

Protein Domains for SMYD1 Gene

InterPro:
Blocks:
  • Nuclear protein SET
  • Zn-finger, MYND type

Suggested Antigen Peptide Sequences for SMYD1 Gene

GenScript: Design optimal peptide antigens:
  • Hypothetical rhabdomyosarcoma antigen MU-RMS-40.9A (Q5GJ33_HUMAN)
  • SET and MYND domain-containing protein 1 (SMYD1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NB12

UniProtKB/Swiss-Prot:

SMYD1_HUMAN :
  • The SET domain is split between the S-sequence (residues 1-49) and the core SET domain (residues 181-258), however the two segments still come together to form a conserved SET domain fold.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Domain:
  • The SET domain is split between the S-sequence (residues 1-49) and the core SET domain (residues 181-258), however the two segments still come together to form a conserved SET domain fold.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with SMYD1: view

Function for SMYD1 Gene

Molecular function for SMYD1 Gene

UniProtKB/Swiss-Prot Function:
Methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. Acts as a transcriptional repressor. Essential for cardiomyocyte differentiation and cardiac morphogenesis.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60260, Rhea:RHEA-COMP:15537, Rhea:RHEA-COMP:15547, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.354; Evidence={ECO:0000250|UniProtKB:P97443};.
UniProtKB/Swiss-Prot Induction:
By serum response factor SRF and myogenin. SRF binds to the CArG site and MYOG binds to the E-box element on SMYD1 promoter.

Enzyme Numbers (IUBMB) for SMYD1 Gene

Phenotypes From GWAS Catalog for SMYD1 Gene

Gene Ontology (GO) - Molecular Function for SMYD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003714 transcription corepressor activity IEA --
GO:0005515 protein binding IEA,IPI 23455924
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with SMYD1: view
genes like me logo Genes that share phenotypes with SMYD1: view

Animal Models for SMYD1 Gene

MGI Knock Outs for SMYD1:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMYD1

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SMYD1 Gene

Localization for SMYD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMYD1 Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMYD1 gene
Compartment Confidence
nucleus 4
extracellular 2
cytoskeleton 2
cytosol 2
plasma membrane 1
mitochondrion 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for SMYD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with SMYD1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SMYD1 Gene

Pathways & Interactions for SMYD1 Gene

genes like me logo Genes that share pathways with SMYD1: view

Pathways by source for SMYD1 Gene

2 BioSystems pathways for SMYD1 Gene
2 KEGG pathways for SMYD1 Gene
1 GeneTex pathway for SMYD1 Gene

Gene Ontology (GO) - Biological Process for SMYD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006338 chromatin remodeling IEA --
GO:0007507 heart development IEA --
GO:0010831 positive regulation of myotube differentiation IDA 19783823
GO:0032259 methylation IEA --
GO:0034968 histone lysine methylation IBA 21873635
genes like me logo Genes that share ontologies with SMYD1: view

No data available for SIGNOR curated interactions for SMYD1 Gene

Drugs & Compounds for SMYD1 Gene

No Compound Related Data Available

Transcripts for SMYD1 Gene

mRNA/cDNA for SMYD1 Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMYD1

Alternative Splicing Database (ASD) splice patterns (SP) for SMYD1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12
SP1: -
SP2: -
SP3:
SP4: - - - - - - - - - - - -

Relevant External Links for SMYD1 Gene

GeneLoc Exon Structure for
SMYD1

Expression for SMYD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SMYD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMYD1 Gene

This gene is overexpressed in Muscle - Skeletal (x20.4), Heart - Left Ventricle (x20.2), and Heart - Atrial Appendage (x6.0).

Protein differential expression in normal tissues from HIPED for SMYD1 Gene

This gene is overexpressed in Heart (32.6), Fetal heart (18.8), and Tonsil (15.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SMYD1 Gene



Protein tissue co-expression partners for SMYD1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SMYD1

SOURCE GeneReport for Unigene cluster for SMYD1 Gene:

Hs.516176

mRNA Expression by UniProt/SwissProt for SMYD1 Gene:

Q8NB12-SMYD1_HUMAN
Tissue specificity: Expression seems mostly restricted to heart and skeletal muscle.

Evidence on tissue expression from TISSUES for SMYD1 Gene

  • Muscle(4.8)
  • Heart(4.7)
genes like me logo Genes that share expression patterns with SMYD1: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SMYD1 Gene

Orthologs for SMYD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SMYD1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SMYD1 29 30
  • 97.49 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SMYD1 29 30
  • 92.87 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SMYD1 29 30
  • 92.24 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Smyd1 29
  • 89.59 (n)
Mouse
(Mus musculus)
Mammalia Smyd1 29 16 30
  • 89.45 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SMYD1 30
  • 88 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SMYD1 30
  • 87 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SMYD1 29 30
  • 78.69 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SMYD1 30
  • 81 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia smyd1 29
  • 72.68 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1817 29
Zebrafish
(Danio rerio)
Actinopterygii smyd1b 29 30
  • 67.63 (n)
OneToMany
CU469500.4 30
  • 61 (a)
OneToMany
smyd1a 30
  • 60 (a)
OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.922 29
Fruit Fly
(Drosophila melanogaster)
Insecta Bzd 30
  • 22 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea set-14 30
  • 20 (a)
ManyToMany
set-18 30
  • 19 (a)
ManyToMany
set-30 30
  • 16 (a)
ManyToMany
set-10 30
  • 16 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 36 (a)
OneToOne
Species where no ortholog for SMYD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SMYD1 Gene

ENSEMBL:
Gene Tree for SMYD1 (if available)
TreeFam:
Gene Tree for SMYD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMYD1: view image
Alliance of Genome Resources:
Additional Orthologs for SMYD1

Paralogs for SMYD1 Gene

Paralogs for SMYD1 Gene

(3) SIMAP similar genes for SMYD1 Gene using alignment to 4 proteins:

  • SMYD1_HUMAN
  • C9JUP3_HUMAN
  • E9PHG3_HUMAN
  • Q5GJ33_HUMAN
genes like me logo Genes that share paralogs with SMYD1: view

Variants for SMYD1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMYD1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs113636517 Benign: not provided 88,087,989(+) C/A
NM_198274.4(SMYD1):c.442C>A (p.Arg148=)
SYNONYMOUS
rs13403507 Benign: not provided 88,096,694(+) G/A
NM_198274.4(SMYD1):c.798G>A (p.Leu266=)
SYNONYMOUS
rs375801077 Likely Benign: not provided 88,067,978(+) T/A
NM_198274.4(SMYD1):c.114T>A (p.Ala38=)
SYNONYMOUS
rs61731026 Benign: not provided 88,103,066(+) G/T
NM_198274.4(SMYD1):c.897G>T (p.Gln299His)
MISSENSE
rs1542087 -- p.Gln164Pro

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SMYD1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SMYD1 Gene

Variant ID Type Subtype PubMed ID
dgv61n16 CNV deletion 17901297
dgv6947n54 CNV gain 21841781
nsv1072005 CNV deletion 25765185
nsv1130752 CNV deletion 24896259
nsv1148611 CNV deletion 26484159
nsv582383 CNV gain 21841781
nsv582384 CNV loss 21841781
nsv582386 CNV loss 21841781
nsv834289 CNV gain 17160897

Variation tolerance for SMYD1 Gene

Residual Variation Intolerance Score: 77% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.74; 78.84% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMYD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMYD1
Leiden Open Variation Database (LOVD)
SMYD1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMYD1 Gene

Disorders for SMYD1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SMYD1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
hypertrophic cardiomyopathy
  • familial hypertrophic cardiomyopathy
- elite association - COSMIC cancer census association via MalaCards
Search SMYD1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SMYD1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SMYD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SMYD1 Gene

Publications for SMYD1 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  2. SMYD1, the myogenic activator, is a direct target of serum response factor and myogenin. (PMID: 19783823) Li D … Liu M (Nucleic acids research 2009) 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. Bop encodes a muscle-restricted protein containing MYND and SET domains and is essential for cardiac differentiation and morphogenesis. (PMID: 11923873) Gottlieb PD … Srivastava D (Nature genetics 2002) 2 3

Products for SMYD1 Gene

Sources for SMYD1 Gene