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Aliases for PRDM6 Gene

Aliases for PRDM6 Gene

  • PR/SET Domain 6 2 3 5
  • PR Domain-Containing Protein 6 3 4
  • PR Domain Containing 6 2 3
  • PR Domain 6 2 3
  • Putative Histone-Lysine N-Methyltransferase PRDM6 3
  • PR-Domain Zinc Finger Protein 6 3
  • PR Domain Zinc Finger Protein 6 4
  • EC 2.1.1.43 4
  • PRISM 3
  • KMT8C 3
  • PDA3 3
  • PFM3 4

External Ids for PRDM6 Gene

Previous GeneCards Identifiers for PRDM6 Gene

  • GC05P122055
  • GC05P122751
  • GC05P122455
  • GC05P122480
  • GC05P122452
  • GC05U900559
  • GC05P117612
  • GC05P122424
  • GC05P123089

Summaries for PRDM6 Gene

GeneCards Summary for PRDM6 Gene

PRDM6 (PR/SET Domain 6) is a Protein Coding gene. Diseases associated with PRDM6 include Patent Ductus Arteriosus 3 and Familial Patent Arterial Duct. Among its related pathways are Lysine degradation. GO annotations related to this gene include nucleic acid binding and histone-lysine N-methyltransferase activity. An important paralog of this gene is PRDM14.

UniProtKB/Swiss-Prot for PRDM6 Gene

  • Putative histone methyltransferase that acts as a transcriptional repressor of smooth muscle gene expression. Promotes the transition from differentiated to proliferative smooth muscle by suppressing differentiation and maintaining the proliferative potential of vascular smooth muscle cells. Also plays a role in endothelial cells by inhibiting endothelial cell proliferation, survival and differentiation. It is unclear whether it has histone methyltransferase activity in vivo. According to some authors, it does not act as a histone methyltransferase by itself and represses transcription by recruiting EHMT2/G9a. According to others, it possesses histone methyltransferase activity when associated with other proteins and specifically methylates Lys-20 of histone H4 in vitro. Lys-20 methylation represents a specific tag for epigenetic transcriptional repression (By similarity).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRDM6 Gene

Genomics for PRDM6 Gene

Regulatory Elements for PRDM6 Gene

Enhancers for PRDM6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05F123035 0.5 ENCODE 11.8 +0.7 654 2.5 ARID4B SIN3A DMAP1 ZNF48 YY1 GLIS2 ZNF263 SP3 SP5 REST PPIC PRDM6 ENSG00000260686 ENSG00000249996
GH05F122773 1 ENCODE 9.2 -260.2 -260234 4.0 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 SNX2 LOX SRFBP1 ENSG00000260686 PRDM6 PPIC RN7SL689P
GH05F122758 0.5 ENCODE 9.2 -276.0 -275993 2.6 PKNOX1 ESRRA ZNF146 ZNF175 ZNF384 FEZF1 YY1 HIC1 ZNF316 ZFHX2 PPIC ENSG00000260686 PRDM6 RN7SL689P LOC105379152 SNX2 LOC101927379
GH05F122843 1 ENCODE 9.2 -189.9 -189885 4.8 PKNOX1 ARID4B SIN3A FEZF1 DMAP1 YY1 FOS SP3 SP5 REST PPIC SNX24 SNX2 ENSG00000260686 PRDM6 RN7SL689P GC05M122843 GC05P122965
GH05F122779 0.5 Ensembl 9.2 -255.9 -255885 0.6 SPI1 PRDM6 RN7SL689P SNX2 ENSG00000260686
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PRDM6 on UCSC Golden Path with GeneCards custom track

Promoters for PRDM6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001288747 615 2400 ARID4B SIN3A DMAP1 ZNF48 YY1 GLIS2 ZNF263 SP3 SP5 REST

Genomic Location for PRDM6 Gene

Chromosome:
5
Start:
123,035,985 bp from pter
End:
123,194,266 bp from pter
Size:
158,282 bases
Orientation:
Plus strand

Genomic View for PRDM6 Gene

Genes around PRDM6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM6 Gene

Proteins for PRDM6 Gene

  • Protein details for PRDM6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQX0-PRDM6_HUMAN
    Recommended name:
    Putative histone-lysine N-methyltransferase PRDM6
    Protein Accession:
    Q9NQX0
    Secondary Accessions:
    • B5MCJ4
    • Q9NQW9

    Protein attributes for PRDM6 Gene

    Size:
    595 amino acids
    Molecular mass:
    64452 Da
    Quaternary structure:
    • Interacts with HDAC1, HDAC2, HDAC3, CBX1 and EP300.
    SequenceCaution:
    • Sequence=AAF78078.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAF78079.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PRDM6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRDM6 Gene

Post-translational modifications for PRDM6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PRDM6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PRDM6 Gene

Domains & Families for PRDM6 Gene

Protein Domains for PRDM6 Gene

Suggested Antigen Peptide Sequences for PRDM6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NQX0

UniProtKB/Swiss-Prot:

PRDM6_HUMAN :
  • Contains 1 SET domain.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
  • Contains 4 C2H2-type zinc fingers.
Domain:
  • Contains 1 SET domain.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Similarity:
  • Contains 4 C2H2-type zinc fingers.
genes like me logo Genes that share domains with PRDM6: view

Function for PRDM6 Gene

Molecular function for PRDM6 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
UniProtKB/Swiss-Prot Function:
Putative histone methyltransferase that acts as a transcriptional repressor of smooth muscle gene expression. Promotes the transition from differentiated to proliferative smooth muscle by suppressing differentiation and maintaining the proliferative potential of vascular smooth muscle cells. Also plays a role in endothelial cells by inhibiting endothelial cell proliferation, survival and differentiation. It is unclear whether it has histone methyltransferase activity in vivo. According to some authors, it does not act as a histone methyltransferase by itself and represses transcription by recruiting EHMT2/G9a. According to others, it possesses histone methyltransferase activity when associated with other proteins and specifically methylates Lys-20 of histone H4 in vitro. Lys-20 methylation represents a specific tag for epigenetic transcriptional repression (By similarity).

Enzyme Numbers (IUBMB) for PRDM6 Gene

Gene Ontology (GO) - Molecular Function for PRDM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0018024 histone-lysine N-methyltransferase activity IEA --
GO:0042803 protein homodimerization activity IEA --
genes like me logo Genes that share ontologies with PRDM6: view
genes like me logo Genes that share phenotypes with PRDM6: view

Animal Models for PRDM6 Gene

MGI Knock Outs for PRDM6:

Animal Model Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PRDM6

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PRDM6 Gene

Localization for PRDM6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM6 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PRDM6 Gene COMPARTMENTS Subcellular localization image for PRDM6 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for PRDM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with PRDM6: view

Pathways & Interactions for PRDM6 Gene

SuperPathways for PRDM6 Gene

SuperPathway Contained pathways
1 Lysine degradation
genes like me logo Genes that share pathways with PRDM6: view

Pathways by source for PRDM6 Gene

1 KEGG pathway for PRDM6 Gene

Gene Ontology (GO) - Biological Process for PRDM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016569 covalent chromatin modification IEA --
GO:0022008 neurogenesis IEA --
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with PRDM6: view

No data available for SIGNOR curated interactions for PRDM6 Gene

Drugs & Compounds for PRDM6 Gene

(2) Drugs for PRDM6 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-Adenosylmethionine Approved Nutra 0
s-adenosylhomocysteine Experimental Pharma 0
genes like me logo Genes that share compounds with PRDM6: view

Transcripts for PRDM6 Gene

mRNA/cDNA for PRDM6 Gene

(2) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PRDM6 Gene

PR domain containing 6:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PRDM6

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM6 Gene

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

Relevant External Links for PRDM6 Gene

GeneLoc Exon Structure for
PRDM6
ECgene alternative splicing isoforms for
PRDM6

Expression for PRDM6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PRDM6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PRDM6 Gene

This gene is overexpressed in Artery - Aorta (x12.0), Bladder (x7.4), Artery - Tibial (x5.6), and Artery - Coronary (x4.7).

Protein differential expression in normal tissues from HIPED for PRDM6 Gene

This gene is overexpressed in Cerebrospinal fluid (43.5) and Heart (25.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PRDM6 Gene



Protein tissue co-expression partners for PRDM6 Gene

NURSA nuclear receptor signaling pathways regulating expression of PRDM6 Gene:

PRDM6

SOURCE GeneReport for Unigene cluster for PRDM6 Gene:

Hs.135118
genes like me logo Genes that share expression patterns with PRDM6: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for PRDM6 Gene

Orthologs for PRDM6 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM6 Gene

Organism Taxonomy Gene Similarity Type Details
platypus
(Ornithorhynchus anatinus)
Mammalia PRDM6 35
  • 99 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PRDM6 34 35
  • 97.7 (n)
dog
(Canis familiaris)
Mammalia PRDM6 34 35
  • 92.82 (n)
cow
(Bos Taurus)
Mammalia PRDM6 34 35
  • 91.71 (n)
rat
(Rattus norvegicus)
Mammalia Prdm6 34
  • 88.89 (n)
mouse
(Mus musculus)
Mammalia Prdm6 34 16 35
  • 87.16 (n)
oppossum
(Monodelphis domestica)
Mammalia PRDM6 35
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRDM6 34 35
  • 82.16 (n)
lizard
(Anolis carolinensis)
Reptilia PRDM6 35
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm6 34
  • 79.77 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.12311 34
zebrafish
(Danio rerio)
Actinopterygii prdm6 35
  • 91 (a)
OneToMany
PRDM6 (2 of 2) 35
  • 87 (a)
OneToMany
LOC101886516 34
  • 75.24 (n)
worm
(Caenorhabditis elegans)
Secernentea set-17 35
  • 17 (a)
OneToMany
Species where no ortholog for PRDM6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 PRDM6 Gene

ENSEMBL:
Gene Tree for PRDM6 (if available)
TreeFam:
Gene Tree for PRDM6 (if available)

Paralogs for PRDM6 Gene

Variants for PRDM6 Gene

Sequence variations from dbSNP and Humsavar for PRDM6 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
VAR_077015 Patent ductus arteriosus 3 (PDA3) [MIM:617039]
VAR_077016 Patent ductus arteriosus 3 (PDA3) [MIM:617039]
rs879253872 Pathogenic 123,170,997(+) AAGCC(A/G)GCTCC nc-transcript-variant, reference, missense
rs879255278 Pathogenic 123,180,296(+) CATCC(A/G)AACCC nc-transcript-variant, downstream-variant-500B, reference, missense
rs879255279 Pathogenic 123,099,849(+) CATCT(C/G)CGCGG nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for PRDM6 Gene

Variant ID Type Subtype PubMed ID
esv2730710 CNV deletion 23290073
esv2730712 CNV deletion 23290073
esv2730713 CNV deletion 23290073
esv3575879 CNV gain 25503493
esv3575880 CNV gain 25503493
nsv1016658 CNV loss 25217958
nsv1017500 CNV loss 25217958
nsv4979 CNV insertion 18451855
nsv520349 CNV loss 19592680
nsv950128 CNV deletion 24416366

Variation tolerance for PRDM6 Gene

Gene Damage Index Score: 12.09; 93.82% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PRDM6 Gene

Human Gene Mutation Database (HGMD)
PRDM6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRDM6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM6 Gene

Disorders for PRDM6 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PRDM6 Gene - From: ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
patent ductus arteriosus 3
  • pda3
familial patent arterial duct
patent ductus arteriosus
  • ductus arteriosus, patent
chromosome 1p36 deletion syndrome
  • 1p36 deletion syndrome
left ventricular noncompaction
  • left ventricular hypertrabeculation
- elite association - COSMIC cancer census association via MalaCards
Search PRDM6 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PRDM6

Genetic Association Database (GAD)
PRDM6
Human Genome Epidemiology (HuGE) Navigator
PRDM6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PRDM6
genes like me logo Genes that share disorders with PRDM6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PRDM6 Gene

Publications for PRDM6 Gene

  1. Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. (PMID: 27716515) Li N. … Mani A. (Am. J. Hum. Genet. 2016) 2 3 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. PRISM/PRDM6, a transcriptional repressor that promotes the proliferative gene program in smooth muscle cells. (PMID: 16537907) Davis C.A. … Olson E.N. (Mol. Cell. Biol. 2006) 2 3 64
  4. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X. … Chen J. (Mol. Syst. Biol. 2015) 3 64
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64

Products for PRDM6 Gene

Sources for PRDM6 Gene

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