This gene encodes a protein that belongs to a conserved family of histone methyltransferases that predominantly act as negative regulators of transcription. The encoded protein contains an N-terminal Su(var)3-9, Enhancer-of-zeste, and Trithorax (SET) domain and a double zinc-finger domain. Knockout of this gene in mouse results in mistargeting by neurons of the dorsal telenceph... See more...

Aliases for PRDM8 Gene

Aliases for PRDM8 Gene

  • PR/SET Domain 8 2 3 5
  • PR Domain Zinc Finger Protein 8 3 4
  • PR Domain 8 2 3
  • PFM5 3 4
  • PR-Domain Containing Protein 8 3
  • PR Domain-Containing Protein 8 4
  • PR Domain Containing 8 2
  • EC 2.1.1.- 4
  • EPM10 3
  • KMT8D 3

External Ids for PRDM8 Gene

Previous GeneCards Identifiers for PRDM8 Gene

  • GC04P080993
  • GC04P081391
  • GC04P081498
  • GC04P081564
  • GC04P081565
  • GC04P081462
  • GC04P081325
  • GC04P081107
  • GC04P076850

Summaries for PRDM8 Gene

Entrez Gene Summary for PRDM8 Gene

  • This gene encodes a protein that belongs to a conserved family of histone methyltransferases that predominantly act as negative regulators of transcription. The encoded protein contains an N-terminal Su(var)3-9, Enhancer-of-zeste, and Trithorax (SET) domain and a double zinc-finger domain. Knockout of this gene in mouse results in mistargeting by neurons of the dorsal telencephalon, abnormal itch-like behavior, and impaired differentiation of rod bipolar cells. In humans, the protein has been shown to interact with the phosphatase laforin and the ubiquitin ligase malin, which regulate glycogen construction in the cytoplasm. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

GeneCards Summary for PRDM8 Gene

PRDM8 (PR/SET Domain 8) is a Protein Coding gene. Diseases associated with PRDM8 include Epilepsy, Progressive Myoclonic, 10 and Progressive Myoclonus Epilepsy. Gene Ontology (GO) annotations related to this gene include chromatin binding and histone methyltransferase activity. An important paralog of this gene is ZNF488.

UniProtKB/Swiss-Prot Summary for PRDM8 Gene

  • Probable histone methyltransferase, preferentially acting on 'Lys-9' of histone H3 (By similarity). Involved in the control of steroidogenesis through transcriptional repression of steroidogenesis marker genes such as CYP17A1 and LHCGR (By similarity). Forms with BHLHE22 a transcriptional repressor complex controlling genes involved in neural development and neuronal differentiation (By similarity). In the retina, it is required for rod bipolar and type 2 OFF-cone bipolar cell survival (By similarity).

Additional gene information for PRDM8 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRDM8 Gene

Genomics for PRDM8 Gene

GeneHancer (GH) Regulatory Elements for PRDM8 Gene

Promoters and enhancers for PRDM8 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
GH04J080182 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 511.9 +0.7 734 5.1 ZBTB40 CTCF USF1 RBAK TEAD4 ZNF639 ZNF10 ZIC2 POLR2A ZBTB10 PRDM8 lnc-PRDM8-4 LOC105377303 ENSG00000248719
GH04J080197 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 509 +14.1 14059 2.4 ZIC2 ZBTB10 ZNF423 ZBTB26 MXI1 ZNF341 WT1 SP2 ZBTB17 ZNF76 PRDM8 ENSG00000248719 ANTXR2 HSALNG0035460 lnc-PRDM8-4
GH04J080123 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 15.9 -57.5 -57544 4.6 CTCF GTF2E2 JUND PHB2 FOS ZBTB5 AFF1 REST NR3C1 EP300 ANTXR2 lnc-ANTXR2-3 PRDM8 ENSG00000248719 RPSAP39
GH04J080077 Promoter/Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 15.4 -105.0 -105009 2.8 FOS EP300 CTCF POLR2H NFE2 FOSL1 JUND GATA2 POLR2A JUN KPNA2P1 ANTXR2 PRDM8 ENSG00000248719 RF00004-089 lnc-PRDM8-6 lnc-ANTXR2-3
GH04J080137 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 12.2 -42.2 -42199 8.1 PHB2 ZBTB5 AFF1 TARDBP DNMT1 HES1 NR3C1 TOE1 MYC EP300 PRDM8 ANTXR2 lnc-ANTXR2-3 RPSAP39
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRDM8 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRDM8

Top Transcription factor binding sites by QIAGEN in the PRDM8 gene promoter:
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AP-2gamma
  • c-Myb
  • C/EBPbeta
  • CUTL1
  • GATA-1
  • Nkx2-5

Genomic Locations for PRDM8 Gene

Genomic Locations for PRDM8 Gene
chr4:80,183,741-80,204,329
(GRCh38/hg38)
Size:
20,589 bases
Orientation:
Plus strand
chr4:81,105,033-81,125,483
(GRCh37/hg19)
Size:
20,451 bases
Orientation:
Plus strand

Genomic View for PRDM8 Gene

Genes around PRDM8 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM8 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM8 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM8 Gene

Proteins for PRDM8 Gene

  • Protein details for PRDM8 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQV8-PRDM8_HUMAN
    Recommended name:
    PR domain zinc finger protein 8
    Protein Accession:
    Q9NQV8
    Secondary Accessions:
    • A8K7X2
    • Q6IQ36

    Protein attributes for PRDM8 Gene

    Size:
    689 amino acids
    Molecular mass:
    71663 Da
    Quaternary structure:
    • Interacts with EPM2A and NHLRC1. This interaction sequesters EPM2A and NHLRC1 to the nucleus (PubMed:22961547). Interacts with BHLHE22 (By similarity).
    SequenceCaution:
    • Sequence=AAF87241.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for PRDM8 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRDM8 Gene

Post-translational modifications for PRDM8 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PRDM8 Gene

Domains & Families for PRDM8 Gene

Gene Families for PRDM8 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for PRDM8 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PRDM8 Gene

GenScript: Design optimal peptide antigens:
  • PR domain-containing protein 8 (PRDM8_HUMAN)
  • PRDM8 protein (Q05CA1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NQV8

UniProtKB/Swiss-Prot:

PRDM8_HUMAN :
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with PRDM8: view

Function for PRDM8 Gene

Molecular function for PRDM8 Gene

UniProtKB/Swiss-Prot Function:
Probable histone methyltransferase, preferentially acting on 'Lys-9' of histone H3 (By similarity). Involved in the control of steroidogenesis through transcriptional repression of steroidogenesis marker genes such as CYP17A1 and LHCGR (By similarity). Forms with BHLHE22 a transcriptional repressor complex controlling genes involved in neural development and neuronal differentiation (By similarity). In the retina, it is required for rod bipolar and type 2 OFF-cone bipolar cell survival (By similarity).

Enzyme Numbers (IUBMB) for PRDM8 Gene

Phenotypes From GWAS Catalog for PRDM8 Gene

Gene Ontology (GO) - Molecular Function for PRDM8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IEA,IPI 22961547
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PRDM8: view
genes like me logo Genes that share phenotypes with PRDM8: view

Human Phenotype Ontology for PRDM8 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PRDM8 Gene

MGI Knock Outs for PRDM8:

miRNA for PRDM8 Gene

miRTarBase miRNAs that target PRDM8

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for PRDM8 Gene

Localization for PRDM8 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM8 Gene

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 PRDM8 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PRDM8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 22961547
genes like me logo Genes that share ontologies with PRDM8: view

Pathways & Interactions for PRDM8 Gene

PathCards logo

SuperPathways for PRDM8 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PRDM8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007399 nervous system development IEA --
GO:0014003 oligodendrocyte development IBA 21873635
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with PRDM8: view

No data available for Pathways by source and SIGNOR curated interactions for PRDM8 Gene

Drugs & Compounds for PRDM8 Gene

No Compound Related Data Available

Transcripts for PRDM8 Gene

mRNA/cDNA for PRDM8 Gene

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

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM8 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13
SP1: -
SP2: - - - - - -
SP3: -
SP4: - - - - - -
SP5:
SP6: - - - - - - - -
SP7: - - - - - - -

Relevant External Links for PRDM8 Gene

GeneLoc Exon Structure for
PRDM8

Expression for PRDM8 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PRDM8 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PRDM8 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (51.7) and Retina (17.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PRDM8 Gene



Protein tissue co-expression partners for PRDM8 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRDM8

SOURCE GeneReport for Unigene cluster for PRDM8 Gene:

Hs.373642

mRNA Expression by UniProt/SwissProt for PRDM8 Gene:

Q9NQV8-PRDM8_HUMAN
Tissue specificity: Expressed in brain, heart, skeletal muscle, testes, prostate.

Evidence on tissue expression from TISSUES for PRDM8 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with PRDM8: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRDM8 Gene

Orthologs for PRDM8 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM8 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PRDM8 31 30
  • 97.93 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PRDM8 31 30
  • 91.87 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PRDM8 31 30
  • 89.35 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PRDM8 31
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Prdm8 17 31 30
  • 84.93 (n)
rat
(Rattus norvegicus)
Mammalia Prdm8 30
  • 84.61 (n)
oppossum
(Monodelphis domestica)
Mammalia PRDM8 31
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRDM8 31
  • 48 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PRDM8 31
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm8 30
  • 63.62 (n)
zebrafish
(Danio rerio)
Actinopterygii prdm8b 31 30
  • 64.31 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG13287 31
  • 21 (a)
OneToMany
Species where no ortholog for PRDM8 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for PRDM8 Gene

ENSEMBL:
Gene Tree for PRDM8 (if available)
TreeFam:
Gene Tree for PRDM8 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRDM8: view image

Paralogs for PRDM8 Gene

Paralogs for PRDM8 Gene

genes like me logo Genes that share paralogs with PRDM8: view

Variants for PRDM8 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRDM8 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
639513 Uncertain Significance: Epilepsy, progressive myoclonic, 10 80,203,223(+) T/TGCCGCTGCA INFRAME_INSERTION
640230 Uncertain Significance: Epilepsy, progressive myoclonic, 10 80,203,275(+) C/G MISSENSE_VARIANT
642805 Uncertain Significance: Epilepsy, progressive myoclonic, 10 80,202,346(+) A/C MISSENSE_VARIANT
643837 Uncertain Significance: Epilepsy, progressive myoclonic, 10 80,202,537(+) G/A MISSENSE_VARIANT
648808 Uncertain Significance: Epilepsy, progressive myoclonic, 10 80,203,183(+) C/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for PRDM8 Gene

Structural Variations from Database of Genomic Variants (DGV) for PRDM8 Gene

Variant ID Type Subtype PubMed ID
esv29411 CNV loss 19812545
nsv594739 CNV gain 21841781
nsv594740 CNV loss 21841781

Variation tolerance for PRDM8 Gene

Residual Variation Intolerance Score: 33.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.11; 38.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRDM8 Gene

Human Gene Mutation Database (HGMD)
PRDM8
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRDM8

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM8 Gene

Disorders for PRDM8 Gene

MalaCards: The human disease database

(9) MalaCards diseases for PRDM8 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
epilepsy, progressive myoclonic, 10
  • epm10
progressive myoclonus epilepsy
  • progressive myoclonic epilepsy
dyskeratosis congenita
  • zinsser-cole-engman syndrome
unverricht-lundborg syndrome
  • myoclonic epilepsy of unverricht and lundborg
epilepsy
  • epilepsy syndrome
- elite association - COSMIC cancer census association via MalaCards
Search PRDM8 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PRDM8_HUMAN
  • Epilepsy, progressive myoclonic 10 (EPM10) [MIM:616640]: A progressive myoclonus epilepsy characterized by progressive dysarthria, myoclonus, ataxia, cognitive decline, psychosis, dementia and spasticity, with onset in childhood. There is variability between patients. {ECO:0000269 PubMed:22961547}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PRDM8

genes like me logo Genes that share disorders with PRDM8: view

No data available for Genatlas for PRDM8 Gene

Publications for PRDM8 Gene

  1. Early-onset Lafora body disease. (PMID: 22961547) Turnbull J … Minassian BA (Brain : a journal of neurology 2012) 3 4 54
  2. Bhlhb5 and Prdm8 form a repressor complex involved in neuronal circuit assembly. (PMID: 22284184) Ross SE … Greenberg ME (Neuron 2012) 2 3 54
  3. Genome-wide association study identifies eight loci associated with blood pressure. (PMID: 19430483) Newton-Cheh C … Munroe PB (Nature genetics 2009) 3 41 54
  4. 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 54
  5. DNA methylation in PRDM8 is indicative for dyskeratosis congenita. (PMID: 26909595) Weidner CI … Wagner W (Oncotarget 2016) 3 54

Products for PRDM8 Gene

Sources for PRDM8 Gene