The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. An elevated expression level of this gene has been observed in PC12 cells treated with nerve growth factor, beta poly... See more...

Aliases for PRDM4 Gene

Aliases for PRDM4 Gene

  • PR/SET Domain 4 2 3 5
  • PFM1 2 3 4
  • PR Domain Zinc Finger Protein 4 3 4
  • PR Domain-Containing Protein 4 3 4
  • PR Domain Containing 4 2 3
  • PR Domain 4 2 3
  • PR-Domain Zinc-Finger Protein PFM1 3
  • EC 2.1.1.- 4
  • PRDM4 5

External Ids for PRDM4 Gene

Previous GeneCards Identifiers for PRDM4 Gene

  • GC12M107237
  • GC12M108007
  • GC12M106629
  • GC12M108126
  • GC12M105186

Summaries for PRDM4 Gene

Entrez Gene Summary for PRDM4 Gene

  • The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. An elevated expression level of this gene has been observed in PC12 cells treated with nerve growth factor, beta polypeptide (NGF). This gene is located in a chromosomal region that is thought to contain tumor suppressor genes. [provided by RefSeq, Jul 2008]

GeneCards Summary for PRDM4 Gene

PRDM4 (PR/SET Domain 4) is a Protein Coding gene. Diseases associated with PRDM4 include Reflex Epilepsy and Pseudo-Von Willebrand Disease. Among its related pathways are Signaling by GPCR and Development HGF signaling pathway. Gene Ontology (GO) annotations related to this gene include methyltransferase activity. An important paralog of this gene is ZNF592.

UniProtKB/Swiss-Prot Summary for PRDM4 Gene

  • May function as a transcription factor involved in cell differentiation.

Additional gene information for PRDM4 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRDM4 Gene

Genomics for PRDM4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PRDM4 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRDM4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRDM4

Top Transcription factor binding sites by QIAGEN in the PRDM4 gene promoter:
  • AML1a
  • C/EBPalpha
  • FOXC1
  • FOXF2
  • POU2F1
  • POU2F1a
  • Roaz
  • ZIC2

Genomic Locations for PRDM4 Gene

Genomic Locations for PRDM4 Gene
chr12:107,732,866-107,761,272
(GRCh38/hg38)
Size:
28,407 bases
Orientation:
Minus strand
chr12:108,126,643-108,155,049
(GRCh37/hg19)
Size:
28,407 bases
Orientation:
Minus strand

Genomic View for PRDM4 Gene

Genes around PRDM4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM4 Gene

Proteins for PRDM4 Gene

  • Protein details for PRDM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UKN5-PRDM4_HUMAN
    Recommended name:
    PR domain zinc finger protein 4
    Protein Accession:
    Q9UKN5
    Secondary Accessions:
    • Q9UFA6

    Protein attributes for PRDM4 Gene

    Size:
    801 amino acids
    Molecular mass:
    87920 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PRDM4 Gene

neXtProt entry for PRDM4 Gene

Post-translational modifications for PRDM4 Gene

  • Ubiquitination at Lys412
  • Modification sites at PhosphoSitePlus

Other Protein References for PRDM4 Gene

No data available for DME Specific Peptides for PRDM4 Gene

Domains & Families for PRDM4 Gene

Gene Families for PRDM4 Gene

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

Protein Domains for PRDM4 Gene

Suggested Antigen Peptide Sequences for PRDM4 Gene

GenScript: Design optimal peptide antigens:
  • PR domain-containing protein 4 (PRDM4_HUMAN)
  • PRDM4 protein (Q6NUK0_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UKN5

UniProtKB/Swiss-Prot:

PRDM4_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 PRDM4: view

Function for PRDM4 Gene

Molecular function for PRDM4 Gene

UniProtKB/Swiss-Prot Function:
May function as a transcription factor involved in cell differentiation.
GENATLAS Biochemistry:
PR domain containing 4,widely expressed,involved in cell differentiation control and in tumorigenesis

Enzyme Numbers (IUBMB) for PRDM4 Gene

Phenotypes From GWAS Catalog for PRDM4 Gene

Gene Ontology (GO) - Molecular Function for PRDM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA --
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding ISS --
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific ISS --
GO:0003676 nucleic acid binding IEA --
genes like me logo Genes that share ontologies with PRDM4: view
genes like me logo Genes that share phenotypes with PRDM4: view

Animal Models for PRDM4 Gene

MGI Knock Outs for PRDM4:
  • Prdm4 Prdm4<tm1b(EUCOMM)Hmgu>
  • Prdm4 Prdm4<tm1b(EUCOMM)Liz>
  • Prdm4 Prdm4<tm2.1Liz>
  • Prdm4 Prdm4<tm1a(EUCOMM)Liz>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM4

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PRDM4 Gene

Localization for PRDM4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM4 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 PRDM4 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PRDM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0035097 histone methyltransferase complex NAS 23048031
genes like me logo Genes that share ontologies with PRDM4: view

Pathways & Interactions for PRDM4 Gene

genes like me logo Genes that share pathways with PRDM4: view

Pathways by source for PRDM4 Gene

Gene Ontology (GO) - Biological Process for PRDM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006366 transcription by RNA polymerase II IEA --
GO:0010468 regulation of gene expression IBA 21873635
GO:0032259 methylation IEA --
GO:0043985 histone H4-R3 methylation NAS 23048031
GO:0045893 positive regulation of transcription, DNA-templated IBA --
genes like me logo Genes that share ontologies with PRDM4: view

No data available for SIGNOR curated interactions for PRDM4 Gene

Drugs & Compounds for PRDM4 Gene

No Compound Related Data Available

Transcripts for PRDM4 Gene

mRNA/cDNA for PRDM4 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM4

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM4 Gene

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

Relevant External Links for PRDM4 Gene

GeneLoc Exon Structure for
PRDM4

Expression for PRDM4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PRDM4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRDM4

SOURCE GeneReport for Unigene cluster for PRDM4 Gene:

Hs.506655

mRNA Expression by UniProt/SwissProt for PRDM4 Gene:

Q9UKN5-PRDM4_HUMAN
Tissue specificity: Expressed in many tissues. Highly expressed in ovary, testis, pancreas, brain, heart and prostate.

Evidence on tissue expression from TISSUES for PRDM4 Gene

  • Nervous system(2.9)
genes like me logo Genes that share expression patterns with PRDM4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRDM4 Gene

Orthologs for PRDM4 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PRDM4 30 31
  • 99.63 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PRDM4 30 31
  • 94.84 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PRDM4 30 31
  • 93.8 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PRDM4 31
  • 91 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Prdm4 30 17 31
  • 90.79 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Prdm4 30
  • 89.46 (n)
Oppossum
(Monodelphis domestica)
Mammalia PRDM4 31
  • 86 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PRDM4 30 31
  • 80.64 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PRDM4 31
  • 81 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia prdm4 30
  • 70.38 (n)
African clawed frog
(Xenopus laevis)
Amphibia prdm4-prov 30
Zebrafish
(Danio rerio)
Actinopterygii prdm4 30 31
  • 64.35 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG43347 31
  • 6 (a)
OneToMany
Species where no ortholog for PRDM4 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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 PRDM4 Gene

ENSEMBL:
Gene Tree for PRDM4 (if available)
TreeFam:
Gene Tree for PRDM4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRDM4: view image

Paralogs for PRDM4 Gene

(18) SIMAP similar genes for PRDM4 Gene using alignment to 5 proteins:

  • PRDM4_HUMAN
  • F8VRG2_HUMAN
  • F8VZQ2_HUMAN
  • H0YIF6_HUMAN
  • Q6NUK0_HUMAN
genes like me logo Genes that share paralogs with PRDM4: view

Variants for PRDM4 Gene

Additional dbSNP identifiers (rs#s) for PRDM4 Gene

Structural Variations from Database of Genomic Variants (DGV) for PRDM4 Gene

Variant ID Type Subtype PubMed ID
nsv1038935 CNV gain 25217958
nsv560091 CNV gain 21841781
nsv820093 CNV loss 19587683

Variation tolerance for PRDM4 Gene

Residual Variation Intolerance Score: 5.19% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.23; 24.72% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRDM4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRDM4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRDM4 Gene

Disorders for PRDM4 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PRDM4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
reflex epilepsy
  • epilepsy, sensory-induced
pseudo-von willebrand disease
  • vwdp
porokeratosis
  • porokeratosis of mibelli
brittle cornea syndrome 2
  • fragilitas oculi with joint hyperextensibility
- elite association - COSMIC cancer census association via MalaCards
Search PRDM4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PRDM4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with PRDM4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PRDM4 Gene

Publications for PRDM4 Gene

  1. PFM1 (PRDM4), a new member of the PR-domain family, maps to a tumor suppressor locus on human chromosome 12q23-q24.1. (PMID: 10552934) Yang XH … Huang S (Genomics 1999) 2 3 4 23
  2. 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 41
  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. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. PRDM4 mediates YAP-induced cell invasion by activating leukocyte-specific integrin β2 expression. (PMID: 29669796) Liu H … Zhao B (EMBO reports 2018) 3

Products for PRDM4 Gene

Sources for PRDM4 Gene