PRDM14 Gene (Protein Coding)

PR/SET Domain 14

GC08M070063
GIFtS:
41
This gene encodes a member of the PRDI-BF1 and RIZ homology domain containing (PRDM) family of transcriptional regulators. The encoded protein may possess histone methyltransferase activity and plays a critical role in cell pluripotency by suppressing the expression of differentiation marker genes. Expression of this gene may play a role in breast cancer. [provided by RefSeq, D... See more...

Aliases for PRDM14 Gene

Aliases for PRDM14 Gene

  • PR/SET Domain 14 2 3 5
  • PR Domain Zinc Finger Protein 14 3 4
  • PR Domain-Containing Protein 14 3 4
  • PR Domain 14 2 3
  • PR Domain Containing 14 2
  • PR Domain-Containing 14 3
  • EC 2.1.1.- 4
  • PRDM14 5
  • PFM11 3

External Ids for PRDM14 Gene

Previous GeneCards Identifiers for PRDM14 Gene

  • GC08M070904
  • GC08M070687
  • GC08M071013
  • GC08M071127
  • GC08M070963
  • GC08M066457

Summaries for PRDM14 Gene

Entrez Gene Summary for PRDM14 Gene

  • This gene encodes a member of the PRDI-BF1 and RIZ homology domain containing (PRDM) family of transcriptional regulators. The encoded protein may possess histone methyltransferase activity and plays a critical role in cell pluripotency by suppressing the expression of differentiation marker genes. Expression of this gene may play a role in breast cancer. [provided by RefSeq, Dec 2011]

GeneCards Summary for PRDM14 Gene

PRDM14 (PR/SET Domain 14) is a Protein Coding gene. Diseases associated with PRDM14 include Brain Germinoma and Pineal Region Germinoma. Among its related pathways are Developmental Biology and Mesodermal Commitment Pathway. Gene Ontology (GO) annotations related to this gene include methyltransferase activity. An important paralog of this gene is ZBTB20.

UniProtKB/Swiss-Prot Summary for PRDM14 Gene

  • Transcription factor that has both positive and negative roles on transcription. Required for the maintenance of embryonic stem cell identity and the reacquisition of pluripotency in somatic cells. May play an essential role in germ cell development at 2 levels: the reacquisition of potential pluripotency, including SOX2 up-regulation, and successful epigenetic reprogramming, characterized by EHMT1 repression. Its association with CBFA2T2 is required for the functions in pluripotency and germ cell formation (By similarity). Directly up-regulates the expression of pluripotency gene POU5F1 through its proximal enhancer. Binds to the DNA consensus sequence 5'-GGTC[TC]CTAA-3'.

Additional gene information for PRDM14 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRDM14 Gene

Genomics for PRDM14 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PRDM14 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
GH08J070073 Promoter/Enhancer 1.5 EPDnew FANTOM5 Ensembl ENCODE 259.7 +0.8 793 4.2 ETS1 SIN3A CTCF YY1 SMARCA4 TAF1 BMI1 EGR1 EZH2 NANOG PRDM14 LOC101929759 SLCO5A1 RF00017-7119
GH08J069953 Enhancer 0.4 Ensembl 11.8 +117.4 117392 1 RXRA HNF4A NR2F2 RNU1-101P PRDM14 SLCO5A1 LOC101929759 SDCBPP2 RF00876-026
GH08J070042 Enhancer 0.2 Ensembl 12.3 +29.2 29193 1.4 PRDM14 RNU1-101P LOC101929759 SLCO5A1 piR-57460-647 RF00017-7119
GH08J070089 Promoter 0.8 CraniofacialAtlas 0.4 -16.7 -16673 0.4 ZNF217 ZIC2 CEBPB CTCF MBD1 RB1 L3MBTL2 ZXDB HLF ZEB2 LOC101929759 SLCO5A1 RF00017-7120 RNU1-101P RF00003-089 PRDM14 NCOA2
GH08J070074 Enhancer 0.4 Ensembl ENCODE 0.7 -3.3 -3330 1.2 JUND LOC101929759 SLCO5A1 PRDM14 RF00003-089 RNU1-101P RF00017-7119 NCOA2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRDM14 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRDM14

Top Transcription factor binding sites by QIAGEN in the PRDM14 gene promoter:
  • AML1a
  • STAT1
  • STAT1alpha
  • STAT1beta
  • STAT2
  • STAT3
  • STAT4
  • STAT5A
  • STAT5B
  • STAT6

Genomic Locations for PRDM14 Gene

Latest Assembly
chr8:70,051,613-70,071,693
(GRCh38/hg38)
Size:
20,081 bases
Orientation:
Minus strand

Previous Assembly
chr8:70,963,886-70,983,487
(GRCh37/hg19 by Entrez Gene)
Size:
19,602 bases
Orientation:
Minus strand

chr8:70,963,886-70,983,928
(GRCh37/hg19 by Ensembl)
Size:
20,043 bases
Orientation:
Minus strand

Genomic View for PRDM14 Gene

Genes around PRDM14 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM14 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM14 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PRDM14 Gene

Proteins for PRDM14 Gene

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  • Protein details for PRDM14 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9GZV8-PRD14_HUMAN
    Recommended name:
    PR domain zinc finger protein 14
    Protein Accession:
    Q9GZV8
    Secondary Accessions:
    • Q86UX9

    Protein attributes for PRDM14 Gene

    Size:
    571 amino acids
    Molecular mass:
    64062 Da
    Quaternary structure:
    • Interacts with CBFA2T2.

neXtProt entry for PRDM14 Gene

Protein Expression for PRDM14 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PRDM14 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PRDM14 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PRDM14 Gene

Domains & Families for PRDM14 Gene

Gene Families for PRDM14 Gene

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

Protein Domains for PRDM14 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PRDM14 Gene

GenScript: Design optimal peptide antigens:
  • PR domain-containing protein 14 (PRD14_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9GZV8

UniProtKB/Swiss-Prot:

PRD14_HUMAN :
  • The first 5 zinc fingers, but not the last one, are required for DNA-binding and transcriptional activity.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Domain:
  • The first 5 zinc fingers, but not the last one, are required for DNA-binding and transcriptional activity.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with PRDM14: view

Function for PRDM14 Gene

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  1. Animal Models for research
  2. CRISPR products for research
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  6. Cell Lines for research

Molecular function for PRDM14 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor that has both positive and negative roles on transcription. Required for the maintenance of embryonic stem cell identity and the reacquisition of pluripotency in somatic cells. May play an essential role in germ cell development at 2 levels: the reacquisition of potential pluripotency, including SOX2 up-regulation, and successful epigenetic reprogramming, characterized by EHMT1 repression. Its association with CBFA2T2 is required for the functions in pluripotency and germ cell formation (By similarity). Directly up-regulates the expression of pluripotency gene POU5F1 through its proximal enhancer. Binds to the DNA consensus sequence 5'-GGTC[TC]CTAA-3'.

Enzyme Numbers (IUBMB) for PRDM14 Gene

Phenotypes From GWAS Catalog for PRDM14 Gene

Gene Ontology (GO) - Molecular Function for PRDM14 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA,IBA 21873635
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 21516116
GO:0008168 methyltransferase activity IEA --
genes like me logo Genes that share ontologies with PRDM14: view
genes like me logo Genes that share phenotypes with PRDM14: view

Animal Models for PRDM14 Gene

MGI Knock Outs for PRDM14:
  • Prdm14 Prdm14<tm1a(EUCOMM)Wtsi>
  • Prdm14 Prdm14<tm1b(EUCOMM)Wtsi>
  • Prdm14 Prdm14<tm1e(EUCOMM)Wtsi>
  • Prdm14 Prdm14<tm1Sait>

Animal Models for research

Targeted motifs for PRDM14 Gene
HOMER Transcription Factor Regulatory Elements motif PRDM14
  • Consensus sequence: AGGTCTCTAACC Submotif: canonical Cell Type: H1 GEO ID: GSE22767

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM14

No data available for Human Phenotype Ontology , miRNA and Transcription Factor Targets for PRDM14 Gene

Localization for PRDM14 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM14 Gene

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 PRDM14 gene
Compartment Confidence
nucleus 5
extracellular 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endosome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PRDM14 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm IDA,TAS --
genes like me logo Genes that share ontologies with PRDM14: view

Pathways & Interactions for PRDM14 Gene

genes like me logo Genes that share pathways with PRDM14: view

Pathways by source for PRDM14 Gene

1 BioSystems pathway for PRDM14 Gene

SIGNOR curated interactions for PRDM14 Gene

Activates:

Gene Ontology (GO) - Biological Process for PRDM14 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0000902 cell morphogenesis IEA --
GO:0001708 cell fate specification IEA --
GO:0001827 inner cell mass cell fate commitment IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
genes like me logo Genes that share ontologies with PRDM14: view

Drugs & Compounds for PRDM14 Gene

Products:

  1. Drug products for research
No Compound Related Data Available

Transcripts for PRDM14 Gene

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  1. CRISPR products for research
  2. miRNA products for research
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mRNA/cDNA for PRDM14 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
2 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 PRDM14

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM14 Gene

No ASD Table

Relevant External Links for PRDM14 Gene

GeneLoc Exon Structure for
PRDM14

Expression for PRDM14 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PRDM14 Gene

mRNA expression in normal human tissues for PRDM14 Gene
mRNA expression by GTEx for PRDM14 GenemRNA expression by BioGPS for PRDM14 Gene

mRNA differential expression in normal tissues according to GTEx for PRDM14 Gene

This gene is overexpressed in Testis (x44.4) and Kidney - Cortex (x4.6).

Protein differential expression in normal tissues from HIPED for PRDM14 Gene

This gene is overexpressed in Cerebrospinal fluid (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PRDM14 Gene



Protein tissue co-expression partners for PRDM14 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRDM14

SOURCE GeneReport for Unigene cluster for PRDM14 Gene:

Hs.736037

mRNA Expression by UniProt/SwissProt for PRDM14 Gene:

Q9GZV8-PRD14_HUMAN
Tissue specificity: Expressed in embryonic stem cells. Tends to be overexpressed in breast cancer (at protein level).

Evidence on tissue expression from TISSUES for PRDM14 Gene

  • Nervous system(2.6)
  • Skin(2.4)
  • Muscle(2)
genes like me logo Genes that share expression patterns with PRDM14: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PRDM14 Gene

Orthologs for PRDM14 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM14 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PRDM14 30 31
  • 99.53 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia PRDM14 31
  • 89 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PRDM14 30 31
  • 85.68 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PRDM14 30 31
  • 83.77 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia PRDM14 31
  • 78 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia LOC100365184 30
  • 77.02 (n)
Mouse
(Mus musculus)
 Mammalia Prdm14 30 17 31
  • 76.11 (n)
 OneToOne
Chicken
(Gallus gallus)
 Aves PRDM14 31
  • 72 (a)
 OneToOne
LOC100858709 30
  • 66.1 (n)
Lizard
(Anolis carolinensis)
 Reptilia PRDM14 31
  • 63 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia prdm14 30
  • 62.24 (n)
Zebrafish
(Danio rerio)
 Actinopterygii prdm14 30 31
  • 65.44 (n)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea F47E1.3 31 32
  • 31 (a)
 OneToOne
Species where no ortholog for PRDM14 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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 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)

Evolution for PRDM14 Gene

ENSEMBL:
Gene Tree for PRDM14 (if available)
TreeFam:
Gene Tree for PRDM14 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRDM14: view image

Paralogs for PRDM14 Gene

Paralogs for PRDM14 Gene

(3) SIMAP similar genes for PRDM14 Gene using alignment to 2 proteins:

  • PRD14_HUMAN
  • C9JMM8_HUMAN
genes like me logo Genes that share paralogs with PRDM14: view

Variants for PRDM14 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRDM14 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
rs3750228 - p.Lys244Glu

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PRDM14 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 PRDM14 Gene

Variant ID Type Subtype PubMed ID
nsv1023889 CNV gain+loss 25217958
nsv1034456 CNV gain 25217958
nsv1068714 OTHER inversion 25765185
nsv508513 CNV deletion 20534489
nsv527289 CNV gain 19592680
nsv611487 CNV loss 21841781
nsv831352 CNV gain 17160897

Variation tolerance for PRDM14 Gene

Residual Variation Intolerance Score: 31.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.80; 83.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRDM14 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRDM14

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM14 Gene

Disorders for PRDM14 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PRDM14 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
brain germinoma
  • germinoma of the brain
pineal region germinoma
  • pineal germinoma
testicular cancer
  • childhood neoplasm of the testis
breast cancer
  • breast cancer, familial
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PRDM14

Genetic Association Database
(GAD)
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 PRDM14: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PRDM14 Gene

Publications for PRDM14 Gene

  1. Co-repressor CBFA2T2 regulates pluripotency and germline development. (PMID: 27281218) Tu S … Reinberg D (Nature 2016) 3 4
  2. A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. (PMID: 20953172) Chia NY … Ng HH (Nature 2010) 3 4
  3. Gene amplification and overexpression of PRDM14 in breast cancers. (PMID: 17942894) Nishikawa N … Tokino T (Cancer research 2007) 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. 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

ExternalLinks

View latest publications for PRDM14 gene in Mastermind

Products for PRDM14 Gene

Sources for PRDM14 Gene