This tumor suppressor gene is a member of a nuclear histone/protein methyltransferase superfamily. It encodes a zinc finger protein that can bind to retinoblastoma protein, estrogen receptor, and the TPA-responsive element (MTE) of the heme-oxygenase-1 gene. Although the functions of this protein have not been fully characterized, it may (1) play a role in transcriptional regul... See more...

Aliases for PRDM2 Gene

Aliases for PRDM2 Gene

  • PR/SET Domain 2 2 3 5
  • Retinoblastoma Protein-Interacting Zinc Finger Protein 2 3 4
  • MTE-Binding Protein 2 3 4
  • Retinoblastoma Protein-Binding Zinc Finger Protein 2 3
  • PR Domain Containing 2, With ZNF Domain 2 3
  • PR Domain Zinc Finger Protein 2 3 4
  • Zinc-Finger DNA-Binding Protein 2 3
  • PR Domain-Containing Protein 2 3 4
  • Lysine N-Methyltransferase 8 3 4
  • GATA-3 Binding Protein G3B 2 3
  • Zinc Finger Protein RIZ 3 4
  • PR Domain 2 2 3
  • MTB-ZF 3 4
  • KMT8 3 4
  • RIZ 3 4
  • GATA-3-Binding Protein G3B 4
  • EC 2.1.1.355 4
  • HUMHOXY1 3
  • KMT8A 3
  • RIZ1 3
  • RIZ2 3

External Ids for PRDM2 Gene

Previous GeneCards Identifiers for PRDM2 Gene

  • GC01P013428
  • GC01P013210
  • GC01P013394
  • GC01P013776
  • GC01P013899
  • GC01P014026
  • GC01P012544

Summaries for PRDM2 Gene

Entrez Gene Summary for PRDM2 Gene

  • This tumor suppressor gene is a member of a nuclear histone/protein methyltransferase superfamily. It encodes a zinc finger protein that can bind to retinoblastoma protein, estrogen receptor, and the TPA-responsive element (MTE) of the heme-oxygenase-1 gene. Although the functions of this protein have not been fully characterized, it may (1) play a role in transcriptional regulation during neuronal differentiation and pathogenesis of retinoblastoma, (2) act as a transcriptional activator of the heme-oxygenase-1 gene, and (3) be a specific effector of estrogen action. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

GeneCards Summary for PRDM2 Gene

PRDM2 (PR/SET Domain 2) is a Protein Coding gene. Diseases associated with PRDM2 include Retinoblastoma and Wilms Tumor 5. Among its related pathways are PKMTs methylate histone lysines and Metabolism. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and histone-lysine N-methyltransferase activity. An important paralog of this gene is ZNF407.

UniProtKB/Swiss-Prot Summary for PRDM2 Gene

  • S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates 'Lys-9' of histone H3. May function as a DNA-binding transcription factor. Binds to the macrophage-specific TPA-responsive element (MTE) of the HMOX1 (heme oxygenase 1) gene and may act as a transcriptional activator of this gene.

Gene Wiki entry for PRDM2 Gene

Additional gene information for PRDM2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRDM2 Gene

Genomics for PRDM2 Gene

GeneHancer (GH) Regulatory Elements for PRDM2 Gene

Promoters and enhancers for PRDM2 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
GH01J013747 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.2 +50.3 50333 5.1 HNRNPK EP300 ZSCAN5C SIN3A POLR2G SP1 PHF8 ZFX CTCF ZNF639 PRDM2 lnc-LRRC38-2 piR-39858-004
GH01J013699 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 26 +2.1 2057 6.1 ZBTB40 SIN3A NRF1 USF1 SP1 PHF8 ZFX EP300 POLR2A ZBTB26 lnc-LRRC38-8 PRDM2 piR-39858-004
GH01J013727 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 28.8 +31.0 30983 6.8 ZBTB40 SIN3A SP1 ZIC2 ZNF263 RELA MEF2C RCOR1 POLR2A NFYB PRDM2 ENSG00000253085 piR-39858-004 lnc-LRRC38-2
GH01J013757 Enhancer 0.8 ENCODE dbSUPER 11.8 +59.0 59041 2.8 ZNF217 CTBP1 CTCF RBM25 SIN3A ZNF316 ZNF384 MAFF MAFK JUND PRDM2 ENSG00000253085 lnc-LRRC38-2 piR-39858-004
GH01J013726 Enhancer 0.7 ENCODE dbSUPER 12.5 +25.7 25724 0.5 CTCF TRIM28 RAD21 TRIM22 SMC3 GATA3 ZBTB48 ZNF664 BCLAF1 ZNF143 PRDM2 ENSG00000253085 piR-39858-004 lnc-LRRC38-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRDM2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRDM2

Top Transcription factor binding sites by QIAGEN in the PRDM2 gene promoter:
  • FOXJ2
  • FOXJ2 (long isoform)
  • p300

Genomic Locations for PRDM2 Gene

Genomic Locations for PRDM2 Gene
chr1:13,700,198-13,825,079
(GRCh38/hg38)
Size:
124,882 bases
Orientation:
Plus strand
chr1:14,026,693-14,151,574
(GRCh37/hg19)
Size:
124,882 bases
Orientation:
Plus strand

Genomic View for PRDM2 Gene

Genes around PRDM2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM2 Gene

Proteins for PRDM2 Gene

  • Protein details for PRDM2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13029-PRDM2_HUMAN
    Recommended name:
    PR domain zinc finger protein 2
    Protein Accession:
    Q13029
    Secondary Accessions:
    • B1AJZ4
    • B5MC68
    • Q13149
    • Q14550
    • Q5THJ1
    • Q5VUL9

    Protein attributes for PRDM2 Gene

    Size:
    1718 amino acids
    Molecular mass:
    188915 Da
    Quaternary structure:
    • Binds to the retinoblastoma protein (RB). Interacts with GATA3.
    Miscellaneous:
    • [Isoform 3]: Produced by alternative initiation at Met-202 of isoform 1.
    SequenceCaution:
    • Sequence=BAA08110.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PRDM2 Gene

    Alternative splice isoforms for PRDM2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRDM2 Gene

Post-translational modifications for PRDM2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PRDM2 Gene

Domains & Families for PRDM2 Gene

Gene Families for PRDM2 Gene

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

Protein Domains for PRDM2 Gene

Blocks:
  • C2H2-type zinc finger signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PRDM2 Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger protein RIZ (PRDM2_HUMAN)
  • PR domain containing 2, with ZNF domain (Q5THJ0_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13029

UniProtKB/Swiss-Prot:

PRDM2_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 PRDM2: view

Function for PRDM2 Gene

Molecular function for PRDM2 Gene

UniProtKB/Swiss-Prot Function:
S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates 'Lys-9' of histone H3. May function as a DNA-binding transcription factor. Binds to the macrophage-specific TPA-responsive element (MTE) of the HMOX1 (heme oxygenase 1) gene and may act as a transcriptional activator of this gene.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60276, Rhea:RHEA-COMP:15538, Rhea:RHEA-COMP:15546, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.355;.
GENATLAS Biochemistry:
PR domain containing 2,retinoblastoma RB1 protein interacting zinc finger RIZ,with two alternative spliced forms,280kDa (RIZ1),250kDa (RIZ2),acting as a putative tumor suppressor,with RIZ1 commonly underexpressed in breast cancer and other carcinomas

Enzyme Numbers (IUBMB) for PRDM2 Gene

Phenotypes From GWAS Catalog for PRDM2 Gene

Gene Ontology (GO) - Molecular Function for PRDM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IMP 8654390
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS 19274049
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IMP 8654390
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with PRDM2: view
genes like me logo Genes that share phenotypes with PRDM2: view

Animal Models for PRDM2 Gene

MGI Knock Outs for PRDM2:

Animal Model Products

Clone Products

  • Addgene plasmids for PRDM2

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PRDM2 Gene

Localization for PRDM2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM2 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 PRDM2 gene
Compartment Confidence
nucleus 5
golgi apparatus 4
plasma membrane 2
cytosol 2
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PRDM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,NAS 7538672
GO:0005654 nucleoplasm IDA --
GO:0005794 Golgi apparatus IDA --
genes like me logo Genes that share ontologies with PRDM2: view

Pathways & Interactions for PRDM2 Gene

PathCards logo

SuperPathways for PRDM2 Gene

genes like me logo Genes that share pathways with PRDM2: view

Pathways by source for PRDM2 Gene

1 BioSystems pathway for PRDM2 Gene
2 KEGG pathways for PRDM2 Gene
1 GeneTex pathway for PRDM2 Gene

SIGNOR curated interactions for PRDM2 Gene

Activates:

Gene Ontology (GO) - Biological Process for PRDM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated NAS 7590293
GO:0008340 determination of adult lifespan IEA --
GO:0032259 methylation IEA --
GO:0034968 histone lysine methylation IEA --
GO:0045893 positive regulation of transcription, DNA-templated IBA 21873635
genes like me logo Genes that share ontologies with PRDM2: view

Drugs & Compounds for PRDM2 Gene

(12) Drugs for PRDM2 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Zinc Approved, Investigational Pharma 2822
D-Lysine Approved, Experimental Nutra Full agonist, Agonist 0
s-adenosylhomocysteine Experimental Pharma 0
heme Pharma Agonist 0

(6) Additional Compounds for PRDM2 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with PRDM2: view

Transcripts for PRDM2 Gene

mRNA/cDNA for PRDM2 Gene

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

Clone Products

  • Addgene plasmids for PRDM2

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM2 Gene

No ASD Table

Relevant External Links for PRDM2 Gene

GeneLoc Exon Structure for
PRDM2

Expression for PRDM2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PRDM2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PRDM2 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (65.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PRDM2 Gene



Protein tissue co-expression partners for PRDM2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRDM2

SOURCE GeneReport for Unigene cluster for PRDM2 Gene:

Hs.371823

mRNA Expression by UniProt/SwissProt for PRDM2 Gene:

Q13029-PRDM2_HUMAN
Tissue specificity: Highly expressed in retinoblastoma cell lines and in brain tumors. Also expressed in a number of other cell lines and in brain, heart, skeletal muscle, liver and spleen. Isoform 1 is expressed in testis at much higher level than isoform 3.

Evidence on tissue expression from TISSUES for PRDM2 Gene

  • Nervous system(4.8)
  • Liver(4.3)
  • Eye(4.2)
  • Bone marrow(2.1)
genes like me logo Genes that share expression patterns with PRDM2: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRDM2 Gene

Orthologs for PRDM2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PRDM2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PRDM2 31 30
  • 99.32 (n)
OneToOne
dog
(Canis familiaris)
Mammalia -- 31
  • 97 (a)
OneToMany
-- 31
  • 88 (a)
OneToMany
PRDM2 30
  • 84.36 (n)
mouse
(Mus musculus)
Mammalia Prdm2 17 31 30
  • 83.26 (n)
cow
(Bos Taurus)
Mammalia PRDM2 31 30
  • 82.94 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Prdm2 30
  • 82.81 (n)
oppossum
(Monodelphis domestica)
Mammalia PRDM2 31
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PRDM2 31
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRDM2 31 30
  • 73.14 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PRDM2 31
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm2 30
  • 64.61 (n)
Str.11503 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.19643 30
zebrafish
(Danio rerio)
Actinopterygii prdm2b 31 30
  • 56.83 (n)
OneToOne
Species where no ortholog for PRDM2 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)
  • worm (Caenorhabditis elegans)

Evolution for PRDM2 Gene

ENSEMBL:
Gene Tree for PRDM2 (if available)
TreeFam:
Gene Tree for PRDM2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRDM2: view image

Paralogs for PRDM2 Gene

(6) SIMAP similar genes for PRDM2 Gene using alignment to 7 proteins:

  • PRDM2_HUMAN
  • D6RAA0_HUMAN
  • D6RED5_HUMAN
  • D6RJM6_HUMAN
  • H0Y9J3_HUMAN
  • Q5THJ1_HUMAN
  • S4R3F7_HUMAN
genes like me logo Genes that share paralogs with PRDM2: view

Variants for PRDM2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRDM2 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
716658 Benign: not provided 13,780,617(+) C/T MISSENSE_VARIANT,INTRON_VARIANT
791148 Benign: not provided 13,780,983(+) C/T MISSENSE_VARIANT,INTRON_VARIANT
rs41269807 Likely Benign: not specified 13,780,865(+) T/A MISSENSE_VARIANT,INTRON_VARIANT
rs17350795 - p.Ser450Asn
rs2076324 - p.Asp283Glu

Additional dbSNP identifiers (rs#s) for PRDM2 Gene

Structural Variations from Database of Genomic Variants (DGV) for PRDM2 Gene

Variant ID Type Subtype PubMed ID
esv2744086 CNV deletion 23290073
esv3577741 CNV loss 25503493
nsv3187 CNV deletion 18451855
nsv473350 CNV novel sequence insertion 20440878
nsv474268 CNV novel sequence insertion 20440878
nsv545567 CNV gain 21841781
nsv954813 CNV duplication 24416366

Variation tolerance for PRDM2 Gene

Residual Variation Intolerance Score: 49.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.01; 68.46% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRDM2 Gene

Human Gene Mutation Database (HGMD)
PRDM2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRDM2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM2 Gene

Disorders for PRDM2 Gene

MalaCards: The human disease database

(8) MalaCards diseases for PRDM2 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
retinoblastoma
  • rb1
wilms tumor 5
  • nephroblastoma
medulloblastoma
  • mdb
gastric cancer
  • gastric cancer, somatic
breast cancer
  • breast cancer, familial
- elite association - COSMIC cancer census association via MalaCards
Search PRDM2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PRDM2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PRDM2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PRDM2 Gene

Publications for PRDM2 Gene

  1. The retinoblastoma protein binds to RIZ, a zinc-finger protein that shares an epitope with the adenovirus E1A protein. (PMID: 7538672) Buyse IM … Huang S (Proceedings of the National Academy of Sciences of the United States of America 1995) 2 3 4 23 54
  2. The RIZ Pro704 insertion-deletion polymorphism, bone mineral density and fracture risk: the Rotterdam study. (PMID: 18037365) Stolk L … Uitterlinden AG (Bone 2008) 3 23 41 54
  3. Structural studies of the SET domain from RIZ1 tumor suppressor. (PMID: 18082620) Briknarová K … Huang S (Biochemical and biophysical research communications 2008) 3 4 23 54
  4. Genetic polymorphisms in the Rb-binding zinc finger gene RIZ and the risk of lung cancer. (PMID: 17693662) Yoon KA … Lee JS (Carcinogenesis 2007) 3 23 41 54
  5. Inactivation of a histone methyltransferase by mutations in human cancers. (PMID: 14633678) Kim KC … Huang S (Cancer research 2003) 3 4 23 54

Products for PRDM2 Gene

Sources for PRDM2 Gene