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Aliases for PRDM13 Gene

Aliases for PRDM13 Gene

  • PR/SET Domain 13 2 3 5
  • PR Domain Containing 13 2 3
  • PR Domain 13 2 3
  • PFM10 3 4
  • PR Domain Zinc Finger Protein 13 3
  • PR-Domain Containing Protein 13 3
  • PR Domain-Containing Protein 13 4
  • MU-MB-20.220 3
  • EC 2.1.1.- 4

External Ids for PRDM13 Gene

Previous GeneCards Identifiers for PRDM13 Gene

  • GC06P099922
  • GC06P100071
  • GC06P100100
  • GC06P100161
  • GC06P097494
  • GC06P100054

Summaries for PRDM13 Gene

GeneCards Summary for PRDM13 Gene

PRDM13 (PR/SET Domain 13) is a Protein Coding gene. Diseases associated with PRDM13 include Childhood Medulloblastoma. Gene Ontology (GO) annotations related to this gene include chromatin binding and methyltransferase activity. An important paralog of this gene is PRDM16.

UniProtKB/Swiss-Prot for PRDM13 Gene

  • May be involved in transcriptional regulation.

Additional gene information for PRDM13 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRDM13 Gene

Genomics for PRDM13 Gene

GeneHancer (GH) Regulatory Elements for PRDM13 Gene

Promoters and enhancers for PRDM13 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I099606 Promoter 0.8 EPDnew 550.8 +0.0 34 0.1 SUZ12 CTBP2 ZBTB33 EZH2 PRDM13 GC06P099636
GH06I099611 Enhancer 0.7 ENCODE 0.8 +4.6 4588 0.1 LEF1 BACH1 BATF IRF4 RELA ZNF316 EGR1 ATF7 NFE2 PRDM10 PRDM13 GC06P099636
GH06I099588 Enhancer 0.9 ENCODE 0.4 -18.0 -17969 0.4 ZSCAN4 INSM2 KLF17 MZF1 SIN3A ZNF2 RAD21 ZNF335 ZNF213 ZNF366 GC06M099587 ENSG00000279170 RPS3P5 PRDM13
GH06I099612 Enhancer 0.8 Ensembl 0.4 +7.0 6996 2.6 ZNF76 GLI4 ZNF2 RARA ZNF335 GLIS2 SCRT2 ZNF548 ZNF391 EGR2 PNISR LOC101927365 PRDM13 GC06P099636
GH06I099592 Enhancer 0.5 Ensembl 0.4 -13.6 -13645 0.6 HLF CEBPA CEBPB CEBPG EP300 CCNC GC06M099587 PRDM13
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PRDM13 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRDM13 gene promoter:

Genomic Locations for PRDM13 Gene

Genomic Locations for PRDM13 Gene
8,849 bases
Plus strand

Genomic View for PRDM13 Gene

Genes around PRDM13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM13 Gene

Proteins for PRDM13 Gene

  • Protein details for PRDM13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    PR domain zinc finger protein 13
    Protein Accession:
    Secondary Accessions:
    • Q5TGC1
    • Q5TGC2

    Protein attributes for PRDM13 Gene

    707 amino acids
    Molecular mass:
    73981 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAG13448.1; Type=Miscellaneous discrepancy; Note=Non-canonical splice intron-exon junction.; Evidence={ECO:0000305}; Sequence=CAI19763.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI22063.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

neXtProt entry for PRDM13 Gene

Post-translational modifications for PRDM13 Gene

No Post-translational modifications

Other Protein References for PRDM13 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PRDM13 Gene

Domains & Families for PRDM13 Gene

Gene Families for PRDM13 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for PRDM13 Gene

Suggested Antigen Peptide Sequences for PRDM13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with PRDM13: view

Function for PRDM13 Gene

Molecular function for PRDM13 Gene

UniProtKB/Swiss-Prot Function:
May be involved in transcriptional regulation.

Enzyme Numbers (IUBMB) for PRDM13 Gene

Phenotypes From GWAS Catalog for PRDM13 Gene

Gene Ontology (GO) - Molecular Function for PRDM13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with PRDM13: view
genes like me logo Genes that share phenotypes with PRDM13: view

Animal Models for PRDM13 Gene

MGI Knock Outs for PRDM13:

Animal Model Products

CRISPR Products

miRNA for PRDM13 Gene

miRTarBase miRNAs that target PRDM13

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PRDM13 Gene

Localization for PRDM13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM13 Gene

Subcellular locations from

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 PRDM13 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for PRDM13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with PRDM13: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PRDM13 Gene

Pathways & Interactions for PRDM13 Gene

SuperPathways for PRDM13 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PRDM13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016571 histone methylation IEA --
GO:0022008 neurogenesis IEA --
genes like me logo Genes that share ontologies with PRDM13: view

No data available for Pathways by source and SIGNOR curated interactions for PRDM13 Gene

Drugs & Compounds for PRDM13 Gene

No Compound Related Data Available

Transcripts for PRDM13 Gene

mRNA/cDNA for PRDM13 Gene

(1) REFSEQ mRNAs :
(3) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM13 Gene

No ASD Table

Relevant External Links for PRDM13 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PRDM13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRDM13 Gene

mRNA differential expression in normal tissues according to GTEx for PRDM13 Gene

This gene is overexpressed in Brain - Hypothalamus (x14.2), Testis (x12.4), and Brain - Spinal cord (cervical c-1) (x7.1).

Protein differential expression in normal tissues from HIPED for PRDM13 Gene

This gene is overexpressed in Breast (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PRDM13 Gene

Protein tissue co-expression partners for PRDM13 Gene

NURSA nuclear receptor signaling pathways regulating expression of PRDM13 Gene:


SOURCE GeneReport for Unigene cluster for PRDM13 Gene:

genes like me logo Genes that share expression patterns with PRDM13: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRDM13 Gene

Orthologs for PRDM13 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PRDM13 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PRDM13 33 34
  • 99.62 (n)
(Bos Taurus)
Mammalia PRDM13 33 34
  • 88.12 (n)
(Ornithorhynchus anatinus)
Mammalia PRDM13 34
  • 86 (a)
(Rattus norvegicus)
Mammalia Prdm13 33
  • 83.1 (n)
(Mus musculus)
Mammalia Prdm13 33 16 34
  • 82.19 (n)
(Canis familiaris)
Mammalia PRDM13 34
  • 75 (a)
(Monodelphis domestica)
Mammalia PRDM13 34
  • 72 (a)
(Anolis carolinensis)
Reptilia PRDM13 34
  • 48 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm13 33
  • 62.82 (n)
(Danio rerio)
Actinopterygii prdm13 33 34
  • 64.17 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG13296 34
  • 26 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 34
  • 12 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1775 34
  • 15 (a)
Species where no ortholog for PRDM13 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • 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 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 PRDM13 Gene

Gene Tree for PRDM13 (if available)
Gene Tree for PRDM13 (if available)

Paralogs for PRDM13 Gene

Paralogs for PRDM13 Gene

(14) SIMAP similar genes for PRDM13 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PRDM13: view

Variants for PRDM13 Gene

Sequence variations from dbSNP and Humsavar for PRDM13 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs373935217 uncertain-significance, not specified 99,613,227(+) G/A/C coding_sequence_variant, missense_variant
rs751190925 uncertain-significance, not specified 99,613,836(+) G/A/T coding_sequence_variant, missense_variant
rs1000154305 -- 99,605,038(+) G/A upstream_transcript_variant
rs1000441901 -- 99,610,511(+) A/G intron_variant
rs1000644538 -- 99,609,748(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PRDM13 Gene

Variant ID Type Subtype PubMed ID
nsv830741 CNV gain 17160897
nsv1029536 CNV loss 25217958

Variation tolerance for PRDM13 Gene

Residual Variation Intolerance Score: 77.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.60; 91.29% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRDM13 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM13 Gene

Disorders for PRDM13 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PRDM13 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
childhood medulloblastoma
  • pediatric medulloblastoma
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PRDM13

genes like me logo Genes that share disorders with PRDM13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PRDM13 Gene

Publications for PRDM13 Gene

  1. Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. (PMID: 21102462) Elks CE … Murray A (Nature genetics 2010) 3 44 58
  2. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4 58
  3. Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity. (PMID: 25546159) Satoh A … Imai S (Aging cell 2015) 3 58
  4. The PcG protein hPc2 interacts with the N-terminus of histone demethylase JARID1B and acts as a transcriptional co-repressor. (PMID: 19336002) Zhou W … Zhang L (BMB reports 2009) 3 58
  5. Novel tumor antigens identified by autologous antibody screening of childhood medulloblastoma cDNA libraries. (PMID: 12800201) Behrends U … Mautner J (International journal of cancer 2003) 3 58

Products for PRDM13 Gene

Sources for PRDM13 Gene

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