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    PRDM9 PR/SET domain 9 [ Homo sapiens (human) ]

    Gene ID: 56979, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PRDM9provided by HGNC
    Official Full Name
    PR/SET domain 9provided by HGNC
    Primary source
    HGNC:HGNC:13994
    See related
    Ensembl:ENSG00000164256 MIM:609760; AllianceGenome:HGNC:13994
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PFM6; KMT8B; MSBP3; ZNF899; MEISETZ
    Summary
    The protein encoded by this gene is a zinc finger protein with histone methyltransferase activity that catalyzes histone H3 lysine 4 trimethylation (H3K4me3) during meiotic prophase. This protein contains multiple domains, including a Kruppel-associated box (KRAB) domain, an SSX repression domain (SSXRD), a PRD1-BF1 and RIZ homologous region, a subclass of SET (PR/SET) domain, and a tandem array of C2H2 zinc fingers. The zinc finger array recognizes a short sequence motif, leading to local H3K4me3, and meiotic recombination hotspot activity. The observed allelic variation alters the DNA-binding sequence specificity of the protein, resulting in distinct meiotic recombination hotspots amongst individuals and populations. Multiple alternate alleles of this gene have been described. [provided by RefSeq, Jul 2015]
    Expression
    Restricted expression toward testis (RPKM 2.2) See more
    Orthologs
    mouse all
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    Genomic context

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    See PRDM9 in Genome Data Viewer
    Location:
    5p14.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (23507155..23528093)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (23614868..23635807)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (23507264..23528202)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374688 Neighboring gene uncharacterized LOC124901171 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:23465882-23467081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:23506773-23507272 Neighboring gene TRPC6 pseudogene 9 Neighboring gene uncharacterized LOC124901158

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Rare allelic forms of PRDM9 associated with childhood leukemogenesis. Hussin J, et al. Genome Res, 2013 Mar. PMID 23222848, Free PMC Article
    2. The red queen model of recombination hotspots evolution in the light of archaic and modern human genomes. Lesecque Y, et al. PLoS Genet, 2014 Nov. PMID 25393762, Free PMC Article
    3. Primate evolution of the recombination regulator PRDM9. Schwartz JJ, et al. Nat Commun, 2014 Jul 8. PMID 25001002, Free PMC Article
    4. Allelic variants of PRDM9 associated with high hyperdiploid childhood acute lymphoblastic leukaemia. Woodward EL, et al. Br J Haematol, 2014 Sep. PMID 24754746
    5. X marks the spot: PRDM9 rescues hybrid sterility by finding hidden treasure in the genome. Zelazowski MJ, et al. Nat Struct Mol Biol, 2016 Apr. PMID 27045445, Free PMC Article

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FBLN5 was Regulated by PRDM9, and Promoted Senescence and Osteogenic Differentiation of Human Periodontal Ligament Stem Cells.
      Title: FBLN5 was Regulated by PRDM9, and Promoted Senescence and Osteogenic Differentiation of Human Periodontal Ligament Stem Cells.
    2. Cancer Associated PRDM9: Implications for Linking Genomic Instability and Meiotic Recombination.
      Title: Cancer Associated PRDM9: Implications for Linking Genomic Instability and Meiotic Recombination.
    3. Association of Single Nucleotide Polymorphisms in the PYGO2 and PRDM9 Genes with Idiopathic Azoospermia in Iranian Infertile Male Patients.
      Title: Association of Single Nucleotide Polymorphisms in the PYGO2 and PRDM9 Genes with Idiopathic Azoospermia in Iranian Infertile Male Patients.
    4. PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2.
      Title: PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2.
    5. Pathogenic variants of meiotic double strand break (DSB) formation genes PRDM9 and ANKRD31 in premature ovarian insufficiency.
      Title: Pathogenic variants of meiotic double strand break (DSB) formation genes PRDM9 and ANKRD31 in premature ovarian insufficiency.
    6. The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain.
      Title: The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain.
    7. ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair.
      Title: ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair.
    8. Recent findings have highlighted an unexpected molecular control of the distribution of meiotic double-strand breaks (DSBs) in mammals by a rapidly evolving gene in trans, PR-domain-containing 9 (PRDM9), and specific DNA sequence motifs in cis
      Title: The Control of Meiotic Recombination in the Human Genome.
    9. PRDM9 expression in tumors is significantly higher than in healthy neighboring tissues. Aberrant expression of PRDM9 is associated with genomic instability in cancers.
      Title: Aberrant PRDM9 expression impacts the pan-cancer genomic landscape.
    10. PRDM9 activity leads to the erosion of its own binding sites and the rapid evolution of its DNA-binding domain. PRDM9 may also contribute to reproductive isolation, as it is involved in hybrid sterility potentially due to a reduction of its activity in specific heterozygous contexts. [Review]
      Title: PRDM9, a driver of the genetic map.
    Submit: New GeneRIF Correction See all GeneRIFs (36)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Fine-scale recombination rate differences between sexes, populations and individuals.
    EBI GWAS Catalog
    The landscape of recombination in African Americans.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H3K36 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K36 methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K36 methyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables histone H3K36 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K4 methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K4 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4K20 monomethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4K20me methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables recombination hotspot binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables recombination hotspot binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables recombination hotspot binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables transcription cis-regulatory region binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in double-strand break repair involved in meiotic recombination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in female gamete generation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in homologous chromosome pairing at meiosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in male gamete generation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within meiotic gene conversion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of fertilization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of reciprocal meiotic recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of reciprocal meiotic recombination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase PRDM9
    Names
    PR domain 9
    PR domain containing 9
    PR domain zinc finger protein 9
    [histone H3]-lysine36 N-trimethyltransferase PRDM9
    [histone H3]-lysine4 N-trimethyltransferase PRDM9
    [histone H3]-lysine9 N-trimethyltransferase PRDM9
    [histone H4]-N-methyl-L-lysine20 N-methyltransferase PRDM9
    [histone H4]-lysine20 N-methyltransferase PRDM9
    histone methyl transferase
    minisatellite binding protein 3 (115kD)
    protein-lysine N-methyltransferase PRDM9
    NP_001363829.1
    NP_064612.2

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001310214.3 → NP_001297143.1  histone-lysine N-methyltransferase PRDM9 isoform PRDM9 A

      See identical proteins and their annotated locations for NP_001297143.1

      Status: REVIEWED

      Source sequence(s)
      AK301776, AL704903, DB518225, DB636359
      UniProtKB/TrEMBL
      A0AAG2UW24
      Conserved Domains (7) summary
      smart00317
      Location:246 → 364
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00349
      Location:27 → 85
      KRAB; krueppel associated box
      COG5048
      Location:611 → 878
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:750 → 770
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:27 → 62
      KRAB; KRAB box
      pfam09514
      Location:171 → 201
      SSXRD; SSXRD motif
      pfam13465
      Location:846 → 870
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001376900.1 → NP_001363829.1  histone-lysine N-methyltransferase PRDM9 isoform PRDM9 B

      Status: REVIEWED

      Source sequence(s)
      AC025451
      Consensus CDS
      CCDS43307.1
      UniProtKB/Swiss-Prot
      B4DX22, Q27Q50, Q9NQV7
      Related
      ENSP00000425471.2, ENST00000502755.6
      Conserved Domains (5) summary
      COG5048
      Location:611 → 878
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:750 → 770
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam09514
      Location:171 → 201
      SSXRD; SSXRD motif
      cd19193
      Location:240 → 368
      PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
      cl02581
      Location:27 → 85
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    3. NM_020227.4 → NP_064612.2  histone-lysine N-methyltransferase PRDM9 isoform PRDM9 B

      See identical proteins and their annotated locations for NP_064612.2

      Status: REVIEWED

      Source sequence(s)
      AC025451
      Consensus CDS
      CCDS43307.1
      UniProtKB/Swiss-Prot
      B4DX22, Q27Q50, Q9NQV7
      Related
      ENSP00000296682.4, ENST00000296682.4
      Conserved Domains (5) summary
      COG5048
      Location:611 → 878
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:750 → 770
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam09514
      Location:171 → 201
      SSXRD; SSXRD motif
      cd19193
      Location:240 → 368
      PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
      cl02581
      Location:27 → 85
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      23507155..23528093
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791779.1 Reference GRCh38.p14 PATCHES

      Range
      137172..158109
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      23614868..23635807
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NQV7.2 GenPept UniProtKB/Swiss-Prot:Q9NQV7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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