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

Gene ID: 56979, updated on 5-Mar-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
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Genomic context

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Location:
5p14.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (23507155..23528093)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (23614868..23635807)
105.20220307 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: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Aberrant PRDM9 expression impacts the pan-cancer genomic landscape. Houle AA, et al. Genome Res, 2018 Nov. PMID 30341163, Free PMC Article
  2. The Control of Meiotic Recombination in the Human Genome. Ergoren MC. Crit Rev Eukaryot Gene Expr, 2018. PMID 30311566
  3. Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence. Patel A, et al. J Biol Chem, 2017 Sep 29. PMID 28801461, Free PMC Article
  4. An exploratory study of predisposing genetic factors for DiGeorge/velocardiofacial syndrome. Vergés L, et al. Sci Rep, 2017 Jan 6. PMID 28059126, Free PMC Article
  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 (44) 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)

Genotypes

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/Swiss-Prot
    Q9NQV7
    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_2023_10

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.

Chemical Information
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