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

Summary

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

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_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Cancer Associated PRDM9: Implications for Linking Genomic Instability and Meiotic Recombination.
Title: Cancer Associated PRDM9: Implications for Linking Genomic Instability and Meiotic Recombination.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
The landscape of recombination in African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

L28288 (e-PCR)
- UniSTS:15648

PRDM9_3659 (e-PCR)
- UniSTS:462457

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

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

NP_064612.2

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

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)

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
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
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