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PRDM9 - PR/SET domain 9 Gene

Also Known as PFM6; KMT8B; MSBP3; ZNF899; MEISETZ

Species: Homo sapiens

Gene Type: protein coding

Gene ID: 56979

About PRDM9

Cytogenetic location: 5p14.2 Genomic coordinates (GRCh38): 5:23,507,155-23,528,093 (from NCBI)

This gene has 3 transcripts (splice variants), 74 orthologues and 62 paralogues. Restricted expression toward testis (RPKM 2.2).

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]

PRDM9 Products (3)

mRNA	Protein	Name
NM_001310214.3	NP_001297143.1	histone-lysine N-methyltransferase PRDM9 isoform PRDM9 A
NM_001376900.1	NP_001363829.1	histone-lysine N-methyltransferase PRDM9 isoform PRDM9 B
NM_020227.4	NP_064612.2	histone-lysine N-methyltransferase PRDM9 isoform PRDM9 B

Gene Ontology

Molecular Function
Biological Process

Molecular Function GO Annotation	Evidence	References	Source
enables histone H3K36 methyltransferase activity	IMP IMP: Inferred from mutant phenotype	24634223	GOA
enables histone H3K4 methyltransferase activity	IDA IDA: Inferred from direct assay	24095733	GOA
enables histone H3K4 methyltransferase activity	IMP IMP: Inferred from mutant phenotype	24634223	GOA
enables recombination hotspot binding	IDA IDA: Inferred from direct assay	26833727	GOA
enables recombination hotspot binding	IMP IMP: Inferred from mutant phenotype	20044539	GOA
enables transcription cis-regulatory region binding	IMP IMP: Inferred from mutant phenotype	29072575	GOA

Biological Process GO Annotation	Evidence	References	Source
acts upstream of or within meiotic gene conversion	IDA IDA: Inferred from direct assay	21750151	GOA
acts upstream of or within positive regulation of reciprocal meiotic recombination	IMP IMP: Inferred from mutant phenotype	21750151	GOA

EXP: Inferred from Experiment IDA: Inferred from direct assay IPI: Inferred from physical interaction IMP: Inferred from mutant phenotype IGI: Inferred from genetic interaction IEP: Inferred from expression pattern

PRDM9 Protein Structure

KRAB

SSXRD

zf-H2C2_2

0
200
400
600
800
894 a.a.

Protein Preferred Names	Protein Names
histone-lysine N-methyltransferase PRDM9	PR domain 9

Related Diseases

Diseases	Alias
Genetic Non-Acquired Premature Ovarian Failure
Spastic Paraplegia 4, Autosomal Dominant	SPG4 Hereditary Spastic Paraplegia 4 Fsp2 Autosomal Dominant Spastic Paraplegia Type 4 Familial Spastic Paraplegia, Autosomal Dominant, 2 Autosomal Dominant Spastic Paraplegia 4 Familial Spastic Paraplegia Autosomal Dominant 2 Paraplegia, Spastic, Autosomal Dominant, Type 4
Haverhill Fever	Streptobacillosis Streptobacillary Rat-Bite Fever Streptobacillary Fever Rat-Bite Fever Due To Streptobacillus Moniliformis Erythema Arthriticum Epidemicum Epidemic Arthritic Erythema
Spastic Paraplegia 24, Autosomal Recessive	SPG24 Spastic Paraplegia 24 Hereditary Spastic Paraplegia 24 Autosomal Recessive Spastic Paraplegia Type 24 Autosomal Recessive Spastic Paraplegia 24
Alacrima, Achalasia, And Mental Retardation Syndrome	AAMR Alacrima, Achalasia, And Intellectual Disability Syndrome Alacrima, Achalasia, And Impaired Intellectual Development Syndrome Intellectual Disability
Male Infertility	Infertility, Male Infertility Male Male Sterility Absolute Infertility
Neuropathy, Hereditary, With Liability To Pressure Palsies	Tomaculous Neuropathy Hereditary Neuropathy With Liability To Pressure Palsies HNPP Polyneuropathy, Familial Recurrent Neuropathy, Recurrent, With Pressure Palsies Current Pressure-Sensitive Neuropathy Familial Recurrent Polyneuropathy Heterozygous Microdeletion 17p11.2p12 Potato-Grubbing Palsy Tulip-Bulb Digger'S Palsy Compression Neuropathy Entrapment Neuropathy Familial Pressure Sensitive Neuropathy Hereditary Motor And Sensory Neuropathy Hereditary Pressure Sensitive Neuropathy Inherited Tendency To Pressure Palsies Hereditary Liability To Pressure Palsies Nerve Compression Syndrome Entrapment Neuropathies Hereditary Motor And Sensory Neuropathies
Potocki-Lupski Syndrome	PTLS Chromosome 17p11.2 Duplication Syndrome 17p11.2 Microduplication Syndrome Duplication 17p11.2 Syndrome Trisomy 17p11.2 Potocki-Lupski Syndrome (Dup(17)(P11.2p11.2)) 17p11.2 Duplication Syndrome Dup(17)(P11.2p11.2) Pls Chromosome 17, Trisomy 17p11 2
Spermatogenic Failure	Azoospermia Spgf Spermatogenic Failure, Susceptibility To Absent Sperm Aspermatogenesis Infertility Due To Azoospermia Hypospermatogenesis Azoospermatism
Williams-Beuren Syndrome	Williams Syndrome WBS Wms Deletion 7q11.23 Monosomy 7q11.23 Chromosome 7q11.23 Deletion Syndrome, 1.5- To 1.8-Mb Fanconi Schlesinger Syndrome Beuren Syndrome Elfin Facies Syndrome Elfin Facies With Hypercalcemia Hypercalcemia-Supravalvar Aortic Stenosis Ws
Charcot-Marie-Tooth Disease	Cmt Hmsn Hereditary Motor And Sensory Neuropathy Pma Cmt - Charcot-Marie-Tooth Disease Charcot Marie Tooth Disease Charcot-Marie-Tooth Hereditary Neuropathy Charcot-Marie-Tooth Syndrome Peroneal Muscular Atrophy Hereditary Motor And Sensory Neuropathies

Diseases	Alias
Waldenstroem'S Macroglobulinemia	Waldenstroem'S Macroglobulinemia Waldenstroem'S Macroglobulinemia Macroglobulinemia Of Waldenstrom Lymphoplasmacytic Lymphoma With Igm Gammopathy Lymphoplasmacytic Lymphoma Waldenstroem'S Macroglobulinemia Waldenstroem'S Macroglobulinemia Macroglobulinemia Of Waldenstrom Lymphoplasmacytic Lymphoma With Igm Gammopathy Lymphoplasmacytic Lymphoma

Related Agents

Pre-clinical Phase

Pre-clinical Phase

Bioactive Molecules (5)

Cat. No.	Product Name	Effect	Purity	Rare Diseases
HY-114209	MRK-740	Inhibitor	99.13%	Unkown
HY-RS11073	PRDM9 Human Pre-designed siRNA Set A	Pre-designed Set	/	Unkown
HY-176820	MRK-740-NC	Inhibitor	/	Unkown
HY-RS19230	Prdm9 Mouse Pre-designed siRNA Set A	Pre-designed Set	/	Unkown
HY-RS25719	Prdm9 Rat Pre-designed siRNA Set A	Pre-designed Set	/	Unkown

Orthologs Information

Species	Symbol	Source	ID
Mus musculus	PRDM9	MGD	MGI:2384854
Rattus norvegicus	PRDM9	RGD	RGD:1305247
Others	PRDM9	NCBI