Seroatlas · Human Serome Atlas

PRDM9

Histone-lysine N-methyltransferase PRDM9

Also known as: KMT8B, Meisetz, MSBP3, PFM6, PRDM9_HUMAN, ZNF899

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q9NQV7
Gene
PRDM9
Ensembl
ENSG00000164256
Chromosome
5
Canonical length
894 aa
Protein class
Enzymes, Predicted intracellular proteins, Transcription factors
Quaternary structure
Homodimer

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

894 residues, UniProt reviewed canonical sequence.

>Q9NQV7|PRDM9
     1  MSPEKSQEES PEEDTERTER KPMVKDAFKD ISIYFTKEEW AEMGDWEKTR YRNVKRNYNA
    61  LITIGLRATR PAFMCHRRQA IKLQVDDTED SDEEWTPRQQ VKPPWMALRV EQRKHQKGMP
   121  KASFSNESSL KELSRTANLL NASGSEQAQK PVSPSGEAST SGQHSRLKLE LRKKETERKM
   181  YSLRERKGHA YKEVSEPQDD DYLYCEMCQN FFIDSCAAHG PPTFVKDSAV DKGHPNRSAL
   241  SLPPGLRIGP SGIPQAGLGV WNEASDLPLG LHFGPYEGRI TEDEEAANNG YSWLITKGRN
   301  CYEYVDGKDK SWANWMRYVN CARDDEEQNL VAFQYHRQIF YRTCRVIRPG CELLVWYGDE
   361  YGQELGIKWG SKWKKELMAG REPKPEIHPC PSCCLAFSSQ KFLSQHVERN HSSQNFPGPS
   421  ARKLLQPENP CPGDQNQEQQ YPDPHSRNDK TKGQEIKERS KLLNKRTWQR EISRAFSSPP
   481  KGQMGSCRVG KRIMEEESRT GQKVNPGNTG KLFVGVGISR IAKVKYGECG QGFSVKSDVI
   541  THQRTHTGEK LYVCRECGRG FSWKSHLLIH QRIHTGEKPY VCRECGRGFS WQSVLLTHQR
   601  THTGEKPYVC RECGRGFSRQ SVLLTHQRRH TGEKPYVCRE CGRGFSRQSV LLTHQRRHTG
   661  EKPYVCRECG RGFSWQSVLL THQRTHTGEK PYVCRECGRG FSWQSVLLTH QRTHTGEKPY
   721  VCRECGRGFS NKSHLLRHQR THTGEKPYVC RECGRGFRDK SHLLRHQRTH TGEKPYVCRE
   781  CGRGFRDKSN LLSHQRTHTG EKPYVCRECG RGFSNKSHLL RHQRTHTGEK PYVCRECGRG
   841  FRNKSHLLRH QRTHTGEKPY VCRECGRGFS DRSSLCYHQR THTGEKPYVC REDE

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PRDM9 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Intracellular
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.45
Highest tissue expression
4.1 nTPM

Expression across tissuesHPA

Tissue

  • testis: 4.1 nTPM
  • epididymis: 1.5 nTPM
  • skin: 0.2 nTPM
  • bone marrow: 0.1 nTPM
  • adipose tissue: 0 nTPM
  • adrenal gland: 0 nTPM

Single-cell type

  • early primary spermatocytes: 73 nCPM
  • epididymal principal cells: 15 nCPM
  • late primary spermatocytes: 3.5 nCPM
  • late spermatids: 3.2 nCPM
  • early spermatids: 2.7 nCPM
  • undifferentiated spermatogonia: 2.4 nCPM

Immune cell

  • neutrophil: 1.1 nTPM
  • basophil: 0.7 nTPM
  • NK-cell: 0.5 nTPM
  • classical monocyte: 0.2 nTPM
  • naive B-cell: 0.2 nTPM
  • gdT-cell: 0.1 nTPM

Brain region

  • white matter: 2.6 nTPM
  • choroid plexus: 2.2 nTPM
  • medulla oblongata: 2 nTPM
  • pons: 1.9 nTPM
  • basal ganglia: 1.8 nTPM
  • hypothalamus: 1.8 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PRDM9.

Disease | GeneticClinVar

3 pathogenic / likely-pathogenic of 176 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
1.32
gnomAD pLI
0
gnomAD missense Z
-0.75
DepMap mean gene effect
0.17
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PRDM9 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PRDM9 as an antibody target. Whether an autoantibody or antibody against PRDM9 could matter depends on whether native PRDM9 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PRDM9 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label PRDM9 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PRDM9. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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