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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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PRDM2
PR/SET domain 2
Chromosome 1 · 1p36.21
NCBI Gene: 7799Ensembl: ENSG00000116731.23HGNC: HGNC:9347UniProt: Q13029
100PubMed Papers
20Diseases
0Drugs
1Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
RNA polymerase II transcription regulatory region sequence-specific DNA bindingnegative regulation of transcription by RNA polymerase IInucleoplasmDNA-binding transcription activator activity, RNA polymerase II-specificAbruptio Placentaeliver diseasebrain aneurysmbile duct disorder
✦AI Summary

PRDM2 (PR/SET domain 2), also known as RIZ, is a histone methyltransferase that catalyzes lysine-9 methylation of histone H3 1. The gene produces two major isoforms through alternative splicing: RIZ1 (PR-domain positive) and RIZ2 (PR-domain negative), which differ functionally in their ability to regulate transcription 1. PRDM2 functions as a DNA-binding transcription factor with zinc-finger domains that mediate protein-DNA interactions and may activate genes like HMOX1 2. At the mechanistic level, PRDM2 regulates gene expression through epigenetic modifications and transcriptional control, with distinct isoforms showing differential effects on T lymphocyte differentiation and activation 3. Disease relevance is substantial: an imbalance between RIZ1 and RIZ2 isoforms is implicated in multiple malignancies, where the PR-positive RIZ1 is typically lost or downregulated while RIZ2 remains elevated in cancer cells 1. PRDM2 promoter methylation suppresses expression in lung cancer, and demethylating agents can restore expression and inhibit cancer cell growth 4. Mutations and deletions in PRDM2 occur frequently in hepatocellular carcinoma 5, and hypoxia-induced alternative splicing of PRDM2 produces frameshift mutations promoting tumor adaptation 6. Clinically, PRDM2 variants associate with polycystic ovary syndrome subtypes 7, suggesting diagnostic and therapeutic potential across multiple disease contexts.

Sources cited
1
PRDM2/RIZ structure, isoform imbalance in cancer, RIZ1 as estradiol target, and role in disease pathophysiology
PMID: 29883756
2
PRDM2 histone methyltransferase function, PR domain catalytic activity, zinc-finger mediated interactions, RIZ1/RIZ2 isoform differences, and role in systemic diseases
PMID: 40867614
3
PRDM2 (RIZ1 and RIZ2) transcripts in T lymphocyte activation and differentiation through epigenetic regulation
PMID: 36964555
4
PRDM2 methylation in lung cancer cells, demethylation-induced expression upregulation, and growth suppression
PMID: 24966940
5
PRDM2 deletion in hepatocellular carcinoma with RIZ1 loss/underexpression and tumor suppressive functions
PMID: 10862032
6
Hypoxia-induced PRDM2 alternative splicing producing frameshift mutations affecting cancer cell adaptation
PMID: 37988165
7
PRDM2 genetic association with polycystic ovary syndrome reproductive subtype
PMID: 32574161
8
PRDM2 mutations enriched in colorectal cancer involving chromatin remodeling and histone methylation pathways
PMID: 24755471
Disease Associationsⓘ20
Abruptio PlacentaeOpen Targets
0.37Weak
liver diseaseOpen Targets
0.34Weak
brain aneurysmOpen Targets
0.33Weak
bile duct disorderOpen Targets
0.31Weak
Flexion contractureOpen Targets
0.26Weak
hepatocellular carcinomaOpen Targets
0.22Weak
gliomaOpen Targets
0.21Weak
papillary renal cell carcinomaOpen Targets
0.21Weak
non-small cell lung carcinomaOpen Targets
0.20Weak
lung adenocarcinomaOpen Targets
0.20Weak
breast carcinomaOpen Targets
0.20Weak
lung carcinomaOpen Targets
0.20Weak
injuryOpen Targets
0.20Weak
undifferentiated pleomorphic sarcomaOpen Targets
0.20Weak
embryonal rhabdomyosarcomaOpen Targets
0.19Weak
alveolar rhabdomyosarcomaOpen Targets
0.19Weak
esophageal squamous cell carcinomaOpen Targets
0.19Weak
meningiomaOpen Targets
0.19Weak
gastric carcinomaOpen Targets
0.19Weak
urinary bladder carcinomaOpen Targets
0.19Weak
Pathogenic Variants1
NM_001393986.1(PRDM2):c.4283_4295del (p.Leu1428fs)Likely pathogenic
Flexion contracture
☆☆☆☆→ Residue 1428
View on ClinVar ↗
Related Genes
MSL1Shared pathway100%HDGFL1Shared pathway100%HIPK4Shared pathway100%HMGB4Shared pathway100%NAA40Shared pathway100%NSD1Shared pathway100%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
51%
Brain
40%
Heart
32%
Lung
31%
Liver
15%
Gene Interaction Network
Click a node to explore
PRDM2MSL1HDGFL1HIPK4HMGB4NAA40NSD1
PROTEIN STRUCTURE
Preparing viewer…
PDB2QPW · 1.79 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.30Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.21 [0.15–0.30]
RankingsWhere PRDM2 stands among ~20K protein-coding genes
  • #4,799of 20,598
    Most Researched100 · top quartile
  • #4,888of 5,498
    Most Pathogenic Variants1
  • #1,116of 17,882
    Most Constrained (LOEUF)0.30 · top 10%
Genes detectedPRDM2
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Human PRDM2: Structure, function and pathophysiology.
PMID: 29883756
Biochim Biophys Acta Gene Regul Mech · 2018
1.00
2
Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer.
PMID: 24755471
Cancer Res · 2014
0.90
3
Distinct subtypes of polycystic ovary syndrome with novel genetic associations: An unsupervised, phenotypic clustering analysis.
PMID: 32574161
PLoS Med · 2020
0.80
4
AEP-cleaved DDX3X induces alternative RNA splicing events to mediate cancer cell adaptation in harsh microenvironments.
PMID: 37988165
J Clin Invest · 2023
0.70
5
Exploring the putative role of PRDM1 and PRDM2 transcripts as mediators of T lymphocyte activation.
PMID: 36964555
J Transl Med · 2023
0.60