PRDM1

Chr 6

PR/SET domain 1

Also known as: BLIMP-1, BLIMP1, PRDI-BF1

NCBI Gene: 639ENSG00000057657UniProt: O75626

This gene encodes a protein that acts as a repressor of beta-interferon gene expression. The protein binds specifically to the PRDI (positive regulatory domain I element) of the beta-IFN gene promoter. Transcription of this gene increases upon virus induction. Two alternatively spliced transcript variants that encode different isoforms have been reported. [provided by RefSeq, Jul 2008]

111
ClinVar variants
15
Pathogenic / LP
0.96
pLI score· haploinsufficient
0
Active trials
Clinical Summary— PRDM1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.96). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
15 Pathogenic / Likely Pathogenic· 82 VUS of 111 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.33LOEUF
pLI 0.956
Z-score 4.15
OE 0.15 (0.07–0.33)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.77Z-score
OE missense 0.78 (0.71–0.84)
380 obs / 490.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.15 (0.07–0.33)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.78 (0.71–0.84)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.86
0≤1.21.6
LoF obs/exp: 4 / 27.5Missense obs/exp: 380 / 490.3Syn Z: 1.54

ClinVar Variant Classifications

111 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic15
VUS82
Likely Benign9
Benign4
Conflicting1
15
Pathogenic
82
VUS
9
Likely Benign
4
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
15
0
15
Likely Pathogenic
0
0
0
0
0
VUS
1
74
7
0
82
Likely Benign
0
5
0
4
9
Benign
0
3
0
1
4
Conflicting
—1
Total182225111

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PRDM1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Landscape of pathogenic mutations in premature ovarian insufficiency.
Ke H et al.·Nat Med
2023
Simplified algorithm for genetic subtyping in diffuse large B-cell lymphoma.
Shen R et al.·Signal Transduct Target Ther
2023
Genetic ablation of PRDM1 in antitumor T cells enhances therapeutic efficacy of adoptive immunotherapy.
Yoshikawa T et al.·Blood
2022
BLIMP1 and NR4A3 transcription factors reciprocally regulate antitumor CAR T cell stemness and exhaustion.
Jung IY et al.·Sci Transl Med
2022
Fatty Acids Invigorate Tumor-Resident Memory T Cells.
Chakraborty P et al.·Cancer Res
2023
High-grade B-cell lymphoma not otherwise specified, with diffuse large B-cell lymphoma gene expression signatures: Genomic analysis and potential therapeutics.
Lone W et al.·Am J Hematol
2025
Transethnic meta-analysis identifies GSDMA and PRDM1 as susceptibility genes to systemic sclerosis.
Terao C et al.·Ann Rheum Dis
2017Review
Epigenetics of the antibody and autoantibody response.
Moroney JB et al.·Curr Opin Immunol
2020Review
Somatic IRF4 mutations and thymic tropism in primary mediastinal large B-cell lymphoma.
Rai S et al.·Blood
2025
Plasmablast-like lymphoma cells as a distinct subpopulation confer multidrug resistance in PCNSL.
Liang F et al.·Neuro Oncol
2025
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
PRDM1 restricts bladder cancer progression and enhances chemosensitivity by suppressing OTUD6A-mediated deubiquitination of CDC6.
Cui J et al.·Cell Death Dis
2026🔓 Open Access
PRDM1 Knockdown Promotes Ferroptosis and Sunitinib Sensitivity by Modulating the PI3K/Akt Signaling Through Inhibition of ESM1 Transcription in Renal Cell Carcinoma.
Zhang YS et al.·Kaohsiung J Med Sci
2026
PRDM1+ Malignant Cells Mediate an Immunosuppressive Landscape and Resistance to Neoadjuvant Chemoradiotherapy and Immunotherapy in Esophageal Squamous Cell Carcinoma.
Shen D et al.·Adv Sci (Weinh)
2026
ZFP36L1-mediated PRDM1 mRNA degradation inhibits inflammatory activation of Kupffer cells and ameliorates DCD liver ischemic-reperfusion injury.
Du P et al.·Biochim Biophys Acta Mol Basis Dis
2026
PRDM1-driven SLC30A9 overexpression contributes to the malignant phenotype of cervical cancer cells via promoting mitochondrial hyperfunction.
Wang H et al.·Cell Death Dis
2025🔓 Open Access
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools