PRDM1 (PR/SET Domain 1): A Master Regulator of B-Cell Differentiation and Tumor Suppressor
Explore the genomic architecture, expression, mutations, and clinical significance of the PRDM1 gene, a key transcription factor in immune function and cancer.
Gene Information Card
| Symbol | PRDM1 |
|---|---|
| Full Name | PR/SET domain 1 |
| Gene Type | Protein coding |
| Chromosomal Location | 6q21 |
| NCBI Gene ID | 639 ncbi.nlm.nih.gov/gene/639 |
| Ensembl ID | ENSG00000057657 |
| UniProt ID | O75626 |
| OMIM ID | 603423 |
| HGNC ID | 9346 |
| Aliases | Blimp-1, PRDI-BF1, MGC117339 |
Description
PRDM1 (PR/SET domain 1) encodes a zinc finger transcription factor known as Blimp-1 (B-lymphocyte-induced maturation protein-1). It is a master regulator of terminal differentiation in B cells, plasma cell formation, and immune responses. PRDM1 also functions as a tumor suppressor in several cancers, particularly in diffuse large B-cell lymphoma (DLBCL) and natural killer/T-cell lymphoma. The protein contains a PR domain (similar to SET domain) and five zinc finger motifs, mediating DNA binding and transcriptional repression. PRDM1 is involved in epigenetic regulation and is critical for maintaining immune homeostasis.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Diffuse large B-cell lymphoma (DLBCL) | Inactivation of PRDM1 via deletion or mutation leads to loss of tumor suppressor function, promoting B-cell lymphoma development. | ClinVar, COSMIC, NCBI Gene |
| Multiple myeloma | PRDM1 is essential for plasma cell differentiation; dysregulation contributes to myeloma pathogenesis, though mutations are less common. | OMIM, NCBI Gene |
| Natural killer/T-cell lymphoma | PRDM1 is frequently inactivated by deletions or epigenetic silencing, contributing to tumor progression. | COSMIC, NCBI Gene |
| Immunodeficiency (rare) | Biallelic loss-of-function mutations in PRDM1 can cause combined immunodeficiency with B-cell differentiation defects. | OMIM, ClinVar |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Spleen | High (nTPM ~ 50) | High expression in immune tissues |
| Bone Marrow | Moderate (nTPM ~ 20) | Plasma cells present |
| Lymph Node | High (nTPM ~ 40) | Germinal center B cells |
| Blood | Low (nTPM ~ 5) | Peripheral blood leukocytes |
| Liver | Low (nTPM ~ 1) | Minimal expression |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| Ramos (Burkitt lymphoma) | Low | B-cell line with low PRDM1 expression |
| U266 (Multiple myeloma) | High | Plasma cell line with high PRDM1 expression |
| K562 (CML) | Low | Myeloid line with minimal expression |
| HeLa (Cervical cancer) | Low | Epithelial line with low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.268C>T (p.Arg90*) | Nonsense | Rare (0.1% in general population) | Loss of function, truncated protein |
| c.1120delC (p.Leu374fs) | Frameshift | Somatic in DLBCL (~5%) | Loss of function, protein truncation |
| c.1450G>A (p.Gly484Arg) | Missense | Somatic in NK/T-cell lymphoma (~3%) | Altered DNA binding affinity |
| Whole gene deletion | Copy number loss | Somatic in DLBCL (~20%) | Loss of heterozygosity, tumor suppressor inactivation |
Mutation functional classification
Loss of Function (LOF)
Most PRDM1 mutations in cancer are loss-of-function, including nonsense, frameshift, and deletions, leading to loss of transcriptional repression and tumor suppressor activity.
Gain of Function (GOF)
Gain-of-function mutations are rare; some missense variants may alter target gene specificity but are not well characterized.
Dominant Negative (DN)
Truncated PRDM1 proteins can exert dominant-negative effects by interfering with wild-type protein function, though evidence is limited.
View complete mutation data：
Gene Ontology (GO)
| • DNA-binding transcription factor activity | • RNA polymerase II cis-regulatory region sequence-specific DNA binding |
| • Protein homodimerization activity | • Chromatin binding |
| • Negative regulation of transcription by RNA polymerase II | • Positive regulation of transcription by RNA polymerase II |
| • B cell differentiation | • Plasma cell differentiation |
| • Immune response | • Apoptotic process |
Pathways
• B cell receptor signaling pathway
• Plasma cell differentiation
• IL-4 signaling pathway
• p53 signaling pathway (via regulation of target genes)
• Epigenetic regulation of gene expression
Protein Summary
The PRDM1 protein (Blimp-1) is a 825-amino acid transcription factor with an N-terminal PR domain (similar to SET methyltransferases) and five C2H2 zinc finger motifs. It binds to specific DNA sequences to repress target genes involved in B-cell identity and promote plasma cell differentiation. Blimp-1 recruits histone-modifying enzymes such as G9a and HDAC2 to mediate epigenetic silencing. It is essential for antibody secretion and immune memory. In cancer, loss of PRDM1 leads to uncontrolled B-cell proliferation and lymphoma development.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| PRDM16 Knockout HEK293 Cell Line | EDJ-KQ3350 | Human | 63976 | Details Get a Quote |
| PRDM14 Knockout HEK293 Cell Line | EDJ-KQ3683 | Human | 63978 | Details Get a Quote |
| PRDM1 Knockout HEK293 Cell Line | EDJ-KQ4134 | Human | 639 | Details Get a Quote |
| PRDM15 Knockout HEK293 Cell Line | EDJ-KQ12218 | Human | 63977 | Details Get a Quote |
| PRDM11 Knockout HEK293 Cell Line | EDJ-KQ14143 | Human | 56981 | Details Get a Quote |
| PRDM10 Knockout HEK293 Cell Line | EDJ-KQ14888 | Human | 56980 | Details Get a Quote |
| PRDM12 Knockout HEK293 Cell Line | EDJ-KQ14889 | Human | 59335 | Details Get a Quote |
| PRDM13 Knockout HEK293 Cell Line | EDJ-KQ14890 | Human | 59336 | Details Get a Quote |
| PRDM16 Knockout HCT 116 Cell Line | EDJ-KQ25007 | Human | 63976 | Details Get a Quote |
| PRDM15 Knockout A-549 Cell Line | EDJ-KQ40963 | Human | 63977 | Details Get a Quote |
| PRDM15 Knockout HCT 116 Cell Line | EDJ-KQ40964 | Human | 63977 | Details Get a Quote |
| PRDM15 Knockout HeLa Cell Line | EDJ-KQ40965 | Human | 63977 | Details Get a Quote |
| PRDM1 Knockout A-549 Cell Line | EDJ-KQ26556 | Human | 639 | Details Get a Quote |
| PRDM1 Knockout HCT 116 Cell Line | EDJ-KQ26557 | Human | 639 | Details Get a Quote |
| PRDM1 Knockout HeLa Cell Line | EDJ-KQ26558 | Human | 639 | Details Get a Quote |
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