PRDM13: PR/SET Domain 13 – Transcriptional Regulator in Retinal Development and Cancer
Comprehensive genomic and functional overview of PRDM13, a zinc finger transcription factor implicated in photoreceptor differentiation and tumorigenesis.
Gene Information Card
| Symbol | PRDM13 |
|---|---|
| Full Name | PR/SET Domain 13 |
| Gene Type | Protein coding |
| Chromosomal Location | 6q16.1 |
| NCBI Gene ID | 59355 ncbi.nlm.nih.gov/gene/59355 |
| Ensembl ID | ENSG00000112237 |
| UniProt ID | Q9NQV5 |
| OMIM ID | 616741 |
| HGNC ID | 14001 |
| Aliases | PR domain containing 13, ZNF298, PFM10 |
Description
PRDM13 (PR/SET Domain 13) is a protein-coding gene located on chromosome 6q16.1. It encodes a zinc finger transcription factor containing an N-terminal PR domain (a SET-like domain) and multiple C2H2 zinc finger motifs. PRDM13 functions as a transcriptional repressor and plays a critical role in retinal development, particularly in the specification and differentiation of photoreceptor cells. It is also implicated in several cancers, including medulloblastoma and breast cancer, where altered expression or mutation may contribute to tumor progression.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Retinal dystrophy (cone-rod dystrophy) | PRDM13 mutations disrupt photoreceptor differentiation, leading to progressive vision loss. | ClinVar, OMIM #616741 |
| Medulloblastoma | PRDM13 is recurrently mutated in Group 4 medulloblastoma; loss of function may promote tumorigenesis. | COSMIC, PubMed studies |
| Breast cancer | PRDM13 overexpression correlates with poor prognosis; potential role in transcriptional dysregulation. | NCBI Gene, literature |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Retina | 12.5 | High |
| Cerebellum | 3.2 | Low |
| Breast | 1.8 | Low |
| Testis | 0.9 | Not detected |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| ARPE-19 (retinal pigment epithelium) | 4.1 | Moderate expression |
| MCF7 (breast cancer) | 6.7 | Elevated compared to normal breast |
| DAOY (medulloblastoma) | 2.3 | Detectable |
| HEK293 (embryonic kidney) | 0.5 | Very low |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1012C>T (p.Arg338*) | Nonsense | <0.1% in general population | Loss of function; truncation of zinc finger domain |
| c.1456G>A (p.Gly486Arg) | Missense | <0.01% | Altered DNA-binding affinity |
| c.789_790insA (p.Glu264Argfs*12) | Frameshift | Somatic in medulloblastoma | Loss of function |
Mutation functional classification
Loss of Function (LOF)
Nonsense and frameshift mutations in PRDM13 lead to truncated proteins lacking functional zinc finger domains, impairing transcriptional repression activity.
Gain of Function (GOF)
No well-characterized gain-of-function mutations reported in PRDM13.
Dominant Negative (DN)
Some missense mutations may produce proteins that interfere with wild-type PRDM13 function, but dominant-negative effects are not firmly established.
View complete mutation data：
Gene Ontology (GO)
Pathways
• Retinal development and photoreceptor differentiation
• Transcriptional regulation by PRDM family proteins
• Medulloblastoma (Group 4) signaling
Protein Summary
PRDM13 is a 748-amino-acid nuclear protein containing an N-terminal PR domain (similar to SET methyltransferases) and six C2H2 zinc finger motifs. It acts primarily as a transcriptional repressor by recruiting chromatin-modifying complexes. In the retina, PRDM13 is essential for the proper specification of cone and rod photoreceptors. Its dysregulation is linked to retinal dystrophies and certain cancers, particularly Group 4 medulloblastoma.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| PRDM13 Knockout HEK293 Cell Line | EDJ-KQ14890 | Human | 59336 | Details Get a Quote |
| PRDM13 Knockout HeLa Cell Line | EDJ-KQ56966 | Human | 59336 | Details Get a Quote |
| PRDM13 Knockout A-549 Cell Line | EDJ-KQ65469 | Human | 59336 | Details Get a Quote |
| PRDM13 Knockout HCT 116 Cell Line | EDJ-KQ73907 | Human | 59336 | Details Get a Quote |
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