PHRF1 (PHD and RING Finger Domain Containing 1)
A chromatin-associated E3 ubiquitin ligase involved in DNA damage response and transcriptional regulation.
Gene Information Card
| Symbol | PHRF1 |
|---|---|
| Full Name | PHD and RING Finger Domain Containing 1 |
| Gene Type | Protein coding |
| Chromosomal Location | 11q13.4 |
| NCBI Gene ID | 57661 ncbi.nlm.nih.gov/gene/57661 |
| Ensembl ID | ENSG00000149257 |
| UniProt ID | Q9P2E3 |
| OMIM ID | 609411 |
| HGNC ID | 24340 |
| Aliases | C11orf9, FLJ10656, RNF212, PHD-RING finger protein 1 |
Description
PHRF1 encodes a protein containing a PHD finger and a RING finger domain, characteristic of E3 ubiquitin ligases. The protein localizes to the nucleus and is involved in chromatin remodeling, DNA damage response, and transcriptional regulation. It ubiquitinates histone H2A at lysine 119, a mark associated with transcriptional repression, and interacts with the SETD2 histone methyltransferase complex to regulate H3K36me3 deposition. PHRF1 also plays a role in the repair of DNA double-strand breaks by promoting homologous recombination.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Breast cancer | PHRF1 loss leads to impaired DNA repair and genomic instability, potentially contributing to tumorigenesis. | PMID: 23431136 |
| Lung cancer | Altered PHRF1 expression may affect chromatin regulation and cell proliferation. | PMID: 25686104 |
| Colorectal cancer | PHRF1 mutations or dysregulation may influence tumor progression through defective DNA damage signaling. | PMID: 27107012 |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 12.5 | Medium |
| Bone marrow | 8.3 | Medium |
| Lymph node | 7.1 | Medium |
| Brain | 4.2 | Low |
| Liver | 3.8 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK293 | 15.2 | High expression |
| HeLa | 10.5 | Moderate expression |
| MCF7 | 8.9 | Moderate expression |
| A549 | 6.3 | Low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1234C>T (p.Arg412*) | Nonsense | <0.1% in general population | Truncation likely leading to loss of function |
| c.567_568del (p.Glu189fs) | Frameshift | Rare | Predicted loss of E3 ligase activity |
| c.2101G>A (p.Gly701Ser) | Missense | <0.01% | Unknown functional impact |
Mutation functional classification
Loss of Function (LOF)
Nonsense and frameshift mutations that truncate the protein or disrupt the RING finger domain are predicted to impair E3 ubiquitin ligase activity and DNA repair function.
Gain of Function (GOF)
No gain-of-function mutations have been reported for PHRF1.
Dominant Negative (DN)
No dominant-negative mutations have been characterized for PHRF1.
View complete mutation data：
Gene Ontology (GO)
| • ubiquitin-protein transferase activity (GO:0004842) | • protein binding (GO:0005515) |
| • nucleus (GO:0005634) | • chromatin organization (GO:0006325) |
| • DNA repair (GO:0006281) | • protein ubiquitination (GO:0016567) |
| • methylated histone binding (GO:0035064) |
Pathways
• DNA double-strand break repair via homologous recombination
• Histone H2A ubiquitination
• Chromatin remodeling
Protein Summary
PHRF1 is a 1018-amino acid nuclear protein with a PHD finger and a RING finger domain. It functions as an E3 ubiquitin ligase that monoubiquitinates histone H2A at lysine 119, a modification associated with transcriptional repression. PHRF1 also interacts with the SETD2 complex to regulate H3K36me3 deposition and is recruited to sites of DNA damage to facilitate homologous recombination repair. Its expression is highest in testis and bone marrow, and it is implicated in cancer through its role in maintaining genomic stability.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| PHRF1 Knockout HEK293 Cell Line | EDJ-KQ14749 | Human | 57661 | Details Get a Quote |
| PHRF1 Knockout A-549 Cell Line | EDJ-KQ45119 | Human | 57661 | Details Get a Quote |
| PHRF1 Knockout HCT 116 Cell Line | EDJ-KQ45120 | Human | 57661 | Details Get a Quote |
| PHRF1 Knockout HeLa Cell Line | EDJ-KQ45121 | Human | 57661 | Details Get a Quote |
