PHF2: PHD Finger Protein 2 – A Histone Demethylase in Transcriptional Regulation
Comprehensive genomic and functional overview of PHF2, a JmjC-domain-containing histone demethylase implicated in development and cancer.
Gene Information Card
| Symbol | PHF2 |
|---|---|
| Full Name | PHD finger protein 2 |
| Gene Type | Protein-coding |
| Chromosomal Location | 9q22.31 |
| NCBI Gene ID | 5253 ncbi.nlm.nih.gov/gene/5253 |
| Ensembl ID | ENSG00000107165 |
| UniProt ID | O75152 |
| OMIM ID | 604350 |
| HGNC ID | 8920 |
| Aliases | KDM7C, JHDM1E, GRC5, CENP-35 |
Description
PHF2 (PHD finger protein 2) encodes a histone demethylase that specifically demethylates lysine 9 on histone H3 (H3K9me2) and lysine 27 on histone H3 (H3K27me2), acting as a transcriptional activator. It contains a PHD finger domain and a JmjC domain. PHF2 is involved in cell cycle regulation, chromatin remodeling, and development. Mutations and altered expression have been linked to various cancers and developmental disorders.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Breast cancer | PHF2 acts as a tumor suppressor; loss of expression promotes proliferation and metastasis via H3K9me2 accumulation at tumor suppressor gene promoters. | PMID: 25910206 |
| Colorectal cancer | PHF2 downregulation correlates with poor prognosis; demethylase activity regulates Wnt/β-catenin signaling. | PMID: 27626308 |
| Hepatocellular carcinoma | PHF2 suppresses tumor growth by demethylating H3K9me2 at CDKN1A promoter, inducing p21 expression. | PMID: 29367642 |
| Intellectual disability | Homozygous loss-of-function mutations in PHF2 cause autosomal recessive intellectual disability with microcephaly. | PMID: 25064873 |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | Medium |
| Liver | 8.3 | Low |
| Kidney | 10.1 | Medium |
| Testis | 15.2 | High |
| Lung | 7.8 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HeLa | 14.0 | Cervical cancer cell line |
| HEK293 | 11.5 | Embryonic kidney cells |
| MCF7 | 9.2 | Breast cancer cell line |
| HepG2 | 8.7 | Hepatocellular carcinoma cell line |
| K562 | 6.4 | Leukemia cell line |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1051C>T (p.Arg351*) | Nonsense | <0.1% | Loss of function; truncation of JmjC domain |
| c.1462G>A (p.Gly488Arg) | Missense | <0.1% | Likely loss of function; disrupts catalytic activity |
| c.1975_1976del (p.Leu659fs) | Frameshift | <0.1% | Loss of function; premature termination |
| c.1A>G (p.Met1?) | Start loss | <0.1% | Loss of function; no translation initiation |
Mutation functional classification
Loss of Function (LOF)
Nonsense, frameshift, and start-loss mutations that truncate or abolish PHF2 protein expression or catalytic activity.
Gain of Function (GOF)
No gain-of-function mutations reported in curated databases.
Dominant Negative (DN)
No dominant-negative mutations reported in curated databases.
View complete mutation data：
Gene Ontology (GO)
| • histone H3-K9 demethylation | • histone H3-K27 demethylation |
| • chromatin remodeling | • transcription |
| • DNA-templated | • cell cycle |
| • PHD finger domain binding | • zinc ion binding |
| • nucleus |
Pathways
• Chromatin modifying enzymes
• Transcriptional regulation by histone demethylation
• Wnt signaling pathway (via β-catenin regulation)
Protein Summary
PHF2 is a 1,090-amino-acid protein containing an N-terminal PHD finger domain and a central JmjC domain. It functions as a histone demethylase specific for H3K9me2 and H3K27me2, converting them to monomethyl and unmethylated states. The protein localizes to the nucleus and interacts with transcription factors such as ARID5B and CENP-C. PHF2 is involved in cell cycle progression, DNA damage response, and differentiation. Its expression is regulated in a tissue-specific manner, with highest levels in testis and brain.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| PHF2 Knockout HEK293 Cell Line | EDJ-KQ2175 | Human | 5253 | Details Get a Quote |
| PHF21B Knockout HEK293 Cell Line | EDJ-KQ7400 | Human | 112885 | Details Get a Quote |
| PHF24 Knockout HEK293 Cell Line | EDJ-KQ7982 | Human | 23349 | Details Get a Quote |
| PHF20L1 Knockout HEK293 Cell Line | EDJ-KQ10920 | Human | 51105 | Details Get a Quote |
| PHF20 Knockout HEK293 Cell Line | EDJ-KQ10985 | Human | 51230 | Details Get a Quote |
| PHF21A Knockout HEK293 Cell Line | EDJ-KQ11045 | Human | 51317 | Details Get a Quote |
| PHF23 Knockout HEK293 Cell Line | EDJ-KQ14744 | Human | 79142 | Details Get a Quote |
| PHF21A Knockout A-549 Cell Line | EDJ-KQ38952 | Human | 51317 | Details Get a Quote |
| PHF21A Knockout HeLa Cell Line | EDJ-KQ38954 | Human | 51317 | Details Get a Quote |
| PHF2 Knockout A-549 Cell Line | EDJ-KQ22384 | Human | 5253 | Details Get a Quote |
| PHF2 Knockout HCT 116 Cell Line | EDJ-KQ22385 | Human | 5253 | Details Get a Quote |
| PHF2 Knockout HeLa Cell Line | EDJ-KQ22386 | Human | 5253 | Details Get a Quote |
| PHF21A Knockout HCT 116 Cell Line | EDJ-KQ37645 | Human | 51317 | Details Get a Quote |
| PHF20L1 Knockout A-549 Cell Line | EDJ-KQ38674 | Human | 51105 | Details Get a Quote |
| PHF20L1 Knockout HCT 116 Cell Line | EDJ-KQ38675 | Human | 51105 | Details Get a Quote |
Displaying Records 1 To 15 Of 25 Records
