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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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PHF2
PHD finger protein 2
Chromosome 9 · 9q22.31
NCBI Gene: 5253Ensembl: ENSG00000197724.13HGNC: HGNC:8920UniProt: O75151
81PubMed Papers
20Diseases
0Drugs
1Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
zinc ion bindingprotein demethylationtranscription initiation-coupled chromatin remodelingkinetochoreAbnormality of the skeletal systemmathematical abilityirritable bowel syndromeurinary system disease
✦AI Summary

PHF2 (PHD finger protein 2) is a histone demethylase that serves as a tumor suppressor through multiple epigenetic mechanisms. PHF2 catalyzes demethylation of histone H3 lysine 9 (H3K9me2) and H4 lysine 20 (H4K20me3), with activity regulated by phosphorylation—PKA phosphorylation activates its enzymatic function 1, while AMPK phosphorylation at S655 enhances H3K9me2 demethylation activity to suppress cancer metastasis 2. PHF2 functions as a coactivator with ARID5B in transcriptional regulation and maintains pericentromeric heterochromatin stability essential for genome integrity and neural progenitor proliferation 3. Beyond histone modification, PHF2 acts as an E3 ubiquitin ligase targeting SREBP1c to suppress lipogenesis in hepatocellular carcinoma 4. Clinically, PHF2 dysfunction associates with multiple malignancies. Down-expression correlates with poor prognosis, lymph node metastasis, and proliferation in breast cancer 5. Inactivating frameshift mutations occur in colorectal and gastric cancers with high microsatellite instability 6. Reduced PHF2 expression driven by risk alleles at locus 9q22.33 promotes nasopharyngeal carcinoma cell proliferation 7. Additionally, PHF2 upregulation contributes to neuroinflammation in Alzheimer's disease; PHF2 knockdown reduces inflammatory gene expression and improves cognitive outcomes 8. Genetic association studies identify PHF2 as a susceptibility locus for irritable bowel syndrome 9.

Sources cited
1
PHF2 is a lysine demethylase activated by PKA phosphorylation; demethylates H3K9me2 and H4K20me3; functions as coactivator with ARID5B
PMID: 21532585
2
AMPK phosphorylates PHF2 at S655, enhancing H3K9me2 demethylation activity and suppressing lung cancer metastasis
PMID: 36872368
3
PHF2 maintains pericentromeric heterochromatin stability through H3K9me2 balance, essential for neural progenitor proliferation and genome integrity
PMID: 38890452
4
PHF2 functions as E3 ubiquitin ligase of SREBP1c tumor suppressor in hepatocellular carcinoma; palmitoylation triggers PHF2 degradation
PMID: 37828054
5
PHF2 is down-expressed in breast cancer; low expression associates with lymph node metastasis, poor prognosis, and ectopic PHF2 inhibits cancer cell proliferation
PMID: 35558021
6
PHF2 harbors frameshift mutations in colorectal and gastric cancers with high microsatellite instability, suggesting inactivation as tumor suppressor
PMID: 27744626
7
PHF2 at locus 9q22.33 acts as nasopharyngeal carcinoma susceptibility gene; risk alleles reduce PHF2 expression and promote cell proliferation
PMID: 37352861
8
PHF2 is upregulated in Alzheimer's disease and regulates inflammatory genes; PHF2 knockdown reduces neuroinflammation and improves cognitive function
PMID: 40849543
9
PHF2/FAM120A is identified as genetic susceptibility locus for irritable bowel syndrome
PMID: 34741163
Disease Associationsⓘ20
Abnormality of the skeletal systemOpen Targets
0.49Moderate
mathematical abilityOpen Targets
0.44Moderate
irritable bowel syndromeOpen Targets
0.39Weak
urinary system diseaseOpen Targets
0.38Weak
insomniaOpen Targets
0.32Weak
health study participationOpen Targets
0.32Weak
asthmaOpen Targets
0.31Weak
Neck painOpen Targets
0.31Weak
Sleep DisorderOpen Targets
0.30Weak
erectile dysfunctionOpen Targets
0.30Weak
intelligenceOpen Targets
0.28Weak
major depressive disorderOpen Targets
0.28Weak
dysthymic disorderOpen Targets
0.27Weak
fungal infectious diseaseOpen Targets
0.24Weak
schizophreniaOpen Targets
0.21Weak
sleep apneaOpen Targets
0.19Weak
Abnormal urine sodium concentrationOpen Targets
0.18Weak
post-traumatic stress disorderOpen Targets
0.17Weak
COVID-19Open Targets
0.17Weak
abortionOpen Targets
0.13Weak
Pathogenic Variants1
NM_005392.4(PHF2):c.2749C>T (p.Gln917Ter)Likely pathogenic
not provided
★☆☆☆2022→ Residue 917
View on ClinVar ↗
Related Genes
ARID5BProtein interaction80%KDM3BProtein interaction70%MSL1Shared pathway33%HDGFL1Shared pathway33%HIPK4Shared pathway33%HMGB4Shared pathway33%
Tissue Expression6 tissues
Ovary
100%
Brain
95%
Heart
89%
Bone Marrow
83%
Lung
73%
Liver
37%
Gene Interaction Network
Click a node to explore
PHF2ARID5BKDM3BMSL1HDGFL1HIPK4HMGB4
PROTEIN STRUCTURE
Preparing viewer…
PDB7M10 · 1.15 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.33Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.24 [0.17–0.33]
RankingsWhere PHF2 stands among ~20K protein-coding genes
  • #5,883of 20,598
    Most Researched81
  • #4,959of 5,498
    Most Pathogenic Variants1
  • #1,373of 17,882
    Most Constrained (LOEUF)0.33 · top 10%
Genes detectedPHF2
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Palmitoylation-driven PHF2 ubiquitination remodels lipid metabolism through the SREBP1c axis in hepatocellular carcinoma.
PMID: 37828054
Nat Commun · 2023
1.00
2
Phosphorylation of PHF2 by AMPK releases the repressive H3K9me2 and inhibits cancer metastasis.
PMID: 36872368
Signal Transduct Target Ther · 2023
0.90
3
The expression and biological function of the PHF2 gene in breast cancer.
PMID: 35558021
RSC Adv · 2018
0.80
4
Histone Demethylase Gene PHF2 Is Mutated in Gastric and Colorectal Cancers.
PMID: 27744626
Pathol Oncol Res · 2017
0.70
5
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders.
PMID: 34741163
Nat Genet · 2021
0.60