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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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PHF12
PHD finger protein 12
Chromosome 17 · 17q11.2
NCBI Gene: 57649Ensembl: ENSG00000109118.15HGNC: HGNC:20816UniProt: Q96QT6
60PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
negative regulation of transcription by RNA polymerase IItranscription repressor complexSin3-type complextranscription corepressor activityneurodegenerative diseasedevelopmental disorder of mental healthNeurodevelopmental disordercomplex neurodevelopmental disorder
✦AI Summary

PHF12 (PHD finger protein 12) functions as a transcriptional repressor and key scaffolding subunit of SIN3 chr17-remodeling complexes. As a core component of these complexes, PHF12 stabilizes the assembly by contacting each subunit domain and recruits the H3 histone tail to serve as the substrate receptor 1. The SIN3B complex containing PHF12 represses transcription by recognizing H3K27ac marks and recruiting histone deacetylase activity to counteract histone acetyltransferase activity, thereby mitigating histone acetylation and RNA polymerase II progression at transcribed regions 1. PHF12 may also function in a SIN3A-independent manner through recruitment of TLE5 complexes 2. Clinically, PHF12 dysregulation is implicated in multiple malignancies. In non-small cell lung cancer, PHF12 is upregulated and promotes tumorigenesis by transcriptionally regulating HDAC1 expression and activating EGFR/AKT signaling 3. In lung squamous cell carcinoma, PHF12 upregulation driven by lncRNA RP11-116G8.5 promotes cancer cell proliferation and invasion 4. PHF12 suppression by MYC-mediated m6A modifications also contributes to MYC-driven lymphoma progression 5. Additionally, PHF12 variants are associated with age-related macular degeneration and intraocular pressure regulation 67, and PHF12 expression patterns show diagnostic potential for prostate cancer detection 8.

Sources cited
1
PHF12 is a key scaffolding subunit of SIN3 complexes that stabilizes assembly, recruits H3 histone tail, and enables H3K27ac recognition for transcriptional repression
PMID: 37137925
2
PHF12 may function in SIN3A-independent transcriptional repression through recruitment of TLE5 complexes
PMID: 11390640
3
PHF12 is upregulated in non-small cell lung cancer and promotes tumorigenesis by transcriptionally regulating HDAC1 and activating EGFR/AKT signaling
PMID: 39075515
4
PHF12 upregulation in lung squamous cell carcinoma promotes cancer cell proliferation and invasion when regulated by lncRNA RP11-116G8.5
PMID: 34500373
5
PHF12 is a MYC-repressed gene whose m6A-modified transcripts are targets of MYC-driven cancer progression mechanisms
PMID: 33426808
6
Rare coding variants in PHF12 are identified in families with age-related macular degeneration
PMID: 32246154
7
PHF12 shows suggestive gene-based association with intraocular pressure regulation
PMID: 25525164
8
PHF12 expression in urine sediment is an independent predictor for prostate cancer discrimination
PMID: 26856686
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.45Moderate
developmental disorder of mental healthOpen Targets
0.37Weak
Neurodevelopmental disorderOpen Targets
0.37Weak
complex neurodevelopmental disorderOpen Targets
0.37Weak
autism spectrum disorderOpen Targets
0.09Suggestive
neoplasmOpen Targets
0.07Suggestive
non-small cell lung carcinomaOpen Targets
0.07Suggestive
lung cancerOpen Targets
0.06Suggestive
systemic lupus erythematosusOpen Targets
0.06Suggestive
triple-negative breast cancerOpen Targets
0.04Suggestive
atrial fibrillationOpen Targets
0.03Suggestive
breast cancerOpen Targets
0.03Suggestive
cancerOpen Targets
0.02Suggestive
venous thromboembolismOpen Targets
0.01Suggestive
Low back painOpen Targets
0.01Suggestive
Andersen-Tawil syndromeOpen Targets
0.01Suggestive
lung adenocarcinomaOpen Targets
0.01Suggestive
infectionOpen Targets
0.01Suggestive
obesityOpen Targets
0.01Suggestive
squamous cell lung carcinomaOpen Targets
0.01Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
HDAC1Protein interaction99%HDAC2Protein interaction98%KDM5AProtein interaction98%BRMS1Protein interaction98%MORF4L1Protein interaction97%EMSYProtein interaction97%
Tissue Expression6 tissues
Bone Marrow
100%
Lung
70%
Ovary
58%
Brain
52%
Liver
47%
Heart
36%
Gene Interaction Network
Click a node to explore
PHF12HDAC1HDAC2KDM5ABRMS1MORF4L1EMSY
PROTEIN STRUCTURE
Preparing viewer…
PDB8BPB · 2.80 Å · EM
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.12Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.06 [0.03–0.12]
RankingsWhere PHF12 stands among ~20K protein-coding genes
  • #7,694of 20,598
    Most Researched60
  • #99of 17,882
    Most Constrained (LOEUF)0.12 · top 1%
Genes detectedPHF12
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
MYC promotes cancer progression by modulating m
PMID: 33426808
EMBO Rep · 2021
1.00
2
LncRNA RP11-116G8.5 promotes the progression of lung squamous cell carcinoma through sponging miR-3150b-3p/miR-6870-5p to upregulate PHF12/FOXP4.
PMID: 34500373
Pathol Res Pract · 2021
0.90
3
Family-based exome sequencing identifies rare coding variants in age-related macular degeneration.
PMID: 32246154
Hum Mol Genet · 2020
0.80
4
Exome array analysis identifies CAV1/CAV2 as a susceptibility locus for intraocular pressure.
PMID: 25525164
Invest Ophthalmol Vis Sci · 2014
0.70
5
Frequent loss of heterozygosity at the DCC locus in gastric cancer.
PMID: 1591722
Cancer Res · 1992
0.60