PHF3 Gene

HGNC Family	Zinc fingers
Name	PHD finger protein 3
Description	This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nPHF3 is a member of a family of PHD finger‐containing proteins that appears to play a role in transcriptional regulation and tumor suppression. Initially described as the third member of a PHD finger gene family—with a domain architecture that includes a PHD (LAP) motif and regions homologous to the transcription factor TFIIS—PHF3 is ubiquitously expressed in normal tissues such as the brain but is significantly reduced or lost in glioblastoma, suggesting that its downregulation may contribute to glioma development. In parallel, serological studies identified that glioblastoma patients frequently develop autoantibodies against PHF3, with such immune responses correlating with substantially prolonged survival, thereby indicating potential utility as a prognostic biomarker."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n\nDissecting its genetic associations beyond brain tumors, genome‐wide analyses have identified the PHF3 locus within a broader PHF3-PTP4A1 region as being associated with an increased risk for alcohol dependence. Multiple single nucleotide polymorphisms mapping to this linkage disequilibrium block not only show consistent associations across diverse populations but also exhibit strong cis-acting regulatory effects on gene expression. These findings implicate PHF3 dysregulation as a contributory factor in the neurobiological pathways underlying alcohol dependence."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n\nAt the molecular level, PHF3 functions as a regulatory hub by directly interfacing with the transcription machinery. Its SPOC domain specifically docks onto the C-terminal domain of RNA polymerase II, preferentially binding tandem phosphorylated Serine-2 marks across adjacent repeats. This interaction not only mediates proper transcriptional elongation and minimizes Pol II stalling but also couples gene expression with mRNA stability mechanisms. In neurons, the loss of PHF3 activity triggers derepression of key neuronal genes and aberrant differentiation, underscoring its pivotal role in the coordination of transcription and mRNA decay."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "U Fischer, A K Struss, D Hemmer, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PHF3 expression is frequently reduced in glioma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cytogenet Cell Genet (2001)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1159/000048804"}], "href": "https://doi.org/10.1159/000048804"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "11856869"}], "href": "https://pubmed.ncbi.nlm.nih.gov/11856869"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Christian Philipp Pallasch, Anne-Katrin Struss, Angela Munnia, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Autoantibodies against GLEA2 and PHF3 in glioblastoma: tumor-associated autoantibodies correlated with prolonged survival."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Int J Cancer (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/ijc.20929"}], "href": "https://doi.org/10.1002/ijc.20929"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15906353"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15906353"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Lingjun Zuo, Clarence K Zhang, Fei Wang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS One (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pone.0026726"}], "href": "https://doi.org/10.1371/journal.pone.0026726"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22096494"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22096494"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Lingjun Zuo, Kesheng Wang, Guilin Wang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Common PTP4A1-PHF3-EYS variants are specific for alcohol dependence."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Addict (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/j.1521-0391.2013.12115.x"}], "href": "https://doi.org/10.1111/j.1521-0391.2013.12115.x"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24961364"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24961364"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Lisa-Marie Appel, Vedran Franke, Melania Bruno, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41467-021-26360-2"}], "href": "https://doi.org/10.1038/s41467-021-26360-2"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "34667177"}], "href": "https://pubmed.ncbi.nlm.nih.gov/34667177"}]}]}]}
Proteins	PHF3_HUMAN
NCBI Gene ID	23469
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

PHF3 has 4,624 functional associations with biological entities spanning 8 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 111 datasets.

Click the + buttons to view associations for PHF3 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

PHF3 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by PHF3 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PHF3 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of PHF3 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of PHF3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of PHF3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PHF3 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of PHF3 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PHF3 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PHF3 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of PHF3 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of PHF3 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Gene Mutation Profiles	cell lines with PHF3 gene mutations from the CCLE Cell Line Gene Mutation Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with PHF3 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with PHF3 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of PHF3 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of PHF3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of PHF3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of PHF3 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing PHF3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing PHF3 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing PHF3 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with PHF3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with PHF3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of PHF3 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with PHF3 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Disease Associations	diseases associated with PHF3 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by PHF3 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with PHF3 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with PHF3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with PHF3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with PHF3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at PHF3 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of PHF3 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of PHF3 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing PHF3 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD High Level Gene-Disease Associations	diseases associated with PHF3 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of PHF3 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with PHF3 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing PHF3 from the GeneSigDB Published Gene Signatures dataset.
	GEO Signatures of Differentially Expressed Genes for Diseases	disease perturbations changing expression of PHF3 gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset.