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GeneE
27 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PHF6
PHD finger protein 6
Chromosome X Β· Xq26.2
NCBI Gene: 84295Ensembl: ENSG00000156531.19HGNC: HGNC:18145UniProt: Q8IWS0
174PubMed Papers
21Diseases
0Drugs
55Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
RNA bindingprotein bindingtubulin bindingenzyme bindingBorjeson-Forssman-Lehmann syndromeneurodegenerative diseasegenetic disorderacute myeloid leukemia
✦AI Summary

PHF6 (PHD finger protein 6) is an X-linked epigenetic regulator that functions as a transcriptional modifier through chrX remodeling. The protein contains conserved plant homeodomain (PHD) zinc finger domains that enable DNA binding and interaction with chrX-associated complexes 1. PHF6 cooperates with nucleosome remodeling and deacetylation (NuRD) complexes and SWI/SNF chrX remodeling complexes to maintain active chrX states at promoters and enhancers, facilitating RNA Polymerase II transcriptional progression 2. In hematopoiesis, PHF6 maintains lineage-specific chrX architecture that supports B-cell and T-cell identity genes 3. Germline PHF6 mutations cause BΓΆrjeson-Forssman-Lehmann syndrome, an X-linked neurodevelopmental disorder 1. Somatic PHF6 mutations are frequent in hematologic malignancies, occurring in ~38% of adult T-ALL, ~16% of pediatric T-ALL, ~3% of AML, and ~20% of MPAL 3. PHF6 mutations associate with adverse outcomes in AML 4 and myeloid neoplasms, particularly when co-occurring with RUNX1 mutations 5. However, PHF6 demonstrates lineage-dependent effects: while acting as a tumor suppressor in T-ALL, it functions as an oncogene in certain B-ALL and solid tumors, suggesting tissue-specific roles 36. NGS-based stratification identifies PHF6 mutations as favorable prognostic indicators in T-ALL when occurring without high-risk alterations 7.

Sources cited
1
PHF6 role in epigenetic regulation and hematopoiesis; mutation frequencies in various leukemias; dual tumor suppressor/oncogene function depending on cell lineage
PMID: 36008597
2
PHF6 structure, DNA binding capability, interaction with NuRD complex, and association with BFLS and leukemias
PMID: 24554700
3
PHF6 cooperates with SWI/SNF complexes at promoters to maintain active chromatin and facilitate RNA Polymerase II progression
PMID: 39181868
4
PHF6 mutations associated with reduced overall survival in AML
PMID: 22417203
5
PHF6 interacts with RUNX1 at enhancers; negative prognostic role especially with RUNX1 co-mutations in myeloid neoplasms
PMID: 38418452
6
PHF6 mutations identify low-risk T-ALL subgroup in NGS-based stratification
PMID: 38848537
7
PHF6 demonstrates tissue-specific roles as tumor suppressor in some cancers and oncogene in others including breast and colorectal cancers
PMID: 26561469
Disease Associationsβ“˜21
Borjeson-Forssman-Lehmann syndromeOpen Targets
0.82Strong
neurodegenerative diseaseOpen Targets
0.54Moderate
genetic disorderOpen Targets
0.51Moderate
acute myeloid leukemiaOpen Targets
0.50Moderate
Intellectual disabilityOpen Targets
0.46Moderate
T-cell acute lymphoblastic leukemiaOpen Targets
0.38Weak
lymphoid neoplasmOpen Targets
0.37Weak
breast ductal adenocarcinomaOpen Targets
0.37Weak
carcinoma of liver and intrahepatic biliary tractOpen Targets
0.37Weak
Endometrial Endometrioid AdenocarcinomaOpen Targets
0.37Weak
Ovarian Endometrioid Adenocarcinoma with Squamous DifferentiationOpen Targets
0.37Weak
acute lymphoblastic leukemiaOpen Targets
0.34Weak
Autosomal dominant spastic paraplegia type 4Open Targets
0.34Weak
hereditary spastic paraplegia 4Open Targets
0.34Weak
HirsutismOpen Targets
0.33Weak
neoplasmOpen Targets
0.30Weak
lung adenocarcinomaOpen Targets
0.30Weak
bladder transitional cell carcinomaOpen Targets
0.30Weak
gliomaOpen Targets
0.29Weak
chronic lymphocytic leukemiaOpen Targets
0.29Weak
Boerjeson-Forssman-Lehmann syndromeUniProt
Pathogenic Variants55
NM_001015877.2(PHF6):c.820C>T (p.Arg274Ter)Pathogenic
Inborn genetic diseases|not provided|See cases|Borjeson-Forssman-Lehmann syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 274
NM_001015877.2(PHF6):c.1024C>T (p.Arg342Ter)Pathogenic
Borjeson-Forssman-Lehmann syndrome|not provided|Intellectual disability
β˜…β˜…β˜†β˜†2024β†’ Residue 342
NM_001015877.2(PHF6):c.134G>A (p.Cys45Tyr)Pathogenic
Borjeson-Forssman-Lehmann syndrome|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 45
NM_001015877.2(PHF6):c.346C>T (p.Arg116Ter)Pathogenic
Borjeson-Forssman-Lehmann syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 116
NM_001015877.2(PHF6):c.673C>T (p.Arg225Ter)Pathogenic
Borjeson-Forssman-Lehmann syndrome|Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 225
NM_001015877.2(PHF6):c.2T>C (p.Met1Thr)Pathogenic
Borjeson-Forssman-Lehmann syndrome|Hereditary spastic paraplegia 4|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 1
NM_001015877.2(PHF6):c.940A>G (p.Ile314Val)Likely pathogenic
not provided|PHF6-related disorder
β˜…β˜†β˜†β˜†2026β†’ Residue 314
NM_001015877.2(PHF6):c.181dup (p.Ser61fs)Pathogenic
Borjeson-Forssman-Lehmann syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 61
NM_001015877.2(PHF6):c.375-1G>APathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_001015877.2(PHF6):c.385C>T (p.Arg129Ter)Pathogenic
Borjeson-Forssman-Lehmann syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 129
NM_001015877.2(PHF6):c.958G>A (p.Gly320Arg)Likely pathogenic
Borjeson-Forssman-Lehmann syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 320
NM_001015877.2(PHF6):c.417A>T (p.Glu139Asp)Pathogenic
Borjeson-Forssman-Lehmann syndrome|Nonpapillary renal cell carcinoma
β˜…β˜†β˜†β˜†2024β†’ Residue 139
NM_001015877.2(PHF6):c.904C>T (p.His302Tyr)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2024β†’ Residue 302
NM_001015877.2(PHF6):c.-46-2A>GPathogenic
Early onset severe obesity
β˜…β˜†β˜†β˜†2023
NM_001015877.2(PHF6):c.392A>T (p.His131Leu)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 131
NM_001015877.2(PHF6):c.729+2T>CLikely pathogenic
Borjeson-Forssman-Lehmann syndrome|Nonpapillary renal cell carcinoma
β˜…β˜†β˜†β˜†2023
NM_001015877.2(PHF6):c.769A>G (p.Arg257Gly)Pathogenic
Borjeson-Forssman-Lehmann syndrome|not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 257
NM_001015877.2(PHF6):c.241-5_255delPathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2023
NM_001015877.2(PHF6):c.88C>T (p.Gln30Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 30
NM_001015877.2(PHF6):c.965A>C (p.Tyr322Ser)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2022β†’ Residue 322
View on ClinVar β†—
Related Genes
CTR9Protein interaction100%CDC73Protein interaction100%RBBP4Protein interaction96%NPM1Protein interaction94%TLX3Protein interaction90%KMT2AProtein interaction90%
Tissue Expression6 tissues
Ovary
100%
Brain
71%
Bone Marrow
49%
Heart
38%
Lung
27%
Liver
25%
Gene Interaction Network
Click a node to explore
PHF6CTR9CDC73RBBP4NPM1TLX3KMT2A
PROTEIN STRUCTURE
Preparing viewer…
PDB4NN2 Β· 1.47 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.39Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.21 [0.12–0.39]
RankingsWhere PHF6 stands among ~20K protein-coding genes
  • #2,526of 20,598
    Most Researched174 Β· top quartile
  • #1,240of 5,498
    Most Pathogenic Variants55 Β· top quartile
  • #1,877of 17,882
    Most Constrained (LOEUF)0.39 Β· top quartile
Genes detectedPHF6
Sources retrieved27 papers
Response timeβ€”
πŸ“„ Sources
27β–Ό
1
PMID: 23556151
1.00
2
T-Cell Acute Lymphoblastic Leukemia: Biomarkers and Their Clinical Usefulness.
PMID: 34440292
Genes (Basel) Β· 2021
0.90
3
Prognostic relevance of integrated genetic profiling in acute myeloid leukemia.
PMID: 22417203
N Engl J Med Β· 2012
0.80
4
Genomic and global gene expression profiling in pediatric and young adult acute leukemia with PICALM::MLLT10 Fusion.
PMID: 38429501
Leukemia Β· 2024
0.72
5
NGS-based stratification refines the risk stratification in T-ALL and identifies a very-high-risk subgroup of patients.
PMID: 38848537
Blood Β· 2024
0.70