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Aliases for PHF6 Gene

Aliases for PHF6 Gene

  • PHD Finger Protein 6 2 3 5
  • PHD-Like Zinc Finger Protein 3 4
  • Centromere Protein 31 2 3
  • CENP-31 3 4
  • Borjeson-Forssman-Lehmann Syndrome 2
  • KIAA1823 4
  • BFLS 3
  • BORJ 3

External Ids for PHF6 Gene

Previous HGNC Symbols for PHF6 Gene

  • BFLS
  • BORJ

Previous GeneCards Identifiers for PHF6 Gene

  • GC00U991174
  • GC0XP130353
  • GC0XP131452
  • GC0XP132212
  • GC0XP133232
  • GC0XP133334
  • GC0XP133507
  • GC0XP122905

Summaries for PHF6 Gene

Entrez Gene Summary for PHF6 Gene

  • This gene is a member of the plant homeodomain (PHD)-like finger (PHF) family. It encodes a protein with two PHD-type zinc finger domains, indicating a potential role in transcriptional regulation, that localizes to the nucleolus. Mutations affecting the coding region of this gene or the splicing of the transcript have been associated with Borjeson-Forssman-Lehmann syndrome (BFLS), a disorder characterized by mental retardation, epilepsy, hypogonadism, hypometabolism, obesity, swelling of subcutaneous tissue of the face, narrow palpebral fissures, and large ears. Alternate splicing results in multiple transcript variants, encoding different isoforms. [provided by RefSeq, Jun 2010]

GeneCards Summary for PHF6 Gene

PHF6 (PHD Finger Protein 6) is a Protein Coding gene. Diseases associated with PHF6 include Borjeson-Forssman-Lehmann Syndrome and Mental Retardation Epilepsy. GO annotations related to this gene include poly(A) RNA binding and histone binding. An important paralog of this gene is PHF11.

UniProtKB/Swiss-Prot for PHF6 Gene

  • Transcriptional regulator that associates with ribosomal RNA promoters and suppresses ribosomal RNA (rRNA) transcription.

Gene Wiki entry for PHF6 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF6 Gene

Genomics for PHF6 Gene

Regulatory Elements for PHF6 Gene

Enhancers for PHF6 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PHF6 on UCSC Golden Path with GeneCards custom track

Promoters for PHF6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PHF6 on UCSC Golden Path with GeneCards custom track

Genomic Location for PHF6 Gene

134,373,253 bp from pter
134,428,792 bp from pter
55,540 bases
Plus strand

Genomic View for PHF6 Gene

Genes around PHF6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF6 Gene

Proteins for PHF6 Gene

  • Protein details for PHF6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    PHD finger protein 6
    Protein Accession:
    Secondary Accessions:
    • A8K230
    • B4E0G4
    • D3DTG3
    • E9PC97
    • Q5JRC7
    • Q5JRC8
    • Q96JK3
    • Q9BRU0

    Protein attributes for PHF6 Gene

    365 amino acids
    Molecular mass:
    41290 Da
    Quaternary structure:
    • Interacts with UBTF. Interacts with the NuRD complex component RBBP4 (via the nucleolar localization motif), the interaction mediates transcriptional repression activity.
    • Sequence=BAB47452.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PHF6 Gene

    Alternative splice isoforms for PHF6 Gene


neXtProt entry for PHF6 Gene

Proteomics data for PHF6 Gene at MOPED

Post-translational modifications for PHF6 Gene

  • Ubiquitination at Lys 118
  • Modification sites at PhosphoSitePlus

Other Protein References for PHF6 Gene

No data available for DME Specific Peptides for PHF6 Gene

Domains & Families for PHF6 Gene

Gene Families for PHF6 Gene

Protein Domains for PHF6 Gene


Suggested Antigen Peptide Sequences for PHF6 Gene

Graphical View of Domain Structure for InterPro Entry



  • The PHD-type zinc finger 1 mediates both nucleolar localization and interaction with UBTF.
  • Contains 2 C2HC-type zinc fingers.
  • The PHD-type zinc finger 1 mediates both nucleolar localization and interaction with UBTF.
  • The ePHD2 domain folds as an integrated structural module comprizing the C2HC-type zinc finger (pre-PHD) and the atypical PHD-type 2 zinc finger. It mediates non-specific binding to dsDNA, but doesnt bind histones in contrast to many PHD-type zinc fingers.
  • Contains 2 C2HC-type zinc fingers.
  • Contains 2 PHD-type zinc fingers.
genes like me logo Genes that share domains with PHF6: view

Function for PHF6 Gene

Molecular function for PHF6 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional regulator that associates with ribosomal RNA promoters and suppresses ribosomal RNA (rRNA) transcription.

Gene Ontology (GO) - Molecular Function for PHF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0008270 zinc ion binding IEA --
GO:0042826 histone deacetylase binding IPI 22720776
GO:0043021 ribonucleoprotein complex binding IPI 22720776
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with PHF6: view
genes like me logo Genes that share phenotypes with PHF6: view

Human Phenotype Ontology for PHF6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for PHF6 Gene

Localization for PHF6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF6 Gene

Nucleus. Nucleus, nucleolus. Chromosome, centromere, kinetochore. Note=Nuclear, it particularly localizes to the nucleolus.

Subcellular locations from

Jensen Localization Image for PHF6 Gene COMPARTMENTS Subcellular localization image for PHF6 gene
Compartment Confidence
nucleus 5
extracellular 1

No data available for Gene Ontology (GO) - Cellular Components for PHF6 Gene

Pathways & Interactions for PHF6 Gene

SuperPathways for PHF6 Gene

No Data Available

SIGNOR curated interactions for PHF6 Gene


Gene Ontology (GO) - Biological Process for PHF6 Gene


No data available for Pathways by source for PHF6 Gene

Drugs & Compounds for PHF6 Gene

(1) Drugs for PHF6 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PHF6: view

Transcripts for PHF6 Gene

Unigene Clusters for PHF6 Gene

PHD finger protein 6:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PHF6 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12
SP1: - -
SP2: - -
SP3: -
SP5: - -

Relevant External Links for PHF6 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PHF6 Gene

mRNA expression in normal human tissues for PHF6 Gene

Protein differential expression in normal tissues from HIPED for PHF6 Gene

This gene is overexpressed in Lung (39.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PHF6 Gene

SOURCE GeneReport for Unigene cluster for PHF6 Gene Hs.356501

mRNA Expression by UniProt/SwissProt for PHF6 Gene

Tissue specificity: Ubiquitously expressed.
genes like me logo Genes that share expression patterns with PHF6: view

Protein tissue co-expression partners for PHF6 Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PHF6 Gene

Orthologs for PHF6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PHF6 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PHF6 35
  • 95.8 (n)
  • 99.73 (a)
PHF6 36
  • 89 (a)
(Canis familiaris)
Mammalia PHF6 35
  • 97.63 (n)
  • 99.73 (a)
PHF6 36
  • 100 (a)
(Mus musculus)
Mammalia Phf6 35
  • 92.49 (n)
  • 97.53 (a)
Phf6 16
Phf6 36
  • 98 (a)
(Pan troglodytes)
Mammalia PHF6 35
  • 100 (n)
  • 100 (a)
PHF6 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Phf6 35
  • 91.78 (n)
  • 97.54 (a)
(Monodelphis domestica)
Mammalia PHF6 36
  • 93 (a)
(Ornithorhynchus anatinus)
Mammalia PHF6 36
  • 95 (a)
(Gallus gallus)
Aves PHF6 35
  • 84.47 (n)
  • 89.59 (a)
PHF6 36
  • 90 (a)
(Anolis carolinensis)
Reptilia PHF6 36
  • 87 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia phf6 35
  • 74.75 (n)
  • 77.41 (a)
Str.15049 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.12568 35
(Danio rerio)
Actinopterygii phf6 35
  • 67.32 (n)
  • 70.95 (a)
wufa22g03 35
phf6 36
  • 71 (a)
Species with no ortholog for PHF6:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PHF6 Gene

Gene Tree for PHF6 (if available)
Gene Tree for PHF6 (if available)

Paralogs for PHF6 Gene

Paralogs for PHF6 Gene

(1) SIMAP similar genes for PHF6 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with PHF6: view

Variants for PHF6 Gene

Sequence variations from dbSNP and Humsavar for PHF6 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
VAR_017633 Boerjeson-Forssman-Lehmann syndrome (BFLS)
VAR_017634 Boerjeson-Forssman-Lehmann syndrome (BFLS)
VAR_017635 Boerjeson-Forssman-Lehmann syndrome (BFLS)
VAR_017636 Boerjeson-Forssman-Lehmann syndrome (BFLS)
VAR_017637 Boerjeson-Forssman-Lehmann syndrome (BFLS)

Structural Variations from Database of Genomic Variants (DGV) for PHF6 Gene

Variant ID Type Subtype PubMed ID
nsv521188 CNV Loss 19592680

Variation tolerance for PHF6 Gene

Residual Variation Intolerance Score: 22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.28; 6.20% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHF6 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF6 Gene

Disorders for PHF6 Gene

MalaCards: The human disease database

(7) MalaCards diseases for PHF6 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PHF6 in MalaCards View complete list of genes associated with diseases


  • Boerjeson-Forssman-Lehmann syndrome (BFLS) [MIM:301900]: A X-linked recessive disorder characterized by moderate to severe mental retardation, epilepsy, hypogonadism, hypometabolism, obesity with marked gynecomastia, swelling of subcutaneous tissue of the face, narrow palpebral fissure and large but not deformed ears. {ECO:0000269 PubMed:12415272}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PHF6

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PHF6: view

No data available for Genatlas for PHF6 Gene

Publications for PHF6 Gene

  1. Mutations in PHF6 are associated with Boerjeson-Forssman-Lehmann syndrome. (PMID: 12415272) Lower K.M. … Gecz J. (Nat. Genet. 2002) 2 3 4 23 67
  2. Mutation screening in Borjeson-Forssman-Lehmann syndrome: identification of a novel de novo PHF6 mutation in a female patient. (PMID: 15994862) Crawford J. … GAccz J. (J. Med. Genet. 2006) 3 23
  3. A novel PHF6 mutation results in enhanced exon skipping and mild BAPrjeson-Forssman-Lehmann syndrome. (PMID: 15466013) VallAce D. … Picketts D.J. (J. Med. Genet. 2004) 2 3
  4. The clinical picture of the BAPrjeson-Forssman-Lehmann syndrome in males and heterozygous females with PHF6 mutations. (PMID: 14756673) Turner G. … Partington M. (Clin. Genet. 2004) 3 23
  5. Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. (PMID: 25281560) Lambert J.P. … Gingras A.C. (J Proteomics 2015) 3

Products for PHF6 Gene

Sources for PHF6 Gene