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Aliases for PHF6 Gene

Aliases for PHF6 Gene

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

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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 Lys118
  • Modification sites at PhosphoSitePlus

Other Protein References for PHF6 Gene

No data available for DME Specific Peptides for PHF6 Gene

Domains for PHF6 Gene

Gene Families for PHF6 Gene

  • PHF :Zinc fingers, PHD-type

Protein Domains for PHF6 Gene


Suggested Antigen Peptide Sequences for PHF6 Gene

Graphical View of Domain Structure for InterPro Entry



  • Q8IWS0
  • 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:0005515 protein binding IPI 22720776
GO:0008270 zinc ion binding IEA --
GO:0015631 tubulin binding IPI 22720776
GO:0019899 enzyme binding IPI 22720776
genes like me logo Genes that share ontologies with PHF6: view

Phenotypes for PHF6 Gene

GenomeRNAi human phenotypes for PHF6:
genes like me logo Genes that share phenotypes with PHF6: view

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting 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

Gene Ontology (GO) - Cellular Components for PHF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000777 condensed chromosome kinetochore IEA --
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA 22720776
GO:0005730 nucleolus IDA --
genes like me logo Genes that share ontologies with PHF6: view

Pathways for PHF6 Gene

SuperPathways for PHF6 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PHF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with PHF6: view

No data available for Pathways by source for PHF6 Gene

Compounds for PHF6 Gene

(1) Novoseek inferred chemical compound relationships for PHF6 Gene

Compound -log(P) Hits PubMed IDs
zinc 30.6 2
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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression 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 expressions with PHF6: view

No data available for 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
(Pan troglodytes)
Mammalia PHF6 35
  • 100 (n)
  • 100 (a)
PHF6 36
  • 100 (a)
(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)
(Monodelphis domestica)
Mammalia PHF6 36
  • 93 (a)
(Ornithorhynchus anatinus)
Mammalia PHF6 36
  • 95 (a)
(Rattus norvegicus)
Mammalia Phf6 35
  • 91.78 (n)
  • 97.54 (a)
(Gallus gallus)
Aves PHF6 35
  • 84.47 (n)
  • 89.59 (a)
PHF6 36
  • 90 (a)
(Anolis carolinensis)
Reptilia PHF6 36
  • 87 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.12568 35
tropical clawed frog
(Silurana tropicalis)
Amphibia phf6 35
  • 74.75 (n)
  • 77.41 (a)
Str.15049 35
(Danio rerio)
Actinopterygii phf6 35
  • 67.32 (n)
  • 70.95 (a)
phf6 36
  • 71 (a)
wufa22g03 35
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

Selected 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 MAF
rs2355970 -- 134,408,943(-) TGAAG(C/T)CAGGA intron-variant
rs2355971 -- 134,379,132(-) CCCCT(C/G)TTCCT intron-variant
rs2355972 -- 134,379,055(-) CAAAC(A/G)CAGTT intron-variant
rs2355973 -- 134,372,640(-) TTATC(A/C)CAATC upstream-variant-2KB
rs2355974 -- 134,372,544(-) ccatg(A/C/T)ctggg upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
nsv521188 CNV Loss 19592680

Relevant External Links for PHF6 Gene

HapMap Linkage Disequilibrium report
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

MalaCards: The human disease database. (3) Diseases for PHF6 Gene including...

Search for PHF6 Gene in MalaCards »

(1) OMIM Diseases for PHF6 Gene (300414)


  • 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.

(2) University of Copenhagen DISEASES for PHF6 Gene

(2) Novoseek inferred disease relationships for PHF6 Gene

Disease -log(P) Hits PubMed IDs
borjeson-forssman-lehmann syndrome 98.1 5
obesity 41.3 1
genes like me logo Genes that share disorders with PHF6: view

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
  2. 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
  3. 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
  4. Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11347906) Nagase T. … Ohara O. (DNA Res. 2001) 3 4
  5. PHF6 regulates cell cycle progression by suppressing ribosomal RNA synthesis. (PMID: 23229552) Wang J. … Chen J. (J. Biol. Chem. 2013) 3 4

Products for PHF6 Gene

Sources for PHF6 Gene

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