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Symbol PHF6 contributors: mct/npt - updated : 23-06-2015
HGNC name PHD finger protein 6
HGNC id 18145
Corresponding disease
BFLS Börjeson-Forssman-Lehmann syndrome
Location Xq26.2      Physical location : 133.507.341 - 133.562.821
Synonym name PHD-like zinc finger protein 6
Synonym symbol(s) KIAA1823, MGC14797, BORJ
TYPE functioning gene
STRUCTURE 55.48 kb     10 Exon(s)
10 Kb 5' upstream gene genomic sequence study
MAPPING cloned Y linked N status provisional
Physical map
HS6ST2 Xq26.1-q26.2 heparan sulfate 6-O-sulfotransferase 2 USP26 Xq26.2 ubiquitin specific protease 26 LOC51270 Xq26.2 E2F-like protein GPC4 Xq26.1 glypican 4 GPC3 Xq26.1 glypican 3 LOC347475 Xq26.3 hypothetical gene supported by BC017958 LOC392544 X hypothetical gene supported by NM_152729 PHF6 Xq26 PHD finger protein 6 HPRT1 Xq26.1 hypoxanthine phosphoribosyltransferase 1 (Lesch-Nyhan syndrome) MGC16121 Xq26.3 hypothetical protein MGC16121 PLAC1 Xq26 placenta-specific 1 LOC159090 Xq26.3 similar to hypothetical protein MGC17347 LOC159091 Xq26.3 hypothetical protein BC017868 DJ473B4 Xq26.3 hypothetical protein dJ473B4 LOC340581 Xq26.3 hypothetical protein LOC340581 LOC392545 X similar to high mobility group protein homolog HMG4 LOC389887 X similar to RIKEN cDNA 1110012O05 CXX1 Xq26 CAAX box 1 DKFZP564B147 Xq26.3 DKFZP564B147 protein LOC159049 Xq26.3 hypothetical LOC159049 FLJ20527 Xq26.3 hypothetical protein FLJ20527 LOC392546 X similar to hypothetical protein FLJ20527 LOC389888 X similar to hypothetical protein FLJ20527 LOC389889 X hypothetical gene supported by BC061642 ZNF75 Xq26 zinc finger protein 75 (D8C6) FLJ23614 Xq26.3 hypothetical protein FLJ23614 LOC392547 X similar to KIAA0445 protein LOC203522 Xq26.3 hypothetical protein LOC203522 LOC392548 X similar to C-ets-2 protein LOC139587 Xq26.3 similar to sarcoma antigen; putative tumor antigen MGC27005 Xq26.3 hypothetical protein MGC27005 SAGE Xq28 hypothetical protein MGC27005 LOC93380 Xq26.3 hypothetical protein LOC93380 SLC9A6 Xq26.3 solute carrier family 9 (sodium/hydrogen exchanger), isoform 6 LOC392549 X similar to Glyceraldehyde 3-phosphate dehydrogenase, liver (GAPDH) LOC139542 Xq26.3 similar to E2F transcription factor 6 isoform a FHL1 Xq26 four and a half LIM domains 1 FLJ12649 Xq26.3 hypothetical protein FLJ12649 GPR112 Xq26.3 G protein-coupled receptor 112
TRANSCRIPTS type messenger
identificationnb exonstypebpproduct
ProteinkDaAAspecific expressionYearPubmed
8 splicing 1236 - 312 - Lower, Crawford (2006)
10 splicing 4772 41.2 365 - Lower, Vallee (2004)
  • also called the PHF6B
  • inclusion of the intron 10
  • - splicing - - - - Vallee (2004)
  • also called PHF6 delta exon 3
  • maintained in the nucleolus, lacking exon 3(exon skipping)
  • in normal or mild form of BFLS patients
  • 11 - 4442 - 365 - Crawford (2006)
    also called PHF6A
    Type ubiquitous
       expressed in (based on citations)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Digestiveintestinesmall intestine  highly
    Hearing/Equilibriumearinnercochlea highly
    Lymphoid/Immunelymph node   highly
     spinal cord    
    Reproductivefemale systemovary   
    Urinarybladder   highly
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    cell lineage
    cell lines
    at STAGE
    physiological period fetal
    Text liver
  • two PHD-like zinc finger domains with a proposed role in controlling gene expression, that are imperfect PHD domains and may have functions that differ from other PHD domains, and its nucleolus localization mainly depends on its PHD1 domain
  • four nuclear localization signals (Van Vlierberghe 2010)
  • plant homeodomain (PHD)-like finger (PHF) family
  • CATEGORY transcription factor
    SUBCELLULAR LOCALIZATION     intracellular
    basic FUNCTION
  • may be playing a role in transcriptional regulation
  • playing an important role in cell growth and poliferation which may be achieved via its participation in ribosomes biogenesis (at the RNA and/or protein level)
  • new X-linked tumor suppressor in T--cell acute lymphoblastic leukemia (Van Vlierberghe 2010)
  • nucleolus, ribosomal RNA promoter-associated protein
  • key function of PHF6 is involved in regulating rRNA synthesis, which may contribute to its roles in cell cycle control, genomic maintenance, and tumor suppression
  • tumor suppressor function of PHF6 may be associated with its regulatory role in rRNA synthesis, which contributes to genome maintenance
  • is required for normal cell cycle progression
  • caretaker tumor suppressor, which functions by ensuring proper rRNA synthesis to maintain genomic stability
  • CELLULAR PROCESS nucleotide, transcription, regulation
    a component
    DNA binding
    small molecule metal binding,
  • Zn2+
  • protein
  • localizes to the nucleolus, directly interacts with upstream binding factor (UBTF), and suppresses ribosomal RNA (rRNA) transcription by affecting the protein level of UBTF
  • UBTF, a transcription factor required for the expression of ribosomal RNAs, is a major PHF6-associated protein (23229552)
  • cell & other
    Other phosphorylated during mitosis and by the ATM and ATR kinases upon DNA damage, which suggests a dynamic regulation of PHF6 during cell cycle and DNA repair (Van Vlierberghe 2010)
    corresponding disease(s) BFLS
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    tumoral somatic mutation      
    truncating or missense mutations in 38 p100 of adult and ~16 p100 of pediatric -T-ALL (Van Vlierberghe 2010)
    Variant & Polymorphism
    Candidate gene
    Therapy target