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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. Among its related pathways are Mesodermal Commitment Pathway. 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 CIViC summary , 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XG134372 1.3 FANTOM5 ENCODE 9.5 +0.7 748 3.3 HDGF PKNOX1 ATF1 ARID4B SIN3A ZNF48 YY1 ETS1 GLIS2 GATA2 PHF6 GC0XP134446
GH0XG134171 1.5 FANTOM5 ENCODE dbSUPER 1.9 -199.6 -199619 4.8 ZNF76 ETS1 GLIS2 ZNF143 EGR2 ZNF202 SP3 CEBPB ZNF398 CBX8 CCDC160 GPC3 PHF6 MIR106A GC0XM134203 GC0XM134201 ENSG00000283638
GH0XG134388 0.7 Ensembl ENCODE 0.4 +15.8 15819 0.7 CEBPB HMBOX1 MIR503HG PHF6 GC0XP134446
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000248920 647 2601 HDGF PKNOX1 ATF1 ARID4B SIN3A YY1 ETS1 GLIS2 GATA2 FOS

Genomic Location for PHF6 Gene

Chromosome:
X
Start:
134,373,253 bp from pter
End:
134,428,792 bp from pter
Size:
55,540 bases
Orientation:
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:
    Q8IWS0-PHF6_HUMAN
    Recommended name:
    PHD finger protein 6
    Protein Accession:
    Q8IWS0
    Secondary Accessions:
    • A8K230
    • B4E0G4
    • D3DTG3
    • E9PC97
    • Q5JRC7
    • Q5JRC8
    • Q96JK3
    • Q9BRU0

    Protein attributes for PHF6 Gene

    Size:
    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.
    SequenceCaution:
    • 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

    UniProtKB/Swiss-Prot:

neXtProt entry for PHF6 Gene

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 & 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

Q8IWS0

UniProtKB/Swiss-Prot:

PHF6_HUMAN :
  • The PHD-type zinc finger 1 mediates both nucleolar localization and interaction with UBTF.
Domain:
  • 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 pre-PHD-type 2 zinc finger and the PHD-type 2 zinc finger. It mediates non-specific binding to dsDNA, but doesnt bind histones in contrast to many 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:0003723 RNA binding IDA 22658674
GO:0005515 protein binding IPI 22720776
GO:0008270 zinc ion binding IEA --
GO:0015631 tubulin binding IPI 22720776
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 Models for PHF6 Gene

MGI Knock Outs for PHF6:
  • Phf6 tm1b(EUCOMM)Wtsi

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , 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

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHF6 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for PHF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000776 kinetochore IEA --
GO:0000777 condensed chromosome kinetochore IEA --
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA 22720776
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with PHF6: view

Pathways & Interactions for PHF6 Gene

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

Pathways by source for PHF6 Gene

2 BioSystems pathways for PHF6 Gene

SIGNOR curated interactions for PHF6 Gene

Inactivates:

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

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:

CRISPR Products

Inhibitory RNA Products

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: -
SP4:
SP5: - -

Relevant External Links for PHF6 Gene

GeneLoc Exon Structure for
PHF6
ECgene alternative splicing isoforms for
PHF6

Expression for PHF6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for PHF6 Gene



Protein tissue co-expression partners for PHF6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PHF6 Gene:

PHF6

SOURCE GeneReport for Unigene cluster for PHF6 Gene:

Hs.356501

mRNA Expression by UniProt/SwissProt for PHF6 Gene:

Q8IWS0-PHF6_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for PHF6 Gene

  • Nervous system(4.6)
  • Bone marrow(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PHF6 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • skull
Thorax:
  • breast
  • lung
  • rib
  • rib cage
Pelvis:
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vas deferens
  • vulva
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
General:
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with PHF6: view

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
chimpanzee
(Pan troglodytes)
Mammalia PHF6 34 35
  • 100 (n)
dog
(Canis familiaris)
Mammalia PHF6 34 35
  • 97.63 (n)
cow
(Bos Taurus)
Mammalia PHF6 34 35
  • 95.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PHF6 35
  • 95 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PHF6 35
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Phf6 34 16 35
  • 92.49 (n)
rat
(Rattus norvegicus)
Mammalia Phf6 34
  • 91.78 (n)
chicken
(Gallus gallus)
Aves PHF6 34 35
  • 84.47 (n)
lizard
(Anolis carolinensis)
Reptilia PHF6 35
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phf6 34
  • 74.75 (n)
Str.15049 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.12568 34
zebrafish
(Danio rerio)
Actinopterygii phf6 34 35
  • 67.32 (n)
wufa22g03 34
Species where no ortholog for PHF6 was found in the sources mined by GeneCards:
  • 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

ENSEMBL:
Gene Tree for PHF6 (if available)
TreeFam:
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
rs104894917 Pathogenic, Boerjeson-Forssman-Lehmann syndrome (BFLS) [MIM:301900] 134,413,937(+) ATGCC(A/G)AGAAG reference, missense
rs104894918 Pathogenic, Boerjeson-Forssman-Lehmann syndrome (BFLS) [MIM:301900] 134,413,923(+) ACTGC(A/G)TATAT reference, missense
rs104894919 Pathogenic, Boerjeson-Forssman-Lehmann syndrome (BFLS) [MIM:301900] 134,415,055(+) CATCA(A/G)GAGCA reference, missense
rs132630298 Pathogenic, Boerjeson-Forssman-Lehmann syndrome (BFLS) [MIM:301900] 134,393,556(+) AACAT(G/T)TCACA reference, missense
rs28935179 Boerjeson-Forssman-Lehmann syndrome (BFLS) [MIM:301900]

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)
PHF6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF6

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

Disorders for PHF6 Gene

MalaCards: The human disease database

(9) 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

UniProtKB/Swiss-Prot

PHF6_HUMAN
  • 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, ECO:0000269 PubMed:23229552, ECO:0000269 PubMed:23906836}. 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:
PHF6
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 22 64
  2. Structural and functional insights into the human BAPrjeson-Forssman-Lehmann syndrome-associated protein PHF6. (PMID: 24554700) Liu Z. … Shi Y. (J. Biol. Chem. 2014) 3 4 64
  3. PHF6 regulates cell cycle progression by suppressing ribosomal RNA synthesis. (PMID: 23229552) Wang J. … Chen J. (J. Biol. Chem. 2013) 3 4 64
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64
  5. 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 22 64

Products for PHF6 Gene

Sources for PHF6 Gene

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