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Aliases for PHF8 Gene

Aliases for PHF8 Gene

  • PHD Finger Protein 8 2 3 4
  • ZNF422 3 4 6
  • Jumonji C Domain-Containing Histone Demethylase 1F 2 3
  • EC 1.14.11.27 4 63
  • KIAA1111 4 6
  • MRXSSD 3 6
  • Histone Lysine Demethylase PHF8 3
  • JHDM1F 3

External Ids for PHF8 Gene

Previous GeneCards Identifiers for PHF8 Gene

  • GC0XM052930
  • GC0XM053846
  • GC0XM051017

Summaries for PHF8 Gene

Entrez Gene Summary for PHF8 Gene

  • The protein encoded by this gene is a histone lysine demethylase that preferentially acts on histones in the monomethyl or dimethyl states. The encoded protein requires Fe(2+) ion, 2-oxoglutarate, and oxygen for its catalytic activity. Defects in this gene are a cause of mental retardation syndromic X-linked Siderius type (MRXSSD). Four transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]

GeneCards Summary for PHF8 Gene

PHF8 (PHD Finger Protein 8) is a Protein Coding gene. Diseases associated with PHF8 include x-linked intellectual disability, siderius type and mental retardation, x-linked, syndromic, siderius type. Among its related pathways are Cell Cycle, Mitotic and Cell Cycle, Mitotic. GO annotations related to this gene include chromatin binding and methylated histone binding. An important paralog of this gene is KDM2B.

UniProtKB/Swiss-Prot for PHF8 Gene

  • Histone lysine demethylase with selectivity for the di- and monomethyl states that plays a key role cell cycle progression, rDNA transcription and brain development. Demethylates mono- and dimethylated histone H3 Lys-9 residue (H3K9Me1 and H3K9Me2), dimethylated H3 Lys-27 (H3K27Me2) and monomethylated histone H4 Lys-20 residue (H4K20Me1). Acts as a transcription activator as H3K9Me1, H3K9Me2, H3K27Me2 and H4K20Me1 are epigenetic repressive marks. Involved in cell cycle progression by being required to control G1-S transition. Acts as a coactivator of rDNA transcription, by activating polymerase I (pol I) mediated transcription of rRNA genes. Required for brain development, probably by regulating expression of neuron-specific genes. Only has activity toward H4K20Me1 when nucleosome is used as a substrate and when not histone octamer is used as substrate. May also have weak activity toward dimethylated H3 Lys-36 (H3K36Me2), however, the relevance of this result remains unsure in vivo. Specifically binds trimethylated Lys-4 of histone H3 (H3K4me3), affecting histone demethylase specificity: has weak activity toward H3K9Me2 in absence of H3K4me3, while it has high activity toward H3K9me2 when binding H3K4me3.

Gene Wiki entry for PHF8 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF8 Gene

Genomics for PHF8 Gene

Regulatory Elements for PHF8 Gene

Genomic Location for PHF8 Gene

Start:
53,936,676 bp from pter
End:
54,048,958 bp from pter
Size:
112,283 bases
Orientation:
Minus strand

Genomic View for PHF8 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PHF8 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF8 Gene

Proteins for PHF8 Gene

  • Protein details for PHF8 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UPP1-PHF8_HUMAN
    Recommended name:
    Histone lysine demethylase PHF8
    Protein Accession:
    Q9UPP1
    Secondary Accessions:
    • B3KMV4
    • B7Z911
    • Q5H9U5
    • Q5JPR9
    • Q5JPS0
    • Q5JPS2
    • Q5JPS3
    • Q5VUJ4
    • Q7Z6D4
    • Q9HAH2

    Protein attributes for PHF8 Gene

    Size:
    1060 amino acids
    Molecular mass:
    117864 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Note=Binds 1 Fe(2+) ion per subunit.;
    Quaternary structure:
    • Interacts with POLR1B, UBTF, SETD1A, HCFC1, E2F1 and ZNF711.
    SequenceCaution:
    • Sequence=BAA83063.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAB13877.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAI45929.1; Type=Erroneous termination; Positions=419; Note=Translated as Arg.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PHF8 Gene

    Alternative splice isoforms for PHF8 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHF8 Gene

Proteomics data for PHF8 Gene at MOPED

Selected DME Specific Peptides for PHF8 Gene

Post-translational modifications for PHF8 Gene

  • Phosphorylation at Ser-69 and Ser-120 are required for dissociation from chromatin and accumulation of H4K20Me1 levels during prophase.
  • Ubiquitination at Lys467, Lys486, and Lys732
  • Modification sites at PhosphoSitePlus

Domains for PHF8 Gene

Gene Families for PHF8 Gene

HGNC:
  • KDM :Chromatin-modifying enzymes / K-demethylases
  • PHF :Zinc fingers, PHD-type

Protein Domains for PHF8 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UPP1

UniProtKB/Swiss-Prot:

PHF8_HUMAN :
  • Q9UPP1
Domain:
  • The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 promotes its access to H3K9me2
  • The linker region is a critical determinant of demethylase specificity. It enables the active site of JmjC to reach the target H3K9me2 when the PHD-type zinc finger binds to H3K4me3
  • Contains 1 JmjC domain.
Family:
  • Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.
Similarity:
  • Contains 1 PHD-type zinc finger.
genes like me logo Genes that share domains with PHF8: view

Function for PHF8 Gene

Molecular function for PHF8 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties: Kinetic parameters: KM=134 uM for histone H3 H3K9Me2 {ECO:0000269 PubMed:20023638}; KM=8 uM for histone H3 H3K4me3 and H3K9Me2 {ECO:0000269 PubMed:20023638};
UniProtKB/Swiss-Prot CatalyticActivity: Protein N(6),N(6)-dimethyl-L-lysine + 2-oxoglutarate + O(2) = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO(2)
UniProtKB/Swiss-Prot CatalyticActivity: Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O(2) = protein L-lysine + succinate + formaldehyde + CO(2)
UniProtKB/Swiss-Prot Function: Histone lysine demethylase with selectivity for the di- and monomethyl states that plays a key role cell cycle progression, rDNA transcription and brain development. Demethylates mono- and dimethylated histone H3 Lys-9 residue (H3K9Me1 and H3K9Me2), dimethylated H3 Lys-27 (H3K27Me2) and monomethylated histone H4 Lys-20 residue (H4K20Me1). Acts as a transcription activator as H3K9Me1, H3K9Me2, H3K27Me2 and H4K20Me1 are epigenetic repressive marks. Involved in cell cycle progression by being required to control G1-S transition. Acts as a coactivator of rDNA transcription, by activating polymerase I (pol I) mediated transcription of rRNA genes. Required for brain development, probably by regulating expression of neuron-specific genes. Only has activity toward H4K20Me1 when nucleosome is used as a substrate and when not histone octamer is used as substrate. May also have weak activity toward dimethylated H3 Lys-36 (H3K36Me2), however, the relevance of this result remains unsure in vivo. Specifically binds trimethylated Lys-4 of histone H3 (H3K4me3), affecting histone demethylase specificity: has weak activity toward H3K9Me2 in absence of H3K4me3, while it has high activity toward H3K9me2 when binding H3K4me3.

Enzyme Numbers (IUBMB) for PHF8 Gene

Gene Ontology (GO) - Molecular Function for PHF8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IDA 20622854
GO:0005506 iron ion binding IDA 20023638
GO:0005515 protein binding IPI 20208542
GO:0008270 zinc ion binding IDA 20023638
GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors IDA 20023638
genes like me logo Genes that share ontologies with PHF8: view

Phenotypes for PHF8 Gene

GenomeRNAi human phenotypes for PHF8:
genes like me logo Genes that share phenotypes with PHF8: view

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for PHF8 Gene

Localization for PHF8 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF8 Gene

Nucleus. Nucleus, nucleolus. Note=Recruited to H3K4me3 sites on chromatin during interphase. Dissociates from chromatin when cells enter mitosis.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PHF8 Gene COMPARTMENTS Subcellular localization image for PHF8 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for PHF8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA 20208542
GO:0015630 microtubule cytoskeleton --
GO:0031965 nuclear membrane IDA --
genes like me logo Genes that share ontologies with PHF8: view

Pathways for PHF8 Gene

genes like me logo Genes that share pathways with PHF8: view

Pathways by source for PHF8 Gene

Gene Ontology (GO) - Biological Process for PHF8 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000082 G1/S transition of mitotic cell cycle IMP 20622854
GO:0000278 mitotic cell cycle TAS --
GO:0006325 chromatin organization TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0007420 brain development ISS --
genes like me logo Genes that share ontologies with PHF8: view

Transcripts for PHF8 Gene

Unigene Clusters for PHF8 Gene

PHD finger protein 8:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PHF8 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b ·
SP1: - - - - - -
SP2: - - -
SP3: - -
SP4: - - -
SP5: - -
SP6:
SP7: - -
SP8:
SP9:
SP10:
SP11:
SP12:

ExUns: 17c ^ 18 ^ 19a · 19b · 19c ^ 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b ^ 25a · 25b · 25c · 25d ^ 26a · 26b ^ 27a · 27b · 27c
SP1: - - - -
SP2: - - - -
SP3: - - -
SP4: - -
SP5: - -
SP6:
SP7:
SP8: - -
SP9: -
SP10: - -
SP11:
SP12:

Relevant External Links for PHF8 Gene

GeneLoc Exon Structure for
PHF8
ECgene alternative splicing isoforms for
PHF8

Expression for PHF8 Gene

mRNA expression in normal human tissues for PHF8 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for PHF8 Gene

SOURCE GeneReport for Unigene cluster for PHF8 Gene Hs.133352

genes like me logo Genes that share expressions with PHF8: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PHF8 Gene

Orthologs for PHF8 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PHF8 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHF8 35
  • 99.88 (n)
  • 99.76 (a)
PHF8 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PHF8 35
  • 93.33 (n)
  • 96.39 (a)
PHF8 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PHF8 35
  • 93.52 (n)
  • 97.07 (a)
PHF8 36
  • 95 (a)
OneToOne
mouse
(Mus musculus)
Mammalia 4921501E09Rik 36
  • 67 (a)
OneToMany
Phf8 35
  • 90.84 (n)
  • 94.62 (a)
Phf8 16
Phf8 36
  • 95 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia PHF8 36
  • 72 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHF8 36
  • 71 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Phf8 35
  • 90.97 (n)
  • 94.92 (a)
lizard
(Anolis carolinensis)
Reptilia PHF8 36
  • 72 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia LOC398683 35
tropical clawed frog
(Silurana tropicalis)
Amphibia phf8 35
  • 67.28 (n)
  • 71.34 (a)
Str.10718 35
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3567 35
zebrafish
(Danio rerio)
Actinopterygii phf8 35
  • 64.65 (n)
  • 67.52 (a)
phf8 36
  • 63 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea jmjd-1.1 36
  • 27 (a)
ManyToMany
jmjd-1.2 36
  • 20 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD1 36
  • 29 (a)
OneToMany
Species with no ortholog for PHF8:
  • 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • 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)
  • 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)

Evolution for PHF8 Gene

ENSEMBL:
Gene Tree for PHF8 (if available)
TreeFam:
Gene Tree for PHF8 (if available)

Paralogs for PHF8 Gene

Paralogs for PHF8 Gene

genes like me logo Genes that share paralogs with PHF8: view

Variants for PHF8 Gene

Sequence variations from dbSNP and Humsavar for PHF8 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs1132024 -- 53,942,975(-) AGAAG(C/G)GACTT intron-variant, utr-variant-3-prime
rs1132583 -- 53,936,893(-) AGCCC(A/C)CCGCT utr-variant-3-prime
rs2516101 -- 54,045,724(-) CTCCA(C/T)GCATT upstream-variant-2KB, intron-variant
rs3204832 -- 53,938,273(-) TGAAA(A/C/G/T)CACCT utr-variant-3-prime, intron-variant
rs3747473 -- 54,044,898(-) TCGAA(A/G)GTGCT utr-variant-5-prime, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for PHF8 Gene

Variant ID Type Subtype PubMed ID
nsv435891 CNV Deletion 17901297
esv2740175 CNV Deletion 23290073
nsv524220 CNV Gain 19592680
esv2675498 CNV Deletion 23128226

Relevant External Links for PHF8 Gene

HapMap Linkage Disequilibrium report
PHF8
Human Gene Mutation Database (HGMD)
PHF8
Locus Specific Mutation Databases (LSDB)
PHF8

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF8 Gene

Disorders for PHF8 Gene

(1) OMIM Diseases for PHF8 Gene (300560)

UniProtKB/Swiss-Prot

PHF8_HUMAN
  • Mental retardation, X-linked, syndromic, Siderius type (MRXSSD) [MIM:300263]: A syndrome characterized by mild to borderline mental retardation with or without cleft lip/cleft palate. {ECO:0000269 PubMed:16199551, ECO:0000269 PubMed:17661819}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for PHF8 Gene

Relevant External Links for PHF8

Genetic Association Database (GAD)
PHF8
Human Genome Epidemiology (HuGE) Navigator
PHF8
genes like me logo Genes that share disorders with PHF8: view

Publications for PHF8 Gene

  1. Mutations in PHF8 are associated with X linked mental retardation and cleft lip/cleft palate. (PMID: 16199551) Laumonnier F. … Briault S. (J. Med. Genet. 2005) 3 4 23
  2. Screening of mutations in the PHF8 gene and identification of a novel mutation in a Finnish family with XLMR and cleft lip/cleft palate. (PMID: 17661819) Koivisto A.M. … Jaervelae I. (Clin. Genet. 2007) 3 4 23
  3. Crystal structure of the PHF8 Jumonji domain, an N(epsilon)-methyl lysine demethylase. (PMID: 20067792) Yue W.W. … McDonough M.A. (FEBS Lett. 2010) 3 4 23
  4. PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. (PMID: 20208542) Feng W. … Grummt I. (Nat. Struct. Mol. Biol. 2010) 3 4 23
  5. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10470851) Kikuno R. … Ohara O. (DNA Res. 1999) 2 3 4

Products for PHF8 Gene

Sources for PHF8 Gene

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