PHF2 Gene (Protein Coding)

PHD Finger Protein 2

GC09P093576
GIFtS:
39
This gene encodes a protein which contains a zinc finger-like PHD (plant homeodomain) finger, distinct from other classes of zinc finger motifs, and a hydrophobic and highly conserved domain. The PHD finger shows the typical Cys4-His-Cys3 arrangement. PHD finger genes are thought to belong to a diverse group of transcriptional regulators possibly affecting eukaryotic gene expre... See more...

Aliases for PHF2 Gene

Aliases for PHF2 Gene

  • PHD Finger Protein 2 2 3 4 5
  • CENP-35 2 3 4
  • Jumonji C Domain-Containing Histone Demethylase 1E 2 3
  • Lysine-Specific Demethylase PHF2 3 4
  • Centromere Protein 35 2 3
  • KIAA0662 2 4
  • JHDM1E 2 3
  • KDM7C 2 3
  • GRC5 3 4
  • EC 1.14.11.- 4
  • PHF2 5

External Ids for PHF2 Gene

Previous GeneCards Identifiers for PHF2 Gene

  • GC09U990060
  • GC09P088066
  • GC09P089638
  • GC09P091680
  • GC09P093418
  • GC09P095378
  • GC09P096338
  • GC09P066069

Summaries for PHF2 Gene

Entrez Gene Summary for PHF2 Gene

  • This gene encodes a protein which contains a zinc finger-like PHD (plant homeodomain) finger, distinct from other classes of zinc finger motifs, and a hydrophobic and highly conserved domain. The PHD finger shows the typical Cys4-His-Cys3 arrangement. PHD finger genes are thought to belong to a diverse group of transcriptional regulators possibly affecting eukaryotic gene expression by influencing chromatin structure. [provided by RefSeq, Jul 2008]

GeneCards Summary for PHF2 Gene

PHF2 (PHD Finger Protein 2) is a Protein Coding gene. Diseases associated with PHF2 include Dissociative Disorder and Culler-Jones Syndrome. Among its related pathways are Chromatin Regulation / Acetylation and Chromatin organization. Gene Ontology (GO) annotations related to this gene include transcription coactivator activity and methylated histone binding. An important paralog of this gene is PHF8.

UniProtKB/Swiss-Prot Summary for PHF2 Gene

  • Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA.

Additional gene information for PHF2 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PHF2 Gene

Genomics for PHF2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PHF2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PHF2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PHF2

Top Transcription factor binding sites by QIAGEN in the PHF2 gene promoter:
  • AREB6
  • ITF-2
  • Meis-1
  • Meis-1a
  • MyoD
  • RSRFC4
  • Tal-1beta
  • TBP
  • TFIID

Genomic Locations for PHF2 Gene

Latest Assembly
chr9:93,576,584-93,679,587
(GRCh38/hg38)
Size:
103,004 bases
Orientation:
Plus strand

Previous Assembly
chr9:96,338,866-96,441,869
(GRCh37/hg19 by Entrez Gene)
Size:
103,004 bases
Orientation:
Plus strand

chr9:96,338,689-96,441,869
(GRCh37/hg19 by Ensembl)
Size:
103,181 bases
Orientation:
Plus strand

Genomic View for PHF2 Gene

Genes around PHF2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PHF2 Gene

Proteins for PHF2 Gene

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  • Protein details for PHF2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75151-PHF2_HUMAN
    Recommended name:
    Lysine-specific demethylase PHF2
    Protein Accession:
    O75151
    Secondary Accessions:
    • Q4VXG0
    • Q8N3K2
    • Q9Y6N4

    Protein attributes for PHF2 Gene

    Size:
    1096 amino acids
    Molecular mass:
    120775 Da
    Quaternary structure:
    • Component of the PHF2-ARID5B complex, at least composed of PHF2 and ARID5B. Interacts with HNF4A and NR1H4.
    SequenceCaution:
    • Sequence=BAA31637.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PHF2 Gene

neXtProt entry for PHF2 Gene

Protein Expression for PHF2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PHF2 Gene

  • Phosphorylated by PKA on specific serine residues, leading to the formation of an active lysine demethylase complex.
  • Ubiquitination at Lys175, Lys412, and Lys427
  • Modification sites at PhosphoSitePlus

Other Protein References for PHF2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PHF2 Gene

Domains & Families for PHF2 Gene

Gene Families for PHF2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PHF2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PHF2 Gene

GenScript: Design optimal peptide antigens:
  • PHD finger protein 2 (PHF2_HUMAN)
  • PHF2 protein (Q6P2C5_HUMAN)
  • PHF2 protein (Q8N359_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75151

UniProtKB/Swiss-Prot:

PHF2_HUMAN :
  • The PHD-type zinc finger mediates the binding to H3K4me2 and H3K4me3.
  • Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.
Domain:
  • The PHD-type zinc finger mediates the binding to H3K4me2 and H3K4me3.
Family:
  • Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.
genes like me logo Genes that share domains with PHF2: view

Function for PHF2 Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
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  6. Cell Lines for research

Molecular function for PHF2 Gene

UniProtKB/Swiss-Prot Function:
Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA.
UniProtKB/Swiss-Prot EnzymeRegulation:
Enzymatically inactive by itself, and become active following phosphorylation by PKA.
GENATLAS Biochemistry:
PHD finger protein 2,Drosophila polycomb group homolog,PcG,widespread expressed

Enzyme Numbers (IUBMB) for PHF2 Gene

Phenotypes From GWAS Catalog for PHF2 Gene

Gene Ontology (GO) - Molecular Function for PHF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003712 transcription coregulator activity IBA 21873635
GO:0003713 transcription coactivator activity IDA 21532585
GO:0005506 iron ion binding IDA 21167174
GO:0005515 protein binding IPI 21532585
GO:0008270 zinc ion binding IDA 20129925
genes like me logo Genes that share ontologies with PHF2: view
genes like me logo Genes that share phenotypes with PHF2: view

Animal Models for PHF2 Gene

MGI Knock Outs for PHF2:
  • Phf2 Phf2<tm1.1Yima>

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHF2

No data available for Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for PHF2 Gene

Localization for PHF2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF2 Gene

Nucleus, nucleolus. Chromosome, centromere, kinetochore.

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 PHF2 gene
Compartment Confidence
nucleus 5
cytosol 3
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli rim (3)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PHF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000775 chromosome, centromeric region IEA --
GO:0000776 kinetochore IEA,IDA 20813266
GO:0000777 condensed chromosome kinetochore IEA --
GO:0000785 chromatin IBA --
GO:0005634 nucleus TAS 10051327
genes like me logo Genes that share ontologies with PHF2: view

Pathways & Interactions for PHF2 Gene

genes like me logo Genes that share pathways with PHF2: view

Pathways by source for PHF2 Gene

1 Cell Signaling Technology pathway for PHF2 Gene

Gene Ontology (GO) - Biological Process for PHF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001889 liver development TAS 21532585
GO:0006325 chromatin organization IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0006482 protein demethylation IBA,IDA 21532585
GO:0033169 histone H3-K9 demethylation IEA --
genes like me logo Genes that share ontologies with PHF2: view

No data available for SIGNOR curated interactions for PHF2 Gene

Drugs & Compounds for PHF2 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for PHF2 Gene

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mRNA/cDNA for PHF2 Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHF2

Alternative Splicing Database (ASD) splice patterns (SP) for PHF2 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ·
SP1:
SP2:
SP3:
SP4: -
SP5:
SP6: - - - - - -
SP7:

ExUns: 18c ^ 19a · 19b · 19c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6: - -
SP7:

Relevant External Links for PHF2 Gene

GeneLoc Exon Structure for
PHF2

Expression for PHF2 Gene

Products:

  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PHF2 Gene

mRNA expression in normal human tissues for PHF2 Gene
mRNA expression by BioGPS for PHF2 GenemRNA expression by GTEx for PHF2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PHF2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (16.4), Placenta (10.9), CD8 Tcells (8.6), and Pancreatic juice (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PHF2 Gene



Protein tissue co-expression partners for PHF2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PHF2

SOURCE GeneReport for Unigene cluster for PHF2 Gene:

Hs.211441

mRNA Expression by UniProt/SwissProt for PHF2 Gene:

O75151-PHF2_HUMAN
Tissue specificity: Widely expressed, including in liver (at protein level).

Evidence on tissue expression from TISSUES for PHF2 Gene

  • Nervous system(4.4)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with PHF2: view

Primer products for research

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PHF2 Gene

Orthologs for PHF2 Gene

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

Orthologs for PHF2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PHF2 30 31
  • 98.72 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia PHF2 31
  • 96 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PHF2 30 31
  • 88.65 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Phf2 30 17 31
  • 87.3 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PHF2 30 31
  • 87.14 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Phf2 30
  • 86.32 (n)
Oppossum
(Monodelphis domestica)
 Mammalia PHF2 31
  • 83 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves PHF2 30 31
  • 74.72 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia PHF2 31
  • 81 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia phf2 30
  • 71.05 (n)
Zebrafish
(Danio rerio)
 Actinopterygii phf2 30 31
  • 68.47 (n)
 OneToOne
wufa14c10 30
Worm
(Caenorhabditis elegans)
 Secernentea F29B9.2a 32
  • 33 (a)
F29B9.2b 32
  • 33 (a)
spt-3 32
  • 27 (a)
jmjd-1.1 31
  • 24 (a)
 ManyToMany
jmjd-1.2 31
  • 19 (a)
 ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes JHD1 31
  • 27 (a)
 OneToMany
Species where no ortholog for PHF2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 Vase (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 PHF2 Gene

ENSEMBL:
Gene Tree for PHF2 (if available)
TreeFam:
Gene Tree for PHF2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PHF2: view image

Paralogs for PHF2 Gene

Paralogs for PHF2 Gene

(2) SIMAP similar genes for PHF2 Gene using alignment to 4 proteins:

  • PHF2_HUMAN
  • E7ET14_HUMAN
  • Q6P2C5_HUMAN
  • Q8N359_HUMAN

Pseudogenes.org Pseudogenes for PHF2 Gene

genes like me logo Genes that share paralogs with PHF2: view

Variants for PHF2 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PHF2 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
993631 Uncertain Significance: none provided 93,676,611(+) GAA/G
NM_005392.4(PHF2):c.2857_2858del (p.Lys953fs) 		FRAMESHIFT
rs10992837 Benign: not provided 93,660,207(+) G/A
NM_005392.4(PHF2):c.1345G>A (p.Val449Ile) 		MISSENSE
rs10992855 Benign: not provided 93,676,725(+) G/T
NM_005392.4(PHF2):c.2964G>T (p.Pro988=) 		SYNONYMOUS
rs138464551 Benign: not provided 93,663,633(+) C/T
NM_005392.4(PHF2):c.1935C>T (p.Leu645=) 		SYNONYMOUS
rs140677384 Benign: not provided 93,673,594(+) G/A
NM_005392.4(PHF2):c.2358G>A (p.Pro786=) 		SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PHF2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PHF2 Gene

Variant ID Type Subtype PubMed ID
dgv4485e59 CNV duplication 20981092
dgv7688n100 CNV gain 25217958
esv1581383 CNV deletion 17803354
esv2631126 CNV insertion 19546169
esv2668862 CNV deletion 23128226
esv2738788 CNV deletion 23290073
esv2738789 CNV deletion 23290073
esv2738790 CNV deletion 23290073
esv2738791 CNV deletion 23290073
esv2738792 CNV deletion 23290073
esv28910 CNV loss 19812545
esv3350789 CNV duplication 20981092
esv3358961 CNV duplication 20981092
esv3421237 CNV duplication 20981092
esv3440136 CNV duplication 20981092
esv3573292 CNV loss 25503493
nsv1036609 CNV gain 25217958
nsv1076192 CNV deletion 25765185
nsv1110039 CNV deletion 24896259
nsv1137483 CNV deletion 24896259
nsv1139996 CNV duplication 24896259
nsv1145256 CNV deletion 24896259
nsv1149043 CNV duplication 26484159
nsv509311 CNV insertion 20534489
nsv512992 CNV insertion 21212237
nsv519449 CNV loss 19592680
nsv824984 CNV gain 20364138
nsv824985 CNV gain 20364138

Variation tolerance for PHF2 Gene

Residual Variation Intolerance Score: 35% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.61; 96.54% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHF2 Gene

Human Gene Mutation Database (HGMD)
PHF2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF2 Gene

Disorders for PHF2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PHF2 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
dissociative disorder
  • dissociative disease
culler-jones syndrome
  • cjs
autism spectrum disorder
  • asd
- elite association - COSMIC cancer census association via MalaCards
Search PHF2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PHF2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with PHF2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PHF2 Gene

Publications for PHF2 Gene

  1. Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation. (PMID: 20129925) Wen H … Shi X (The Journal of biological chemistry 2010) 2 3 4
  2. PHF2, a novel PHD finger gene located on human chromosome 9q22. (PMID: 10051327) Hasenpusch-Theil K … Frischauf AM (Mammalian genome : official journal of the International Mammalian Genome Society 1999) 2 3 4
  3. PKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B. (PMID: 21532585) Baba A … Kato S (Nature cell biology 2011) 3 4
  4. Structural basis for human PHF2 Jumonji domain interaction with metal ions. (PMID: 21167174) Horton JR … Cheng X (Journal of molecular biology 2011) 3 4
  5. The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics. (PMID: 20813266) Ohta S … Rappsilber J (Cell 2010) 3 4

ExternalLinks

View latest publications for PHF2 gene in Mastermind

Products for PHF2 Gene

  • Addgene plasmids for PHF2

Sources for PHF2 Gene