Aliases for PHF19 Gene

Aliases for PHF19 Gene

  • PHD Finger Protein 19 2 3 4 5
  • PCL3 2 3 4
  • Tudor Domain Containing 19B 2 3
  • Polycomb-Like Protein 3 3 4
  • TDRD19B 2 3
  • MTF2L1 2 3
  • Polycomb-Like 3 2
  • Polycomb Like 3 3
  • DKFZP727G051 2
  • PHF19 5
  • HPCL3 4

External Ids for PHF19 Gene

Previous GeneCards Identifiers for PHF19 Gene

  • GC09M118994
  • GC09M120698
  • GC09M122657
  • GC09M123617
  • GC09M093235

Summaries for PHF19 Gene

GeneCards Summary for PHF19 Gene

PHF19 (PHD Finger Protein 19) is a Protein Coding gene. Diseases associated with PHF19 include Hereditary Lymphedema and Hereditary Lymphedema I. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include methylated histone binding. An important paralog of this gene is MTF2.

UniProtKB/Swiss-Prot Summary for PHF19 Gene

  • Polycomb group (PcG) that specifically binds histone H3 trimethylated at 'Lys-36' (H3K36me3) and recruits the PRC2 complex. Probably involved in the transition from an active state to a repressed state in embryonic stem cells: acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting H3K36me3 histone demethylases RIOX1 or KDM2B, leading to demethylation of H3K36 and recruitment of the PRC2 complex that mediates H3K27me3 methylation, followed by de novo silencing. Recruits the PRC2 complex to CpG islands and contributes to embryonic stem cell self-renewal. Also binds dimethylated at 'Lys-36' (H3K36me2). Isoform 1 and isoform 2 inhibit transcription from an HSV-tk promoter.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PHF19 Gene

Genomics for PHF19 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PHF19 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J120867 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.3 +32.9 32851 3.1 CTCF ZBTB33 PRDM10 POLR2A BACH1 JUND LARP7 ZNF143 ZIC2 RBFOX2 lnc-PSMD5-5 PHF19 CUTALP TRAF1 PSMD5
GH09J120871 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.3 +26.2 26214 8.1 GATAD2A TEAD4 PRDM10 POLR2A BACH1 TARDBP JUND FOXA1 LARP7 ZIC2 PHF19 CUTALP TRAF1 PSMD5 lnc-PSMD5-5
GH09J120901 Enhancer 1 Ensembl ENCODE dbSUPER 600.7 -1.6 -1649 6.5 POLR2A SMAD5 ZNF740 BCLAF1 CBFB ZFHX2 STAT5A EBF1 RCOR1 ATF2 PHF19 CUTALP TRAF1
GH09J120900 Enhancer 0.5 ENCODE dbSUPER 600.7 +1.8 1802 0.2 PYGO2 ZBED1 PHF19 CUTALP TRAF1 lnc-PSMD5-5 PSMD5
GH09J121618 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 4.7 -719.1 -719117 4.6 GATAD2A CTCF PRDM10 PRDM1 SP1 CEBPA MNT CEBPB ZBTB48 YY1 DAB2IP ENSG00000229854 PHF19 RF00951-157 RF00017-7861 LOC107987125
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PHF19 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PHF19

Top Transcription factor binding sites by QIAGEN in the PHF19 gene promoter:
  • LCR-F1
  • Nkx2-2
  • RORalpha2

Genomic Locations for PHF19 Gene

Genomic Locations for PHF19 Gene
chr9:120,855,651-120,902,160
(GRCh38/hg38)
Size:
46,510 bases
Orientation:
Minus strand
chr9:123,617,931-123,639,606
(GRCh37/hg19)
Size:
21,676 bases
Orientation:
Minus strand

Genomic View for PHF19 Gene

Genes around PHF19 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF19 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF19 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF19 Gene

Proteins for PHF19 Gene

  • Protein details for PHF19 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5T6S3-PHF19_HUMAN
    Recommended name:
    PHD finger protein 19
    Protein Accession:
    Q5T6S3
    Secondary Accessions:
    • Q32NF2
    • Q5T6S4
    • Q6N038
    • Q8TBL6
    • Q9UFS9

    Protein attributes for PHF19 Gene

    Size:
    580 amino acids
    Molecular mass:
    65591 Da
    Quaternary structure:
    • Associated component of the PRC2 complex. Interacts with EZH2 (via its Tudor domain). Isoform 1 interacts with SUZ12; isoform 2 does not interact with SUZ12. Interacts with RIOX1.
    SequenceCaution:
    • Sequence=CAE45832.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
    Miscellaneous:
    • Down-regulated in spheroid melanoma cells that display an invasive phenotype, characterized by a higher motility, a poor proliferation rate and a gain of pluripotency gene expression. PHF19 favors the proliferation and reduces the transmigration capacity of melanoma cell lines, 2 properties of invasive cells, suggesting that down-regulation may participate in the switch from proliferative to invasive states in melanoma cells (PubMed:22487681).

    Three dimensional structures from OCA and Proteopedia for PHF19 Gene

    Alternative splice isoforms for PHF19 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHF19 Gene

Post-translational modifications for PHF19 Gene

  • Ubiquitination at Lys554
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PHF19 Gene

Domains & Families for PHF19 Gene

Gene Families for PHF19 Gene

Protein Domains for PHF19 Gene

Suggested Antigen Peptide Sequences for PHF19 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ16269 fis, clone MESAN2016552, highly similar to Homo sapiens PHD finger protein 19 (PHF19), transcript variant 1, mRNA (B3KV88_HUMAN)
  • cDNA FLJ53261, highly similar to Homo sapiens PHD finger protein 19 (PHF19), transcript variant 1, mRNA (B7Z8H3_HUMAN)
  • Polycomb-like protein 3 (PHF19_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5T6S3

UniProtKB/Swiss-Prot:

PHF19_HUMAN :
  • The Tudor domain recognizes and binds H3K36me3 (PubMed:23273982, PubMed:23160351, PubMed:23104054 and PubMed:23228662). May also bind H3K27me3, with a lower affinity (PubMed:23160351).
  • Belongs to the Polycomblike family.
Domain:
  • The Tudor domain recognizes and binds H3K36me3 (PubMed:23273982, PubMed:23160351, PubMed:23104054 and PubMed:23228662). May also bind H3K27me3, with a lower affinity (PubMed:23160351).
Family:
  • Belongs to the Polycomblike family.
genes like me logo Genes that share domains with PHF19: view

Function for PHF19 Gene

Molecular function for PHF19 Gene

UniProtKB/Swiss-Prot Function:
Polycomb group (PcG) that specifically binds histone H3 trimethylated at 'Lys-36' (H3K36me3) and recruits the PRC2 complex. Probably involved in the transition from an active state to a repressed state in embryonic stem cells: acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting H3K36me3 histone demethylases RIOX1 or KDM2B, leading to demethylation of H3K36 and recruitment of the PRC2 complex that mediates H3K27me3 methylation, followed by de novo silencing. Recruits the PRC2 complex to CpG islands and contributes to embryonic stem cell self-renewal. Also binds dimethylated at 'Lys-36' (H3K36me2). Isoform 1 and isoform 2 inhibit transcription from an HSV-tk promoter.

Phenotypes From GWAS Catalog for PHF19 Gene

Gene Ontology (GO) - Molecular Function for PHF19 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA 21873635
GO:0003682 chromatin binding IBA 21873635
GO:0005515 protein binding IPI 23104054
GO:0035064 methylated histone binding IBA,IDA 23104054
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PHF19: view
genes like me logo Genes that share phenotypes with PHF19: view

Animal Models for PHF19 Gene

MGI Knock Outs for PHF19:
  • Phf19 Phf19<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

miRNA for PHF19 Gene

miRTarBase miRNAs that target PHF19

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHF19

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PHF19 Gene

Localization for PHF19 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF19 Gene

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 PHF19 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1

Gene Ontology (GO) - Cellular Components for PHF19 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm TAS --
GO:0035098 colocalizes_with ESC/E(Z) complex IBA,IDA 23104054
genes like me logo Genes that share ontologies with PHF19: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PHF19 Gene

Pathways & Interactions for PHF19 Gene

genes like me logo Genes that share pathways with PHF19: view

Pathways by source for PHF19 Gene

1 Cell Signaling Technology pathway for PHF19 Gene

Gene Ontology (GO) - Biological Process for PHF19 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0006325 chromatin organization IBA 21873635
GO:0006355 regulation of transcription, DNA-templated IBA 21873635
GO:0019827 stem cell population maintenance IEA --
GO:0045814 negative regulation of gene expression, epigenetic TAS --
genes like me logo Genes that share ontologies with PHF19: view

No data available for SIGNOR curated interactions for PHF19 Gene

Drugs & Compounds for PHF19 Gene

No Compound Related Data Available

Transcripts for PHF19 Gene

mRNA/cDNA for PHF19 Gene

5 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHF19

Alternative Splicing Database (ASD) splice patterns (SP) for PHF19 Gene

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

ExUns: 17b ^ 18a · 18b ^ 19a · 19b
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for PHF19 Gene

GeneLoc Exon Structure for
PHF19

Expression for PHF19 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PHF19 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Bone (Muscoskeletal System)

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PHF19 Gene



Protein tissue co-expression partners for PHF19 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PHF19

SOURCE GeneReport for Unigene cluster for PHF19 Gene:

Hs.460124

mRNA Expression by UniProt/SwissProt for PHF19 Gene:

Q5T6S3-PHF19_HUMAN
Tissue specificity: Isoform 1 is expressed in thymus, heart, lung and kidney. Isoform 2 is predominantly expressed in placenta, skeletal muscle and kidney, whereas isoform 1 is predominantly expressed in liver and peripheral blood leukocytes. Overexpressed in many types of cancers, including colon, skin, lung, rectal, cervical, uterus, liver cancers, in cell lines derived from different stages of melanoma and in glioma cell lines.

Evidence on tissue expression from TISSUES for PHF19 Gene

  • Skin(4.4)
  • Lung(2.4)
  • Nervous system(2.3)
  • Intestine(2)
genes like me logo Genes that share expression patterns with PHF19: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PHF19 Gene

Orthologs for PHF19 Gene

This gene was present in the common ancestor of animals.

Orthologs for PHF19 Gene

Organism Taxonomy Gene Similarity Type Details
Cow
(Bos Taurus)
Mammalia PHF19 30 31
  • 92.13 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Phf19 30
  • 88.12 (n)
Mouse
(Mus musculus)
Mammalia Phf19 30 17 31
  • 87.49 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PHF19 31
  • 83 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia PHF19 31
  • 78 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PHF19 31
  • 78 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PHF19 30 31
  • 77.32 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PHF19 31
  • 42 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia phf19 30
  • 70.39 (n)
Str.1129 30
Zebrafish
(Danio rerio)
Actinopterygii phf13 30
  • 68.46 (n)
phf19 31
  • 66 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Pcl 30 31
  • 48.65 (n)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.6624 31
  • 41 (a)
OneToMany
Species where no ortholog for PHF19 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)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chimpanzee (Pan troglodytes)
  • 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)
  • 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 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 PHF19 Gene

ENSEMBL:
Gene Tree for PHF19 (if available)
TreeFam:
Gene Tree for PHF19 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PHF19: view image

Paralogs for PHF19 Gene

Paralogs for PHF19 Gene

(2) SIMAP similar genes for PHF19 Gene using alignment to 5 proteins:

  • PHF19_HUMAN
  • B0QZ50_HUMAN
  • B0QZ51_HUMAN
  • B0QZ72_HUMAN
  • F5H8K3_HUMAN
genes like me logo Genes that share paralogs with PHF19: view

Variants for PHF19 Gene

Additional dbSNP identifiers (rs#s) for PHF19 Gene

Structural Variations from Database of Genomic Variants (DGV) for PHF19 Gene

Variant ID Type Subtype PubMed ID
esv2759713 CNV loss 17122850
nsv1051370 CNV gain 25217958
nsv8566 CNV gain 18304495
nsv950936 CNV deletion 24416366

Variation tolerance for PHF19 Gene

Residual Variation Intolerance Score: 24.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.64; 31.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHF19 Gene

Human Gene Mutation Database (HGMD)
PHF19
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF19

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PHF19 Gene

Disorders for PHF19 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PHF19 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
hereditary lymphedema
  • milroy disease
hereditary lymphedema i
  • nonne-milroy lymphedema
melanoma
  • malignant melanoma
- elite association - COSMIC cancer census association via MalaCards
Search PHF19 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PHF19

genes like me logo Genes that share disorders with PHF19: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PHF19 Gene

Publications for PHF19 Gene

  1. A novel human homologue of Drosophila polycomblike gene is up-regulated in multiple cancers. (PMID: 15563832) Wang S … Zhu J (Gene 2004) 2 3 4
  2. Tudor domains of the PRC2 components PHF1 and PHF19 selectively bind to histone H3K36me3. (PMID: 23228662) Qin S … Min J (Biochemical and biophysical research communications 2013) 3 4
  3. An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. (PMID: 23273982) Cai L … Wang GG (Molecular cell 2013) 3 4
  4. Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation. (PMID: 23160351) Brien GL … Bracken AP (Nature structural & molecular biology 2012) 3 4
  5. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. (PMID: 23104054) Ballaré C … Di Croce L (Nature structural & molecular biology 2012) 3 4

Products for PHF19 Gene

Sources for PHF19 Gene