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Aliases for PHF23 Gene

Aliases for PHF23 Gene

  • PHD Finger Protein 23 2 3 3 5
  • PDH-Containing Protein JUNE-1 3 4
  • PHD Finger Protein 23a 3
  • HJUNE-1b 3

External Ids for PHF23 Gene

Previous GeneCards Identifiers for PHF23 Gene

  • GC17M007080
  • GC17M007082
  • GC17M007138
  • GC17M007030

Summaries for PHF23 Gene

GeneCards Summary for PHF23 Gene

PHF23 (PHD Finger Protein 23) is a Protein Coding gene. An important paralog of this gene is PHF13.

UniProtKB/Swiss-Prot for PHF23 Gene

  • Acts as a negative regulator of autophagy, through promoting ubiquitination and degradation of LRSAM1, an E3 ubiquitin ligase that promotes autophagy in response to starvation or infecting bacteria.

Additional gene information for PHF23 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF23 Gene

Genomics for PHF23 Gene

GeneHancer (GH) Regulatory Elements for PHF23 Gene

Promoters and enhancers for PHF23 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
GH17J007233 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 650.7 +1.1 1063 11.3 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 DVL2 GABARAP PHF23 CNTROB SNORD10 WRAP53 NEURL4 POLR2A KIAA0753 KCTD11
GH17J007312 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.4 -74.8 -74823 4 HDGF PKNOX1 SMAD1 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 GPS2 GC17M007314 NEURL4 EIF5A ACAP1 SLC2A4 ENSG00000202251 CLDN7 CTDNEP1 ELP5
GH17J007177 Promoter/Enhancer 1.4 Ensembl ENCODE 10.7 +61.9 61873 1.7 ATF1 ARID4B SIN3A DMAP1 YY1 GLIS2 ZNF143 ATF7 SP3 RXRA GC17P007176 ASGR1 ENSG00000262067 LOC105371508 SPEM1 SLC16A11 ACADVL DLG4 SLC16A13 ELP5
GH17J007171 Enhancer 1.1 Ensembl ENCODE 10.7 +66.0 66042 4.2 FOXA2 SIN3A YBX1 GLI4 YY1 ZNF143 ZNF207 KLF7 ZNF548 KLF13 DVL2 CNTROB WRAP53 CYB5D1 NEURL4 NLGN2 SENP3 LOC100996842 SNORD10 ELP5
GH17J007141 Enhancer 0.6 ENCODE 10.4 +97.8 97843 1.3 SMARCE1 PKNOX1 GATAD2B DPF2 ZNF507 ZNF217 CTBP1 GATA3 CUX1 TCF7L2 GC17M007141 RPL7AP64 ASGR2 SLC16A11 ASGR1 DVL2 PHF23 GABARAP CLDN7 ENSG00000202251
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PHF23 on UCSC Golden Path with GeneCards custom track

Genomic Locations for PHF23 Gene

Genomic Locations for PHF23 Gene
chr17:7,235,028-7,239,722
(GRCh38/hg38)
Size:
4,695 bases
Orientation:
Minus strand
chr17:7,138,347-7,143,041
(GRCh37/hg19)

Genomic View for PHF23 Gene

Genes around PHF23 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF23 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF23 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF23 Gene

Proteins for PHF23 Gene

  • Protein details for PHF23 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BUL5-PHF23_HUMAN
    Recommended name:
    PHD finger protein 23
    Protein Accession:
    Q9BUL5
    Secondary Accessions:
    • A1DZ74
    • B3KVH8
    • B4DLK6
    • D3DTN4
    • Q8IZK0
    • Q96HG7
    • Q9H5X0

    Protein attributes for PHF23 Gene

    Size:
    403 amino acids
    Molecular mass:
    43818 Da
    Quaternary structure:
    • Interacts with LRSAM1.
    SequenceCaution:
    • Sequence=ABK59096.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB15498.1; Type=Frameshift; Positions=241; Evidence={ECO:0000305};

    Alternative splice isoforms for PHF23 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHF23 Gene

Post-translational modifications for PHF23 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PHF23 Gene

Domains & Families for PHF23 Gene

Gene Families for PHF23 Gene

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

Protein Domains for PHF23 Gene

Graphical View of Domain Structure for InterPro Entry

Q9BUL5

UniProtKB/Swiss-Prot:

PHF23_HUMAN :
  • The PHD-type zinc-finger domain is required for interaction with LRSAM1 and negative regulation of autophagy.
  • Belongs to the PHF23 family.
Domain:
  • The PHD-type zinc-finger domain is required for interaction with LRSAM1 and negative regulation of autophagy.
Family:
  • Belongs to the PHF23 family.
genes like me logo Genes that share domains with PHF23: view

Function for PHF23 Gene

Molecular function for PHF23 Gene

UniProtKB/Swiss-Prot Function:
Acts as a negative regulator of autophagy, through promoting ubiquitination and degradation of LRSAM1, an E3 ubiquitin ligase that promotes autophagy in response to starvation or infecting bacteria.

Phenotypes From GWAS Catalog for PHF23 Gene

Gene Ontology (GO) - Molecular Function for PHF23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IBA --
GO:0005515 protein binding IPI 25484098
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PHF23: view
genes like me logo Genes that share phenotypes with PHF23: view

Animal Model Products

CRISPR Products

miRNA for PHF23 Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHF23

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PHF23 Gene

Localization for PHF23 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF23 Gene

Nucleus. Cytoplasm. Note=Mainly present in the nucleus and part in the cytoplasm. {ECO:0000269 PubMed:25484098}.

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 PHF23 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PHF23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with PHF23: view

Pathways & Interactions for PHF23 Gene

SuperPathways for PHF23 Gene

No Data Available

Interacting Proteins for PHF23 Gene

Gene Ontology (GO) - Biological Process for PHF23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy IEA --
GO:0007076 mitotic chromosome condensation IBA --
GO:0031398 positive regulation of protein ubiquitination IMP 25484098
GO:1901097 negative regulation of autophagosome maturation IMP 25484098
GO:1902902 negative regulation of autophagosome assembly IMP 25484098
genes like me logo Genes that share ontologies with PHF23: view

No data available for Pathways by source and SIGNOR curated interactions for PHF23 Gene

Drugs & Compounds for PHF23 Gene

No Compound Related Data Available

Transcripts for PHF23 Gene

Unigene Clusters for PHF23 Gene

PHD finger protein 23:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHF23

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHF23 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d ^ 5 ^ 6
SP1: -
SP2: -
SP3: -

Relevant External Links for PHF23 Gene

GeneLoc Exon Structure for
PHF23
ECgene alternative splicing isoforms for
PHF23

Expression for PHF23 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PHF23 Gene

Protein differential expression in normal tissues from HIPED for PHF23 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (18.8), NK cells (12.3), CD8 Tcells (10.1), and Placenta (8.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PHF23 Gene



Protein tissue co-expression partners for PHF23 Gene

NURSA nuclear receptor signaling pathways regulating expression of PHF23 Gene:

PHF23

SOURCE GeneReport for Unigene cluster for PHF23 Gene:

Hs.644724

mRNA Expression by UniProt/SwissProt for PHF23 Gene:

Q9BUL5-PHF23_HUMAN
Tissue specificity: Widely expressed in human tissues and various cell lines.

Evidence on tissue expression from TISSUES for PHF23 Gene

  • Nervous system(4.7)
  • Intestine(4.4)
  • Liver(4.3)
  • Blood(4.1)
  • Lung(2.9)
  • Skin(2.9)
  • Heart(2)
  • Muscle(2)
genes like me logo Genes that share expression patterns with PHF23: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PHF23 Gene

Orthologs for PHF23 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PHF23 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHF23 34 33
  • 99.67 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PHF23 34 33
  • 92.86 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PHF23 34 33
  • 92.22 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Phf23 16 34 33
  • 90.86 (n)
rat
(Rattus norvegicus)
Mammalia Phf23 33
  • 90.76 (n)
oppossum
(Monodelphis domestica)
Mammalia PHF23 34
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHF23 34
  • 39 (a)
OneToOne
chicken
(Gallus gallus)
Aves -- 34
  • 34 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 33 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.6085 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.5594 33
zebrafish
(Danio rerio)
Actinopterygii phf23a 34 33
  • 62.18 (n)
OneToMany
phf23b 34
  • 46 (a)
OneToMany
Dr.27169 33
sea squirt
(Ciona savignyi)
Ascidiacea Cin.4327 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4327 33
Species where no ortholog for PHF23 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 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 PHF23 Gene

ENSEMBL:
Gene Tree for PHF23 (if available)
TreeFam:
Gene Tree for PHF23 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PHF23: view image

Paralogs for PHF23 Gene

Paralogs for PHF23 Gene

genes like me logo Genes that share paralogs with PHF23: view

Variants for PHF23 Gene

Sequence variations from dbSNP and Humsavar for PHF23 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000459012 -- 7,240,108(-) A/C upstream_transcript_variant
rs1000557803 -- 7,240,386(-) G/A upstream_transcript_variant
rs1000598225 -- 7,235,015(-) G/A/C downstream_transcript_variant
rs1000676156 -- 7,234,567(-) C/T downstream_transcript_variant
rs1002226595 -- 7,236,423(-) G/T coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for PHF23 Gene

Variant ID Type Subtype PubMed ID
esv2422288 CNV deletion 17116639
esv2665200 CNV deletion 23128226
esv2669909 CNV deletion 23128226
esv28577 CNV loss 19812545
esv3639861 CNV loss 21293372
esv3639862 CNV loss 21293372
nsv1070384 CNV deletion 25765185
nsv457659 CNV loss 19166990
nsv574322 CNV loss 21841781
nsv952118 CNV deletion 24416366

Variation tolerance for PHF23 Gene

Residual Variation Intolerance Score: 20.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.86; 17.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHF23 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF23

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF23 Gene

Disorders for PHF23 Gene

UniProtKB/Swiss-Prot

PHF23_HUMAN
  • Note=A chromosomal aberration involving PHF23 is found in a patient with acute myeloid leukemia (AML). Translocation t(11;17)(p15;p13) with NUP98.

Additional Disease Information for PHF23

No disorders were found for PHF23 Gene.

No data available for MalaCards and Genatlas for PHF23 Gene

Publications for PHF23 Gene

  1. PHF23 (plant homeodomain finger protein 23) negatively regulates cell autophagy by promoting ubiquitination and degradation of E3 ligase LRSAM1. (PMID: 25484098) Wang Z … Chen Y (Autophagy 2014) 3 4 58
  2. Genome-wide association study identifies multiple loci influencing human serum metabolite levels. (PMID: 22286219) Kettunen J … Ripatti S (Nature genetics 2012) 3 44 58
  3. A novel NUP98-PHF23 fusion resulting from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia. (PMID: 17287853) Reader JC … Ning Y (Leukemia 2007) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for PHF23 Gene

Sources for PHF23 Gene

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