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    PHF23 PHD finger protein 23 [ Homo sapiens (human) ]

    Gene ID: 79142, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PHF23provided by HGNC
    Official Full Name
    PHD finger protein 23provided by HGNC
    Primary source
    HGNC:HGNC:28428
    See related
    Ensembl:ENSG00000040633 MIM:612910; AllianceGenome:HGNC:28428
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    hJUNE-1b
    Summary
    Predicted to enable metal ion binding activity. Involved in negative regulation of autophagosome assembly; negative regulation of autophagosome maturation; and positive regulation of protein ubiquitination. Located in nucleoplasm. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in esophagus (RPKM 12.0), testis (RPKM 11.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHF23 in Genome Data Viewer
    Location:
    17p13.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (7235038..7240828, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (7135965..7140642, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (7138357..7142776, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene acyl-CoA dehydrogenase very long chain Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7128275-7128774 Neighboring gene microRNA 324 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:7132793-7133992 Neighboring gene dishevelled segment polarity protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8090 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7142377-7143026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11605 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7144925-7145476 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7145477-7146028 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8094 Neighboring gene GABA type A receptor-associated protein Neighboring gene CTD nuclear envelope phosphatase 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7154656-7155243 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7155244-7155832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8097 Neighboring gene elongator acetyltransferase complex subunit 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8098 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7164637-7165600 Neighboring gene Sharpr-MPRA regulatory region 7888 Neighboring gene claudin 7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. A novel NUP98-PHF23 fusion resulting from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia. Reader JC, et al. Leukemia, 2007 Apr. PMID 17287853
    2. PHF23 promotes NSCLC proliferation, metastasis, and chemoresistance via stabilization of ACTN4 and activation of the ERK pathway. Cheng M, et al. Cell Death Dis, 2023 Aug 25. PMID 37626047, Free PMC Article
    3. Mechanistic insights into chromatin targeting by leukemic NUP98-PHF23 fusion. Zhang Y, et al. Nat Commun, 2020 Jul 3. PMID 32620764, Free PMC Article
    4. PHF23 (plant homeodomain finger protein 23) negatively regulates cell autophagy by promoting ubiquitination and degradation of E3 ligase LRSAM1. Wang Z, et al. Autophagy, 2014. PMID 25484098, Free PMC Article
    5. Genome-wide association study identifies multiple loci influencing human serum metabolite levels. Kettunen J, et al. Nat Genet, 2012 Jan 29. PMID 22286219, Free PMC Article

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHF23 promotes NSCLC proliferation, metastasis, and chemoresistance via stabilization of ACTN4 and activation of the ERK pathway.
      Title: PHF23 promotes NSCLC proliferation, metastasis, and chemoresistance via stabilization of ACTN4 and activation of the ERK pathway.
    2. Mechanistic insights into chromatin targeting by leukemic NUP98-PHF23 fusion.
      Title: Mechanistic insights into chromatin targeting by leukemic NUP98-PHF23 fusion.
    3. Plant homeodomain finger protein 23 negatively regulates cell autophagy by promoting ubiquitination and degradation of E3 ligase LRSAM1
      Title: PHF23 (plant homeodomain finger protein 23) negatively regulates cell autophagy by promoting ubiquitination and degradation of E3 ligase LRSAM1.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC2941, FLJ16355, FLJ22884

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of protein ubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 23
    Names
    PDH-containing protein JUNE-1
    PHD finger protein 23a

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001284517.2 → NP_001271446.1  PHD finger protein 23 isoform 2

      See identical proteins and their annotated locations for NP_001271446.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AK297040, BY994418, DA131173, EF071959
      Consensus CDS
      CCDS67144.1
      UniProtKB/Swiss-Prot
      Q9BUL5
      Related
      ENSP00000460738.1, ENST00000571362.5
      Conserved Domains (1) summary
      cd15631
      Location:274 → 317
      PHD_PHF23; PHD finger found in PHD finger protein 23 (PHF23)

    2. NM_001284518.2 → NP_001271447.1  PHD finger protein 23 isoform 3

      See identical proteins and their annotated locations for NP_001271447.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate 5' exon and uses an alternate start codon compared to variant 1. It encodes isoform 3 which has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AK122901, BY994418, EF071959
      Consensus CDS
      CCDS67143.1
      UniProtKB/Swiss-Prot
      Q9BUL5
      Related
      ENSP00000414607.2, ENST00000454255.6
      Conserved Domains (1) summary
      cd15631
      Location:337 → 380
      PHD_PHF23; PHD finger found in PHD finger protein 23 (PHF23)

    3. NM_024297.3 → NP_077273.2  PHD finger protein 23 isoform 1

      See identical proteins and their annotated locations for NP_077273.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC002509, BC008630, DA131173
      Consensus CDS
      CCDS42250.1
      UniProtKB/Swiss-Prot
      A1DZ74, B3KVH8, B4DLK6, D3DTN4, Q8IZK0, Q96HG7, Q9BUL5, Q9H5X0
      Related
      ENSP00000322579.3, ENST00000320316.8
      Conserved Domains (1) summary
      cd15631
      Location:341 → 384
      PHD_PHF23; PHD finger found in PHD finger protein 23 (PHF23)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      7235038..7240828 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047436728.1 → XP_047292684.1  PHD finger protein 23 isoform X2

    2. XM_024450938.2 → XP_024306706.1  PHD finger protein 23 isoform X1

      Conserved Domains (1) summary
      cd15631
      Location:345 → 388
      PHD_PHF23; PHD finger found in PHD finger protein 23 (PHF23)

    3. XM_024450942.2 → XP_024306710.1  PHD finger protein 23 isoform X3

      UniProtKB/TrEMBL
      I3L1N0
      Conserved Domains (1) summary
      cd15631
      Location:211 → 254
      PHD_PHF23; PHD finger found in PHD finger protein 23 (PHF23)

    4. XM_047436729.1 → XP_047292685.1  PHD finger protein 23 isoform X3

      UniProtKB/TrEMBL
      I3L1N0

    5. XM_024450940.2 → XP_024306708.1  PHD finger protein 23 isoform X3

      UniProtKB/TrEMBL
      I3L1N0
      Conserved Domains (1) summary
      cd15631
      Location:211 → 254
      PHD_PHF23; PHD finger found in PHD finger protein 23 (PHF23)

    6. XM_024450939.2 → XP_024306707.1  PHD finger protein 23 isoform X3

      UniProtKB/TrEMBL
      I3L1N0
      Conserved Domains (1) summary
      cd15631
      Location:211 → 254
      PHD_PHF23; PHD finger found in PHD finger protein 23 (PHF23)

    7. XM_047436730.1 → XP_047292686.1  PHD finger protein 23 isoform X3

      UniProtKB/TrEMBL
      I3L1N0
      Related
      ENSP00000458953.1, ENST00000576955.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      7135965..7140642 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317168.1 → XP_054173143.1  PHD finger protein 23 isoform X1

    2. XM_054317172.1 → XP_054173147.1  PHD finger protein 23 isoform X3

      UniProtKB/TrEMBL
      I3L1N0

    3. XM_054317169.1 → XP_054173144.1  PHD finger protein 23 isoform X3

      UniProtKB/TrEMBL
      I3L1N0

    4. XM_054317170.1 → XP_054173145.1  PHD finger protein 23 isoform X3

      UniProtKB/TrEMBL
      I3L1N0

    5. XM_054317171.1 → XP_054173146.1  PHD finger protein 23 isoform X3

      UniProtKB/TrEMBL
      I3L1N0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BUL5.1 GenPept UniProtKB/Swiss-Prot:Q9BUL5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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