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

Gene ID: 79142, updated on 5-Mar-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, Apr 2022]
Expression
Ubiquitous expression in esophagus (RPKM 12.0), testis (RPKM 11.9) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (7235038..7240828, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (7135965..7140642, complement)
105.20220307 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
  • 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. Mechanistic insights into chromatin targeting by leukemic NUP98-PHF23 fusion. Zhang Y, et al. Nat Commun, 2020 Jul 3. PMID 32620764, Free PMC Article
  2. 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
  3. 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
  4. 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
  5. Systematic identification of molecular links between core and candidate genes in breast cancer. Arroyo R, et al. J Mol Biol, 2015 Mar 27. PMID 25640309

See all (28) 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_2023_10

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

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