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    PHF8 PHD finger protein 8 [ Homo sapiens (human) ]

    Gene ID: 23133, updated on 4-Nov-2024

    Summary

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    Official Symbol
    PHF8provided by HGNC
    Official Full Name
    PHD finger protein 8provided by HGNC
    Primary source
    HGNC:HGNC:20672
    See related
    Ensembl:ENSG00000172943 MIM:300560; AllianceGenome:HGNC:20672
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    KDM7B; JHDM1F; MRXSSD; ZNF422
    Summary
    The protein encoded by this gene is a histone lysine demethylase that preferentially acts on histones in the monomethyl or dimethyl states. The encoded protein requires Fe(2+) ion, 2-oxoglutarate, and oxygen for its catalytic activity. The protein has an N-terminal PHD finger and a central Jumonji C domain. This gene is thought to function as a transcription activator. Defects in this gene are a cause of syndromic X-linked Siderius type intellectual disability (MRXSSD) and over-expression of this gene is associated with several forms of cancer. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]
    Expression
    Broad expression in testis (RPKM 19.3), ovary (RPKM 6.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHF8 in Genome Data Viewer
    Location:
    Xp11.22
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (53936680..54048936, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (53226407..53338824, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (53963113..54071569, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene MRPS18C pseudogene 7 Neighboring gene RNA, 5S ribosomal pseudogene 505 Neighboring gene Sharpr-MPRA regulatory region 5322 Neighboring gene MPRA-validated peak7381 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29669 Neighboring gene Sharpr-MPRA regulatory region 9958 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:54091510-54091662 Neighboring gene family with sequence similarity 120 member C Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:54154862-54155382 Neighboring gene ribosomal protein L37 pseudogene 24 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20861 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20863 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:54242133-54242784 Neighboring gene WNK lysine deficient protein kinase 3 Neighboring gene ribosomal protein L7a pseudogene 71

    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. Features of the PHF8/KIAA1718 histone demethylase. Suganuma T, et al. Cell Res, 2010 Aug. PMID 20644565
    2. PIP2 epigenetically represses rRNA genes transcription interacting with PHF8. Ulicna L, et al. Biochim Biophys Acta Mol Cell Biol Lipids, 2018 Mar. PMID 29246768
    3. The histone demethylase PHF8 promotes adult acute lymphoblastic leukemia through interaction with the MEK/ERK signaling pathway. Fu Y, et al. Biochem Biophys Res Commun, 2018 Feb 12. PMID 29330049
    4. Histone demethylase PHF8 promotes epithelial to mesenchymal transition and breast tumorigenesis. Shao P, et al. Nucleic Acids Res, 2017 Feb 28. PMID 27899639, Free PMC Article
    5. c-MYC drives histone demethylase PHF8 during neuroendocrine differentiation and in castration-resistant prostate cancer. Maina PK, et al. Oncotarget, 2016 Nov 15. PMID 27689328, Free PMC Article

    See all (117) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Histone demethylase PHF8 protected against chondrocyte injury and alleviated posttraumatic osteoarthritis by epigenetically enhancing WWP2 expression.
      Title: Histone demethylase PHF8 protected against chondrocyte injury and alleviated posttraumatic osteoarthritis by epigenetically enhancing WWP2 expression.
    2. Homocysteine metabolites impair the PHF8/H4K20me1/mTOR/autophagy pathway by upregulating the expression of histone demethylase PHF8-targeting microRNAs in human vascular endothelial cells and mice.
      Title: Homocysteine metabolites impair the PHF8/H4K20me1/mTOR/autophagy pathway by upregulating the expression of histone demethylase PHF8-targeting microRNAs in human vascular endothelial cells and mice.
    3. Histone demethylase PHF8 facilitates the development of chronic myeloid leukaemia by directly targeting BCR::ABL1.
      Title: Histone demethylase PHF8 facilitates the development of chronic myeloid leukaemia by directly targeting BCR::ABL1.
    4. Loss of PHF8 induces a viral mimicry response by activating endogenous retrotransposons.
      Title: Loss of PHF8 induces a viral mimicry response by activating endogenous retrotransposons.
    5. PHF8-GLUL axis in lipid deposition and tumor growth of clear cell renal cell carcinoma.
      Title: PHF8-GLUL axis in lipid deposition and tumor growth of clear cell renal cell carcinoma.
    6. NEDD4L represses prostate cancer cell proliferation via modulating PHF8 through the ubiquitin-proteasome pathway.
      Title: NEDD4L represses prostate cancer cell proliferation via modulating PHF8 through the ubiquitin-proteasome pathway.
    7. The histone demethylase PHF8 regulates TGFbeta signaling and promotes melanoma metastasis.
      Title: The histone demethylase PHF8 regulates TGFβ signaling and promotes melanoma metastasis.
    8. Histone demethylase PHF8 promotes cell growth and metastasis of non-small-cell lung cancer through activating Wnt/beta-catenin signaling pathway.
      Title: Histone demethylase PHF8 promotes cell growth and metastasis of non-small-cell lung cancer through activating Wnt/β-catenin signaling pathway.
    9. Disrupting PHF8-TOPBP1 connection elicits a breast tumor-specific vulnerability to chemotherapeutics.
      Title: Disrupting PHF8-TOPBP1 connection elicits a breast tumor-specific vulnerability to chemotherapeutics.
    10. Analysis of a Set of KDM5C Regulatory Genes Mutated in Neurodevelopmental Disorders Identifies Temporal Coexpression Brain Signatures.
      Title: Analysis of a Set of KDM5C Regulatory Genes Mutated in Neurodevelopmental Disorders Identifies Temporal Coexpression Brain Signatures.
    Submit: New GeneRIF Correction See all GeneRIFs (48)

    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

    Associated conditions

    Description Tests
    Syndromic X-linked intellectual disability Siderius type
    MedGen: C1846055 OMIM: 300263 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-08-26)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-08-26)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Case-case genome-wide association analysis shows markers differentially associated with schizophrenia and bipolar disorder and implicates calcium channel genes.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1111, DKFZp686E0868

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 2-oxoglutarate-dependent dioxygenase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K27me2/H3K27me3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K36 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K36me/H3K36me2 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K9me/H3K9me2 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4K20 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone demethylase activity TAS
    Traceable Author Statement
    more info
    		  
    enables iron ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in G1/S transition of mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in brain development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of rDNA heterochromatin formation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase I IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone lysine demethylase PHF8
    Names
    [histone H3]-dimethyl-L-lysine(36) demethylase PHF8
    [histone H3]-dimethyl-L-lysine(9) demethylase PHF8
    jumonji C domain-containing histone demethylase 1F
    lysine demethylase 7B
    zinc finger protein 422
    NP_001171825.1
    NP_001171826.1
    NP_001171827.1
    NP_055922.1
    XP_005262053.1
    XP_005262056.1
    XP_005262057.1
    XP_011529080.1
    XP_047297890.1
    XP_047297891.1
    XP_047297892.1
    XP_047297893.1
    XP_054182694.1
    XP_054182695.1
    XP_054182696.1
    XP_054182697.1
    XP_054182698.1
    XP_054182699.1
    XP_054182700.1
    XP_054182701.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_021309.1 RefSeqGene

      Range
      5664..113457
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001184896.1 → NP_001171825.1  histone lysine demethylase PHF8 isoform 1

      See identical proteins and their annotated locations for NP_001171825.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AB029034, AL732374, BC053861, DA458639
      Consensus CDS
      CCDS55420.1
      UniProtKB/Swiss-Prot
      B3KMV4, B7Z911, Q5H9U5, Q5JPR9, Q5JPS0, Q5JPS2, Q5JPS3, Q5VUJ4, Q7Z6D4, Q9HAH2, Q9UPP1
      UniProtKB/TrEMBL
      A0A8J8YW94
      Related
      ENSP00000350676.5, ENST00000357988.9
      Conserved Domains (3) summary
      smart00558
      Location:235 → 298
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15642
      Location:42 → 93
      PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
      cl21464
      Location:270 → 370
      cupin_like; Conserved domain found in cupin and related proteins

    2. NM_001184897.2 → NP_001171826.1  histone lysine demethylase PHF8 isoform 3

      See identical proteins and their annotated locations for NP_001171826.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence, the 3' UTR and coding sequence, and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has a shorter N-terminus, longer and distinct C-terminus, and lacks an internal segment compared to isoform 1.
      Source sequence(s)
      AB029034, AK304272, AL589872, AL732374, BC053861, BE676640
      UniProtKB/TrEMBL
      A0A8J8YW94
      Conserved Domains (4) summary
      smart00558
      Location:199 → 262
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15642
      Location:6 → 57
      PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
      pfam02373
      Location:234 → 334
      JmjC; JmjC domain, hydroxylase
      pfam17811
      Location:338 → 441
      JHD; Jumonji helical domain

    3. NM_001184898.2 → NP_001171827.1  histone lysine demethylase PHF8 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and the 3' UTR and coding sequence compared to variant 1. The resulting isoform (4) has a shorter N-terminus and a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AF091081, BC042108
      Consensus CDS
      CCDS55419.1
      UniProtKB/TrEMBL
      A0A8J8YW94
      Related
      ENSP00000319473.8, ENST00000322659.12
      Conserved Domains (3) summary
      smart00558
      Location:199 → 262
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15642
      Location:6 → 57
      PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
      cl21464
      Location:234 → 334
      cupin_like; Conserved domain found in cupin and related proteins

    4. NM_015107.3 → NP_055922.1  histone lysine demethylase PHF8 isoform 2

      See identical proteins and their annotated locations for NP_055922.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AL589872, AL732374, BC053861, BE676640
      Consensus CDS
      CCDS14355.1
      UniProtKB/TrEMBL
      A0A8J8YW94
      Related
      ENSP00000338868.6, ENST00000338154.11
      Conserved Domains (3) summary
      smart00558
      Location:199 → 262
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15642
      Location:6 → 57
      PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
      cl21464
      Location:234 → 334
      cupin_like; Conserved domain found in cupin and related proteins

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      53936680..54048936 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005261996.2 → XP_005262053.1  histone lysine demethylase PHF8 isoform X1

      See identical proteins and their annotated locations for XP_005262053.1

      UniProtKB/TrEMBL
      A0A8J8YW94
      Conserved Domains (3) summary
      smart00558
      Location:235 → 298
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15642
      Location:42 → 93
      PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
      cl21464
      Location:270 → 370
      cupin_like; Conserved domain found in cupin and related proteins

    2. XM_011530778.2 → XP_011529080.1  histone lysine demethylase PHF8 isoform X1

      See identical proteins and their annotated locations for XP_011529080.1

      UniProtKB/TrEMBL
      A0A8J8YW94
      Conserved Domains (3) summary
      smart00558
      Location:235 → 298
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15642
      Location:42 → 93
      PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
      cl21464
      Location:270 → 370
      cupin_like; Conserved domain found in cupin and related proteins

    3. XM_047441934.1 → XP_047297890.1  histone lysine demethylase PHF8 isoform X2

      UniProtKB/Swiss-Prot
      B3KMV4, B7Z911, Q5H9U5, Q5JPR9, Q5JPS0, Q5JPS2, Q5JPS3, Q5VUJ4, Q7Z6D4, Q9HAH2, Q9UPP1

    4. XM_005262000.2 → XP_005262057.1  histone lysine demethylase PHF8 isoform X4

      UniProtKB/TrEMBL
      A0A8J8YW94
      Conserved Domains (4) summary
      smart00558
      Location:235 → 298
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15642
      Location:42 → 93
      PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
      pfam02373
      Location:270 → 370
      JmjC; JmjC domain, hydroxylase
      pfam17811
      Location:374 → 477
      JHD; Jumonji helical domain

    5. XM_047441935.1 → XP_047297891.1  histone lysine demethylase PHF8 isoform X3

      UniProtKB/TrEMBL
      H0Y3N9
      Related
      ENSP00000379578.3, ENST00000396282.7

    6. XM_005261999.2 → XP_005262056.1  histone lysine demethylase PHF8 isoform X3

      See identical proteins and their annotated locations for XP_005262056.1

      UniProtKB/TrEMBL
      A0A8J8YW94, H0Y3N9
      Conserved Domains (3) summary
      smart00558
      Location:199 → 262
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15642
      Location:6 → 57
      PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
      cl21464
      Location:234 → 334
      cupin_like; Conserved domain found in cupin and related proteins

    7. XM_047441937.1 → XP_047297893.1  histone lysine demethylase PHF8 isoform X6

    8. XM_047441936.1 → XP_047297892.1  histone lysine demethylase PHF8 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      53226407..53338824 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326720.1 → XP_054182695.1  histone lysine demethylase PHF8 isoform X1

    2. XM_054326719.1 → XP_054182694.1  histone lysine demethylase PHF8 isoform X1

    3. XM_054326721.1 → XP_054182696.1  histone lysine demethylase PHF8 isoform X2

      UniProtKB/Swiss-Prot
      B3KMV4, B7Z911, Q5H9U5, Q5JPR9, Q5JPS0, Q5JPS2, Q5JPS3, Q5VUJ4, Q7Z6D4, Q9HAH2, Q9UPP1

    4. XM_054326724.1 → XP_054182699.1  histone lysine demethylase PHF8 isoform X4

    5. XM_054326722.1 → XP_054182697.1  histone lysine demethylase PHF8 isoform X3

      UniProtKB/TrEMBL
      H0Y3N9

    6. XM_054326723.1 → XP_054182698.1  histone lysine demethylase PHF8 isoform X3

      UniProtKB/TrEMBL
      H0Y3N9

    7. XM_054326726.1 → XP_054182701.1  histone lysine demethylase PHF8 isoform X6

    8. XM_054326725.1 → XP_054182700.1  histone lysine demethylase PHF8 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UPP1.3 GenPept UniProtKB/Swiss-Prot:Q9UPP1

    Gene LinkOut

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