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

Gene ID: 23133, updated on 3-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. X-linked mental retardation associated with cleft lip/palate maps to Xp11.3-q21.3. Siderius LE, et al. Am J Med Genet, 1999 Jul 30. PMID 10398231
  2. PHF8 Plays an Oncogene Function in Hepatocellular Carcinoma Formation. Ye H, et al. Oncol Res, 2019 May 7. PMID 30764899, Free PMC Article
  3. Histone demethylase PHF8 promotes cell growth and metastasis of non-small-cell lung cancer through activating Wnt/β-catenin signaling pathway. Hu Y, et al. Histol Histopathol, 2021 Aug. PMID 34100557
  4. 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
  5. PIP2 epigenetically represses rRNA genes transcription interacting with PHF8. Ulicna L, et al. Biochim Biophys Acta Mol Cell Biol Lipids, 2018 Mar. PMID 29246768

See all (116) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. The histone demethylase PHF8 regulates TGFbeta signaling and promotes melanoma metastasis.
    Title: The histone demethylase PHF8 regulates TGFβ signaling and promotes melanoma metastasis.
  7. 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.
  8. 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.
  9. 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.
  10. MYC Regulates PHF8, Which Promotes the Progression of Gastric Cancer by Suppressing miR-22-3p.
    Title: MYC Regulates PHF8, Which Promotes the Progression of Gastric Cancer by Suppressing miR-22-3p.
Submit: New GeneRIF Correction See all GeneRIFs (47)

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
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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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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

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