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

Gene ID: 23133, updated on 11-Jul-2019

Summary

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
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

Genomic context

See PHF8 in Genome Data Viewer
Location:
Xp11.22
Exon count:
28
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (53936680..54048935, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (53963113..54075368, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein S18C pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 505 Neighboring gene family with sequence similarity 120C Neighboring gene ribosomal protein L37 pseudogene 24 Neighboring gene WNK lysine deficient protein kinase 3 Neighboring gene ribosomal protein L7a pseudogene 71

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Siderius X-linked mental retardation syndrome
MedGen: C1846055 OMIM: 300263 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-09-20)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-09-20)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Cell Cycle, organism-specific biosystem (from REACTOME)
    Cell Cycle, organism-specific biosystem
    Cell Cycle
  • Cell Cycle, Mitotic, organism-specific biosystem (from REACTOME)
    Cell Cycle, Mitotic, organism-specific biosystemThe replication of the genome and the subsequent segregation of chromosomes into daughter cells are controlled by a series of events collectively known as the cell cycle. DNA replication is carried o...
  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Condensation of Prophase Chromosomes, organism-specific biosystem (from REACTOME)
    Condensation of Prophase Chromosomes, organism-specific biosystemIn mitotic prophase, the action of the condensin II complex enables initial chromosome condensation.The condensin II complex subunit NCAPD3 binds monomethylated histone H4 (H4K20me1), thereby associa...
  • Ectoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Ectoderm Differentiation, organism-specific biosystemModel depicting ectoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
    HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
  • M Phase, organism-specific biosystem (from REACTOME)
    M Phase, organism-specific biosystemMitosis, or the M phase, involves nuclear division and cytokinesis, where two identical daughter cells are produced. Mitosis involves prophase, prometaphase, metaphase, anaphase, and telophase. Fin...
  • Mitotic Prophase, organism-specific biosystem (from REACTOME)
    Mitotic Prophase, organism-specific biosystemDuring prophase, the chromatin in the nucleus condenses, and the nucleolus disappears. Centrioles begin moving to the opposite poles or sides of the cell. Some of the fibers that extend from the cen...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1111, DKFZp686E0868

Gene Ontology Provided by GOA

Process Evidence Code Pubs
G1/S transition of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
brain development ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K27 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K36 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H4-K20 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of chromatin silencing at rDNA IDA
Inferred from Direct Assay
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase I IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
nuclear membrane IDA
Inferred from Direct Assay
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IC
Inferred by Curator
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone lysine demethylase PHF8
Names
jumonji C domain-containing histone demethylase 1F
NP_001171825.1
NP_001171826.1
NP_001171827.1
NP_055922.1
XP_005262053.1
XP_005262054.1
XP_005262056.1
XP_005262057.1
XP_011529080.1
XP_016884850.1
XP_016884851.1

NCBI Reference Sequences (RefSeq)

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
    5963..113457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001184896.1NP_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
    Q9UPP1
    Related
    ENSP00000350676.5, ENST00000357988.9
    Conserved Domains (3) summary
    smart00558
    Location:235298
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:4293
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:270370
    cupin_like; Conserved domain found in cupin and related proteins
  2. NM_001184897.1NP_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, AL732374, BC053861, BE676640
    Consensus CDS
    CCDS55418.1
    UniProtKB/Swiss-Prot
    Q9UPP1
    Related
    ENSP00000340051.6, ENST00000338946.10
    Conserved Domains (3) summary
    smart00558
    Location:199262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:657
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:234334
    cupin_like; Conserved domain found in cupin and related proteins
  3. NM_001184898.2NP_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
    O95327
    Related
    ENSP00000319473.8, ENST00000322659.12
    Conserved Domains (3) summary
    smart00558
    Location:199262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:657
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:234334
    cupin_like; Conserved domain found in cupin and related proteins
  4. NM_015107.3NP_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/Swiss-Prot
    Q9UPP1
    Related
    ENSP00000338868.6, ENST00000338154.10
    Conserved Domains (3) summary
    smart00558
    Location:199262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:657
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:234334
    cupin_like; Conserved domain found in cupin and related proteins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    53936680..54048935 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for XP_005262053.1

    Conserved Domains (3) summary
    smart00558
    Location:235298
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:4293
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:270370
    cupin_like; Conserved domain found in cupin and related proteins
  2. XM_005262000.1XP_005262057.1  histone lysine demethylase PHF8 isoform X4

    Conserved Domains (3) summary
    smart00558
    Location:235298
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:4293
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:270370
    cupin_like; Conserved domain found in cupin and related proteins
  3. XM_011530778.1XP_011529080.1  histone lysine demethylase PHF8 isoform X1

    See identical proteins and their annotated locations for XP_011529080.1

    Conserved Domains (3) summary
    smart00558
    Location:235298
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:4293
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:270370
    cupin_like; Conserved domain found in cupin and related proteins
  4. XM_005261997.4XP_005262054.1  histone lysine demethylase PHF8 isoform X2

    See identical proteins and their annotated locations for XP_005262054.1

    Conserved Domains (3) summary
    smart00558
    Location:199262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:657
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:234334
    cupin_like; Conserved domain found in cupin and related proteins
  5. XM_017029361.2XP_016884850.1  histone lysine demethylase PHF8 isoform X2

    Conserved Domains (3) summary
    smart00558
    Location:199262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:657
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:234334
    cupin_like; Conserved domain found in cupin and related proteins
  6. XM_005261999.1XP_005262056.1  histone lysine demethylase PHF8 isoform X2

    See identical proteins and their annotated locations for XP_005262056.1

    Related
    ENSP00000379578.2, ENST00000396282.6
    Conserved Domains (3) summary
    smart00558
    Location:199262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:657
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:234334
    cupin_like; Conserved domain found in cupin and related proteins
  7. XM_017029362.2XP_016884851.1  histone lysine demethylase PHF8 isoform X3

    UniProtKB/Swiss-Prot
    Q9UPP1
    Conserved Domains (3) summary
    smart00558
    Location:199262
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd15642
    Location:657
    PHD_PHF8; PHD finger found in histone lysine demethylase PHF8
    cl21464
    Location:234334
    cupin_like; Conserved domain found in cupin and related proteins
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