Seroatlas · Human Serome Atlas

PHF8

Histone lysine demethylase PHF8

Also known as: JHDM1F, KDM7B, KIAA1111, PHF8_HUMAN, ZNF422

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9UPP1
Gene: PHF8
Ensembl: ENSG00000172943
Chromosome: X
Canonical length: 1060 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Potential drug targets, Predicted intracellular proteins
Subcellular location: Nucleoplasm

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

1060 residues, UniProt reviewed canonical sequence.

>Q9UPP1|PHF8
     1  MNRSRAIVQR GRVLPPPAPL DTTNLAGRRT LQGRAKMASV PVYCLCRLPY DVTRFMIECD
    61  MCQDWFHGSC VGVEEEKAAD IDLYHCPNCE VLHGPSIMKK RRGSSKGHDT HKGKPVKTGS
   121  PTFVRELRSR TFDSSDEVIL KPTGNQLTVE FLEENSFSVP ILVLKKDGLG MTLPSPSFTV
   181  RDVEHYVGSD KEIDVIDVTR QADCKMKLGD FVKYYYSGKR EKVLNVISLE FSDTRLSNLV
   241  ETPKIVRKLS WVENLWPEEC VFERPNVQKY CLMSVRDSYT DFHIDFGGTS VWYHVLKGEK
   301  IFYLIRPTNA NLTLFECWSS SSNQNEMFFG DQVDKCYKCS VKQGQTLFIP TGWIHAVLTP
   361  VDCLAFGGNF LHSLNIEMQL KAYEIEKRLS TADLFRFPNF ETICWYVGKH ILDIFRGLRE
   421  NRRHPASYLV HGGKALNLAF RAWTRKEALP DHEDEIPETV RTVQLIKDLA REIRLVEDIF
   481  QQNVGKTSNI FGLQRIFPAG SIPLTRPAHS TSVSMSRLSL PSKNGSKKKG LKPKELFKKA
   541  ERKGKESSAL GPAGQLSYNL MDTYSHQALK TGSFQKAKFN ITGACLNDSD DDSPDLDLDG
   601  NESPLALLMS NGSTKRVKSL SKSRRTKIAK KVDKARLMAE QVMEDEFDLD SDDELQIDER
   661  LGKEKATLII RPKFPRKLPR AKPCSDPNRV REPGEVEFDI EEDYTTDEDM VEGVEGKLGN
   721  GSGAGGILDL LKASRQVGGP DYAALTEAPA SPSTQEAIQG MLCMANLQSS SSSPATSSLQ
   781  AWWTGGQDRS SGSSSSGLGT VSNSPASQRT PGKRPIKRPA YWRTESEEEE ENASLDEQDS
   841  LGACFKDAEY IYPSLESDDD DPALKSRPKK KKNSDDAPWS PKARVTPTLP KQDRPVREGT
   901  RVASIETGLA AAAAKLAQQE LQKAQKKKYI KKKPLLKEVE QPRPQDSNLS LTVPAPTVAA
   961  TPQLVTSSSP LPPPEPKQEA LSGSLADHEY TARPNAFGMA QANRSTTPMA PGVFLTQRRP
  1021  SVGSQSNQAG QGKRPKKGLA TAKQRLGRIL KIHRNGKLLL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PHF8 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.53
Highest tissue expression: 33 nTPM

Expression across tissuesHPA

Tissue

epididymis: 33 nTPM
testis: 31 nTPM
thymus: 13 nTPM
seminal vesicle: 13 nTPM
liver: 12 nTPM
tonsil: 12 nTPM

Single-cell type

choroid plexus epithelial cells: 119 nCPM
undifferentiated spermatogonia: 116 nCPM
early primary spermatocytes: 101 nCPM
epididymal principal cells: 96 nCPM
renal collecting duct intercalated cells: 90 nCPM
sertoli cells: 86 nCPM

Immune cell

basophil: 6.5 nTPM
T-reg: 5.6 nTPM
MAIT T-cell: 5.3 nTPM
intermediate monocyte: 5 nTPM
neutrophil: 4.3 nTPM
eosinophil: 4.2 nTPM

Brain region

choroid plexus: 40 nTPM
white matter: 25 nTPM
cerebral cortex: 23 nTPM
basal ganglia: 22 nTPM
pons: 21 nTPM
thalamus: 21 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PHF8.

Disease | AllUniProt

Conditions PHF8 is implicated in, by any mechanism.

Intellectual developmental disorder, X-linked, syndromic, Siderius type (MRXSSD) MIM:300263

Disease | GeneticClinVar

30 pathogenic / likely-pathogenic of 375 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Syndromic X-linked intellectual disability Siderius type
Intellectual disability
Inborn genetic diseases
PHF8-related disorder

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.26
gnomAD pLI: 1
gnomAD missense Z: 3.98
DepMap mean gene effect: -0.09
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PHF8 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PHF8 as an antibody target. Whether an autoantibody or antibody against PHF8 could matter depends on whether native PHF8 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PHF8 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label PHF8 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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