Seroatlas · Human Serome Atlas

PNKP

Bifunctional polynucleotide phosphatase/kinase

Also known as: PNK, PNKP_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
Q96T60
Gene
PNKP
Ensembl
ENSG00000039650
Chromosome
19
Canonical length
521 aa
Protein class
Disease related genes, Enzymes, Human disease related genes, Metabolic proteins, Potential drug targets, Predicted intracellular proteins
Subcellular location
Nucleoplasm,Nucleoli

OverviewNCBI Gene

This locus represents a gene involved in DNA repair. In response to ionizing radiation or oxidative damage, the protein encoded by this locus catalyzes 5' phosphorylation and 3' dephosphorylation of nucleic acids. Mutations at this locus have been associated with microcephaly, seizures, and developmental delay.[provided by RefSeq, Sep 2010]

Canonical amino-acid sequenceUniProt

521 residues, UniProt reviewed canonical sequence.

>Q96T60|PNKP
     1  MGEVEAPGRL WLESPPGGAP PIFLPSDGQA LVLGRGPLTQ VTDRKCSRTQ VELVADPETR
    61  TVAVKQLGVN PSTTGTQELK PGLEGSLGVG DTLYLVNGLH PLTLRWEETR TPESQPDTPP
   121  GTPLVSQDEK RDAELPKKRM RKSNPGWENL EKLLVFTAAG VKPQGKVAGF DLDGTLITTR
   181  SGKVFPTGPS DWRILYPEIP RKLRELEAEG YKLVIFTNQM SIGRGKLPAE EFKAKVEAVV
   241  EKLGVPFQVL VATHAGLYRK PVTGMWDHLQ EQANDGTPIS IGDSIFVGDA AGRPANWAPG
   301  RKKKDFSCAD RLFALNLGLP FATPEEFFLK WPAAGFELPA FDPRTVSRSG PLCLPESRAL
   361  LSASPEVVVA VGFPGAGKST FLKKHLVSAG YVHVNRDTLG SWQRCVTTCE TALKQGKRVA
   421  IDNTNPDAAS RARYVQCARA AGVPCRCFLF TATLEQARHN NRFREMTDSS HIPVSDMVMY
   481  GYRKQFEAPT LAEGFSAILE IPFRLWVEPR LGRLYCQFSE G

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PNKP 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)
0.3
Highest tissue expression
46 nTPM

Expression across tissuesHPA

Tissue

  • adrenal gland: 46 nTPM
  • spleen: 38 nTPM
  • pituitary gland: 38 nTPM
  • kidney: 33 nTPM
  • thyroid gland: 32 nTPM
  • pancreas: 29 nTPM

Single-cell type

  • epididymal principal cells: 291 nCPM
  • adrenal cortex cells: 139 nCPM
  • breast lactating cells: 77 nCPM
  • leydig cells: 76 nCPM
  • syncytiotrophoblasts: 73 nCPM
  • parietal cells: 73 nCPM

Immune cell

  • neutrophil: 24 nTPM
  • non-classical monocyte: 18 nTPM
  • eosinophil: 17 nTPM
  • classical monocyte: 12 nTPM
  • naive B-cell: 12 nTPM
  • intermediate monocyte: 12 nTPM

Brain region

  • choroid plexus: 40 nTPM
  • cerebral cortex: 22 nTPM
  • hippocampal formation: 19 nTPM
  • pons: 19 nTPM
  • midbrain: 19 nTPM
  • medulla oblongata: 18 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PNKP.

Disease | AllUniProt

Conditions PNKP is implicated in, by any mechanism.

  • Microcephaly, seizures, and developmental delay (MCSZ) MIM:613402
  • Ataxia-oculomotor apraxia 4 (AOA4) MIM:616267

Disease | GeneticClinVar

145 pathogenic / likely-pathogenic of 1,270 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

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)
1.21
gnomAD pLI
0
gnomAD missense Z
-1.31
DepMap mean gene effect
-0.4
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% 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 PNKP 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 PNKP as an antibody target. Whether an autoantibody or antibody against PNKP could matter depends on whether native PNKP is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PNKP 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 PNKP as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PNKP. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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