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Aliases for PNKP Gene

Aliases for PNKP Gene

  • Polynucleotide Kinase 3'-Phosphatase 2
  • Polynucleotide Kinase 3-Phosphatase 2 3
  • DNA 5-Kinase/3-Phosphatase 3 4
  • EIEE10 3 6
  • MCSZ 3 6
  • PNK 3 6
  • Homo Sapiens Polynucleotide Kinase 3-Phosphatase (PNKP) 3
  • Bifunctional Polynucleotide Phosphatase/Kinase 3
  • Polynucleotide Kinase-3-Phosphatase 4
  • AOA4 3

External Ids for PNKP Gene

Summaries for PNKP Gene

Entrez Gene Summary for PNKP 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]

GeneCards Summary for PNKP Gene

PNKP (Polynucleotide Kinase 3'-Phosphatase) is a Protein Coding gene. Diseases associated with PNKP include microcephaly, seizures, and developmental delay and doid:4019. Among its related pathways are Cell Cycle / Checkpoint Control and Chks in Checkpoint Regulation. GO annotations related to this gene include double-stranded DNA binding and endonuclease activity. An important paralog of this gene is APTX.

UniProtKB/Swiss-Prot for PNKP Gene

  • Plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3-phosphates from, or by phosphorylating 5-hydroxyl groups on, the ribose sugar of the DNA backbone.

Gene Wiki entry for PNKP Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PNKP Gene

Genomics for PNKP Gene

Genomic Location for PNKP Gene

49,861,203 bp from pter
49,867,909 bp from pter
6,707 bases
Minus strand

Genomic View for PNKP Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PNKP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PNKP Gene

Regulatory Elements for PNKP Gene

Proteins for PNKP Gene

  • Protein details for PNKP Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Bifunctional polynucleotide phosphatase/kinase
    Protein Accession:
    Secondary Accessions:
    • Q9BUL2
    • Q9P1V2
    • Q9UKU8
    • Q9UNF8
    • Q9UNI0

    Protein attributes for PNKP Gene

    521 amino acids
    Molecular mass:
    57076 Da
    Quaternary structure:
    • Monomer.
    • Sequence=AAD47379.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PNKP Gene

    Alternative splice isoforms for PNKP Gene


neXtProt entry for PNKP Gene

Proteomics data for PNKP Gene at MOPED

Post-translational modifications for PNKP Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PNKP Gene

Domains for PNKP Gene


  • The FHA domain binds threonine-phosphorylated peptides from XRCC1/4, and is responsible for the recruitment of PNKP to the sites of DNA repair. The affinity is ten times greater if peptides are also phosphorylated on the serine preceeding the phosphothreonine.:
    • Q96T60
  • Contains 1 FHA domain.:
    • Q96T60
  • In the N-terminal section; belongs to the DNA 3 phosphatase family.:
    • Q96T60
genes like me logo Genes that share domains with PNKP: view

No data available for Gene Families for PNKP Gene

Function for PNKP Gene

Molecular function for PNKP Gene

GENATLAS Biochemistry: polynucleotide kinase-3 phosphatase,facilitating DNA repair of DNA strand breaks caused by oxidative damage
UniProtKB/Swiss-Prot CatalyticActivity: A 3-phosphopolynucleotide + H(2)O = a polynucleotide + phosphate
UniProtKB/Swiss-Prot CatalyticActivity: ATP + 5-dephospho-DNA = ADP + 5-phospho-DNA
UniProtKB/Swiss-Prot Function: Plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3-phosphates from, or by phosphorylating 5-hydroxyl groups on, the ribose sugar of the DNA backbone.

Gene Ontology (GO) - Molecular Function for PNKP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003684 damaged DNA binding NAS 10446193
GO:0003690 double-stranded DNA binding TAS 10446193
GO:0004519 endonuclease activity NAS 10446192
GO:0005515 protein binding IPI 19155274
GO:0005524 ATP binding NAS 10446192
genes like me logo Genes that share ontologies with PNKP: view

Phenotypes for PNKP Gene

GenomeRNAi human phenotypes for PNKP:
genes like me logo Genes that share phenotypes with PNKP: view

miRNA for PNKP Gene

miRTarBase miRNAs that target PNKP

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for PNKP Gene

Localization for PNKP Gene

Subcellular locations from UniProtKB/Swiss-Prot for PNKP Gene

Subcellular locations from

Jensen Localization Image for PNKP Gene COMPARTMENTS Subcellular localization image for PNKP gene
Compartment Confidence
nucleus 5
cytosol 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for PNKP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 10446193
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
GO:0016020 membrane IDA 19946888
genes like me logo Genes that share ontologies with PNKP: view

Pathways for PNKP Gene

genes like me logo Genes that share pathways with PNKP: view

Pathways by source for PNKP Gene

1 GeneGo (Thomson Reuters Life Sciences Research) pathway for PNKP Gene
1 Qiagen pathway for PNKP Gene
2 Cell Signaling Technology pathways for PNKP Gene

Gene Ontology (GO) - Biological Process for PNKP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000718 nucleotide-excision repair, DNA damage removal NAS 10446193
GO:0006261 DNA-dependent DNA replication NAS 10446192
GO:0006281 DNA repair TAS --
GO:0006284 base-excision repair TAS --
GO:0006979 response to oxidative stress IDA 10446192
genes like me logo Genes that share ontologies with PNKP: view

Compounds for PNKP Gene

(4) HMDB Compounds for PNKP Gene

Compound Synonyms Cas Number PubMed IDs
Adenosine triphosphate
  • 5'-(tetrahydrogen triphosphate) Adenosine
  • adenosindiphosphorsaeure
  • NFB Orthophosphate
  • Dihydrogen oxide

(5) Novoseek inferred chemical compound relationships for PNKP Gene

Compound -log(P) Hits PubMed IDs
polynucleotide 93.6 21
phosphonate 79.1 7
atp 27.5 3
adenylate 14.4 1
oxygen 0 1
genes like me logo Genes that share compounds with PNKP: view

Transcripts for PNKP Gene

Unigene Clusters for PNKP Gene

Polynucleotide kinase 3-phosphatase:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PNKP Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b · 4c · 4d ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^
SP1: - - - -
SP2: - - - - -
SP3: -
SP4: -
SP5: - -
SP6: - - - - - - -
SP8: - - -
SP9: - -

ExUns: 17 ^ 18

Relevant External Links for PNKP Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PNKP Gene

mRNA expression in normal human tissues for PNKP Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for PNKP Gene

SOURCE GeneReport for Unigene cluster for PNKP Gene Hs.78016

mRNA Expression by UniProt/SwissProt for PNKP Gene

Tissue specificity: Expressed in many tissues with highest expression in spleen and testis, and lowest expression in small intestine (PubMed:10446192). Expressed in higher amount in pancreas, heart and kidney and at lower levels in brain, lung and liver (PubMed:10446193).
genes like me logo Genes that share expressions with PNKP: view

Orthologs for PNKP Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PNKP Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PNKP 36
  • 98.82 (n)
  • 98.96 (a)
  • 99 (a)
(Bos Taurus)
Mammalia PNKP 36
  • 86.53 (n)
  • 83.42 (a)
  • 85 (a)
(Canis familiaris)
Mammalia PNKP 36
  • 84.84 (n)
  • 86.56 (a)
  • 87 (a)
(Mus musculus)
Mammalia Pnkp 36
  • 79.55 (n)
  • 81.35 (a)
Pnkp 16
Pnkp 37
  • 81 (a)
(Monodelphis domestica)
Mammalia PNKP 37
  • 64 (a)
(Ornithorhynchus anatinus)
Mammalia PNKP 37
  • 76 (a)
(Rattus norvegicus)
Mammalia Pnkp 36
  • 80.45 (n)
  • 81.54 (a)
(Anolis carolinensis)
Reptilia PNKP 37
  • 53 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.13565 36
tropical clawed frog
(Silurana tropicalis)
Amphibia pnkp 36
  • 58.19 (n)
  • 56.75 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5541 36
(Danio rerio)
Actinopterygii pnkp 36
  • 59.62 (n)
  • 57.29 (a)
pnkp 37
  • 47 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG9601 36
  • 48.86 (n)
  • 41.88 (a)
CG9601 37
  • 37 (a)
CG9601 38
  • 40 (a)
(Caenorhabditis elegans)
Secernentea F21D5.5 36
  • 47.57 (n)
  • 46.22 (a)
F21D5.5 37
  • 41 (a)
F21D5.5 38
  • 45 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HNT3 37
  • 7 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU08151 36
  • 50.15 (n)
  • 40.84 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes pnk1 36
  • 44.8 (n)
  • 37.94 (a)
Species with no ortholog for PNKP:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PNKP Gene

Gene Tree for PNKP (if available)
Gene Tree for PNKP (if available)

Paralogs for PNKP Gene

Paralogs for PNKP Gene

Selected SIMAP similar genes for PNKP Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with PNKP: view

Variants for PNKP Gene

Sequence variations from dbSNP and Humsavar for PNKP Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type MAF
rs1290647 -- 49,862,907(+) TCCCC(A/C/T)CTCCG intron-variant
rs1290648 -- 49,863,106(+) CTTAG(A/G)GCCAG intron-variant
rs1290649 Likely benign 49,865,104(+) CTCCC(A/T)CAGCC intron-variant
rs2125346 -- 49,868,203(+) GGGGT(G/T)TCACC upstream-variant-2KB
rs2257103 -- 49,866,809(+) ATTTC(C/T)CGATG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PNKP Gene

Variant ID Type Subtype PubMed ID
nsv9739 CNV Gain+Loss 18304495
nsv912269 CNV Loss 21882294
dgv53n68 CNV Loss 17160897
nsv912272 CNV Loss 21882294
dgv3974n71 CNV Loss 21882294
dgv54n68 CNV Loss 17160897
nsv526372 CNV Loss 19592680
nsv524068 CNV Loss 19592680
esv2677406 CNV Deletion 23128226

Relevant External Links for PNKP Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

Disorders for PNKP Gene

(1) OMIM Diseases for PNKP Gene (605610)


  • Microcephaly, seizures, and developmental delay (MCSZ) [MIM:613402]: A disease characterized by infantile-onset seizures, microcephaly, severe intellectual disability and delayed motor milestones with absent speech or only achieving a few words. Most patients also have behavioral problems with hyperactivity. Microcephaly is progressive and without neuronal migration or structural abnormalities, consistent with primary microcephaly. {ECO:0000269 PubMed:20118933}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for PNKP Gene

Relevant External Links for PNKP

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with PNKP: view

Publications for PNKP Gene

  1. Molecular cloning of the human gene, PNKP, encoding a polynucleotide kinase 3'-phosphatase and evidence for its role in repair of DNA strand breaks caused by oxidative damage. (PMID: 10446192) Jilani A. … Lasko D.D. (J. Biol. Chem. 1999) 2 3 4 23
  2. Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK. (PMID: 19155274) Ali A.A. … Oliver A.W. (Nucleic Acids Res. 2009) 3 4 23
  3. Molecular characterization of a human DNA kinase. (PMID: 10446193) Karimi-Busheri F. … Weinfeld M. (J. Biol. Chem. 1999) 2 3 4
  4. Polynucleotide kinase 3' phosphatase variant, dietary variables and risk of adenoma recurrence in the Polyp Prevention Trial. (PMID: 18414202) Murphy G. … Lanza E. (Eur. J. Cancer Prev. 2008) 3 23 49
  5. Mutations in PNKP cause microcephaly, seizures and defects in DNA repair. (PMID: 20118933) Shen J. … Walsh C.A. (Nat. Genet. 2010) 3 4

Products for PNKP Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • DNA Damage Signaling Pathway in human,mouse,rat
    • DNA Repair in human,mouse,rat
    • Nitric Oxide Signaling Pathway in human,mouse,rat
    • Oxidative Stress in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate PNKP
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for PNKP
    • Block miRNA regulation of PNKP using miScript Target Protectors
    • Addgene plasmids for PNKP

    Sources for PNKP Gene

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