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Aliases for PNKP Gene

Aliases for PNKP Gene

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

External Ids for PNKP Gene

Previous GeneCards Identifiers for PNKP Gene

  • GC19M051022
  • GC19M050732
  • GC19M055040
  • GC19M055056
  • GC19M050364
  • GC19M046740

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 Ataxia-Oculomotor Apraxia 4 and Microcephaly, Seizures, And Developmental Delay. Among its related pathways are DNA damage_NHEJ mechanisms of DSBs repair 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

Regulatory Elements for PNKP Gene

Enhancers for PNKP Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

Enhancers around PNKP on UCSC Golden Path with GeneCards custom track

Promoters for PNKP Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for PNKP Gene

Chromosome:
19
Start:
49,859,882 bp from pter
End:
49,878,351 bp from pter
Size:
18,470 bases
Orientation:
Minus strand

Genomic View for PNKP Gene

Genes around PNKP on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PNKP Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PNKP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PNKP Gene

Proteins for PNKP Gene

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

    Protein Symbol:
    Q96T60-PNKP_HUMAN
    Recommended name:
    Bifunctional polynucleotide phosphatase/kinase
    Protein Accession:
    Q96T60
    Secondary Accessions:
    • Q9BUL2
    • Q9P1V2
    • Q9UKU8
    • Q9UNF8
    • Q9UNI0

    Protein attributes for PNKP Gene

    Size:
    521 amino acids
    Molecular mass:
    57076 Da
    Quaternary structure:
    • Monomer.
    SequenceCaution:
    • 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

    UniProtKB/Swiss-Prot:

neXtProt entry for PNKP Gene

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 & Families for PNKP Gene

Gene Families for PNKP Gene

Suggested Antigen Peptide Sequences for PNKP Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96T60

UniProtKB/Swiss-Prot:

PNKP_HUMAN :
  • 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.
  • In the N-terminal section; belongs to the DNA 3 phosphatase family.
Domain:
  • 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.
  • Contains 1 FHA domain.
Family:
  • In the N-terminal section; belongs to the DNA 3 phosphatase family.
genes like me logo Genes that share domains with PNKP: view

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

Human Phenotype Ontology for PNKP Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for PNKP Gene

miRTarBase miRNAs that target PNKP

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PNKP

Flow Cytometry Products

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

Localization for PNKP Gene

Subcellular locations from UniProtKB/Swiss-Prot for PNKP Gene

Subcellular locations from

COMPARTMENTS
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:0005739 mitochondrion IEA --
GO:0016020 membrane IDA 19946888
genes like me logo Genes that share ontologies with PNKP: view

Pathways & Interactions for PNKP Gene

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

Pathways by source for PNKP Gene

1 GeneGo (Thomson Reuters) pathway for PNKP Gene
1 Qiagen pathway for PNKP Gene

SIGNOR curated interactions for PNKP Gene

Is activated by:

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 IGI 10446192
GO:0006979 response to oxidative stress IDA 10446192
GO:0009314 response to radiation TAS 10446192
genes like me logo Genes that share ontologies with PNKP: view

Drugs & Compounds for PNKP Gene

(5) Drugs for PNKP Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Adenosine triphosphate Approved Nutra 0

(5) Additional Compounds for PNKP Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
Phosphate
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
14265-44-2
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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PNKP

Flow Cytometry Products

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: - - - - - - -
SP7:
SP8: - - -
SP9: - -

ExUns: 17 ^ 18
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for PNKP Gene

GeneLoc Exon Structure for
PNKP
ECgene alternative splicing isoforms for
PNKP

Expression for PNKP Gene

mRNA expression in normal human tissues for PNKP Gene

Protein differential expression in normal tissues from HIPED for PNKP Gene

This gene is overexpressed in Heart (15.5), Lymph node (11.2), and Peripheral blood mononuclear cells (9.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PNKP Gene



Protein tissue co-expression partners for PNKP Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PNKP Gene:

PNKP

SOURCE GeneReport for Unigene cluster for PNKP Gene:

Hs.78016

mRNA Expression by UniProt/SwissProt for PNKP Gene:

Q96T60-PNKP_HUMAN
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 expression patterns with PNKP: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PNKP Gene

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
cow
(Bos Taurus)
Mammalia PNKP 34
  • 86.53 (n)
  • 83.42 (a)
PNKP 35
  • 85 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PNKP 34
  • 84.84 (n)
  • 86.56 (a)
PNKP 35
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pnkp 34
  • 79.55 (n)
  • 81.35 (a)
Pnkp 16
Pnkp 35
  • 81 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PNKP 34
  • 98.82 (n)
  • 98.96 (a)
PNKP 35
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pnkp 34
  • 80.45 (n)
  • 81.54 (a)
oppossum
(Monodelphis domestica)
Mammalia PNKP 35
  • 64 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PNKP 35
  • 76 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PNKP 35
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pnkp 34
  • 58.19 (n)
  • 56.75 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.13565 34
zebrafish
(Danio rerio)
Actinopterygii pnkp 34
  • 59.62 (n)
  • 57.29 (a)
pnkp 35
  • 47 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5541 34
fruit fly
(Drosophila melanogaster)
Insecta CG9601 36
  • 40 (a)
CG9601 34
  • 48.86 (n)
  • 41.88 (a)
CG9601 35
  • 37 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F21D5.5 36
  • 45 (a)
F21D5.5 34
  • 47.57 (n)
  • 46.22 (a)
F21D5.5 35
  • 41 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HNT3 35
  • 7 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU08151 34
  • 50.15 (n)
  • 40.84 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes pnk1 34
  • 44.8 (n)
  • 37.94 (a)
Species where no ortholog for PNKP was found in the sources mined by GeneCards:
  • 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

ENSEMBL:
Gene Tree for PNKP (if available)
TreeFam:
Gene Tree for PNKP (if available)

Paralogs for PNKP Gene

Paralogs for PNKP Gene

(1) 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
rs3739168 - 49,867,147(-) GAGCG(A/C/T)CCCCC reference, missense
rs3739173 - 49,866,409(-) AGTGG(C/T)AGTGA reference, missense
rs3739185 - 49,864,364(-) CCACA(A/C/T)GCTCT reference, missense
rs3739186 - 49,864,229(-) TCTTG(A/T)ACCCA reference, missense
rs3739206 - 49,861,464(-) CATGG(G/T)CATGT reference, missense

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

Variant ID Type Subtype PubMed ID
dgv53n68 CNV loss 17160897
dgv54n68 CNV loss 17160897
esv2677406 CNV deletion 23128226
esv3644628 CNV gain 21293372
esv3644629 CNV loss 21293372
nsv1140251 OTHER inversion 24896259
nsv524068 CNV loss 19592680
nsv526372 CNV loss 19592680
nsv953600 CNV deletion 24416366
nsv9739 CNV gain+loss 18304495

Variation tolerance for PNKP Gene

Residual Variation Intolerance Score: 65.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.73; 57.59% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PNKP Gene

Human Gene Mutation Database (HGMD)
PNKP
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PNKP

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PNKP Gene

Disorders for PNKP Gene

MalaCards: The human disease database

(6) MalaCards diseases for PNKP Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
ataxia-oculomotor apraxia 4
  • ataxia-oculomotor apraxia type 4
microcephaly, seizures, and developmental delay
  • epileptic encephalopathy, early infantile, 10
ohtahara syndrome
  • epileptic encephalopathy, early infantile, 15
apraxia
  • dyspraxia
microcephaly
  • microcephalus
- elite association - COSMIC cancer census association via MalaCards
Search PNKP in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PNKP_HUMAN
  • Ataxia-oculomotor apraxia 4 (AOA4) [MIM:616267]: An autosomal recessive disease characterized by cerebellar ataxia, oculomotor apraxia, areflexia and peripheral neuropathy. {ECO:0000269 PubMed:25728773}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 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, ECO:0000269 PubMed:27232581}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PNKP

Genetic Association Database (GAD)
PNKP
Human Genome Epidemiology (HuGE) Navigator
PNKP
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PNKP
genes like me logo Genes that share disorders with PNKP: view

No data available for Genatlas for PNKP Gene

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 22 65
  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 22 65
  3. 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 22 46 65
  4. Molecular characterization of a human DNA kinase. (PMID: 10446193) Karimi-Busheri F. … Weinfeld M. (J. Biol. Chem. 1999) 2 3 4 65
  5. Mutations in PNKP cause recessive ataxia with oculomotor apraxia type 4. (PMID: 25728773) Bras J. … Guerreiro R. (Am. J. Hum. Genet. 2015) 3 4 65

Products for PNKP Gene

Sources for PNKP Gene

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