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PNKP Gene

protein-coding   GIFtS: 65
GCID: GC19M050364

Polynucleotide Kinase 3'-Phosphatase

  See PNKP-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Polynucleotide Kinase 3'-Phosphatase1 2     PNK2 5
DNA 5'-Kinase/3'-Phosphatase2 3     Bifunctional Polynucleotide Phosphatase/Kinase2
EIEE102 5     Homo Sapiens Polynucleotide Kinase 3'-Phosphatase (PNKP)2
MCSZ2 5     Polynucleotide Kinase-3'-Phosphatase3

External Ids:    HGNC: 91541   Entrez Gene: 112842   Ensembl: ENSG000000396507   OMIM: 6056105   UniProtKB: Q96T603   

Export aliases for PNKP gene to outside databases

Previous GC identifers: GC19M051022 GC19M050732 GC19M055040 GC19M055056 GC19M046740


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 ohtahara syndrome. 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: PNKP_HUMAN, Q96T60
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 Wiki entry for PNKP Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NC_018930.2  NT_011109.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the PNKP gene promoter:
         p53   Sp1   SREBP-1c   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): PNKP promoter sequence
   Search Chromatin IP Primers for PNKP

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PNKP


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.3-q13.4   Ensembl cytogenetic band:  19q13.33   HGNC cytogenetic band: 19q13.3-q13.4

PNKP Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PNKP gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M050364:  view genomic region     (about GC identifiers)

Start:
50,364,460 bp from pter      End:
50,371,166 bp from pter
Size:
6,707 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: PNKP_HUMAN, Q96T60 (See protein sequence)
Recommended Name: Bifunctional polynucleotide phosphatase/kinase  
Size: 521 amino acids; 57076 Da
Subunit: Monomer (By similarity)
Sequence caution: Sequence=AAD47379.1; Type=Frameshift; Positions=Several;
2 PDB 3D structures from and Proteopedia for PNKP:
2BRF (3D)        2W3O (3D)    
Secondary accessions: Q9P1V2 Q9UKU8 Q9UNF8 Q9UNI0

Explore the universe of human proteins at neXtProt for PNKP: NX_Q96T60

Explore proteomics data for PNKP at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See PNKP Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_009185.2  
    ENSEMBL proteins: 
     ENSP00000323511   ENSP00000472300   ENSP00000468896   ENSP00000473137   ENSP00000469826  
     ENSP00000471097   ENSP00000470346   ENSP00000469848   ENSP00000470887  

    PNKP Human Recombinant Protein Products:

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    antibodies-online proteins for PNKP (6 products) 

     
    antibodies-online peptides for PNKP

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    Selected InterPro protein domains (see all 8):
     IPR008984 SMAD_FHA_domain
     IPR023214 HAD-like_dom
     IPR006549 HAD-SF_hydro_IIIA
     IPR013954 PNK3P
     IPR027417 P-loop_NTPase

    Graphical View of Domain Structure for InterPro Entry Q96T60

    ProtoNet protein and cluster: Q96T60

    1 Blocks protein domain: IPB013954 Polynucleotide kinase 3 phosphatase

    UniProtKB/Swiss-Prot: PNKP_HUMAN, Q96T60
    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
    Similarity: In the N-terminal section; belongs to the DNA 3' phosphatase family
    Similarity: Contains 1 FHA domain


    Find genes that share domains with PNKP           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PNKP_HUMAN, Q96T60
    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
    Catalytic activity: A 3'-phosphopolynucleotide + H(2)O = a polynucleotide + phosphate
    Catalytic activity: ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA

         Genatlas biochemistry entry for PNKP:
    polynucleotide kinase-3 phosphatase,facilitating DNA repair of DNA strand breaks caused by oxidative damage

         Gene Ontology (GO): Selected molecular function terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003684damaged DNA binding NAS10446193
    GO:0003690double-stranded DNA binding TAS10446193
    GO:0004519endonuclease activity NAS10446192
    GO:0005515protein binding IPI19155274
    GO:0005524ATP binding NAS10446192
         
    Find genes that share ontologies with PNKP           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for PNKP:
     Decreased telomerase activity  PARP inhibitor sensitization 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for PNKP

    miRNA
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    miRTarBase miRNAs that target PNKP:
    hsa-mir-26b-5p (MIRT029605)

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PNKP_HUMAN, Q96T60: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    peroxisome1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--

    Find genes that share ontologies with PNKP           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for PNKP About    
    See pathways by source

    SuperPathContained pathways About
    1Cell Cycle / Checkpoint Control
    Cell Cycle / Checkpoint Control0.32
    DNA Damage0.32
    2Non-homologous end-joining
    DNA damage NHEJ mechanisms of DSBs repair0.37
    3Chks in Checkpoint Regulation
    DNA Repair Mechanisms0.32


    Find genes that share SuperPaths with PNKP           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for PNKP
        DNA Repair Mechanisms

    2 Cell Signaling Technology (CST) Pathways for PNKP
        Cell Cycle / Checkpoint Control
    DNA Damage

    1 GeneGo (Thomson Reuters) Pathway for PNKP
        DNA damage NHEJ mechanisms of DSBs repair


        Pathway & Disease-focused RT2 Profiler PCR Arrays including PNKP: 
              DNA Damage Signaling Pathway in human mouse rat
              Oxidative Stress in human mouse rat
              Nitric Oxide Signaling Pathway in human mouse rat
              DNA Repair in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for PNKP

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for PNKP (Q96T601, 2, 3 ENSP000003235114) via UniProtKB, MINT, STRING, and/or I2D (see all 56)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    XRCC4Q134261, 2, 3, ENSP000003420114EBI-1045072,EBI-717592 MINT-51171 MINT-8200112 MINT-8200097 MINT-51174 MINT-51172 MINT-8200126 MINT-51173 MINT-51175 I2D: score=4 STRING: ENSP00000342011
    TRIM37O949722, 3, ENSP000002622944MINT-67355 I2D: score=5 STRING: ENSP00000262294
    SMAD5Q997172, 3MINT-61828 I2D: score=3 
    XRCC1P188871, 2, 3, ENSP000002628874EBI-1045072,EBI-947466 MINT-8200077 I2D: score=5 STRING: ENSP00000262887
    TP53BP1Q128882, 3, ENSP000003714754MINT-8199157 I2D: score=1 STRING: ENSP00000371475
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000718nucleotide-excision repair, DNA damage removal NAS10446193
    GO:0006261DNA-dependent DNA replication NAS10446192
    GO:0006281DNA repair IGI10446192
    GO:0006979response to oxidative stress IDA10446192
    GO:0009314response to radiation TAS10446192

    Find genes that share ontologies with PNKP           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PNKP

    4 HMDB Compounds for PNKP    About this table
    CompoundSynonyms CAS #PubMed Ids
    ADPadenosindiphosphorsaeure (see all 8)58-64-0--
    Adenosine triphosphate5'-(tetrahydrogen triphosphate) Adenosine (see all 24)56-65-5--
    PhosphateNFB Orthophosphate (see all 13)14265-44-2--
    WaterDihydrogen oxide (see all 2)7732-18-5--

    5 Novoseek inferred chemical compound relationships for PNKP gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    polynucleotide 93.6 23 10446192 (2), 11586300 (1), 16982218 (1), 13679147 (1) (see all 20)
    phosphonate 79.1 7 16648365 (2), 16982218 (1), 17116430 (1), 10446192 (1) (see all 6)
    atp 27.5 3 1621950 (1), 18007613 (1), 10446192 (1)
    adenylate 14.4 1 11842120 (1)
    oxygen 0 1 11586300 (1)



    Find genes that share compounds with PNKP           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PNKP gene: 
    NM_007254.3  

    Unigene Cluster for PNKP:

    Polynucleotide kinase 3'-phosphatase
    Hs.78016  [show with all ESTs]
    Unigene Representative Sequence: BC013034
    15 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000595081 ENST00000594661 ENST00000322344(uc002pqg.3 uc002pqi.3 uc021uxx.1 uc002pqj.3)
    ENST00000599454 ENST00000596014 ENST00000593946 ENST00000600910 ENST00000600573
    ENST00000597965 ENST00000601816 ENST00000593706 ENST00000598020 ENST00000595792
    ENST00000599543 ENST00000596726
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      QuantiFast Probe-based Assays in human, mouse, rat PNKP

    Additional mRNA sequence: 

    AF120499.1 AF125807.1 AF126486.1 BC002519.2 BC009339.2 BC013034.2 BC033822.1 

    17 DOTS entries:

    DT.211706  DT.121429426  DT.100789769  DT.40275406  DT.100789766  DT.121429538  DT.100789779  DT.121429380 
    DT.100769341  DT.100789767  DT.100789780  DT.40202941  DT.95219672  DT.95219688  DT.75102180  DT.95219695 
    DT.121429373 

    Selected AceView cDNA sequences (see all 205):

    BM052781 BI761490 BX279591 CR599191 AL042657 BI908075 CA433726 BC002519 
    BC033822 BU543115 CD366787 CD671425 CR615833 CR594341 BF507485 BM974887 
    CR590331 BM664223 CR598028 CR620645 BQ877856 BU541073 BQ008966 BQ002105 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for PNKP (see all 9)    About this scheme

    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:                                      -                 -                                                                                                   

    ExUns: 17 ^ 18
    SP1:            
    SP2:            
    SP3:            
    SP4:            
    SP5:            


    ECgene alternative splicing isoforms for PNKP

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PNKP expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TATGGCTACA
    PNKP Expression
    About this image


    PNKP expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Telencephalon
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    PNKP Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PNKP Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.78016

    UniProtKB/Swiss-Prot: PNKP_HUMAN, Q96T60
    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)

        Pathway & Disease-focused RT2 Profiler PCR Arrays including PNKP: 
              DNA Damage Signaling Pathway in human mouse rat
              Oxidative Stress in human mouse rat
              Nitric Oxide Signaling Pathway in human mouse rat
              DNA Repair in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PNKP

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for PNKP gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pnkp1 , 5 polynucleotide kinase 3'- phosphatase1, 5 79.55(n)1
    81.35(a)1
      7 (28.94 cM)5
    590471  NM_021549.21  NP_067524.21 
     448571395 
    lizard
    (Anolis carolinensis)
    Reptilia PNKP6
    polynucleotide kinase 3'-phosphatase
    53(a)
    1 ↔ 1
    6(79802832-79820107)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.135652 Xenopus laevis transcribed sequence with weak similarity more 71.77(n)    BJ070151.1 
    zebrafish
    (Danio rerio)
    Actinopterygii pnkp1 polynucleotide kinase 3'-phosphatase 59.62(n)
    57.29(a)
      569462  NM_001077578.2  NP_001071046.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG96011 , 3 CG96011 40(a)3
    48.86(n)1
    41.88(a)1
      84F133
    409941  NM_141535.31  NP_649792.31 
    worm
    (Caenorhabditis elegans)
    Secernentea F21D5.51 , 3 polynucleotide kinase 3' phosphatase3
    F21D5.51
    45(a)3
    47.57(n)1
    46.22(a)1
      IV(8735986-8739560)3
    1776811  NM_069102.31  NP_501503.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes HNT36
    DNA 5' AMP hydrolase involved in DNA repair; membe...
    7(a)
    1 → many
    XV(811671-812324) YOR258W


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PNKP gene
    APTX2  
    1 SIMAP similar gene for PNKP using alignment to 7 protein entries:     PNKP_HUMAN (see all proteins):
    APTX

    Find genes that share paralogs with PNKP           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PNKP (see all 391)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0638354
    Epileptic encephalopathy, early infantile, 10 (EIEE10)4--see VAR_0638352 L F mis40--------
    VAR_0638364
    Epileptic encephalopathy, early infantile, 10 (EIEE10)4--see VAR_0638362 E K mis40--------
    rs37607101,2
    C--50371438(+) tttttA/Gtattt 1 -- us2k10--------
    rs113258291,2
    C,F--50371648(+) TTTTTT/-CCCTT 1 -- us2k1 trp33Minor allele frequency- -:0.50NA CSA 6
    rs1397940501,2
    --50540858(+) TACGTC/TTCCCC 1 -- ds50010--------
    rs1140085561,2
    F--50540960(+) AGCCCG/AGGAAC 1 -- ds50011Minor allele frequency- A:0.02WA 118
    rs1431889411,2
    --50540983(+) GCTCTC/TGGCTG 1 -- ds50010--------
    rs713533401,2
    C,F--50541007(+) CCCCCA/C/GCGAAT 1 -- ds50011NA 2
    rs1489139361,2
    --50541008(+) CCCCCC/GGAATC 1 -- ds50010--------
    rs1151696151,2
    C,F--50541022(+) AGACCC/TGCAGG 1 -- ds50011Minor allele frequency- T:0.02WA 118

    HapMap Linkage Disequilibrium report for PNKP (50364460 - 50371166 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for PNKP:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2677406CNV Deletion23128226
    nsv912269CNV Loss21882294
    nsv912272CNV Loss21882294
    dgv54n68CNV Loss17160897
    dgv53n68CNV Loss17160897
    dgv3974n71CNV Loss21882294
    nsv524068CNV Loss19592680
    nsv526372CNV Loss19592680
    nsv9739CNV Gain+Loss18304495

    Human Gene Mutation Database (HGMD): PNKP
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PNKP
    DNA2.0 Custom Variant and Variant Library Synthesis for PNKP

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 605610   
    OMIM disorders: 613402  
    UniProtKB/Swiss-Prot: PNKP_HUMAN, Q96T60
  • Epileptic encephalopathy, early infantile, 10 (EIEE10) [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. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 5 diseases for PNKP:    
    About MalaCards
    microcephaly, seizures, and developmental delay    ohtahara syndrome    doid:4019    epileptic encephalopathy, early infantile, 17
    microcephaly

    3 diseases from the University of Copenhagen DISEASES database for PNKP:
    Ohtahara syndrome     Apraxia     DOID:4019

    Find genes that share disorders with PNKP           About GenesLikeMe

    Genetic Association Database (GAD): PNKP
    Human Genome Epidemiology (HuGE) Navigator: PNKP (5 documents)

    Export disorders for PNKP gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PNKP gene, integrated from 10 sources (see all 80):
    (articles sorted by number of sources associating them with PNKP)
        Utopia: connect your pdf to the dynamic
    world of online information

    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. (PubMed id 10446192)1, 2, 3, 9 Jilani A....Lasko D.D. (J. Biol. Chem. 1999)
    2. Molecular characterization of a human DNA kinase. (PubMed id 10446193)1, 2, 3 Karimi-Busheri F....Weinfeld M. (J. Biol. Chem. 1999)
    3. Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK. (PubMed id 19155274)1, 2, 9 Ali A.A.... Oliver A.W. (Nucleic Acids Res. 2009)
    4. Polynucleotide kinase 3' phosphatase variant, dietary variables and risk of adenoma recurrence in the Polyp Prevention Trial. (PubMed id 18414202)1, 4, 9 Murphy G....Lanza E. (Eur. J. Cancer Prev. 2008)
    5. Mutations in PNKP cause microcephaly, seizures and defects in DNA repair. (PubMed id 20118933)1, 2 Shen J.... Walsh C.A. (Nat. Genet. 2010)
    6. Variation within DNA repair pathway genes and risk of multiple sclerosis. (PubMed id 20522537)1, 4 Briggs F.B....Barcellos L.F. (Am. J. Epidemiol. 2010)
    7. Association between genetic variants in the base excision repair pathway and outcomes after hematopoietic cell transplantations. (PubMed id 20226869)1, 4 Thyagarajan B....Arora M. (Biol. Blood Marrow Transplant. 2010)
    8. Polymorphisms in the base excision repair pathway and graft-versus-host disease. (PubMed id 20574454)1, 4 Arora M....Thyagarajan B. (Leukemia 2010)
    9. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    10. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (Nature 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 11284 HGNC: 9154 AceView: PNKP Ensembl:ENSG00000039650 euGenes: HUgn11284
    ECgene: PNKP H-InvDB: PNKP

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PNKP Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for PNKP Genetics and Cytogenetics in Oncology and Haematology
    NIEHS-SNPshttp://egp.gs.washington.edu/data/pnkp/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PNKP gene:
    Search GeneIP for patents involving PNKP

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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