ENSG00000039650


Homo sapiens

Features
Gene ID: ENSG00000039650
  
Biological name :PNKP
  
Synonyms : PNKP / polynucleotide kinase 3-phosphatase / Q96T60
  
Possible biological names infered from orthology :
  
Species: Homo sapiens
  
Chr. number: 19
Strand: -1
Band: q13.33
Gene start: 49859882
Gene end: 49878351
  
Corresponding Affymetrix probe sets: 218961_s_at (Human Genome U133 Plus 2.0 Array)   
  
Cross references: Ensembl peptide - ENSP00000473137
Ensembl peptide - ENSP00000491347
Ensembl peptide - ENSP00000490791
Ensembl peptide - ENSP00000490737
Ensembl peptide - ENSP00000490539
Ensembl peptide - ENSP00000489983
Ensembl peptide - ENSP00000489771
Ensembl peptide - ENSP00000486898
Ensembl peptide - ENSP00000486707
Ensembl peptide - ENSP00000486500
Ensembl peptide - ENSP00000486037
Ensembl peptide - ENSP00000323511
Ensembl peptide - ENSP00000468896
Ensembl peptide - ENSP00000469826
Ensembl peptide - ENSP00000469848
Ensembl peptide - ENSP00000470346
Ensembl peptide - ENSP00000470887
Ensembl peptide - ENSP00000471097
Ensembl peptide - ENSP00000472300
NCBI entrez gene - 11284     See in Manteia.
OMIM - 605610
RefSeq - NM_007254
RefSeq Peptide - NP_009185
swissprot - A0A1B0GVJ3
swissprot - A0A1B0GU66
swissprot - A0A0D9SFU1
swissprot - A0A0D9SFL2
swissprot - A0A0D9SFD6
swissprot - A0A0D9SEV0
swissprot - M0QX49
swissprot - M0QYH2
swissprot - M0QYI1
swissprot - M0R000
swissprot - M0R097
swissprot - M0R3C8
swissprot - A0A1W2PP58
swissprot - Q96T60
swissprot - A0A1B0GW61
swissprot - A0A1B0GW17
Ensembl - ENSG00000039650
  
Related genetic diseases (OMIM): 613402 - Microcephaly, seizures, and developmental delay, 613402
  616267 - Ataxia-oculomotor apraxia 4, 616267
See expression report in BioGPS
See gene description in Wikigenes
See gene description in GeneCards
See co-cited genes in PubMed


Ortholog prediction (from Ensembl)
Ortholog nameID Species
 pnkpENSDARG00000100455Danio rerio
 PnkpENSMUSG00000002963Mus musculus


Paralog prediction (from Ensembl)
Paralog nameIDSimilarity(%)
APTX / Q7Z2E3 / aprataxinENSG0000013707415


Protein motifs (from Interpro)
Interpro ID Name
 IPR006549  HAD-superfamily hydrolase,subfamily IIIA
 IPR006550  Polynucleotide kinase 3-phosphatase, metazoan
 IPR006551  Polynucleotide 3"-phosphatase
 IPR008984  SMAD/FHA domain superfamily
 IPR013954  Polynucleotide kinase 3 phosphatase
 IPR023214  HAD superfamily
 IPR027417  P-loop containing nucleoside triphosphate hydrolase
 IPR036412  HAD-like superfamily


Gene Ontology (GO)
TypeGO IDTermEv.Code
 biological_processGO:0000718 nucleotide-excision repair, DNA damage removal NAS
 biological_processGO:0006261 DNA-dependent DNA replication NAS
 biological_processGO:0006281 DNA repair IGI
 biological_processGO:0006974 cellular response to DNA damage stimulus IEA
 biological_processGO:0006979 response to oxidative stress IDA
 biological_processGO:0008152 metabolic process IEA
 biological_processGO:0009314 response to radiation TAS
 biological_processGO:0010836 negative regulation of protein ADP-ribosylation IMP
 biological_processGO:0016310 phosphorylation IEA
 biological_processGO:0016311 dephosphorylation IDA
 biological_processGO:0032212 positive regulation of telomere maintenance via telomerase IMP
 biological_processGO:0042769 DNA damage response, detection of DNA damage NAS
 biological_processGO:0046939 nucleotide phosphorylation IDA
 biological_processGO:0051973 positive regulation of telomerase activity IMP
 biological_processGO:0090305 nucleic acid phosphodiester bond hydrolysis IEA
 biological_processGO:0098504 DNA 3" dephosphorylation involved in DNA repair IBA
 biological_processGO:0098506 polynucleotide 3" dephosphorylation IEA
 biological_processGO:1904355 positive regulation of telomere capping IMP
 cellular_componentGO:0005634 nucleus IDA
 cellular_componentGO:0005654 nucleoplasm TAS
 cellular_componentGO:0005730 nucleolus IDA
 cellular_componentGO:0005739 mitochondrion IEA
 cellular_componentGO:0016020 membrane HDA
 molecular_functionGO:0000166 nucleotide binding IEA
 molecular_functionGO:0003684 damaged DNA binding NAS
 molecular_functionGO:0003690 double-stranded DNA binding TAS
 molecular_functionGO:0003824 catalytic activity IEA
 molecular_functionGO:0004519 endonuclease activity NAS
 molecular_functionGO:0005515 protein binding IEA
 molecular_functionGO:0005524 ATP binding NAS
 molecular_functionGO:0016301 kinase activity IEA
 molecular_functionGO:0016740 transferase activity IEA
 molecular_functionGO:0016787 hydrolase activity IEA
 molecular_functionGO:0017076 purine nucleotide binding NAS
 molecular_functionGO:0046403 polynucleotide 3"-phosphatase activity TAS
 molecular_functionGO:0046404 ATP-dependent polydeoxyribonucleotide 5"-hydroxyl-kinase activity IEA


Pathways (from Reactome)
Pathway description
APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway


Phenotype (from MGI, Zfin or HPO)
IDPhenotypeDefinition Genetic BG
 HP:0000007 Autosomal recessive inheritance "A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele)." [HPO:curators]
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 HP:0000253 Microcephaly, progressive "Progressive microcephaly is diagnosed when the head circumference falls progressively behind age- and gender-dependent norms." [HPO:curators]
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 HP:0000657 Oculomotor apraxia 
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 HP:0000752 Hyperactivity 
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 HP:0001250 Seizures "Seizures are an intermittent `abnormality of the central nervous system` (FMA:HP:0002011) due to a sudden, excessive, disorderly discharge of cerebral neurons and characterized clinically by some combination of disturbance of sensation, loss of consciousness, impairment of psychic function, or convulsive movements." [HPO:probinson]
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 HP:0001251 Ataxia "Ataxia is a nonspecific neurological sign and symptom consisting of gross lack of coordination of muscle movements. Ataxia is caused by dysfunction of one or more parts of the nervous system including the cerebellum, the sensory nervous system, the vestibular system, or the cerebral cortex." [HPO:curators]
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 HP:0001265 Hyporeflexia 
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 HP:0001270 Motor retardation 
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 HP:0001272 Cerebellar atrophy 
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 HP:0001284 Areflexia 
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 HP:0001290 Generalized hypotonia "Generalized muscular hypotonia (abnormally low muscle tone)." [HPO:curators]
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 HP:0001332 Dystonia "An abnormally increased muscular tone that causes fixed abnormal postures. There is a slow, intermittent twisting motion that leads to exaggerated turning and posture of the extremities and trunk." [HPO:curators]
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 HP:0002079 Hypoplasia of the corpus callosum "Underdevelopment of the corpus callosum." [HPO:curators]
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 HP:0002119 Ventriculomegaly 
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 HP:0002445 Tetraplegia 
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 HP:0003202 Amyotrophy "The presence of muscular atrophy (which is also known as amyotrophy)." [HPO:curators]
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 HP:0003678 Rapidly progressive 
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 HP:0009830 Peripheral neuropathy "Peripheral neuropathy is a general term for any disorder of the peripheral nervous system. The main clinical features used to classify peripheral neuropathy are distribution, type (mainly demyelinating versus mainly axonal), duration, and course." [HPO:curators]
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 HP:0009879 Cortical gyral simplification "An abnormal reduction of the number and complexity of the pattern of gyrations of the cerebral cortex." [HPO:curators]
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 HP:0010864 Mental retardation, severe "Moderate mental retardation is defined as an intelligence quotient (IQ) in the range of 20-34." [HPO:probinson]
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 HP:0100543 Cognitive impairment "Abnormality in the process of thought including the ability to process information." [HPO:sdoelken]
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 HP:0200134 Epileptic encephalopathy 
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Interacting proteins (from Reactome)
Interactor ID Name Interaction type
 ENSG00000070501 POLB / P06746 / DNA polymerase beta  / complex / reaction
 ENSG00000073050 XRCC1 / P18887 / X-ray repair cross complementing 1  / complex / reaction
 ENSG00000005156 LIG3 / P49916 / DNA ligase 3  / complex / reaction
 ENSG00000140398 NEIL1 / Q96FI4 / nei like DNA glycosylase 1  / complex / reaction






 

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