Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	11284
Gene name	Polynucleotide kinase 3'-phosphatase
Gene symbol	PNKP
Synonyms (NCBI Gene)	AOA4CMT2B2EIEE10MCSZPNK
Chromosome	19
Chromosome location	19q13.33
Summary	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 associa

Show/Hide all (63)

SNP ID	Visualize variation	Clinical significance	Consequence
rs3739173	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs3739200	->G	Conflicting-interpretations-of-pathogenicity	Intron variant
rs34472250	C>G,T	Likely-benign, uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs75203375	C>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant
rs115259839	G>A,C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs116192442	G>A	Benign-likely-benign, likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs142143566	C>T	Benign, likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs144284975	G>A,C	Benign, likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, synonymous variant, coding sequence variant
rs145904995	C>T	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity, benign-likely-benign	Synonymous variant, coding sequence variant
rs151180981	G>A	Benign, likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs199919568	A>C,G	Conflicting-interpretations-of-pathogenicity	Splice donor variant
rs201503405	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs267606956	C>A,T	Pathogenic	Missense variant, coding sequence variant, stop gained
rs267606957	G>A,C	Pathogenic	Missense variant, coding sequence variant
rs371834726	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant
rs372148913	G>A	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs372404688	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs374745816	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Intron variant
rs375781731	G>A	Pathogenic	Coding sequence variant, stop gained
rs376854895	C>G,T	Conflicting-interpretations-of-pathogenicity, likely-benign, uncertain-significance, benign, likely-pathogenic	Missense variant, coding sequence variant
rs532550120	C>G,T	Conflicting-interpretations-of-pathogenicity, likely-benign, uncertain-significance	Coding sequence variant, missense variant, synonymous variant
rs539286945	G>A,C	Pathogenic	Stop gained, coding sequence variant, missense variant
rs571119317	G>A	Benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs587784365	->GTCGATGGCGACCCGTT	Pathogenic	Frameshift variant, coding sequence variant
rs587784366	TACCTGGCGC>-	Pathogenic-likely-pathogenic, likely-pathogenic, pathogenic	Intron variant, coding sequence variant, splice donor variant
rs730882224	->GTCGATGGCGACCCGTT	Likely-pathogenic	Frameshift variant, coding sequence variant
rs747244348	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Synonymous variant, coding sequence variant
rs750550558	->TT	Likely-pathogenic	Intron variant
rs752902474	AGGAGGGGGGTCAGGGG>-,AGGAGGGGGGTCAGGGGAGGAGGGGGGTCAGGGG	Pathogenic	Intron variant
rs756746191	G>C	Pathogenic	Coding sequence variant, missense variant
rs760249644	->CTACCTGGCGCGGCTCGCG	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, splice donor variant
rs764379536	CTCGCGGCGTCTGG>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs766530579	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs767645983	T>G	Pathogenic	Splice acceptor variant
rs768847609	->GACC	Pathogenic	Coding sequence variant, frameshift variant
rs772727116	C>T	Pathogenic	Coding sequence variant, stop gained
rs786203983	C>A	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs786205207	GGT>-	Likely-pathogenic, pathogenic	Coding sequence variant, inframe deletion
rs794727920	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Synonymous variant, coding sequence variant
rs796052850	G>A	Pathogenic	Coding sequence variant, stop gained
rs796052859	->A	Likely-pathogenic, pathogenic	Coding sequence variant, stop gained
rs796052860	TCGCGGC>-,TCGCGGCTCGCGGC	Likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs796052861	->ACCTGGCG	Pathogenic	Splice donor variant, coding sequence variant
rs796052862	->CTCGG	Pathogenic	Frameshift variant, coding sequence variant
rs796052863	TGT>-	Likely-pathogenic	Coding sequence variant, inframe deletion
rs879255541	->C	Likely-pathogenic	Frameshift variant, coding sequence variant
rs886037744	->CGGCT	Pathogenic	Frameshift variant, coding sequence variant
rs959497903	C>A,T	Likely-pathogenic	Splice donor variant
rs1057518102	C>T	Likely-pathogenic	Splice donor variant
rs1057520630	C>G,T	Pathogenic	Splice donor variant
rs1064794452	TC>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1131691883	GAGCTCGAAGCCGG>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1247055716	C>A	Pathogenic	Splice donor variant
rs1338672803	A>C,G	Likely-pathogenic	Missense variant, coding sequence variant
rs1389034284	->A	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1555810849	CTGGCGCGGCTC>-,CTGGCGCGGCTCCCTGGCGCGGCTC	Uncertain-significance, likely-pathogenic	Coding sequence variant, splice donor variant
rs1555810891	->GGGCTGTCTCACACGTGGTCACACAGCGCTGCCAGGAGCCTAGCGTGTC	Likely-pathogenic	Coding sequence variant, stop gained, inframe indel
rs1568659036	GCTCGCGGCGTCTGGGTTTGTGTTGTCGATGGCGACCCGTTTCCCTTGCTTCAGGGCTGTCTCACACGTGGTCACACAGCGCTGCCAGG>-	Pathogenic	Frameshift variant, coding sequence variant
rs1568660279	T>C	Likely-pathogenic	Splice acceptor variant
rs1568662343	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs1568663209	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1600416052	->GTTGTCGATGGCGACCC	Pathogenic	Frameshift variant, coding sequence variant
rs1600423552	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant

Show/Hide all (1)

miRTarBase ID	miRNA	Experiments	Reference
MIRT029605	hsa-miR-26b-5p	Microarray	19088304

Show/Hide all (43)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0003684	Function	Damaged DNA binding	NAS	10446193
GO:0003690	Function	Double-stranded DNA binding	TAS	10446193
GO:0003824	Function	Catalytic activity	IEA
GO:0004519	Function	Endonuclease activity	NAS	10446192
GO:0005515	Function	Protein binding	IPI	15385968, 16189514, 19155274, 21637298, 25416956, 25609649, 26496610, 28514442, 32296183, 32814053, 33961781, 38225382
GO:0005524	Function	ATP binding	IEA
GO:0005524	Function	ATP binding	NAS	10446192
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	10446193
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005730	Component	Nucleolus	IDA
GO:0006261	Process	DNA-templated DNA replication	NAS	10446192
GO:0006281	Process	DNA repair	IBA
GO:0006281	Process	DNA repair	IEA
GO:0006281	Process	DNA repair	IGI	10446192
GO:0006287	Process	Base-excision repair, gap-filling	TAS
GO:0006289	Process	Nucleotide-excision repair	TAS	10446193
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	IDA	15385968, 28453785
GO:0006974	Process	DNA damage response	IEA
GO:0006979	Process	Response to oxidative stress	IDA	10446192
GO:0009314	Process	Response to radiation	NAS	10446193
GO:0009314	Process	Response to radiation	TAS	10446192
GO:0016020	Component	Membrane	HDA	19946888
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0017076	Function	Purine nucleotide binding	NAS	10446193
GO:0032206	Process	Positive regulation of telomere maintenance	IMP	21531765
GO:0035861	Component	Site of double-strand break	IDA	28453785
GO:0035861	Component	Site of double-strand break	IEA
GO:0046403	Function	Polynucleotide 3'-phosphatase activity	IBA
GO:0046403	Function	Polynucleotide 3'-phosphatase activity	IDA	10446192, 10446193
GO:0046403	Function	Polynucleotide 3'-phosphatase activity	IEA
GO:0046403	Function	Polynucleotide 3'-phosphatase activity	TAS
GO:0046404	Function	ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	IBA
GO:0046404	Function	ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	IDA	10446193
GO:0046404	Function	ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	IEA
GO:0051734	Function	ATP-dependent polynucleotide 5'-hydroxyl-kinase activity	IEA
GO:2001034	Process	Positive regulation of double-strand break repair via nonhomologous end joining	IMP	12032095

MIM	HGNC	e!Ensembl
605610	9154	ENSG00000039650

Q96T60

Protein name

Bifunctional polynucleotide phosphatase/kinase (DNA 5'-kinase/3'-phosphatase) (Polynucleotide kinase-3'-phosphatase) [Includes: Polynucleotide 3'-phosphatase (EC 3.1.3.32) (2'(3')-polynucleotidase); Polynucleotide 5'-hydroxyl-kinase (EC 2.7.1.78)]

Protein 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 (PubMed:10446192, PubMed:10446193, PubMed:15385968, PubMed:20852255, PubMed:28453785). Throug

PDB

2BRF , 2W3O

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF17913	FHA_2	10 → 107	FHA domain	Domain
PF08645	PNK3P	166 → 328	Polynucleotide kinase 3 phosphatase	Family
PF13671	AAA_33	367 → 407		Domain
PF13671	AAA_33	399 → 489		Domain

Tissue specificity

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 (

Sequence

MGEVEAPGRLWLESPPGGAPPIFLPSDGQALVLGRGPLTQVTDRKCSRTQVELVADPETR
TVAVKQLGVNPSTTGTQELKPGLEGSLGVGDTLYLVNGLHPLTLRWEETRTPESQPDTPP
GTPLVSQDEKRDAELPKKRMRKSNPGWENLEKLLVFTAAGVKPQGKVAGFDLDGTLITTR
SGKVFPTGPSDWRILYPEIPRKLRELEAEGYKLVIFTNQMSIGRGKLPAEEFKAKVEAVV
EKLGVPFQVLVATHAGLYRKPVTGMWDHLQEQANDGTPISIGDSIFVGDAAGRPANWAPG
RKKKDFSCADRLFALNLGLPFATPEEFFLKWPAAGFELPAFDPRTVSRSGPLCLPESRAL
LSASPEVVVAVGFPGAGKSTFLKKHLVSAGYVHVNRDTLGSWQRCVTTCETALKQGKRVA
IDNTNPDAASRARYVQCARAAGVPCRCFLFTATLEQARHNNRFREMTDSSHIPVSDMVMY
GYRKQFEAPTLAEGFSAILEIPFRLWVEPRLGRLYCQFSEG

Sequence length

521

Interactions

View interactions

	KEGG		Reactome
	Base excision repair		APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway

1214

Show/Hide Causal Diseases (14)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the nervous system	Pathogenic; Likely pathogenic	rs267606956, rs587784365, rs768847609	RCV001813953 RCV001813954 RCV001814226
Ataxia - oculomotor apraxia type 4	Pathogenic; Likely pathogenic	rs1477525034, rs982113263, rs786203983, rs886037744, rs1555810613, rs786205207, rs587784365, rs756746191	RCV001335536 RCV002497869 RCV000167523 RCV000167524 RCV000167525 RCV000170438 RCV000167521 RCV000853401
Ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia	Likely pathogenic; Pathogenic	rs587784366	RCV000825541
Cerebellar atrophy	Likely pathogenic	rs730882224	RCV000162138
Charcot-Marie-Tooth disease type 2B2	Likely pathogenic; Pathogenic	rs982113263, rs786205207, rs796052862, rs2122334749, rs1247055716	RCV002497869 RCV001093540 RCV001814094 RCV003990465 RCV001328605
Developmental and epileptic encephalopathy, 12	Likely pathogenic; Pathogenic	rs1391913873, rs2122319491, rs1337771339, rs1163218519, rs2074810148, rs1057520630, rs149614720, rs138249970, rs766419491, rs2122315348, rs1413085852, rs965965834, rs1309576866, rs2122333424, rs1170743406 View all (57 more)	RCV001379489 RCV001389015 RCV001384335 RCV001381085 RCV001384137 RCV002541158 RCV001970322 RCV001923081 RCV002027658 RCV002037658 RCV001950872 RCV001943423 RCV001899543 RCV001994753 RCV001890349 RCV002035465 RCV002037963 RCV002036262 RCV001946592 RCV001992260 RCV001951493 RCV001070856 RCV000648410 RCV003526220 RCV001226527 RCV002607730 RCV003108614 RCV002512794 RCV000706286 RCV002676527 RCV002715283 RCV001387495 RCV003638640 RCV001857632 RCV005055689 RCV000550810 RCV002801539 RCV000798839 RCV002893882 RCV003005461 RCV003002797 RCV003034787 RCV003036041 RCV003525515 RCV003525844 RCV003525753 RCV003527119 RCV003526805 RCV003527540 RCV003639001 RCV003639756 RCV003639927 RCV003639869 RCV003640281 RCV003813968 RCV003857160 RCV001378231 RCV001231907 RCV000821367 RCV003114620 RCV001376960 RCV002532707 RCV000704636 RCV005092093 RCV000812409 RCV000807769 RCV001860590 RCV001059979 RCV001043154 RCV001058986 RCV001224000 RCV001217975 RCV001212535 RCV001214794 RCV001240620 RCV001880168
Global developmental delay	Likely pathogenic	rs730882224	RCV000162138
Intellectual disability	Pathogenic	rs587784365	RCV001257702
Microcephaly, seizures, and developmental delay	Pathogenic; Likely pathogenic	rs2122319422, rs982113263, rs762003634, rs587784366, rs786203983, rs2514633587, rs786205207, rs267606956, rs587784365, rs267606957, rs752902474, rs770344860, rs1247055716, rs1600416052, rs2514637165, rs2514644062 View all (1 more)	RCV001731174 RCV002497869 RCV003339880 RCV000147346 RCV001813762 RCV002470636 RCV000500375 RCV000005119 RCV000005120 RCV000005121 RCV000194165 RCV003340935 RCV000502084 RCV000995611 RCV001255835 RCV001255766
Nonpapillary renal cell carcinoma	Pathogenic	rs767645983	RCV005892190
Ovarian serous cystadenocarcinoma	Likely pathogenic; Pathogenic	rs1057520630	RCV005922457
PNKP-related disorder	Likely pathogenic; Pathogenic	rs982113263, rs587784366, rs760131892, rs752902474, rs1212228078, rs1247055716, rs2074784617	RCV004579583 RCV004700470 RCV004539747 RCV003335190 RCV003995126 RCV004535608 RCV004536078
Primary microcephaly	Likely pathogenic	rs730882224	RCV000162138
Seizure	Pathogenic	rs587784365	RCV005401280

Show/Hide Unknown Diseases (14)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Abnormal cerebral morphology	Conflicting classifications of pathogenicity	rs199919568, rs774995635	RCV002274937 RCV002275195
Adrenocortical carcinoma, hereditary	Conflicting classifications of pathogenicity	rs199919568	RCV005892187
Cervical cancer	Likely benign	rs776421692	RCV005926111
Colon adenocarcinoma	Conflicting classifications of pathogenicity	rs199919568	RCV005892185
Epileptic encephalopathy	Benign; Likely benign	rs3739205	RCV000268050
Familial cancer of breast	Benign; Likely benign; Uncertain significance	rs142199280, rs142032281, rs368832563	RCV005886527 RCV005892191 RCV005869484
Gastric cancer	Benign; Likely benign	rs142199280	RCV005886529
Hepatocellular carcinoma	Conflicting classifications of pathogenicity	rs199919568	RCV005892186
Malignant tumor of urinary bladder	Benign; Likely benign; Uncertain significance	rs142199280, rs377619541	RCV005886528 RCV005930499
Melanoma	-; Uncertain significance	rs2122334749, rs142032281	RCV005930213 RCV005892192
Microcephaly	Conflicting classifications of pathogenicity	rs199919568	RCV005625406
Pyridoxine-dependent epilepsy	Uncertain significance	rs763116781	RCV000678825
Uterine carcinosarcoma	Uncertain significance	rs751424212	RCV005913550
Uterine corpus endometrial carcinoma	Conflicting classifications of pathogenicity	rs115259839, rs199919568	RCV005892048 RCV005892189

Show/Hide Text Mining Associations (34)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenoma	Associate	18414202
Amyotrophic Lateral Sclerosis	Associate	32005289
Apraxia oculomotor Cogan type	Associate	35326432
Ataxia	Associate	25728773, 27165045, 30039206
Autosomal Recessive Primary Microcephaly	Associate	34697416
Brain Neoplasms	Associate	35354845
Cerebellar Diseases	Associate	32980744, 35326432
Charcot Marie Tooth Disease	Associate	30039206, 32504494, 34697416
Charcot Marie Tooth disease Type 2B2	Associate	30039206, 32504494
Charcot Marie Tooth disease X linked recessive 2	Associate	31167812
Colorectal Neoplasms	Associate	35271294
Developmental Disabilities	Associate	22508754, 25728773, 32980744, 37916443
Drug Related Side Effects and Adverse Reactions	Associate	23883586
Early onset ataxia with oculomotor apraxia and hypoalbuminemia	Associate	27165045
Edema	Associate	27165045
Embryo Loss	Associate	37061005
Genetic Diseases Inborn	Associate	25728773
Glioblastoma	Associate	35354845
Glioma	Associate	35354845
Heredodegenerative Disorders Nervous System	Associate	20118933, 28922417
Machado Joseph Disease	Associate	25590633
Microcephaly	Associate	20118933, 22508754, 25728773, 28821613, 30039206, 32504494, 32980744, 34697416, 35354845, 35412344, 37916443
Neoplasms	Associate	23883586, 35354845
Neoplastic Syndromes Hereditary	Associate	28453785, 31167812
Neurodegenerative Diseases	Associate	25590633, 32504494, 37061005
Neurodegenerative Diseases	Inhibit	30148840
Neurodevelopmental Disorders	Associate	32504494
Neurologic Manifestations	Associate	20118933, 31533039, 37061005
Osteolysis syndrome recessive	Associate	35412344
Prostatic Neoplasms	Associate	29320576, 33569050
Seizures	Associate	20118933, 22508754, 25728773, 32504494, 32980744, 34697416, 37916443
Spinocerebellar ataxia autosomal recessive 1	Associate	25728773
Squamous Cell Carcinoma of Head and Neck	Stimulate	28415784
Zika Virus Infection	Associate	35412344

PNKP (polynucleotide kinase 3'-phosphatase)