PNKP

Chr 19q13.33

polynucleotide kinase 3'-phosphatase

Aliases:: PNK
MANE:: ENST00000322344.8

OMIM: 605610 ↗NCBI: 11284 ↗Ensembl ↗

Annotations refreshed 1 month ago.

Predicted protein structure

AlphaFold predicted structure

PNKP · Q96T60

v62025-08-01

Predicted Aligned Error matrix for PNKP — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

90.9/ 100

Very high

521 residues

Confidence breakdown

Very high(≥ 90)83%
Confident(70–90)9%
Low(50–70)1%
Very low(< 50)7%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

Ataxia and cerebellar anomalies - narrow panel
BIALLELIC, autosomal or pseudoautosomal
Childhood onset dystonia, chorea or related movement disorder
BIALLELIC, autosomal or pseudoautosomal
DDG2P
BIALLELIC, autosomal or pseudoautosomal
Early onset or syndromic epilepsy
BIALLELIC, autosomal or pseudoautosomal
Fetal anomalies
BIALLELIC, autosomal or pseudoautosomal
Hereditary ataxia
BIALLELIC, autosomal or pseudoautosomal
Hereditary ataxia with onset in adulthood
BIALLELIC, autosomal or pseudoautosomal
Hereditary neuropathy
BIALLELIC, autosomal or pseudoautosomal

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Disease associations (Open Targets)

Ataxia-oculomotor apraxia type 4
0.80
microcephaly, seizures, and developmental delay
0.80
Spinocerebellar ataxia with axonal neuropathy type 2
0.75
early-infantile DEE
0.69
Microcephaly - seizures - developmental delay
0.65
Charcot-Marie-Tooth disease type 2B2
0.61
developmental and epileptic encephalopathy, 12
0.56
hereditary disease
0.54
genetic developmental and epileptic encephalopathy
0.54
Abnormality of the nervous system
0.45

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

Bifunctional polynucleotide phosphatase/kinase

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). 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 (PubMed:10446192, PubMed:10446193)