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Guo, L. PNKP Gene. Encyclopedia. Available online: (accessed on 21 May 2024).
Guo L. PNKP Gene. Encyclopedia. Available at: Accessed May 21, 2024.
Guo, Lily. "PNKP Gene" Encyclopedia, (accessed May 21, 2024).
Guo, L. (2020, December 25). PNKP Gene. In Encyclopedia.
Guo, Lily. "PNKP Gene." Encyclopedia. Web. 25 December, 2020.

polynucleotide kinase 3'-phosphatase


1. Introduction

The PNKP gene provides instructions for making the polynucleotide kinase-phosphatase (PNKP) enzyme. This enzyme is critical for repairing broken strands of DNA molecules. It can help fix damage that affects one DNA strand (single-strand breaks) or both strands (double-strand breaks). At the site of the damage, the PNKP enzyme modifies the broken ends of the DNA strands so that they can be joined back together.

2. Health Conditions Related to Genetic Changes

2.1. Ataxia with oculomotor apraxia

At least nine PNKP gene mutations have been found to cause ataxia with oculomotor apraxia type 4. This condition is characterized by poor coordination and balance (ataxia) and problems with side-to-side movement of the eyes (oculomotor apraxia). These problems are due to the breakdown (degeneration) of nerve cells in the part of the brain that coordinates movement (the cerebellum).

PNKP gene mutations that cause ataxia with oculomotor apraxia type 4 lead to production of an unstable enzyme that is quickly broken down in the cell. Shortage of the PNKP enzyme prevents efficient repair of damaged DNA. Researchers suggest that the repair of single-strand breaks is particularly impaired in ataxia with oculomotor apraxia type 4. It is thought that single-strand DNA damage increases after birth as the brain grows. Without repair, the accumulating damage leads to a loss of nerve cell in the brain, resulting in the movement problems characteristic of ataxia with oculomotor apraxia type 4.

2.2. Microcephaly, seizures, and developmental delay

At least six mutations in the PNKP gene have been found to cause microcephaly, seizures, and developmental delay (MCSZ). This condition is characterized by problems with brain development before birth that result in an unusually small head size (microcephaly), recurrent seizures (epilepsy), and delayed development of speech and motor skills. Rarely, affected individuals also have difficulty coordinating movements (ataxia) due to degeneration of nerve cells in the cerebellum.

PNKP gene mutations that cause MCSZ lead to production of an unstable enzyme that is quickly broken down in the cell. Shortage of the PNKP enzyme prevents efficient repair of damaged DNA. Researchers suggest that, in contrast to ataxia with oculomotor apraxia type 4 (described above), the repair of double-strand breaks is particularly impaired in MCSZ. The accumulating damage is especially harmful to nerve cells. It is thought that excessive DNA damage before birth leads to the death of nerve cell precursors, impairing normal brain development and causing microcephaly and the other neurological features of MCSZ.

It is unclear why mutations in the same gene, even the same mutation in some cases, can have different effects on single-strand or double-strand DNA damage repair and cause either ataxia with oculomotor apraxia type 4 or MCSZ.

3. Other Names for This Gene

  • AOA4
  • bifunctional polynucleotide phosphatase/kinase
  • DNA 5'-kinase/3'-phosphatase
  • EIEE10
  • Homo sapiens polynucleotide kinase 3'-phosphatase (PNKP)
  • MCSZ
  • PNK


  1. Aceytuno RD, Piett CG, Havali-Shahriari Z, Edwards RA, Rey M, Ye R, Javed F,Fang S, Mani R, Weinfeld M, Hammel M, Tainer JA, Schriemer DC, Lees-Miller SP,Glover JNM. Structural and functional characterization of the PNKP-XRCC4-LigIVDNA repair complex. Nucleic Acids Res. 2017 Jun 2;45(10):6238-6251. doi:10.1093/nar/gkx275.
  2. Bras J, Alonso I, Barbot C, Costa MM, Darwent L, Orme T, Sequeiros J, Hardy J,Coutinho P, Guerreiro R. Mutations in PNKP cause recessive ataxia with oculomotorapraxia type 4. Am J Hum Genet. 2015 Mar 5;96(3):474-9. doi:10.1016/j.ajhg.2015.01.005.
  3. Breslin C, Mani RS, Fanta M, Hoch N, Weinfeld M, Caldecott KW. The Rev1interacting region (RIR) motif in the scaffold protein XRCC1 mediates alow-affinity interaction with polynucleotide kinase/phosphatase (PNKP) during DNAsingle-strand break repair. J Biol Chem. 2017 Sep 29;292(39):16024-16031. doi:10.1074/jbc.M117.806638.
  4. Dumitrache LC, McKinnon PJ. Polynucleotide kinase-phosphatase (PNKP) mutationsand neurologic disease. Mech Ageing Dev. 2017 Jan;161(Pt A):121-129. doi:10.1016/j.mad.2016.04.009.
  5. Poulton C, Oegema R, Heijsman D, Hoogeboom J, Schot R, Stroink H, WillemsenMA, Verheijen FW, van de Spek P, Kremer A, Mancini GM. Progressive cerebellaratrophy and polyneuropathy: expanding the spectrum of PNKP mutations.Neurogenetics. 2013 Feb;14(1):43-51. doi: 10.1007/s10048-012-0351-8.
  6. Reynolds JJ, Walker AK, Gilmore EC, Walsh CA, Caldecott KW. Impact of PNKPmutations associated with microcephaly, seizures and developmental delay onenzyme activity and DNA strand break repair. Nucleic Acids Res. 2012Aug;40(14):6608-19. doi: 10.1093/nar/gks318.
  7. Shen J, Gilmore EC, Marshall CA, Haddadin M, Reynolds JJ, Eyaid W, Bodell A,Barry B, Gleason D, Allen K, Ganesh VS, Chang BS, Grix A, Hill RS, Topcu M,Caldecott KW, Barkovich AJ, Walsh CA. Mutations in PNKP cause microcephaly,seizures and defects in DNA repair. Nat Genet. 2010 Mar;42(3):245-9. doi:10.1038/ng.526.
  8. Shimada M, Dumitrache LC, Russell HR, McKinnon PJ. Polynucleotidekinase-phosphatase enables neurogenesis via multiple DNA repair pathways tomaintain genome stability. EMBO J. 2015 Oct 1;34(19):2465-80. doi:10.15252/embj.201591363.
  9. Weinfeld M, Mani RS, Abdou I, Aceytuno RD, Glover JN. Tidying up loose ends:the role of polynucleotide kinase/phosphatase in DNA strand break repair. Trends Biochem Sci. 2011 May;36(5):262-71. doi: 10.1016/j.tibs.2011.01.006.
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