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Gene

PNKP

polynucleotide kinase 3'-phosphatase

Summary

Cytogenetic location
19q13.33
Coordinates
Chromosome 19: 49,861,204–49,867,576 (GRCh38)
Exons
17 exons across 6.4 kb
Protein
521 amino acids
Inheritance
Autosomal recessive
Also known as
PNK
MANE Select transcript
ENST00000322344.8NM_007254.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Dystonia, Myotonia, Paroxysmal Dyskinesia

    • Inherited Dystonia

      Umbrella term covering inherited dystonias, including DYT-TOR1A early-onset generalized dystonia, DYT-THAP1, myoclonus-dystonia (SGCE) and KMT2B-related dystonia.

      • 3 GenCC submitters rate it definitive or strong

Broader groupings

  • Autosomal Recessive Cerebellar Ataxias (incl. CANVAS and AVED)

    • Autosomal Recessive Cerebellar AtaxiaAutosomal recessive

      One of 57 genes linked to it

      A group of recessively inherited ataxias caused by biallelic variants in genes such as RFC1, FXN, SACS, TTPA, SETX, APTX, PNKP, ANO10 and SYNE1.

      • 3 GenCC submitters rate it definitive or strong
      What knowing changes

      Ataxia with vitamin E deficiency (TTPA) is treatable with vitamin E supplements; other forms are managed with physiotherapy and symptom care, and relatives can be offered carrier testing.

  • Epilepsy (Full Panel)

    • Epilepsy

      One of 171 genes linked to it

      A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How PNKP is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 19, with a bracket where PNKP sits. PNKP and 43 genes near it on chromosome 19, from 49,364,390 to 50,364,389.Chromosome 1919q13.33p13.3p13.2p13.13p13.12p13.11p12p11q11q12q13.11q13.12q13.13q13.2q13.31q13.32q13.33q13.41q13.42q13.4349.4 Mb49.6 Mb49.8 Mb50 Mb50.2 MbDKKL1: 49,361,783–49,375,120, forward strandDKKL1KASH5: 49,388,219–49,417,990, forward strandKASH5PTH2: 49,422,419–49,423,660, reverse strandPTH2GFY: 49,423,749–49,428,987, forward strandGFYSLC17A7: 49,429,399–49,443,197, reverse strandPIH1D1: 49,446,291–49,453,537, reverse strandALDH16A1: 49,453,146–49,471,052, forward strand: 49,462,752–49,486,231, forward strandFLT3LG: 49,474,150–49,486,233, forward strandFLT3LGRPL13A: 49,487,510–49,493,057, forward strandRPL13ARPS11: 49,496,233–49,499,903, forward strandRPS11FCGRT: 49,506,806–49,526,917, forward strandFCGRTRCN3: 49,526,534–49,579,703, forward strandRCN3NOSIP: 49,555,207–49,592,927, reverse strandNOSIPPRRG2: 49,580,646–49,591,004, forward strandPRRG2PRR12: 49,591,108–49,626,439, forward strandPRR12RRAS: 49,634,555–49,640,211, reverse strandRRASSCAF1: 49,640,488–49,658,649, forward strandIRF3: 49,659,569–49,665,864, reverse strandBCL2L12: 49,664,622–49,673,917, forward strandBCL2L12PRMT1: 49,675,786–49,689,029, forward strandPRMT1ADM5: 49,688,953–49,690,575, forward strandADM5CPT1C: 49,690,898–49,713,733, forward strandCPT1CTSKS: 49,739,753–49,763,329, reverse strandTSKSAP2A1: 49,766,912–49,807,114, forward strandAP2A1FUZ: 49,806,866–49,817,376, reverse strandFUZMED25: 49,818,269–49,840,384, forward strandPTOV1: 49,850,735–49,860,744, forward strandPTOV1PNKP: 49,861,204–49,867,576, reverse strandPNKPAKT1S1: 49,869,023–49,879,470, reverse strandAKT1S1TBC1D17: 49,877,501–49,888,751, forward strandTBC1D17IL4I1: 49,889,654–49,929,926, reverse strandIL4I1NUP62: 49,906,825–49,929,926, reverse strandNUP62: 49,909,501–49,958,391, reverse strandATF5: 49,923,910–49,933,935, forward strandATF5SIGLEC11: 49,948,910–49,961,172, reverse strandSIGLEC16: 49,969,600–49,975,819, forward strandVRK3: 49,974,537–50,025,946, reverse strandVRK3ZNF473: 50,025,714–50,053,414, forward strandZNF473IZUMO2: 50,152,537–50,163,281, reverse strandIZUMO2MYH14: 50,188,181–50,310,545, forward strandMYH14KCNC3: 50,311,937–50,333,515, reverse strandKCNC3NR1H2: 50,329,639–50,383,404, forward strandNR1H2NAPSA: 50,358,472–50,369,342, reverse strandNAPSADiagram of PNKP: 17 exons on the reverse strand of chromosome 19Exon 17: 2 known disease-causing sitesExon 16: 1 known disease-causing siteExon 15: 6 known disease-causing sitesExon 14: 8 known disease-causing sitesExon 13: 1 known disease-causing siteExon 12: 2 known disease-causing sitesExon 11: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 4: 3 known disease-causing sitesExon 3: 1 known disease-causing siteExon 2: 3 known disease-causing sitesExon 17: 49,861,204–49,861,365, 162 basesExon 16: 49,861,449–49,861,510, 62 basesExon 15: 49,861,608–49,861,695, 88 basesExon 14: 49,861,772–49,861,881, 110 basesExon 13: 49,862,044–49,862,105, 62 basesExon 12: 49,862,185–49,862,281, 97 basesExon 11: 49,862,371–49,862,463, 93 basesExon 10: 49,862,538–49,862,608, 71 basesExon 9: 49,862,690–49,862,738, 49 basesExon 8: 49,863,689–49,863,760, 72 basesExon 7: 49,863,964–49,864,071, 108 basesExon 6: 49,864,179–49,864,236, 58 basesExon 5: 49,864,324–49,864,403, 80 basesExon 4: 49,865,127–49,865,426, 300 basesExon 3: 49,866,399–49,866,445, 47 basesExon 2: 49,867,054–49,867,217, 164 basesExon 1: 49,867,469–49,867,576, 108 bases17161514131211109876543215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 1.7 kb of the gene's 6.4 kb; 1,566 of those bases code for the protein.

How a genome test reads PNKP

41

positions in PNKP where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 6.4 kb of PNKP, introns included, not only the 1.7 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). PNKP gene: polynucleotide kinase 3'-phosphatase. Retrieved 17 October 2026, from https://dantelabs.com/genes/pnkp

Vancouver

Dante Labs. PNKP gene: polynucleotide kinase 3'-phosphatase [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/pnkp

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