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Gene

PNPT1

polyribonucleotide nucleotidyltransferase 1

Summary

Cytogenetic location
2p16.1
Coordinates
Chromosome 2: 55,634,061–55,693,844 (GRCh38)
Exons
28 exons across 59.8 kb
Protein
783 amino acids
Also known as
PNPase, OLD35, old-35
Previous symbols
DFNB70
MANE Select transcript
ENST00000447944.7NM_033109.5
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

  • Primary Mitochondrial Disease

    • Combined Oxidative Phosphorylation Deficiency

      Disorders, usually caused by nuclear genes involved in mitochondrial protein production, that reduce several respiratory chain complexes at once and often cause severe multisystem disease in childhood.

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

      Knowing can end a diagnostic search and guide surveillance and supportive care.

Broader groupings

  • Hearing Loss and Deafness

    • Nonsyndromic Genetic Hearing Loss

      One of 97 genes linked to it

      Inherited hearing loss without other medical features, including the common recessive forms caused by GJB2, OTOF, SLC26A4, STRC and many other genes, as well as dominant, X-linked and mitochondrial forms.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Knowing the genetic cause can guide hearing support and cochlear implant decisions, gene-therapy trial eligibility (for example OTOF) and family counselling.

  • Leigh Syndrome

    • One of 69 genes linked to it

      A progressive neurological disease defined by specific neuropathological features associating brainstem and basal ganglia lesions.

      • ClinGen rates the link moderate

How PNPT1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where PNPT1 sits. PNPT1 and 7 genes near it on chromosome 2, from 55,163,953 to 56,163,952.Chromosome 22p16.1p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.355.2 Mb55.4 Mb55.6 Mb55.8 Mb56 MbCLHC1: 55,172,547–55,232,563, reverse strandCLHC1RPS27A: 55,229,447–55,236,649, forward strandRPS27AMTIF2: 55,236,218–55,270,263, reverse strandMTIF2CCDC88A: 55,287,363–55,420,042, reverse strandCCDC88ACFAP36: 55,519,559–55,545,501, forward strandCFAP36PPP4R3B: 55,547,292–55,618,880, reverse strandPPP4R3BPNPT1: 55,634,061–55,693,844, reverse strandPNPT1EFEMP1: 55,810,992–55,924,271, reverse strandEFEMP1Diagram of PNPT1: 28 exons on the reverse strand of chromosome 2Exon 26: 1 known disease-causing siteExon 25: 2 known disease-causing sitesExon 22: 1 known disease-causing siteExon 20: 1 known disease-causing siteExon 19: 4 known disease-causing sitesExon 18: 1 known disease-causing siteExon 17: 3 known disease-causing sitesExon 14: 1 known disease-causing siteExon 12: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 4: 2 known disease-causing sitesExon 1: 1 known disease-causing siteExon 28: 55,634,061–55,636,392, 2,332 basesExon 27: 55,637,552–55,637,599, 48 basesExon 26: 55,640,627–55,640,705, 79 basesExon 25: 55,643,158–55,643,213, 56 basesExon 24: 55,643,319–55,643,425, 107 basesExon 23: 55,644,637–55,644,720, 84 basesExon 22: 55,645,349–55,645,432, 84 basesExon 21: 55,646,259–55,646,322, 64 basesExon 20: 55,646,415–55,646,486, 72 basesExon 19: 55,647,347–55,647,453, 107 basesExon 18: 55,654,900–55,654,953, 54 basesExon 17: 55,656,131–55,656,220, 90 basesExon 16: 55,656,305–55,656,371, 67 basesExon 15: 55,660,157–55,660,193, 37 basesExon 14: 55,661,956–55,662,026, 71 basesExon 13: 55,666,991–55,667,093, 103 basesExon 12: 55,667,862–55,667,958, 97 basesExon 11: 55,671,319–55,671,376, 58 basesExon 10: 55,671,995–55,672,046, 52 basesExon 9: 55,672,893–55,673,079, 187 basesExon 8: 55,679,682–55,679,795, 114 basesExon 7: 55,680,712–55,680,759, 48 basesExon 6: 55,680,855–55,680,918, 64 basesExon 5: 55,683,785–55,683,834, 50 basesExon 4: 55,684,943–55,685,048, 106 basesExon 3: 55,686,370–55,686,444, 75 basesExon 2: 55,687,645–55,687,705, 61 basesExon 1: 55,693,663–55,693,844, 182 bases2825201510515′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 4.5 kb of the gene's 59.8 kb; 2,352 of those bases code for the protein.

How a genome test reads PNPT1

29

positions in PNPT1 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 59.8 kb of PNPT1, introns included, not only the 4.5 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.). PNPT1 gene: polyribonucleotide nucleotidyltransferase 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/pnpt1

Vancouver

Dante Labs. PNPT1 gene: polyribonucleotide nucleotidyltransferase 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pnpt1

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