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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PNPT1
polyribonucleotide nucleotidyltransferase 1
Chromosome 2 Β· 2p16.1
NCBI Gene: 87178Ensembl: ENSG00000138035.16HGNC: HGNC:23166UniProt: Q8TCS8
121PubMed Papers
23Diseases
0Drugs
71Pathogenic Variants
FUNCTIONAL ROLE
Hub GeneTransporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
regulation of cellular senescenceprotein homotrimerizationnuclear polyadenylation-dependent mRNA catabolic processmitochondrial mRNA polyadenylationcombined oxidative phosphorylation defect type 13autosomal recessive nonsyndromic hearing loss 70deafnessspinocerebellar ataxia type 25
✦AI Summary

PNPT1 encodes polynucleotide phosphorylase (PNPase), a 3'-to-5' exoribonuclease localized to the mitochondrial intermembrane space and matrix 1. Primary functions include catalyzing phosphorolysis of single-stranded polyribonucleotides and serving as a core component of the mitochondrial degradosome (mtEXO) complex, which degrades double-stranded RNA with 3'-to-5' directionality 1. PNPT1 processes non-coding mitochondrial transcripts, facilitates mRNA polyadenylation, and mediates cytoplasmic RNA import into mitochondria 2. Additionally, PNPT1 functions as a cytoplasmic exoribonuclease degrading specific mRNAs and microRNAs, and participates in oxidized RNA surveillance 3. A critical protective mechanism involves PNPT1 restricting accumulation of mitochondrial double-stranded RNA (mt-dsRNA) and preventing its cytoplasmic escape, thereby suppressing MDA5-driven antiviral signaling and preventing inflammatory responses 12. Mutations in PNPT1 cause mt-dsRNA accumulation coupled with interferon upregulation 1. PNPT1 deficiency also triggers the mt-dsRNA-PKR-eIF2Ξ± axis, leading to translational arrest and renal tubular atrophy in chr2 kidney disease 4. Clinically, PNPT1 mutations associate with autosomal recessive deafness (DFNB70) presenting with sensorineural hearing loss and vestibular dysfunction 5, and spinocerebellar ataxia 25 6. PNPT1 reduction occurs in metabolic-associated fatty liver disease and hepatocellular carcinoma, suggesting context-dependent roles in disease progression 78.

Sources cited
1
PNPT1 localizes to mitochondrial intermembrane space/matrix; degrades mitochondrial dsRNA and prevents cytoplasmic escape; mutations cause mt-dsRNA accumulation and interferon activation
PMID: 30046113
2
Reduced PNPT1 in senescent cells promotes mt-dsRNA accumulation and inflammatory SASP response
PMID: 39191740
3
PNPT1 deficiency causes renal tubular injury via mt-dsRNA-PKR-eIF2Ξ± axis-mediated translation arrest
PMID: 36869030
4
PNPT1 mutations cause spinocerebellar ataxia 25 (SCA25)
PMID: 37479376
5
PNPT1 encodes 3'-5' exoribonuclease involved in mitochondrial RNA degradation and surveillance; overexpression associated with poor liver cancer prognosis
PMID: 36232701
6
Compound heterozygous PNPT1 variants cause DFNB70 with prelingual profound sensorineural hearing loss and vestibular dysfunction
PMID: 34374074
7
PNPT1 is reduced in metabolic-associated fatty liver disease and regulates lipid metabolism and mitochondrial stability through Mcl-1 mRNA degradation
PMID: 39218215
8
PNPT1 is overexpressed in hepatocellular carcinoma and promotes epithelial phenotype maintenance
PMID: 39522317
Disease Associationsβ“˜23
combined oxidative phosphorylation defect type 13Open Targets
0.81Strong
autosomal recessive nonsyndromic hearing loss 70Open Targets
0.75Strong
deafnessOpen Targets
0.69Moderate
spinocerebellar ataxia type 25Open Targets
0.68Moderate
genetic disorderOpen Targets
0.51Moderate
open-angle glaucomaOpen Targets
0.49Moderate
glaucomaOpen Targets
0.47Moderate
hearing lossOpen Targets
0.46Moderate
hypothyroidismOpen Targets
0.40Weak
hearing loss, autosomal recessiveOpen Targets
0.37Weak
DystoniaOpen Targets
0.37Weak
Neurodevelopmental disorderOpen Targets
0.33Weak
myxedemaOpen Targets
0.32Weak
neurodegenerative diseaseOpen Targets
0.30Weak
Global developmental delayOpen Targets
0.30Weak
cholelithiasisOpen Targets
0.27Weak
diverticular diseaseOpen Targets
0.26Weak
Barrett's esophagusOpen Targets
0.25Weak
autoimmune thyroid diseaseOpen Targets
0.24Weak
thyroid diseaseOpen Targets
0.24Weak
Combined oxidative phosphorylation deficiency 13UniProt
Deafness, autosomal recessive, 70, with or without adult-onset neurodegenerationUniProt
Spinocerebellar ataxia 25UniProt
Pathogenic Variants71
NM_033109.5(PNPT1):c.1519G>T (p.Ala507Ser)Pathogenic
not provided|Combined oxidative phosphorylation defect type 13|Neurodevelopmental disorder|Combined oxidative phosphorylation defect type 13;Autosomal recessive nonsyndromic hearing loss 70|Inborn genetic diseases|Spinocerebellar ataxia type 25|Autosomal recessive nonsyndromic hearing loss 70|PNPT1-related disorder
β˜…β˜…β˜†β˜†2026β†’ Residue 507
NM_033109.5(PNPT1):c.407G>A (p.Arg136His)Pathogenic
Combined oxidative phosphorylation defect type 13|not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 136
NM_033109.5(PNPT1):c.1174_1175del (p.Gln392fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 392
NM_033109.5(PNPT1):c.1849C>T (p.Arg617Ter)Pathogenic
Global developmental delay|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 617
NM_033109.5(PNPT1):c.1223del (p.Lys407_Ser408insTer)Pathogenic
not provided|Combined oxidative phosphorylation defect type 13
β˜…β˜…β˜†β˜†2025β†’ Residue 407
NM_033109.5(PNPT1):c.574C>T (p.Arg192Ter)Pathogenic
Autosomal recessive nonsyndromic hearing loss 70|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 192
NM_033109.5(PNPT1):c.419C>T (p.Pro140Leu)Likely pathogenic
PNPT1-related disorder|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 140
NM_033109.5(PNPT1):c.1390C>T (p.Arg464Ter)Pathogenic
Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 464
NM_033109.5(PNPT1):c.1818T>G (p.Val606=)Pathogenic
Autosomal recessive nonsyndromic hearing loss 70;Combined oxidative phosphorylation defect type 13|not provided|Combined oxidative phosphorylation defect type 13
β˜…β˜…β˜†β˜†2023β†’ Residue 606
NM_033109.5(PNPT1):c.1906+1G>ALikely pathogenic
Combined oxidative phosphorylation defect type 13|not provided
β˜…β˜…β˜†β˜†2023
NM_033109.5(PNPT1):c.223-1G>ALikely pathogenic
not provided
β˜…β˜…β˜†β˜†2023
NM_033109.5(PNPT1):c.1528G>C (p.Ala510Pro)Pathogenic
Combined oxidative phosphorylation defect type 13|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 510
NM_033109.5(PNPT1):c.394C>T (p.Arg132Ter)Pathogenic
not provided|Combined oxidative phosphorylation defect type 13
β˜…β˜…β˜†β˜†2022β†’ Residue 132
NM_033109.5(PNPT1):c.310C>T (p.Gln104Ter)Pathogenic
Combined oxidative phosphorylation defect type 13
β˜…β˜†β˜†β˜†2026β†’ Residue 104
NM_033109.5(PNPT1):c.828dup (p.Phe277fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 277
NM_033109.5(PNPT1):c.16dup (p.Tyr6fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 6
NM_033109.5(PNPT1):c.1258del (p.Asp420fs)Pathogenic
Monogenic hearing loss
β˜…β˜†β˜†β˜†2025β†’ Residue 420
NM_033109.5(PNPT1):c.2043del (p.Tyr682fs)Likely pathogenic
Spinocerebellar ataxia type 25
β˜…β˜†β˜†β˜†2025β†’ Residue 682
NM_033109.5(PNPT1):c.1285-2A>GLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_033109.5(PNPT1):c.976+1G>TLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
View on ClinVar β†—
Related Genes
POLR2BProtein interaction100%RPS15Protein interaction98%EXOSC10Protein interaction97%EXOSC8Protein interaction97%EXOSC7Protein interaction97%EXOSC3Protein interaction97%
Tissue Expression6 tissues
Heart
100%
Bone Marrow
69%
Liver
62%
Brain
55%
Lung
53%
Ovary
51%
Gene Interaction Network
Click a node to explore
PNPT1POLR2BRPS15EXOSC10EXOSC8EXOSC7EXOSC3
PROTEIN STRUCTURE
Preparing viewer…
PDB3U1K Β· 2.13 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.64LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.49 [0.38–0.64]
RankingsWhere PNPT1 stands among ~20K protein-coding genes
  • #3,891of 20,598
    Most Researched121 Β· top quartile
  • #1,024of 5,498
    Most Pathogenic Variants71 Β· top quartile
  • #4,575of 17,882
    Most Constrained (LOEUF)0.64
Genes detectedPNPT1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Mitochondrial double-stranded RNA triggers antiviral signalling in humans.
PMID: 30046113
Nature Β· 2018
1.00
2
Release of mitochondrial dsRNA into the cytosol is a key driver of the inflammatory phenotype of senescent cells.
PMID: 39191740
Nat Commun Β· 2024
0.90
3
Polynucleotide phosphorylase protects against renal tubular injury via blocking mt-dsRNA-PKR-eIF2Ξ± axis.
PMID: 36869030
Nat Commun Β· 2023
0.80
4
Autosomal dominant cerebellar ataxias: new genes and progress towards treatments.
PMID: 37479376
Lancet Neurol Β· 2023
0.70
5
SP1 and NFY Regulate the Expression of
PMID: 36232701
Int J Mol Sci Β· 2022
0.60