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PNPT1 polyribonucleotide nucleotidyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 87178, updated on 26-Nov-2024

Summary

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Official Symbol
PNPT1provided by HGNC
Official Full Name
polyribonucleotide nucleotidyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:23166
See related
Ensembl:ENSG00000138035 MIM:610316; AllianceGenome:HGNC:23166
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
OLD35; SCA25; DFNB70; PNPASE; old-35; COXPD13
Summary
The protein encoded by this gene belongs to the evolutionary conserved polynucleotide phosphorylase family comprised of phosphate dependent 3'-to-5' exoribonucleases implicated in RNA processing and degradation. This enzyme is predominantly localized in the mitochondrial intermembrane space and is involved in import of RNA to mitochondria. Mutations in this gene have been associated with combined oxidative phosphorylation deficiency-13 and autosomal recessive nonsyndromic deafness-70. Related pseudogenes are found on chromosomes 3 and 7. [provided by RefSeq, Dec 2012]
Expression
Ubiquitous expression in thyroid (RPKM 6.2), testis (RPKM 5.9) and 25 other tissues See more
Orthologs
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Genomic context

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See PNPT1 in Genome Data Viewer
Location:
2p16.1
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (55634061..55693844, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (55631213..55690978, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (55861196..55920979, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA12 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:55794160-55794660 Neighboring gene protein phosphatase 4 regulatory subunit 3B Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:55843714-55844639 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:55844640-55845564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11500 Neighboring gene PPP4R3B divergent transcript Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:55877194-55877806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15786 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:55935598-55935772 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:55944176-55944368 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:55950709-55951210 Neighboring gene uncharacterized LOC107985811 Neighboring gene uncharacterized LOC112268416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:56063682-56064458 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:56064459-56065235 Neighboring gene EGF containing fibulin extracellular matrix protein 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Polyribonucleotide nucleotidyltransferase 1 participates in metabolic-associated fatty liver disease pathogenesis by affecting lipid metabolism and mitochondrial homeostasis. Guan C, et al. Mol Metab, 2024 Nov. PMID 39218215, Free PMC Article
  2. Is PNPT1-related hearing loss ever non-syndromic? Whole exome sequencing of adult siblings expands the natural history of PNPT1-related disorders. Eaton A, et al. Am J Med Genet A, 2018 Nov. PMID 30244537
  3. Crystal structure of dimeric human PNPase reveals why disease-linked mutants suffer from low RNA import and degradation activities. Golzarroshan B, et al. Nucleic Acids Res, 2018 Sep 19. PMID 30020492, Free PMC Article
  4. Defective mitochondrial RNA processing due to PNPT1 variants causes Leigh syndrome. Matilainen S, et al. Hum Mol Genet, 2017 Sep 1. PMID 28645153
  5. Novel biallelic mutations in the PNPT1 gene encoding a mitochondrial-RNA-import protein PNPase cause delayed myelination. Sato R, et al. Clin Genet, 2018 Feb. PMID 28594066

See all (112) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Polyribonucleotide nucleotidyltransferase 1 participates in metabolic-associated fatty liver disease pathogenesis by affecting lipid metabolism and mitochondrial homeostasis.
    Title: Polyribonucleotide nucleotidyltransferase 1 participates in metabolic-associated fatty liver disease pathogenesis by affecting lipid metabolism and mitochondrial homeostasis.
  2. Human PNPase causes RNA stabilization and accumulation of R-loops in the Escherichia coli model system.
    Title: Human PNPase causes RNA stabilization and accumulation of R-loops in the Escherichia coli model system.
  3. SP1 and NFY Regulate the Expression of PNPT1, a Gene Encoding a Mitochondrial Protein Involved in Cancer.
    Title: SP1 and NFY Regulate the Expression of PNPT1, a Gene Encoding a Mitochondrial Protein Involved in Cancer.
  4. Heterozygous PNPT1 Variants Cause Spinocerebellar Ataxia Type 25.
    Title: Heterozygous PNPT1 Variants Cause Spinocerebellar Ataxia Type 25.
  5. Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase.
    Title: Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase.
  6. Heterogeneity of PNPT1 neuroimaging: mitochondriopathy, interferonopathy or both?
    Title: Heterogeneity of PNPT1 neuroimaging: mitochondriopathy, interferonopathy or both?
  7. PNPT1, MYO15A, PTPRQ, and SLC12A2-associated genetic and phenotypic heterogeneity among hearing impaired assortative mating families in Southern India.
    Title: PNPT1, MYO15A, PTPRQ, and SLC12A2-associated genetic and phenotypic heterogeneity among hearing impaired assortative mating families in Southern India.
  8. Crystallographic modeling of the PNPT1:c.1453A>G variant as a cause of mitochondrial dysfunction and autosomal recessive deafness; expanding the neuroimaging and clinical features.
    Title: Crystallographic modeling of the PNPT1:c.1453A>G variant as a cause of mitochondrial dysfunction and autosomal recessive deafness; expanding the neuroimaging and clinical features.
  9. Ocular Manifestations of PNPT1-Related Neuropathy.
    Title: Ocular Manifestations of PNPT1-Related Neuropathy.
  10. PNPT1 and PCGF3 variants associated with angiotensin-converting enzyme inhibitor-induced cough: a nested case-control genome-wide study.
    Title: PNPT1 and PCGF3 variants associated with angiotensin-converting enzyme inhibitor-induced cough: a nested case-control genome-wide study.
Submit: New GeneRIF Correction See all GeneRIFs (43)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Autosomal recessive nonsyndromic hearing loss 70
MedGen: C1824925 OMIM: 614934 GeneReviews: Not available
Compare labs
Combined oxidative phosphorylation defect type 13
MedGen: C4706283 OMIM: 614932 GeneReviews: Not available
Compare labs
Spinocerebellar ataxia type 25
MedGen: C1837518 OMIM: 608703 GeneReviews: Hereditary Ataxia Overview
Compare labs

EBI GWAS Catalog

Description
Many sequence variants affecting diversity of adult human height.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3'-5'-RNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 3'-5'-RNA exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 3'-5'-RNA exonuclease activity TAS
Traceable Author Statement
more info
  
enables RNA binding HDA PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables miRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables poly(G) binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables poly(U) RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables polyribonucleotide nucleotidyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables polyribonucleotide nucleotidyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in RNA import into mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to interferon-beta IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to oxidative stress IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in liver regeneration IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mitochondrial RNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitochondrial RNA 3'-end processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitochondrial RNA 5'-end processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitochondrial RNA catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mitochondrial RNA catabolic process TAS
Traceable Author Statement
more info
  
involved_in mitochondrial mRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitochondrial mRNA catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mitochondrial mRNA polyadenylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitochondrion organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of growth IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nuclear polyadenylation-dependent mRNA catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of miRNA catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of mitochondrial RNA catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein homooligomerization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein homotrimerization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in rRNA import into mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of cell cycle IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of cellular respiration ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of cellular senescence IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to cAMP IEA
Inferred from Electronic Annotation
more info
  
involved_in response to growth hormone IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
part_of mitochondrial degradosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial intermembrane space IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
located_in mitochondrion HTP PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ribosome IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
polyribonucleotide nucleotidyltransferase 1, mitochondrial
Names
3'-5' RNA exonuclease OLD35
PNPase 1
PNPase old-35
polynucleotide phosphorylase 1
polynucleotide phosphorylase-like protein
NP_149100.2
XP_005264686.1
XP_016860661.1
XP_047302117.1
XP_054200311.1
XP_054200312.1
XP_054200313.1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033012.1 RefSeqGene

    Range
    5067..64850
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_033109.5 → NP_149100.2  polyribonucleotide nucleotidyltransferase 1, mitochondrial precursor

    See identical proteins and their annotated locations for NP_149100.2

    Status: REVIEWED

    Source sequence(s)
    AC015982, AJ458465, AW731791, BC009057, BU943827, CR749867, DB461021
    Consensus CDS
    CCDS1856.1
    UniProtKB/Swiss-Prot
    Q53SU0, Q68CN1, Q7Z7D1, Q8IWX1, Q8TCS8, Q96T05, Q9BRU3, Q9BVX0
    Related
    ENSP00000400646.2, ENST00000447944.7
    Conserved Domains (6) summary
    smart00316
    Location:679 → 750
    S1; Ribosomal protein S1-like RNA-binding domain
    cd11363
    Location:49 → 273
    RNase_PH_PNPase_1; Polyribonucleotide nucleotidyltransferase, repeat 1
    cd11364
    Location:366 → 596
    RNase_PH_PNPase_2; Polyribonucleotide nucleotidyltransferase, repeat 2
    PRK11824
    Location:49 → 752
    PRK11824; polynucleotide phosphorylase/polyadenylase; Provisional
    pfam03726
    Location:282 → 363
    PNPase; Polyribonucleotide nucleotidyltransferase, RNA binding domain
    cl00098
    Location:605 → 664
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    55634061..55693844 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005172.2 → XP_016860661.1  polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1

    Conserved Domains (6) summary
    smart00316
    Location:599 → 670
    S1; Ribosomal protein S1-like RNA-binding domain
    cd11364
    Location:286 → 516
    RNase_PH_PNPase_2; Polyribonucleotide nucleotidyltransferase, repeat 2
    PRK11824
    Location:1 → 672
    PRK11824; polynucleotide phosphorylase/polyadenylase; Provisional
    pfam03726
    Location:202 → 283
    PNPase; Polyribonucleotide nucleotidyltransferase, RNA binding domain
    cl00098
    Location:525 → 584
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    cl03114
    Location:1 → 193
    RNase_PH; RNase PH-like 3'-5' exoribonucleases

  2. XM_005264629.3 → XP_005264686.1  polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1

    Conserved Domains (6) summary
    smart00316
    Location:599 → 670
    S1; Ribosomal protein S1-like RNA-binding domain
    cd11364
    Location:286 → 516
    RNase_PH_PNPase_2; Polyribonucleotide nucleotidyltransferase, repeat 2
    PRK11824
    Location:1 → 672
    PRK11824; polynucleotide phosphorylase/polyadenylase; Provisional
    pfam03726
    Location:202 → 283
    PNPase; Polyribonucleotide nucleotidyltransferase, RNA binding domain
    cl00098
    Location:525 → 584
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    cl03114
    Location:1 → 193
    RNase_PH; RNase PH-like 3'-5' exoribonucleases

  3. XM_047446161.1 → XP_047302117.1  polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    55631213..55690978 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054344337.1 → XP_054200312.1  polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1

  2. XM_054344336.1 → XP_054200311.1  polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1

  3. XM_054344338.1 → XP_054200313.1  polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TCS8.2 GenPept UniProtKB/Swiss-Prot:Q8TCS8

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