PNPT1 polyribonucleotide nucleotidyltransferase 1 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Heterozygous PNPT1 Variants Cause Spinocerebellar Ataxia Type 25.
Title: Heterozygous PNPT1 Variants Cause Spinocerebellar Ataxia Type 25.
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.
Heterogeneity of PNPT1 neuroimaging: mitochondriopathy, interferonopathy or both?
Title: Heterogeneity of PNPT1 neuroimaging: mitochondriopathy, interferonopathy or both?
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.
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.
Ocular Manifestations of PNPT1-Related Neuropathy.
Title: Ocular Manifestations of PNPT1-Related Neuropathy.
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	not available
Combined oxidative phosphorylation defect type 13 MedGen: C4706283 OMIM: 614932 GeneReviews: Not available	not available
Spinocerebellar ataxia type 25 MedGen: C1837518 OMIM: 608703 GeneReviews: Hereditary Ataxia Overview	not available

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC139196P1 (e-PCR)
- UniSTS:270883

PMC156606P3 (e-PCR)
- UniSTS:271410

PMC156606P4 (e-PCR)
- UniSTS:271411

D8S2279 (e-PCR)
- UniSTS:473907

D10S16 (e-PCR)
- UniSTS:155756

D15S1477 (e-PCR)
- UniSTS:474482

D1S1425 (e-PCR)
- UniSTS:149621

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 more info	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 more info	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

EC 2.7.7.8

XP_005264686.1

EC 2.7.7.8

XP_016860661.1

EC 2.7.7.8

XP_047302117.1

EC 2.7.7.8

XP_054200311.1

EC 2.7.7.8

XP_054200312.1

EC 2.7.7.8

XP_054200313.1

EC 2.7.7.8

NCBI Reference Sequences (RefSeq)

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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

NG_033012.1 RefSeqGene

Range

5067..64850

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

55634061..55693844 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

55631213..55690978 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054344337.1 → XP_054200312.1 polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1
XM_054344336.1 → XP_054200311.1 polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1
XM_054344338.1 → XP_054200313.1 polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X2