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PDE12 phosphodiesterase 12 [ Homo sapiens (human) ]

Gene ID: 201626, updated on 5-Mar-2024

Summary

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Official Symbol
PDE12provided by HGNC
Official Full Name
phosphodiesterase 12provided by HGNC
Primary source
HGNC:HGNC:25386
See related
Ensembl:ENSG00000174840 MIM:616519; AllianceGenome:HGNC:25386
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
2-PDE; 2'-PDE
Summary
Enables 3'-5'-exoribonuclease activity. Involved in several processes, including RNA metabolic process; cellular response to cytokine stimulus; and regulation of mitochondrial mRNA stability. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in adrenal (RPKM 3.9), thyroid (RPKM 3.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
3p14.3
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (57556274..57656495)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (57596636..57696867)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (57542001..57642222)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene dynein axonemal heavy chain 12 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:57529659-57530209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:57543831-57544463 Neighboring gene RNA, U6 small nuclear 108, pseudogene Neighboring gene RNA, U6 small nuclear 483, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19989 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:57582608-57583807 Neighboring gene RNA, U6atac small nuclear 26, pseudogene Neighboring gene ARF4 antisense RNA 1 Neighboring gene ADP ribosylation factor 4 Neighboring gene DENN domain containing 6A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14481 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:57678132-57678632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14483 Neighboring gene DENND6A divergent transcript Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:57737311-57738510 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:57741142-57742044 and GRCh37_chr3:57742045-57742946 Neighboring gene MPRA-validated peak4671 silencer Neighboring gene sarcolemma associated protein Neighboring gene PDHA1 pseudogene 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. PDE12 in type 1 diabetes. Tekin H, et al. Sci Rep, 2022 Oct 28. PMID 36307540, Free PMC Article
  2. The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors. Wood ER, et al. J Biol Chem, 2015 Aug 7. PMID 26055709, Free PMC Article
  3. Crystallization and preliminary X-ray crystallographic analysis of human phosphodiesterase 12. Kohno T, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2010 May 1. PMID 20445249, Free PMC Article
  4. PDE12 removes mitochondrial RNA poly(A) tails and controls translation in human mitochondria. Rorbach J, et al. Nucleic Acids Res, 2011 Sep 1. PMID 21666256, Free PMC Article
  5. Identification of 2'-phosphodiesterase, which plays a role in the 2-5A system regulated by interferon. Kubota K, et al. J Biol Chem, 2004 Sep 3. PMID 15231837

See all (60) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PDE12 disrupts mitochondrial oxidative phosphorylation and mediates mitochondrial dysfunction to induce oral mucosal epithelial barrier damage in oral submucous fibrosis.
    Title: PDE12 disrupts mitochondrial oxidative phosphorylation and mediates mitochondrial dysfunction to induce oral mucosal epithelial barrier damage in oral submucous fibrosis.
  2. PDE12 in type 1 diabetes.
    Title: PDE12 in type 1 diabetes.
  3. PDE12 is a negative regulator of the antiviral innate immune response.
    Title: The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors.
  4. 2'-phosphodiesterase is a mitochondrial protein that specifically removes poly(A) extensions from mitochondrial mRNAs both in vitro and in mitochondria of cultured cells.
    Title: PDE12 removes mitochondrial RNA poly(A) tails and controls translation in human mitochondria.
  5. 2'-PDE locates to the mitochondrial matrix of human cells, and comprise an active 3'-5' exoribonuclease exhibiting a preference for oligo-adenosine RNA like canonical cytoplasmic deadenylases.
    Title: Human 2'-phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  7. crystals of phosphodiesterase 12 belonged to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 111.3, c = 192.4 A, and diffracted to 2.5 A resolution.
    Title: Crystallization and preliminary X-ray crystallographic analysis of human phosphodiesterase 12.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables oligoribonucleotidase activity TAS
Traceable Author Statement
more info
  
enables poly(A)-specific ribonuclease activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in antiviral innate immune response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to dsRNA IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to interferon-alpha IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cellular response to type II interferon IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in defense response to virus TAS
Traceable Author Statement
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mitochondrial mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nucleic acid metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of viral genome replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of mitochondrial mRNA stability IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in mitochondrial matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial matrix IMP
Inferred from Mutant Phenotype
more info
 PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
2',5'-phosphodiesterase 12
Names
2'-phosphodiesterase
mitochondrial deadenylase
NP_001309105.1
NP_001309106.1
NP_808881.3

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.

mRNA and Protein(s)

  1. NM_001322176.2 → NP_001309105.1  2',5'-phosphodiesterase 12 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. These differences result in a shorter protein (isoform 2) with a distinct C-terminus, compared to isoform 1. Isoform 2 may lack phospodiesterase or deadenylase activty.
    Source sequence(s)
    AC092418, AC114480, BM713922
    Conserved Domains (1) summary
    cl00490
    Location:299 → 462
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

  2. NM_001322177.2 → NP_001309106.1  2',5'-phosphodiesterase 12 isoform 3 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 3' coding region and 3' UTR, compared to variant 1. These differences result in a shorter protein (isoform 3) with a distinct C-terminus, compared to isoform 1. Isoform 3 may lack phospodiesterase or deadenylase activty.
    Source sequence(s)
    AC092418, BC034978, U79276
    Consensus CDS
    CCDS82792.1
    UniProtKB/TrEMBL
    F6T1Q0
    Related
    ENSP00000420626.1, ENST00000487257.1
    Conserved Domains (1) summary
    cl00490
    Location:299 → 462
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

  3. NM_177966.7 → NP_808881.3  2',5'-phosphodiesterase 12 isoform 1 precursor

    See identical proteins and their annotated locations for NP_808881.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes the canonical protein (isoform 1).
    Source sequence(s)
    AC092418, AL831824, U79276
    Consensus CDS
    CCDS33772.1
    UniProtKB/Swiss-Prot
    B4DTU8, Q6L8Q7, Q8IYU3, Q8NDU2, Q8TE78
    Related
    ENSP00000309142.7, ENST00000311180.9
    Conserved Domains (1) summary
    cl00490
    Location:299 → 608
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    57556274..57656495
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    57596636..57696867
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6L8Q7.2 GenPept UniProtKB/Swiss-Prot:Q6L8Q7

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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