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CNP 2',3'-cyclic nucleotide 3' phosphodiesterase [ Homo sapiens (human) ]

Gene ID: 1267, updated on 5-Mar-2024

Summary

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Official Symbol
CNPprovided by HGNC
Official Full Name
2',3'-cyclic nucleotide 3' phosphodiesteraseprovided by HGNC
Primary source
HGNC:HGNC:2158
See related
Ensembl:ENSG00000173786 MIM:123830; AllianceGenome:HGNC:2158
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
CNP1; HLD20
Summary
Predicted to enable 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity. Involved in substantia nigra development. Located in several cellular components, including extracellular space; microtubule; and plasma membrane. Implicated in hypomyelinating leukodystrophy 20; multiple sclerosis; and schizophrenia. Biomarker of alcoholic liver cirrhosis; multiple sclerosis; and restless legs syndrome. [provided by Alliance of Genome Resources, Apr 2022]
Annotation information
Note: CNP (Gene ID: 1267) and NPPC (Gene ID: 4880) share the CNP symbol/alias in common. CNP is a widely used alternative name for C-type natriuretic peptide (NPPC), which can be confused with the official symbol for 2',3'-cyclic-nucleotide 3'-phosphodiesterase (CNP). [06 Jul 2018]
Expression
Broad expression in brain (RPKM 130.3), kidney (RPKM 16.0) and 18 other tissues See more
Orthologs
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Genomic context

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See CNP in Genome Data Viewer
Location:
17q21.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (41966795..41977740)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (42823292..42834237)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (40118813..40129758)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATP citrate lyase Neighboring gene uncharacterized LOC124904005 Neighboring gene MPRA-validated peak2844 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:40066298-40067497 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8505 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40085993-40086896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12176 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40091696-40092276 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:40102816-40102967 Neighboring gene outer dynein arm docking complex subunit 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40110957-40111564 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40111565-40112170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40112171-40112776 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40112777-40113382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8508 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40119287-40119844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40119845-40120402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40120403-40120960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12179 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:40140463-40140963 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:40139962-40140462 Neighboring gene DnaJ heat shock protein family (Hsp40) member C7 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:40162959-40163488 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:40168666-40169865 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12182 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40180775-40181563 Neighboring gene NFKB inhibitor interacting Ras like 2 Neighboring gene zinc finger protein 385C Neighboring gene chromosome 17 open reading frame 113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8511

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. CNP deficiency causes severe hypomyelinating leukodystrophy in humans. Al-Abdi L, et al. Hum Genet, 2020 May. PMID 32128616
  2. 2',3'-cyclic nucleotide 3'-phosphodiesterases inhibit hepatitis B virus replication. Ma H, et al. PLoS One, 2013. PMID 24260477, Free PMC Article
  3. Differential expression of 2',3'-cyclic-nucleotide 3'-phosphodiesterase and neural lineage markers correlate with glioblastoma xenograft infiltration and patient survival. Zorniak M, et al. Clin Cancer Res, 2012 Jul 1. PMID 22589395, Free PMC Article
  4. No relationship between 2',3'-cyclic nucleotide 3'-phosphodiesterase and schizophrenia in the Chinese Han population: an expression study and meta-analysis. Che R, et al. BMC Med Genet, 2009 Apr 6. PMID 19348671, Free PMC Article
  5. Effect of a functional single nucleotide polymorphism in the 2',3'-cyclic nucleotide 3'-phosphodiesterase gene on the expression of oligodendrocyte-related genes in schizophrenia. Iwamoto K, et al. Psychiatry Clin Neurosci, 2008 Feb. PMID 18289148

See all (149) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Circ-AFF2/miR-650/CNP axis promotes proliferation, inflammatory response, migration, and invasion of rheumatoid arthritis synovial fibroblasts.
    Title: Circ-AFF2/miR-650/CNP axis promotes proliferation, inflammatory response, migration, and invasion of rheumatoid arthritis synovial fibroblasts.
  2. Catatonia-related executive dysfunction and brain atrophy of Cnp(-/-) mice fail to improve under PLX5622.
    Title: Genetically induced brain inflammation by Cnp deletion transiently benefits from microglia depletion.
  3. CNP deficiency causes severe hypomyelinating leukodystrophy.
    Title: CNP deficiency causes severe hypomyelinating leukodystrophy in humans.
  4. 2',3'-Cyclic-nucleotide 3'-phosphodiesterase contributes to epithelial-mesenchymal transition of lens epithelial cells through the notch signalling pathway
    Title: 2',3'-Cyclic-nucleotide 3'-phosphodiesterase contributes to epithelial-mesenchymal transition of lens epithelial cells through the notch signalling pathway.
  5. CNP and RtcA fine-tune XBP1 output during ER stress
    Title: The cyclic phosphodiesterase CNP and RNA cyclase RtcA fine-tune noncanonical XBP1 splicing during ER stress.
  6. This study showed that the expression of CNPase protein was significantly decreased but increase expression mrna in ventral prefrontal white matter in major depressive disorder.
    Title: Oligodendrocyte morphometry and expression of myelin - Related mRNA in ventral prefrontal white matter in major depressive disorder.
  7. kidneys express 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase), and renal CNPase mediates in part the renal 2',3'-cAMP-adenosine pathway
    Title: Role of 2',3'-cyclic nucleotide 3'-phosphodiesterase in the renal 2',3'-cAMP-adenosine pathway.
  8. 2',3'-cyclic nucleotide 3'-phosphodiesterases inhibit hepatitis B virus replication.
    Title: 2',3'-cyclic nucleotide 3'-phosphodiesterases inhibit hepatitis B virus replication.
  9. No Alzheimer disease-associated differences in CNP and DPYSL2 promoter DNA methylation were observed.
    Title: CNP and DPYSL2 mRNA expression and promoter methylation levels in brain of Alzheimer's disease patients.
  10. CNP binds to the structural protein Gag and blocks HIV-1 particle assembly after Gag and viral RNA have associated with the plasma membrane.
    Title: Inhibition of HIV-1 particle assembly by 2',3'-cyclic-nucleotide 3'-phosphodiesterase.
Submit: New GeneRIF Correction See all GeneRIFs (32)

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
Leukodystrophy, hypomyelinating, 20
MedGen: C5436730 OMIM: 619071 GeneReviews: Not available
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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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag CNP targets the MA domain of the HIV-1 Gag protein following its association with the plasma membrane. CNP is packaged into the interior of virions and is resistant to digestion by subtilisin PubMed
gag CNP inhibits cell-associated HIV-1 Gag processing and reduces particulate CA protein in the supernatant of transfected cells PubMed
gag CNP binds directly to HIV-1 Gag and inhibits an early step in virion assembly in cells. HIV-1 Gag E40K mutant abolishes the inhibition of Gag assembly by CNP PubMed
Tat tat HIV-1 Tat decreases the intracellular levels of cAMP and CREB ser-133 phosphorylation through a signal transduction pathway involving sequential activation of phosphatidylinositol 3-kinase, AKT, and cyclic nucleoside phosphodiesterases PubMed
capsid gag CNP inhibits cell-associated HIV-1 Gag processing and reduces particulate CA protein in the supernatant of transfected cells PubMed

Go to the HIV-1, Human Interaction Database

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 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables cyclic nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in adult locomotory behavior IEA
Inferred from Electronic Annotation
more info
  
involved_in axonogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in chemical synaptic transmission TAS
Traceable Author Statement
more info
 PubMed 
involved_in cyclic nucleotide catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in forebrain development IEA
Inferred from Electronic Annotation
more info
  
involved_in oligodendrocyte differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of mitochondrial membrane permeability IEA
Inferred from Electronic Annotation
more info
  
involved_in response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
  
involved_in response to toxic substance IEA
Inferred from Electronic Annotation
more info
  
involved_in substantia nigra development HEP PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
  
located_in extracellular exosome HDA PubMed 
located_in extracellular space IDA
Inferred from Direct Assay
more info
  
located_in melanosome IEA
Inferred from Electronic Annotation
more info
  
located_in membrane HDA PubMed 
located_in microvillus IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrial inner membrane IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrial outer membrane IEA
Inferred from Electronic Annotation
more info
  
located_in myelin sheath abaxonal region IEA
Inferred from Electronic Annotation
more info
  
located_in myelin sheath adaxonal region IEA
Inferred from Electronic Annotation
more info
  
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in pseudopodium IEA
Inferred from Electronic Annotation
more info
  
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
2',3'-cyclic-nucleotide 3'-phosphodiesterase
Names
2', 3' cyclic nucleotide 3' phosphohydrolase
CNPase
NP_001317145.1
NP_149124.3
XP_011522642.1
XP_054171055.1

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_001330216.2 → NP_001317145.1  2',3'-cyclic-nucleotide 3'-phosphodiesterase isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC125257, HY337437
    Consensus CDS
    CCDS82123.1
    Conserved Domains (2) summary
    pfam05881
    Location:166 → 379
    CNPase; 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase)
    pfam13671
    Location:32 → 146
    AAA_33; AAA domain

  2. NM_033133.5 → NP_149124.3  2',3'-cyclic-nucleotide 3'-phosphodiesterase isoform 1

    See identical proteins and their annotated locations for NP_149124.3

    Status: VALIDATED

    Source sequence(s)
    AC125257
    Consensus CDS
    CCDS11414.2
    UniProtKB/Swiss-Prot
    P09543
    Related
    ENSP00000377470.2, ENST00000393892.8
    Conserved Domains (2) summary
    pfam05881
    Location:186 → 399
    CNPase; 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase)
    pfam13671
    Location:52 → 166
    AAA_33; AAA domain

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    41966795..41977740
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011524340.3 → XP_011522642.1  2',3'-cyclic-nucleotide 3'-phosphodiesterase isoform X1

    See identical proteins and their annotated locations for XP_011522642.1

    Related
    ENSP00000377466.1, ENST00000393888.1
    Conserved Domains (2) summary
    pfam05881
    Location:166 → 379
    CNPase; 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase)
    pfam13671
    Location:32 → 146
    AAA_33; AAA domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    42823292..42834237
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054315080.1 → XP_054171055.1  2',3'-cyclic-nucleotide 3'-phosphodiesterase isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P09543.2 GenPept UniProtKB/Swiss-Prot:P09543

Gene LinkOut

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