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

    Gene ID: 1267, updated on 28-Oct-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 cytoplasm; extracellular space; and microtubule. 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, Oct 2024]
    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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (41966795..41977740)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (42823292..42834237)
    RS_2024_09 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 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. cDNA cloning and amino acid sequence of human brain 2',3'-cyclic-nucleotide 3'-phosphodiesterase. Kurihara T, et al. Biochem Biophys Res Commun, 1988 Apr 29. PMID 2835044
    2. Leydig cells of the human testis possess astrocyte and oligodendrocyte marker molecules. Davidoff MS, et al. Acta Histochem, 2002. PMID 11993850
    3. Crystallization and preliminary X-ray crystallographic studies of human 2',3'-cyclic nucleotide 3'-phosphodiesterase. Sakamoto Y, et al. Acta Crystallogr D Biol Crystallogr, 2004 Nov. PMID 15502338
    4. Crystal structure of the catalytic fragment of human brain 2',3'-cyclic-nucleotide 3'-phosphodiesterase. Sakamoto Y, et al. J Mol Biol, 2005 Feb 25. PMID 15713463
    5. CNP deficiency causes severe hypomyelinating leukodystrophy in humans. Al-Abdi L, et al. Hum Genet, 2020 May. PMID 32128616

    See all (165) 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
    		not available

    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 microtubule IDA
    Inferred from Direct Assay
    more info
    		 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_2024_08

    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

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

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