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    CNPY3 canopy FGF signaling regulator 3 [ Homo sapiens (human) ]

    Gene ID: 10695, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CNPY3provided by HGNC
    Official Full Name
    canopy FGF signaling regulator 3provided by HGNC
    Primary source
    HGNC:HGNC:11968
    See related
    Ensembl:ENSG00000137161 MIM:610774; AllianceGenome:HGNC:11968
    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
    CAG4A; DEE60; ERDA5; TNRC5; EIEE60; PRAT4A
    Summary
    This gene encodes a protein that binds members of the toll-like receptor protein family and functions as a chaperone to aid in folding and export of these proteins. Alternative splicing results in multiple transcript variants. Naturally occuring readthrough transcription occurs between this locus and the downstream GNMT (glycine N-methyltransferase) gene and is represented with GeneID:107080644. [provided by RefSeq, Jan 2016]
    Expression
    Ubiquitous expression in spleen (RPKM 21.7), bone marrow (RPKM 19.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CNPY3 in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (42928002..42939294)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42757067..42768434)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (42895740..42907032)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24576 Neighboring gene peroxisomal biogenesis factor 39 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17209 Neighboring gene pre T cell antigen receptor alpha Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:42896611-42897112 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:42897113-42897614 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24580 Neighboring gene CNPY3-GNMT readthrough Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:42906342-42906844 Neighboring gene long intergenic non-protein coding RNA 2976 Neighboring gene RPL24 pseudogene 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. The TLR-chaperone CNPY3 is a critical regulator of NLRP3-inflammasome activation. Ghait M, et al. Eur J Immunol, 2022 Jun. PMID 35334124
    2. A novel rare variant of CNPY3 from familial NMOSD impairs the TLR-mediated immune response. Mo Y, et al. J Neuroimmunol, 2023 Apr 15. PMID 36931208
    3. A single base mutation in the PRAT4A gene reveals differential interaction of PRAT4A with Toll-like receptors. Kiyokawa T, et al. Int Immunol, 2008 Nov. PMID 18780723
    4. Toll-like receptor and accessory molecule mRNA expression in humans and mice as well as in murine autoimmunity, transient inflammation, and progressive fibrosis. Ramaiah SK, et al. Int J Mol Sci, 2013 Jun 26. PMID 23803655, Free PMC Article
    5. Biallelic Variants in CNPY3, Encoding an Endoplasmic Reticulum Chaperone, Cause Early-Onset Epileptic Encephalopathy. Mutoh H, et al. Am J Hum Genet, 2018 Feb 1. PMID 29394991, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel rare variant of CNPY3 from familial NMOSD impairs the TLR-mediated immune response.
      Title: A novel rare variant of CNPY3 from familial NMOSD impairs the TLR-mediated immune response.
    2. The TLR-chaperone CNPY3 is a critical regulator of NLRP3-inflammasome activation.
      Title: The TLR-chaperone CNPY3 is a critical regulator of NLRP3-inflammasome activation.
    3. The data suggest that CNPY3 performs essential roles in brain function, in addition to known Toll-like receptor-dependent immune responses.
      Title: Biallelic Variants in CNPY3, Encoding an Endoplasmic Reticulum Chaperone, Cause Early-Onset Epileptic Encephalopathy.
    4. a mechanism for the differential trafficking of TLR1 I602S variants, and highlight the distinct roles for PRAT4A and PRAT4B in the regulation of TLR1 surface expression.
      Title: Cell surface trafficking of TLR1 is differentially regulated by the chaperones PRAT4A and PRAT4B.
    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

    Associated conditions

    Description Tests
    Developmental and epileptic encephalopathy, 60
    MedGen: C4693663 OMIM: 617929 GeneReviews: Not available
    		Compare labs

    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

    Readthrough CNPY3-GNMT

    Readthrough gene: CNPY3-GNMT, Included gene: GNMT

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    protein canopy homolog 3
    Names
    CAG repeat containing
    CTG repeat protein 4a
    expanded repeat-domain protein CAG/CTG 5
    protein associated with TLR4
    protein associated with Toll-like receptor 4A
    trinucleotide repeat-containing gene 5 protein

    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_001318842.1 → NP_001305771.1  protein canopy homolog 3 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon and uses an alternate splice site in the 5' region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is longer than isoform (1).
      Source sequence(s)
      AI202110, AK124196, BC011767, BQ063472
      Conserved Domains (1) summary
      pfam11938
      Location:48 → 227
      DUF3456; TLR4 regulator and MIR-interacting MSAP

    2. NM_001318845.1 → NP_001305774.1  protein canopy homolog 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' coding region and initiates translation at an alternate start codon compared to variant 1. The encoded isoform (2) has a distinct, shorter N-terminus than isoform 1.
      Source sequence(s)
      AI202110, AK124196, BC011767
      Conserved Domains (1) summary
      pfam11938
      Location:4 → 105
      DUF3456; TLR4 regulator and MIR-interacting MSAP

    3. NM_001318847.2 → NP_001305776.1  protein canopy homolog 3 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains an alternate exon in the 5' region, lacks multiple 3' exons, and extends past a splice site used in variant 1, resulting in a distinct 3' coding region and 3' UTR. The encoded isoform (5) has a shorter, distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK124196, CA431321, CK429647
      Conserved Domains (1) summary
      pfam11938
      Location:48 → 92
      DUF3456; TLR4 regulator and MIR-interacting MSAP

    4. NM_001318848.2 → NP_001305777.1  protein canopy homolog 3 isoform 6 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks multiple 3' exons and extends past a splice site used in variant 1, resulting in a distinct 3' coding region and 3' UTR. The encoded isoform (6) has a shorter, distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK124196, BQ680146, CA431321
      Conserved Domains (1) summary
      pfam11938
      Location:48 → 124
      DUF3456; TLR4 regulator and MIR-interacting MSAP

    5. NM_006586.5 → NP_006577.2  protein canopy homolog 3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_006577.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AI202110, AL035587, BC004423
      Consensus CDS
      CCDS4875.1
      UniProtKB/Swiss-Prot
      O15412, Q0P6I2, Q8NF54, Q8WTU8, Q9BT09, Q9P0F2
      Related
      ENSP00000361926.4, ENST00000372836.5
      Conserved Domains (1) summary
      pfam11938
      Location:48 → 194
      DUF3456; TLR4 regulator and MIR-interacting MSAP

    RNA

    1. NR_134880.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) contains an alternate exon in the 5' region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI202110, AK124196, BC011767, BG675987

    2. NR_134881.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) has a longer 5' UTR and contains two alternate exons in the 5' region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI202110, AK124196, AL035587, BC011767

    3. NR_134882.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) lacks an internal exon and contains an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI202110, AK124196, BC011767, BI909527

    4. NR_134885.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) uses an alternate splice site in the 5' region, lacks multiple 3' exons, and extends past a splice site used in variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK124196, CA431321, CN302713

    5. NR_134886.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) lacks an exon in the 5' region, lacks multiple 3' exons, and extends past a splice site used in variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq criteria.
      Source sequence(s)
      AK124196, BF528267, CA431321, CN302712

    6. NR_134888.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an exon in the 5' region and lacks an exon in the 3' region, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the open reading frame found in variant 1.
      Source sequence(s)
      AI202110, AK124196, BC011767, HY101691

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      42928002..42939294
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      42757067..42768434
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BT09.1 GenPept UniProtKB/Swiss-Prot:Q9BT09

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