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

Gene ID: 10695, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (42928002..42939294)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42757067..42768434)
105.20220307 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 chromosome 6 open reading frame 226 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: 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. The TLR-chaperone CNPY3 is a critical regulator of NLRP3-inflammasome activation. Ghait M, et al. Eur J Immunol, 2022 Jun. PMID 35334124
  2. 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
  3. 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
  4. 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
  5. PRAT4A-dependent expression of cell surface TLR5 on neutrophils, classical monocytes and dendritic cells. Shibata T, et al. Int Immunol, 2012 Oct. PMID 22836022

See all (39) 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
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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

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_2023_10

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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