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

Summary

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

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_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH18283 (e-PCR)
- UniSTS:56067

GDB:434012 (e-PCR)
- UniSTS:157204

RH93325 (e-PCR)
- UniSTS:91163

D5S2354 (e-PCR)
- UniSTS:473392

D6S1374 (e-PCR)
- UniSTS:153688

SHGC-57523 (e-PCR)
- UniSTS:50523

D1S1425 (e-PCR)
- UniSTS:149621

G35510 (e-PCR)
- UniSTS:44150

D6S322E (e-PCR)
- UniSTS:8579

G64272 (e-PCR)
- UniSTS:158649

RH18149 (e-PCR)
- UniSTS:209601

D6S322E (e-PCR)
- UniSTS:147425

D12S814 (e-PCR)
- UniSTS:33022

Readthrough CNPY3-GNMT

Readthrough gene: CNPY3-GNMT, Included gene: GNMT

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)

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
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
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
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
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

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
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
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
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
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
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