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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CNPY3
canopy FGF signaling regulator 3
Chromosome 6 Β· 6p21.1
NCBI Gene: 10695Ensembl: ENSG00000137161.19HGNC: HGNC:11968UniProt: Q9BT09
44PubMed Papers
21Diseases
0Drugs
8Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingsignaling receptor bindingendoplasmic reticulum lumenendoplasmic reticulumgenetic developmental and epileptic encephalopathyinfantile spasmshypertension, pregnancy-inducedneoplasm
✦AI Summary

CNPY3 (canopy FGF signaling regulator 3) functions as a critical co-chaperone for HSP90B1/GRP94 in the endoplasmic reticulum, specifically required for proper folding and trafficking of Toll-like receptors (TLRs) except TLR3 1. CNPY3 controls TLR exit from the ER and surface expression, consequently regulating both innate and adaptive immune responses 2. Beyond TLR regulation, CNPY3 plays a TLR-independent role in NLRP3-inflammasome activation by regulating caspase-1 localization and autoactivation, affecting IL-1Ξ² and IL-18 processing 1. Disease associations include developmental and epileptic encephalopathy 60, where loss-of-function variants impair both TLR signaling and inflammasome activation 1. A novel C52Y variant identified in familial neuromyelitis optica spectrum disorder shows dominant negative effects on TLR4 surface expression and reduces inflammatory cytokine production 2. Additionally, CNPY3 appears to promote cancer progression in multiple malignancies including breast, colon, and prostate cancers by modulating the tumor microenvironment and enhancing cell migration and invasion 34. The protein's dual roles in immune regulation and cancer progression make it a potential therapeutic target with clinical significance in both inflammatory diseases and oncology.

Sources cited
1
CNPY3 functions as co-chaperone for TLR folding/trafficking and regulates NLRP3-inflammasome activation independently of TLRs
PMID: 35334124
2
CNPY3 C52Y variant from familial NMOSD shows dominant negative effects on TLR4 surface expression and reduces inflammatory responses
PMID: 36931208
3
CNPY3 promotes breast cancer progression and metastasis via modulation of tumor microenvironment
PMID: 41296387
4
CNPY3 correlates with colon cancer aggressiveness and affects cell proliferation, migration, and apoptosis
PMID: 40055606
⚠Limited data available β€” This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜21
genetic developmental and epileptic encephalopathyOpen Targets
0.68Moderate
infantile spasmsOpen Targets
0.61Moderate
hypertension, pregnancy-inducedOpen Targets
0.20Weak
neoplasmOpen Targets
0.09Suggestive
breast cancerOpen Targets
0.07Suggestive
cancerOpen Targets
0.07Suggestive
smoking initiationOpen Targets
0.04Suggestive
gliomaOpen Targets
0.04Suggestive
chronic obstructive pulmonary diseaseOpen Targets
0.03Suggestive
nervous system diseaseOpen Targets
0.02Suggestive
triple-negative breast cancerOpen Targets
0.02Suggestive
gastric cancerOpen Targets
0.02Suggestive
proteostasis deficienciesOpen Targets
0.01Suggestive
Pick diseaseOpen Targets
0.01Suggestive
systemic juvenile idiopathic arthritisOpen Targets
0.01Suggestive
prostate cancerOpen Targets
0.01Suggestive
amyotrophic lateral sclerosisOpen Targets
0.01Suggestive
frontotemporal dementiaOpen Targets
0.01Suggestive
SepsisOpen Targets
0.01Suggestive
Epileptic encephalopathyOpen Targets
0.01Suggestive
Developmental and epileptic encephalopathy 60UniProt
Pathogenic Variants8
NM_006586.5(CNPY3):c.496-3_496-2delLikely pathogenic
Developmental and epileptic encephalopathy, 60|not specified
β˜…β˜†β˜†β˜†2024
NM_006586.5(CNPY3):c.548del (p.Asn183fs)Pathogenic
Developmental and epileptic encephalopathy, 60
β˜…β˜†β˜†β˜†2023β†’ Residue 183
NM_006586.5(CNPY3):c.628C>T (p.Gln210Ter)Likely pathogenic
Developmental and epileptic encephalopathy, 60
β˜…β˜†β˜†β˜†2020β†’ Residue 210
NM_006586.5(CNPY3):c.734_737del (p.Gln245fs)Likely pathogenic
Developmental and epileptic encephalopathy, 60
β˜…β˜†β˜†β˜†2020β†’ Residue 245
NM_006586.5(CNPY3):c.361C>T (p.Arg121Ter)Likely pathogenic
Developmental and epileptic encephalopathy, 60
β˜…β˜†β˜†β˜†β†’ Residue 121
NM_006586.5(CNPY3):c.373G>C (p.Gly125Arg)Pathogenic
Developmental and epileptic encephalopathy, 60
β˜†β˜†β˜†β˜†2020β†’ Residue 125
NM_006586.5(CNPY3):c.702_720dup (p.Ser241delinsGlySerArgArgGlnGluTer)Pathogenic
Developmental and epileptic encephalopathy, 60
β˜†β˜†β˜†β˜†2020β†’ Residue 241
NM_006586.5(CNPY3):c.495+1G>APathogenic
Developmental and epileptic encephalopathy, 60
β˜†β˜†β˜†β˜†2020
View on ClinVar β†—
Related Genes
TLR4Protein interaction100%TLR9Protein interaction97%TLR8Protein interaction96%HSP90B1Protein interaction96%TLR1Protein interaction88%LY96Protein interaction88%
Tissue Expression6 tissues
Bone Marrow
100%
Liver
53%
Lung
48%
Ovary
40%
Brain
29%
Heart
23%
Gene Interaction Network
Click a node to explore
CNPY3TLR4TLR9TLR8HSP90B1TLR1LY96
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9BT09
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.88LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.60 [0.42–0.88]
RankingsWhere CNPY3 stands among ~20K protein-coding genes
  • #9,575of 20,598
    Most Researched44
  • #3,099of 5,498
    Most Pathogenic Variants8
  • #7,848of 17,882
    Most Constrained (LOEUF)0.88
Genes detectedCNPY3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Autozygome and high throughput confirmation of disease genes candidacy.
PMID: 30237576
Genet Med Β· 2019
1.00
2
Thermal Proteome Profiling Strategy Identifies CNPY3 as a Cellular Target of Gambogic Acid for Inducing Prostate Cancer Pyroptosis.
PMID: 38511243
J Med Chem Β· 2024
0.90
3
Exploring the regulatory role of CNPY3 as a prognostic biomarker on human glioma cell migration, invasion and immune infiltration.
PMID: 40171811
Cancer Biomark Β· 2025
0.80
4
CNPY3 Promotes Human Breast Cancer Progression and Metastasis via Modulation of the Tumor Microenvironment.
PMID: 41296387
Curr Issues Mol Biol Β· 2025
0.70
5
CNPY3's regulation of tumor microenvironment and its impact on colon cancer aggressiveness.
PMID: 40055606
Mol Med Β· 2025
0.60