CNPY1

Chr 7

canopy FGF signaling regulator 1

NCBI Gene: 285888ENSG00000146910UniProt: Q3B7I2

Cnpy1 is expressed in the midbrain-hindbrain (MHB) boundary in zebrafish, binds FGFR1 (MIM 136350), and plays a role in FGF signaling (Hirate and Okamoto, 2006 [PubMed 16488878]).[supplied by OMIM, Dec 2008]

99
ClinVar variants
83
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— CNPY1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
83 Pathogenic / Likely Pathogenic· 16 VUS of 99 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.93LOEUF
pLI 0.000
Z-score -0.89
OE 1.47 (0.74–1.93)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.04Z-score
OE missense 1.01 (0.80–1.30)
46 obs / 45.3 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.1.47 (0.74–1.93)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.01 (0.80–1.30)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.63
0≤1.21.6
LoF obs/exp: 6 / 4.1Missense obs/exp: 46 / 45.3Syn Z: 1.16

ClinVar Variant Classifications

99 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic76
Likely Pathogenic7
VUS16
76
Pathogenic
7
Likely Pathogenic
16
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
76
0
76
Likely Pathogenic
0
0
7
0
7
VUS
0
11
5
0
16
Likely Benign
0
0
0
0
0
Benign
0
0
0
0
0
Total01188099

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CNPY1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Autism associated gene, engrailed2, and flanking gene levels are altered in post-mortem cerebellum.
Choi J et al.·PLoS One
2014
Progress in Research on CNPY2 in Diseases.
Chen KQ et al.·Mini Rev Med Chem
2024Review
The role of canopy family proteins: biological mechanism and disease function.
Li X et al.·Mol Biol Rep
2025Review
Characterization of CNPY5 and its family members.
Schildknegt D et al.·Protein Sci
2019
Prenatal phthalate exposure and altered patterns of DNA methylation in cord blood.
Solomon O et al.·Environ Mol Mutagen
2017
Molecular characterization of three NPY receptors (Y2, Y5 and Y7) in chickens: Gene structure, tissue expression, promoter identification, and functional analysis.
He C et al.·Gen Comp Endocrinol
2016Functional
An investigation of obesity susceptibility genes in Northern Han Chinese by targeted resequencing.
Wu Y et al.·Medicine (Baltimore)
2017
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools