CNPY1

canopy FGF signaling regulator 1

Basic information

Region (hg38): 7:155474206-155555450

Links

ENSG00000146910 ∙ NCBI:285888 ∙ OMIM:612493 ∙ HGNC:27786 ∙ Uniprot:Q3B7I2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CNPY1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNPY1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in CNPY1

This is a list of pathogenic ClinVar variants found in the CNPY1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-155507034-C-G		not specified	Uncertain significance (Oct 06, 2021)
7-155507101-C-T		not specified	Uncertain significance (Apr 25, 2023)
7-155508914-A-G		not specified	Uncertain significance (May 06, 2024)
7-155508954-T-C		not specified	Uncertain significance (May 30, 2022)
7-155509003-G-A		not specified	Uncertain significance (Nov 22, 2023)
7-155509010-G-C		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNPY1	protein_coding	protein_coding	ENST00000321736	3	59657

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000215	0.166	124767	0	19	124786	0.0000761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0353	46	45.3	1.01	0.00000192	599
Missense in Polyphen		14	16.305	0.85862		206
Synonymous	1.16	10	15.9	0.630	7.00e-7	151
Loss of Function	-0.887	6	4.07	1.47	1.68e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000585	0.0000585
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000265
Middle Eastern	0.000111	0.000111
South Asian	0.000394	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.685
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.72

Haploinsufficiency Scores

• pHI: 0.0754
• hipred: N
• hipred_score: 0.209

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.107

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cnpy1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: cnpy1
• Affected structure: endodermal cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Cellular component: endoplasmic reticulum