CNPY4

canopy FGF signaling regulator 4

Basic information

Region (hg38): 7:100119634-100125508

Links

ENSG00000166997 ∙ NCBI:245812 ∙ OMIM:610047 ∙ HGNC:28631 ∙ Uniprot:Q8N129 ∙ 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 CNPY4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNPY4 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			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	22	2	0

Variants in CNPY4

This is a list of pathogenic ClinVar variants found in the CNPY4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100119693-A-G		Inborn genetic diseases	Uncertain significance (May 18, 2021)
7-100119720-G-A			Uncertain significance (May 01, 2024)
7-100119721-ATTGT-A		Inborn genetic diseases	Uncertain significance (Jun 06, 2021)
7-100119751-C-T		not specified	Uncertain significance (Jul 31, 2024)
7-100119762-G-A			Likely benign (Mar 01, 2025)
7-100119805-G-A		not specified	Uncertain significance (Aug 19, 2024)
7-100119806-C-T		not specified	Uncertain significance (Jan 20, 2023)
7-100122279-G-C		not specified	Uncertain significance (Sep 26, 2024)
7-100122282-C-G		not specified	Uncertain significance (Nov 03, 2023)
7-100122306-G-A		not specified	Uncertain significance (Jun 17, 2022)
7-100122327-G-A		not specified	Uncertain significance (Jun 13, 2023)
7-100122369-G-A		not specified	Uncertain significance (Nov 22, 2024)
7-100122381-G-C		not specified	Uncertain significance (Aug 23, 2021)
7-100122386-G-C		Autism	Uncertain significance (-)
7-100122522-G-A		not specified	Uncertain significance (Aug 15, 2023)
7-100122545-G-A		not specified	Uncertain significance (May 20, 2024)
7-100122552-G-A		not specified	Uncertain significance (Mar 24, 2023)
7-100122788-A-G		not specified	Uncertain significance (Jan 27, 2025)
7-100124614-T-C		not specified	Uncertain significance (Jun 02, 2023)
7-100124617-C-T		not specified	Uncertain significance (Aug 16, 2022)
7-100124727-T-A		not specified	Uncertain significance (Jun 24, 2022)
7-100124799-G-C		not specified	Uncertain significance (Aug 04, 2024)
7-100124825-G-C		not specified	Uncertain significance (Jan 17, 2025)
7-100124833-G-A		not specified	Likely benign (Nov 22, 2022)
7-100124837-C-A		not specified	Likely benign (Apr 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNPY4	protein_coding	protein_coding	ENST00000262932	6	5899

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.03e-13	0.00583	125644	0	104	125748	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.255	147	139	1.06	0.00000715	1612
Missense in Polyphen		54	57.373	0.94121		673
Synonymous	0.145	52	53.4	0.975	0.00000287	463
Loss of Function	-0.795	18	14.7	1.22	8.57e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00102
Ashkenazi Jewish	0.00	0.00
East Asian	0.00120	0.00120
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000397	0.000396
Middle Eastern	0.00120	0.00120
South Asian	0.000294	0.000294
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of the cell surface expression of TLR4. {ECO:0000269|PubMed:16338228}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.825
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.197
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.327

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnpy4
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: positive regulation of protein localization to plasma membrane
• Cellular component: extracellular region
• Molecular function: molecular_function;signaling receptor binding