CNPY2

canopy FGF signaling regulator 2

Basic information

Region (hg38): 12:56309842-56316119

Previous symbols: [ "TMEM4" ]

Links

ENSG00000257727 ∙ NCBI:10330 ∙ OMIM:605861 ∙ HGNC:13529 ∙ Uniprot:Q9Y2B0 ∙ 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 CNPY2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNPY2 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				1		1
missense			11			11
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	11	1	0

Variants in CNPY2

This is a list of pathogenic ClinVar variants found in the CNPY2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-56310572-T-C		not specified	Uncertain significance (Jan 04, 2024)
12-56310581-C-T		not specified	Uncertain significance (Aug 28, 2023)
12-56310990-T-C		not specified	Uncertain significance (Mar 04, 2024)
12-56310996-G-A		not specified	Uncertain significance (Mar 06, 2025)
12-56311054-A-G		not specified	Uncertain significance (Aug 20, 2024)
12-56311222-G-A		not specified	Uncertain significance (Jun 28, 2024)
12-56311244-G-A			Likely benign (Nov 01, 2022)
12-56311251-A-G		not specified	Uncertain significance (Oct 01, 2024)
12-56311299-C-T		not specified	Uncertain significance (Jan 19, 2024)
12-56314861-G-A		not specified	Uncertain significance (Mar 07, 2025)
12-56314903-A-G		not specified	Uncertain significance (May 14, 2024)
12-56314961-T-C		not specified	Uncertain significance (Jul 26, 2024)
12-56315157-G-A		not specified	Uncertain significance (Jan 08, 2025)
12-56315163-A-T		not specified	Uncertain significance (Jan 22, 2025)
12-56315167-GGTTCC-G		Abnormality of the face;Craniosynostosis syndrome	Likely pathogenic (Aug 01, 2021)
12-56315168-G-C		not specified	Uncertain significance (Dec 27, 2023)
12-56315202-A-G		not specified	Uncertain significance (Mar 03, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNPY2	protein_coding	protein_coding	ENST00000273308	5	6495

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00292	0.947	125721	0	26	125747	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.647	91	110	0.826	0.00000665	1185
Missense in Polyphen		26	35.515	0.73208		381
Synonymous	0.533	36	40.3	0.893	0.00000218	353
Loss of Function	1.71	6	12.6	0.478	7.93e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positive regulator of neurite outgrowth by stabilizing myosin regulatory light chain (MRLC). It prevents MIR-mediated MRLC ubiquitination and its subsequent proteasomal degradation.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.711
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.554
• hipred: N
• hipred_score: 0.328
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnpy2

Gene ontology

• Biological process: negative regulation of gene expression;regulation of low-density lipoprotein particle clearance;positive regulation of low-density lipoprotein particle receptor biosynthetic process
• Cellular component: endoplasmic reticulum
• Molecular function: protein binding