CPNE3

copine 3, the group of Copines

Basic information

Region (hg38): 8:86514434-86561498

Links

ENSG00000085719 ∙ NCBI:8895 ∙ OMIM:604207 ∙ HGNC:2316 ∙ Uniprot:O75131 ∙ 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 CPNE3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE3 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in CPNE3

This is a list of pathogenic ClinVar variants found in the CPNE3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-86528553-C-T		not specified	Uncertain significance (Mar 18, 2024)
8-86528595-A-G		not specified	Uncertain significance (May 18, 2022)
8-86528597-C-A		not specified	Uncertain significance (Mar 18, 2024)
8-86528647-T-A		not specified	Uncertain significance (Aug 19, 2021)
8-86528981-C-A		not specified	Uncertain significance (Jun 09, 2022)
8-86529071-A-G		not specified	Uncertain significance (Aug 26, 2022)
8-86529105-G-A		not specified	Uncertain significance (Feb 28, 2023)
8-86531180-G-A		not specified	Uncertain significance (Feb 12, 2024)
8-86532550-T-G		not specified	Uncertain significance (Nov 23, 2021)
8-86532567-A-G		not specified	Uncertain significance (Nov 13, 2023)
8-86532578-A-G		not specified	Uncertain significance (Jun 06, 2023)
8-86537638-C-T		not specified	Uncertain significance (Mar 23, 2022)
8-86540279-C-T		not specified	Uncertain significance (Aug 23, 2021)
8-86544774-A-T		not specified	Uncertain significance (Jan 23, 2024)
8-86546644-A-G		not specified	Uncertain significance (Dec 27, 2022)
8-86548326-A-G		not specified	Uncertain significance (Apr 27, 2022)
8-86548341-C-T		not specified	Uncertain significance (Mar 15, 2024)
8-86548371-A-G		not specified	Uncertain significance (Aug 17, 2021)
8-86548376-G-A		not specified	Uncertain significance (Jul 27, 2022)
8-86551083-A-G		not specified	Likely benign (Dec 02, 2021)
8-86551097-G-T		not specified	Uncertain significance (Jul 25, 2023)
8-86551190-A-G		not specified	Uncertain significance (Nov 16, 2021)
8-86551201-A-G		not specified	Uncertain significance (Sep 22, 2023)
8-86551214-C-A		not specified	Uncertain significance (May 27, 2022)
8-86554925-C-G		not specified	Uncertain significance (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPNE3	protein_coding	protein_coding	ENST00000521271	15	76668

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.78e-25	0.0000475	125482	0	266	125748	0.00106

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.975	329	283	1.16	0.0000136	3551
Missense in Polyphen		116	102.22	1.1348		1333
Synonymous	0.164	99	101	0.979	0.00000529	980
Loss of Function	-0.825	35	30.1	1.16	0.00000144	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00191	0.00191
Ashkenazi Jewish	0.00199	0.00199
East Asian	0.00615	0.00611
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.00615	0.00611
South Asian	0.00125	0.00124
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent phospholipid-binding protein that plays a role in ERBB2-mediated tumor cell migration in response to growth factor heregulin stimulation (PubMed:20010870). {ECO:0000269|PubMed:20010870}.
• Pathway: Neutrophil degranulation;Metabolism of lipids;Innate Immune System;Immune System;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.943
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.58

Haploinsufficiency Scores

• pHI: 0.332
• hipred: N
• hipred_score: 0.401
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.887

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpne3

Gene ontology

• Biological process: protein phosphorylation;lipid metabolic process;vesicle-mediated transport;positive regulation of cell migration;ERBB2 signaling pathway;neutrophil degranulation;glycerophospholipid biosynthetic process;cellular response to calcium ion;cellular response to growth factor stimulus
• Cellular component: nucleus;nucleolus;cytoplasm;mitochondrion;cytosol;plasma membrane;focal adhesion;cell junction;azurophil granule membrane;extracellular exosome
• Molecular function: RNA binding;protein serine/threonine kinase activity;transporter activity;protein binding;calcium-dependent phospholipid binding;receptor tyrosine kinase binding;calcium-dependent protein binding