CPNE1

copine 1, the group of Copines

Basic information

Region (hg38): 20:35626031-35664956

Links

ENSG00000214078 ∙ NCBI:8904 ∙ OMIM:604205 ∙ HGNC:2314 ∙ Uniprot:Q99829 ∙ 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 CPNE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE1 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			43	7	7	57
Total	0	0	68	8	7

Variants in CPNE1

This is a list of pathogenic ClinVar variants found in the CPNE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-35626297-G-A		not specified	Uncertain significance (Jan 10, 2023)
20-35626305-C-A		not specified	Uncertain significance (Jul 06, 2021)
20-35626328-C-A			Likely benign (Jun 01, 2024)
20-35626333-G-T		not specified	Uncertain significance (Oct 17, 2024)
20-35626587-G-T		not specified	Uncertain significance (Apr 18, 2024)
20-35626712-A-G		not specified	Uncertain significance (Aug 08, 2023)
20-35626724-G-A		not specified	Uncertain significance (Mar 25, 2024)
20-35626730-C-T		not specified	Likely benign (Mar 26, 2024)
20-35626763-G-A		not specified	Uncertain significance (Dec 26, 2023)
20-35626767-C-G		not specified	Uncertain significance (Aug 12, 2024)
20-35626802-T-A		not specified	Uncertain significance (Jun 09, 2022)
20-35627306-G-C		not specified	Uncertain significance (May 01, 2024)
20-35627365-C-T		not specified	Uncertain significance (Oct 22, 2021)
20-35627366-G-A		not specified	Uncertain significance (May 17, 2023)
20-35627386-C-T		not specified	Uncertain significance (Aug 20, 2024)
20-35627387-G-A		not specified	Uncertain significance (Jun 28, 2022)
20-35630480-T-G		not specified	Uncertain significance (Jul 15, 2021)
20-35630759-C-G		not specified	Uncertain significance (Dec 05, 2024)
20-35630910-T-C		not specified	Uncertain significance (Mar 29, 2023)
20-35630929-C-T		not specified	Uncertain significance (Dec 04, 2024)
20-35630977-A-G		not specified	Uncertain significance (Mar 18, 2024)
20-35630988-T-A		not specified	Uncertain significance (Apr 20, 2024)
20-35631126-C-G		not specified	Uncertain significance (Nov 07, 2024)
20-35631269-C-T		not specified	Likely benign (Dec 12, 2023)
20-35631291-T-C		not specified	Uncertain significance (Oct 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPNE1	protein_coding	protein_coding	ENST00000317677	16	38926

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.73e-14	0.185	100225	1579	23944	125748	0.107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0942	316	321	0.985	0.0000193	3521
Missense in Polyphen		116	117.48	0.98737		1442
Synonymous	1.12	106	122	0.871	0.00000689	1079
Loss of Function	1.08	25	31.6	0.792	0.00000156	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.201	0.201
Ashkenazi Jewish	0.141	0.139
East Asian	0.0829	0.0823
Finnish	0.0734	0.0735
European (Non-Finnish)	0.106	0.104
Middle Eastern	0.0829	0.0823
South Asian	0.159	0.157
Other	0.116	0.114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent phospholipid-binding protein that plays a role in calcium-mediated intracellular processes (PubMed:14674885). Involved in the TNF-alpha receptor signaling pathway in a calcium-dependent manner (PubMed:14674885). Exhibits calcium-dependent phospholipid binding properties (PubMed:9430674, PubMed:19539605). Plays a role in neuronal progenitor cell differentiation; induces neurite outgrowth via a AKT-dependent signaling cascade and calcium-independent manner (PubMed:23263657, PubMed:25450385). May recruit target proteins to the cell membrane in a calcium-dependent manner (PubMed:12522145). May function in membrane trafficking (PubMed:9430674). Involved in TNF-alpha- induced NF-kappa-B transcriptional repression by inducing endoprotease processing of the transcription factor NF-kappa-B p65/RELA subunit (PubMed:18212740). Also induces endoprotease processing of NF-kappa-B p50/NFKB1, p52/NFKB2, RELB and REL (PubMed:18212740). {ECO:0000269|PubMed:12522145, ECO:0000269|PubMed:14674885, ECO:0000269|PubMed:18212740, ECO:0000269|PubMed:19539605, ECO:0000269|PubMed:23263657, ECO:0000269|PubMed:25450385, ECO:0000269|PubMed:9430674}.
• Pathway: Neutrophil degranulation;Metabolism of lipids;Innate Immune System;Immune System;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.186

Intolerance Scores

• loftool: 0.866
• rvis_EVS: 1
• rvis_percentile_EVS: 90.72

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.229
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.875

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpne1

Gene ontology

• Biological process: proteolysis;lipid metabolic process;negative regulation of gene expression;vesicle-mediated transport;regulation of I-kappaB kinase/NF-kappaB signaling;neutrophil degranulation;negative regulation of DNA binding;positive regulation of neuron differentiation;glycerophospholipid biosynthetic process;positive regulation of protein kinase B signaling;cellular response to calcium ion;negative regulation of NIK/NF-kappaB signaling;positive regulation of tumor necrosis factor-mediated signaling pathway;neuron projection extension
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;membrane;nuclear membrane;azurophil granule membrane;extracellular exosome
• Molecular function: phosphatidylserine binding;endopeptidase activity;transporter activity;calcium ion binding;protein binding;calcium-dependent phospholipid binding;protein homodimerization activity;NF-kappaB binding