CPNE7

copine 7, the group of Copines

Basic information

Region (hg38): 16:89575757-89597246

Links

ENSG00000178773 ∙ NCBI:27132 ∙ OMIM:605689 ∙ HGNC:2320 ∙ Uniprot:Q9UBL6 ∙ 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 CPNE7 gene.

• Inborn genetic diseases (44 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE7 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				2		2
missense			42	3		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	5	0

Variants in CPNE7

This is a list of pathogenic ClinVar variants found in the CPNE7 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-89575956-G-A		not specified	Uncertain significance (Apr 19, 2023)
16-89577567-G-C		not specified	Uncertain significance (May 23, 2023)
16-89577597-C-G		not specified	Uncertain significance (Aug 26, 2022)
16-89577617-G-A		not specified	Uncertain significance (Aug 16, 2021)
16-89577647-G-A		not specified	Uncertain significance (Jan 05, 2022)
16-89577659-C-T		not specified	Uncertain significance (Dec 21, 2023)
16-89577707-T-C		not specified	Uncertain significance (Dec 22, 2023)
16-89578860-G-A		not specified	Uncertain significance (Dec 07, 2021)
16-89578887-A-C		not specified	Uncertain significance (Aug 16, 2022)
16-89578917-G-C		not specified	Uncertain significance (Dec 09, 2023)
16-89578940-C-A		not specified	Uncertain significance (Mar 06, 2023)
16-89578975-C-T		not specified	Uncertain significance (Feb 07, 2023)
16-89583444-G-C		not specified	Uncertain significance (Oct 27, 2022)
16-89583481-G-A		not specified	Uncertain significance (Jul 13, 2021)
16-89583497-C-T		not specified	Uncertain significance (Apr 06, 2022)
16-89583722-G-T		not specified	Uncertain significance (Feb 17, 2024)
16-89584034-G-A		not specified	Uncertain significance (Apr 12, 2023)
16-89584058-G-A		not specified	Uncertain significance (Mar 20, 2023)
16-89584065-T-C		not specified	Uncertain significance (Dec 22, 2023)
16-89584080-G-A		not specified	Uncertain significance (Jan 04, 2022)
16-89584097-G-A		not specified	Uncertain significance (Sep 23, 2023)
16-89584825-G-A		not specified	Uncertain significance (Jun 02, 2023)
16-89585486-C-T		not specified	Uncertain significance (Nov 17, 2022)
16-89585532-C-G		not specified	Uncertain significance (Aug 15, 2023)
16-89585550-A-G			Likely benign (May 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPNE7	protein_coding	protein_coding	ENST00000268720	17	21479

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.27e-24	0.000310	125682	0	57	125739	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.978	444	390	1.14	0.0000259	4077
Missense in Polyphen		182	157.89	1.1527		1632
Synonymous	-3.43	237	179	1.33	0.0000139	1239
Loss of Function	-0.223	35	33.6	1.04	0.00000167	375

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000531	0.000522
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000332	0.000317
Middle Eastern	0.000167	0.000163
South Asian	0.000275	0.000261
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes. {ECO:0000250|UniProtKB:Q99829}.
• Pathway: Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Intolerance Scores

• loftool: 0.859
• rvis_EVS: -1.34
• rvis_percentile_EVS: 4.65

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.275
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.878

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpne7

Gene ontology

• Biological process: lipid metabolic process;glycerophospholipid biosynthetic process;cellular response to calcium ion
• Cellular component: nucleus;cytoplasm;plasma membrane;extracellular exosome
• Molecular function: transporter activity;protein binding;calcium-dependent phospholipid binding