CPNE8

copine 8, the group of Copines

Basic information

Region (hg38): 12:38646822-38907430

Links

ENSG00000139117 ∙ NCBI:144402 ∙ ∙ HGNC:23498 ∙ Uniprot:Q86YQ8 ∙ 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 CPNE8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE8 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			8			8
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	9	0	0

Variants in CPNE8

This is a list of pathogenic ClinVar variants found in the CPNE8 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-38670798-C-T		not specified	Uncertain significance (Feb 27, 2023)
12-38693805-A-T		not specified	Uncertain significance (Apr 25, 2022)
12-38702896-T-C		not specified	Uncertain significance (May 01, 2024)
12-38762151-T-C		not specified	Uncertain significance (May 21, 2024)
12-38762178-G-A		not specified	Uncertain significance (Apr 25, 2022)
12-38762187-A-T		not specified	Uncertain significance (Jul 17, 2023)
12-38762205-C-A		not specified	Uncertain significance (May 24, 2024)
12-38762209-T-C		not specified	Uncertain significance (Dec 08, 2021)
12-38767656-T-C		not specified	Uncertain significance (Mar 29, 2024)
12-38767708-T-C		not specified	Uncertain significance (Mar 28, 2024)
12-38839935-C-T		not specified	Uncertain significance (Apr 04, 2024)
12-38848587-C-T		not specified	Uncertain significance (Mar 23, 2023)
12-38848667-GGAAA-G			Likely benign (Dec 01, 2022)
12-38873029-C-G		not specified	Uncertain significance (Mar 24, 2023)
12-38905456-C-T		not specified	Uncertain significance (Nov 27, 2023)
12-38905524-C-T		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPNE8	protein_coding	protein_coding	ENST00000331366	20	260609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00802	0.992	125714	0	25	125739	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	197	288	0.684	0.0000136	3679
Missense in Polyphen		78	117.41	0.66435		1547
Synonymous	-0.912	110	98.5	1.12	0.00000466	1025
Loss of Function	3.69	10	32.8	0.305	0.00000147	446

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000956	0.0000922
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000552	0.0000544
Finnish	0.0000471	0.0000462
European (Non-Finnish)	0.000173	0.000167
Middle Eastern	0.0000552	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes. {ECO:0000250|UniProtKB:Q99829}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.568
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.103
• hipred: Y
• hipred_score: 0.601
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.163

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpne8

Gene ontology

• Biological process: biological_process;cellular response to calcium ion
• Cellular component: plasma membrane;extracellular exosome
• Molecular function: molecular_function;calcium-dependent phospholipid binding