CPNE4

copine 4, the group of Copines|MicroRNA protein coding host genes

Basic information

Region (hg38): 3:131533555-132285410

Links

ENSG00000196353 ∙ NCBI:131034 ∙ OMIM:604208 ∙ HGNC:2317 ∙ Uniprot:Q96A23 ∙ 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 CPNE4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE4 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in CPNE4

This is a list of pathogenic ClinVar variants found in the CPNE4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-131535199-G-A		not specified	Uncertain significance (Jul 26, 2021)
3-131535259-C-T		not specified	Uncertain significance (Nov 15, 2021)
3-131535304-C-T		not specified	Uncertain significance (Jan 26, 2022)
3-131535306-C-G		not specified	Uncertain significance (Feb 05, 2024)
3-131542610-C-G		not specified	Uncertain significance (Aug 21, 2023)
3-131542688-C-T		not specified	Uncertain significance (Dec 21, 2021)
3-131549991-C-T		not specified	Uncertain significance (May 03, 2023)
3-131669728-A-G		not specified	Uncertain significance (Nov 07, 2022)
3-131696564-T-C		not specified	Uncertain significance (Aug 22, 2023)
3-131696591-T-C		not specified	Uncertain significance (Oct 05, 2022)
3-131723481-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-131723501-T-C		not specified	Uncertain significance (Jul 28, 2021)
3-131723531-C-T		not specified	Uncertain significance (Sep 27, 2022)
3-131723537-C-T		not specified	Uncertain significance (Jun 18, 2021)
3-131723603-C-T		not specified	Uncertain significance (Dec 22, 2023)
3-131905413-C-T		not specified	Uncertain significance (Nov 21, 2022)
3-131905432-C-T		not specified	Uncertain significance (Feb 21, 2024)
3-131905436-T-A		not specified	Uncertain significance (May 12, 2024)
3-131905439-T-C		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPNE4	protein_coding	protein_coding	ENST00000512055	15	751856

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0859	0.914	125728	0	18	125746	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.65	184	317	0.581	0.0000168	3712
Missense in Polyphen		78	150.79	0.51727		1742
Synonymous	-0.504	124	117	1.06	0.00000644	1024
Loss of Function	3.78	8	30.5	0.262	0.00000154	356

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000905
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.418
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.24

Haploinsufficiency Scores

• pHI: 0.353
• hipred: Y
• hipred_score: 0.735
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.639

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpne4

Gene ontology

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