CPNE6

copine 6, the group of Copines

Basic information

Region (hg38): 14:24070837-24078100

Links

ENSG00000100884 ∙ NCBI:9362 ∙ OMIM:605688 ∙ HGNC:2319 ∙ Uniprot:O95741 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CPNE6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE6 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				1		1
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in CPNE6

This is a list of pathogenic ClinVar variants found in the CPNE6 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24073066-G-A		not specified	Uncertain significance (Jul 05, 2023)
14-24073600-C-A		not specified	Uncertain significance (Mar 07, 2024)
14-24075220-G-A		not specified	Uncertain significance (Apr 20, 2024)
14-24075536-G-A		not specified	Uncertain significance (Mar 15, 2024)
14-24075569-C-T		not specified	Uncertain significance (Sep 01, 2021)
14-24075839-C-T		not specified	Uncertain significance (Jun 07, 2024)
14-24075843-C-T			not provided (-)
14-24076174-A-G		not specified	Uncertain significance (Jan 04, 2022)
14-24076218-C-G		not specified	Uncertain significance (Nov 29, 2023)
14-24076219-G-A		not specified	Uncertain significance (Sep 23, 2023)
14-24076219-G-C		not specified	Uncertain significance (Jun 03, 2022)
14-24076368-G-A		not specified	Uncertain significance (Feb 02, 2024)
14-24076412-G-A		not specified	Uncertain significance (Oct 12, 2021)
14-24076535-C-G		not specified	Uncertain significance (Jun 27, 2023)
14-24076548-G-C		not specified	Uncertain significance (Jan 08, 2024)
14-24076935-G-A		not specified	Uncertain significance (Mar 20, 2024)
14-24076986-C-G		not specified	Uncertain significance (Feb 23, 2023)
14-24077001-G-A		not specified	Uncertain significance (Feb 06, 2023)
14-24077293-G-A		not specified	Uncertain significance (Mar 01, 2023)
14-24077373-T-G		not specified	Uncertain significance (Sep 14, 2021)
14-24077638-C-A			Likely benign (Mar 01, 2022)
14-24077639-G-A		not specified	Uncertain significance (Jun 24, 2022)
14-24077683-G-A		not specified	Uncertain significance (Nov 23, 2021)
14-24077684-C-T		not specified	Uncertain significance (Jun 29, 2023)
14-24077692-C-T		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPNE6	protein_coding	protein_coding	ENST00000397016	15	7264

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.153	0.847	125736	0	10	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.88	196	347	0.565	0.0000219	3609
Missense in Polyphen		49	138.62	0.35348		1509
Synonymous	-0.260	145	141	1.03	0.00000907	1103
Loss of Function	3.96	8	32.2	0.248	0.00000188	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.000102	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent phospholipid-binding protein that plays a role in calcium-mediated intracellular processes. Binds phospholipid membranes in a calcium-dependent manner (By similarity). Plays a role in dendrite formation by melanocytes (PubMed:23999003). {ECO:0000250|UniProtKB:Q9Z140, ECO:0000269|PubMed:23999003}.
• Pathway: Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.53

Haploinsufficiency Scores

• pHI: 0.199
• hipred: Y
• hipred_score: 0.675
• ghis: 0.659

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.747

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpne6

Gene ontology

• Biological process: lipid metabolic process;chemical synaptic transmission;nervous system development;vesicle-mediated transport;glycerophospholipid biosynthetic process;cellular response to calcium ion;positive regulation of dendrite extension
• Cellular component: endosome;plasma membrane;membrane;axon;dendrite;perikaryon;clathrin-coated endocytic vesicle;extracellular exosome
• Molecular function: phosphatidylserine binding;transporter activity;calcium ion binding;protein binding;calcium-dependent phospholipid binding