CPNE7

protein-coding

copine 7, the group of Copines

Gene summary

This gene encodes a member of the copine family, which is composed of calcium-dependent membrane-binding proteins. The gene product contains two N-terminal C2 domains and one von Willebrand factor A domain. The encoded protein may be involved in membrane trafficking. Two alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008]

MANE transcript

NM_153636.3

Inheritance

—

ClinVar variants

U:145B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.04

Max pathogenic AF

—

Genomic locus

chr16:89,575,758-89,597,246

External References & Databases

Ensembl (ENSG00000178773)

Transcript & Mutation Effects

hg38 • Region Span ~21.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CPNE7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 158

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153636.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	2 clinvar		5
missense			139 clinvar	6 clinvar		145
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	145	8	0	153

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153636.3	RefSeq	NP_705900.1	15	MANE Select
ENST00000319518.13	Ensembl	ENSP00000317374.8	15	MANE Select
NM_014427.5	RefSeq	NP_055242.1	17	Standard
ENST00000268720.10	Ensembl	ENSP00000268720.5	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
Metabolism
Glycerophospholipid biosynthesis
Phospholipid metabolism

Biological Process

lipid metabolic process
glycerophospholipid biosynthetic process
cellular response to calcium ion

Molecular Function

transporter activity
protein binding
calcium-dependent phospholipid binding

Cellular Component

nucleus
cytoplasm
plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000268720
Coding exons: 17
Length: 21479
Individuals with no LoFs: 125682
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125739
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.978	444	390	1.14	0.0000259	4077
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00033	0.00032	rare
South Asian	0.00027	0.00026	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes. {ECO:0000250|UniProtKB:Q99829}.;

Intolerance Scores

LoFtool: 0.859
RVIS EVS: -1.34
RVIS percentile EVS: 4.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.878

Gene Damage Prediction

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