CPNE8

protein-coding

copine 8, the group of Copines

Gene summary

Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene is one of several genes that encode a calcium-dependent protein containing two N-terminal type II C2 domains and an integrin A domain-like sequence in the C-terminus. [provided by RefSeq, Jul 2008]

MANE transcript

NM_153634.3

Inheritance

—

ClinVar variants

U:43

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr12:38,646,822-38,907,430

External References & Databases

Ensembl (ENSG00000139117)

Transcript & Mutation Effects

hg38 • Region Span ~260.6 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 CPNE8 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 38

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153634.3. 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			1 clinvar			1
missense			39 clinvar			39
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	43	0	0	43

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153634.3	RefSeq	NP_705898.1	20	MANE Select
ENST00000331366.10	Ensembl	ENSP00000329748.5	20	MANE Select
ENST00000360449.3	Ensembl	ENSP00000353633.3	20	Standard
ENST00000360449.4	Ensembl	ENSP00000353633.3	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

biological_process
cellular response to calcium ion

Molecular Function

molecular_function
calcium-dependent phospholipid binding

Cellular Component

plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000331366
Coding exons: 20
Length: 260609
Individuals with no LoFs: 125714
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125739
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.91	197	288	0.684	0.0000136	3679
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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: 0.127

Intolerance Scores

LoFtool: 0.568
RVIS EVS: -0.4
RVIS percentile EVS: 26.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.163

Gene Damage Prediction

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