CPNE5

protein-coding

copine 5, 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. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. More variants may exist, but their full-length natures could not be determined. [provided by RefSeq, Sep 2015]

MANE transcript

NM_020939.2

Inheritance

—

ClinVar variants

U:67B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr6:36,740,775-36,839,444

External References & Databases

Ensembl (ENSG00000124772)

Transcript & Mutation Effects

hg38 • Region Span ~98.7 kb

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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 CPNE5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 58

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020939.2. 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		3 clinvar	4
missense			59 clinvar		1 clinvar	60
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	67	0	4	71

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020939.2	RefSeq	NP_065990.1	21	MANE Select
ENST00000244751.7	Ensembl	ENSP00000244751.2	21	MANE Select
NM_001314017.1	RefSeq	NP_001300946.1	7	Standard
NM_001314018.2	RefSeq	NP_001300947.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cellular response to calcium ion
positive regulation of dendrite extension

Molecular Function

molecular_function
calcium-dependent phospholipid binding

Cellular Component

plasma membrane
neuron projection
perikaryon
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000244751
Coding exons: 21
Length: 99227
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125747
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.72	234	384	0.609	0.0000248	3889
Missense (PolyPhen)		78	174.03	0.44819		1779
Synonymous	0.611	152	162	0.939	0.0000120	1117
Loss of Function	3.74	13	37.8	0.344	0.00000218	394

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000062	0.000054	rare
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.00013	0.00013	rare
Other	0.00019	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 (By similarity). Plays a role in dendrite formation by melanocytes (PubMed:23999003). {ECO:0000250|UniProtKB:Q99829, ECO:0000269|PubMed:23999003}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.569
RVIS EVS: -1
RVIS percentile EVS: 8.37

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.289

Gene Damage Prediction

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