GeneBe

CPNE3

copine 3, the group of Copines

Basic information

Region (hg38): 8:86514435-86561498

Links

ENSG00000085719 ∙ NCBI:8895 ∙ OMIM:604207 ∙ HGNC:2316 ∙ Uniprot:O75131 ∙ 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 CPNE3 gene.

  • not_specified (55 variants)
  • not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003909.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
54
clinvar
1
clinvar
 55
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 54 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CPNE3protein_codingprotein_codingENST00000521271 1576668
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.78e-250.000047512548202661257480.00106
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.9753292831.160.00001363551
Missense in Polyphen116102.221.13481333
Synonymous0.164991010.9790.00000529980
Loss of Function-0.8253530.11.160.00000144369

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001910.00191
Ashkenazi Jewish0.001990.00199
East Asian0.006150.00611
Finnish0.0003240.000323
European (Non-Finnish)0.0002470.000246
Middle Eastern0.006150.00611
South Asian0.001250.00124
Other0.0003270.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Calcium-dependent phospholipid-binding protein that plays a role in ERBB2-mediated tumor cell migration in response to growth factor heregulin stimulation (PubMed:20010870). {ECO:0000269|PubMed:20010870}.;
Pathway
Neutrophil degranulation;Metabolism of lipids;Innate Immune System;Immune System;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

pRec
0.118

Intolerance Scores

loftool
0.943
rvis_EVS
0.38
rvis_percentile_EVS
75.58

Haploinsufficiency Scores

pHI
0.332
hipred
N
hipred_score
0.401
ghis
0.500

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.887

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cpne3
Phenotype

Gene ontology

Biological process
protein phosphorylation;lipid metabolic process;vesicle-mediated transport;positive regulation of cell migration;ERBB2 signaling pathway;neutrophil degranulation;glycerophospholipid biosynthetic process;cellular response to calcium ion;cellular response to growth factor stimulus
Cellular component
nucleus;nucleolus;cytoplasm;mitochondrion;cytosol;plasma membrane;focal adhesion;cell junction;azurophil granule membrane;extracellular exosome
Molecular function
RNA binding;protein serine/threonine kinase activity;transporter activity;protein binding;calcium-dependent phospholipid binding;receptor tyrosine kinase binding;calcium-dependent protein binding