CPNE3
protein-codingcopine 3, 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 encodes a protein which contains two type II C2 domains in the amino-terminus and an A domain-like sequence in the carboxy-terminus. The A domain mediates interactions between integrins and extracellular ligands. [provided by RefSeq, Aug 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~47.1 kbGenCC 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 CPNE3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003909.5. 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 | 2 | 1 | 3 | |||
| missense | 73 | 1 | 74 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 9 | 9 | ||||
| Total | 0 | 0 | 84 | 2 | 0 | 86 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003900.1 | 15 | MANE Select | |
| Ensembl | ENSP00000477590.1 | 15 | MANE Select | |
| Ensembl | ENSP00000428561.1 | 10 | Standard | |
| Ensembl | ENSP00000427966.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neutrophil degranulation
- Metabolism of lipids
- Innate Immune System
- Immune System
- Metabolism
Biological Process
- protein phosphorylation
- lipid metabolic process
- vesicle-mediated transport
- positive regulation of cell migration
- ERBB2 signaling pathway
Molecular Function
- RNA binding
- protein serine/threonine kinase activity
- transporter activity
- protein binding
- calcium-dependent phospholipid binding
Cellular Component
- nucleus
- nucleolus
- cytoplasm
- mitochondrion
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000521271
- Coding exons
- 15
- Length
- 76668
- Individuals with no LoFs
- 125482
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 266
- Defined
- 125748
- p
- 0.00106
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.975 | 329 | 283 | 1.16 | 0.0000136 | 3551 |
| Missense (PolyPhen) | 116 | 102.22 | 1.1348 | 1333 | ||
| Synonymous | 0.164 | 99 | 101 | 0.979 | 0.00000529 | 980 |
| Loss of Function | -0.825 | 35 | 30.1 | 1.16 | 0.00000144 | 369 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00032 | 0.00031 | rare |
| Latino/Admixed American | 0.0016 | 0.0016 | notable |
| Ashkenazi Jewish | 0.0020 | 0.0020 | notable |
| East Asian | 0.0061 | 0.0061 | notable |
| Finnish | 0.00032 | 0.00032 | rare |
| European (Non-Finnish) | 0.00025 | 0.00025 | rare |
| South Asian | 0.0012 | 0.0012 | notable |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- LoFtool
- 0.943
- RVIS EVS
- 0.38
- RVIS percentile EVS
- 75.58
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.887
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |