CPA3
protein-codingcarboxypeptidase A3, the group of M14 carboxypeptidases
Gene summary
This gene encodes a member of the carboxypeptidase A family of zinc metalloproteases. The encoded preproprotein is proteolytically processed to generate a mature protease that is released by mast cells and may be involved in the degradation of endogenous proteins and the inactivation of venom-associated peptides. Expression of this gene may be elevated in human asthma patients. [provided by RefSeq, Nov 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~31.9 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 CPA3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001870.4. 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 | 1 | 1 | 3 | ||
| missense | 61 | 2 | 2 | 65 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 63 | 3 | 3 | 69 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001861.2 | 11 | MANE Select | |
| Ensembl | ENSP00000296046.3 | 11 | MANE Select | |
| Ensembl | ENSP00000569672.1 | 11 | Standard | |
| Ensembl | ENSP00000569672.1 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Renin-angiotensin system - Homo sapiens (human)
- Protein digestion and absorption - Homo sapiens (human)
- Pancreatic secretion - Homo sapiens (human)
- Peptide hormone metabolism
- Metabolism of proteins
Biological Process
- angiotensin maturation
- proteolysis
Molecular Function
- metallocarboxypeptidase activity
- zinc ion binding
Cellular Component
- extracellular region
- extracellular space
- transport vesicle
- secretory granule
- collagen-containing extracellular matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000296046
- Coding exons
- 11
- Length
- 31941
- Individuals with no LoFs
- 125595
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 152
- Defined
- 125747
- p
- 0.000605
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.695 | 259 | 229 | 1.13 | 0.0000120 | 2754 |
| Missense (PolyPhen) | 102 | 82.964 | 1.2294 | 1025 | ||
| Synonymous | -0.0591 | 79 | 78.3 | 1.01 | 0.00000395 | 748 |
| Loss of Function | 0.266 | 25 | 26.5 | 0.944 | 0.00000154 | 290 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0025 | 0.0025 | notable |
| Latino/Admixed American | 0.00052 | 0.00052 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00055 | 0.00054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00028 | 0.00028 | rare |
| South Asian | 0.0016 | 0.0016 | notable |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.147
Intolerance Scores
- LoFtool
- 0.963
- RVIS EVS
- 1.51
- RVIS percentile EVS
- 95.45
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0624
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |