CPPED1
protein-codingcalcineurin like phosphoesterase domain containing 1
Gene summary
Predicted to enable metal ion binding activity and protein serine/threonine phosphatase activity. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~144.1 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 CPPED1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018340.3. 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 | 0 | |||||
| missense | 70 | 3 | 73 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 71 | 3 | 0 | 74 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060810.2 | 4 | MANE Select | |
| Ensembl | ENSP00000371193.4 | 4 | MANE Select | |
| RefSeq | NP_001092925.1 | 3 | Standard | |
| Ensembl | ENSP00000261660.4 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- protein dephosphorylation
- neutrophil degranulation
Molecular Function
- phosphoprotein phosphatase activity
- metal ion binding
Cellular Component
- extracellular region
- cytosol
- plasma membrane
- azurophil granule lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381774
- Coding exons
- 4
- Length
- 140956
- Individuals with no LoFs
- 124749
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 46
- Defined
- 124795
- p
- 0.000184
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.956 | 232 | 194 | 1.19 | 0.0000121 | 2053 |
| Missense (PolyPhen) | 64 | 54.907 | 1.1656 | 591 | ||
| Synonymous | -1.56 | 111 | 91.9 | 1.21 | 0.00000709 | 596 |
| Loss of Function | 0.404 | 11 | 12.5 | 0.877 | 6.24e-7 | 125 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00067 | 0.00067 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00017 | 0.00017 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000088 | 0.000088 | rare |
| South Asian | 0.00030 | 0.00029 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Protein phosphatase that dephosphorylates AKT family kinase specifically at 'Ser-473', blocking cell cycle progression and promoting cell apoptosis. May play an inhibitory role in glucose uptake by adipocytes. {ECO:0000269|PubMed:23799035, ECO:0000269|PubMed:23939394}.;
Intolerance Scores
- LoFtool
- 0.401
- RVIS EVS
- 1.29
- RVIS percentile EVS
- 93.84
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.629
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |