CPPED1

Chr 16

calcineurin like phosphoesterase domain containing 1

Also known as: CSTP1

NCBI Gene: 55313ENSG00000103381UniProt: Q9BRF8

Predicted to enable metal ion binding activity and phosphoprotein phosphatase activity. Predicted to be involved in chromatin remodeling and regulation of transcription by RNA polymerase II. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2025]

112
ClinVar variants
16
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— CPPED1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
16 Pathogenic / Likely Pathogenic· 77 VUS of 112 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.45LOEUF
pLI 0.000
Z-score 0.40
OE 0.88 (0.55–1.45)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.96Z-score
OE missense 1.19 (1.07–1.33)
232 obs / 194.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.88 (0.55–1.45)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.19 (1.07–1.33)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.21
0≤1.21.6
LoF obs/exp: 11 / 12.5Missense obs/exp: 232 / 194.5Syn Z: -1.56

ClinVar Variant Classifications

112 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic14
Likely Pathogenic2
VUS77
Likely Benign4
14
Pathogenic
2
Likely Pathogenic
77
VUS
4
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
14
0
14
Likely Pathogenic
0
0
2
0
2
VUS
0
67
10
0
77
Likely Benign
0
3
1
0
4
Benign
0
0
0
0
0
Total07027097

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CPPED1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Neuroinflammation Markers in Tear Fluid of Mild Alzheimer's Disease.
Kärkkäinen V et al.·J Mol Neurosci
2025
The neutrophil extracellular traps-related gene signature predicts the prognosis of glioblastoma multiforme.
Sun G et al.·Folia Neuropathol
2024
CircCDK1 blocking IGF2BP2-mediated m6A modification of CPPED1 promotes laryngeal squamous cell carcinoma metastasis via the PI3K/AKT signal pathway.
Li J et al.·Gene
2023
Differential ion mobility mass spectrometry in immunopeptidomics identifies neoantigens carrying colorectal cancer driver mutations.
Minegishi Y et al.·Commun Biol
2022
New candidate loci identified by array-CGH in a cohort of 100 children presenting with syndromic obesity.
Vuillaume ML et al.·Am J Med Genet A
2014Cohort
Deciphering the Cellular Targets of Bioactive Compounds Using a Chloroalkane Capture Tag.
Ohana RF et al.·ACS Chem Biol
2015
Proteomic Signatures and Blood Adenosine Triphosphate Levels as Markers of Empagliflozin Efficacy in Type 2 Diabetes Mellitus and Heart Failure.
Omurzakova U et al.·Horm Metab Res
2025
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools