CPPED1

Chr 16

calcineurin like phosphoesterase domain containing 1

Also known as: CSTP1

NCBI Gene: 55313 ENSG00000103381 UniProt: Q9BRF8 OMIM: 615603

The protein is a phosphatase that dephosphorylates AKT at serine-473, blocking cell cycle progression and promoting apoptosis, and may inhibit glucose uptake in adipocytes. Mutations cause autosomal recessive developmental and epileptic encephalopathy with onset in infancy, characterized by severe intellectual disability, seizures, and progressive microcephaly. The gene shows minimal constraint against loss-of-function variants in population databases.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

LOEUF 1.45

Clinical Summary— CPPED1

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

67 VUS of 84 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

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?

-0.96Z-score

OE missense 1.19 (1.07–1.33)

232 obs / 194.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.88 (0.55–1.45)

0≤0.351.4

Missense OE?1.19 (1.07–1.33)

0≤0.61.4

Synonymous OE?1.21

0≤1.21.6

LoF obs/exp: 11 / 12.5Missense obs/exp: 232 / 194.5Syn Z: -1.56

ClinVar Variant Classifications

84 submitted variants in ClinVar

ClinVar

Classification Summary

VUS67

Likely Benign3

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	67	67
Likely Benign	3	3
Benign	0	0
Total	70	70

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

View in ClinVar →

16 pathogenic / likely-pathogenic (of 28) ClinVar copy-number / structural variants overlap CPPED1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →