PPTC7

Chr 12

protein phosphatase targeting COQ7

Also known as: TA-PP2C, TAPP2C

This mitochondrial protein phosphatase regulates coenzyme Q biosynthesis and mitophagy by dephosphorylating key enzymes and mitophagy receptors. Mutations cause autosomal recessive mitochondrial disease with early-onset encephalopathy, developmental delay, and multisystem involvement. The gene is highly constrained against loss-of-function variants, reflecting its essential role in mitochondrial metabolism.

OMIMResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.36
Clinical SummaryPPTC7
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.94). One damaged copy is likely sufficient to cause disease.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint
0.36LOEUF
pLI 0.938
Z-score 3.12
OE 0.08 (0.030.36)
Highly constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
2.89Z-score
OE missense 0.39 (0.320.48)
70 obs / 178.6 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.08 (0.030.36)
00.351.4
Missense OE0.39 (0.320.48)
00.61.4
Synonymous OE0.95
01.21.6
LoF obs/exp: 1 / 13.2Missense obs/exp: 70 / 178.6Syn Z: 0.32
DN
0.3395th %ile
GOF
0.4283th %ile
LOF
0.75top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.36

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

PPTC7 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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