PLPP6

Chr 9

phospholipid phosphatase 6

Also known as: LPRP-B, PA-PSP, PDP1, PPAPDC2, PSDP, bA6J24.6

NCBI Gene: 403313ENSG00000205808UniProt: Q8IY26

Enables isoprenoid diphosphate phosphatase activity and phosphatase activity. Involved in several processes, including phospholipid dephosphorylation; phospholipid metabolic process; and positive regulation of neutrophil activation. Located in endoplasmic reticulum membrane and nuclear membrane. [provided by Alliance of Genome Resources, Jul 2025]

248
ClinVar variants
167
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— PLPP6
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
167 Pathogenic / Likely Pathogenic· 69 VUS of 248 total submissions
Some data sources returned errors (1)

pubmed: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi

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.
1.74LOEUF
pLI 0.001
Z-score 0.21
OE 0.91 (0.47–1.74)
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.
-0.62Z-score
OE missense 1.13 (1.01–1.28)
190 obs / 167.6 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.0.91 (0.47–1.74)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.13 (1.01–1.28)
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.1.26
0≤1.21.6
LoF obs/exp: 5 / 5.5Missense obs/exp: 190 / 167.6Syn Z: -1.86

ClinVar Variant Classifications

248 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic160
Likely Pathogenic7
VUS69
Likely Benign5
Benign6
160
Pathogenic
7
Likely Pathogenic
69
VUS
5
Likely Benign
6
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
160
0
160
Likely Pathogenic
0
0
7
0
7
VUS
0
54
15
0
69
Likely Benign
0
3
0
2
5
Benign
0
3
3
0
6
Total0601852247

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

View in ClinVar →

Protein Context — Lollipop Plot

PLPP6 · 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

No publications found for PLPP6

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