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3 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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PLPP6
phospholipid phosphatase 6
Chromosome 9 · 9p24.1
NCBI Gene: 403313Ensembl: ENSG00000205808.7HGNC: HGNC:23682UniProt: Q8IY26
23PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
sphingosine-1-phosphate phosphatase activityendoplasmic reticulum membranefarnesyl diphosphate catabolic processphospholipid dephosphorylationrespiratory tract infectious disorderX-linked non-syndromic intellectual disability46,XX testicular disorder of sex developmentThrombocytopenia
✦AI Summary

PLPP6 (phospholipid phosphatase 6) is a magnesium-independent polyisoprenoid diphosphatase that catalyzes sequential dephosphorylation of presqualene, farnesyl, geranyl, and geranylgeranyl diphosphates 123. The enzyme plays multiple metabolic roles: it regulates innate immunity by dephosphorylating presqualene diphosphate, which inhibits polymorphonuclear neutrophil activation 14; participates in cholesterol and sterol biosynthesis through presqualene and farnesyl diphosphate dephosphorylation 3; and contributes to protein prenylation by acting on farnesyl and geranylgeranyl diphosphates 3. Additionally, PLPP6 has lower activity toward phosphatidic acid, lysophosphatidic acid, ceramide-1-P, and sphingosine-1-phosphate, potentially influencing phospholipid and triacylglycerol biosynthesis 53. Clinically, PLPP6 has emerged as a critical gene in chromosome 9-related syndromes, being identified as important for 83% of individuals with 9p deletion syndrome 6. In allergic disease, PLPP6 regulates dendritic cell cholesterol content and macropinocytosis, with PLPP6 knockout mice showing decreased airway allergen sensitization 7.

Sources cited
1
PLPP6 catalyzes dephosphorylation of presqualene diphosphate and functions in innate immune response
PMID: 16464866
2
PLPP6 catalyzes sequential dephosphorylation of polyisoprenoid diphosphates
PMID: 19220020
3
PLPP6 dephosphorylates presqualene, farnesyl, and geranylgeranyl diphosphates; involved in cholesterol biosynthesis and protein prenylation
PMID: 20110354
4
PLPP6-mediated dephosphorylation of presqualene diphosphate inhibits neutrophil activation pathways
PMID: 23568778
5
PLPP6 acts on phosphatidic acid, ceramide-1-P, and lysophosphatidic acid in phospholipid biosynthesis
PMID: 18930839
6
PLPP6 identified as one of 24 important genes for 83% of individuals with 9p deletion syndrome
PMID: 41137173
7
PLPP6 regulates dendritic cell cholesterol content and macropinocytosis; Plpp6 knockout mice show decreased allergen sensitization
PMID: 36238896
Disease Associationsⓘ20
respiratory tract infectious disorderOpen Targets
0.10Weak
X-linked non-syndromic intellectual disabilityOpen Targets
0.05Suggestive
46,XX testicular disorder of sex developmentOpen Targets
0.05Suggestive
ThrombocytopeniaOpen Targets
0.05Suggestive
autosomal dominant macrothrombocytopeniaOpen Targets
0.05Suggestive
X-linked intellectual disability - macrocephaly - macroorchidismOpen Targets
0.05Suggestive
X-linked intellectual disability-macrocephaly-macroorchidism syndromeOpen Targets
0.05Suggestive
46,XY complete gonadal dysgenesisOpen Targets
0.05Suggestive
46,XX ovotesticular disorder of sex developmentOpen Targets
0.05Suggestive
response to antipsychotic drugOpen Targets
0.05Suggestive
Testicular regression syndromeOpen Targets
0.05Suggestive
injuryOpen Targets
0.04Suggestive
cryptorchidismOpen Targets
0.04Suggestive
familial male-limited precocious pubertyOpen Targets
0.04Suggestive
thrombocytopenia 4Open Targets
0.04Suggestive
thrombocytopenia with congenital dyserythropoietic anemiaOpen Targets
0.04Suggestive
hypogonadotropic hypogonadism 11 with or without anosmiaOpen Targets
0.04Suggestive
partial chromosome Y deletionOpen Targets
0.04Suggestive
platelet-type bleeding disorder 15Open Targets
0.04Suggestive
macrothrombocytopenia, isolated, 2, autosomal dominantOpen Targets
0.04Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
ZNG1ACo-mentioned in literature100%BRD10Co-mentioned in literature100%PLPP1Protein interaction94%EPHX2Protein interaction68%DMRT2Co-mentioned in literature67%RCL1Co-mentioned in literature67%
Tissue Expression6 tissues
Liver
100%
Brain
50%
Lung
21%
Ovary
21%
Heart
21%
Bone Marrow
15%
Gene Interaction Network
Click a node to explore
PLPP6ZNG1ABRD10PLPP1EPHX2DMRT2RCL1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q8IY26
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.76LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF1.20 [0.81–1.76]
RankingsWhere PLPP6 stands among ~20K protein-coding genes
  • #13,485of 20,598
    Most Researched23
  • #16,405of 17,882
    Most Constrained (LOEUF)1.76
Genes detectedPLPP6
Sources retrieved3 papers
Response time—
📄 Sources
3
1
Whole-Genome Sequencing Reveals Individual and Cohort Level Insights into Chromosome 9p Syndromes.
PMID: 40196253
medRxiv · 2025
1.00
2
Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes.
PMID: 41137173
Genome Med · 2025
0.67
3
Mouse phospholipid phosphatase 6 regulates dendritic cell cholesterol, macropinocytosis, and allergen sensitization.
PMID: 36238896
iScience · 2022
0.33