PLPP6
protein-codingphospholipid phosphatase 6, the group of Phospholipid phosphatases
Gene summary
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]
- PPAPDC2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PLPP6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_203453.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 54 | 3 | 2 | 59 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 54 | 5 | 2 | 61 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_982278.3 | 1 | MANE Select | |
| Ensembl | ENSP00000371307.2 | 1 | MANE Select |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of lipids
- Metabolism
- Metabolism of steroids
- Cholesterol biosynthesis
Biological Process
- cholesterol biosynthetic process
- phospholipid dephosphorylation
Molecular Function
- hydrolase activity
- lipid phosphatase activity
Cellular Component
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381883
- Coding exons
- 1
- Length
- 2959
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.616 | 190 | 168 | 1.13 | 0.00000837 | 1838 |
| Missense (PolyPhen) | 69 | 68.414 | 1.0086 | 724 | ||
| Synonymous | -1.86 | 104 | 82.5 | 1.26 | 0.00000425 | 669 |
| Loss of Function | 0.205 | 5 | 5.52 | 0.906 | 2.38e-7 | 55 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Phosphatase that dephosphorylates presqualene diphosphate (PSDP) into presqualene monophosphate (PSMP), suggesting that it may be indirectly involved in innate immunity. PSDP is a bioactive lipid that rapidly remodels to presqualene monophosphate PSMP upon cell activation. Displays diphosphate phosphatase activity with a substrate preference for PSDP > FDP > phosphatidic acid. {ECO:0000269|PubMed:16464866}.;
Intolerance Scores
- RVIS EVS
- 0.19
- RVIS percentile EVS
- 67.03
Essentials
- Essential (gene trap)
- N