PLPP3
protein-codingphospholipid phosphatase 3, the group of Phospholipid phosphatases
Gene summary
The protein encoded by this gene is a member of the phosphatidic acid phosphatase (PAP) family. PAPs convert phosphatidic acid to diacylglycerol, and function in de novo synthesis of glycerolipids as well as in receptor-activated signal transduction mediated by phospholipase D. This protein is a membrane glycoprotein localized at the cell plasma membrane. It has been shown to actively hydrolyze extracellular lysophosphatidic acid and short-chain phosphatidic acid. The expression of this gene is found to be enhanced by epidermal growth factor in Hela cells. [provided by RefSeq, Mar 2010]
- PPAP2B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~150.5 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 PLPP3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003713.5. 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 | 3 | 3 | ||||
| missense | 29 | 29 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 33 | 0 | 0 | 33 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003704.3 | 6 | MANE Select | |
| Ensembl | ENSP00000360296.3 | 6 | MANE Select | |
| Ensembl | ENSP00000562883.1 | 4 | Standard | |
| Ensembl | ENSP00000562883.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Fc gamma R-mediated phagocytosis - Homo sapiens (human)
- Glycerolipid metabolism - Homo sapiens (human)
- Ether lipid metabolism - Homo sapiens (human)
- Glycerophospholipid metabolism - Homo sapiens (human)
- Choline metabolism in cancer - Homo sapiens (human)
Biological Process
- negative regulation of protein phosphorylation
- protein dephosphorylation
- lipid metabolic process
- phospholipid metabolic process
- germ cell migration
Molecular Function
- phosphoprotein phosphatase activity
- protein binding
- phosphatidate phosphatase activity
- phosphatase activity
- sphingosine-1-phosphate phosphatase activity
Cellular Component
- Golgi apparatus
- plasma membrane
- integral component of plasma membrane
- adherens junction
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371250
- Coding exons
- 6
- Length
- 150556
- Individuals with no LoFs
- 125664
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 125666
- p
- 0.00000796
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.43 | 134 | 189 | 0.707 | 0.0000112 | 2041 |
| Missense (PolyPhen) | 26 | 65.465 | 0.39716 | 699 | ||
| Synonymous | 0.858 | 67 | 76.6 | 0.875 | 0.00000448 | 605 |
| Loss of Function | 3.00 | 1 | 12.4 | 0.0807 | 6.09e-7 | 149 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the conversion of phosphatidic acid (PA) to diacylglycerol (DG). In addition it hydrolyzes lysophosphatidic acid (LPA), ceramide-1-phosphate (C-1-P) and sphingosine-1- phosphate (S-1-P). The relative catalytic efficiency is LPA = PA > C-1-P > S-1-P. May be involved in cell adhesion and in cell-cell interactions.;
Recessive Scores
- pRec
- 0.179
Intolerance Scores
- RVIS EVS
- -0.41
- RVIS percentile EVS
- 26.23
Essentials
- Essential (gene trap)
- N