PLPP4
protein-codingphospholipid phosphatase 4, the group of Phospholipid phosphatases
Gene summary
Enables diacylglycerol diphosphate phosphatase activity; identical protein binding activity; and phosphatidate phosphatase activity. Involved in phospholipid dephosphorylation and regulation of calcium ion import. Predicted to be located in plasma membrane. Predicted to be active in membrane. Biomarker of breast cancer. [provided by Alliance of Genome Resources, Jul 2025]
- PPAPDC1
- PPAPDC1A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~134.8 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 PLPP4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001030059.3. 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 | 0 | |||||
| missense | 32 | 32 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 32 | 0 | 0 | 32 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001025230.1 | 7 | MANE Select | |
| Ensembl | ENSP00000381302.1 | 7 | MANE Select | |
| RefSeq | NP_001305095.1 | 6 | Standard | |
| RefSeq | NP_001305096.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycerolipid metabolism - Homo sapiens (human)
- Glycerophospholipid metabolism - Homo sapiens (human)
- Role of phospholipids in phagocytosis
- Fcgamma receptor (FCGR) dependent phagocytosis
- Innate Immune System
Biological Process
- blastocyst hatching
- phospholipid metabolic process
- Fc-gamma receptor signaling pathway involved in phagocytosis
- phospholipid dephosphorylation
Molecular Function
- phosphatidate phosphatase activity
- phosphatase activity
- identical protein binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000398250
- Coding exons
- 7
- Length
- 132902
- Individuals with no LoFs
- 124785
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 22
- Defined
- 124807
- p
- 0.0000881
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.15 | 124 | 166 | 0.748 | 0.00000992 | 1753 |
| Missense (PolyPhen) | 40 | 59.242 | 0.6752 | 607 | ||
| Synonymous | 0.991 | 55 | 65.2 | 0.844 | 0.00000421 | 542 |
| Loss of Function | 1.50 | 8 | 14.1 | 0.568 | 7.66e-7 | 158 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00019 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Displays magnesium-independent phosphatidate phosphatase activity in vitro. Catalyzes the conversion of phosphatidic acid to diacylglycerol. {ECO:0000269|PubMed:17590538}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- RVIS EVS
- -0.25
- RVIS percentile EVS
- 35.75