PLPP3
phospholipid phosphatase 3, the group of Phospholipid phosphatases
Basic information
Region (hg38): 1:56494761-56645301
Previous symbols: [ "PPAP2B" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPP3 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 0 |
Variants in PLPP3
This is a list of pathogenic ClinVar variants found in the PLPP3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-56496642-G-A | not specified | Uncertain significance (Dec 01, 2022) | ||
| 1-56496676-C-T | not specified | Uncertain significance (Mar 21, 2022) | ||
| 1-56512115-C-T | not specified | Uncertain significance (Dec 28, 2022) | ||
| 1-56512136-C-T | not specified | Uncertain significance (Apr 08, 2022) | ||
| 1-56524326-T-C | not specified | Uncertain significance (Jan 26, 2023) | ||
| 1-56524475-A-G | not specified | Uncertain significance (Jan 02, 2024) | ||
| 1-56524476-G-A | not specified | Uncertain significance (Jan 02, 2024) | ||
| 1-56524533-G-A | not specified | Uncertain significance (Oct 04, 2022) | ||
| 1-56524535-T-C | not specified | Uncertain significance (Feb 16, 2023) | ||
| 1-56524547-G-A | not specified | Uncertain significance (Jan 19, 2024) | ||
| 1-56537020-T-G | not specified | Uncertain significance (Feb 22, 2023) | ||
| 1-56537037-C-T | not specified | Uncertain significance (Sep 23, 2023) | ||
| 1-56578920-G-A | not specified | Uncertain significance (Feb 08, 2023) | ||
| 1-56578961-C-A | not specified | Uncertain significance (Oct 05, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLPP3 | protein_coding | protein_coding | ENST00000371250 | 6 | 150556 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.917 | 0.0829 | 125664 | 0 | 2 | 125666 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.43 | 134 | 189 | 0.707 | 0.0000112 | 2041 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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.;
- Pathway
- 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);Fat digestion and absorption - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Triacylglyceride Synthesis;Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Prostaglandin formation from arachidonate;Glycerophospholipid metabolism;triacylglycerol biosynthesis;Sphingolipid de novo biosynthesis;Sphingolipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.179
Intolerance Scores
- loftool
- rvis_EVS
- -0.41
- rvis_percentile_EVS
- 26.23
Haploinsufficiency Scores
- pHI
- 0.277
- hipred
- Y
- hipred_score
- 0.752
- ghis
- 0.585
Essentials
- essential_gene_CRISPR
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Mouse Genome Informatics
- Gene name
- Plpp3
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- negative regulation of protein phosphorylation;protein dephosphorylation;lipid metabolic process;phospholipid metabolic process;germ cell migration;regulation of Wnt signaling pathway;sphingolipid biosynthetic process;homotypic cell-cell adhesion;canonical Wnt signaling pathway involved in positive regulation of endothelial cell migration;canonical Wnt signaling pathway involved in positive regulation of cell-cell adhesion;canonical Wnt signaling pathway involved in positive regulation of wound healing;phospholipid dephosphorylation;protein stabilization;positive regulation of DNA-binding transcription factor activity;canonical Wnt signaling pathway
- Cellular component
- Golgi apparatus;plasma membrane;integral component of plasma membrane;adherens junction;membrane
- Molecular function
- phosphoprotein phosphatase activity;protein binding;phosphatidate phosphatase activity;phosphatase activity;sphingosine-1-phosphate phosphatase activity;lipid phosphatase activity