PLPP3

phospholipid phosphatase 3, the group of Phospholipid phosphatases

Basic information

Region (hg38): 1:56494760-56645301

Previous symbols: [ "PPAP2B" ]

Links

ENSG00000162407 ∙ NCBI:8613 ∙ OMIM:607125 ∙ HGNC:9229 ∙ Uniprot:O14495 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLPP3 gene.

• Inborn genetic diseases (9 variants)

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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	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: gnomAD

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: dbNSFP

• 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

• 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_gene_trap: N

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