PLPP1

phospholipid phosphatase 1, the group of Phospholipid phosphatases|MicroRNA protein coding host genes

Basic information

Region (hg38): 5:55424854-55534969

Previous symbols: [ "PPAP2A" ]

Links

ENSG00000067113 ∙ NCBI:8611 ∙ OMIM:607124 ∙ HGNC:9228 ∙ Uniprot:O14494 ∙ 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 PLPP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPP1 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in PLPP1

This is a list of pathogenic ClinVar variants found in the PLPP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-55425225-G-A		not specified	Uncertain significance (Jan 10, 2023)
5-55425234-T-C		not specified	Uncertain significance (Dec 20, 2023)
5-55425235-T-A		not specified	Uncertain significance (Jul 05, 2023)
5-55425277-C-T		not specified	Uncertain significance (Oct 26, 2024)
5-55425280-C-G		not specified	Uncertain significance (Oct 06, 2021)
5-55425910-C-T		not specified	Uncertain significance (Jun 11, 2024)
5-55425964-C-T		not specified	Uncertain significance (Jun 11, 2021)
5-55425994-G-A		not specified	Uncertain significance (Dec 04, 2024)
5-55467892-A-C		not specified	Uncertain significance (Dec 19, 2023)
5-55467906-T-C		not specified	Uncertain significance (Sep 29, 2023)
5-55467971-A-T		not specified	Uncertain significance (Dec 31, 2023)
5-55468070-G-A		not specified	Uncertain significance (Mar 20, 2024)
5-55468080-A-G		not specified	Uncertain significance (Oct 03, 2022)
5-55491007-T-C		not specified	Uncertain significance (Oct 26, 2024)
5-55491010-C-T		not specified	Uncertain significance (Jan 23, 2023)
5-55491021-T-A		not specified	Uncertain significance (Feb 23, 2023)
5-55491079-T-C		not specified	Uncertain significance (Jun 29, 2023)
5-55534576-C-G		not specified	Uncertain significance (Dec 03, 2021)
5-55534587-G-T		not specified	Uncertain significance (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPP1	protein_coding	protein_coding	ENST00000264775	6	110197

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0964	0.897	125736	0	9	125745	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.541	134	153	0.877	0.00000766	1843
Missense in Polyphen		41	59.399	0.69025		707
Synonymous	0.579	53	58.6	0.904	0.00000324	555
Loss of Function	2.35	4	13.2	0.302	6.86e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000219	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.000219	0.000217
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Broad-specificity phosphohydrolase that dephosphorylates exogenous bioactive glycerolipids and sphingolipids. Catalyzes the conversion of phosphatidic acid (PA) to diacylglycerol (DG). Pivotal regulator of lysophosphatidic acid (LPA) signaling in the cardiovascular system. Major enzyme responsible of dephosphorylating LPA in platelets, which terminates signaling actions of LPA. May control circulating, and possibly also regulate localized, LPA levels resulting from platelet activation. It has little activity towards ceramide-1-phosphate (C-1-P) and sphingosine-1-phosphate (S-1-P). The relative catalytic efficiency is LPA > PA > S-1-P > C-1-P. It's down-regulation may contribute to the development of colon adenocarcinoma. {ECO:0000269|PubMed:12909631}.
• 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);Sphingolipid Metabolism;Familial lipoprotein lipase deficiency;Gaucher Disease;Globoid Cell Leukodystrophy;Metachromatic Leukodystrophy (MLD);Plasmalogen Synthesis;Glycerolipid Metabolism;Fabry disease;Glycerol Kinase Deficiency;Phospholipid Biosynthesis;D-glyceric acidura;Krabbe disease;Androgen receptor signaling pathway;Sphingolipid Metabolism;Triacylglyceride Synthesis;Metabolism of lipids;Metabolism;p73 transcription factor network;Glycosphingolipid metabolism;Prostaglandin formation from arachidonate;Glycerophospholipid metabolism;triacylglycerol biosynthesis;Sphingolipid de novo biosynthesis;Sphingolipid metabolism;Fc-epsilon receptor I signaling in mast cells (Consensus)

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.655
• hipred: Y
• hipred_score: 0.640
• ghis: 0.573

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Plpp1
• Phenotype: homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: plpp1b
• Affected structure: intersegmental vessel
• Phenotype tag: abnormal
• Phenotype quality: decreased functionality

Gene ontology

• Biological process: protein dephosphorylation;lipid metabolic process;phospholipid metabolic process;protein kinase C-activating G protein-coupled receptor signaling pathway;negative regulation of cell population proliferation;germ cell migration;regulation of lipid metabolic process;sphingolipid biosynthetic process;intracellular steroid hormone receptor signaling pathway;androgen receptor signaling pathway;phospholipid dephosphorylation
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;extracellular exosome
• Molecular function: phosphatidate phosphatase activity;phosphatase activity;sphingosine-1-phosphate phosphatase activity;lipid phosphatase activity