PLPP2

phospholipid phosphatase 2, the group of Phospholipid phosphatases

Basic information

Region (hg38): 19:281039-291403

Previous symbols: [ "PPAP2C" ]

Links

ENSG00000141934 ∙ NCBI:8612 ∙ OMIM:607126 ∙ HGNC:9230 ∙ Uniprot:O43688 ∙ 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 PLPP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPP2 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			24	3		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	26	3	0

Variants in PLPP2

This is a list of pathogenic ClinVar variants found in the PLPP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-281405-G-A		PLPP2-related disorder	Likely benign (May 25, 2022)
19-281408-A-C		not specified	Uncertain significance (Oct 17, 2023)
19-281424-G-T		not specified	Uncertain significance (Mar 22, 2023)
19-281432-C-T		not specified	Uncertain significance (Oct 12, 2022)
19-281503-G-A		not specified	Uncertain significance (Mar 18, 2024)
19-281534-A-G		PLPP2-related disorder	Likely benign (May 25, 2022)
19-282148-C-G		not specified	Uncertain significance (Oct 06, 2021)
19-282159-T-A		not specified	Uncertain significance (Apr 12, 2022)
19-282181-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-282190-G-A		not specified	Uncertain significance (Aug 12, 2022)
19-282274-G-A		not specified	Uncertain significance (Apr 22, 2022)
19-282304-C-T		not specified	Uncertain significance (Apr 04, 2023)
19-282766-T-C		not specified	Uncertain significance (Dec 14, 2021)
19-287481-C-T		not specified	Uncertain significance (Jan 02, 2024)
19-287511-C-T		not specified	Uncertain significance (Sep 28, 2021)
19-287546-C-G		not specified	Uncertain significance (Feb 15, 2023)
19-287597-A-G		not specified	Uncertain significance (May 30, 2023)
19-287599-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-287600-A-G		not specified	Uncertain significance (May 13, 2024)
19-287703-G-A			Likely benign (Jan 01, 2024)
19-287742-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-288055-T-C		not specified	Uncertain significance (Nov 10, 2022)
19-288066-G-A		not specified	Uncertain significance (Jan 08, 2024)
19-288075-T-A		not specified	Uncertain significance (Feb 28, 2024)
19-288081-C-T		not specified	Uncertain significance (Mar 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPP2	protein_coding	protein_coding	ENST00000327790	6	10354

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000831	0.939	125702	0	41	125743	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.492	151	169	0.894	0.0000109	1931
Missense in Polyphen		51	63.417	0.8042		728
Synonymous	0.409	73	77.6	0.941	0.00000543	666
Loss of Function	1.66	7	13.6	0.514	8.51e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000213	0.000211
Middle Eastern	0.000544	0.000544
South Asian	0.0000982	0.0000980
Other	0.000163	0.000163

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 PA > C-1-P > LPA > S-1-P.
• 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);Familial lipoprotein lipase deficiency;Glycerolipid Metabolism;Glycerol Kinase Deficiency;D-glyceric acidura;Triacylglyceride Synthesis;Metabolism of lipids;Metabolism;triacylglycerol biosynthesis;Sphingolipid de novo biosynthesis;Sphingolipid metabolism (Consensus)

Intolerance Scores

• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.69

Haploinsufficiency Scores

• pHI: 0.454
• hipred: N
• hipred_score: 0.454
• ghis: 0.427

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Plpp2
• Phenotype: normal phenotype

Gene ontology

• Biological process: protein dephosphorylation;phospholipid metabolic process;sphingolipid biosynthetic process;phospholipid dephosphorylation
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: phosphoprotein phosphatase activity;protein binding;phosphatidate phosphatase activity;phosphatase activity;sphingosine-1-phosphate phosphatase activity;lipid phosphatase activity