PLPPR2

phospholipid phosphatase related 2, the group of Phospholipid phosphatase related

Basic information

Region (hg38): 19:11355386-11365698

Links

ENSG00000105520 ∙ NCBI:64748 ∙ OMIM:619591 ∙ HGNC:29566 ∙ Uniprot:Q96GM1 ∙ 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 PLPPR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPPR2 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				1		1
missense			24	3		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	4	0

Variants in PLPPR2

This is a list of pathogenic ClinVar variants found in the PLPPR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-11359632-A-T		not specified	Uncertain significance (Feb 22, 2023)
19-11359668-G-T		not specified	Uncertain significance (Aug 26, 2024)
19-11359843-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-11359858-C-T		not specified	Uncertain significance (Aug 04, 2024)
19-11359864-C-T		not specified	Uncertain significance (Nov 09, 2023)
19-11359878-G-A		not specified	Likely benign (Mar 14, 2023)
19-11361255-G-A		not specified	Uncertain significance (Aug 13, 2021)
19-11361269-G-T		not specified	Uncertain significance (Sep 10, 2024)
19-11361352-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-11362552-C-T			Likely benign (Aug 01, 2022)
19-11362555-G-A		not specified	Uncertain significance (Jun 21, 2021)
19-11363759-G-A		not specified	Uncertain significance (Nov 09, 2021)
19-11363831-C-A		not specified	Uncertain significance (Aug 02, 2022)
19-11364166-C-G		not specified	Likely benign (Nov 09, 2024)
19-11364191-C-T		not specified	Uncertain significance (Nov 14, 2023)
19-11364351-G-A		not specified	Likely benign (Sep 11, 2024)
19-11364364-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-11364419-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-11364422-C-T		not specified	Uncertain significance (Sep 13, 2022)
19-11364428-G-A		not specified	Uncertain significance (Sep 26, 2024)
19-11364430-G-A		not specified	Uncertain significance (Jan 24, 2023)
19-11364436-C-T		not specified	Uncertain significance (Apr 04, 2023)
19-11364442-C-G		not specified	Uncertain significance (Nov 22, 2024)
19-11364497-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-11364508-G-A		not specified	Uncertain significance (Jun 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPPR2	protein_coding	protein_coding	ENST00000591608	8	10313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.00975	125137	0	1	125138	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	203	283	0.717	0.0000192	2645
Missense in Polyphen		58	110.11	0.52677		1077
Synonymous	0.401	128	134	0.956	0.00000969	995
Loss of Function	3.75	1	18.3	0.0546	0.00000108	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000885	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Signaling by GPCR;Signal Transduction;Lysosphingolipid and LPA receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;triacylglycerol biosynthesis (Consensus)

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• ghis: 0.496

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Plppr2

Gene ontology

• Biological process: phospholipid metabolic process;phospholipid dephosphorylation
• Cellular component: integral component of plasma membrane
• Molecular function: phosphatidate phosphatase activity;phosphatase activity;lipid phosphatase activity