PLPPR3

phospholipid phosphatase related 3, the group of Phospholipid phosphatase related

Basic information

Region (hg38): 19:812488-821955

Links

ENSG00000129951 ∙ NCBI:79948 ∙ OMIM:610391 ∙ HGNC:23497 ∙ Uniprot:Q6T4P5 ∙ 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 PLPPR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPPR3 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			98	1		99
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	98	2	0

Variants in PLPPR3

This is a list of pathogenic ClinVar variants found in the PLPPR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-812577-G-A		not specified	Uncertain significance (Jan 22, 2025)
19-812589-G-A		not specified	Uncertain significance (Dec 18, 2023)
19-812595-A-T		not specified	Uncertain significance (Nov 09, 2022)
19-812632-C-T		not specified	Uncertain significance (May 01, 2024)
19-812638-C-G		not specified	Uncertain significance (Jul 31, 2024)
19-812649-A-G		not specified	Uncertain significance (Apr 13, 2023)
19-812676-G-C		not specified	Uncertain significance (Nov 15, 2024)
19-812682-C-G		not specified	Uncertain significance (Jan 21, 2025)
19-812691-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-812700-G-T		not specified	Uncertain significance (Mar 11, 2024)
19-812701-C-A		not specified	Uncertain significance (Jun 26, 2024)
19-812712-G-A		not specified	Uncertain significance (Aug 04, 2023)
19-812722-G-A		not specified	Uncertain significance (Apr 19, 2023)
19-812725-G-C		not specified	Uncertain significance (Jul 14, 2021)
19-812725-G-T		not specified	Uncertain significance (Nov 09, 2024)
19-812739-G-A		not specified	Uncertain significance (Sep 19, 2022)
19-812740-T-C		not specified	Uncertain significance (Dec 21, 2023)
19-812752-C-T		not specified	Uncertain significance (Jun 18, 2024)
19-812779-C-G		not specified	Uncertain significance (Sep 26, 2023)
19-812820-C-G		not specified	Uncertain significance (Dec 28, 2022)
19-812823-G-C		not specified	Uncertain significance (May 05, 2023)
19-812847-C-T		not specified	Uncertain significance (Oct 30, 2023)
19-812853-G-T		not specified	Uncertain significance (Feb 01, 2025)
19-812918-C-G		not specified	Uncertain significance (Oct 12, 2022)
19-812946-T-C		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPPR3	protein_coding	protein_coding	ENST00000359894	6	9450

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00956	0.981	124854	2	392	125248	0.00157

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.880	333	381	0.873	0.0000285	4592
Missense in Polyphen		217	263.35	0.824		2969
Synonymous	-1.92	240	205	1.17	0.0000190	1622
Loss of Function	2.26	6	15.6	0.384	6.68e-7	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00921	0.00919
Ashkenazi Jewish	0.0108	0.0107
East Asian	0.000218	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.000641	0.000637
Middle Eastern	0.000218	0.000218
South Asian	0.00	0.00
Other	0.00230	0.00229

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)

Recessive Scores

• pRec: 0.103

Haploinsufficiency Scores

• pHI: 0.251
• hipred: N
• hipred_score: 0.490
• ghis: 0.483

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Plppr3

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