PLPPR3

protein-coding

phospholipid phosphatase related 3, the group of Phospholipid phosphatase related

Gene summary

The proteins in the lipid phosphate phosphatase (LPP) family, including PRG2, are integral membrane proteins that modulate bioactive lipid phosphates including phosphatidate, lysophosphatidate, and sphingosine-1-phosphate in the context of cell migration, neurite retraction, and mitogenesis (Brauer et al., 2003 [PubMed 12730698]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_001270366.2

Inheritance

—

ClinVar variants

U:173B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr19:812,488-821,955

External References & Databases

Ensembl (ENSG00000129951)

Transcript & Mutation Effects

hg38 • Region Span ~9.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PLPPR3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 179

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001270366.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			172 clinvar	1 clinvar		173
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	173	2	0	175

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001270366.2	RefSeq	NP_001257295.1	7	MANE Select
ENST00000520876.8	Ensembl	ENSP00000430297.1	7	MANE Select
NM_024888.3	RefSeq	NP_079164.1	6	Standard
ENST00000359894.6	Ensembl	ENSP00000352962.2	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by GPCR
Signal Transduction
Lysosphingolipid and LPA receptors
Class A/1 (Rhodopsin-like receptors)
GPCR ligand binding

Biological Process

phospholipid metabolic process
phospholipid dephosphorylation

Molecular Function

phosphatidate phosphatase activity
phosphatase activity
lipid phosphatase activity

Cellular Component

integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359894
Coding exons: 6
Length: 9450
Individuals with no LoFs: 124854
Homozygous LoFs: 2
Heterozygous LoFs: 392
Defined: 125248
p: 0.00157

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.880	333	381	0.873	0.0000285	4592
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0065	0.0065	notable
Latino/Admixed American	0.0027	0.0027	notable
Ashkenazi Jewish	0.011	0.011	notable
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00064	0.00064	rare
South Asian	0	0.0	absent
Other	0.0023	0.0023	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.103

Essentials

Essential (gene trap): N