LPAR2

protein-coding

lysophosphatidic acid receptor 2, the group of Lysophosphatidic acid receptors

Gene summary

This gene encodes a member of family I of the G protein-coupled receptors, as well as the EDG family of proteins. This protein functions as a lysophosphatidic acid (LPA) receptor and contributes to Ca2+ mobilization, a critical cellular response to LPA in cells, through association with Gi and Gq proteins. An alternative splice variant has been described but its full length sequence has not been determined. [provided by RefSeq, Jul 2008]

Previous symbols:

EDG4

MANE transcript

NM_001395660.1

Inheritance

—

ClinVar variants

U:42B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr19:19,623,655-19,628,930

External References & Databases

Ensembl (ENSG00000064547)

Transcript & Mutation Effects

hg38 • Region Span ~5.3 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 LPAR2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395660.1. 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					4 clinvar	4
missense			42 clinvar		1 clinvar	43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	0	5	47

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 99 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395660.1	RefSeq	NP_001382589.1	2	MANE Select
ENST00000407877.8	Ensembl	ENSP00000384665.3	2	MANE Select
ENST00000542587.5	Ensembl	ENSP00000443256.2	2	Standard
ENST00000542587.6	Ensembl	ENSP00000443256.2	2	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
lpar2a	Danio rerio	Structure: hemoglobin biosynthetic process Quality: increased occurrence abnormal

Gene / Model

Organism

Observed Phenotype

lpar2a

Danio rerio

Structure: hemoglobin biosynthetic process

Quality: increased occurrence

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

PI3K-Akt signaling pathway - Homo sapiens (human)
Rap1 signaling pathway - Homo sapiens (human)
Phospholipase D signaling pathway - Homo sapiens (human)
Pathways in cancer - Homo sapiens (human)
Neuroactive ligand-receptor interaction - Homo sapiens (human)

Biological Process

G protein-coupled receptor signaling pathway
activation of phospholipase C activity
positive regulation of cytosolic calcium ion concentration

Molecular Function

G protein-coupled receptor activity
protein binding
lipid binding
lysophosphatidic acid receptor activity

Cellular Component

plasma membrane
integral component of plasma membrane
cell surface
endocytic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000542587
Coding exons: 2
Length: 5263
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 26
Defined: 125746
p: 0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.85	163	244	0.667	0.0000171	2200
Missense (PolyPhen)		41	81.141	0.50529		823
Synonymous	1.11	89	103	0.861	0.00000665	802
Loss of Function	1.87	4	10.5	0.380	7.07e-7	90

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.000091	0.000088	rare
South Asian	0.000035	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Receptor for lysophosphatidic acid (LPA), a mediator of diverse cellular activities. Seems to be coupled to the G(i)/G(o), G(12)/G(13), and G(q) families of heteromeric G proteins. Plays a key role in phospholipase C-beta (PLC-beta) signaling pathway. Stimulates phospholipase C (PLC) activity in a manner that is independent of RALA activation. {ECO:0000269|PubMed:15143197, ECO:0000269|PubMed:19306925}.;

Recessive Scores

pRec: 0.158

Intolerance Scores

LoFtool: 0.567
RVIS EVS: -0.34
RVIS percentile EVS: 30.37

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.744

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium