GeneBe

LPAR1

protein-coding

lysophosphatidic acid receptor 1, the group of Lysophosphatidic acid receptors

Gene summary

The integral membrane protein encoded by this gene is a lysophosphatidic acid (LPA) receptor from a group known as EDG receptors. These receptors are members of the G protein-coupled receptor superfamily. Utilized by LPA for cell signaling, EDG receptors mediate diverse biologic functions, including proliferation, platelet aggregation, smooth muscle contraction, inhibition of neuroblastoma cell differentiation, chemotaxis, and tumor cell invasion. Many transcript variants encoding a few different isoforms have been identified for this gene. [provided by RefSeq, Oct 2020]

Previous symbols:
  • EDG2

MANE transcript

NM_001351411.2

Inheritance

—

ClinVar variants

U:41B:2

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr9:110,873,263-111,038,470

External References & Databases

Ensembl (ENSG00000198121)NCBI Gene (1902)OMIM (602282)HGNC:3166GenCCUniProt (Q92633)AlphaFoldClinVar (LPAR1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~165.2 kb
Loading mutation effect viewer...

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 LPAR1 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 38
EBV-positive nodal T- and NK-cell lymphomaTotal: 1
not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001351411.2. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
 3
missense
39
clinvar
1
clinvar
 40
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total00411143
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 167 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001351411.2RefSeqNP_001338340.13MANE Select
ENST00000683809.1EnsemblENSP00000506912.13MANE Select
NM_001351397.2RefSeqNP_001338326.13Standard
NM_001351398.2RefSeqNP_001338327.13Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
lpar1Danio rerio

Structure: thoracic duct

Quality: aplastic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • PI3K-Akt signaling pathway - Homo sapiens (human)
  • Gap junction - Homo sapiens (human)
  • Rap1 signaling pathway - Homo sapiens (human)
  • Phospholipase D signaling pathway - Homo sapiens (human)
  • Pathways in cancer - Homo sapiens (human)

Biological Process

  • activation of MAPK activity
  • G protein-coupled receptor signaling pathway
  • adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
  • activation of phospholipase C activity
  • positive regulation of cytosolic calcium ion concentration

Molecular Function

  • G-protein alpha-subunit binding
  • G protein-coupled receptor activity
  • protein binding
  • PDZ domain binding
  • lysophosphatidic acid binding

Cellular Component

  • endosome
  • plasma membrane
  • integral component of plasma membrane
  • cell surface
  • endocytic vesicle

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000374431
Coding exons
3
Length
165439
Individuals with no LoFs
125675
Homozygous LoFs
0
Heterozygous LoFs
6
Defined
125681
p
0.0000239
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.421262290.5510.00001352411
Missense (PolyPhen)2777.5190.3483941
Synonymous-0.5068377.31.070.00000419733
Loss of Function2.21310.90.2765.45e-7124

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish0.000200.00020rare
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000270.000026rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Receptor for lysophosphatidic acid (LPA) (PubMed:9070858, PubMed:19306925, PubMed:25025571, PubMed:26091040). Plays a role in the reorganization of the actin cytoskeleton, cell migration, differentiation and proliferation, and thereby contributes to the responses to tissue damage and infectious agents. Activates downstream signaling cascades via the G(i)/G(o), G(12)/G(13), and G(q) families of heteromeric G proteins. Signaling inhibits adenylyl cyclase activity and decreases cellular cAMP levels (PubMed:26091040). Signaling triggers an increase of cytoplasmic Ca(2+) levels (PubMed:19656035, PubMed:19733258, PubMed:26091040). Activates RALA; this leads to the activation of phospholipase C (PLC) and the formation of inositol 1,4,5-trisphosphate (PubMed:19306925). Signaling mediates activation of down-stream MAP kinases (By similarity). Contributes to the regulation of cell shape. Promotes Rho-dependent reorganization of the actin cytoskeleton in neuronal cells and neurite retraction (PubMed:26091040). Promotes the activation of Rho and the formation of actin stress fibers (PubMed:26091040). Promotes formation of lamellipodia at the leading edge of migrating cells via activation of RAC1 (By similarity). Through its function as lysophosphatidic acid receptor, plays a role in chemotaxis and cell migration, including responses to injury and wounding (PubMed:18066075, PubMed:19656035, PubMed:19733258). Plays a role in triggering inflammation in response to bacterial lipopolysaccharide (LPS) via its interaction with CD14. Promotes cell proliferation in response to lysophosphatidic acid. Required for normal skeleton development. May play a role in osteoblast differentiation. Required for normal brain development. Required for normal proliferation, survival and maturation of newly formed neurons in the adult dentate gyrus. Plays a role in pain perception and in the initiation of neuropathic pain (By similarity). {ECO:0000250|UniProtKB:P61793, ECO:0000269|PubMed:18066075, ECO:0000269|PubMed:19306925, ECO:0000269|PubMed:19656035, ECO:0000269|PubMed:19733258, ECO:0000269|PubMed:25025571, ECO:0000269|PubMed:26091040, ECO:0000269|PubMed:9070858, ECO:0000305|PubMed:11093753, ECO:0000305|PubMed:9069262}.;

Recessive Scores

pRec
0.166

Intolerance Scores

LoFtool
0.616
RVIS EVS
-0.56
RVIS percentile EVS
19.31

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.00577

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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