LPAR1
Chr 9lysophosphatidic acid receptor 1
Also known as: EDG2, Gpcr26, LPA1, Mrec1.3, VZG1, edg-2, rec.1.3, vzg-1
The lysophosphatidic acid receptor 1 functions as a G protein-coupled receptor that binds lysophosphatidic acid and regulates actin cytoskeleton reorganization, cell migration, proliferation, and neuronal development including neurite retraction and formation of new neurons in the adult brain. Gain-of-function mutations in LPAR1 cause neurodevelopmental disorders, though the specific inheritance pattern requires further clinical characterization. The pathogenic mechanism involves excessive receptor activation leading to dysregulated cellular signaling that disrupts normal brain development and neuronal function.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Moderately missense-constrained (top ~2.5%)
This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
83 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 29 | 0 | 29 |
Likely Pathogenic | 0 | 0 | 4 | 0 | 4 |
VUS | 0 | 38 | 3 | 0 | 41 |
Likely Benign | 0 | 1 | 0 | 0 | 1 |
Benign | 0 | 0 | 0 | 1 | 1 |
| Total | 0 | 39 | 36 | 1 | 76 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
LPAR1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools