LPAR1
lysophosphatidic acid receptor 1, the group of Lysophosphatidic acid receptors
Basic information
Region (hg38): 9:110873263-111038470
Previous symbols: [ "EDG2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPAR1 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 | |||||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 1 |
Variants in LPAR1
This is a list of pathogenic ClinVar variants found in the LPAR1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-110875485-G-A | not specified | Uncertain significance (Jan 24, 2024) | ||
| 9-110875510-C-T | not specified | Uncertain significance (Jun 28, 2022) | ||
| 9-110875602-G-A | not specified | Uncertain significance (Dec 05, 2022) | ||
| 9-110875671-A-G | not specified | Uncertain significance (Oct 20, 2023) | ||
| 9-110941433-C-T | not specified | Uncertain significance (Oct 26, 2021) | ||
| 9-110941483-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 9-110941484-A-T | not specified | Uncertain significance (Oct 26, 2022) | ||
| 9-110941685-C-T | not specified | Uncertain significance (Aug 27, 2024) | ||
| 9-110941694-T-C | not specified | Uncertain significance (Apr 23, 2024) | ||
| 9-110941705-A-G | not specified | Uncertain significance (Dec 20, 2021) | ||
| 9-110941760-G-A | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 9-110941779-C-T | Benign (May 04, 2018) | |||
| 9-110941897-A-G | not specified | Uncertain significance (Sep 27, 2021) | ||
| 9-110941973-G-A | not specified | Uncertain significance (Jan 09, 2024) | ||
| 9-110941982-G-A | not specified | Uncertain significance (Sep 01, 2021) | ||
| 9-110942033-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 9-110942104-C-T | not specified | Uncertain significance (Aug 10, 2024) | ||
| 9-110942132-C-T | not specified | Uncertain significance (Mar 30, 2024) | ||
| 9-110942155-T-C | not specified | Uncertain significance (Dec 19, 2023) | ||
| 9-110972105-A-G | not specified | Uncertain significance (Nov 17, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LPAR1 | protein_coding | protein_coding | ENST00000374431 | 3 | 165439 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.186 | 0.804 | 125675 | 0 | 6 | 125681 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.42 | 126 | 229 | 0.551 | 0.0000135 | 2411 |
| Missense in Polyphen | 27 | 77.519 | 0.3483 | 941 | ||
| Synonymous | -0.506 | 83 | 77.3 | 1.07 | 0.00000419 | 733 |
| Loss of Function | 2.21 | 3 | 10.9 | 0.276 | 5.45e-7 | 124 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000199 | 0.000198 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000267 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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}.;
- Pathway
- 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);Neuroactive ligand-receptor interaction - Homo sapiens (human);Small Ligand GPCRs;Myometrial Relaxation and Contraction Pathways;NOTCH1 regulation of human endothelial cell calcification;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Signaling by GPCR;Signal Transduction;rho-selective guanine exchange factor akap13 mediates stress fiber formation;Lysosphingolipid and LPA receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;G alpha (q) signalling events;GPCR downstream signalling;LPA receptor mediated events
(Consensus)
Recessive Scores
- pRec
- 0.166
Intolerance Scores
- loftool
- 0.616
- rvis_EVS
- -0.56
- rvis_percentile_EVS
- 19.31
Haploinsufficiency Scores
- pHI
- 0.572
- hipred
- Y
- hipred_score
- 0.632
- ghis
- 0.584
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.00577
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lpar1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- lpar1
- Affected structure
- thoracic duct
- Phenotype tag
- abnormal
- Phenotype quality
- aplastic
Gene ontology
- 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;regulation of cell shape;negative regulation of neuron projection development;oligodendrocyte development;cerebellum development;optic nerve development;corpus callosum development;bleb assembly;positive regulation of Rho protein signal transduction;myelination;positive regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of MAPK cascade;negative regulation of cAMP-mediated signaling;positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway;positive regulation of stress fiber assembly;cell chemotaxis;positive regulation of dendritic spine development;cellular response to oxygen levels;positive regulation of smooth muscle cell chemotaxis;cellular response to 1-oleoyl-sn-glycerol 3-phosphate
- Cellular component
- endosome;plasma membrane;integral component of plasma membrane;cell surface;endocytic vesicle;neuronal cell body;dendritic spine;dendritic shaft
- Molecular function
- G-protein alpha-subunit binding;G protein-coupled receptor activity;protein binding;PDZ domain binding;lysophosphatidic acid binding;lysophosphatidic acid receptor activity