LPAR4
lysophosphatidic acid receptor 4, the group of Lysophosphatidic acid receptors
Basic information
Region (hg38): X:78747709-78758714
Previous symbols: [ "GPR23" ]
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 LPAR4 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 | 0 | |||||
| missense | 14 | 16 | ||||
| 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 | 1 | 1 |
Variants in LPAR4
This is a list of pathogenic ClinVar variants found in the LPAR4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-78754873-G-A | not specified | Uncertain significance (Feb 02, 2024) | ||
| X-78755002-G-A | Likely benign (Jul 06, 2018) | |||
| X-78755029-C-A | Benign (Apr 16, 2018) | |||
| X-78755069-G-A | not specified | Uncertain significance (Aug 17, 2021) | ||
| X-78755108-A-G | not specified | Uncertain significance (Aug 19, 2023) | ||
| X-78755273-A-T | not specified | Uncertain significance (Oct 12, 2021) | ||
| X-78755333-C-A | not specified | Uncertain significance (Apr 27, 2022) | ||
| X-78755423-C-A | not specified | Uncertain significance (Jan 10, 2022) | ||
| X-78755441-G-C | not specified | Uncertain significance (Feb 15, 2023) | ||
| X-78755458-T-C | not specified | Uncertain significance (Apr 01, 2024) | ||
| X-78755522-T-C | not specified | Uncertain significance (Jan 22, 2024) | ||
| X-78755546-T-C | not specified | Uncertain significance (Mar 23, 2022) | ||
| X-78755611-C-G | not specified | Uncertain significance (Jun 22, 2021) | ||
| X-78755699-C-A | not specified | Uncertain significance (Sep 25, 2023) | ||
| X-78755812-C-T | not specified | Uncertain significance (Jun 10, 2022) | ||
| X-78755862-G-C | not specified | Uncertain significance (May 13, 2024) | ||
| X-78755869-T-C | not specified | Uncertain significance (Aug 02, 2021) | ||
| X-78755963-T-C | not specified | Uncertain significance (Jan 23, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LPAR4 | protein_coding | protein_coding | ENST00000435339 | 1 | 9386 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00223 | 0.540 | 125514 | 3 | 3 | 125520 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.939 | 105 | 136 | 0.773 | 0.00000972 | 2447 |
| Missense in Polyphen | 36 | 56.641 | 0.63558 | 1022 | ||
| Synonymous | -0.364 | 51 | 47.8 | 1.07 | 0.00000312 | 759 |
| Loss of Function | 0.224 | 4 | 4.51 | 0.886 | 3.37e-7 | 100 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000367 | 0.0000367 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000722 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000491 | 0.0000353 |
| Middle Eastern | 0.0000722 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for lysophosphatidic acid (LPA), a mediator of diverse cellular activities. Transduces a signal by increasing the intracellular calcium ions and by stimulating adenylyl cyclase activity. The rank order of potency for agonists of this receptor is 1-oleoyl- > 1-stearoyl- > 1-palmitoyl- > 1-myristoyl- > 1- alkyl- > 1-alkenyl-LPA. {ECO:0000269|PubMed:12724320}.;
- Pathway
- 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);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;GPCRs, Class A Rhodopsin-like;Nucleotide GPCRs;Signaling by GPCR;Signal Transduction;P2Y receptors;Nucleotide-like (purinergic) receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling;LPA4-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- loftool
- 0.275
- rvis_EVS
- 0.28
- rvis_percentile_EVS
- 71.08
Haploinsufficiency Scores
- pHI
- 0.752
- hipred
- N
- hipred_score
- 0.398
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.649
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lpar4
- Phenotype
- 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); respiratory system phenotype; embryo phenotype; skeleton phenotype; immune system phenotype; muscle phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; craniofacial phenotype;
Gene ontology
- Biological process
- G protein-coupled receptor signaling pathway;positive regulation of Rho protein signal transduction;positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway
- Cellular component
- plasma membrane;integral component of plasma membrane;nuclear body;intracellular membrane-bounded organelle
- Molecular function
- G protein-coupled receptor activity;lysophosphatidic acid binding;lysophosphatidic acid receptor activity