LPAR4
protein-codinglysophosphatidic acid receptor 4, the group of Lysophosphatidic acid receptors
Gene summary
This gene encodes a member of the lysophosphatidic acid receptor family. It may also be related to the P2Y receptors, a family of receptors that bind purine and pyrimidine nucleotides and are coupled to G proteins. The encoded protein may play a role in monocytic differentiation. [provided by RefSeq, Feb 2009]
- GPR23
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.0 kbGenCC 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 LPAR4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001278000.3. 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 | 3 | 3 | ||||
| missense | 43 | 1 | 1 | 45 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 47 | 1 | 1 | 49 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001264929.1 | 1 | MANE Select | |
| Ensembl | ENSP00000478261.1 | 1 | MANE Select | |
| RefSeq | NP_005287.1 | 1 | Standard | |
| Ensembl | ENSP00000408205.2 | 1 | Standard |
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
- positive regulation of Rho protein signal transduction
- positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway
Molecular Function
- G protein-coupled receptor activity
- lysophosphatidic acid binding
- lysophosphatidic acid receptor activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- nuclear body
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000435339
- Coding exons
- 1
- Length
- 9386
- Individuals with no LoFs
- 125514
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 3
- Defined
- 125520
- p
- 0.0000239
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.939 | 105 | 136 | 0.773 | 0.00000972 | 2447 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000037 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000072 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000049 | 0.000035 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- LoFtool
- 0.275
- RVIS EVS
- 0.28
- RVIS percentile EVS
- 71.08
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.649
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |