LPAR3

lysophosphatidic acid receptor 3, the group of Lysophosphatidic acid receptors

Basic information

Region (hg38): 1:84811601-84893206

Previous symbols: [ "EDG7" ]

Links

ENSG00000171517 ∙ NCBI:23566 ∙ OMIM:605106 ∙ HGNC:14298 ∙ Uniprot:Q9UBY5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LPAR3 gene.

• Inborn genetic diseases (20 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPAR3 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					2	2
missense			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	3

Variants in LPAR3

This is a list of pathogenic ClinVar variants found in the LPAR3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-84813938-G-T		not specified	Uncertain significance (Jan 10, 2022)
1-84813953-G-A		not specified	Uncertain significance (May 24, 2023)
1-84813989-T-A		not specified	Uncertain significance (Mar 06, 2023)
1-84814024-T-C		not specified	Uncertain significance (Aug 04, 2023)
1-84814046-C-T			Benign (Jun 05, 2018)
1-84814083-T-C			Benign (Jun 05, 2018)
1-84814165-A-C		not specified	Uncertain significance (Jan 23, 2023)
1-84865402-G-A		not specified	Uncertain significance (Sep 30, 2021)
1-84865430-G-A		not specified	Uncertain significance (Jul 14, 2022)
1-84865498-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-84865499-G-C		not specified	Uncertain significance (Apr 24, 2023)
1-84865556-C-A		not specified	Uncertain significance (Dec 17, 2023)
1-84865604-T-C		not specified	Uncertain significance (Aug 05, 2023)
1-84865631-T-C		not specified	Uncertain significance (Mar 30, 2022)
1-84865689-C-A		not specified	Uncertain significance (Jun 16, 2023)
1-84865717-C-T		not specified	Uncertain significance (May 26, 2022)
1-84865730-T-C		not specified	Uncertain significance (Oct 06, 2022)
1-84865748-C-T		not specified	Uncertain significance (Nov 30, 2021)
1-84865779-A-C			Benign (Jun 04, 2018)
1-84865808-G-A		not specified	Uncertain significance (Apr 07, 2022)
1-84865819-C-T		not specified	Uncertain significance (Jan 26, 2023)
1-84865834-G-A		not specified	Uncertain significance (Nov 07, 2022)
1-84865873-T-C		not specified	Uncertain significance (May 17, 2023)
1-84865874-A-T		not specified	Uncertain significance (Dec 03, 2021)
1-84865889-A-G		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPAR3	protein_coding	protein_coding	ENST00000440886	2	81612

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.679	0.317	125726	0	21	125747	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.257	195	205	0.950	0.0000124	2340
Missense in Polyphen		85	92.096	0.92295		1062
Synonymous	0.514	81	87.1	0.930	0.00000597	713
Loss of Function	2.29	1	8.00	0.125	3.44e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000347	0.000347
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000571	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000277	0.0000264
Middle Eastern	0.0000571	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for lysophosphatidic acid (LPA), a mediator of diverse cellular activities. May play a role in the development of ovarian cancer. Seems to be coupled to the G(i)/G(o) and G(q) families of heteromeric G proteins.
• 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;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: 0.120

Intolerance Scores

• loftool: 0.492
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.219
• hipred: Y
• hipred_score: 0.611
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.220

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lpar3
• Phenotype: homeostasis/metabolism phenotype; embryo phenotype; reproductive system phenotype

Zebrafish Information Network

• Gene name: lpar3
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: activation of MAPK activity;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;positive regulation of cytosolic calcium ion concentration;chemical synaptic transmission;bleb assembly;positive regulation of collateral sprouting;positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway;positive regulation of calcium ion transport
• Cellular component: plasma membrane;integral component of plasma membrane;axon
• Molecular function: G-protein alpha-subunit binding;G protein-coupled receptor activity;phospholipid binding;lipid binding;lysophosphatidic acid receptor activity