LPAR2

lysophosphatidic acid receptor 2, the group of Lysophosphatidic acid receptors

Basic information

Region (hg38): 19:19623655-19628930

Previous symbols: [ "EDG4" ]

Links

ENSG00000064547 ∙ NCBI:9170 ∙ OMIM:605110 ∙ HGNC:3168 ∙ Uniprot:Q9HBW0 ∙ 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 LPAR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPAR2 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					4	4
missense			22		1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	23	0	5

Variants in LPAR2

This is a list of pathogenic ClinVar variants found in the LPAR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19624282-G-A		not specified	Uncertain significance (Jul 06, 2021)
19-19624289-C-A		not specified	Uncertain significance (Feb 26, 2024)
19-19624351-C-T		not specified	Uncertain significance (Aug 17, 2021)
19-19624354-G-A		not specified	Uncertain significance (Oct 20, 2023)
19-19624392-C-T		not specified	Uncertain significance (Mar 19, 2024)
19-19624404-C-T		not specified	Uncertain significance (Jun 13, 2024)
19-19624405-G-A		not specified	Uncertain significance (Oct 20, 2023)
19-19624419-C-T		not specified	Uncertain significance (Apr 25, 2023)
19-19624439-A-G			Benign (Dec 31, 2019)
19-19624459-C-T		not specified	Uncertain significance (May 20, 2024)
19-19626578-G-A			Benign (Dec 31, 2019)
19-19626593-C-T		not specified	Uncertain significance (Oct 02, 2023)
19-19626623-C-T		not specified	Uncertain significance (Dec 14, 2023)
19-19626635-C-A		not specified	Uncertain significance (Apr 12, 2022)
19-19626638-C-A		not specified	Uncertain significance (Jun 03, 2022)
19-19626656-C-T		not specified	Uncertain significance (Jan 23, 2023)
19-19626659-G-T		not specified	Uncertain significance (Mar 31, 2023)
19-19626682-G-T		not specified	Uncertain significance (Sep 25, 2023)
19-19626711-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-19626728-C-T		not specified	Uncertain significance (May 28, 2024)
19-19626745-G-A			Benign (Feb 13, 2018)
19-19626756-G-A		not specified	Uncertain significance (Nov 08, 2022)
19-19626854-C-T		not specified	Uncertain significance (Feb 23, 2023)
19-19626871-C-T			Benign (Jul 13, 2018)
19-19626879-C-T		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPAR2	protein_coding	protein_coding	ENST00000542587	2	5263

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0367	0.932	125720	0	26	125746	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	163	244	0.667	0.0000171	2200
Missense in Polyphen		41	81.141	0.50529		823
Synonymous	1.11	89	103	0.861	0.00000665	802
Loss of Function	1.87	4	10.5	0.380	7.07e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000192	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.000192	0.000185
European (Non-Finnish)	0.0000915	0.0000879
Middle Eastern	0.000273	0.000272
South Asian	0.0000349	0.0000327
Other	0.000332	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for lysophosphatidic acid (LPA), a mediator of diverse cellular activities. Seems to be coupled to the G(i)/G(o), G(12)/G(13), and G(q) families of heteromeric G proteins. Plays a key role in phospholipase C-beta (PLC-beta) signaling pathway. Stimulates phospholipase C (PLC) activity in a manner that is independent of RALA activation. {ECO:0000269|PubMed:15143197, ECO:0000269|PubMed:19306925}.
• 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: 0.158

Intolerance Scores

• loftool: 0.567
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.120
• hipred: Y
• hipred_score: 0.669
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.744

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lpar2
• 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); hematopoietic system phenotype; normal phenotype; respiratory system phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: lpar2a
• Affected structure: hemoglobin biosynthetic process
• Phenotype tag: abnormal
• Phenotype quality: increased occurrence

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;activation of phospholipase C activity;positive regulation of cytosolic calcium ion concentration
• Cellular component: plasma membrane;integral component of plasma membrane;cell surface;endocytic vesicle
• Molecular function: G protein-coupled receptor activity;protein binding;lipid binding;lysophosphatidic acid receptor activity