LPAR5

lysophosphatidic acid receptor 5, the group of Lysophosphatidic acid receptors

Basic information

Region (hg38): 12:6618835-6635960

Previous symbols: [ "GPR93", "GPR92" ]

Links

ENSG00000184574 ∙ NCBI:57121 ∙ OMIM:606926 ∙ HGNC:13307 ∙ Uniprot:Q9H1C0 ∙ 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 LPAR5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPAR5 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	0

Variants in LPAR5

This is a list of pathogenic ClinVar variants found in the LPAR5 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-6620264-G-C		not specified	Uncertain significance (Dec 15, 2023)
12-6620273-G-A		not specified	Uncertain significance (Oct 02, 2023)
12-6620345-C-G		not specified	Uncertain significance (Jun 29, 2023)
12-6620345-C-T		not specified	Uncertain significance (Mar 01, 2024)
12-6620420-C-T		not specified	Uncertain significance (May 05, 2023)
12-6620426-C-G		not specified	Uncertain significance (Aug 21, 2023)
12-6620440-G-A		not specified	Uncertain significance (Jan 31, 2022)
12-6620444-C-T		not specified	Uncertain significance (May 23, 2023)
12-6620504-G-A		not specified	Uncertain significance (Feb 27, 2024)
12-6620519-G-C		not specified	Uncertain significance (Oct 04, 2022)
12-6620552-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-6620615-C-G		not specified	Uncertain significance (Dec 27, 2022)
12-6620644-A-T		not specified	Uncertain significance (May 13, 2024)
12-6620657-G-C		not specified	Uncertain significance (Dec 02, 2022)
12-6620689-C-G		not specified	Uncertain significance (Apr 07, 2022)
12-6620699-A-G		not specified	Uncertain significance (Sep 26, 2022)
12-6620719-T-C		not specified	Uncertain significance (Jan 10, 2023)
12-6620767-C-G		not specified	Uncertain significance (Mar 24, 2023)
12-6620792-C-T		not specified	Uncertain significance (Mar 29, 2022)
12-6620833-C-T		not specified	Uncertain significance (Feb 12, 2024)
12-6620842-C-T		not specified	Uncertain significance (Jan 30, 2024)
12-6620849-G-A		not specified	Uncertain significance (Oct 04, 2022)
12-6620962-G-A		not specified	Uncertain significance (Jun 07, 2024)
12-6621076-C-T		not specified	Uncertain significance (May 15, 2023)
12-6621083-C-T		not specified	Uncertain significance (Nov 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPAR5	protein_coding	protein_coding	ENST00000329858	1	17613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0514	0.869	125136	0	29	125165	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	191	243	0.787	0.0000175	2279
Missense in Polyphen		67	80.337	0.83398		864
Synonymous	1.32	108	127	0.851	0.00000966	875
Loss of Function	1.46	3	7.22	0.416	4.23e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000644	0.0000618
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.000102	0.0000935
European (Non-Finnish)	0.000166	0.000159
Middle Eastern	0.000110	0.000109
South Asian	0.000132	0.000131
Other	0.000380	0.000327

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for lysophosphatidic acid (LPA), a mediator of diverse cellular activities.
• 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);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;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 (Consensus)

Recessive Scores

• pRec: 0.105

Haploinsufficiency Scores

• pHI: 0.0927
• hipred: N
• hipred_score: 0.272
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.359

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lpar5
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;biological_process
• Cellular component: cellular_component;plasma membrane;integral component of membrane
• Molecular function: molecular_function;G protein-coupled receptor activity