LPAR6

lysophosphatidic acid receptor 6, the group of Lysophosphatidic acid receptors

Basic information

Region (hg38): 13:48389567-48444704

Previous symbols: [ "P2RY5" ]

Links

ENSG00000139679 ∙ NCBI:10161 ∙ OMIM:609239 ∙ HGNC:15520 ∙ Uniprot:P43657 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypotrichosis 8 (Strong), mode of inheritance: AR
• isolated familial wooly hair disorder (Supportive), mode of inheritance: AD
• hypotrichosis simplex (Supportive), mode of inheritance: AD
• hypotrichosis 8 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypotrichosis 8	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	18461368; 18297070; 18297072; 21070332; 21426374

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LPAR6 gene.

• Hypotrichosis 8 (4 variants)
• Wooly hair, autosomal recessive 1, with or without hypotrichosis (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPAR6 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				8		8
missense		7	21	4	3	35
nonsense	1			1		2
start loss	1					1
frameshift	2	1	1	1	4	9
inframe indel				1	1	2
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				2	2	4
Total	4	8	22	17	10

Highest pathogenic variant AF is 0.0000131

Variants in LPAR6

This is a list of pathogenic ClinVar variants found in the LPAR6 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-48411303-G-T			Benign (May 16, 2021)
13-48411385-T-C			Likely benign (Mar 07, 2022)
13-48411460-C-A		Inborn genetic diseases	Uncertain significance (May 10, 2024)
13-48411491-T-A		Inborn genetic diseases	Uncertain significance (Dec 17, 2023)
13-48411499-CA-C		Hypotrichosis 8	Likely pathogenic (-)
13-48411503-C-A		Retinoblastoma • not specified	Benign/Likely benign (Jan 05, 2024)
13-48411591-C-T		Hypotrichosis 8	Likely pathogenic (-)
13-48411594-A-G		Hypotrichosis 8	Likely pathogenic (-)
13-48411605-G-T		Retinoblastoma	Likely benign (May 28, 2019)
13-48411609-A-G		Inborn genetic diseases	Uncertain significance (Aug 30, 2022)
13-48411623-T-G			Likely benign (Dec 27, 2023)
13-48411630-A-G		Inborn genetic diseases	Likely benign (Mar 02, 2023)
13-48411668-A-G		LPAR6-related disorder	Likely benign (Jan 03, 2024)
13-48411682-T-A		Hypotrichosis 8	Likely pathogenic (-)
13-48411696-A-G		Inborn genetic diseases	Uncertain significance (Mar 01, 2023)
13-48411715-T-C		Inborn genetic diseases	Uncertain significance (Feb 02, 2022)
13-48411717-A-G		Inborn genetic diseases	Uncertain significance (May 05, 2022)
13-48411727-C-T		Inborn genetic diseases	Uncertain significance (May 06, 2022)
13-48411798-T-C		Inborn genetic diseases	Likely benign (Apr 04, 2023)
13-48411837-G-A		Hypotrichosis 8	Uncertain significance (-)
13-48411839-A-G		LPAR6-related disorder	Benign/Likely benign (Aug 01, 2024)
13-48411853-C-G		Inborn genetic diseases	Uncertain significance (Dec 13, 2021)
13-48411859-C-T		Hypotrichosis 8	Pathogenic/Likely pathogenic (Jun 11, 2024)
13-48411862-T-A		Wooly hair, autosomal recessive 1, with or without hypotrichosis • Hypotrichosis 8	Likely pathogenic (-)
13-48411884-A-G			Likely benign (Apr 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPAR6	protein_coding	protein_coding	ENST00000378434	1	55134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000713	0.770	125680	0	42	125722	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.114	174	178	0.976	0.00000819	2280
Missense in Polyphen		69	70.559	0.9779		946
Synonymous	0.727	56	63.4	0.884	0.00000308	656
Loss of Function	1.01	6	9.33	0.643	4.42e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.0000545	0.0000544
South Asian	0.000588	0.000588
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to oleoyl-L-alpha-lysophosphatidic acid (LPA). Intracellular cAMP is involved in the receptor activation. Important for the maintenance of hair growth and texture. {ECO:0000269|PubMed:18297070}.
• Disease: DISEASE: Woolly hair autosomal recessive 1 with or without hypotrichosis (ARWH1) [MIM:278150]: A hair shaft disorder characterized by fine and tightly curled hair. Compared to normal curly hair that is observed in some populations, woolly hair grows slowly and stops growing after a few inches. Under light microscopy, woolly hair shows some structural anomalies, including trichorrhexis nodosa and tapered ends. Some individuals exhibit features of hypotrichosis. {ECO:0000269|PubMed:18297072}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypotrichosis 8 (HYPT8) [MIM:278150]: A condition characterized by the presence of less than the normal amount of hair and abnormal hair follicles and shafts, which are thin and atrophic. The disorder affects the trunk and extremities as well as the scalp, and the eyebrows and eyelashes may also be involved, whereas beard, pubic, and axillary hairs are largely spared. In addition, patients can develop hyperkeratotic follicular papules, erythema, and pruritus in affected areas. In some patients with congenital hypotrichosis, monilethrix-like hairs showing elliptical nodes have been observed. {ECO:0000269|PubMed:18297070}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: PI3K-Akt 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 (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.937
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.213
• hipred: N
• hipred_score: 0.292
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.192

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lpar6
• Phenotype: hematopoietic system phenotype

Zebrafish Information Network

• Gene name: lpar6a
• Affected structure: intersegmental vessel
• Phenotype tag: abnormal
• Phenotype quality: decreased functionality

Gene ontology

• Biological process: blastocyst hatching;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;intracellular membrane-bounded organelle
• Molecular function: G protein-coupled receptor activity