LGR6

leucine rich repeat containing G protein-coupled receptor 6, the group of G protein-coupled receptors, Class A orphans

Basic information

Region (hg38): 1:202193799-202319781

Links

ENSG00000133067 ∙ NCBI:59352 ∙ OMIM:606653 ∙ HGNC:19719 ∙ Uniprot:Q9HBX8 ∙ 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 LGR6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGR6 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	4
missense			57	2	1	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	57	4	3

Variants in LGR6

This is a list of pathogenic ClinVar variants found in the LGR6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-202194068-C-A		not specified	Uncertain significance (Oct 06, 2021)
1-202194108-A-C		not specified	Uncertain significance (Jul 19, 2022)
1-202227953-A-G		not specified	Uncertain significance (Nov 16, 2021)
1-202235956-G-A		not specified	Uncertain significance (Jul 16, 2021)
1-202235963-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-202235978-C-A		not specified	Uncertain significance (Jul 25, 2023)
1-202276308-G-A		not specified	Uncertain significance (May 03, 2023)
1-202276316-G-A		not specified	Uncertain significance (Jun 07, 2023)
1-202276370-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-202276392-A-G		not specified	Uncertain significance (Nov 10, 2022)
1-202276467-G-A		not specified	Uncertain significance (Mar 03, 2022)
1-202276487-T-G		not specified	Uncertain significance (Mar 21, 2022)
1-202276491-C-T		not specified	Uncertain significance (Apr 03, 2023)
1-202297508-A-T		not specified	Likely benign (Nov 07, 2023)
1-202297545-G-A		not specified	Uncertain significance (Jan 17, 2024)
1-202303295-A-G		not specified	Uncertain significance (Feb 05, 2024)
1-202304570-G-A			Benign/Likely benign (Dec 01, 2022)
1-202306884-C-T		not specified	Uncertain significance (Dec 28, 2022)
1-202306917-C-A		not specified	Uncertain significance (Feb 10, 2022)
1-202307364-C-G		not specified	Uncertain significance (Dec 07, 2023)
1-202309059-C-T		not specified	Uncertain significance (Dec 26, 2023)
1-202309101-G-T		not specified	Uncertain significance (Mar 02, 2023)
1-202309154-A-G		not specified	Uncertain significance (Oct 24, 2023)
1-202310191-C-G			Benign (Jun 26, 2018)
1-202310295-T-C		not specified	Uncertain significance (Jun 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGR6	protein_coding	protein_coding	ENST00000367278	18	125881

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000294	1.00	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	482	553	0.872	0.0000320	6143
Missense in Polyphen		170	223.76	0.75975		2606
Synonymous	0.496	245	255	0.960	0.0000155	2105
Loss of Function	3.31	16	38.0	0.421	0.00000177	431

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000148
Ashkenazi Jewish	0.000215	0.000198
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000152	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.000427	0.000425
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for R-spondins that potentiates the canonical Wnt signaling pathway and acts as a marker of multipotent stem cells in the epidermis. Upon binding to R-spondins (RSPO1, RSPO2, RSPO3 or RSPO4), associates with phosphorylated LRP6 and frizzled receptors that are activated by extracellular Wnt receptors, triggering the canonical Wnt signaling pathway to increase expression of target genes. In contrast to classical G-protein coupled receptors, does not activate heterotrimeric G-proteins to transduce the signal. May act as a tumor suppressor. {ECO:0000269|PubMed:21727895, ECO:0000269|PubMed:22615920}.
• Pathway: GPCRs, Other;Signaling by WNT;Signal Transduction;Regulation of FZD by ubiquitination;TCF dependent signaling in response to WNT (Consensus)

Intolerance Scores

• loftool: 0.232
• rvis_EVS: -0.1
• rvis_percentile_EVS: 45.69

Haploinsufficiency Scores

• pHI: 0.132
• hipred: Y
• hipred_score: 0.663
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0700

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lgr6
• Phenotype: normal phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;Wnt signaling pathway;positive regulation of Wnt signaling pathway;positive regulation of cell migration;positive regulation of canonical Wnt signaling pathway;bone regeneration
• Cellular component: plasma membrane;integral component of plasma membrane;vesicle;trans-Golgi network membrane
• Molecular function: transmembrane signaling receptor activity;G protein-coupled receptor activity;protein binding;protein-hormone receptor activity