LGR5

leucine rich repeat containing G protein-coupled receptor 5, the group of G protein-coupled receptors, Class A orphans

Basic information

Region (hg38): 12:71439798-71586310

Previous symbols: [ "GPR67", "GPR49" ]

Links

ENSG00000139292

∙ NCBI:8549 ∙ OMIM:606667 ∙ HGNC:4504 ∙ Uniprot:O75473 ∙ 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 LGR5 gene.

not_specified (105 variants)
not_provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGR5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003667.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	1 clinvar	6
missense			98 clinvar	7 clinvar	2 clinvar	107
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	98	12	3

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGR5	protein_coding	protein_coding	ENST00000266674	18	146541

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.50e-8	0.999	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.144	474	465	1.02	0.0000235	5890
Missense in Polyphen		142	175.09	0.81099		2387
Synonymous	-0.299	197	192	1.03	0.0000105	1825
Loss of Function	2.92	19	38.5	0.493	0.00000182	496

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000537	0.000536
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000327	0.000325
Middle Eastern	0.000163	0.000163
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Receptor for R-spondins that potentiates the canonical Wnt signaling pathway and acts as a stem cell marker of the intestinal epithelium and the hair follicle. 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. Involved in the development and/or maintenance of the adult intestinal stem cells during postembryonic development. {ECO:0000269|PubMed:21693646, ECO:0000269|PubMed:21727895, ECO:0000269|PubMed:21909076, ECO:0000269|PubMed:22815884, ECO:0000269|PubMed:23809763}.;
Pathway: Signaling by WNT;Signal Transduction;Regulation of FZD by ubiquitination;TCF dependent signaling in response to WNT (Consensus)

Recessive Scores

pRec: 0.141

Intolerance Scores

loftool: 0.396
rvis_EVS: 1.56
rvis_percentile_EVS: 95.68

Haploinsufficiency Scores

pHI: 0.639
hipred: Y
hipred_score: 0.591
ghis: 0.403

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.621

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Lgr5
Phenotype: renal/urinary system phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; 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); endocrine/exocrine gland phenotype;

Gene ontology

Biological process: hair follicle development;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;activation of adenylate cyclase activity;hormone-mediated signaling pathway;oocyte differentiation;regulation of cell population proliferation;inner ear development;positive regulation of canonical Wnt signaling pathway;epithelial cell proliferation involved in renal tubule morphogenesis
Cellular component: plasma membrane;integral component of plasma membrane;trans-Golgi network membrane
Molecular function: transmembrane signaling receptor activity;G protein-coupled receptor activity;protein binding;G protein-coupled peptide receptor activity;protein-hormone receptor activity