GPBAR1

G protein-coupled bile acid receptor 1, the group of G protein-coupled bile acid receptor

Basic information

Region (hg38): 2:218259495-218263861

Links

ENSG00000179921 ∙ NCBI:151306 ∙ OMIM:610147 ∙ HGNC:19680 ∙ Uniprot:Q8TDU6 ∙ 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 GPBAR1 gene.

• not provided (55 variants)
• GPBAR1-related condition (10 variants)
• Inborn genetic diseases (10 variants)
• not specified (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPBAR1 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			13	3	1	17
missense			42	3	2	47
nonsense						0
start loss						0
frameshift			2			2
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	58	7	3

Variants in GPBAR1

This is a list of pathogenic ClinVar variants found in the GPBAR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-218262724-G-A		GPBAR1-related disorder	Conflicting classifications of pathogenicity (Dec 09, 2019)
2-218262745-C-G			Benign (Jan 01, 2023)
2-218262758-C-G			Uncertain significance (Jan 09, 2018)
2-218262794-C-T			Uncertain significance (Jun 19, 2018)
2-218262797-G-A			Uncertain significance (May 15, 2018)
2-218262814-C-G			Uncertain significance (Jan 16, 2018)
2-218262817-G-A			Uncertain significance (Mar 15, 2017)
2-218262819-A-G		not specified	Uncertain significance (Feb 27, 2024)
2-218262836-G-C		not specified	Uncertain significance (Jan 31, 2024)
2-218262841-C-T			Likely benign (Dec 20, 2018)
2-218262852-G-A		GPBAR1-related disorder • not specified	Uncertain significance (Mar 07, 2023)
2-218262861-G-A			Uncertain significance (Jul 10, 2017)
2-218262875-G-A		GPBAR1-related disorder	Uncertain significance (Feb 22, 2024)
2-218262877-C-T		GPBAR1-related disorder	Likely benign (Mar 31, 2023)
2-218262879-GCTT-G		not specified • GPBAR1-related disorder	Benign/Likely benign (Sep 19, 2019)
2-218262913-C-T		GPBAR1-related disorder	Conflicting classifications of pathogenicity (Apr 16, 2021)
2-218262920-C-G			Uncertain significance (Oct 03, 2017)
2-218262926-T-C		GPBAR1-related disorder	Likely benign (Nov 29, 2022)
2-218262941-GGGCTG-CA		GPBAR1-related disorder	Uncertain significance (Feb 19, 2024)
2-218262946-G-A		GPBAR1-related disorder	Likely benign (Sep 09, 2019)
2-218262959-C-T			Uncertain significance (Nov 08, 2017)
2-218262962-C-T			Uncertain significance (Sep 08, 2017)
2-218262963-G-A		GPBAR1-related disorder	Uncertain significance (Mar 02, 2023)
2-218262986-G-A		not specified	Uncertain significance (Jan 10, 2022)
2-218263017-C-T			Uncertain significance (Feb 01, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPBAR1	protein_coding	protein_coding	ENST00000522678	1	4364

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.36e-9	0.0159	124527	0	133	124660	0.000534

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0957	199	203	0.981	0.0000135	2023
Missense in Polyphen		76	83.584	0.90926		885
Synonymous	0.539	90	96.7	0.930	0.00000600	790
Loss of Function	-1.61	11	6.55	1.68	2.85e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000117	0.000117
Ashkenazi Jewish	0.00	0.00
East Asian	0.00351	0.00351
Finnish	0.0000979	0.0000928
European (Non-Finnish)	0.000377	0.000363
Middle Eastern	0.00351	0.00351
South Asian	0.000632	0.000621
Other	0.000689	0.000660

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for bile acid. Bile acid-binding induces its internalization, activation of extracellular signal-regulated kinase and intracellular cAMP production. May be involved in the suppression of macrophage functions by bile acids. {ECO:0000269|PubMed:12419312, ECO:0000269|PubMed:12524422}.
• Pathway: Olfactory receptor activity;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.990
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpbar1
• Phenotype: renal/urinary system phenotype; immune system phenotype; liver/biliary system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;cell surface bile acid receptor signaling pathway;regulation of bicellular tight junction assembly
• Cellular component: cytoplasm;plasma membrane;integral component of membrane
• Molecular function: bile acid receptor activity;G protein-coupled bile acid receptor activity