OXGR1

oxoglutarate receptor 1, the group of Oxoglutarate receptor

Basic information

Region (hg38): 13:96985713-96994730

Previous symbols: [ "GPR99", "GPR80" ]

Links

ENSG00000165621 ∙ NCBI:27199 ∙ OMIM:606922 ∙ HGNC:4531 ∙ Uniprot:Q96P68 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephrolithiasis, calcium oxalate, 2, with nephrocalcinosis	AD	Renal	The condition involves predisposition to nephrocalcinosis and nephrolithiasis, and management may help manage renal and related sequelae	Renal	36571463

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OXGR1 gene.

• not_specified (53 variants)
• Nephrolithiasis,_calcium_oxalate,_2,_with_or_without_nephrocalcinosis (5 variants)
• not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OXGR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001346194.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense	1	2	51	2		56
nonsense						0
start loss						0
frameshift	1				1	2
splice donor/acceptor (+/-2bp)						0
Total	2	2	51	3	1

Highest pathogenic variant AF is 0.0012453763

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OXGR1	protein_coding	protein_coding	ENST00000298440	1	9012

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000496	0.444	123023	61	2663	125747	0.0109

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0875	182	185	0.982	0.00000957	2215
Missense in Polyphen		51	63.412	0.80427		772
Synonymous	0.390	70	74.3	0.942	0.00000404	681
Loss of Function	0.354	7	8.09	0.866	5.04e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0195	0.0195
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0663	0.0662
Finnish	0.0275	0.0276
European (Non-Finnish)	0.00191	0.00191
Middle Eastern	0.0663	0.0662
South Asian	0.00196	0.00193
Other	0.00554	0.00555

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for alpha-ketoglutarate. Seems to act exclusively through a G(q)-mediated pathway (By similarity). {ECO:0000250}.
• Pathway: Signaling by GPCR;Signal Transduction;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.513
• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.202
• hipred: N
• hipred_score: 0.296
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.279

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oxgr1
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; renal/urinary system phenotype

Gene ontology

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