GPRC6A

G protein-coupled receptor class C group 6 member A, the group of Calcium sensing receptors

Basic information

Region (hg38): 6:116792085-116829083

Links

ENSG00000173612 ∙ NCBI:222545 ∙ OMIM:613572 ∙ HGNC:18510 ∙ Uniprot:Q5T6X5 ∙ 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 GPRC6A gene.

• not_specified (129 variants)
• not_provided (3 variants)
• Disorder_of_sexual_differentiation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPRC6A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000148963.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			122	10	1	133
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	122	11	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPRC6A	protein_coding	protein_coding	ENST00000310357	6	36953

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		115837	1439	8464	125740	0.0402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.178	473	484	0.977	0.0000225	6151
Missense in Polyphen		129	131.07	0.9842		1745
Synonymous	0.423	163	170	0.959	0.00000811	1749
Loss of Function	0.301	26	27.7	0.938	0.00000127	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.648	0.338
Ashkenazi Jewish	0.0833	0.0386
East Asian	0.00520	0.00354
Finnish	0.110	0.0492
European (Non-Finnish)	0.0545	0.0261
Middle Eastern	0.00520	0.00354
South Asian	0.0435	0.0211
Other	0.0736	0.0333

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor activated by amino acids with a preference for basic amino acids such as L-Lys, L-Arg and L-ornithine but also by small and polar amino acids. The L-alpha amino acids respond is augmented by divalent cations Ca(2+) and Mg(2+). Activated by extracellular calcium and osteocalcin. Seems to act through a G(q)/G(11) and G(i)-coupled pathway. Mediates the non-genomic effects of androgens in multiple tissue. May coordinate nutritional and hormonal anabolic signals through the sensing of extracellular amino acids, osteocalcin, divalent ions and its responsiveness to anabolic steroids. {ECO:0000269|PubMed:15576628, ECO:0000269|PubMed:20947496}.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Class C/3 (Metabotropic glutamate/pheromone receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0994

Intolerance Scores

• loftool: 0.135
• rvis_EVS: 1.63
• rvis_percentile_EVS: 96.06

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0298

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;calcium-mediated signaling;response to amino acid
• Cellular component: plasma membrane;integral component of plasma membrane;cell surface
• Molecular function: G protein-coupled receptor activity;signaling receptor activity