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.

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.

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				1		1
missense			48	3	1	52
nonsense						0
start loss						0
frameshift					2	2
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	4	4

Variants in GPRC6A

This is a list of pathogenic ClinVar variants found in the GPRC6A region.

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

Position	Type	Phenotype	Significance	ClinVar
6-116792266-C-T		not specified	Uncertain significance (Jul 28, 2021)
6-116792269-G-T			Benign (Aug 29, 2018)
6-116792344-C-G		not specified	Uncertain significance (Aug 02, 2022)
6-116792370-C-G		not specified	Uncertain significance (Jun 06, 2023)
6-116792395-A-G		not specified	Likely benign (May 26, 2023)
6-116792403-C-G		not specified	Uncertain significance (Jul 12, 2022)
6-116792422-C-A		not specified	Uncertain significance (Feb 14, 2023)
6-116792425-T-C		not specified	Uncertain significance (Aug 16, 2022)
6-116792561-T-G		not specified	Uncertain significance (Jun 11, 2021)
6-116792578-T-C		not specified	Uncertain significance (Aug 12, 2021)
6-116792598-A-AGG			Benign (Aug 29, 2018)
6-116792599-T-TA			Benign (Feb 18, 2020)
6-116792602-T-TTCC			Benign (Aug 29, 2018)
6-116792647-A-G		not specified	Uncertain significance (Mar 11, 2024)
6-116792695-T-C		not specified	Uncertain significance (May 04, 2023)
6-116792738-T-C		not specified	Likely benign (Feb 05, 2024)
6-116792761-A-G		not specified	Uncertain significance (Jan 30, 2024)
6-116792788-G-A		not specified	Uncertain significance (Nov 18, 2022)
6-116792812-G-A		not specified	Uncertain significance (Oct 05, 2023)
6-116792869-A-C		not specified	Uncertain significance (Jan 23, 2024)
6-116792887-G-A			Likely benign (Aug 01, 2023)
6-116792932-G-A		not specified	Uncertain significance (Jul 12, 2023)
6-116793007-C-T		not specified	Uncertain significance (Feb 13, 2024)
6-116793029-C-G		not specified	Uncertain significance (Jun 03, 2022)
6-116793041-C-T		not specified	Uncertain significance (Sep 27, 2021)

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
5.59e-17	0.0132	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

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.219

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

Mouse Genome Informatics

• Gene name: Gprc6a
• 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); growth/size/body region 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; cellular phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; liver/biliary system phenotype; skeleton phenotype; renal/urinary system phenotype

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