GPRC5C

G protein-coupled receptor class C group 5 member C, the group of G protein-coupled receptors, Class C orphans

Basic information

Region (hg38): 17:74424851-74451653

Links

ENSG00000170412 ∙ NCBI:55890 ∙ OMIM:605949 ∙ HGNC:13309 ∙ Uniprot:Q9NQ84 ∙ 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 GPRC5C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPRC5C 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			27	2	1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	29	4	1

Variants in GPRC5C

This is a list of pathogenic ClinVar variants found in the GPRC5C region.

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

Position	Type	Phenotype	Significance	ClinVar
17-74432043-G-C		not specified	Uncertain significance (Sep 01, 2021)
17-74432079-G-A		not specified	Likely benign (Nov 30, 2021)
17-74432138-G-C		not specified	Uncertain significance (May 27, 2022)
17-74439803-G-A		not specified	Uncertain significance (Dec 13, 2023)
17-74439843-G-A		not specified	Uncertain significance (Feb 10, 2022)
17-74439952-C-T		not specified	Uncertain significance (Nov 29, 2023)
17-74439981-A-G			Benign (Feb 26, 2018)
17-74440110-G-A		not specified	Uncertain significance (Sep 15, 2021)
17-74440140-C-T		not specified	Uncertain significance (Mar 31, 2023)
17-74440201-A-C		not specified	Uncertain significance (Oct 06, 2021)
17-74440213-G-A		not specified	Uncertain significance (May 15, 2024)
17-74440230-C-T		not specified	Uncertain significance (Mar 20, 2023)
17-74440254-G-A		not specified	Uncertain significance (May 23, 2023)
17-74440368-G-A		not specified	Uncertain significance (Oct 12, 2021)
17-74440411-C-G		not specified	Uncertain significance (Oct 28, 2023)
17-74440491-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-74440518-A-G		not specified	Uncertain significance (Sep 22, 2023)
17-74440525-C-T		not specified	Uncertain significance (May 04, 2023)
17-74440533-G-A		not specified	Likely benign (Mar 25, 2024)
17-74440560-A-C		not specified	Uncertain significance (Nov 18, 2022)
17-74440561-T-C		not specified	Uncertain significance (Dec 28, 2023)
17-74440629-G-A		not specified	Uncertain significance (Mar 20, 2024)
17-74440716-G-T		not specified	Uncertain significance (Aug 30, 2021)
17-74440721-C-A		not specified	Uncertain significance (Mar 16, 2024)
17-74440734-C-T		not specified	Uncertain significance (Nov 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPRC5C	protein_coding	protein_coding	ENST00000392627	4	26803

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000474	0.970	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.523	285	311	0.916	0.0000192	3124
Missense in Polyphen		91	116.27	0.78265		1204
Synonymous	-1.19	157	139	1.13	0.00000949	1050
Loss of Function	1.93	8	16.4	0.487	7.06e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000351	0.000351
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00109	0.00106
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This retinoic acid-inducible G-protein coupled receptor provide evidence for a possible interaction between retinoid and G-protein signaling pathways. {ECO:0000250}.
• Pathway: GPCRs, Class C Metabotropic glutamate, pheromone (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.183
• rvis_EVS: -0.99
• rvis_percentile_EVS: 8.6

Haploinsufficiency Scores

• pHI: 0.206
• hipred: N
• hipred_score: 0.197
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.941

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gprc5c
• Phenotype: hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;activation of protein kinase activity
• Cellular component: plasma membrane;integral component of plasma membrane;cytoplasmic vesicle membrane;vesicle;receptor complex;extracellular exosome
• Molecular function: G protein-coupled receptor activity;protein kinase activator activity