GPRC5A

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

Basic information

Region (hg38): 12:12891558-12917937

Previous symbols: [ "RAI3" ]

Links

ENSG00000013588 ∙ NCBI:9052 ∙ OMIM:604138 ∙ HGNC:9836 ∙ Uniprot:Q8NFJ5 ∙ 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 GPRC5A gene.

• Inborn genetic diseases (13 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPRC5A 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				3		3
missense			12	2	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	5	1

Variants in GPRC5A

This is a list of pathogenic ClinVar variants found in the GPRC5A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-12908320-C-G			Benign (Jan 25, 2018)
12-12908347-C-T		not specified	Uncertain significance (Jan 02, 2024)
12-12908348-G-A			Likely benign (Jan 25, 2018)
12-12908361-G-A		not specified	Uncertain significance (Feb 01, 2023)
12-12908386-T-C		not specified	Uncertain significance (Jul 13, 2022)
12-12908422-A-G		not specified	Uncertain significance (May 11, 2022)
12-12908434-G-A		not specified	Uncertain significance (Jan 03, 2024)
12-12908494-C-T		not specified	Uncertain significance (Dec 06, 2022)
12-12908507-C-T			Likely benign (Dec 01, 2022)
12-12908524-G-C		not specified	Uncertain significance (Jun 05, 2023)
12-12908584-T-C		not specified	Uncertain significance (Jan 04, 2024)
12-12908769-A-C		not specified	Uncertain significance (Jun 01, 2023)
12-12908769-A-T		not specified	Uncertain significance (Jan 20, 2023)
12-12908793-A-G			Likely benign (Mar 01, 2023)
12-12908942-C-T			Likely benign (Dec 09, 2017)
12-12908991-G-A		not specified	Uncertain significance (Dec 28, 2022)
12-12909004-A-G		not specified	Uncertain significance (Dec 14, 2021)
12-12909012-G-A		not specified	Uncertain significance (Jul 25, 2023)
12-12909024-G-T		not specified	Uncertain significance (Jan 04, 2024)
12-12909064-G-A		not specified	Likely benign (May 23, 2023)
12-12912091-A-T		not specified	Uncertain significance (Jan 31, 2024)
12-12912093-A-G		not specified	Uncertain significance (Jan 06, 2023)
12-12912493-G-T		not specified	Uncertain significance (Mar 01, 2024)
12-12912532-G-A		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPRC5A	protein_coding	protein_coding	ENST00000014914	3	27156

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.79e-8	0.149	125163	2	581	125746	0.00232

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.617	233	208	1.12	0.0000124	2323
Missense in Polyphen		81	74.079	1.0934		911
Synonymous	-0.338	93	88.9	1.05	0.00000571	752
Loss of Function	0.000600	11	11.0	1.00	6.52e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00167	0.00167
Ashkenazi Jewish	0.00318	0.00318
East Asian	0.0000544	0.0000544
Finnish	0.00116	0.00116
European (Non-Finnish)	0.00386	0.00384
Middle Eastern	0.0000544	0.0000544
South Asian	0.00108	0.00108
Other	0.00229	0.00228

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan receptor. Could be involved in modulating differentiation and maintaining homeostasis of epithelial cells. This retinoic acid-inducible GPCR provide evidence for a possible interaction between retinoid and G-protein signaling pathways. Functions as a negative modulator of EGFR signaling (By similarity). May act as a lung tumor suppressor (PubMed:18000218). {ECO:0000250|UniProtKB:Q8BHL4, ECO:0000269|PubMed:18000218}.
• Pathway: GPCRs, Class C Metabotropic glutamate, pheromone;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.322
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.78

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.170
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.770

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gprc5a
• Phenotype: respiratory system phenotype; normal phenotype; neoplasm; immune system phenotype

Gene ontology

• Biological process: signal transduction;negative regulation of epidermal growth factor-activated receptor activity;G protein-coupled receptor signaling pathway;activation of protein kinase activity
• Cellular component: nucleolus;plasma membrane;integral component of plasma membrane;cytoplasmic vesicle membrane;vesicle;intracellular membrane-bounded organelle;receptor complex;extracellular exosome
• Molecular function: G protein-coupled receptor activity;protein binding;protein kinase activator activity;cadherin binding