GPRC5D

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

Basic information

Region (hg38): 12:12940575-12952170

Links

ENSG00000111291 ∙ NCBI:55507 ∙ OMIM:607437 ∙ HGNC:13310 ∙ Uniprot:Q9NZD1 ∙ 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 GPRC5D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPRC5D 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						0
missense			21	3		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	0

Variants in GPRC5D

This is a list of pathogenic ClinVar variants found in the GPRC5D region.

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

Position	Type	Phenotype	Significance	ClinVar
12-12942263-G-C		not specified	Uncertain significance (Aug 07, 2024)
12-12942265-G-A		not specified	Likely benign (Oct 05, 2023)
12-12942275-G-A		not specified	Uncertain significance (Sep 09, 2024)
12-12942325-C-T		not specified	Uncertain significance (Nov 25, 2024)
12-12949505-G-C		not specified	Uncertain significance (Jul 29, 2022)
12-12949566-G-C		not specified	Uncertain significance (May 27, 2022)
12-12949576-C-T		not specified	Likely benign (Aug 17, 2021)
12-12949610-C-T		not specified	Likely benign (Jun 06, 2023)
12-12949634-A-G		not specified	Uncertain significance (Jun 11, 2024)
12-12949666-G-A		not specified	Uncertain significance (Oct 02, 2023)
12-12949677-C-A		not specified	Uncertain significance (Dec 08, 2023)
12-12949701-G-T		not specified	Uncertain significance (Oct 27, 2023)
12-12949706-C-T		not specified	Uncertain significance (Feb 27, 2024)
12-12949720-G-A		not specified	Uncertain significance (Jul 30, 2023)
12-12949780-T-C		not specified	Uncertain significance (Dec 15, 2023)
12-12949804-C-T		not specified	Uncertain significance (Aug 30, 2021)
12-12949807-C-T		not specified	Uncertain significance (Nov 10, 2022)
12-12949826-C-T		not specified	Uncertain significance (Jul 26, 2022)
12-12949885-T-C		not specified	Uncertain significance (Dec 22, 2023)
12-12949898-G-A		not specified	Uncertain significance (Jan 03, 2024)
12-12949917-C-T		not specified	Uncertain significance (Jul 12, 2022)
12-12949947-C-A		not specified	Uncertain significance (Oct 02, 2023)
12-12949990-A-G		not specified	Uncertain significance (Aug 21, 2023)
12-12950048-T-G		not specified	Uncertain significance (Jun 18, 2024)
12-12950105-A-G		not specified	Uncertain significance (Nov 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPRC5D	protein_coding	protein_coding	ENST00000228887	3	11373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00125	0.963	124748	1	997	125746	0.00398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.623	168	192	0.874	0.0000106	2243
Missense in Polyphen		47	63.756	0.73719		805
Synonymous	-0.928	93	82.3	1.13	0.00000507	712
Loss of Function	1.85	7	14.6	0.478	8.88e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00868	0.00871
Ashkenazi Jewish	0.00159	0.00159
East Asian	0.0000544	0.0000544
Finnish	0.00199	0.00199
European (Non-Finnish)	0.00605	0.00605
Middle Eastern	0.0000544	0.0000544
South Asian	0.00222	0.00219
Other	0.00310	0.00310

dbNSFP

Source: dbNSFP

• Pathway: GPCRs, Class C Metabotropic glutamate, pheromone (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.320
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0930

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gprc5d

Gene ontology

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