GPRC5D

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the G protein-coupled receptor family; however, the specific function of this gene has not yet been determined. [provided by RefSeq, Jul 2008]

MANE transcript

NM_018654.2

Inheritance

—

ClinVar variants

U:47B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr12:12,940,575-12,952,170

External References & Databases

Ensembl (ENSG00000111291)

Transcript & Mutation Effects

hg38 • Region Span ~11.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GPRC5D variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 48

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018654.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			46 clinvar	3 clinvar		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	47	3	0	50

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018654.2	RefSeq	NP_061124.1	3	MANE Select
ENST00000228887.6	Ensembl	ENSP00000228887.1	3	MANE Select
ENST00000396333.3	Ensembl	ENSP00000379624.3	2	Standard
ENST00001137650.1	Ensembl	ENSP00000801953.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

GPCRs, Class C Metabotropic glutamate, pheromone

Biological Process

G protein-coupled receptor signaling pathway
activation of protein kinase activity

Molecular Function

G protein-coupled receptor activity
protein kinase activator activity

Cellular Component

plasma membrane
integral component of membrane
receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000228887
Coding exons: 3
Length: 11373
Individuals with no LoFs: 124748
Homozygous LoFs: 1
Heterozygous LoFs: 997
Defined: 125746
p: 0.00398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.623	168	192	0.874	0.0000106	2243
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0073	0.0073	notable
Latino/Admixed American	0.0014	0.0014	notable
Ashkenazi Jewish	0.0016	0.0016	notable
East Asian	0.000054	0.000054	rare
Finnish	0.0020	0.0020	notable
European (Non-Finnish)	0.0061	0.0060	notable
South Asian	0.0022	0.0022	notable
Other	0.0031	0.0031	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.320
RVIS EVS: 0.09
RVIS percentile EVS: 60.47

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0930

Gene Damage Prediction

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