MRGPRX3

protein-coding

MAS related GPR family member X3, the group of G protein-coupled receptors, Class A orphans

Gene summary

This gene encodes a member of the mas-related/sensory neuron specific subfamily of G protein coupled receptors. The encoded protein may be involved in sensory neuron regulation and in the modulation of pain. [provided by RefSeq, Oct 2009]

MANE transcript

NM_001370464.1

Inheritance

—

ClinVar variants

U:84B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chr11:18,120,955-18,138,488

External References & Databases

Ensembl (ENSG00000179826)

Transcript & Mutation Effects

hg38 • Region Span ~17.5 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 MRGPRX3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 93

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370464.1. 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						0
missense			84 clinvar	9 clinvar	1 clinvar	94
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	84	9	1	94

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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_001370464.1	RefSeq	NP_001357393.1	1	MANE Select
ENST00000621697.2	Ensembl	ENSP00000481943.1	1	MANE Select
NM_054031.4	RefSeq	NP_473372.3	1	Standard
ENST00000396275.2	Ensembl	ENSP00000379571.2	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

G protein-coupled receptor signaling pathway

Molecular Function

G protein-coupled receptor activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396275
Coding exons: 1
Length: 17526

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.85	262	190	1.38	0.0000127	2067
Missense (PolyPhen)		41	35.007	1.1712		508
Synonymous	-2.29	115	87.7	1.31	0.00000626	710
Loss of Function

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Orphan receptor. Probably involved in the function of nociceptive neurons. May regulate nociceptor function and/or development, including the sensation or modulation of pain. Potently activated by enkephalins (By similarity). {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.735
RVIS EVS: 1.46
RVIS percentile EVS: 95.23

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.104

Gene Damage Prediction

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