MRGPRX3

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

Basic information

Region (hg38): 11:18120955-18138488

Links

ENSG00000179826 ∙ NCBI:117195 ∙ OMIM:607229 ∙ HGNC:17980 ∙ Uniprot:Q96LB0 ∙ 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 MRGPRX3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRGPRX3 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			37	4	1	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	4	1

Variants in MRGPRX3

This is a list of pathogenic ClinVar variants found in the MRGPRX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-18137206-G-C		not specified	Uncertain significance (Aug 30, 2021)
11-18137250-C-A		not specified	Uncertain significance (Jun 17, 2024)
11-18137251-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-18137297-G-T		not specified	Likely benign (May 02, 2024)
11-18137352-G-C		not specified	Uncertain significance (Oct 29, 2021)
11-18137371-C-T		not specified	Uncertain significance (Dec 12, 2023)
11-18137384-T-C		not specified	Uncertain significance (Jan 09, 2024)
11-18137410-G-A		not specified	Uncertain significance (Nov 08, 2022)
11-18137416-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-18137427-C-A		not specified	Uncertain significance (Mar 06, 2023)
11-18137450-C-T		not specified	Uncertain significance (Feb 23, 2023)
11-18137459-G-T		not specified	Uncertain significance (Jun 28, 2022)
11-18137473-C-T		not specified	Uncertain significance (Mar 24, 2023)
11-18137498-G-A		not specified	Likely benign (May 04, 2022)
11-18137510-C-A		not specified	Uncertain significance (Dec 21, 2022)
11-18137594-A-G		not specified	Likely benign (Nov 27, 2023)
11-18137621-C-T		not specified	Uncertain significance (Apr 11, 2023)
11-18137689-T-C		not specified	Uncertain significance (Dec 20, 2021)
11-18137699-G-A		not specified	Uncertain significance (Jan 04, 2024)
11-18137705-C-T		not specified	Uncertain significance (Jan 26, 2022)
11-18137713-G-A		not specified	Uncertain significance (Dec 19, 2022)
11-18137714-T-G		not specified	Uncertain significance (Dec 19, 2022)
11-18137736-C-A		not specified	Uncertain significance (Jul 25, 2023)
11-18137747-C-T		not specified	Uncertain significance (Feb 21, 2024)
11-18137770-G-A		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRGPRX3	protein_coding	protein_coding	ENST00000396275	1	17526

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0731
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.104

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrgpra9

Gene ontology

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