MS4A2

membrane spanning 4-domains A2, the group of Membrane spanning 4-domains

Basic information

Region (hg38): 11:60088261-60098467

Previous symbols: [ "FCER1B", "IGER", "APY" ]

Links

ENSG00000149534 ∙ NCBI:2206 ∙ OMIM:147138 ∙ HGNC:7316 ∙ Uniprot:Q01362 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• IgE responsiveness, atopic (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MS4A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A2 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				1	1	2
missense			15	1	2	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding				1		1
Total	0	0	15	4	3

Variants in MS4A2

This is a list of pathogenic ClinVar variants found in the MS4A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60088757-A-G		MS4A2-related disorder	Likely benign (May 23, 2019)
11-60088780-T-C		MS4A2-related disorder	Benign (Mar 22, 2019)
11-60089686-TCA-T		MS4A2-related disorder	Likely benign (Jun 05, 2019)
11-60089693-G-A		not specified	Uncertain significance (Mar 18, 2024)
11-60089708-G-T		not specified	Uncertain significance (Mar 08, 2024)
11-60089727-A-C		not specified	Uncertain significance (Jun 05, 2023)
11-60089736-C-T		not specified	Uncertain significance (Jun 11, 2021)
11-60089757-C-T		not specified	Uncertain significance (Dec 26, 2023)
11-60089806-G-A		MS4A2-related disorder	Likely benign (Jun 05, 2019)
11-60089813-T-C		not specified	Uncertain significance (May 03, 2023)
11-60090354-G-A		not specified	Uncertain significance (Mar 11, 2024)
11-60090432-T-A		not specified	Uncertain significance (Dec 15, 2022)
11-60092820-T-C		not specified	Uncertain significance (Sep 20, 2023)
11-60092826-A-G		not specified	Uncertain significance (Dec 05, 2022)
11-60092838-C-T		not specified	Uncertain significance (Oct 13, 2023)
11-60093432-C-A		not specified	Uncertain significance (Feb 06, 2023)
11-60093449-C-T			Benign (Jun 29, 2018)
11-60093494-A-G		not specified	Uncertain significance (Dec 01, 2022)
11-60093497-T-A		not specified	Uncertain significance (May 11, 2022)
11-60093499-C-T		not specified	Uncertain significance (Mar 18, 2024)
11-60093978-G-C		not specified	Uncertain significance (May 26, 2022)
11-60094059-C-A			Benign (Jun 18, 2018)
11-60095567-G-T		not specified	Uncertain significance (May 22, 2023)
11-60095591-A-G		not specified	Uncertain significance (Mar 19, 2024)
11-60095631-A-G		RECLASSIFIED - POLYMORPHISM	Benign (Sep 01, 2001)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A2	protein_coding	protein_coding	ENST00000278888	7	7711

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.60e-9	0.0687	124940	8	798	125746	0.00321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.309	133	123	1.08	0.00000555	1568
Missense in Polyphen		44	34.698	1.2681		467
Synonymous	-0.677	50	44.3	1.13	0.00000210	482
Loss of Function	-0.332	12	10.8	1.11	4.59e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000416	0.000416
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0221	0.0220
European (Non-Finnish)	0.00273	0.00273
Middle Eastern	0.00	0.00
South Asian	0.000100	0.0000980
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: High affinity receptor that binds to the Fc region of immunoglobulins epsilon. Aggregation of FCER1 by multivalent antigens is required for the full mast cell response, including the release of preformed mediators (such as histamine) by degranulation and de novo production of lipid mediators and cytokines. Also mediates the secretion of important lymphokines. Binding of allergen to receptor-bound IgE leads to cell activation and the release of mediators responsible for the manifestations of allergy.
• Pathway: Fc epsilon RI signaling pathway - Homo sapiens (human);Asthma - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Fc Epsilon Receptor I Signaling in Mast Cells;fc epsilon receptor i signaling in mast cells;Fc-epsilon receptor I signaling in mast cells (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.793
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.44

Haploinsufficiency Scores

• pHI: 0.0371
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.584

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a2
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: inflammatory response;immune response;Fc-epsilon receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane;Fc-epsilon receptor I complex
• Molecular function: IgE binding