MS4A1

membrane spanning 4-domains A1, the group of CD molecules|Membrane spanning 4-domains

Basic information

Region (hg38): 11:60455846-60470752

Previous symbols: [ "CD20" ]

Links

ENSG00000156738 ∙ NCBI:931 ∙ OMIM:112210 ∙ HGNC:7315 ∙ Uniprot:P11836 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• common variable immunodeficiency (Supportive), mode of inheritance: AD
• immunodeficiency, common variable, 5 (Limited), mode of inheritance: Unknown
• immunodeficiency, common variable, 5 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency, common variable, 5	AR	Allergy/Immunology/Infectious	Individuals may be susceptible to recurrent infections (eg, respiratory infections have been reported), and antiinfectious prophylaxis (including with IVIG therapy) and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious	20038800

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MS4A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MS4A1 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				26	4	30
missense			94	2		96
nonsense			1			1
start loss						0
frameshift			4			4
inframe indel			3			3
splice donor/acceptor (+/-2bp)			2	1		3
splice region			4	3		7
non coding			2	14	5	21
Total	0	0	106	43	9

Variants in MS4A1

This is a list of pathogenic ClinVar variants found in the MS4A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60461057-CA-C		Immunodeficiency, common variable, 5	Uncertain significance (Jan 27, 2023)
11-60462204-C-T			Benign (Jun 20, 2021)
11-60462383-A-G			Likely benign (Nov 04, 2021)
11-60462384-C-T		not specified	Uncertain significance (Nov 24, 2023)
11-60462409-T-A		not specified	Uncertain significance (Dec 17, 2024)
11-60462412-C-T			Uncertain significance (Jan 20, 2025)
11-60462413-G-A			Likely benign (Oct 13, 2023)
11-60462414-G-A			Uncertain significance (Feb 26, 2024)
11-60462416-A-G			Likely benign (Apr 12, 2023)
11-60462417-G-C			Uncertain significance (Feb 18, 2024)
11-60462419-G-T		not specified	Likely benign (Jun 21, 2023)
11-60462421-C-T			Uncertain significance (Sep 20, 2022)
11-60462422-A-G			Likely benign (Oct 07, 2023)
11-60462424-T-C		not specified	Uncertain significance (Oct 22, 2024)
11-60462425-G-A			Uncertain significance (Dec 28, 2023)
11-60462429-G-T			Uncertain significance (Feb 27, 2022)
11-60462433-C-T		not specified	Uncertain significance (Feb 02, 2025)
11-60462434-T-C			Likely benign (Oct 18, 2022)
11-60462439-C-A			Uncertain significance (Nov 27, 2023)
11-60462440-T-C			Likely benign (Nov 06, 2023)
11-60462441-A-G			Uncertain significance (May 14, 2024)
11-60462444-C-A			Uncertain significance (Feb 07, 2024)
11-60462444-C-T			Uncertain significance (Oct 03, 2024)
11-60462448-C-A			Uncertain significance (May 25, 2022)
11-60462451-G-T			Uncertain significance (Apr 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MS4A1	protein_coding	protein_coding	ENST00000534668	6	15009

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000508	0.686	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.143	151	156	0.968	0.00000737	1965
Missense in Polyphen		31	44.651	0.69427		626
Synonymous	-0.416	58	54.1	1.07	0.00000283	557
Loss of Function	0.932	8	11.4	0.702	4.79e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000365	0.000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein may be involved in the regulation of B-cell activation and proliferation.
• Disease: DISEASE: Immunodeficiency, common variable, 5 (CVID5) [MIM:613495]: A primary immunodeficiency characterized by antibody deficiency, hypogammaglobulinemia, recurrent bacterial infections and an inability to mount an antibody response to antigen. The defect results from a failure of B-cell differentiation and impaired secretion of immunoglobulins; the numbers of circulating B-cells is usually in the normal range, but can be low. {ECO:0000269|PubMed:20038800}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Hematopoietic cell lineage - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• loftool: 0.694
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.146
• ghis: 0.630

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.919

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ms4a1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: humoral immune response;response to bacterium;B cell proliferation
• Cellular component: extracellular space;nucleus;plasma membrane;integral component of plasma membrane;external side of plasma membrane;extracellular exosome
• Molecular function: epidermal growth factor receptor binding;protein binding;MHC class II protein complex binding