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.

not_provided (168 variants)
not_specified (35 variants)
Immunodeficiency,_common_variable,_5 (8 variants)
MS4A1-related_disorder (3 variants)

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. These statistics are base on transcript: NM_000152866.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				28 clinvar	3 clinvar	31
missense			115 clinvar	2 clinvar		117
nonsense			1 clinvar			1
start loss						0
frameshift			5 clinvar			5
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	123	30	3

Loading clinvar variants...

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