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MS4A1 membrane spanning 4-domains A1 [ Homo sapiens (human) ]

Gene ID: 931, updated on 5-Mar-2024

Summary

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Official Symbol
MS4A1provided by HGNC
Official Full Name
membrane spanning 4-domains A1provided by HGNC
Primary source
HGNC:HGNC:7315
See related
Ensembl:ENSG00000156738 MIM:112210; AllianceGenome:HGNC:7315
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
B1; S7; Bp35; CD20; FMC7; CVID5; LEU-16
Summary
This gene encodes a member of the membrane-spanning 4A gene family. Members of this nascent protein family are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns among hematopoietic cells and nonlymphoid tissues. This gene encodes a B-lymphocyte surface molecule which plays a role in the development and differentiation of B-cells into plasma cells. This family member is localized to 11q12, among a cluster of family members. Alternative splicing of this gene results in two transcript variants which encode the same protein. [provided by RefSeq, Jul 2008]
Expression
Biased expression in lymph node (RPKM 206.7), spleen (RPKM 109.2) and 2 other tissues See more
Orthologs
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Genomic context

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See MS4A1 in Genome Data Viewer
Location:
11q12.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (60455847..60470752)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (60406975..60421883)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (60223320..60238225)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene membrane spanning 4-domains A14 Neighboring gene membrane spanning 4-domains A5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4770 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:60258497-60259236 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:60259237-60259974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4772 Neighboring gene membrane spanning 4-domains A12 Neighboring gene membrane spanning 4-domains A13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3372

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. MS4A1 as a Potential Independent Prognostic Factor of Breast Cancer Related to Lipid Metabolism and Immune Microenvironment Based on TCGA Database Analysis. Li S, et al. Med Sci Monit, 2022 Jan 29. PMID 35091527, Free PMC Article
  2. CD20 positive CD8 T cells are a unique and transcriptionally-distinct subset of T cells with distinct transmigration properties. Vlaming M, et al. Sci Rep, 2021 Oct 15. PMID 34654826, Free PMC Article
  3. MS4A1 expression and function in T cells in the colorectal cancer tumor microenvironment. Mudd TW Jr, et al. Cell Immunol, 2021 Feb. PMID 33352466, Free PMC Article
  4. Binding mechanisms of therapeutic antibodies to human CD20. Kumar A, et al. Science, 2020 Aug 14. PMID 32792392
  5. Pharmacokinetics and safety of IBI301 versus rituximab in patients with CD20(+) B-cell lymphoma: a multicenter, randomized, double-blind, parallel-controlled study. Jiang B, et al. Sci Rep, 2020 Jul 15. PMID 32669656, Free PMC Article

See all (160) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Novel cell subtypes of SPP1 + S100P+, MS4A1-SPP1 + S100P+ were key subpopulations in intrahepatic cholangiocarcinoma.
    Title: Novel cell subtypes of SPP1 + S100P+, MS4A1-SPP1 + S100P+ were key subpopulations in intrahepatic cholangiocarcinoma.
  2. MS4A1 as a Potential Independent Prognostic Factor of Breast Cancer Related to Lipid Metabolism and Immune Microenvironment Based on TCGA Database Analysis.
    Title: MS4A1 as a Potential Independent Prognostic Factor of Breast Cancer Related to Lipid Metabolism and Immune Microenvironment Based on TCGA Database Analysis.
  3. CD20 positive CD8 T cells are a unique and transcriptionally-distinct subset of T cells with distinct transmigration properties.
    Title: CD20 positive CD8 T cells are a unique and transcriptionally-distinct subset of T cells with distinct transmigration properties.
  4. CD20 expression, TrkB activation and functional activity of diffuse large B cell lymphoma-derived small extracellular vesicles.
    Title: CD20 expression, TrkB activation and functional activity of diffuse large B cell lymphoma-derived small extracellular vesicles.
  5. Differential effects of CD20+ B cells and PD-L1+ immune cells on pathologic complete response and outcome: comparison between inflammatory breast cancer and locally advanced breast cancer patients.
    Title: Differential effects of CD20+ B cells and PD-L1+ immune cells on pathologic complete response and outcome: comparison between inflammatory breast cancer and locally advanced breast cancer patients.
  6. CD20-positive primary nasal peripheral T-cell lymphoma: An analysis of one case and review of the literature.
    Title: CD20-positive primary nasal peripheral T-cell lymphoma: An analysis of one case and review of the literature.
  7. MS4A1 expression and function in T cells in the colorectal cancer tumor microenvironment.
    Title: MS4A1 expression and function in T cells in the colorectal cancer tumor microenvironment.
  8. Pharmacokinetics and safety of IBI301 versus rituximab in patients with CD20(+) B-cell lymphoma: a multicenter, randomized, double-blind, parallel-controlled study.
    Title: Pharmacokinetics and safety of IBI301 versus rituximab in patients with CD20(+) B-cell lymphoma: a multicenter, randomized, double-blind, parallel-controlled study.
  9. STIM1 knock-down decreases the affinity of obinutuzumab for CD20 by altering CD20 localization to Triton-soluble membrane.
    Title: STIM1 knock-down decreases the affinity of obinutuzumab for CD20 by altering CD20 localization to Triton-soluble membrane.
  10. CD20 deletion has no effect upon B-cell receptor signaling or calcium flux. Also B-cell survival and proliferation is unaffected in the absence of CD20.
    Title: CD20 is dispensable for B-cell receptor signaling but is required for proper actin polymerization, adhesion and migration of malignant B cells.
Submit: New GeneRIF Correction See all GeneRIFs (115)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Immunodeficiency, common variable, 5
MedGen: C3150740 OMIM: 613495 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120-treated plasmacytoid dendritic cells show a reduced capacity to stimulate B cell growth and differentiation through downregulation of CD20 and CD38 PubMed
env HIV-1 gp120 downregulates CD79B from the surface of dual-positive CD79b/CD20 B cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Potential readthrough

Included gene: MS4A5

Homology

Clone Names

  • MGC3969

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables MHC class II protein complex binding HDA PubMed 
enables epidermal growth factor receptor binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables immunoglobulin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in B cell activation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in B cell differentiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in B cell proliferation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in B cell receptor signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in calcium ion import into cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cell surface receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in humoral immune response NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of calcium ion import across plasma membrane IEA
Inferred from Electronic Annotation
more info
  
involved_in protein tetramerization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to bacterium IEA
Inferred from Electronic Annotation
more info
  
involved_in store-operated calcium entry IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cell surface IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular exosome HDA PubMed 
located_in extracellular space HDA PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in plasma membrane raft IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
B-lymphocyte antigen CD20
Names
B-lymphocyte cell-surface antigen B1
CD20 antigen
CD20 receptor
leukocyte surface antigen Leu-16
membrane-spanning 4-domains, subfamily A, member 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_023388.1 RefSeqGene

    Range
    5001..19944
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_140

mRNA and Protein(s)

  1. NM_021950.4 → NP_068769.2  B-lymphocyte antigen CD20

    See identical proteins and their annotated locations for NP_068769.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks a portion of the 5' UTR, compared to variant 1, but encodes the same protein.
    Source sequence(s)
    AP001034, BC002807, CD691924
    Consensus CDS
    CCDS31570.1
    UniProtKB/Swiss-Prot
    A6NMS4, B4DT24, P08984, P11836, Q13963
    UniProtKB/TrEMBL
    A8K803
    Related
    ENSP00000501369.1, ENST00000674194.1
    Conserved Domains (1) summary
    pfam04103
    Location:51 → 216
    CD20; CD20-like family

  2. NM_152866.3 → NP_690605.1  B-lymphocyte antigen CD20

    See identical proteins and their annotated locations for NP_690605.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript variant. Variants 1, 2 and 3 both encode the same protein.
    Source sequence(s)
    AP001034, AW504475, BC002807, CD691924
    Consensus CDS
    CCDS31570.1
    UniProtKB/Swiss-Prot
    A6NMS4, B4DT24, P08984, P11836, Q13963
    UniProtKB/TrEMBL
    A8K803
    Related
    ENSP00000314620.7, ENST00000345732.9
    Conserved Domains (1) summary
    pfam04103
    Location:51 → 216
    CD20; CD20-like family

  3. NM_152867.2 → NP_690606.1  B-lymphocyte antigen CD20

    Status: REVIEWED

    Source sequence(s)
    AP001034, AP003127
    Consensus CDS
    CCDS31570.1
    UniProtKB/Swiss-Prot
    A6NMS4, B4DT24, P08984, P11836, Q13963
    UniProtKB/TrEMBL
    A8K803
    Related
    ENSP00000433277.1, ENST00000534668.6
    Conserved Domains (1) summary
    pfam04103
    Location:51 → 216
    CD20; CD20-like family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    60455847..60470752
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    60406975..60421883
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P11836.1 GenPept UniProtKB/Swiss-Prot:P11836

Gene LinkOut

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