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Aliases for MS4A1 Gene

Aliases for MS4A1 Gene

  • Membrane Spanning 4-Domains A1 2 3 5
  • Membrane-Spanning 4-Domains, Subfamily A, Member 1 2 3
  • Leukocyte Surface Antigen Leu-16 3 4
  • CD20 Antigen 3 4
  • CD20 3 4
  • Bp35 3 4
  • Membrane-Spanning 4-Domains Subfamily A Member 1 4
  • B-Lymphocyte Cell-Surface Antigen B1 3
  • B-Lymphocyte Surface Antigen B1 4
  • B-Lymphocyte Antigen CD20 3
  • CD20 Receptor 3
  • LEU-16 3
  • CVID5 3
  • MS4A2 3
  • B1 3
  • S7 3

External Ids for MS4A1 Gene

Previous HGNC Symbols for MS4A1 Gene

  • CD20

Previous GeneCards Identifiers for MS4A1 Gene

  • GC11P062617
  • GC11P061736
  • GC11P059998
  • GC11P059979
  • GC11P060225
  • GC11P056570

Summaries for MS4A1 Gene

Entrez Gene Summary for MS4A1 Gene

  • 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]

GeneCards Summary for MS4A1 Gene

MS4A1 (Membrane Spanning 4-Domains A1) is a Protein Coding gene. Diseases associated with MS4A1 include Immunodeficiency, Common Variable, 5 and Ms4a1-Related Common Variable Immune Deficiency. Among its related pathways are Hematopoietic cell lineage and Hematopoietic Stem Cell Differentiation Pathways and Lineage-specific Markers. GO annotations related to this gene include epidermal growth factor receptor binding and MHC class II protein complex binding.

UniProtKB/Swiss-Prot for MS4A1 Gene

  • This protein may be involved in the regulation of B-cell activation and proliferation.

Gene Wiki entry for MS4A1 Gene

Additional gene information for MS4A1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MS4A1 Gene

Genomics for MS4A1 Gene

Regulatory Elements for MS4A1 Gene

Enhancers for MS4A1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11H060388 1.2 Ensembl ENCODE dbSUPER 24.5 -66.2 -66157 2.3 PKNOX1 TBL1XR1 SIN3A MAX BMI1 BATF RUNX3 IKZF2 CHD2 ZNF687 MS4A14 MS4A1 MS4A5 GC11M060363
GH11H060376 1.4 Ensembl ENCODE dbSUPER 13.6 -77.7 -77684 2.9 PKNOX1 BATF YY1 FOS ETV6 RUNX3 CREM IKZF2 GATAD2B ELF1 MS4A14 MS4A1 TMEM109 MS4A7 GC11P060374
GH11H060445 1.2 Ensembl ENCODE dbSUPER 13.5 -9.1 -9134 1.6 HDGF PKNOX1 IRF2 TRIM22 JUNB BATF GATA3 POLR2A IKZF1 ZNF512 MS4A1 MS4A12 MS4A13 MS4A6E MS4A18 MS4A7 MS4A5
GH11H060396 1 Ensembl ENCODE dbSUPER 11.6 -58.7 -58695 2 EED RUNX3 SPI1 MS4A14 MS4A1 MS4A5 GC11M060363
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around MS4A1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for MS4A1 Gene

Genomic Locations for MS4A1 Gene
15,009 bases
Plus strand

Genomic View for MS4A1 Gene

Genes around MS4A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MS4A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MS4A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MS4A1 Gene

Proteins for MS4A1 Gene

  • Protein details for MS4A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    B-lymphocyte antigen CD20
    Protein Accession:
    Secondary Accessions:
    • A6NMS4
    • B4DT24
    • P08984
    • Q13963

    Protein attributes for MS4A1 Gene

    297 amino acids
    Molecular mass:
    33077 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for MS4A1 Gene

    Alternative splice isoforms for MS4A1 Gene


neXtProt entry for MS4A1 Gene

Post-translational modifications for MS4A1 Gene

  • Phosphorylated. Might be functionally regulated by protein kinase(s).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for MS4A1

No data available for DME Specific Peptides for MS4A1 Gene

Domains & Families for MS4A1 Gene

Gene Families for MS4A1 Gene

Human Protein Atlas (HPA):
  • CD markers
  • Disease related genes
  • FDA approved drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for MS4A1 Gene

Suggested Antigen Peptide Sequences for MS4A1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the MS4A family.
  • Belongs to the MS4A family.
genes like me logo Genes that share domains with MS4A1: view

Function for MS4A1 Gene

Molecular function for MS4A1 Gene

GENATLAS Biochemistry:
membrane-spanning 4-domains,subfamily A,member 1,expressed in most cells,complexing with an alpha chain and a homodimeric gamma subunit
UniProtKB/Swiss-Prot Function:
This protein may be involved in the regulation of B-cell activation and proliferation.

Phenotypes From GWAS Catalog for MS4A1 Gene

Gene Ontology (GO) - Molecular Function for MS4A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005154 epidermal growth factor receptor binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0023026 MHC class II protein complex binding IDA 20458337
genes like me logo Genes that share ontologies with MS4A1: view
genes like me logo Genes that share phenotypes with MS4A1: view

Human Phenotype Ontology for MS4A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for MS4A1 Gene

MGI Knock Outs for MS4A1:

Animal Model Products

Clone Products

  • Addgene plasmids for MS4A1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for MS4A1 Gene

Localization for MS4A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MS4A1 Gene

Cell membrane; Multi-pass membrane protein. Cell membrane; Lipid-anchor.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for MS4A1 gene
Compartment Confidence
plasma membrane 5
extracellular 5

Gene Ontology (GO) - Cellular Components for MS4A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 22664934
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane NAS 2448768
GO:0009897 external side of plasma membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with MS4A1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for MS4A1 Gene

Pathways & Interactions for MS4A1 Gene

genes like me logo Genes that share pathways with MS4A1: view

Gene Ontology (GO) - Biological Process for MS4A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006959 humoral immune response NAS 2448768
GO:0042100 B cell proliferation NAS 2448768
GO:0042113 B cell activation IEA --
genes like me logo Genes that share ontologies with MS4A1: view

No data available for SIGNOR curated interactions for MS4A1 Gene

Drugs & Compounds for MS4A1 Gene

(19) Drugs for MS4A1 Gene - From: DrugBank, PharmGKB, DGIdb, FDA Approved Drugs, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
rituximab Approved Pharma antibody, Target Therapeutic Antibodies 1771
ofatumumab Approved Pharma antibody, inhibitor, Target Therapeutic Antibodies 0
Tositumomab Approved Pharma antibody, Target 0
ibritumomab tiuxetan Approved Pharma antibody, Target Therapeutic Antibodies 0
Obinutuzumab Approved Pharma Target, antibody 108

(3) Additional Compounds for MS4A1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with MS4A1: view

Transcripts for MS4A1 Gene

Unigene Clusters for MS4A1 Gene

Membrane-spanning 4-domains, subfamily A, member 1:
Representative Sequences:

Clone Products

  • Addgene plasmids for MS4A1

Alternative Splicing Database (ASD) splice patterns (SP) for MS4A1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b · 9c · 9d ^ 10 ^ 11a · 11b
SP1: - - - - - - - -
SP2: - -
SP3: - - - -
SP4: - - - - - - - -
SP5: - - - - - -
SP7: -
SP8: - - - -
SP9: - -
SP10: - - - -
SP12: - -

Relevant External Links for MS4A1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MS4A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MS4A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for MS4A1 Gene

This gene is overexpressed in Spleen (x12.5) and Small Intestine - Terminal Ileum (x5.5).

Protein differential expression in normal tissues from HIPED for MS4A1 Gene

This gene is overexpressed in Blymphocyte (27.9), Lymph node (27.9), Monocytes (6.7), and Peripheral blood mononuclear cells (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for MS4A1 Gene

Protein tissue co-expression partners for MS4A1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of MS4A1 Gene:


SOURCE GeneReport for Unigene cluster for MS4A1 Gene:


mRNA Expression by UniProt/SwissProt for MS4A1 Gene:

Tissue specificity: Expressed on B-cells.

Evidence on tissue expression from TISSUES for MS4A1 Gene

  • Blood(4.7)
  • Spleen(3.3)
  • Lymph node(2.9)
  • Intestine(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for MS4A1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • ear
  • eye
  • head
  • hypothalamus
  • meninges
  • middle ear
  • neck
  • pituitary gland
  • sinus
  • skull
  • thyroid
  • bronchus
  • heart
  • lung
  • adrenal gland
  • intestine
  • large intestine
  • liver
  • small intestine
  • spleen
  • stomach
  • anus
  • rectum
  • uterus
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • lymph node
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with MS4A1: view

Orthologs for MS4A1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for MS4A1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia MS4A1 34 33
  • 99.21 (n)
(Canis familiaris)
Mammalia MS4A1 33 34
  • 84.01 (n)
(Rattus norvegicus)
Mammalia Ms4a1 33
  • 83.11 (n)
(Mus musculus)
Mammalia Ms4a1 34 16 33
  • 82.87 (n)
(Bos Taurus)
Mammalia MS4A1 33 34
  • 78.9 (n)
(Ornithorhynchus anatinus)
Mammalia MS4A1 34
  • 53 (a)
(Monodelphis domestica)
Mammalia MS4A1 34
  • 51 (a)
Species where no ortholog for MS4A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for MS4A1 Gene

Gene Tree for MS4A1 (if available)
Gene Tree for MS4A1 (if available)

Paralogs for MS4A1 Gene

(2) SIMAP similar genes for MS4A1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with MS4A1: view

No data available for Paralogs for MS4A1 Gene

Variants for MS4A1 Gene

Sequence variations from dbSNP and Humsavar for MS4A1 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1000042904 -- 60,467,412(+) GCTGG(A/G)ATTAC intron-variant
rs1000329142 -- 60,461,115(+) AACTT(C/T)CATTC intron-variant, utr-variant-5-prime
rs1000446602 -- 60,460,783(+) ATTGC(C/T)TTCTC intron-variant
rs1000596835 -- 60,455,250(+) AAAAG(A/T)GCTAT upstream-variant-2KB
rs1000836010 -- 60,467,868(+) CATCG(C/T)TAATT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for MS4A1 Gene

Variant ID Type Subtype PubMed ID
nsv555151 CNV loss 21841781
nsv508635 CNV deletion 20534489
nsv471730 CNV loss 16327809
esv4679 CNV loss 18987735
esv3626558 CNV loss 21293372
esv28830 CNV loss 19812545
esv2744572 CNV deletion 23290073
esv2744569 CNV deletion 23290073
esv2661434 CNV deletion 23128226
dgv51n111 CNV deletion 26073780
dgv391e212 CNV loss 25503493

Variation tolerance for MS4A1 Gene

Residual Variation Intolerance Score: 56.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.93; 19.20% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for MS4A1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MS4A1 Gene

Disorders for MS4A1 Gene

MalaCards: The human disease database

(17) MalaCards diseases for MS4A1 Gene - From: HGMD, OMIM, ClinVar, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
immunodeficiency, common variable, 5
  • antibody deficiency due to cd20 defect
ms4a1-related common variable immune deficiency
  • immunodeficiency, common variable, 5
common variable immunodeficiency
  • acquired agammaglobulinemia
pityriasis lichenoides
chronic lymphocytic leukemia
  • b-cell chronic lymphocytic leukemia
- elite association - COSMIC cancer census association via MalaCards
Search MS4A1 in MalaCards View complete list of genes associated with diseases


  • 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.

Relevant External Links for MS4A1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with MS4A1: view

No data available for Genatlas for MS4A1 Gene

Publications for MS4A1 Gene

  1. CD20 deficiency in humans results in impaired T cell-independent antibody responses. (PMID: 20038800) Kuijpers TW … van Lier RA (The Journal of clinical investigation 2010) 3 4 22 60
  2. Mutation or polymorphism of the CD20 gene is not associated with the response to R-CHOP in diffuse large B cell lymphoma patients. (PMID: 19054557) Sar A … Demetrick DJ (Leukemia research 2009) 3 22 45 60
  3. CD20 mutations involving the rituximab epitope are rare in diffuse large B-cell lymphomas and are not a significant cause of R-CHOP failure. (PMID: 19211644) Johnson NA … Gascoyne RD (Haematologica 2009) 3 22 45 60
  4. Isolation and structure of a cDNA encoding the B1 (CD20) cell-surface antigen of human B lymphocytes. (PMID: 2448768) Tedder TF … Saito H (Proceedings of the National Academy of Sciences of the United States of America 1988) 2 3 4 60
  5. Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for type I/II distinction of CD20 antibodies. (PMID: 21444918) Niederfellner G … Klein C (Blood 2011) 3 4 60

Products for MS4A1 Gene

Sources for MS4A1 Gene

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