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 d... See more...

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
  • B-Lymphocyte Antigen CD20 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
  • 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 Common Variable Immunodeficiency. Among its related pathways are Dendritic Cells Developmental Lineage Pathway and Hematopoietic cell lineage. Gene Ontology (GO) annotations related to this gene include epidermal growth factor receptor binding and MHC class II protein complex binding. An important paralog of this gene is MS4A14.

UniProtKB/Swiss-Prot Summary for MS4A1 Gene

  • B-lymphocyte-specific membrane protein that plays a role in the regulation of cellular calcium influx necessary for the development, differentiation, and activation of B-lymphocytes (PubMed:3925015, PubMed:7684739, PubMed:12920111). Functions as a store-operated calcium (SOC) channel component promoting calcium influx after activation by the B-cell receptor/BCR (PubMed:7684739, PubMed:12920111, PubMed:18474602).

Gene Wiki entry for MS4A1 Gene

Additional gene information for MS4A1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for MS4A1 Gene

Genomics for MS4A1 Gene

GeneHancer (GH) Regulatory Elements for MS4A1 Gene

Promoters and enhancers for MS4A1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J060454 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 764.6 +0.9 899 8.5 ZNF24 SP1 ETV6 RELA NKRF POLR2A MAFK MLLT1 ZNF687 CREM MS4A1 MS4A14 MS4A5 MS4A7 MS4A2 PATL1 ENSG00000255008 TMEM109 piR-32677-072
GH11J060376 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 13.6 -76.5 -76547 5.2 SP1 GATA3 TCF7L2 ZNF217 ETV6 POLR2A MLLT1 ZNF687 CREM RELA MS4A14 MS4A7 piR-35674-069 MS4A1 TMEM109 lnc-MS4A7-1 MS4A6E
GH11J060388 Enhancer 0.7 ENCODE dbSUPER 24.5 -66.2 -66157 2.3 SP1 MAX ZNF687 IKZF1 IKZF2 PKNOX1 RUNX3 BMI1 NBN BATF MS4A14 MS4A1 MS4A5 piR-35674-069 MS4A7 lnc-MS4A7-1 MS4A6E
GH11J060476 Enhancer 1 Ensembl ENCODE dbSUPER 12 +21.9 21948 3 ZBTB40 ETV6 CREM IKZF2 PKNOX1 EED BCL11A RUNX3 IKZF1 JUNB MS4A1 MS4A7 piR-32677-072
GH11J060396 Promoter/Enhancer 0.9 EPDnew ENCODE dbSUPER 11.7 -58.7 -58694 2 CREB1 EED RUNX3 IRF4 MS4A14 MS4A1 MS4A5 piR-35674-069 lnc-MS4A7-1 MS4A6E
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MS4A1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the MS4A1 gene promoter:
  • AP-1
  • ATF-2
  • c-Fos
  • c-Jun

Genomic Locations for MS4A1 Gene

Genomic Locations for MS4A1 Gene
chr11:60,455,752-60,470,760
(GRCh38/hg38)
Size:
15,009 bases
Orientation:
Plus strand
chr11:60,223,225-60,238,233
(GRCh37/hg19)
Size:
15,009 bases
Orientation:
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:
    P11836-CD20_HUMAN
    Recommended name:
    B-lymphocyte antigen CD20
    Protein Accession:
    P11836
    Secondary Accessions:
    • A6NMS4
    • B4DT24
    • P08984
    • Q13963

    Protein attributes for MS4A1 Gene

    Size:
    297 amino acids
    Molecular mass:
    33077 Da
    Quaternary structure:
    • Forms homotetramers (PubMed:7684739, PubMed:18474602). Interacts with the heavy and light chains of cell surface IgM, the antigen-binding components of the BCR (PubMed:18474602).

    Three dimensional structures from OCA and Proteopedia for MS4A1 Gene

    Alternative splice isoforms for MS4A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MS4A1 Gene

Post-translational modifications for MS4A1 Gene

  • Phosphorylated on serines and threonines in resting B-cells. Protein kinase C/PKC can use CD20 as substrate.
  • 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

HGNC:
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

GenScript: Design optimal peptide antigens:
  • cDNA FLJ51650, moderately similar to B-lymphocyte antigen CD20 (B4DT24_HUMAN)
  • Membrane-spanning 4-domains subfamily A member 1 (CD20_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P11836

UniProtKB/Swiss-Prot:

CD20_HUMAN :
  • Belongs to the MS4A family.
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

UniProtKB/Swiss-Prot Function:
B-lymphocyte-specific membrane protein that plays a role in the regulation of cellular calcium influx necessary for the development, differentiation, and activation of B-lymphocytes (PubMed:3925015, PubMed:7684739, PubMed:12920111). Functions as a store-operated calcium (SOC) channel component promoting calcium influx after activation by the B-cell receptor/BCR (PubMed:7684739, PubMed:12920111, PubMed:18474602).
GENATLAS Biochemistry:
membrane-spanning 4-domains,subfamily A,member 1,expressed in most cells,complexing with an alpha chain and a homodimeric gamma subunit

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:0019865 immunoglobulin binding IDA 18474602
GO:0023026 MHC class II protein complex binding HDA 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

CRISPR 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. Note=Constitutively associated with membrane rafts. {ECO:0000269 PubMed:12920111}.

Subcellular locations from

COMPARTMENTS
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
nucleus 4
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for MS4A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space HDA 22664934
GO:0005634 nucleus IDA --
GO:0005886 plasma membrane IEA,IDA --
GO:0005887 integral component of plasma membrane NAS 2448768
GO:0009897 external side of plasma membrane IEA --
genes like me logo Genes that share ontologies with MS4A1: view

Pathways & Interactions for MS4A1 Gene

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

SIGNOR curated interactions for MS4A1 Gene

Other effect:

Gene Ontology (GO) - Biological Process for MS4A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002115 store-operated calcium entry IMP 12920111
GO:0006959 humoral immune response NAS 2448768
GO:0009617 response to bacterium IEA --
GO:0030183 B cell differentiation IDA 3925015
GO:0042100 B cell proliferation NAS 2448768
genes like me logo Genes that share ontologies with MS4A1: view

Drugs & Compounds for MS4A1 Gene

(16) Drugs for MS4A1 Gene - From: DrugBank, PharmGKB, DGIdb, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
rituximab Approved Pharma Target, antibody Therapeutic Antibodies 2022
ofatumumab Approved Pharma Target, inhibitor, antibody Therapeutic Antibodies 118
Tositumomab Approved, Investigational Pharma Target, antibody 0
ibritumomab tiuxetan Approved, Investigational Pharma Target, antibody Therapeutic Antibodies 0
Obinutuzumab Approved, Investigational Pharma Target, antibody 144

(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

mRNA/cDNA for MS4A1 Gene

CRISPR Products

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: - - - - - -
SP6:
SP7: -
SP8: - - - -
SP9: - -
SP10: - - - -
SP11:
SP12: - -

Relevant External Links for MS4A1 Gene

GeneLoc Exon Structure for
MS4A1
ECgene alternative splicing isoforms for
MS4A1

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 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:

MS4A1

SOURCE GeneReport for Unigene cluster for MS4A1 Gene:

Hs.712553

mRNA Expression by UniProt/SwissProt for MS4A1 Gene:

P11836-CD20_HUMAN
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
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • head
  • hypothalamus
  • meninges
  • middle ear
  • neck
  • pituitary gland
  • sinus
  • skull
  • thyroid
Thorax:
  • bronchus
  • heart
  • lung
Abdomen:
  • adrenal gland
  • intestine
  • large intestine
  • liver
  • small intestine
  • spleen
  • stomach
Pelvis:
  • anus
  • rectum
  • uterus
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • 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
chimpanzee
(Pan troglodytes)
Mammalia MS4A1 33 32
  • 99.21 (n)
OneToOne
dog
(Canis familiaris)
Mammalia MS4A1 33 32
  • 84.01 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ms4a1 32
  • 83.11 (n)
mouse
(Mus musculus)
Mammalia Ms4a1 17 33 32
  • 82.87 (n)
cow
(Bos Taurus)
Mammalia MS4A1 33 32
  • 78.9 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia MS4A1 33
  • 53 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia MS4A1 33
  • 51 (a)
OneToOne
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

ENSEMBL:
Gene Tree for MS4A1 (if available)
TreeFam:
Gene Tree for MS4A1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for MS4A1: view image

Paralogs for MS4A1 Gene

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

  • CD20_HUMAN
  • B4DT24_HUMAN
  • E9PKH8_HUMAN
  • E9PPL6_HUMAN
genes like me logo Genes that share paralogs with MS4A1: view

Variants for MS4A1 Gene

Sequence variations from dbSNP and Humsavar for MS4A1 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs267603055 uncertain-significance, Common variable immunodeficiency 5 60,464,323(+) G/A/C coding_sequence_variant, missense_variant, synonymous_variant
rs201491900 uncertain-significance, not provided 60,462,424(+) T/C coding_sequence_variant, missense_variant
rs2070770 benign, not provided 60,463,058(+) C/T coding_sequence_variant, synonymous_variant
rs1000042904 -- 60,467,412(+) G/A intron_variant
rs1000329142 -- 60,461,115(+) C/T 5_prime_UTR_variant, intron_variant

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

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

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)

Additional Variant Information for MS4A1 Gene

Human Gene Mutation Database (HGMD)
MS4A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
MS4A1

SNP Genotyping and Copy Number Assay Products

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

Disorders for MS4A1 Gene

MalaCards: The human disease database

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

- elite association - COSMIC cancer census association via MalaCards
Search MS4A1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CD20_HUMAN
  • 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.

Additional Disease Information for MS4A1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 23 56
  2. 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 23 43 56
  3. 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 23 43 56
  4. Transfection of the CD20 cell surface molecule into ectopic cell types generates a Ca2+ conductance found constitutively in B lymphocytes. (PMID: 7684739) Bubien JK … Tedder TF (The Journal of cell biology 1993) 3 4 23 56
  5. 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 56

Products for MS4A1 Gene

Sources for MS4A1 Gene