Human Gene MS4A2 (uc021qka.1) Description and Page Index
  Description: Homo sapiens membrane-spanning 4-domains, subfamily A, member 2 (MS4A2), transcript variant 3, mRNA.
RefSeq Summary (NM_001256916): The allergic response involves the binding of allergen to receptor-bound IgE followed by cell activation and the release of mediators responsible for the manifestations of allergy. The IgE-receptor, a tetramer composed of an alpha, beta, and 2 disulfide-linked gamma chains, is found on the surface of mast cells and basophils. This gene encodes the beta subunit of the high affinity IgE receptor which is 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 family member is localized to 11q12, among a cluster of membrane-spanning 4A gene family members. Alternative splicing results in multiple transcript variants encoding distinct proteins. Additional transcript variants have been described but require experimental validation. [provided by RefSeq, Mar 2012].
Transcript (Including UTRs)
   Position: hg19 chr11:59,856,137-59,865,940 Size: 9,804 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr11:59,856,239-59,863,129 Size: 6,891 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr11:59,856,137-59,865,940)mRNA (may differ from genome)Protein (199 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
Stanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=High affinity immunoglobulin epsilon receptor subunit beta; Short=FcERI; AltName: Full=Fc epsilon receptor I beta-chain; AltName: Full=IgE Fc receptor subunit beta; AltName: Full=Membrane-spanning 4-domains subfamily A member 2;
FUNCTION: High affinity receptor that binds to the Fc region of immunoglobulins epsilon. Aggregation of FCER1 by multivalent antigens is required for the full mast cell response, including the release of preformed mediators (such as histamine) by degranulation and de novo production of lipid mediators and cytokines. Also mediates the secretion of important lymphokines. Binding of allergen to receptor-bound IgE leads to cell activation and the release of mediators responsible for the manifestations of allergy.
SUBUNIT: Tetramer of an alpha chain, a beta chain, and two disulfide linked gamma chains. Binds LILRB1. Interacts with FGR, FES/FPS and LYN (By similarity).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Found on the surface of mast cells and basophils.
PTM: Phosphorylated on tyrosine residues by LYN (By similarity).
POLYMORPHISM: Variant Glu-237 has been found to be present in about 5.3% of a 1004 individuals population sample in Australia. It seems to be a risk factor for atopic dermatitis and asthma.
SIMILARITY: Belongs to the MS4A family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): MS4A2
CDC HuGE Published Literature: MS4A2
Positive Disease Associations: asthma, aspirin-induced , Asthma| , Hyperresponsiveness , immunoglobulin E receptor-mediated histamine release from basophils , periodontitis , Total IgE , Total serum IgE. specific IgE. AR
Related Studies:
  1. asthma, aspirin-induced
    Kim, S. H. et al. 2006, A polymorphism of MS4A2 (-109T>C) encoding the beta-chain of the high-affinity immunoglobulin E receptor (FcepsilonR1beta) is associated with a susceptibility to aspirin-intolerant asthma, Clin Exp Allergy 2006 36(7) 877-83. [PubMed 16839402]
    FcepsilonR1beta-109T > C polymorphism may increase expression of MS4A2 by mast cells, leading to enhanced release of proinflammatory mediators in the asthmatic airway, contributing to increased susceptibility to AIA.
  2. Asthma|
    Angela J Rogers , et al. American journal of respiratory and critical care medicine 2009 179(12):1084-90, Assessing the reproducibility of asthma candidate gene associations, using genome-wide data., American journal of respiratory and critical care medicine 2009 179(12):1084-90. [PubMed 19264973]
    We replicated asthma associations for a minority of candidate genes.
  3. Hyperresponsiveness
    Trabetti E 1998, , Journal of medical genetics. 1998 Aug;35(8):680-1. [PubMed 9719379]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: MS4A2
Diseases sorted by gene-association score: atopy* (416), hand dermatosis (17), neurodermatitis (15), allergic asthma (13), nasal cavity disease (9), nose disease (9), allergic rhinitis (9), dermatographia (9), atopic dermatitis (8), food allergy (8), upper respiratory tract disease (8), byssinosis (8), allergic hypersensitivity disease (7), fruit allergy (7), irritant dermatitis (7), physical urticaria (7), cholinergic urticaria (7), asthma (6), bronchial disease (6), conjunctivitis (6), occupational dermatitis (6), respiratory system disease (6), vernal conjunctivitis (5), conjunctival disease (4), hypersensitivity reaction disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.19 RPKM in Lung
Total median expression: 13.29 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -15.90102-0.156 Picture PostScript Text
3' UTR -710.572811-0.253 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007237 - CD20-like

Pfam Domains:
PF04103 - CD20-like family

ModBase Predicted Comparative 3D Structure on Q01362
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0019863 IgE binding

Biological Process:
GO:0006954 inflammatory response
GO:0006955 immune response
GO:0007165 signal transduction
GO:0007166 cell surface receptor signaling pathway
GO:0038095 Fc-epsilon receptor signaling pathway

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0009897 external side of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0032998 Fc-epsilon receptor I complex

-  Descriptions from all associated GenBank mRNAs
  AK304487 - Homo sapiens cDNA FLJ60221 complete cds, highly similar to High affinity immunoglobulin epsilon receptor subunit beta.
AK310142 - Homo sapiens cDNA, FLJ17184.
D10583 - Homo sapiens mRNA for IgE receptor beta subunit, complete cds.
BC074800 - Homo sapiens membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide), mRNA (cDNA clone MGC:104074 IMAGE:30915525), complete cds.
BC074843 - Homo sapiens membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide), mRNA (cDNA clone MGC:103840 IMAGE:30915222), complete cds.
AB590499 - Synthetic construct DNA, clone: pFN21AE1738, Homo sapiens MS4A2 gene for membrane-spanning 4-domains, subfamily A, member 2, without stop codon, in Flexi system.
KJ891151 - Synthetic construct Homo sapiens clone ccsbBroadEn_00545 MS4A2 gene, encodes complete protein.
KR712129 - Synthetic construct Homo sapiens clone CCSBHm_00036022 MS4A2 (MS4A2) mRNA, encodes complete protein.
JF411082 - Homo sapiens high affinity IgE receptor beta subunit splice variant (MS4A2) mRNA, complete cds, alternatively spliced.
X66187 - H.sapiens FceRI mRNA, partial CDS.
JD317391 - Sequence 298415 from Patent EP1572962.
JD498928 - Sequence 479952 from Patent EP1572962.
JD145276 - Sequence 126300 from Patent EP1572962.
JD350606 - Sequence 331630 from Patent EP1572962.
JD165073 - Sequence 146097 from Patent EP1572962.
JD552846 - Sequence 533870 from Patent EP1572962.
JD291374 - Sequence 272398 from Patent EP1572962.
JD083711 - Sequence 64735 from Patent EP1572962.
JD239688 - Sequence 220712 from Patent EP1572962.
JD320642 - Sequence 301666 from Patent EP1572962.
JD121274 - Sequence 102298 from Patent EP1572962.
JD098709 - Sequence 79733 from Patent EP1572962.
JD375053 - Sequence 356077 from Patent EP1572962.
JD406951 - Sequence 387975 from Patent EP1572962.
JD212722 - Sequence 193746 from Patent EP1572962.
JD198111 - Sequence 179135 from Patent EP1572962.
JD413412 - Sequence 394436 from Patent EP1572962.
JD246960 - Sequence 227984 from Patent EP1572962.
JD246959 - Sequence 227983 from Patent EP1572962.
JD344145 - Sequence 325169 from Patent EP1572962.
JD344146 - Sequence 325170 from Patent EP1572962.
JD056616 - Sequence 37640 from Patent EP1572962.
JD170863 - Sequence 151887 from Patent EP1572962.
JD545169 - Sequence 526193 from Patent EP1572962.
JD283303 - Sequence 264327 from Patent EP1572962.
JD497098 - Sequence 478122 from Patent EP1572962.
JD275276 - Sequence 256300 from Patent EP1572962.
JD275277 - Sequence 256301 from Patent EP1572962.
JD204598 - Sequence 185622 from Patent EP1572962.
JD443394 - Sequence 424418 from Patent EP1572962.
JD138263 - Sequence 119287 from Patent EP1572962.
JD175840 - Sequence 156864 from Patent EP1572962.
JD332241 - Sequence 313265 from Patent EP1572962.
JD351583 - Sequence 332607 from Patent EP1572962.
JD522767 - Sequence 503791 from Patent EP1572962.
JD139824 - Sequence 120848 from Patent EP1572962.
JD451669 - Sequence 432693 from Patent EP1572962.
JD364934 - Sequence 345958 from Patent EP1572962.
JD320099 - Sequence 301123 from Patent EP1572962.
JD385186 - Sequence 366210 from Patent EP1572962.
JD477290 - Sequence 458314 from Patent EP1572962.
JD264016 - Sequence 245040 from Patent EP1572962.
JD313626 - Sequence 294650 from Patent EP1572962.
JD474296 - Sequence 455320 from Patent EP1572962.
JD043262 - Sequence 24286 from Patent EP1572962.
JD166428 - Sequence 147452 from Patent EP1572962.
JD292130 - Sequence 273154 from Patent EP1572962.
JD283630 - Sequence 264654 from Patent EP1572962.
JD351139 - Sequence 332163 from Patent EP1572962.
JD084339 - Sequence 65363 from Patent EP1572962.
JD113611 - Sequence 94635 from Patent EP1572962.
JD175458 - Sequence 156482 from Patent EP1572962.
JD293571 - Sequence 274595 from Patent EP1572962.
JD399867 - Sequence 380891 from Patent EP1572962.
JD106681 - Sequence 87705 from Patent EP1572962.
JD512883 - Sequence 493907 from Patent EP1572962.
JD363472 - Sequence 344496 from Patent EP1572962.
JD171766 - Sequence 152790 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04664 - Fc epsilon RI signaling pathway
hsa05310 - Asthma

BioCarta from NCI Cancer Genome Anatomy Project
h_fcer1Pathway - Fc Epsilon Receptor I Signaling in Mast Cells

Reactome (by CSHL, EBI, and GO)

Protein Q01362 (Reactome details) participates in the following event(s):

R-HSA-2454202 Fc epsilon receptor (FCERI) signaling
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: APY, FCER1B, FCERB_HUMAN, IGER, NM_001256916, NP_001243845, Q01362, Q54A81
UCSC ID: uc021qka.1
RefSeq Accession: NM_001256916
Protein: Q01362 (aka FCERB_HUMAN)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001256916.1
exon count: 6CDS single in 3' UTR: no RNA size: 3529
ORF size: 600CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1387.00frame shift in genome: no % Coverage: 99.55
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.