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MS4A4A membrane spanning 4-domains A4A [ Homo sapiens (human) ]

Gene ID: 51338, updated on 5-Mar-2024

Summary

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Official Symbol
MS4A4Aprovided by HGNC
Official Full Name
membrane spanning 4-domains A4Aprovided by HGNC
Primary source
HGNC:HGNC:13371
See related
Ensembl:ENSG00000110079 MIM:606547; AllianceGenome:HGNC:13371
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
MS4A4; MS4A7; 4SPAN1; CD20L1; CD20-L1; HDCME31P
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, similar intron/exon splice boundaries, and display unique expression patterns in hematopoietic cells and nonlymphoid tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
Expression
Broad expression in placenta (RPKM 28.4), gall bladder (RPKM 18.9) and 20 other tissues See more
Orthologs
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Genomic context

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See MS4A4A 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 (60280666..60308970)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (60231961..60260258)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (60048139..60076443)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4763 Neighboring gene membrane spanning 4-domains A6A Neighboring gene CRISPRi-validated cis-regulatory element chr11.2530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4764 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:59968587-59969442 Neighboring gene membrane spanning 4-domains A4E Neighboring gene microRNA 6503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3371 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:60086754-60087254 Neighboring gene Sharpr-MPRA regulatory region 5454 Neighboring gene membrane spanning 4-domains A6E Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4766 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:60135080-60135586 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4767 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4769 Neighboring gene membrane spanning 4-domains A7

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. The FcεRIβ homologue, MS4A4A, promotes FcεRI signal transduction and store-operated Ca(2+) entry in human mast cells. Arthur GK, et al. Cell Signal, 2020 Jul. PMID 32240745, Free PMC Article
  2. MS4A4A: a novel cell surface marker for M2 macrophages and plasma cells. Sanyal R, et al. Immunol Cell Biol, 2017 Aug. PMID 28303902
  3. The MS4A gene cluster is a key modulator of soluble TREM2 and Alzheimer's disease risk. Deming Y, et al. Sci Transl Med, 2019 Aug 14. PMID 31413141, Free PMC Article
  4. The macrophage tetraspan MS4A4A enhances dectin-1-dependent NK cell-mediated resistance to metastasis. Mattiola I, et al. Nat Immunol, 2019 Aug. PMID 31263276, Free PMC Article
  5. The CD20 homologue MS4A4 directs trafficking of KIT toward clathrin-independent endocytosis pathways and thus regulates receptor signaling and recycling. Cruse G, et al. Mol Biol Cell, 2015 May 1. PMID 25717186, Free PMC Article

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The FcepsilonRIbeta homologue, MS4A4A, promotes FcepsilonRI signal transduction and store-operated Ca(2+) entry in human mast cells.
    Title: The FcεRIβ homologue, MS4A4A, promotes FcεRI signal transduction and store-operated Ca(2+) entry in human mast cells.
  2. MS4A4A is a tetraspan molecule selectively expressed in macrophages during differentiation and polarization, essential for dectin-1-dependent activation of natural killer cell-mediated resistance to metastasis.
    Title: The macrophage tetraspan MS4A4A enhances dectin-1-dependent NK cell-mediated resistance to metastasis.
  3. MS4A4A is expressed at the plasma membrane in monocytes but not in granulocytes or lymphocytes.
    Title: MS4A4A: a novel cell surface marker for M2 macrophages and plasma cells.
  4. MS4A4A expression is significantly upregulated in human masticatory mucosa during wound healing
    Title: Human gingiva transcriptome during wound healing.
  5. MS4A4 in human mast cells effects ligand-induced KIT endocytosis pathways and reduced receptor recycling to the cell surface, thus promoting KIT signaling in the endosomes while reducing that in the plasma membrane.
    Title: The CD20 homologue MS4A4 directs trafficking of KIT toward clathrin-independent endocytosis pathways and thus regulates receptor signaling and recycling.
  6. Single nucleotide polymorphisms in APOE-epsilon4, CLU and MS4A4A influence both Alzheimer disease risk and cerebrospinal fluid Amyloid-beta1-42 levels.
    Title: Genetic loci associated with Alzheimer's disease and cerebrospinal fluid biomarkers in a Finnish case-control cohort.
  7. Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease.
    Title: Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease.
EBI GWAS Catalog

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC22311

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
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 raft IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
membrane-spanning 4-domains subfamily A member 4A
Names
CD20 antigen-like 1
Fc epsilon receptor beta subunit homolog
epididymis secretory sperm binding protein
four-span transmembrane protein 1
membrane-spanning 4-domains, subfamily A, member 4

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.

mRNA and Protein(s)

  1. NM_001243266.2 → NP_001230195.1  membrane-spanning 4-domains subfamily A member 4A isoform 3

    See identical proteins and their annotated locations for NP_001230195.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame coding exon compared to variant 1. This results in a shorter isoform (3) missing an internal protein segment compared to isoform 1.
    Source sequence(s)
    AP003127, AP003970
    Consensus CDS
    CCDS58135.1
    UniProtKB/TrEMBL
    A0A7P0T8A0
    Related
    ENSP00000434506.1, ENST00000532114.6
    Conserved Domains (1) summary
    pfam04103
    Location:65 → 157
    CD20; CD20-like family

  2. NM_024021.4 → NP_076926.2  membrane-spanning 4-domains subfamily A member 4A isoform 2

    See identical proteins and their annotated locations for NP_076926.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an additional exon at the 5' end compared to variant 1. This results in translation initiation from an in-frame downstream AUG, and an isoform (2) with a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AP003127, AP003970
    UniProtKB/TrEMBL
    A0A384MDW1, B2RA46
    Related
    ENSP00000505293.1, ENST00000680757.1
    Conserved Domains (1) summary
    pfam04103
    Location:46 → 188
    CD20; CD20-like family

  3. NM_148975.3 → NP_683876.1  membrane-spanning 4-domains subfamily A member 4A isoform 1

    See identical proteins and their annotated locations for NP_683876.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript, and encodes the longest isoform (1).
    Source sequence(s)
    AP003127, AP003970
    Consensus CDS
    CCDS7982.1
    UniProtKB/Swiss-Prot
    Q8TEZ6, Q96JQ5, Q96PG7, Q9BY18, Q9H3V3, Q9P1S3
    UniProtKB/TrEMBL
    A8K7S4
    Related
    ENSP00000338648.4, ENST00000337908.5
    Conserved Domains (1) summary
    pfam04103
    Location:65 → 207
    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
    60280666..60308970
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    60231961..60260258
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96JQ5.1 GenPept UniProtKB/Swiss-Prot:Q96JQ5

Gene LinkOut

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