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    MS4A6A membrane spanning 4-domains A6A [ Homo sapiens (human) ]

    Gene ID: 64231, updated on 10-Dec-2024

    Summary

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    Official Symbol
    MS4A6Aprovided by HGNC
    Official Full Name
    membrane spanning 4-domains A6Aprovided by HGNC
    Primary source
    HGNC:HGNC:13375
    See related
    Ensembl:ENSG00000110077 MIM:606548; AllianceGenome:HGNC:13375
    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
    CDA01; MS4A6; 4SPAN3; CD20L3; MST090; MSTP090; 4SPAN3.2
    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. The gene encoding this protein is localized to 11q12.1, among a cluster of family members. Alternative splicing of this gene results in several transcript variants that encode different protein isoforms. [provided by RefSeq, Oct 2011]
    Expression
    Broad expression in lymph node (RPKM 27.7), spleen (RPKM 26.2) and 22 other tissues See more
    Orthologs
    all
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    Genomic context

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    See MS4A6A in Genome Data Viewer
    Location:
    11q12.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (60171607..60184666, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (60122891..60135951, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (59939080..59952139, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene membrane spanning 4-domains A2 Neighboring gene long intergenic non-protein coding RNA 2705 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:59935886-59937085 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4763 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 membrane spanning 4-domains A4A

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Involvement of microglia-expressed MS4A6A in the onset of glioblastoma. Lv W, et al. Eur J Neurosci, 2024 May. PMID 38488530
    2. Alzheimer's disease susceptibility variants in the MS4A6A gene are associated with altered levels of MS4A6A expression in blood. Proitsi P, et al. Neurobiol Aging, 2014 Feb. PMID 24064185
    3. MS4A6A genotypes are associated with the atrophy rates of Alzheimer's disease related brain structures. Ma J, et al. Oncotarget, 2016 Sep 13. PMID 27244883, Free PMC Article
    4. Identification of redundancy between human FcεRIβ and MS4A6A proteins points toward additional complex mechanisms for FcεRI trafficking and signaling. Bitting K, et al. Allergy, 2023 May. PMID 36424895, Free PMC Article
    5. The prevalence of CD33 and MS4A6A variant in Chinese Han population with Alzheimer's disease. Deng YL, et al. Hum Genet, 2012 Jul. PMID 22382309

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Involvement of microglia-expressed MS4A6A in the onset of glioblastoma.
      Title: Involvement of microglia-expressed MS4A6A in the onset of glioblastoma.
    2. Identification of redundancy between human FcepsilonRIbeta and MS4A6A proteins points toward additional complex mechanisms for FcepsilonRI trafficking and signaling.
      Title: Identification of redundancy between human FcεRIβ and MS4A6A proteins points toward additional complex mechanisms for FcεRI trafficking and signaling.
    3. Meta analysis validated the Alzheimer disease protective association for MS4A6A (rs610932) variants.
      Title: Updated Meta-Analysis of BIN1, CR1, MS4A6A, CLU, and ABCA7 Variants in Alzheimer's Disease.
    4. rs610932 MS4A6A is not associated with late-onset Alzheimer's disease.
      Title: Validating GWAS Variants from Microglial Genes Implicated in Alzheimer's Disease.
    5. these findings reveal that MS4A6A genotypes affect Alzheimer's disease specific brain structures
      Title: MS4A6A genotypes are associated with the atrophy rates of Alzheimer's disease related brain structures.
    6. Study found enrichment of epistasis in gonadotropin-releasing hormone signaling with risk single-nucleotide polymorphisms in APOE and MS4A6A. Results suggest that in addition to APOE, MS4A6A polymorphisms should be considered in hormone trials targeting gonadotropins.
      Title: APOE and MS4A6A interact with GnRH signaling in Alzheimer's disease: Enrichment of epistatic effects.
    7. Its mutation plays a role in pathogenesis of Alzheimer's disease.
      Title: Mutation analysis of the MS4A and TREM gene clusters in a case-control Alzheimer's disease data set.
    8. identified the significant associations of the GBA L444P mutation and DYRK1A rs8126696 T allele with the earlier age at onset (AAO) in Parkinson's disease (PD) patients, and the A allele at MS4A6A rs610932 with the delayed AAO of PD.
      Title: The GBA, DYRK1A and MS4A6A polymorphisms influence the age at onset of Chinese Parkinson patients.
    9. Common variants in ABCA7 and MS4A6A are associated with cortical and hippocampal atrophy.
      Title: Common variants in ABCA7 and MS4A6A are associated with cortical and hippocampal atrophy.
    10. high levels of MS4A6A contribute to altered turnover or production of cells with an anti-inflammatory neuroprotective phenotype in favor of cells with a damaging pro-inflammatory phenotype believed to contribute to AD pathology.
      Title: Alzheimer's disease susceptibility variants in the MS4A6A gene are associated with altered levels of MS4A6A expression in blood.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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 ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease.
    EBI GWAS Catalog
    Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease.
    EBI GWAS Catalog
    Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular 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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope transmembrane glycoprotein gp41 env A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 downregulates the expression of membrane-spanning 4-domains, subfamily A, member 6A (MS4A6A) in peptide-treated PBMCs 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

    Homology

    Clone Names

    • MGC22650, MGC131944

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell surface receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    membrane-spanning 4-domains subfamily A member 6A
    Names
    CD20 antigen-like 3
    CD20-like precusor
    HAIRB-iso
    MS4A6A-polymorph
    four-span transmembrane protein 3
    four-span transmembrane protein 3.1
    four-span transmembrane protein 3.2
    membrane-spanning 4-domains, subfamily A, member 6A

    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_033978.2 RefSeqGene

      Range
      6583..17169
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001247999.2 → NP_001234928.1  membrane-spanning 4-domains subfamily A member 6A isoform 4

      See identical proteins and their annotated locations for NP_001234928.1

      Status: REVIEWED

      Source sequence(s)
      AP003970
      Consensus CDS
      CCDS58134.1
      UniProtKB/TrEMBL
      B4DUN6
      Related
      ENSP00000392770.3, ENST00000426738.6
      Conserved Domains (1) summary
      pfam04103
      Location:75 → 236
      CD20; CD20-like family

    2. NM_001330275.1 → NP_001317204.1  membrane-spanning 4-domains subfamily A member 6A isoform 5

      Status: REVIEWED

      Source sequence(s)
      AA731356, BQ003409, CB853877, DC297033, EL735363
      Consensus CDS
      CCDS81568.1
      UniProtKB/TrEMBL
      B4DUN6, E9PSA9
      Related
      ENSP00000435844.1, ENST00000529054.5
      Conserved Domains (1) summary
      pfam04103
      Location:75 → 236
      CD20; CD20-like family

    3. NM_022349.4 → NP_071744.2  membrane-spanning 4-domains subfamily A member 6A isoform 2

      See identical proteins and their annotated locations for NP_071744.2

      Status: REVIEWED

      Source sequence(s)
      AP003970
      Consensus CDS
      CCDS44615.1
      UniProtKB/TrEMBL
      Q32NC2
      Related
      ENSP00000431901.1, ENST00000528851.6
      Conserved Domains (1) summary
      pfam04103
      Location:47 → 208
      CD20; CD20-like family

    4. NM_152851.2 → NP_690590.1  membrane-spanning 4-domains subfamily A member 6A isoform 3

      See identical proteins and their annotated locations for NP_690590.1

      Status: REVIEWED

      Source sequence(s)
      AB013104, BC022854, CD684503, DA979138
      Consensus CDS
      CCDS44616.1
      UniProtKB/Swiss-Prot
      Q9H2W1
      Related
      ENSP00000392921.2, ENST00000420732.6
      Conserved Domains (1) summary
      pfam04103
      Location:47 → 159
      CD20; CD20-like family

    5. NM_152852.3 → NP_690591.1  membrane-spanning 4-domains subfamily A member 6A isoform 1

      See identical proteins and their annotated locations for NP_690591.1

      Status: REVIEWED

      Source sequence(s)
      AF212240, AK291870, BC022854
      Consensus CDS
      CCDS7981.1
      UniProtKB/Swiss-Prot
      A8K755, F8W9K1, Q7Z4E8, Q8TBV7, Q8TEZ4, Q8TEZ5, Q96PG6, Q9H2L1, Q9H2N3, Q9H2W1, Q9H3V1, Q9HC76
      UniProtKB/TrEMBL
      Q32NC2
      Related
      ENSP00000436979.1, ENST00000530839.6
      Conserved Domains (1) summary
      pfam04103
      Location:47 → 208
      CD20; CD20-like family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      60171607..60184666 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005274177.4 → XP_005274234.1  membrane-spanning 4-domains subfamily A member 6A isoform X1

      See identical proteins and their annotated locations for XP_005274234.1

      UniProtKB/TrEMBL
      B4DUN6, E9PSA9
      Conserved Domains (1) summary
      pfam04103
      Location:75 → 236
      CD20; CD20-like family

    2. XM_006718660.3 → XP_006718723.1  membrane-spanning 4-domains subfamily A member 6A isoform X2

      Conserved Domains (1) summary
      pfam04103
      Location:78 → 191
      CD20; CD20-like family

    3. XM_024448652.2 → XP_024304420.1  membrane-spanning 4-domains subfamily A member 6A isoform X1

      UniProtKB/TrEMBL
      B4DUN6, E9PSA9
      Conserved Domains (1) summary
      pfam04103
      Location:75 → 236
      CD20; CD20-like family

    4. XM_047427402.1 → XP_047283358.1  membrane-spanning 4-domains subfamily A member 6A isoform X4

      UniProtKB/TrEMBL
      B4DW64

    5. XM_006718661.3 → XP_006718724.1  membrane-spanning 4-domains subfamily A member 6A isoform X3

      UniProtKB/TrEMBL
      B4DW64
      Conserved Domains (1) summary
      pfam04103
      Location:78 → 191
      CD20; CD20-like family

    6. XM_047427403.1 → XP_047283359.1  membrane-spanning 4-domains subfamily A member 6A isoform X5

      UniProtKB/TrEMBL
      B4DW64

    7. XM_017018125.2 → XP_016873614.1  membrane-spanning 4-domains subfamily A member 6A isoform X7

    8. XM_011545209.2 → XP_011543511.1  membrane-spanning 4-domains subfamily A member 6A isoform X6

      Conserved Domains (1) summary
      pfam04103
      Location:75 → 148
      CD20; CD20-like family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      60122891..60135951 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369633.1 → XP_054225608.1  membrane-spanning 4-domains subfamily A member 6A isoform X2

    2. XM_054369631.1 → XP_054225606.1  membrane-spanning 4-domains subfamily A member 6A isoform X1

      UniProtKB/TrEMBL
      B4DUN6, E9PSA9

    3. XM_054369632.1 → XP_054225607.1  membrane-spanning 4-domains subfamily A member 6A isoform X1

      UniProtKB/TrEMBL
      B4DUN6, E9PSA9

    4. XM_054369635.1 → XP_054225610.1  membrane-spanning 4-domains subfamily A member 6A isoform X4

      UniProtKB/TrEMBL
      B4DW64

    5. XM_054369634.1 → XP_054225609.1  membrane-spanning 4-domains subfamily A member 6A isoform X3

      UniProtKB/TrEMBL
      B4DW64

    6. XM_054369636.1 → XP_054225611.1  membrane-spanning 4-domains subfamily A member 6A isoform X5

      UniProtKB/TrEMBL
      B4DW64

    7. XM_054369638.1 → XP_054225613.1  membrane-spanning 4-domains subfamily A member 6A isoform X7

    8. XM_054369637.1 → XP_054225612.1  membrane-spanning 4-domains subfamily A member 6A isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H2W1.1 GenPept UniProtKB/Swiss-Prot:Q9H2W1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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