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    MS4A4E membrane spanning 4-domains A4E [ Homo sapiens (human) ]

    Gene ID: 643680, updated on 10-Dec-2024

    Summary

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    Official Symbol
    MS4A4Eprovided by HGNC
    Official Full Name
    membrane spanning 4-domains A4Eprovided by HGNC
    Primary source
    HGNC:HGNC:14284
    See related
    Ensembl:ENSG00000214787 MIM:608401; AllianceGenome:HGNC:14284
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Most MS4A genes, including MS4A4E, encode proteins with at least 4 potential transmembrane domains and N- and C-terminal cytoplasmic domains encoded by distinct exons.[supplied by OMIM, Apr 2004]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    all
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    Genomic context

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    See MS4A4E in Genome Data Viewer
    Location:
    11q12.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (60200270..60243137, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (60151543..60194426, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (59967743..60010610, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes 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 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 microRNA 6503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3370 Neighboring gene membrane spanning 4-domains A4A 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

    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. Population-based analysis of Alzheimer's disease risk alleles implicates genetic interactions. Ebbert MT, et al. Biol Psychiatry, 2014 May 1. PMID 23954108, Free PMC Article
    2. Genetic variants associated with risk of Alzheimer's disease contribute to cognitive change in midlife: The Atherosclerosis Risk in Communities Study. Bressler J, et al. Am J Med Genet B Neuropsychiatr Genet, 2017 Apr. PMID 27781389, Free PMC Article
    3. Interaction between variants in CLU and MS4A4E modulates Alzheimer's disease risk. Ebbert MTW, et al. Alzheimers Dement, 2016 Feb. PMID 26449541, Free PMC Article
    4. Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. Hollingworth P, et al. Nat Genet, 2011 May. PMID 21460840, Free PMC Article
    5. Structural organization of the human MS4A gene cluster on Chromosome 11q12. Liang Y, et al. Immunogenetics, 2001 Jul. PMID 11486273

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Addition of the minor allele for rs670139 (MS4A4E), rs9331896 (CLU), and rs12155159 (NME8) was nominally associated with change on the DWRT, DSST, and WFT, respectively, in whites. For rs670139 and rs9331896 the association was only significant in individuals bearing at least one APOE 4 allele in stratified analyses.
      Title: Genetic variants associated with risk of Alzheimer's disease contribute to cognitive change in midlife: The Atherosclerosis Risk in Communities Study.
    2. We replicated the rs11136000 (CLU)- rs670139 (MS4A4E) interaction, demonstrated an association in APOE epsilon4 negative subjects, and reported evidence of a possible dominant effect for MS4A4E.
      Title: Interaction between variants in CLU and MS4A4E modulates Alzheimer's disease risk.
    3. ABCA7 and the MS4A6A/MS4A4E gene cluster are new Alzheimer's disease susceptibility loci.
      Title: Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    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
    Genome-wide association study evaluating lipoprotein-associated phospholipase A2 mass and activity at baseline and after rosuvastatin therapy.
    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)

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    putative membrane-spanning 4-domains subfamily A member 4E

    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_001351235.2 → NP_001338164.1  putative membrane-spanning 4-domains subfamily A member 4E isoform 1

      Status: VALIDATED

      Source sequence(s)
      AK300102, AP003970
      UniProtKB/TrEMBL
      B4DT89

    2. NM_001393391.1 → NP_001380320.1  putative membrane-spanning 4-domains subfamily A member 4E isoform 2

      Status: VALIDATED

      Source sequence(s)
      AP003970
      Consensus CDS
      CCDS91480.1
      UniProtKB/TrEMBL
      A0A494C1L8
      Related
      ENSP00000499123.1, ENST00000651255.1
      Conserved Domains (1) summary
      pfam04103
      Location:61 → 152
      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
      60200270..60243137 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011545416.3 → XP_011543718.1  putative membrane-spanning 4-domains subfamily A member 4E isoform X1

      Conserved Domains (1) summary
      pfam04103
      Location:61 → 152
      CD20; CD20-like family

    2. XM_017018641.2 → XP_016874130.1  putative membrane-spanning 4-domains subfamily A member 4E isoform X2

    RNA

    1. XR_007062493.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      60151543..60194426 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369644.1 → XP_054225619.1  putative membrane-spanning 4-domains subfamily A member 4E isoform X1

    2. XM_054369645.1 → XP_054225620.1  putative membrane-spanning 4-domains subfamily A member 4E isoform X2

    RNA

    1. XR_008488423.1 RNA Sequence

    2. XR_008488424.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96PG1.2 GenPept UniProtKB/Swiss-Prot:Q96PG1

    Gene LinkOut

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

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