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

Gene ID: 64231, updated on 3-Apr-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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Location:
11q12.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (60171607..60184666, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (60122891..60135951, complement)
105.20220307 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: 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. 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
  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. 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,
  4. APOE and MS4A6A interact with GnRH signaling in Alzheimer's disease: Enrichment of epistatic effects. Cáceres A, et al. Alzheimers Dement, 2017 Apr. PMID 27337227
  5. Common variants in ABCA7 and MS4A6A are associated with cortical and hippocampal atrophy. Ramirez LM, et al. Neurobiol Aging, 2016 Mar. PMID 26923404

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. rs610932 MS4A6A is not associated with late-onset Alzheimer's disease.
    Title: Validating GWAS Variants from Microglial Genes Implicated in Alzheimer's Disease.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. data revealed the allele (T) of the rs3865444 polymorphism of the CD33 gene and the allele (C) of the rs610932 polymorphism of the MS4A6A gene may contribute to Alzheimer's disease risk in the Chinese Han population
    Title: The prevalence of CD33 and MS4A6A variant in Chinese Han population with Alzheimer's disease.
Submit: New GeneRIF Correction See all GeneRIFs (12)

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)

Genotypes

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, ENST00000530839.5
    Conserved Domains (1) summary
    pfam04103
    Location:47 → 208
    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
    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

  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

  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
    E9PSA9

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

    UniProtKB/TrEMBL
    E9PSA9

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

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

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

  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

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