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Aliases for MS4A6A Gene

Aliases for MS4A6A Gene

  • Membrane Spanning 4-Domains A6A 2 3 5
  • Membrane-Spanning 4-Domains, Subfamily A, Member 6A 2 3
  • Four-Span Transmembrane Protein 3 3 4
  • CD20 Antigen-Like 3 3 4
  • 4SPAN3 3 4
  • CD20L3 3 4
  • MS4A6 3 4
  • Membrane-Spanning 4-Domains Subfamily A Member 6A 3
  • Four-Span Transmembrane Protein 3.1 3
  • Four-Span Transmembrane Protein 3.2 3
  • CD20-Like Precusor 3
  • MS4A6A-Polymorph 3
  • HAIRB-Iso 3
  • 4SPAN3.2 3
  • MSTP090 3
  • MST090 3
  • CDA01 3

External Ids for MS4A6A Gene

Previous HGNC Symbols for MS4A6A Gene

  • MS4A6

Previous GeneCards Identifiers for MS4A6A Gene

  • GC11M062333
  • GC11M061452
  • GC11M059714
  • GC11M059695
  • GC11M059464
  • GC11M059939
  • GC11M056287

Summaries for MS4A6A Gene

Entrez Gene Summary for MS4A6A Gene

  • 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]

GeneCards Summary for MS4A6A Gene

MS4A6A (Membrane Spanning 4-Domains A6A) is a Protein Coding gene. Diseases associated with MS4A6A include Hydrocephalus, Normal-Pressure and Communicating Hydrocephalus. An important paralog of this gene is MS4A6E.

UniProtKB/Swiss-Prot for MS4A6A Gene

  • May be involved in signal transduction as a component of a multimeric receptor complex.

Additional gene information for MS4A6A Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MS4A6A Gene

Genomics for MS4A6A Gene

GeneHancer (GH) Regulatory Elements for MS4A6A Gene

Promoters and enhancers for MS4A6A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I060181 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 558.4 +0.5 504 5.5 HDAC1 BMI1 YBX1 CHAMP1 TCF12 ATF7 IKZF2 RUNX3 NCOA1 ZNF592 MS4A6A MS4A2 MS4A6E LOC105369319
GH11I059753 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4.7 +429.0 428979 4.3 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 CBX5 E2F8 STX3 ENSG00000254477 PATL1 LOC101927226 MS4A6A OSBP FABP5P7 GC11P059703
GH11I059666 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 5.7 +515.9 515939 3.8 HDGF PKNOX1 FOXA2 SMAD1 MLX ARNT ARID4B SIN3A YY1 SLC30A9 PATL1 LOC105369318 STX3 LOC101927226 ENSG00000255008 MS4A6A
GH11I060192 Enhancer 1.3 Ensembl ENCODE dbSUPER 8.1 -10.2 -10180 3.7 PKNOX1 ATF1 ARNT IRF4 ZNF280A TCF12 ZNF766 ZNF143 ATF7 RUNX3 LOC101927226 PATL1 MS4A6A MS4A6E MS4A2 MIR6503
GH11I060363 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 6.9 -179.3 -179281 1.7 SMARCA5 CTCF ZNF654 ZBTB6 RB1 HLF MAX TRIM22 REST RAD21 MS4A14 MS4A7 MS4A6E MS4A5 MS4A12 MS4A18 MS4A6A MS4A4A GC11P060374 GC11M060363
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around MS4A6A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the MS4A6A gene promoter:

Genomic Locations for MS4A6A Gene

Genomic Locations for MS4A6A Gene
13,060 bases
Minus strand

Genomic View for MS4A6A Gene

Genes around MS4A6A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MS4A6A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MS4A6A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MS4A6A Gene

Proteins for MS4A6A Gene

  • Protein details for MS4A6A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Membrane-spanning 4-domains subfamily A member 6A
    Protein Accession:
    Secondary Accessions:
    • A8K755
    • F8W9K1
    • Q7Z4E8
    • Q8TBV7
    • Q8TEZ4
    • Q8TEZ5
    • Q96PG6
    • Q9H2L1
    • Q9H2N3
    • Q9H3V1
    • Q9HC76

    Protein attributes for MS4A6A Gene

    248 amino acids
    Molecular mass:
    26943 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAG44626.1; Type=Frameshift; Positions=115; Evidence={ECO:0000305}; Sequence=AAG44672.1; Type=Frameshift; Positions=68, 103; Evidence={ECO:0000305};

    Alternative splice isoforms for MS4A6A Gene


neXtProt entry for MS4A6A Gene

Post-translational modifications for MS4A6A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for MS4A6A Gene

Domains & Families for MS4A6A Gene

Gene Families for MS4A6A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for MS4A6A Gene

Suggested Antigen Peptide Sequences for MS4A6A Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the MS4A family.
  • Belongs to the MS4A family.
genes like me logo Genes that share domains with MS4A6A: view

Function for MS4A6A Gene

Molecular function for MS4A6A Gene

UniProtKB/Swiss-Prot Function:
May be involved in signal transduction as a component of a multimeric receptor complex.

Phenotypes From GWAS Catalog for MS4A6A Gene

genes like me logo Genes that share phenotypes with MS4A6A: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for MS4A6A Gene

Localization for MS4A6A Gene

Subcellular locations from UniProtKB/Swiss-Prot for MS4A6A Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for MS4A6A gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for MS4A6A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with MS4A6A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for MS4A6A Gene

Pathways & Interactions for MS4A6A Gene

SuperPathways for MS4A6A Gene

No Data Available

Interacting Proteins for MS4A6A Gene

Gene Ontology (GO) - Biological Process for MS4A6A Gene


No data available for Pathways by source and SIGNOR curated interactions for MS4A6A Gene

Drugs & Compounds for MS4A6A Gene

No Compound Related Data Available

Transcripts for MS4A6A Gene

Unigene Clusters for MS4A6A Gene

Membrane-spanning 4-domains, subfamily A, member 6A:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for MS4A6A Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b · 11c ^ 12a · 12b
SP1: - - -
SP2: - -
SP3: - - -
SP4: - - - - - - - -
SP5: - -
SP6: - - -
SP7: -

Relevant External Links for MS4A6A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MS4A6A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MS4A6A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for MS4A6A Gene

This gene is overexpressed in Whole Blood (x13.2) and Spleen (x5.8).

Protein differential expression in normal tissues from HIPED for MS4A6A Gene

This gene is overexpressed in Pancreas (19.8), Gallbladder (16.6), Monocytes (9.7), Urinary Bladder (9.2), and Placenta (9.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for MS4A6A Gene

NURSA nuclear receptor signaling pathways regulating expression of MS4A6A Gene:


SOURCE GeneReport for Unigene cluster for MS4A6A Gene:


mRNA Expression by UniProt/SwissProt for MS4A6A Gene:

Tissue specificity: Variable expression in some B-cell, myelomonocytic, and erythroleukemia cell lines.

Evidence on tissue expression from TISSUES for MS4A6A Gene

  • Blood(4.4)
  • Liver(4.4)
  • Lymph node(4.4)
  • Spleen(4.4)
  • Muscle(4.3)
  • Nervous system(2.3)
  • Intestine(2)
  • Lung(2)
genes like me logo Genes that share expression patterns with MS4A6A: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for MS4A6A Gene

Orthologs for MS4A6A Gene

This gene was present in the common ancestor of mammals.

Orthologs for MS4A6A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia MS4A6A 33 34
  • 98.65 (n)
(Canis familiaris)
Mammalia LOC612553 33
  • 73.06 (n)
-- 34
  • 51 (a)
(Mus musculus)
Mammalia Ms4a6d 33 16 34
  • 66.94 (n)
Gm10212 34
  • 57 (a)
Ms4a6c 34
  • 48 (a)
Ms4a6b 34
  • 47 (a)
(Rattus norvegicus)
Mammalia Ms4a6a 33
  • 66.94 (n)
Species where no ortholog for MS4A6A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for MS4A6A Gene

Gene Tree for MS4A6A (if available)
Gene Tree for MS4A6A (if available)

Paralogs for MS4A6A Gene

Paralogs for MS4A6A Gene

genes like me logo Genes that share paralogs with MS4A6A: view

Variants for MS4A6A Gene

Sequence variations from dbSNP and Humsavar for MS4A6A Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000113673 -- 60,184,011(-) C/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000156217 -- 60,171,295(-) T/A downstream_transcript_variant
rs1000547958 -- 60,183,779(-) T/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000965604 -- 60,175,341(-) C/T downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1001202392 -- 60,176,031(-) A/G genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for MS4A6A Gene

Variant ID Type Subtype PubMed ID
esv2674897 CNV deletion 23128226
esv2744568 CNV deletion 23290073
esv33843 CNV loss 17666407
esv3626553 CNV loss 21293372
nsv468579 CNV gain 19166990
nsv524137 CNV loss 19592680
nsv555150 CNV gain 21841781
nsv832173 CNV gain 17160897
nsv832174 CNV gain 17160897

Variation tolerance for MS4A6A Gene

Residual Variation Intolerance Score: 77.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.44; 54.72% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MS4A6A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MS4A6A Gene

Disorders for MS4A6A Gene

MalaCards: The human disease database

(2) MalaCards diseases for MS4A6A Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
hydrocephalus, normal-pressure
  • normal pressure hydrocephalus
communicating hydrocephalus
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for MS4A6A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with MS4A6A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MS4A6A Gene

Publications for MS4A6A Gene

  1. Identification of a CD20-, FcepsilonRIbeta-, and HTm4-related gene family: sixteen new MS4A family members expressed in human and mouse. (PMID: 11401424) Liang Y … Tedder TF (Genomics 2001) 2 3 4 58
  2. Structural organization of the human MS4A gene cluster on Chromosome 11q12. (PMID: 11486273) Liang Y … Tedder TF (Immunogenetics 2001) 3 4 22 58
  3. Identification of a new multigene four-transmembrane family (MS4A) related to CD20, HTm4 and beta subunit of the high-affinity IgE receptor. (PMID: 11245982) Ishibashi K … Imai M (Gene 2001) 2 3 4 58
  4. Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. (PMID: 21460840) Hollingworth P … Williams J (Nature genetics 2011) 3 44 58
  5. A Large-scale genetic association study of esophageal adenocarcinoma risk. (PMID: 20453000) Liu CY … Christiani DC (Carcinogenesis 2010) 3 44 58

Products for MS4A6A Gene

Sources for MS4A6A Gene

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