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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

MS4A6A Gene

protein-coding GIFtS: 49
GCID: GC11M059939

membrane-spanning 4-domains, subfamily A, member 6A

(Previous symbol: MS4A6)

Explore 5 diseases affiliated with
MS4A6A via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Membrane-Spanning 4-Domains, Subfamily A, Member 6A¹ ²		MS4A6A-Polymorph¹
MS4A6¹ ² ³ ⁵		MST090²
CD20L3¹ ² ³		MSTP090²
Four-Span Transmembrane Protein 3² ³		CD20-Like Precusor²
4SPAN3² ³		Four-Span Transmembrane Protein 3.1²
CD20 Antigen-Like 3² ³		Four-Span Transmembrane Protein 3.2²
4SPAN3.2²		Membrane-Spanning 4-Domains Subfamily A Member 6A²
HAIRB-Iso¹

External Ids:	HGNC: 13375¹	Entrez Gene: 64231²	Ensembl: ENSG00000110077⁷	OMIM: 606548⁵	UniProtKB: Q9H2W1³

Export aliases for MS4A6A gene to outside databases

Previous GC identifers: GC11M062333 GC11M061452 GC11M060189 GC11M059714 GC11M059695 GC11M059464 GC11M056287

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for MS4A6A:

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)

UniProtKB/Swiss-Prot: M4A6A_HUMAN, Q9H2W1

Function: May be involved in signal transduction as a component of a multimeric receptor complex

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000011.9 NC_018922.1 NT_167190.1

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the MS4A6A gene promoter:
SREBP-1c Brachyury MyoD Tal-1beta Cdc5 SREBP-1b c-Ets-1 SREBP-1a Pax-4a ITF-2
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: MS4A6A promoter sequence

Search SABiosciences Chromatin IP Primers for MS4A6A

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat MS4A6A

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11q12.1 Ensembl cytogenetic band: 11q12.2 HGNC cytogenetic band: 11q12.1

MS4A6A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MS4A6A gene location

GeneLoc information about chromosome 11 GeneLoc Exon Structure

GeneLoc location for GC11M059939: view genomic region (about GC identifiers)

Start:	59,939,080 bp from pter	End:	59,952,139 bp from pter
Size:	13,060 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: M4A6A_HUMAN, Q9H2W1 (See protein sequence)

Recommended Name: Membrane-spanning 4-domains subfamily A member 6A

Size: 248 amino acids; 26943 Da

Subcellular location: Membrane; Multi-pass membrane protein

Sequence caution: Sequence=AAG44626.1; Type=Frameshift; Positions=115; Sequence=AAG44672.1; Type=Frameshift;

Positions=68, 103;

Secondary accessions: A8K755 Q7Z4E8 Q8TBV7 Q8TEZ4 Q8TEZ5 Q96PG6 Q9H2L1 Q9H2N3 Q9H3V1 Q9HC76

Alternative splicing: 4 isoforms: Q9H2W1-1 Q9H2W1-2 Q9H2W1-3 Q9H2W1-4

Explore the universe of human proteins at neXtProt for MS4A6A: NX_Q9H2W1

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q9H2W1

MS4A6A Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (4 alternative transcripts):

NP_001234928.1 NP_071744.2 NP_690590.1 NP_690591.1

ENSEMBL proteins:

ENSP00000431901 ENSP00000392921 ENSP00000436979 ENSP00000436133 ENSP00000435844

ENSP00000403212 ENSP00000436172 ENSP00000435630 ENSP00000431266 ENSP00000433436

ENSP00000433012 ENSP00000437152 ENSP00000315878 ENSP00000392770

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	Browse Sino Biological Recombinant Proteins
	Browse ProSpec Recombinant Proteins
	Uscn Proteins for MS4A6A

Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0016021	integral to membrane	IEA	--

MS4A6A for ontologies About GeneDecksing

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	Uscn ELISAs and CLIAs for MS4A6A

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

MS4A6A for domains About GeneDecksing

1 InterPro domain/family:

IPR007237 CD20-like

Graphical View of Domain Structure for InterPro Entry Q9H2W1

ProtoNet protein and cluster: Q9H2W1

UniProtKB/Swiss-Prot: M4A6A_HUMAN, Q9H2W1

Similarity: Belongs to the MS4A family

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: M4A6A_HUMAN, Q9H2W1

Function: May be involved in signal transduction as a component of a multimeric receptor complex

Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0004872	receptor activity	--	--

MS4A6A for ontologies About GeneDecksing

Phenotypes:
2 GenomeRNAi human phenotypes for MS4A6A:

Decreased Wnt reporter activit

Proliferating cells

1 MGI phenotypic allele

for Ms4a6d (no phenotypes)

MS4A6A for phenotypes About GeneDecksing

Animal Models:
Mouse knock-out Ms4a6d^tm1Lex for MS4A6A

inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for MS4A6A

miRNA Products:		OriGene 3'-UTR Clone (see all 3): MS4A6A Browse MicroRNA Expression Plasmids
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		hsa-miR-590-3p hsa-miR-551b*
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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MS4A6A

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for MS4A6A

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for MS4A6A
Search CenterWatch for drugs/clinical trials and news about MS4A6A / M4A6A

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for MS4A6A gene (4 alternative transcripts):

NM_001247999.1 NM_022349.3 NM_152851.2 NM_152852.2

Unigene Clusters for MS4A6A:

Membrane-spanning 4-domains, subfamily A, member 6A

Hs.523702 [show with all ESTs], Hs.744079 [show with all ESTs]

Unigene Representative Sequences: AK026454, BC108728

18/22 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 22):

ENST00000528851(uc001not.3 uc010rlb.2) ENST00000420732 ENST00000530839

ENST00000533989 ENST00000531914 ENST00000529054 ENST00000412309(uc010rla.2)

ENST00000533023 ENST00000527254 ENST00000529906 ENST00000525549 ENST00000530179

ENST00000526677 ENST00000532169 ENST00000534596 ENST00000533660 ENST00000531531

ENST00000533409

miRNA Products:		OriGene 3'-UTR Clone (see all 3): MS4A6A Browse OriGene MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat MS4A6A
		2 QIAGEN miScript miRNA Assays for microRNAs that regulate MS4A6A:
		hsa-miR-590-3p hsa-miR-551b*
		SwitchGear 3'UTR luciferase reporter plasmid: MS4A6A 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
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		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat MS4A6A

Additional cDNA sequence:

AB013104.1 AF142409.1 AF172819.1 AF212240.1 AF237908.1 AF253977.1 AF261136.1 AF286866.1

AF350502.1 AF350503.1 AF354930.1 AK291870.1 AK300725.1 AK301387.1 BC022854.1 BC108728.1

16 DOTS entries:

DT.444503 DT.91751260 DT.95275355 DT.120703088 DT.40198787 DT.97771393 DT.120703099 DT.91724476

DT.95275356 DT.100826512 DT.91751252 DT.91751254 DT.95275359 DT.75174169 DT.91751268 DT.95331750

24/303 AceView cDNA sequences (see all 303):

CK820365 AI800594 AA736644 CR606472 CR609705 AI375656 BV178641 BI821317

AI199994 NM_152852 CA436521 AA731356 AA975342 CR625448 AI361585 BM695459

AV717594 BI766801 BE467132 AI273141 AI091306 NM_152851 AI933321 R58859

GeneLoc Exon Structure

5/9 Alternative Splicing Database (ASD) splice patterns (SP) for MS4A6A (see all 9) About this scheme

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:																																	-						-

ECgene alternative splicing isoforms for MS4A6A

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

MS4A6A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AATTAGGATA

About this image

MS4A6A expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

1 LifeMap In Vivo Development Anatomical Compartment/Cell

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Bone

Maxillary Process

Bone

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See MS4A6A Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for MS4A6A

SOURCE GeneReport for Unigene clusters: Hs.523702 Hs.744079

UniProtKB/Swiss-Prot: M4A6A_HUMAN, Q9H2W1

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

SABiosciences Custom PCR Arrays for MS4A6A

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In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MS4A6A

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

--

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

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for MS4A6A gene

MS4A6E² MS4A7²

3 SIMAP similar genes for MS4A6A using alignment to 11 protein entries: M4A6A_HUMAN (see all proteins):

MS4A6E MS4A12 MS4A7

MS4A6A for paralogs About GeneDecksing

1 Pseudogenes.org Pseudogene for MS4A6A
PGOHUM00000243553

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 11 pos	Sequence	#	AA Chg	Type	More	#	Pop	Total sample
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs11605252^1,2	C,F,H	--	56287229(+)	`AGTTAC/TGTGTG`	2	--	ut3¹		5	NS EA NA	424
rs112590709^1,2		--	56287352(+)	`ACTCAC/TAGCAT`	2	--	ut3¹		1	CSA	1
rs12286820^1,2	F	--	56287848(+)	`GACCAC/TCTCAA`	2	--	int¹		1	WA	118
rs61282517^1,2	C	--	56288047(+)	`ACATTG/ATTCAC`	2	--	int¹		2	WA	120
rs11821697^1,2	C,H	--	56289014(+)	`gtggcA/Gtgatc`	2	--	int¹		2	NA WA	4
rs114465730^1,2	C,F	--	56289711(+)	`CACCAC/TTCCAT`	2	--	int¹		1	WA	118
rs113078279^1,2	F	--	56290276(+)	`GCTAAC/TGACTC`	2	--	int¹		2	CSA	4
rs11230175^1,2	F,H	--	56290577(+)	`AAAGTG/AAAGGT`	2	--	int¹		7	NS EA NA WA	532
rs7924728^1,2	C,F,A,H	--	56291188(+)	`TCCAGG/AGCACA`	2	--	int¹		5	NS EA WA	530
rs11828298^1,2	C,H	--	56291254(+)	`AGGAAC/TTCACC`	2	--	int¹		3	NA WA	122

HapMap Linkage Disequilibrium report for MS4A6A (59939080 - 59952139 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for MS4A6A
1 CNV: 6929
Human Gene Mutation Database (HGMD): MS4A6A

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing MS4A6A

DNA2.0 Custom Variant and Variant Library Synthesis for MS4A6A

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

MS4A6A for disorders           About GeneDecksing

OMIM gene information: 606548    OMIM disorders: --

5 diseases for MS4A6A:    About MalaCards

hepatitis b alzheimer's disease hepatitis esophagitis

adenocarcinoma

Human Genome Epidemiology (HuGE) Navigator: MS4A6A (2 documents)

Export disorders for MS4A6A gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for MS4A6A gene, integrated from 9 sources (see all 12):
(articles sorted by number of sources associating them with MS4A6A)

Utopia: connect your pdf to the dynamic
world of online information

Identification of a new multigene four-transmembrane family (MS4A) related to CD20, HTm4 and beta subunit of the high-affinity IgE receptor. (PubMed id 11245982)^{1, 2, 3} Ishibashi K.... Imai M. (2001)
Identification of a CD20-, FcepsilonRIbeta-, and HTm4-related gene family: sixteen new MS4A family members expressed in human and mouse. (PubMed id 11401424)^{1, 2, 3} Liang Y. and Tedder T.F. (2001)
Structural organization of the human MS4A gene cluster on chromosome 11q12. (PubMed id 11486273)^{1, 2, 9} Liang Y.... Tedder T.F. (2001)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
The prevalence of CD33 and MS4A6A variant in Chinese H an population with Alzheimer's disease. (PubMed id 22382309)¹ Deng Y.L....Chen S.D. (2012)
Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. (PubMed id 21460840)¹ Hollingworth P....Williams J. (2011)
New genetic associations detected in a host response study to hepatitis B vaccine. (PubMed id 20237496)¹ Davila S....Seielstad M. (2010)
A Large-scale genetic association study of esophageal adenocarcinoma risk. (PubMed id 20453000)¹ Liu C.Y....Christiani D.C. (2010)
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)¹ Kimura K.... Sugano S. (2006)
Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)² Taylor T.D....Sakaki Y. (2006)

(in PubMed, OMIM, and NCBI Bookshelf)
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 64231	HGNC: 13375	AceView: MS4A6A	Ensembl:ENSG00000110077	euGenes: HUgn64231
ECgene: MS4A6A	H-InvDB: MS4A6A

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for MS4A6A	Pharmacogenomics, SNPs, Pathways

Intellectual Property for MS4A6A gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for MS4A6A gene:
Search GeneIP for patents involving MS4A6A

GeneCards and IP:
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MS4A6A Gene

membrane-spanning 4-domains, subfamily A, member 6A

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MS4A6A Gene

membrane-spanning 4-domains, subfamily A, member 6A

Aliasesfor MS4A6A gene

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Protein Domains /Familiesfor MS4A6A gene

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for MS4A6A gene

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for MS4A6A gene

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for MS4A6A gene

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Expression
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for MS4A6A gene

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for MS4A6A gene

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for MS4A6A gene