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MS4A12 membrane spanning 4-domains A12 [ Homo sapiens (human) ]

Gene ID: 54860, updated on 27-Nov-2024

Summary

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Official Symbol
MS4A12provided by HGNC
Official Full Name
membrane spanning 4-domains A12provided by HGNC
Primary source
HGNC:HGNC:13370
See related
Ensembl:ENSG00000071203 MIM:606550; AllianceGenome:HGNC:13370
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
Ms4a10
Summary
The protein encoded by this gene is a cell surface protein found primarily in the apical membrane of colonocytes. Silencing of this gene in colon cancer cells inhibits the proliferation, cell motility, and chemotactic invasion of cells. This gene is part of a cluster of similar genes found on chromosome 11. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]
Expression
Restricted expression toward colon (RPKM 119.7) See more
Orthologs
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Genomic context

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See MS4A12 in Genome Data Viewer
Location:
11q12.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (60492778..60507430)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (60443950..60458574)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (60260251..60274903)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene membrane spanning 4-domains A5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4770 Neighboring gene membrane spanning 4-domains A1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:60258497-60259236 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:60259237-60259974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4772 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3372 Neighboring gene membrane spanning 4-domains A13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4773 Neighboring gene membrane spanning 4-domains A19, pseudogene Neighboring gene uncharacterized LOC105369321

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. Decreased expression of MS4A12 inhibits differentiation and predicts early stage survival in colon cancer. He L, et al. Neoplasma, 2017. PMID 27881006
  2. MS4A12 is a colon-selective store-operated calcium channel promoting malignant cell processes. Koslowski M, et al. Cancer Res, 2008 May 1. PMID 18451174
  3. CLCA4 and MS4A12 as the significant gene biomarkers of primary colorectal cancer. Han J, et al. Biosci Rep, 2020 Aug 28. PMID 32797167, Free PMC Article
  4. Selective activation of tumor growth-promoting Ca2+ channel MS4A12 in colon cancer by caudal type homeobox transcription factor CDX2. Koslowski M, et al. Mol Cancer, 2009 Sep 25. PMID 19781065, 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 (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CLCA4 and MS4A12 as the significant gene biomarkers of primary colorectal cancer.
    Title: CLCA4 and MS4A12 as the significant gene biomarkers of primary colorectal cancer.
  2. In early stage colon cancer, the patients with low MS4A12 expression had a poor survival, while in advanced stage colon cancer MS412 had little prognostic value.
    Title: Decreased expression of MS4A12 inhibits differentiation and predicts early stage survival in colon cancer.
  3. RNA interference of CDX1 and CDX2 and chromatin immunoprecipitation in colon cancer cells revealed that MS4A12 transcript and protein expression is essentially dependent on the presence of endogenous CDX2.
    Title: Selective activation of tumor growth-promoting Ca2+ channel MS4A12 in colon cancer by caudal type homeobox transcription factor CDX2.
  4. MS4A12 is a colon-selective store-operated calcium channel promoting malignant cell processes.
    Title: MS4A12 is a colon-selective store-operated calcium channel promoting malignant cell processes.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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
  

General protein information

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Preferred Names
membrane-spanning 4-domains subfamily A member 12

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_001164470.2 → NP_001157942.1  membrane-spanning 4-domains subfamily A member 12 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AK000224, BP262076, BP262976
    Consensus CDS
    CCDS53638.1
    UniProtKB/Swiss-Prot
    Q9NXJ0
    Related
    ENSP00000440424.1, ENST00000537076.5
    Conserved Domains (1) summary
    pfam04103
    Location:93 → 175
    CD20; CD20-like family

  2. NM_017716.3 → NP_060186.2  membrane-spanning 4-domains subfamily A member 12 isoform 1

    See identical proteins and their annotated locations for NP_060186.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK000224, BP262076
    Consensus CDS
    CCDS7988.1
    UniProtKB/Swiss-Prot
    F5GX98, Q8N6L4, Q9NXJ0
    Related
    ENSP00000016913.4, ENST00000016913.8
    Conserved Domains (1) summary
    pfam04103
    Location:90 → 221
    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
    60492778..60507430
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545117.3 → XP_011543419.1  membrane-spanning 4-domains subfamily A member 12 isoform X1

    See identical proteins and their annotated locations for XP_011543419.1

    UniProtKB/Swiss-Prot
    F5GX98, Q8N6L4, Q9NXJ0
    Conserved Domains (1) summary
    pfam04103
    Location:90 → 221
    CD20; CD20-like family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    60443950..60458574
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NXJ0.2 GenPept UniProtKB/Swiss-Prot:Q9NXJ0

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