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VSTM2A V-set and transmembrane domain containing 2A [ Homo sapiens (human) ]

Gene ID: 222008, updated on 11-Apr-2024

Summary

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Official Symbol
VSTM2Aprovided by HGNC
Official Full Name
V-set and transmembrane domain containing 2Aprovided by HGNC
Primary source
HGNC:HGNC:28499
See related
Ensembl:ENSG00000170419 AllianceGenome:HGNC:28499
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
Also known as
VSTM2
Summary
Predicted to enable identical protein binding activity. Involved in several processes, including positive regulation of brown fat cell differentiation; positive regulation of lipid storage; and positive regulation of white fat cell proliferation. Predicted to be located in extracellular region. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 3.8), prostate (RPKM 1.6) and 4 other tissues See more
Orthologs
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Genomic context

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See VSTM2A in Genome Data Viewer
Location:
7p11.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (54542375..54571067)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (54702348..54731660)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (54610068..54638760)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene solute carrier family 25 member 5 pseudogene 3 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:54582481-54583680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:54609706-54610206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:54612500-54613012 Neighboring gene VSTM2A overlapping transcript 1 Neighboring gene uncharacterized LOC124901635 Neighboring gene RNA, U6 small nuclear 1125, pseudogene

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. VSTM2A Overexpression Is a Sensitive and Specific Biomarker for Mucinous Tubular and Spindle Cell Carcinoma (MTSCC) of the Kidney. Wang L, et al. Am J Surg Pathol, 2018 Dec. PMID 30285995, Free PMC Article
  2. VSTM2A suppresses colorectal cancer and antagonizes Wnt signaling receptor LRP6. Dong Y, et al. Theranostics, 2019. PMID 31588233, Free PMC Article
  3. Amplification of Adipogenic Commitment by VSTM2A. Secco B, et al. Cell Rep, 2017 Jan 3. PMID 28052263, Free PMC Article
  4. Expressed sequence tag analysis of human retina for the NEIBank Project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts. Wistow G, et al. Mol Vis, 2002 Jun 15. PMID 12107411
  5. Charting the molecular links between driver and susceptibility genes in colorectal cancer. Arroyo R, et al. Biochem Biophys Res Commun, 2014 Mar 21. PMID 24412244

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Gene of the month: VSTM2A.
    Title: Gene of the month: VSTM2A.
  2. VSTM2A suppresses colorectal cancer and antagonizes Wnt signaling receptor LRP6.
    Title: VSTM2A suppresses colorectal cancer and antagonizes Wnt signaling receptor LRP6.
  3. VSTM2A overexpression to be a sensitive and specific marker for mucinous tubular and spindle cell carcinoma of the kidney.
    Title: VSTM2A Overexpression Is a Sensitive and Specific Biomarker for Mucinous Tubular and Spindle Cell Carcinoma (MTSCC) of the Kidney.
  4. VSTM2A is produced to preserve and amplify the adipogenic capability of adipose precursors.
    Title: Amplification of Adipogenic Commitment by VSTM2A.
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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC33530

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to BMP stimulus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of brown fat cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of lipid storage IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of white fat cell proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in extracellular region ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
NOT located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
V-set and transmembrane domain-containing protein 2A
Names
V-set and transmembrane domain containing 2
hypothetical protein MGC33530

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_001301009.2 → NP_001287938.1  V-set and transmembrane domain-containing protein 2A isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region due to the use of an alternate splice site in the 3'-terminal exon, compared to variant 1. The encoded isoform (2) has a longer and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BI458531, BI752069, BI758069, BQ639021, DN991972, EY892386
    Consensus CDS
    CCDS75604.1
    UniProtKB/TrEMBL
    F8W8J5
    Related
    ENSP00000384103.3, ENST00000402613.4
    Conserved Domains (2) summary
    smart00410
    Location:33 → 148
    IG_like; Immunoglobulin like
    cl11960
    Location:33 → 138
    Ig; Immunoglobulin domain

  2. NM_001317843.2 → NP_001304772.1  V-set and transmembrane domain-containing protein 2A isoform 3 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks one exon, and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC069313, BC028404, BI553644, BI755592
    Consensus CDS
    CCDS83185.1
    UniProtKB/Swiss-Prot
    Q8TAG5
    Related
    ENSP00000303108.3, ENST00000302287.7
    Conserved Domains (2) summary
    smart00410
    Location:33 → 148
    IG_like; Immunoglobulin like
    cl11960
    Location:33 → 138
    Ig; Immunoglobulin domain

  3. NM_182546.4 → NP_872352.2  V-set and transmembrane domain-containing protein 2A isoform 1 precursor

    See identical proteins and their annotated locations for NP_872352.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the shortest isoform (1).
    Source sequence(s)
    BI458531, BI752069, BI754879, BQ639021, DN991972, EY892386
    Consensus CDS
    CCDS5512.2
    UniProtKB/Swiss-Prot
    A4D2E9, B5MC94, Q8TAG5
    Related
    ENSP00000384967.3, ENST00000407838.7
    Conserved Domains (2) summary
    smart00410
    Location:33 → 148
    IG_like; Immunoglobulin like
    cl11960
    Location:33 → 138
    Ig; Immunoglobulin domain

RNA

  1. NR_133927.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks several exons, uses an alternate 5'-terminal exon, and an alternate splice site in the 3'-terminal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AC069313, AI340204, BI458531, BI667944, BX451729, EY892386

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    54542375..54571067
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715665.4 → XP_006715728.1  V-set and transmembrane domain-containing protein 2A isoform X2

    Conserved Domains (2) summary
    smart00410
    Location:33 → 148
    IG_like; Immunoglobulin like
    cl11960
    Location:33 → 138
    Ig; Immunoglobulin domain

  2. XM_006715666.4 → XP_006715729.1  V-set and transmembrane domain-containing protein 2A isoform X3

    Conserved Domains (2) summary
    smart00410
    Location:33 → 148
    IG_like; Immunoglobulin like
    cl11960
    Location:33 → 138
    Ig; Immunoglobulin domain

  3. XM_017011841.2 → XP_016867330.1  V-set and transmembrane domain-containing protein 2A isoform X1

    UniProtKB/TrEMBL
    B5MCX6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    54702348..54731660
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357566.1 → XP_054213541.1  V-set and transmembrane domain-containing protein 2A isoform X3

  2. XM_054357565.1 → XP_054213540.1  V-set and transmembrane domain-containing protein 2A isoform X2

  3. XM_054357564.1 → XP_054213539.1  V-set and transmembrane domain-containing protein 2A isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TAG5.3 GenPept UniProtKB/Swiss-Prot:Q8TAG5

Gene LinkOut

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