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

    Gene ID: 222008, updated on 10-Dec-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 active in membrane. [provided by Alliance of Genome Resources, Dec 2024]
    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_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (54542375..54571067)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (54702348..54731660)
    RS_2024_09 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. Gene of the month: VSTM2A. Wang L, et al. J Clin Pathol, 2024 Jan 18. PMID 38124011
    2. 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
    3. VSTM2A suppresses colorectal cancer and antagonizes Wnt signaling receptor LRP6. Dong Y, et al. Theranostics, 2019. PMID 31588233, Free PMC Article
    4. Amplification of Adipogenic Commitment by VSTM2A. Secco B, et al. Cell Rep, 2017 Jan 3. PMID 28052263, Free PMC Article
    5. 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

    See all (15) 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)

    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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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_2024_08

    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

      UniProtKB/TrEMBL
      B5MCX6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TAG5.3 GenPept UniProtKB/Swiss-Prot:Q8TAG5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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