Aliases for VSTM2A Gene

Aliases for VSTM2A Gene

  • V-Set And Transmembrane Domain Containing 2A 2 3 5
  • V-Set And Transmembrane Domain-Containing Protein 2A 3 4
  • V-Set And Transmembrane Domain Containing 2 2 3
  • VSTM2 3 4
  • Hypothetical Protein MGC33530 3

External Ids for VSTM2A Gene

Previous HGNC Symbols for VSTM2A Gene

  • VSTM2

Previous GeneCards Identifiers for VSTM2A Gene

  • GC07P054578
  • GC07P054447

Summaries for VSTM2A Gene

GeneCards Summary for VSTM2A Gene

VSTM2A (V-Set And Transmembrane Domain Containing 2A) is a Protein Coding gene. An important paralog of this gene is CD101.

UniProtKB/Swiss-Prot Summary for VSTM2A Gene

  • Plays a role in the regulation of the early stage of white and brown preadipocyte cell differentiation. Promotes adipogenic commitment of preadipocytes by increasing gene expression of the transcription factor PPARG in a BMP4-dependent signaling pathway.

Additional gene information for VSTM2A Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VSTM2A Gene

Genomics for VSTM2A Gene

GeneHancer (GH) Regulatory Elements for VSTM2A Gene

Promoters and enhancers for VSTM2A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07J054541 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.2 190 1.8 EP300 CTCF REST ZBTB26 HDAC2 EZH2 SMC3 ZBTB17 MXI1 YY1 VSTM2A lnc-SEC61G-9
GH07J054291 Enhancer 0.7 Ensembl ENCODE 6.8 -249.9 -249924 1.2 EP300 SMC3 NANOG RAD21 CTCF MAFK BACH1 POLR2A EZH2 VSTM2A lnc-VSTM2A-4 ENSG00000287953
GH07J054572 Enhancer 0.2 Ensembl 11.1 +30.5 30476 0.4 VSTM2A ENSG00000228735 VSTM2A-OT1
GH07J054278 Enhancer 0.2 Ensembl 5.2 -263.1 -263124 2 VSTM2A lnc-VSTM2A-4 ENSG00000287953
GH07J054545 Promoter/Enhancer 1.1 Ensembl ENCODE 0.7 +4.5 4475 1.2 CTCF GABPA ZBTB26 GATAD2B MXI1 ZNF341 MYC SMC3 SP2 ZBTB17 lnc-SEC61G-9 VSTM2A VSTM2A-OT1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VSTM2A on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VSTM2A

Top Transcription factor binding sites by QIAGEN in the VSTM2A gene promoter:
  • FOXD3
  • HOXA9
  • HOXA9B
  • Meis-1
  • Meis-1a
  • RORalpha1
  • SRY

Genomic Locations for VSTM2A Gene

Genomic Locations for VSTM2A Gene
chr7:54,542,325-54,571,080
(GRCh38/hg38)
Size:
28,756 bases
Orientation:
Plus strand
chr7:54,610,018-54,638,773
(GRCh37/hg19)
Size:
28,756 bases
Orientation:
Plus strand

Genomic View for VSTM2A Gene

Genes around VSTM2A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VSTM2A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VSTM2A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VSTM2A Gene

Proteins for VSTM2A Gene

  • Protein details for VSTM2A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TAG5-VTM2A_HUMAN
    Recommended name:
    V-set and transmembrane domain-containing protein 2A
    Protein Accession:
    Q8TAG5
    Secondary Accessions:
    • A4D2E9
    • B5MC94

    Protein attributes for VSTM2A Gene

    Size:
    236 amino acids
    Molecular mass:
    25833 Da
    Quaternary structure:
    • Homodimer.
    SequenceCaution:
    • Sequence=AAH28404.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=EAL23809.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for VSTM2A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VSTM2A Gene

Post-translational modifications for VSTM2A Gene

  • N-glycosylated. N-linked glycosylation is critical for secretion but not for preadipocyte cell differentiation activity.
  • Glycosylation at Asn35 and Asn175
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VSTM2A Gene

Domains & Families for VSTM2A Gene

Gene Families for VSTM2A Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted secreted proteins

Protein Domains for VSTM2A Gene

Blocks:
  • Immunoglobulin subtype
  • Immunoglobulin V-set
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VSTM2A Gene

GenScript: Design optimal peptide antigens:
  • V-set and transmembrane domain-containing protein 2A (VTM2A_HUMAN)
genes like me logo Genes that share domains with VSTM2A: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for VSTM2A Gene

Function for VSTM2A Gene

Molecular function for VSTM2A Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the regulation of the early stage of white and brown preadipocyte cell differentiation. Promotes adipogenic commitment of preadipocytes by increasing gene expression of the transcription factor PPARG in a BMP4-dependent signaling pathway.

Phenotypes From GWAS Catalog for VSTM2A Gene

Gene Ontology (GO) - Molecular Function for VSTM2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042802 identical protein binding ISS --
genes like me logo Genes that share ontologies with VSTM2A: view
genes like me logo Genes that share phenotypes with VSTM2A: view

Animal Model Products

  • Taconic Biosciences Mouse Models for VSTM2A

miRNA for VSTM2A Gene

miRTarBase miRNAs that target VSTM2A

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VSTM2A Gene

Localization for VSTM2A Gene

Subcellular locations from UniProtKB/Swiss-Prot for VSTM2A Gene

Secreted. Note=Secreted by adipose precursor cells (By similarity). Not detected in the nucleus (PubMed:28052263). {ECO:0000250 UniProtKB:Q8R0A6}.

Subcellular locations from

COMPARTMENTS
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 VSTM2A gene
Compartment Confidence
extracellular 4
plasma membrane 1
nucleus 1
endoplasmic reticulum 0

Gene Ontology (GO) - Cellular Components for VSTM2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region ISS --
GO:0005634 NOT nucleus IDA 28052263
GO:0016021 integral component of membrane IBA 21873635
genes like me logo Genes that share ontologies with VSTM2A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VSTM2A Gene

Pathways & Interactions for VSTM2A Gene

PathCards logo

SuperPathways for VSTM2A Gene

No Data Available

Interacting Proteins for VSTM2A Gene

;

Gene Ontology (GO) - Biological Process for VSTM2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010628 positive regulation of gene expression IMP 28052263
GO:0010884 positive regulation of lipid storage IMP 28052263
GO:0030154 cell differentiation IEA --
GO:0070352 positive regulation of white fat cell proliferation IMP 28052263
GO:0071773 cellular response to BMP stimulus ISS --
genes like me logo Genes that share ontologies with VSTM2A: view

No data available for Pathways by source and SIGNOR curated interactions for VSTM2A Gene

Drugs & Compounds for VSTM2A Gene

No Compound Related Data Available

Transcripts for VSTM2A Gene

mRNA/cDNA for VSTM2A Gene

3 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VSTM2A Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c
SP1: - - -
SP2: - - -
SP3: - -
SP4: - -
SP5: -

Relevant External Links for VSTM2A Gene

GeneLoc Exon Structure for
VSTM2A

Expression for VSTM2A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VSTM2A Gene

mRNA differential expression in normal tissues according to GTEx for VSTM2A Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x9.3), Brain - Anterior cingulate cortex (BA24) (x7.1), Brain - Nucleus accumbens (basal ganglia) (x6.5), Brain - Cortex (x6.0), Brain - Hypothalamus (x5.2), Brain - Amygdala (x4.5), and Brain - Caudate (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for VSTM2A Gene

This gene is overexpressed in Vitreous humor (34.5) and Cerebrospinal fluid (34.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VSTM2A Gene



Protein tissue co-expression partners for VSTM2A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VSTM2A

SOURCE GeneReport for Unigene cluster for VSTM2A Gene:

Hs.335933

Evidence on tissue expression from TISSUES for VSTM2A Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with VSTM2A: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VSTM2A Gene

Orthologs for VSTM2A Gene

This gene was present in the common ancestor of chordates.

Orthologs for VSTM2A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VSTM2A 31 30
  • 94.2 (n)
OneToOne
dog
(Canis familiaris)
Mammalia VSTM2A 31 30
  • 92.42 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VSTM2A 31 30
  • 90.05 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Vstm2a 17 31 30
  • 89.83 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VSTM2A 31
  • 83 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VSTM2A 31
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves VSTM2A 31 30
  • 80.97 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VSTM2A 31
  • 74 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii zgc:110852 30
  • 62.85 (n)
VSTM2A (1 of 2) 31
  • 51 (a)
OneToMany
VSTM2A (2 of 2) 31
  • 46 (a)
OneToMany
Species where no ortholog for VSTM2A 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)

Evolution for VSTM2A Gene

ENSEMBL:
Gene Tree for VSTM2A (if available)
TreeFam:
Gene Tree for VSTM2A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VSTM2A: view image

Paralogs for VSTM2A Gene

Paralogs for VSTM2A Gene

(2) SIMAP similar genes for VSTM2A Gene using alignment to 3 proteins:

  • VTM2A_HUMAN
  • B5MCX6_HUMAN
  • F8W8J5_HUMAN
genes like me logo Genes that share paralogs with VSTM2A: view

Variants for VSTM2A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VSTM2A Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
rs17855529 - p.Glu84Lys

Additional dbSNP identifiers (rs#s) for VSTM2A Gene

Structural Variations from Database of Genomic Variants (DGV) for VSTM2A Gene

Variant ID Type Subtype PubMed ID
esv2272226 CNV deletion 18987734
esv2734425 CNV deletion 23290073
nsv1024361 CNV gain 25217958
nsv475524 CNV novel sequence insertion 20440878
nsv950218 CNV deletion 24416366

Variation tolerance for VSTM2A Gene

Residual Variation Intolerance Score: 55.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.64; 45.59% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VSTM2A Gene

Human Gene Mutation Database (HGMD)
VSTM2A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VSTM2A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VSTM2A Gene

Disorders for VSTM2A Gene

Additional Disease Information for VSTM2A

No disorders were found for VSTM2A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VSTM2A Gene

Publications for VSTM2A Gene

  1. Amplification of Adipogenic Commitment by VSTM2A. (PMID: 28052263) Secco B … Laplante M (Cell reports 2017) 2 3 4 54
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  3. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer SW … Tsui LC (Science (New York, N.Y.) 2003) 3 4 54
  4. VSTM2A Overexpression Is a Sensitive and Specific Biomarker for Mucinous Tubular and Spindle Cell Carcinoma (MTSCC) of the Kidney. (PMID: 30285995) Wang L … Mehra R (The American journal of surgical pathology 2018) 3 54
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54

Products for VSTM2A Gene

Sources for VSTM2A Gene