Aliases for VSTM1 Gene

Aliases for VSTM1 Gene

  • V-Set And Transmembrane Domain Containing 1 2 3 5
  • V-Set And Transmembrane Domain-Containing Protein 1 3 4
  • Signal Inhibitory Receptor On Leukocytes-1 3 4
  • UNQ3033 2 3
  • SIRL-1 3 4
  • OSCAR-Like Transcript-1 3
  • LAIR Homolog 3
  • SIRL1 3
  • VSTM1 5

External Ids for VSTM1 Gene

Previous GeneCards Identifiers for VSTM1 Gene

  • GC19M059236
  • GC19M054544
  • GC19M050859

Summaries for VSTM1 Gene

GeneCards Summary for VSTM1 Gene

VSTM1 (V-Set And Transmembrane Domain Containing 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include cytokine activity. An important paralog of this gene is TARM1.

UniProtKB/Swiss-Prot Summary for VSTM1 Gene

  • [Isoform 2]: Behaves as a cytokine, promoting IL17A secretion by CD4+ T-cells, and differentiation and activation of IL17 producing helper T-cells (TH17).
  • [Isoform 1]: Inhibitory immune receptor involved in the regulation of phagocytes.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VSTM1 Gene

Genomics for VSTM1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for VSTM1 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
GH19J054064 Promoter 0.7 EPDnew Ensembl 272.6 +0.1 76 0.2 VSTM1 RF00017-2774 CACNG6
GH19J054062 Promoter 0.5 Ensembl 273.3 +1.2 1165 0.4 SPI1 POLR2A VSTM1 RF00017-2774 HSALNG0127463 CACNG6
GH19J054063 Promoter 0.3 Ensembl 250.7 +0.7 665 0.2 RF00017-2774 VSTM1 CACNG6
GH19J054199 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 13.5 -141.6 -141623 12.4 BCLAF1 SP1 ZNF207 ZNF600 NCOR1 MYC IKZF1 SSRP1 ZNF580 ZNF592 RPS9 HSALNG0127488 PRPF31 LENG8-AS1 LENG8 CNOT3 ZNF525 ENSG00000235681 ZNF845 ZNF761
GH19J054373 Promoter/Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 9.6 -311.0 -310951 2.7 YY1 TRIM22 MAFF ZNF316 CBFB SMARCA5 NFE2 MAFK BHLHE40 SPI1 HSALNG0127520 HSALNG0127521 FCAR LAIR1 LILRB2 OSCAR LILRA5 VSTM1 LILRB3 LILRB4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VSTM1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VSTM1

Top Transcription factor binding sites by QIAGEN in the VSTM1 gene promoter:
  • aMEF-2
  • AREB6
  • c-Rel
  • C/EBPalpha
  • HSF1 (long)
  • HSF1short
  • IRF-2
  • MEF-2
  • MEF-2A
  • SEF-1 (1)

Genomic Locations for VSTM1 Gene

Latest Assembly
chr19:54,040,825-54,063,966
(GRCh38/hg38)
Size:
23,142 bases
Orientation:
Minus strand

Previous Assembly
chr19:54,544,079-54,567,151
(GRCh37/hg19 by Entrez Gene)
Size:
23,073 bases
Orientation:
Minus strand

chr19:54,544,079-54,567,207
(GRCh37/hg19 by Ensembl)
Size:
23,129 bases
Orientation:
Minus strand

Alternative Locations (GRCh38/hg38)

  • chr19(ALT_REF_LOCI_1):15,192-38,264 (-)
  • chr19(ALT_REF_LOCI_2):15,192-38,264 (-)
  • chr19(ALT_REF_LOCI_3):15,192-38,264 (-)
  • chr19(ALT_REF_LOCI_4):15,192-38,264 (-)
  • chr19(ALT_REF_LOCI_5):15,192-38,264 (-)
  • chr19(ALT_REF_LOCI_6):15,192-38,264 (-)
  • chr19(ALT_REF_LOCI_7):15,192-38,264 (-)
  • chr19(ALT_REF_LOCI_8):15,192-38,264 (-)
  • chr19(ALT_REF_LOCI_9):15,192-38,264 (-)

Genomic View for VSTM1 Gene

Genes around VSTM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VSTM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VSTM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VSTM1 Gene

Proteins for VSTM1 Gene

  • Protein details for VSTM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6UX27-VSTM1_HUMAN
    Recommended name:
    V-set and transmembrane domain-containing protein 1
    Protein Accession:
    Q6UX27
    Secondary Accessions:
    • B6A8C6
    • D2DJS3
    • D2DJS4
    • Q496B6
    • Q496B7

    Protein attributes for VSTM1 Gene

    Size:
    236 amino acids
    Molecular mass:
    26109 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • [Isoform 2]: Mainly detected in immune tissues and cells.
    • [Isoform 3]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Alternative splice isoforms for VSTM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VSTM1 Gene

Post-translational modifications for VSTM1 Gene

No data available for DME Specific Peptides for VSTM1 Gene

Domains & Families for VSTM1 Gene

Gene Families for VSTM1 Gene

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

Protein Domains for VSTM1 Gene

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

Suggested Antigen Peptide Sequences for VSTM1 Gene

GenScript: Design optimal peptide antigens:
  • V-set and transmembrane domain containing 1 isoform a (B6A8C6_HUMAN)
  • V-set and transmembrane domain containing 1 isoform b (D2DJS4_HUMAN)
  • V-set and transmembrane domain containing 1 isoform c (D2DJS5_HUMAN)
  • V-set and transmembrane domain containing 1 isoform d (D2DJS6_HUMAN)
  • V-set and transmembrane domain containing 1 isoform e (D2E0V1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6UX27

UniProtKB/Swiss-Prot:

VSTM1_HUMAN :
  • Contains 2 copies of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2-containing phosphatases. Both motives are required for full inhibition of FCER1A-mediated degranulation.
Domain:
  • Contains 2 copies of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2-containing phosphatases. Both motives are required for full inhibition of FCER1A-mediated degranulation.
genes like me logo Genes that share domains with VSTM1: view

Function for VSTM1 Gene

Molecular function for VSTM1 Gene

UniProtKB/Swiss-Prot Function:
[Isoform 2]: Behaves as a cytokine, promoting IL17A secretion by CD4+ T-cells, and differentiation and activation of IL17 producing helper T-cells (TH17).
UniProtKB/Swiss-Prot Function:
[Isoform 1]: Inhibitory immune receptor involved in the regulation of phagocytes.

Phenotypes From GWAS Catalog for VSTM1 Gene

Gene Ontology (GO) - Molecular Function for VSTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005125 cytokine activity IEA --
GO:0005515 protein binding IPI --
genes like me logo Genes that share ontologies with VSTM1: view
genes like me logo Genes that share phenotypes with VSTM1: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VSTM1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for VSTM1 Gene

Localization for VSTM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VSTM1 Gene

[Isoform 1]: Membrane. Single-pass membrane protein.
[Isoform 2]: Secreted.

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 VSTM1 gene
Compartment Confidence
extracellular 4
plasma membrane 3
nucleus 1
mitochondrion 0
peroxisome 0
endoplasmic reticulum 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for VSTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with VSTM1: view

Pathways & Interactions for VSTM1 Gene

PathCards logo

SuperPathways for VSTM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VSTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002376 immune system process IEA --
GO:0007165 signal transduction IEA --
genes like me logo Genes that share ontologies with VSTM1: view

No data available for Pathways by source and SIGNOR curated interactions for VSTM1 Gene

Drugs & Compounds for VSTM1 Gene

No Compound Related Data Available

Transcripts for VSTM1 Gene

mRNA/cDNA for VSTM1 Gene

4 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VSTM1

Alternative Splicing Database (ASD) splice patterns (SP) for VSTM1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5
SP1:
SP2: -

Relevant External Links for VSTM1 Gene

GeneLoc Exon Structure for
VSTM1

Expression for VSTM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VSTM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VSTM1 Gene

This gene is overexpressed in Whole Blood (x42.3) and Pituitary (x4.3).

Protein differential expression in normal tissues from HIPED for VSTM1 Gene

This gene is overexpressed in Monocytes (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VSTM1 Gene



Protein tissue co-expression partners for VSTM1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VSTM1

SOURCE GeneReport for Unigene cluster for VSTM1 Gene:

Hs.444431

mRNA Expression by UniProt/SwissProt for VSTM1 Gene:

Q6UX27-VSTM1_HUMAN
Tissue specificity: Expressed on myeloid (neutrophils, eosinophils and monocytes) but not on lymphoid cells.

Evidence on tissue expression from TISSUES for VSTM1 Gene

  • Bone marrow(4.5)
  • Spleen(4.4)
  • Blood(4.3)
genes like me logo Genes that share expression patterns with VSTM1: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for VSTM1 Gene

Orthologs for VSTM1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for VSTM1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia VSTM1 29 30
  • 99.09 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia VSTM1 29 30
  • 78.12 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia LOC100360054 29
  • 67.93 (n)
Cow
(Bos Taurus)
Mammalia VSTM1 30
  • 45 (a)
OneToOne
Species where no ortholog for VSTM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Chicken (Gallus gallus)
  • 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)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)
  • Zebrafish (Danio rerio)

Evolution for VSTM1 Gene

ENSEMBL:
Gene Tree for VSTM1 (if available)
TreeFam:
Gene Tree for VSTM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VSTM1: view image
Alliance of Genome Resources:
Additional Orthologs for VSTM1

Paralogs for VSTM1 Gene

(10) SIMAP similar genes for VSTM1 Gene using alignment to 9 proteins:

  • VSTM1_HUMAN
  • B6A8C6_HUMAN
  • D2DJS4_HUMAN
  • D2DJS5_HUMAN
  • D2DJS6_HUMAN
  • D2E0V1_HUMAN
  • F5GZW9_HUMAN
  • G8JLN4_HUMAN
  • H7C340_HUMAN
genes like me logo Genes that share paralogs with VSTM1: view

Variants for VSTM1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VSTM1 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs2433724 -- p.Ser163Gly

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for VSTM1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for VSTM1 Gene

Variant ID Type Subtype PubMed ID
dgv6541n54 CNV loss 21841781
dgv6542n54 CNV loss 21841781
dgv6543n54 CNV loss 21841781
dgv6544n54 CNV loss 21841781
dgv6545n54 CNV loss 21841781
dgv6546n54 CNV loss 21841781
dgv663e199 CNV deletion 23128226
esv2552009 CNV deletion 19546169
esv2595621 CNV loss 19546169
esv2718812 CNV deletion 23290073
esv2718849 CNV deletion 23290073
esv27833 CNV gain 19812545
esv3556612 CNV deletion 23714750
esv3644779 CNV loss 21293372
esv3644780 CNV gain 21293372
esv987659 CNV gain 20482838
esv995580 CNV gain 20482838
nsv1057516 CNV gain 25217958
nsv1063127 CNV gain 25217958
nsv1071550 CNV deletion 25765185
nsv1114033 CNV deletion 24896259
nsv182 CNV deletion 15895083
nsv2542 CNV deletion 18451855
nsv435707 CNV deletion 17901297
nsv458782 CNV gain 19166990
nsv498905 CNV loss 21111241
nsv510773 CNV deletion 20534489
nsv580110 CNV gain 21841781
nsv580137 CNV loss 21841781
nsv819771 CNV gain 19587683
nsv820269 CNV gain 19587683
nsv820902 CNV deletion 20802225
nsv828625 CNV loss 20364138
nsv833877 CNV loss 17160897
nsv956562 CNV deletion 24416366
nsv9750 CNV gain 18304495

Variation tolerance for VSTM1 Gene

Residual Variation Intolerance Score: 50.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.64; 78.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VSTM1 Gene

Human Gene Mutation Database (HGMD)
VSTM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VSTM1
Leiden Open Variation Database (LOVD)
VSTM1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VSTM1 Gene

Disorders for VSTM1 Gene

Additional Disease Information for VSTM1

No disorders were found for VSTM1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VSTM1 Gene

Publications for VSTM1 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4
  2. Signal inhibitory receptor on leukocytes-1 is a novel functional inhibitory immune receptor expressed on human phagocytes. (PMID: 20375307) Steevels TA … Meyaard L (Journal of immunology (Baltimore, Md. : 1950) 2010) 3 4
  3. 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
  4. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PMID: 15340161) Zhang Z … Henzel WJ (Protein science : a publication of the Protein Society 2004) 3 4
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for VSTM1 Gene

Sources for VSTM1 Gene