Aliases for VSTM4 Gene

Aliases for VSTM4 Gene

  • V-Set And Transmembrane Domain Containing 4 2 3 5
  • V-Set And Transmembrane Domain-Containing Protein 4 3 4
  • C10orf72 3 4
  • Chromosome 10 Open Reading Frame 72 2

External Ids for VSTM4 Gene

Previous HGNC Symbols for VSTM4 Gene

  • C10orf72

Previous GeneCards Identifiers for VSTM4 Gene

  • GC10M050223

Summaries for VSTM4 Gene

GeneCards Summary for VSTM4 Gene

VSTM4 (V-Set And Transmembrane Domain Containing 4) is a Protein Coding gene. Diseases associated with VSTM4 include Lysosomal Acid Lipase Deficiency and Lysosomal And Lipase Deficiency. An important paralog of this gene is IGSF3.

UniProtKB/Swiss-Prot Summary for VSTM4 Gene

  • Peptide Lv enhances L-type voltage-gated calcium channel (L-VGCC) currents in retinal photoreceptors.

Additional gene information for VSTM4 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VSTM4 Gene

Genomics for VSTM4 Gene

GeneHancer (GH) Regulatory Elements for VSTM4 Gene

Promoters and enhancers for VSTM4 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
GH10J049113 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.4 +14.4 14393 2.5 ZNF639 ZIC2 ZBTB26 REST CTBP1 HDAC2 RBM25 KDM5B ZNF282 SMC3 VSTM4 FAM170B LRRC18 FAM170B-AS1 piR-33313-002
GH10J049186 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 500.2 -59.9 -59861 4.8 NRF1 USF1 EP300 POLR2A AFF1 REST USF2 TOE1 MYC CTBP1 TMEM273 lnc-FAM170B-1 VSTM4 piR-47086-034
GH10J050067 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 9.9 -939.3 -939257 3.2 ZBTB40 ZNF217 EP300 POLR2G USF1 SP1 ZFX ZNF639 ZNF10 ZIC2 WASHC2A FAM21EP lnc-PARG-1 PGBD3 TIMM23B-AGAP6 PARG RNA5SP317 AGAP6 SGMS1 BEND3P1
GH10J049008 Enhancer 0.8 Ensembl ENCODE 17.3 +119.1 119143 4.4 POLR2G POLR2A PBX2 NR2F2 NR2F1 GATA2 MITF NR2F6 SMARCA4 MEIS2 VSTM4 FAM170B ENSG00000226576 FAM170B-AS1 WDFY4 DRGX LRRC18 ENSG00000241577 lnc-LRRC18-110 ENSG00000233665
GH10J049052 Enhancer 1.1 Ensembl ENCODE dbSUPER 11.5 +74.1 74058 4.6 ZIC2 RELA MEF2C BCL11A TCF12 NFIC CTCF POLR2A FOS SRF FAM170B VSTM4 piR-43324 lnc-WDFY4-5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VSTM4 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VSTM4

Genomic Locations for VSTM4 Gene

Genomic Locations for VSTM4 Gene
chr10:49,014,236-49,129,144
(GRCh38/hg38)
Size:
114,909 bases
Orientation:
Minus strand
chr10:50,222,290-50,323,559
(GRCh37/hg19)
Size:
101,270 bases
Orientation:
Minus strand

Genomic View for VSTM4 Gene

Genes around VSTM4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VSTM4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VSTM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VSTM4 Gene

Proteins for VSTM4 Gene

  • Protein details for VSTM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IW00-VSTM4_HUMAN
    Recommended name:
    V-set and transmembrane domain-containing protein 4
    Protein Accession:
    Q8IW00
    Secondary Accessions:
    • B4DNI6
    • Q96MX7

    Protein attributes for VSTM4 Gene

    Size:
    320 amino acids
    Molecular mass:
    36146 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for VSTM4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VSTM4 Gene

Post-translational modifications for VSTM4 Gene

  • Proteolytically cleaved to generate a bioactive peptide.
  • Glycosylation at Asn25, Asn41, Asn89, and Asn144
  • Modification sites at PhosphoSitePlus

Other Protein References for VSTM4 Gene

No data available for DME Specific Peptides for VSTM4 Gene

Domains & Families for VSTM4 Gene

Gene Families for VSTM4 Gene

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

Protein Domains for VSTM4 Gene

Suggested Antigen Peptide Sequences for VSTM4 Gene

GenScript: Design optimal peptide antigens:
  • Uncharacterized Ig-like domain-containing protein C10orf72 (CJ072_HUMAN)
genes like me logo Genes that share domains with VSTM4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for VSTM4 Gene

Function for VSTM4 Gene

Molecular function for VSTM4 Gene

UniProtKB/Swiss-Prot Function:
Peptide Lv enhances L-type voltage-gated calcium channel (L-VGCC) currents in retinal photoreceptors.

Phenotypes From GWAS Catalog for VSTM4 Gene

genes like me logo Genes that share phenotypes with VSTM4: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VSTM4 Gene

Localization for VSTM4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VSTM4 Gene

[Peptide Lv]: Secreted.
Cell membrane; Single-pass type I membrane protein.

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 VSTM4 gene
Compartment Confidence
plasma membrane 4
extracellular 3
peroxisome 1
mitochondrion 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VSTM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IBA 21873635
genes like me logo Genes that share ontologies with VSTM4: view

Pathways & Interactions for VSTM4 Gene

PathCards logo

SuperPathways for VSTM4 Gene

No Data Available

Interacting Proteins for VSTM4 Gene

;

Gene Ontology (GO) - Biological Process for VSTM4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for VSTM4 Gene

Drugs & Compounds for VSTM4 Gene

No Compound Related Data Available

Transcripts for VSTM4 Gene

mRNA/cDNA for VSTM4 Gene

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

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VSTM4 Gene

No ASD Table

Relevant External Links for VSTM4 Gene

GeneLoc Exon Structure for
VSTM4

Expression for VSTM4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VSTM4 Gene

mRNA differential expression in normal tissues according to GTEx for VSTM4 Gene

This gene is overexpressed in Adrenal Gland (x4.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VSTM4 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VSTM4

SOURCE GeneReport for Unigene cluster for VSTM4 Gene:

Hs.522928

Evidence on tissue expression from TISSUES for VSTM4 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with VSTM4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VSTM4 Gene

Orthologs for VSTM4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for VSTM4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VSTM4 31 30
  • 98.75 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VSTM4 31 30
  • 88.82 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Vstm4 17 31 30
  • 86.82 (n)
rat
(Rattus norvegicus)
Mammalia Vstm4 30
  • 85.94 (n)
dog
(Canis familiaris)
Mammalia VSTM4 31 30
  • 85.42 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 80 (a)
OneToMany
-- 31
  • 57 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia VSTM4 31
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves VSTM4 31 30
  • 68.67 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VSTM4 31
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vstm4 30
  • 54.05 (n)
zebrafish
(Danio rerio)
Actinopterygii vstm4b 31 30
  • 57.22 (n)
OneToMany
vstm4a 31
  • 44 (a)
OneToMany
Species where no ortholog for VSTM4 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)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for VSTM4 Gene

ENSEMBL:
Gene Tree for VSTM4 (if available)
TreeFam:
Gene Tree for VSTM4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VSTM4: view image

Paralogs for VSTM4 Gene

Paralogs for VSTM4 Gene

genes like me logo Genes that share paralogs with VSTM4: view

Variants for VSTM4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VSTM4 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
rs138454994 A colorectal cancer sample p.Arg100His
rs13088 - p.Phe68Ser
rs17854124 - p.Lys243Arg

Additional dbSNP identifiers (rs#s) for VSTM4 Gene

Structural Variations from Database of Genomic Variants (DGV) for VSTM4 Gene

Variant ID Type Subtype PubMed ID
esv21974 CNV loss 19812545
esv2761593 CNV gain 21179565
esv2845 CNV loss 18987735
esv3546257 CNV deletion 23714750
esv3578863 CNV loss 25503493
esv3623162 CNV loss 21293372
esv3623163 CNV loss 21293372
esv3623164 CNV loss 21293372
esv6657 CNV loss 19470904
nsv1042677 CNV loss 25217958
nsv1068311 CNV deletion 25765185
nsv1120083 OTHER inversion 24896259
nsv1122526 CNV deletion 24896259
nsv1140452 CNV tandem duplication 24896259
nsv1148869 CNV deletion 26484159
nsv522731 CNV loss 19592680
nsv550817 CNV loss 21841781
nsv550818 CNV gain 21841781
nsv6620 CNV deletion 18451855
nsv831866 CNV gain+loss 17160897

Variation tolerance for VSTM4 Gene

Residual Variation Intolerance Score: 90.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.21; 76.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VSTM4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VSTM4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VSTM4 Gene

Disorders for VSTM4 Gene

MalaCards: The human disease database

(3) MalaCards diseases for VSTM4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
lysosomal acid lipase deficiency
  • cholesteryl ester storage disease; cesd
lysosomal and lipase deficiency
vesicoureteral reflux 1
  • vur1
- elite association - COSMIC cancer census association via MalaCards
Search VSTM4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VSTM4

genes like me logo Genes that share disorders with VSTM4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VSTM4 Gene

Publications for VSTM4 Gene

  1. 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
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  3. Genome-wide meta-analysis identifies new susceptibility loci for migraine. (PMID: 23793025) Anttila V … Palotie A (Nature genetics 2013) 3 54
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3 54
  5. Identification of the human testis protein phosphatase 1 interactome. (PMID: 21382349) Fardilha M … da Cruz e Silva EF (Biochemical pharmacology 2011) 3 54

Products for VSTM4 Gene

Sources for VSTM4 Gene