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VSTM4 V-set and transmembrane domain containing 4 [ Homo sapiens (human) ]

Gene ID: 196740, updated on 11-Apr-2024

Summary

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Official Symbol
VSTM4provided by HGNC
Official Full Name
V-set and transmembrane domain containing 4provided by HGNC
Primary source
HGNC:HGNC:26470
See related
Ensembl:ENSG00000165633 AllianceGenome:HGNC:26470
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
C10orf72
Summary
Predicted to act upstream of or within several processes, including endothelial cell migration; retina blood vessel maintenance; and vasculature development. Predicted to be located in extracellular region and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in adrenal (RPKM 18.4), ovary (RPKM 14.7) and 19 other tissues See more
Orthologs
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Genomic context

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See VSTM4 in Genome Data Viewer
Location:
10q11.23
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (49014236..49115522, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (49863442..49964410, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (50222281..50323567, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene WDFY family member 4 Neighboring gene leucine rich repeat containing 18 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:50156438-50157637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50160179-50160678 Neighboring gene uncharacterized LOC105378298 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:50219965-50220220 Neighboring gene microRNA 4294 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3345 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:50264962-50265148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50316573-50317551 Neighboring gene uncharacterized LOC124902545 Neighboring gene FAM170B antisense RNA 1 Neighboring gene family with sequence similarity 170 member B

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. A genome-wide association study of serum uric acid in African Americans. Charles BA, et al. BMC Med Genomics, 2011 Feb 4. PMID 21294900, Free PMC Article
  2. Identification of the human testis protein phosphatase 1 interactome. Fardilha M, et al. Biochem Pharmacol, 2011 Nov 15. PMID 21382349
  3. Genome-wide meta-analysis identifies new susceptibility loci for migraine. Anttila V, et al. Nat Genet, 2013 Aug. PMID 23793025, Free PMC Article
  4. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. Grupe A, et al. Am J Hum Genet, 2006 Jan. PMID 16385451, Free PMC Article
  5. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
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

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies new susceptibility loci for migraine.
EBI GWAS Catalog

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

  • FLJ31737, MGC44086

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in endothelial cell migration IEA
Inferred from Electronic Annotation
more info
  
involved_in endothelial cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in retina blood vessel maintenance IEA
Inferred from Electronic Annotation
more info
  
involved_in retina vasculature development in camera-type eye IEA
Inferred from Electronic Annotation
more info
  
involved_in sprouting angiogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in vasodilation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
V-set and transmembrane domain-containing protein 4

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_001031746.5 → NP_001026916.2  V-set and transmembrane domain-containing protein 4 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001026916.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC060234, AK056299, AK297931, AW058485, BC041414, HY112498
    Consensus CDS
    CCDS31198.1
    UniProtKB/Swiss-Prot
    B4DNI6, Q8IW00, Q96MX7
    Related
    ENSP00000331062.3, ENST00000332853.9

  2. NM_144984.4 → NP_659421.1  V-set and transmembrane domain-containing protein 4 isoform 2 precursor

    See identical proteins and their annotated locations for NP_659421.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK056299, HY112498
    Consensus CDS
    CCDS7228.1
    UniProtKB/Swiss-Prot
    Q8IW00
    Related
    ENSP00000298454.3, ENST00000298454.3

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    49014236..49115522 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047424711.1 → XP_047280667.1  V-set and transmembrane domain-containing protein 4 isoform X2

  2. XM_017015827.3 → XP_016871316.1  V-set and transmembrane domain-containing protein 4 isoform X1

RNA

  1. XR_001747052.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    49863442..49964410 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054364993.1 → XP_054220968.1  V-set and transmembrane domain-containing protein 4 isoform X2

  2. XM_054364992.1 → XP_054220967.1  V-set and transmembrane domain-containing protein 4 isoform X1

RNA

  1. XR_008488174.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IW00.3 GenPept UniProtKB/Swiss-Prot:Q8IW00

Gene LinkOut

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

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