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VSTM2B V-set and transmembrane domain containing 2B [ Homo sapiens (human) ]

Gene ID: 342865, updated on 10-Oct-2023

Summary

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Official Symbol
VSTM2Bprovided by HGNC
Official Full Name
V-set and transmembrane domain containing 2Bprovided by HGNC
Primary source
HGNC:HGNC:33595
See related
Ensembl:ENSG00000187135 AllianceGenome:HGNC:33595
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
Summary
Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward brain (RPKM 9.7) See more
Orthologs
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Genomic context

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See VSTM2B in Genome Data Viewer
Location:
19q12
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (29525418..29564551)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (32051016..32090146)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (30016325..30055458)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14405 Neighboring gene UQCRFS1 divergent transcript Neighboring gene RNA, 7SL, cytoplasmic 340, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr19:29763000-29763195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14406 Neighboring gene VSTM2B divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29799690-29800520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29802083-29802584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29802585-29803084 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29814030-29814530 Neighboring gene MPRA-validated peak3428 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29862474-29863068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29863069-29863661 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50790 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50793 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29895755-29896381 Neighboring gene Sharpr-MPRA regulatory region 9443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29908074-29908807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29910274-29911005 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50884 Neighboring gene uncharacterized LOC124904683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30025281-30025781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30030190-30030690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30030691-30031191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30053547-30054047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30055952-30056800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30059413-30059913 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:30087367-30087867 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:30086866-30087366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:30100801-30101312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14409 Neighboring gene Sharpr-MPRA regulatory region 12961 Neighboring gene uncharacterized LOC105372353 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:30156127-30156680 Neighboring gene POP4 homolog, ribonuclease P/MRP subunit

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. Genome-wide meta-analysis for severe diabetic retinopathy. Grassi MA, et al. Hum Mol Genet, 2011 Jun 15. PMID 21441570, Free PMC Article
  2. Genetic variants associated with disordered eating. Wade TD, et al. Int J Eat Disord, 2013 Sep. PMID 23568457, Free PMC Article
  3. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. Trynka G, et al. Gut, 2009 Aug. PMID 19240061
  4. The DNA sequence and biology of human chromosome 19. Grimwood J, et al. Nature, 2004 Apr 1. PMID 15057824
  5. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Fasci D, et al. Mol Cell Proteomics, 2018 Oct. PMID 30021884, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
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
Genetic variants associated with disordered eating.
EBI GWAS Catalog
Genome-wide meta-analysis for severe diabetic retinopathy.
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

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
V-set and transmembrane domain-containing protein 2B

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_001146339.2 → NP_001139811.1  V-set and transmembrane domain-containing protein 2B isoform 1 precursor

    See identical proteins and their annotated locations for NP_001139811.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC011474
    Consensus CDS
    CCDS46034.1
    UniProtKB/Swiss-Prot
    A6NLU5
    Related
    ENSP00000335038.6, ENST00000335523.8
    Conserved Domains (2) summary
    smart00410
    Location:34 → 139
    IG_like; Immunoglobulin like
    cl11960
    Location:32 → 138
    Ig; Immunoglobulin domain

  2. NM_001384640.1 → NP_001371569.1  V-set and transmembrane domain-containing protein 2B isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AC011474
    Conserved Domains (2) summary
    smart00410
    Location:34 → 129
    IG_like; Immunoglobulin like
    cd00096
    Location:29 → 33
    Ig; Ig strand A [structural motif]

  3. NM_001384641.1 → NP_001371570.1  V-set and transmembrane domain-containing protein 2B isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC011474
    Conserved Domains (2) summary
    cd00096
    Location:29 → 34
    Ig; Ig strand C' [structural motif]
    cl11960
    Location:20 → 92
    Ig; Immunoglobulin domain

  4. NM_001384642.1 → NP_001371571.1  V-set and transmembrane domain-containing protein 2B isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC011474
    Conserved Domains (2) summary
    cd00096
    Location:16 → 23
    Ig; Ig strand C [structural motif]
    cl11960
    Location:16 → 78
    Ig; Immunoglobulin domain

  5. NM_001384643.1 → NP_001371572.1  V-set and transmembrane domain-containing protein 2B isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC011474
    Conserved Domains (1) summary
    smart00409
    Location:8 → 51
    IG; Immunoglobulin

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    29525418..29564551
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011526902.3 → XP_011525204.1  V-set and transmembrane domain-containing protein 2B isoform X1

    See identical proteins and their annotated locations for XP_011525204.1

    UniProtKB/Swiss-Prot
    A6NLU5
    Conserved Domains (2) summary
    smart00410
    Location:34 → 139
    IG_like; Immunoglobulin like
    cl11960
    Location:32 → 138
    Ig; Immunoglobulin domain

  2. XM_011526903.3 → XP_011525205.1  V-set and transmembrane domain-containing protein 2B isoform X2

    Conserved Domains (2) summary
    smart00410
    Location:34 → 129
    IG_like; Immunoglobulin like
    cd00096
    Location:29 → 33
    Ig; Ig strand A [structural motif]

  3. XM_011526905.3 → XP_011525207.1  V-set and transmembrane domain-containing protein 2B isoform X3

    Conserved Domains (1) summary
    smart00410
    Location:37 → 75
    IG_like; Immunoglobulin like

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    32051016..32090146
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054320837.1 → XP_054176812.1  V-set and transmembrane domain-containing protein 2B isoform X1

    UniProtKB/Swiss-Prot
    A6NLU5

  2. XM_054320838.1 → XP_054176813.1  V-set and transmembrane domain-containing protein 2B isoform X2

  3. XM_054320839.1 → XP_054176814.1  V-set and transmembrane domain-containing protein 2B isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A6NLU5.2 GenPept UniProtKB/Swiss-Prot:A6NLU5

Gene LinkOut

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