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    VANGL2 VANGL planar cell polarity protein 2 [ Homo sapiens (human) ]

    Gene ID: 57216, updated on 10-Dec-2024

    Summary

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    Official Symbol
    VANGL2provided by HGNC
    Official Full Name
    VANGL planar cell polarity protein 2provided by HGNC
    Primary source
    HGNC:HGNC:15511
    See related
    Ensembl:ENSG00000162738 MIM:600533; AllianceGenome:HGNC:15511
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LPP1; LTAP; STB1; STBM; STBM1
    Summary
    The protein encoded by this gene is a membrane protein involved in the regulation of planar cell polarity, especially in the stereociliary bundles of the cochlea. The encoded protein transmits directional signals to individual cells or groups of cells in epithelial sheets. This protein is also involved in the development of the neural plate. [provided by RefSeq, Sep 2011]
    Expression
    Broad expression in skin (RPKM 17.0), brain (RPKM 6.7) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VANGL2 in Genome Data Viewer
    Location:
    1q23.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (160400564..160428670)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159537640..159565747)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160370354..160398460)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1921 Neighboring gene uncharacterized LOC105371466 Neighboring gene nescient helix-loop-helix 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1922 Neighboring gene RNA, U4 small nuclear 42, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:160379091-160379966 Neighboring gene Sharpr-MPRA regulatory region 8449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1923 Neighboring gene uncharacterized LOC105371467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1928 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:160460168-160461367 Neighboring gene SLAM family member 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1929

    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. Contribution of VANGL2 mutations to isolated neural tube defects. Kibar Z, et al. Clin Genet, 2011 Jul. PMID 20738329, Free PMC Article
    2. Mutation analysis of the Vangl2 coding region revealed no common cause for Tetralogy of Fallot. Erdal E, et al. J Int Med Res, 2007 Nov-Dec. PMID 18034999
    3. VANGL2 mutations in human cranial neural-tube defects. Lei YP, et al. N Engl J Med, 2010 Jun 10. PMID 20558380
    4. Asymmetry of VANGL2 in migrating lymphocytes as a tool to monitor activity of the mammalian WNT/planar cell polarity pathway. Kaucká M, et al. Cell Commun Signal, 2015 Jan 28. PMID 25627785, Free PMC Article
    5. Promoter methylation and expression of the VANGL2 gene in the myocardium of pediatric patients with tetralogy of fallot. Yuan Y, et al. Birth Defects Res A Clin Mol Teratol, 2014 Dec. PMID 25200836

    See all (74) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Vangl2 suppresses NF-kappaB signaling and ameliorates sepsis by targeting p65 for NDP52-mediated autophagic degradation.
      Title: Vangl2 suppresses NF-κB signaling and ameliorates sepsis by targeting p65 for NDP52-mediated autophagic degradation.
    2. Expression Profiles of ITGA8 and VANGL2 Are Altered in Congenital Anomalies of the Kidney and Urinary Tract (CAKUT).
      Title: Expression Profiles of ITGA8 and VANGL2 Are Altered in Congenital Anomalies of the Kidney and Urinary Tract (CAKUT).
    3. Core planar cell polarity genes VANGL1 and VANGL2 in predisposition to congenital vertebral malformations.
      Title: Core planar cell polarity genes VANGL1 and VANGL2 in predisposition to congenital vertebral malformations.
    4. Functional analysis of germline VANGL2 variants using rescue assays of vangl2 knockout zebrafish.
      Title: Functional analysis of germline VANGL2 variants using rescue assays of vangl2 knockout zebrafish.
    5. Vangl2 promotes the formation of long cytonemes to enable distant Wnt/beta-catenin signaling.
      Title: Vangl2 promotes the formation of long cytonemes to enable distant Wnt/β-catenin signaling.
    6. integrin alphav regulates VANGL2 protein levels
      Title: VANGL2 protein stability is regulated by integrin αv and the extracellular matrix.
    7. Vangl2 modulates glomerular injury, at least in part by acting as a brake on MMP9, a potentially harmful endogenous enzyme.
      Title: Vangl2, a planar cell polarity molecule, is implicated in irreversible and reversible kidney glomerular injury.
    8. Expression of constitutively active and dominant-negative isoforms of RHOA revealed that it acts downstream of VANGL2.
      Title: Vangl2/RhoA Signaling Pathway Regulates Stem Cell Self-Renewal Programs and Growth in Rhabdomyosarcoma.
    9. VANGL2 interacts with Integrin alphaVbeta3 to regulate matrix metalloproteinase activity and cell adhesion to the extracellular matrix.
      Title: VANGL2 interacts with integrin αv to regulate matrix metalloproteinase activity and cell adhesion to the extracellular matrix.
    10. Our experimental data demonstrate that high expression of Prickle1 and Vangl2 reduce the growth of neuroblastoma cells and indicate different roles of PCP proteins in tumorigenic cells compared to normal cells.
      Title: Planar cell polarity gene expression correlates with tumor cell viability and prognostic outcome in neuroblastoma.
    Submit: New GeneRIF Correction See all GeneRIFs (23)

    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

    Associated conditions

    Description Tests
    Neural tube defect
    MedGen: C0027794 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB.
    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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1215, MGC119403, MGC119404

    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 Wnt signaling pathway, planar cell polarity pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in Wnt signaling pathway, planar cell polarity pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in apical protein localization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cell migration involved in kidney development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in dopaminergic neuron axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in establishment of planar polarity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in establishment of planar polarity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in heart looping ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neural tube closure ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in non-motile cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in serotonergic neuron axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cell-cell junction ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lateral plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    vang-like protein 2
    Names
    loop-tail protein 1 homolog
    loop-tail-associated protein
    strabismus 1
    van Gogh-like protein 2
    vang-like 2 (van gogh, Drosophila)

    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.

    Genomic

    1. NG_023420.1 RefSeqGene

      Range
      4991..33097
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_020335.3 → NP_065068.1  vang-like protein 2

      See identical proteins and their annotated locations for NP_065068.1

      Status: REVIEWED

      Source sequence(s)
      AB033041, AK290981, AL445230, BG059541
      Consensus CDS
      CCDS30915.1
      UniProtKB/Swiss-Prot
      D3DVE9, Q5T212, Q9ULK5
      UniProtKB/TrEMBL
      A8K4L6
      Related
      ENSP00000357040.2, ENST00000368061.3
      Conserved Domains (1) summary
      pfam06638
      Location:34 → 521
      Strabismus; Strabismus protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      160400564..160428670
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509804.2 → XP_011508106.1  vang-like protein 2 isoform X1

      See identical proteins and their annotated locations for XP_011508106.1

      UniProtKB/Swiss-Prot
      D3DVE9, Q5T212, Q9ULK5
      UniProtKB/TrEMBL
      A8K4L6
      Conserved Domains (1) summary
      pfam06638
      Location:34 → 521
      Strabismus; Strabismus protein

    2. XM_005245357.2 → XP_005245414.1  vang-like protein 2 isoform X1

      See identical proteins and their annotated locations for XP_005245414.1

      UniProtKB/Swiss-Prot
      D3DVE9, Q5T212, Q9ULK5
      UniProtKB/TrEMBL
      A8K4L6
      Conserved Domains (1) summary
      pfam06638
      Location:34 → 521
      Strabismus; Strabismus protein

    3. XM_047426020.1 → XP_047281976.1  vang-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      D3DVE9, Q5T212, Q9ULK5
      UniProtKB/TrEMBL
      A8K4L6

    4. XM_011509805.4 → XP_011508107.1  vang-like protein 2 isoform X2

      Conserved Domains (1) summary
      pfam06638
      Location:34 → 267
      Strabismus; Strabismus protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      159537640..159565747
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337805.1 → XP_054193780.1  vang-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      D3DVE9, Q5T212, Q9ULK5
      UniProtKB/TrEMBL
      A8K4L6

    2. XM_054337806.1 → XP_054193781.1  vang-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      D3DVE9, Q5T212, Q9ULK5
      UniProtKB/TrEMBL
      A8K4L6

    3. XM_054337807.1 → XP_054193782.1  vang-like protein 2 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ULK5.2 GenPept UniProtKB/Swiss-Prot:Q9ULK5

    Gene LinkOut

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

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