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    VANGL1 VANGL planar cell polarity protein 1 [ Homo sapiens (human) ]

    Gene ID: 81839, updated on 28-Oct-2024

    Summary

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    Official Symbol
    VANGL1provided by HGNC
    Official Full Name
    VANGL planar cell polarity protein 1provided by HGNC
    Primary source
    HGNC:HGNC:15512
    See related
    Ensembl:ENSG00000173218 MIM:610132; AllianceGenome:HGNC:15512
    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
    LPP2; STB2; STBM2; KITENIN
    Summary
    This gene encodes a member of the tretraspanin family. The encoded protein may be involved in mediating intestinal trefoil factor induced wound healing in the intestinal mucosa. Mutations in this gene are associated with neural tube defects. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]
    Expression
    Ubiquitous expression in esophagus (RPKM 4.2), thyroid (RPKM 3.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VANGL1 in Genome Data Viewer
    Location:
    1p13.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (115641970..115698221)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (115653050..115705924)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (116184591..116240842)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 420, pseudogene Neighboring gene small nucleolar RNA SNORA42/SNORA80 family Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:116184448-116185206 Neighboring gene Sharpr-MPRA regulatory region 4355 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:116214007-116214561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:116238833-116239332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:116253505-116254147 Neighboring gene calsequestrin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1555 Neighboring gene nescient helix-loop-helix 2

    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 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. Molecular cloning and characterization of Strabismus 2 (STB2). Katoh M. Int J Oncol, 2002 May. PMID 11956595
    2. Silencing circular RNA VANGL1 inhibits progression of bladder cancer by regulating miR-1184/IGFBP2 axis. Yang D, et al. Cancer Med, 2020 Jan. PMID 31758655, Free PMC Article
    3. VANGL1 Is Not Associated With the Susceptibility of Adolescent Idiopathic Scoliosis in the Chinese Population. Xu L, et al. Spine (Phila Pa 1976), 2018 May 15. PMID 29189642
    4. Mutation of the Planar Cell Polarity Gene VANGL1 in Adolescent Idiopathic Scoliosis. Andersen MR, et al. Spine (Phila Pa 1976), 2017 Jun 15. PMID 27755493
    5. A novel DNA biosensor integrated with Polypyrrole/streptavidin and Au-PAMAM-CP bionanocomposite probes to detect the rs4839469 locus of the vangl1 gene for dysontogenesis prediction. Li Q, et al. Biosens Bioelectron, 2016 Jun 15. PMID 26914375

    See all (113) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. Myelomeningocele among Pakistani population.
      Title: Myelomeningocele among Pakistani population.
    3. Knockdown of circular RNA VANGL1 inhibits TGF-beta-induced epithelial-mesenchymal transition in melanoma cells by sponging miR-150-5p.
      Title: Knockdown of circular RNA VANGL1 inhibits TGF-β-induced epithelial-mesenchymal transition in melanoma cells by sponging miR-150-5p.
    4. Deletions in VANGL1 are a risk factor for antibody-mediated kidney disease.
      Title: Deletions in VANGL1 are a risk factor for antibody-mediated kidney disease.
    5. Up-regulation of VANGL1 by IGF2BPs and miR-29b-3p attenuates the detrimental effect of irradiation on lung adenocarcinoma.
      Title: Up-regulation of VANGL1 by IGF2BPs and miR-29b-3p attenuates the detrimental effect of irradiation on lung adenocarcinoma.
    6. ErbB4/KITENIN-Mediated Signaling is Activated in Cetuximab-Resistant Colorectal Cancer Cells.
      Title: ErbB4/KITENIN-Mediated Signaling is Activated in Cetuximab-Resistant Colorectal Cancer Cells.
    7. Silencing circular RNA VANGL1 inhibits progression of bladder cancer by regulating miR-1184/IGFBP2 axis.
      Title: Silencing circular RNA VANGL1 inhibits progression of bladder cancer by regulating miR-1184/IGFBP2 axis.
    8. Somatic mutations in planar cell polarity genes in neural tissue from human fetuses with neural tube defects.
      Title: Somatic mutations in planar cell polarity genes in neural tissue from human fetuses with neural tube defects.
    9. Circ-VANGL1 promotes the development of Osteoporosis via binding to miRNA-217 to downregulate RUNX2 expression.
      Title: Circ-VANGL1 promotes the progression of osteoporosis by absorbing miRNA-217 to regulate RUNX2 expression.
    10. Circular RNA circ-VANGL1 is a competing endogenous RNA which contributes to bladder cancer progression by regulating miR-605-3p/VANGL1 pathway.
      Title: Circular RNA circ-VANGL1 as a competing endogenous RNA contributes to bladder cancer progression by regulating miR-605-3p/VANGL1 pathway.
    Submit: New GeneRIF Correction See all GeneRIFs (38)

    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
    Sacral defect with anterior meningocele
    MedGen: C1838568 OMIM: 600145 GeneReviews: Not available
    		Compare labs

    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

    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

    • MGC5338

    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 NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in mucociliary clearance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in pigmentation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lateral plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    vang-like protein 1
    Names
    KAI1 C-terminal interacting tetraspanin
    loop-tail protein 2 homolog
    strabismus 2
    van Gogh-like protein 1
    vang-like 1 (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_016548.1 RefSeqGene

      Range
      5018..61269
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001172411.2 → NP_001165882.1  vang-like protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001165882.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AF481859, AL450389, BM146608
      Consensus CDS
      CCDS53350.1
      UniProtKB/Swiss-Prot
      Q8TAA9
      Related
      ENSP00000358523.3, ENST00000369510.8
      Conserved Domains (1) summary
      pfam06638
      Location:26 → 522
      Strabismus; Strabismus protein

    2. NM_001172412.2 → NP_001165883.1  vang-like protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001165883.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AB057596, AL450389
      Consensus CDS
      CCDS883.1
      UniProtKB/Swiss-Prot
      Q5T1D3, Q5T1D4, Q86WG8, Q8N559, Q8TAA9
      Related
      ENSP00000310800.3, ENST00000310260.7
      Conserved Domains (1) summary
      pfam06638
      Location:25 → 524
      Strabismus; Strabismus protein

    3. NM_138959.3 → NP_620409.1  vang-like protein 1 isoform 1

      See identical proteins and their annotated locations for NP_620409.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AB075805, AL450389, BM552933
      Consensus CDS
      CCDS883.1
      UniProtKB/Swiss-Prot
      Q5T1D3, Q5T1D4, Q86WG8, Q8N559, Q8TAA9
      Related
      ENSP00000347672.2, ENST00000355485.7
      Conserved Domains (1) summary
      pfam06638
      Location:25 → 524
      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
      115641970..115698221
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      115653050..115705924
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TAA9.1 GenPept UniProtKB/Swiss-Prot:Q8TAA9

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