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

Gene ID: 81839, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (115641970..115698221)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (115653050..115705924)
105.20220307 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
  • 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. Myelomeningocele among Pakistani population. Fatima U, et al. J Pak Med Assoc, 2022 May. PMID 35713047
  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 (100) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Myelomeningocele among Pakistani population.
    Title: Myelomeningocele among Pakistani population.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. High KITENIN expression is associated with cholangiocarcinoma.
    Title: Silencing of Kangai 1 C-terminal interacting tetraspanin suppresses progression of cholangiocarcinoma.
Submit: New GeneRIF Correction See all GeneRIFs (37)

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 OMIM: 182940 GeneReviews: Not available
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Sacral defect with anterior meningocele
MedGen: C1838568 OMIM: 600145 GeneReviews: Not available
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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 pigmentation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
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_2023_10

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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