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Aliases for VANGL1 Gene

Aliases for VANGL1 Gene

  • VANGL Planar Cell Polarity Protein 1 2 3 5
  • Vang-Like 1 (Van Gogh, Drosophila) 2 3
  • Loop-Tail Protein 2 Homolog 3 4
  • Van Gogh-Like Protein 1 3 4
  • Strabismus 2 3 4
  • LPP2 3 4
  • STB2 3 4
  • Vang (Van Gogh, Drosophila)-Like 1, Vang, Van Gogh-Like 1 (Drosophila) 2
  • KAI1 C-Terminal Interacting Tetraspanin 3
  • Vang-Like Protein 1 3
  • STBM2 3

External Ids for VANGL1 Gene

Previous GeneCards Identifiers for VANGL1 Gene

  • GC01P116607
  • GC01P115067
  • GC01P115332
  • GC01P115531
  • GC01P115896
  • GC01P115986
  • GC01P116184
  • GC01P114043

Summaries for VANGL1 Gene

Entrez Gene Summary for VANGL1 Gene

  • 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]

GeneCards Summary for VANGL1 Gene

VANGL1 (VANGL Planar Cell Polarity Protein 1) is a Protein Coding gene. Diseases associated with VANGL1 include Caudal Regression Syndrome and Neural Tube Defects. Among its related pathways are Wnt Signaling Pathway and Pluripotency and Wnt / Hedgehog / Notch. An important paralog of this gene is VANGL2.

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VANGL1 Gene

Genomics for VANGL1 Gene

Regulatory Elements for VANGL1 Gene

Enhancers for VANGL1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G115646 1.8 FANTOM5 Ensembl ENCODE dbSUPER 24.5 +7.0 6981 5.5 HDGF PKNOX1 FOXA2 ATF1 WRNIP1 FEZF1 BRCA1 ZNF766 GLIS2 FOS VANGL1 ENSG00000207502 CASQ2
GH01G115641 1.4 ENCODE dbSUPER 24.8 +0.4 433 2.4 HDGF PKNOX1 ARNT SIN3A YBX1 DMAP1 ZNF2 ZNF766 ZNF302 ZNF416 VANGL1 ATP1A1-AS1 ENSG00000207502 CASQ2
GH01G115654 1.3 Ensembl ENCODE dbSUPER 16 +13.3 13324 1.5 BCOR HDAC1 PKNOX1 TAL1 JUN ZMYM3 TCF12 ZNF316 GATA2 NCOR1 VANGL1 CASQ2
GH01G115557 0.7 dbSUPER 22.3 -83.1 -83135 3.2 NFIB ZBTB21 ZIC2 EP300 ATF2 NFIC ZNF316 ZNF629 SCRT2 MAFK VANGL1 ELOCP20 CNOT7P2
GH01G115631 0.8 ENCODE 17.9 -9.2 -9227 1.9 SOX13 ZNF146 ZMYM3 CHD7 THRB TEAD3 GATA3 GATA4 NR2F6 CREM VANGL1 ENSG00000207502 GC01M115622
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VANGL1 on UCSC Golden Path with GeneCards custom track

Promoters for VANGL1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000011831 347 1801 HDGF PKNOX1 ARNT SIN3A YBX1 DMAP1 ZNF2 ZNF766 ZNF302 ZNF416

Genomic Location for VANGL1 Gene

115,641,953 bp from pter
115,698,224 bp from pter
56,272 bases
Plus strand

Genomic View for VANGL1 Gene

Genes around VANGL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VANGL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VANGL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VANGL1 Gene

Proteins for VANGL1 Gene

  • Protein details for VANGL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Vang-like protein 1
    Protein Accession:
    Secondary Accessions:
    • Q5T1D3
    • Q5T1D4
    • Q86WG8
    • Q8N559

    Protein attributes for VANGL1 Gene

    524 amino acids
    Molecular mass:
    59975 Da
    Quaternary structure:
    • Heterodimer with VANGL2. Interacts through its C-terminal region with the N-terminal half of DVL1, DVL2 and DVL3. The PDZ domain of DVL1, DVL2 and DVL3 is required for the interaction (By similarity).
    • Sequence=AAH32773.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for VANGL1 Gene


neXtProt entry for VANGL1 Gene

Post-translational modifications for VANGL1 Gene

  • Ubiquitination at isoforms=2299, isoforms=2310, and Lys382
  • Modification sites at PhosphoSitePlus

Other Protein References for VANGL1 Gene

No data available for DME Specific Peptides for VANGL1 Gene

Domains & Families for VANGL1 Gene

Protein Domains for VANGL1 Gene


Suggested Antigen Peptide Sequences for VANGL1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Vang family.
  • Belongs to the Vang family.
genes like me logo Genes that share domains with VANGL1: view

No data available for Gene Families for VANGL1 Gene

Function for VANGL1 Gene

Gene Ontology (GO) - Molecular Function for VANGL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15205336
genes like me logo Genes that share ontologies with VANGL1: view
genes like me logo Genes that share phenotypes with VANGL1: view

Human Phenotype Ontology for VANGL1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VANGL1 Gene

MGI Knock Outs for VANGL1:

Animal Model Products

  • Taconic Biosciences Mouse Models for VANGL1

CRISPR Products

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for VANGL1 Gene

Localization for VANGL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VANGL1 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VANGL1 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 2
nucleus 2
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for VANGL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0016328 lateral plasma membrane IEA --
genes like me logo Genes that share ontologies with VANGL1: view

Pathways & Interactions for VANGL1 Gene

genes like me logo Genes that share pathways with VANGL1: view

Pathways by source for VANGL1 Gene

1 Cell Signaling Technology pathway for VANGL1 Gene
1 KEGG pathway for VANGL1 Gene

Gene Ontology (GO) - Biological Process for VANGL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0043473 pigmentation IEA --
GO:0060071 Wnt signaling pathway, planar cell polarity pathway NAS 24431302
genes like me logo Genes that share ontologies with VANGL1: view

No data available for SIGNOR curated interactions for VANGL1 Gene

Drugs & Compounds for VANGL1 Gene

No Compound Related Data Available

Transcripts for VANGL1 Gene

Unigene Clusters for VANGL1 Gene

VANGL planar cell polarity protein 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for VANGL1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
SP1: - - -
SP2: - - -
SP3: - -

Relevant External Links for VANGL1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VANGL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VANGL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for VANGL1 Gene

This gene is overexpressed in Lung (55.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VANGL1 Gene

Protein tissue co-expression partners for VANGL1 Gene

NURSA nuclear receptor signaling pathways regulating expression of VANGL1 Gene:


SOURCE GeneReport for Unigene cluster for VANGL1 Gene:


mRNA Expression by UniProt/SwissProt for VANGL1 Gene:

Tissue specificity: According to PubMed:11956595, ubiquitously expressed. According to PubMed:12011995, expressed specifically in testis and ovary.

Evidence on tissue expression from TISSUES for VANGL1 Gene

  • Skin(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VANGL1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • ear
  • eye
  • head
  • meninges
  • neck
  • aorta
  • esophagus
  • heart
  • lung
  • rib
  • rib cage
  • trachea
  • intestine
  • kidney
  • large intestine
  • pancreas
  • small intestine
  • stomach
  • anus
  • ovary
  • pelvis
  • penis
  • placenta
  • rectum
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vagina
  • vulva
  • ankle
  • arm
  • digit
  • elbow
  • finger
  • foot
  • forearm
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with VANGL1: view

Primer Products

No data available for mRNA differential expression in normal tissues for VANGL1 Gene

Orthologs for VANGL1 Gene

This gene was present in the common ancestor of animals.

Orthologs for VANGL1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia VANGL1 34 35
  • 99.49 (n)
(Bos Taurus)
Mammalia VANGL1 34 35
  • 90.46 (n)
(Canis familiaris)
Mammalia VANGL1 34 35
  • 90.39 (n)
(Monodelphis domestica)
Mammalia VANGL1 35
  • 90 (a)
(Mus musculus)
Mammalia Vangl1 34 16 35
  • 88.74 (n)
(Rattus norvegicus)
Mammalia Vangl1 34
  • 88.74 (n)
(Gallus gallus)
Aves VANGL1 34 35
  • 80.59 (n)
(Anolis carolinensis)
Reptilia VANGL1 35
  • 81 (a)
(Danio rerio)
Actinopterygii vangl1 34 35
  • 66.54 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012288 34
  • 53.96 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vang 36 34 35
  • 53.93 (n)
(Caenorhabditis elegans)
Secernentea vang-1 34 35
  • 46.26 (n)
B0410.2a 36
  • 34 (a)
B0410.2b 36
  • 34 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10649 35
  • 50 (a)
Species where no ortholog for VANGL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for VANGL1 Gene

Gene Tree for VANGL1 (if available)
Gene Tree for VANGL1 (if available)

Paralogs for VANGL1 Gene

Paralogs for VANGL1 Gene

(1) SIMAP similar genes for VANGL1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with VANGL1: view

Variants for VANGL1 Gene

Sequence variations from dbSNP and Humsavar for VANGL1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs121918218 Pathogenic, Sacral defect with anterior meningocele (SDAM) [MIM:600145] 115,664,171(+) CCATC(A/G)TCCTG reference, missense
rs121918219 other, Neural tube defects (NTD) [MIM:182940] 115,682,372(+) CCAGC(A/G)AGCAG reference, missense
rs121918220 other, Neural tube defects (NTD) [MIM:182940] 115,683,980(+) GGCCA(C/T)GATTG reference, missense
rs146695372 Neural tube defects (NTD) [MIM:182940] 115,663,704(+) CACCT(C/T)GGAGC reference, missense
rs761123443 other, Neural tube defects (NTD) [MIM:182940] 115,663,998(+) GCCAC(A/G)GGTGT reference, missense

Structural Variations from Database of Genomic Variants (DGV) for VANGL1 Gene

Variant ID Type Subtype PubMed ID
dgv146n106 CNV deletion 24896259
dgv293n100 CNV loss 25217958
dgv517n54 CNV loss 21841781
dgv518n54 CNV loss 21841781
dgv519n54 CNV loss 21841781
dgv69n67 CNV loss 20364138
dgv84e212 CNV loss 25503493
esv2716596 CNV deletion 23290073
esv2760632 CNV gain 21179565
esv27976 CNV loss 19812545
esv2850124 CNV deletion 24192839
esv3539878 CNV deletion 23714750
esv3587290 CNV loss 21293372
esv7661 CNV loss 19470904
esv994532 CNV deletion 20482838
nsv1000760 CNV gain 25217958
nsv1077565 CNV deletion 25765185
nsv2509 CNV deletion 18451855
nsv524619 CNV gain 19592680
nsv547571 CNV loss 21841781
nsv547580 CNV gain+loss 21841781
nsv547585 CNV gain 21841781
nsv831115 CNV gain 17160897

Variation tolerance for VANGL1 Gene

Residual Variation Intolerance Score: 17.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.14; 75.69% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VANGL1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VANGL1 Gene

Disorders for VANGL1 Gene

MalaCards: The human disease database

(20) MalaCards diseases for VANGL1 Gene - From: OMIM, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
caudal regression syndrome
  • sacral defect with anterior meningocele
neural tube defects
  • spina bifida
vangl1-related neural tube defect
  • spina bifida
upper thoracic spina bifida aperta
- elite association - COSMIC cancer census association via MalaCards


  • Neural tube defects (NTD) [MIM:182940]: Congenital malformations of the central nervous system and adjacent structures related to defective neural tube closure during the first trimester of pregnancy. Failure of neural tube closure can occur at any level of the embryonic axis. Common NTD forms include anencephaly, myelomeningocele and spina bifida, which result from the failure of fusion in the cranial and spinal region of the neural tube. NTDs have a multifactorial etiology encompassing both genetic and environmental components. {ECO:0000269 PubMed:17409324, ECO:0000269 PubMed:19319979}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Sacral defect with anterior meningocele (SDAM) [MIM:600145]: Form of caudal dysgenesis. It is present at birth and becomes symptomatic later in life, usually because of obstructive labor in females, chronic constipation, or meningitis. Inheritance is autosomal dominant. {ECO:0000269 PubMed:17409324}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VANGL1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with VANGL1: view

No data available for Genatlas for VANGL1 Gene

Publications for VANGL1 Gene

  1. Molecular cloning and characterization of Strabismus 2 (STB2). (PMID: 11956595) Katoh M. (Int. J. Oncol. 2002) 2 3 4 22 64
  2. Novel mutations in VANGL1 in neural tube defects. (PMID: 19319979) Kibar Z. … Gros P. (Hum. Mutat. 2009) 3 4 46 64
  3. Isolation and characterization of a novel human gene, VANGL1, as a therapeutic target for hepatocellular carcinoma. (PMID: 12011995) Yagyu R. … Nakamura Y. (Int. J. Oncol. 2002) 2 3 4 64
  4. Mutations in VANGL1 associated with neural-tube defects. (PMID: 17409324) Kibar Z. … Gros P. (N. Engl. J. Med. 2007) 3 4 64
  5. Analysis of the planar cell polarity gene Vangl2 and its co-expressed paralogue Vangl1 in neural tube defect patients. (PMID: 15952208) Doudney K. … Stanier P. (Am. J. Med. Genet. A 2005) 3 4 64

Products for VANGL1 Gene

Sources for VANGL1 Gene

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