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Aliases for VANGL2 Gene

Aliases for VANGL2 Gene

  • VANGL Planar Cell Polarity Protein 2 2 3 5
  • Vang-Like 2 (Van Gogh, Drosophila) 2 3
  • Loop-Tail-Associated Protein 2 3
  • Loop-Tail Protein 1 Homolog 3 4
  • Van Gogh-Like Protein 2 3 4
  • Strabismus 1 3 4
  • STB1 3 4
  • Vang (Van Gogh, Drosophila)-Like 2, Vang, Van Gogh-Like 2 (Drosophila) 2
  • Vang, Van Gogh-Like 2 2
  • Vang-Like Protein 2 3
  • Strabismus 2
  • KIAA1215 4
  • STBM1 3
  • LPP1 3
  • LTAP 3
  • STBM 3

External Ids for VANGL2 Gene

Previous GeneCards Identifiers for VANGL2 Gene

  • GC01P158177
  • GC01P156117
  • GC01P157163
  • GC01P157585
  • GC01P157587
  • GC01P157183
  • GC01P158636
  • GC01P131726

Summaries for VANGL2 Gene

Entrez Gene Summary for VANGL2 Gene

  • 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]

GeneCards Summary for VANGL2 Gene

VANGL2 (VANGL Planar Cell Polarity Protein 2) is a Protein Coding gene. Diseases associated with VANGL2 include Neural Tube Defects and Anencephaly. Among its related pathways are Signaling by GPCR and Wnt Signaling Pathway and Pluripotency. An important paralog of this gene is VANGL1.

UniProtKB/Swiss-Prot for VANGL2 Gene

  • Involved in the control of early morphogenesis and patterning of both axial midline structures and the development of neural plate. Plays a role in the regulation of planar cell polarity, particularly in the orientation of stereociliary bundles in the cochlea. Required for polarization and movement of myocardializing cells in the outflow tract and seems to act via RHOA signaling to regulate this process. Required for cell surface localization of FZD3 and FZD6 in the inner ear (By similarity).

Additional gene information for VANGL2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VANGL2 Gene

Genomics for VANGL2 Gene

GeneHancer (GH) Regulatory Elements for VANGL2 Gene

Promoters and enhancers for VANGL2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I160399 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 +0.1 133 2.6 ATF1 SIN3A GLI4 ZNF48 ZNF766 GLIS2 ZNF213 ZNF143 RUNX3 SP3 VANGL2 NCSTN LOC105371466
GH01I160621 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 21.9 +228.0 228046 13.9 HDGF ATF1 PKNOX1 SMAD1 TCF12 ZNF766 ATF7 RUNX3 JUNB ZNF592 VANGL2 ENSG00000228863 COPA NCSTN SLAMF7 NHLH1 RNU4-42P ITLN1 SLAMF6 SLAMF1
GH01I160518 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 16.1 +120.7 120721 4.7 HDGF PKNOX1 SMAD1 IRF4 ZNF766 E2F8 ZNF143 ATF7 RUNX3 JUNB SLAMF6 VANGL2 CD84 SLAMF1 LOC105371467
GH01I160605 Enhancer 1.3 Ensembl ENCODE dbSUPER 24.2 +206.7 206730 3.1 ELF3 HDGF FOXA2 RB1 ARNT KLF17 BMI1 BATF IRF4 RAD21 VANGL2 CD84 ENSG00000228863 SLAMF6 SLAMF1 RNU4-42P LOC646347
GH01I160573 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 13.3 +176.4 176363 6.1 PKNOX1 RB1 ARNT BMI1 ZBTB40 ZNF766 EGR1 ATF7 FOS BCLAF1 CD84 SLAMF7 VANGL2 SLAMF6 SLAMF1 CD48 CD244 ATP1A4 LOC105371468
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VANGL2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VANGL2 gene promoter:

Genomic Locations for VANGL2 Gene

Genomic Locations for VANGL2 Gene
chr1:160,400,574-160,428,678
(GRCh38/hg38)
Size:
28,105 bases
Orientation:
Plus strand
chr1:160,370,364-160,398,468
(GRCh37/hg19)

Genomic View for VANGL2 Gene

Genes around VANGL2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VANGL2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VANGL2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VANGL2 Gene

Proteins for VANGL2 Gene

  • Protein details for VANGL2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9ULK5-VANG2_HUMAN
    Recommended name:
    Vang-like protein 2
    Protein Accession:
    Q9ULK5
    Secondary Accessions:
    • D3DVE9
    • Q5T212

    Protein attributes for VANGL2 Gene

    Size:
    521 amino acids
    Molecular mass:
    59714 Da
    Quaternary structure:
    • Homodimer and heterodimer with VANGL1. 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. Also interacts with the PDZ domains of MAGI3, SCRIB/SCRB1 and FZD3 (By similarity). Interacts with PRICKLE3 (By similarity).
    SequenceCaution:
    • Sequence=BAA86529.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for VANGL2 Gene

Post-translational modifications for VANGL2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VANGL2 Gene

No data available for DME Specific Peptides for VANGL2 Gene

Domains & Families for VANGL2 Gene

Gene Families for VANGL2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted membrane proteins

Protein Domains for VANGL2 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for VANGL2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9ULK5

UniProtKB/Swiss-Prot:

VANG2_HUMAN :
  • Belongs to the Vang family.
Family:
  • Belongs to the Vang family.
genes like me logo Genes that share domains with VANGL2: view

Function for VANGL2 Gene

Molecular function for VANGL2 Gene

UniProtKB/Swiss-Prot Function:
Involved in the control of early morphogenesis and patterning of both axial midline structures and the development of neural plate. Plays a role in the regulation of planar cell polarity, particularly in the orientation of stereociliary bundles in the cochlea. Required for polarization and movement of myocardializing cells in the outflow tract and seems to act via RHOA signaling to regulate this process. Required for cell surface localization of FZD3 and FZD6 in the inner ear (By similarity).

Phenotypes From GWAS Catalog for VANGL2 Gene

Gene Ontology (GO) - Molecular Function for VANGL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 22610794
genes like me logo Genes that share ontologies with VANGL2: view
genes like me logo Genes that share phenotypes with VANGL2: view

Human Phenotype Ontology for VANGL2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VANGL2 Gene

MGI Knock Outs for VANGL2:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for VANGL2 Gene

Localization for VANGL2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VANGL2 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
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 VANGL2 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 3
extracellular 2
nucleus 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for VANGL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001725 stress fiber IEA --
GO:0005886 plasma membrane TAS --
GO:0005911 cell-cell junction ISS,IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with VANGL2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VANGL2 Gene

Pathways & Interactions for VANGL2 Gene

genes like me logo Genes that share pathways with VANGL2: view

Pathways by source for VANGL2 Gene

1 KEGG pathway for VANGL2 Gene

Gene Ontology (GO) - Biological Process for VANGL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001736 establishment of planar polarity ISS,IEA --
GO:0001843 neural tube closure ISS,IEA --
GO:0001942 hair follicle development IEA --
GO:0001947 heart looping IEA,ISS --
GO:0003149 membranous septum morphogenesis IEA --
genes like me logo Genes that share ontologies with VANGL2: view

No data available for SIGNOR curated interactions for VANGL2 Gene

Drugs & Compounds for VANGL2 Gene

No Compound Related Data Available

Transcripts for VANGL2 Gene

mRNA/cDNA for VANGL2 Gene

Unigene Clusters for VANGL2 Gene

VANGL planar cell polarity protein 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VANGL2 Gene

No ASD Table

Relevant External Links for VANGL2 Gene

GeneLoc Exon Structure for
VANGL2
ECgene alternative splicing isoforms for
VANGL2

Expression for VANGL2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VANGL2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VANGL2 Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x4.3).

Protein differential expression in normal tissues from HIPED for VANGL2 Gene

This gene is overexpressed in Nasal epithelium (56.9) and Pancreas (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VANGL2 Gene



NURSA nuclear receptor signaling pathways regulating expression of VANGL2 Gene:

VANGL2

SOURCE GeneReport for Unigene cluster for VANGL2 Gene:

Hs.99477

Evidence on tissue expression from TISSUES for VANGL2 Gene

  • Nervous system(4.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VANGL2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • endocrine
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • head
  • meninges
  • neck
  • skull
Abdomen:
  • adrenal gland
Pelvis:
  • prostate
  • urinary bladder
General:
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with VANGL2: view

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for VANGL2 Gene

Orthologs for VANGL2 Gene

This gene was present in the common ancestor of animals.

Orthologs for VANGL2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VANGL2 33 34
  • 98.54 (n)
cow
(Bos Taurus)
Mammalia VANGL2 33 34
  • 93.99 (n)
mouse
(Mus musculus)
Mammalia Vangl2 33 16 34
  • 89.89 (n)
rat
(Rattus norvegicus)
Mammalia Vangl2 33
  • 89.89 (n)
oppossum
(Monodelphis domestica)
Mammalia VANGL2 34
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 55 (a)
OneToMany
-- 34
  • 36 (a)
OneToMany
dog
(Canis familiaris)
Mammalia VANGL2 34
  • 46 (a)
OneToOne
chicken
(Gallus gallus)
Aves VANGL2 33 34
  • 85.22 (n)
lizard
(Anolis carolinensis)
Reptilia VANGL2 34
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vangl2 33
  • 79.4 (n)
Str.11014 33
zebrafish
(Danio rerio)
Actinopterygii vangl2 33 34
  • 74.66 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vang 35 34
  • 46 (a)
worm
(Caenorhabditis elegans)
Secernentea B0410.2a 35
  • 31 (a)
B0410.2b 35
  • 31 (a)
vang-1 34
  • 30 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10649 34
  • 50 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2933 33
Species where no ortholog for VANGL2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for VANGL2 Gene

ENSEMBL:
Gene Tree for VANGL2 (if available)
TreeFam:
Gene Tree for VANGL2 (if available)

Paralogs for VANGL2 Gene

Paralogs for VANGL2 Gene

(1) SIMAP similar genes for VANGL2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with VANGL2: view

Variants for VANGL2 Gene

Sequence variations from dbSNP and Humsavar for VANGL2 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs267607167 risk-factor, Neural tube defects, susceptibility to, Neural tube defects (NTD) [MIM:182940] 160,421,171(+) C/G/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs267607168 risk-factor, Neural tube defects, susceptibility to, Neural tube defects (NTD) [MIM:182940] 160,425,122(+) T/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
VAR_067221 Neural tube defects (NTD) [MIM:182940] p.Ser84Phe
rs199788326 uncertain-significance, not specified 160,421,085(+) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1000083348 -- 160,425,919(+) A/G 3_prime_UTR_variant, genic_downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for VANGL2 Gene

Variant ID Type Subtype PubMed ID
esv3587713 CNV loss 21293372
nsv1014588 CNV loss 25217958
nsv548056 CNV loss 21841781

Variation tolerance for VANGL2 Gene

Residual Variation Intolerance Score: 16.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.75; 33.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VANGL2 Gene

Human Gene Mutation Database (HGMD)
VANGL2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VANGL2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VANGL2 Gene

Disorders for VANGL2 Gene

MalaCards: The human disease database

(20) MalaCards diseases for VANGL2 Gene - From: HGMD, OMIM, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
neural tube defects
  • neural tube defects, susceptibility to
anencephaly
  • anph
strabismus
  • strabismus, susceptibility to
upper thoracic spina bifida cystica
cervicothoracic spina bifida cystica
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

VANG2_HUMAN
  • 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:20558380}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for VANGL2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VANGL2: view

No data available for Genatlas for VANGL2 Gene

Publications for VANGL2 Gene

  1. VANGL2 mutations in human cranial neural-tube defects. (PMID: 20558380) Lei YP … Wang HY (The New England journal of medicine 2010) 3 4 44 58
  2. A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. (PMID: 19734545) Need AC … Goldstein DB (Human molecular genetics 2009) 3 44 58
  3. Mutation analysis of the Vangl2 coding region revealed no common cause for Tetralogy of Fallot. (PMID: 18034999) Erdal E … Açikel U (The Journal of international medical research 2007) 3 22 58
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for VANGL2 Gene

Sources for VANGL2 Gene

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