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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 Vangl2-Related Neural Tube Defect. Among its related pathways are Wnt Signaling Pathway and Pluripotency and CDK-mediated phosphorylation and removal of Cdc6. 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).

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

Regulatory Elements for VANGL2 Gene

Enhancers for VANGL2 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
GH01G160621 1.8 FANTOM5 Ensembl ENCODE dbSUPER 21.9 +228.0 228047 13.9 HDGF PKNOX1 ATF1 WRNIP1 TCF12 ZNF766 GATA2 ZNF207 JUNB TBX21 VANGL2 RPSAP18 ENSG00000228863 COPA NCSTN ENSG00000272668 SLAMF7 NHLH1 SNHG28 RNU4-42P
GH01G160605 1.5 Ensembl ENCODE dbSUPER 24.2 +206.7 206731 3.1 HDGF CREB3L1 ARNT WRNIP1 ZNF766 CBX5 GATA2 ELK1 ZNF143 REST VANGL2 CD84 ENSG00000228863 SLAMF6 SLAMF1 RNU4-42P LOC646347
GH01G160427 1.9 FANTOM5 Ensembl ENCODE dbSUPER 19 +30.1 30067 6.0 HDGF PKNOX1 SIN3A ZNF766 CBX5 ZNF143 ZNF207 SP3 JUNB REST VANGL2 SLAMF7 SLAMF1 NCSTN ENSG00000228863 NHLH1 ITLN1 CD48 CD244 LY9
GH01G160558 1.3 Ensembl ENCODE dbSUPER 24.8 +159.0 158985 1.9 HDAC1 LEF1 ESRRA ZNF766 ZNF316 GATA2 FOXK2 NR2F6 TRIM24 HES1 VANGL2 SLAMF6 SLAMF1 LY9 CD84 LOC105371468
GH01G160538 1.9 FANTOM5 Ensembl ENCODE dbSUPER 15.9 +141.1 141051 7.2 HDGF PKNOX1 CREB3L1 ARNT YY1 ZNF766 CBX5 ZNF143 ZNF207 JUNB CD84 SLAMF1 VANGL2 ENSG00000228863 TSTD1 SLAMF6 CD48 DCAF8 LOC105371468
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VANGL2 on UCSC Golden Path with GeneCards custom track

Promoters for VANGL2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000014546 226 1601 ATF1 SIN3A GLI4 ZNF48 ZNF766 GLIS2 SP3 YY2 TSHZ1 REST

Genomic Location for VANGL2 Gene

Chromosome:
1
Start:
160,400,574 bp from pter
End:
160,428,678 bp from pter
Size:
28,105 bases
Orientation:
Plus strand

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).
    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

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

No data available for Gene Families for VANGL2 Gene

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).

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

CRISPR Products

Inhibitory RNA 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 IEA,ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with VANGL2: view

Pathways & Interactions for VANGL2 Gene

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

Gene Ontology (GO) - Biological Process for VANGL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001736 establishment of planar polarity IEA,ISS --
GO:0001843 neural tube closure ISS,IEA --
GO:0001942 hair follicle development IEA --
GO:0001947 heart looping ISS,IEA --
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:

CRISPR Products

Inhibitory RNA Products

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
Organs:
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

Primer Products

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 34 35
  • 98.54 (n)
cow
(Bos Taurus)
Mammalia VANGL2 34 35
  • 93.99 (n)
mouse
(Mus musculus)
Mammalia Vangl2 34 16 35
  • 89.89 (n)
rat
(Rattus norvegicus)
Mammalia Vangl2 34
  • 89.89 (n)
oppossum
(Monodelphis domestica)
Mammalia VANGL2 35
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 55 (a)
OneToMany
-- 35
  • 36 (a)
OneToMany
dog
(Canis familiaris)
Mammalia VANGL2 35
  • 46 (a)
OneToOne
chicken
(Gallus gallus)
Aves VANGL2 34 35
  • 85.22 (n)
lizard
(Anolis carolinensis)
Reptilia VANGL2 35
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vangl2 34
  • 79.4 (n)
Str.11014 34
zebrafish
(Danio rerio)
Actinopterygii vangl2 34 35
  • 74.66 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vang 36 35
  • 46 (a)
worm
(Caenorhabditis elegans)
Secernentea B0410.2a 36
  • 31 (a)
B0410.2b 36
  • 31 (a)
vang-1 35
  • 30 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10649 35
  • 50 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2933 34
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 Sequence Context AA Info Type
rs267607167 other, Neural tube defects (NTD) [MIM:182940] 160,421,171(+) GGGTG(C/G/T)GCAAG reference, missense
rs267607168 other, Neural tube defects (NTD) [MIM:182940] 160,425,122(+) GGCCT(C/T)CTTGG reference, missense
VAR_067221 Neural tube defects (NTD) [MIM:182940]
rs1000083348 -- 160,425,919(+) CAGGG(A/G)TACTC utr-variant-3-prime
rs1000087397 -- 160,398,760(+) ACAGG(C/G)TAGCA intron-variant, upstream-variant-2KB

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)

Relevant External Links 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

(24) MalaCards diseases for VANGL2 Gene - From: OMIM, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
neural tube defects
  • spina bifida
vangl2-related neural tube defect
strabismus
anencephaly
  • absence of a large part of the brain and the skull
craniorachischisis
- 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.

Relevant External Links for VANGL2

Genetic Association Database (GAD)
VANGL2
Human Genome Epidemiology (HuGE) Navigator
VANGL2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VANGL2
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 Y.P. … Wang H.Y. (N. Engl. J. Med. 2010) 3 4 46 64
  2. A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. (PMID: 19734545) Need A.C. … Goldstein D.B. (Hum. Mol. Genet. 2009) 3 46 64
  3. Mutation analysis of the Vangl2 coding region revealed no common cause for Tetralogy of Fallot. (PMID: 18034999) Erdal E. … AAsikel U. (J. Int. Med. Res. 2007) 3 22 64
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for VANGL2 Gene

Sources for VANGL2 Gene

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