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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
  • KITENIN 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 Neural Tube Defects and Sacral Defect With Anterior Meningocele. Among its related pathways are Wnt / Hedgehog / Notch and Wnt Signaling Pathway and Pluripotency. An important paralog of this gene is VANGL2.

Additional gene information for VANGL1 Gene

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

GeneHancer (GH) Regulatory Elements for VANGL1 Gene

Promoters and enhancers for VANGL1 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
GH01I115641 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 574.8 +0.4 433 2.4 HDGF PKNOX1 CLOCK ARNT SIN3A YBX1 DMAP1 ZNF2 ZNF766 ZNF213 VANGL1 ATP1A1-AS1 SIKE1 ENSG00000207502 CD58 CASQ2
GH01I115646 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 24.5 +7.0 6980 5.5 HDGF ATF1 PKNOX1 FEZF1 IRF4 BRCA1 ZNF766 GLIS2 ATF7 FOS VANGL1 ENSG00000207502 CASQ2
GH01I115654 Enhancer 1.2 Ensembl ENCODE dbSUPER 16 +13.3 13324 1.5 BCOR HDAC1 MEIS2 PKNOX1 JUN TEAD4 TAL1 ZMYM3 TCF12 MTA3 VANGL1 CASQ2
GH01I115557 Enhancer 0.6 dbSUPER 22.3 -83.1 -83134 3.2 NFIB ZBTB21 ZNF189 ZIC2 ATF2 NFIC SCRT2 ZNF629 CREB1 ATF7 VANGL1 ELOCP20 CNOT7P2
GH01I115676 Enhancer 0.9 FANTOM5 ENCODE 12.4 +36.3 36251 4.4 CTCF BMI1 FOSL1 GATA3 SCRT2 ZNF143 FOSL2 FOS IKZF2 RUNX3 VANGL1 ENSG00000207502 CASQ2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VANGL1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VANGL1 gene promoter:

Genomic Locations for VANGL1 Gene

Genomic Locations for VANGL1 Gene
chr1:115,641,953-115,698,224
(GRCh38/hg38)
Size:
56,272 bases
Orientation:
Plus strand
chr1:116,184,574-116,240,845
(GRCh37/hg19)

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:
    Q8TAA9-VANG1_HUMAN
    Recommended name:
    Vang-like protein 1
    Protein Accession:
    Q8TAA9
    Secondary Accessions:
    • Q5T1D3
    • Q5T1D4
    • Q86WG8
    • Q8N559

    Protein attributes for VANGL1 Gene

    Size:
    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).
    SequenceCaution:
    • Sequence=AAH32773.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for VANGL1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VANGL1 Gene

Post-translational modifications for VANGL1 Gene

  • Ubiquitination at posLast=299299, isoforms=2310, and posLast=382382
  • Modification sites at PhosphoSitePlus

Other Protein References for VANGL1 Gene

Antibody Products

  • R&D Systems Antibodies for VANGL1 (Vang-like Protein 1/VANGL1)
  • Abcam antibodies for VANGL1
  • Santa Cruz Biotechnology (SCBT) Antibodies for VANGL1

No data available for DME Specific Peptides for VANGL1 Gene

Domains & Families for VANGL1 Gene

Gene Families for VANGL1 Gene

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

Protein Domains for VANGL1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for VANGL1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8TAA9

UniProtKB/Swiss-Prot:

VANG1_HUMAN :
  • Belongs to the Vang family.
Family:
  • Belongs to the Vang family.
genes like me logo Genes that share domains with VANGL1: view

Function for VANGL1 Gene

Phenotypes From GWAS Catalog 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

Clone 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

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 VANGL1 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 2
nucleus 2
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
See all subcellular structures

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 KEGG pathway for VANGL1 Gene
1 Cell Signaling Technology 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:

Clone 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: - -
SP4:
SP5:

Relevant External Links for VANGL1 Gene

GeneLoc Exon Structure for
VANGL1
ECgene alternative splicing isoforms for
VANGL1

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:

VANGL1

SOURCE GeneReport for Unigene cluster for VANGL1 Gene:

Hs.515130

mRNA Expression by UniProt/SwissProt for VANGL1 Gene:

Q8TAA9-VANG1_HUMAN
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
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • head
  • meninges
  • neck
Thorax:
  • aorta
  • esophagus
  • heart
  • lung
  • rib
  • rib cage
  • trachea
Abdomen:
  • intestine
  • kidney
  • large intestine
  • pancreas
  • small intestine
  • stomach
Pelvis:
  • anus
  • ovary
  • pelvis
  • penis
  • placenta
  • rectum
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vagina
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • finger
  • foot
  • forearm
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • 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

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
chimpanzee
(Pan troglodytes)
Mammalia VANGL1 33 34
  • 99.49 (n)
cow
(Bos Taurus)
Mammalia VANGL1 33 34
  • 90.46 (n)
dog
(Canis familiaris)
Mammalia VANGL1 33 34
  • 90.39 (n)
oppossum
(Monodelphis domestica)
Mammalia VANGL1 34
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vangl1 33 16 34
  • 88.74 (n)
rat
(Rattus norvegicus)
Mammalia Vangl1 33
  • 88.74 (n)
chicken
(Gallus gallus)
Aves VANGL1 33 34
  • 80.59 (n)
lizard
(Anolis carolinensis)
Reptilia VANGL1 34
  • 81 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii vangl1 33 34
  • 66.54 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012288 33
  • 53.96 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vang 35 33 34
  • 53.93 (n)
worm
(Caenorhabditis elegans)
Secernentea vang-1 33 34
  • 46.26 (n)
B0410.2a 35
  • 34 (a)
B0410.2b 35
  • 34 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10649 34
  • 50 (a)
OneToMany
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

ENSEMBL:
Gene Tree for VANGL1 (if available)
TreeFam:
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 Variation AA Info Type
rs1005223172 uncertain-significance, Neural tube defect, Caudal dysgenesis syndrome 115,697,372(+) C/G 3_prime_UTR_variant
rs10494179 likely-benign, Neural tube defect, Catecholaminergic polymorphic ventricular tachycardia, Caudal dysgenesis syndrome 115,696,747(+) G/A 3_prime_UTR_variant
rs10801933 likely-benign, Caudal dysgenesis syndrome, Neural tube defect, Catecholaminergic polymorphic ventricular tachycardia 115,697,130(+) A/G 3_prime_UTR_variant
rs10923204 likely-benign, Neural tube defect, Caudal dysgenesis syndrome 115,694,402(+) G/T 3_prime_UTR_variant
rs114033235 uncertain-significance, Neural tube defect, Caudal dysgenesis syndrome 115,693,151(+) A/G 3_prime_UTR_variant

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)

Additional Variant Information for VANGL1 Gene

Human Gene Mutation Database (HGMD)
VANGL1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VANGL1

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

Disorders for VANGL1 Gene

MalaCards: The human disease database

(18) MalaCards diseases for VANGL1 Gene - From: HGMD, OMIM, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
neural tube defects
  • neural tube defects, susceptibility to
sacral defect with anterior meningocele
  • sdam
strabismus
  • strabismus, susceptibility to
meningocele
  • spinal meningocele
upper thoracic spina bifida cystica
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

VANG1_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: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.

Additional Disease Information for VANGL1

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 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 (International journal of oncology 2002) 2 3 4 22 58
  2. Novel mutations in VANGL1 in neural tube defects. (PMID: 19319979) Kibar Z … Gros P (Human mutation 2009) 3 4 44 58
  3. Isolation and characterization of a novel human gene, VANGL1, as a therapeutic target for hepatocellular carcinoma. (PMID: 12011995) Yagyu R … Nakamura Y (International journal of oncology 2002) 2 3 4 58
  4. Mutations in VANGL1 associated with neural-tube defects. (PMID: 17409324) Kibar Z … Gros P (The New England journal of medicine 2007) 3 4 58
  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 (American journal of medical genetics. Part A 2005) 3 4 58

Products for VANGL1 Gene

Sources for VANGL1 Gene

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