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] See more...

Aliases for VANGL1 Gene

Aliases for VANGL1 Gene

  • VANGL Planar Cell Polarity Protein 1 2 3 5
  • STB2 2 3 4
  • Vang-Like 1 (Van Gogh, Drosophila) 2 3
  • Loop-Tail Protein 2 Homolog 3 4
  • Van Gogh-Like Protein 1 3 4
  • Vang-Like Protein 1 3 4
  • Strabismus 2 3 4
  • LPP2 3 4
  • Vang (Van Gogh, Drosophila)-Like 1, Vang, Van Gogh-Like 1 (Drosophila) 2
  • KAI1 C-Terminal Interacting Tetraspanin 3
  • KITENIN 3
  • VANGL1 5
  • 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 Sacral Defect With Anterior Meningocele and Neural Tube Defects. Among its related pathways are Wnt / Hedgehog / Notch and Wnt signaling pathway. An important paralog of this gene is VANGL2.

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VANGL1 Gene

Genomics for VANGL1 Gene

GeneHancer (GH) Regulatory Elements Pubs

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
GH01J115641 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 274.7 +0.6 631 2.8 CHD2 TBP ZBTB10 MNT IKZF1 BRCA1 CTCF BHLHE40 ELF1 NONO VANGL1 ATP1A1-AS1 SIKE1 ENSG00000207502 CD58 HE856257 CASQ2
GH01J115646 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 24.5 +7.0 6963 5.5 BCL11A FEZF1 IKZF1 BRCA1 ZIC2 SIN3A GTF2E2 TRIM22 IRF4 EP300 VANGL1 ENSG00000207502 CASQ2 HE856257
GH01J115608 Enhancer 0.8 Ensembl ENCODE 24.3 -33.4 -33420 0.5 ZNF217 CTCF REST TRIM22 SMC3 RAD21 ARID3A CREB1 ZSCAN4 ARID2 VANGL1 RN7SL420P RF00017-302 ENSG00000207502 NGF
GH01J115594 Enhancer 0.8 Ensembl ENCODE 22.1 -46.7 -46669 2.6 DEK CTCF REST TRIM22 SMC3 RAD21 RFX5 MAX ZNF143 GLIS1 piR-54207 VANGL1 ENSG00000207502 CASQ2 NGF-AS1 NGF lnc-CASQ2-1 LOC100287840
GH01J115654 Enhancer 0.9 ENCODE dbSUPER 16.1 +13.3 13307 1.5 MNT BHLHE40 TAL1 ZNF316 SMARCA4 HDAC2 ZBTB33 TCF12 MTA2 NFE2 VANGL1 HE856257 CASQ2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VANGL1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VANGL1

Top Transcription factor binding sites by QIAGEN in the VANGL1 gene promoter:
  • AP-1
  • c-Fos
  • c-Jun
  • Cdc5
  • E4BP4
  • FosB
  • Fra-1
  • JunB
  • Pax-5
  • POU3F2

Genomic Locations for VANGL1 Gene

Latest Assembly
chr1:115,641,970-115,698,224
(GRCh38/hg38)
Size:
56,255 bases
Orientation:
Plus strand

Previous Assembly
chr1:116,184,591-116,240,842
(GRCh37/hg19 by Entrez Gene)
Size:
56,252 bases
Orientation:
Plus strand

chr1:116,184,574-116,240,845
(GRCh37/hg19 by Ensembl)
Size:
56,272 bases
Orientation:
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:
    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 Lys299, Lys310, 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

Gene Families for VANGL1 Gene

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

Protein Domains for VANGL1 Gene

InterPro:
Blocks:
  • Strabismus
ProtoNet:

Suggested Antigen Peptide Sequences for VANGL1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ92368 (Q96J52_HUMAN)
  • Van Gogh-like protein 1 (VANG1_HUMAN)

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:
  • Vangl1 Vangl1<tm1e(KOMP)Wtsi>

Animal Models for research

  • Taconic Biosciences Mouse Models for VANGL1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VANGL1

Clone products for research

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 3
nucleus 3
extracellular 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1
peroxisome 0

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 IBA 21873635
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

PathCards logo

SuperPathways 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

mRNA/cDNA for VANGL1 Gene

3 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VANGL1

Clone products for research

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

Expression for VANGL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for VANGL1 Gene



Protein tissue co-expression partners for VANGL1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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(4.4)

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

Primer products for research

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 30 31
  • 99.49 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia VANGL1 30 31
  • 90.46 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia VANGL1 30 31
  • 90.39 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia VANGL1 31
  • 90 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Vangl1 30 17 31
  • 88.74 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Vangl1 30
  • 88.74 (n)
Chicken
(Gallus gallus)
Aves VANGL1 30 31
  • 80.59 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia VANGL1 31
  • 81 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii vangl1 30 31
  • 66.54 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012288 30
  • 53.96 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta Vang 30 31 32
  • 53.93 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea vang-1 30 31
  • 46.26 (n)
OneToMany
B0410.2a 32
  • 34 (a)
B0410.2b 32
  • 34 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.10649 31
  • 50 (a)
OneToMany
Species where no ortholog for VANGL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for VANGL1: view image

Paralogs for VANGL1 Gene

Paralogs for VANGL1 Gene

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

  • VANG1_HUMAN
  • Q96J52_HUMAN
genes like me logo Genes that share paralogs with VANGL1: view

Variants for VANGL1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VANGL1 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
873558 Uncertain Significance: Neural tube defect; Caudal regression sequence 115,663,909(+) G/A
NM_138959.3(VANGL1):c.453G>A (p.Gly151=)
SYNONYMOUS
873609 Conflicting Interpretations: Neural tube defect; Caudal regression sequence 115,682,419(+) T/C
NM_138959.3(VANGL1):c.868T>C (p.Tyr290His)
MISSENSE
873610 Conflicting Interpretations: Neural tube defect; Caudal regression sequence 115,684,020(+) C/T
NM_138959.3(VANGL1):c.1023C>T (p.Asn341=)
SYNONYMOUS
873611 Conflicting Interpretations: Neural tube defect; Caudal regression sequence 115,684,047(+) T/C
NM_138959.3(VANGL1):c.1050T>C (p.His350=)
SYNONYMOUS
873669 Uncertain Significance: Neural tube defect; Caudal regression sequence 115,691,608(+) T/A
NM_138959.3(VANGL1):c.*229T>A
THREE_PRIME_UTR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for VANGL1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

SNP Genotyping and Copy Number Assays for research

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

Disorders for VANGL1 Gene

MalaCards: The human disease database

(30) MalaCards diseases for VANGL1 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- 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 variants 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 variants affecting the gene represented in this entry.

Additional Disease Information for VANGL1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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 23
  2. Novel mutations in VANGL1 in neural tube defects. (PMID: 19319979) Kibar Z … Gros P (Human mutation 2009) 3 4 41
  3. Mutations in VANGL1 associated with neural-tube defects. (PMID: 17409324) Kibar Z … Gros P (The New England journal of medicine 2007) 3 4 74
  4. 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
  5. Independent mutations at Arg181 and Arg274 of Vangl proteins that are associated with neural tube defects in humans decrease protein stability and impair membrane targeting. (PMID: 25068569) Iliescu A … Gros P (Biochemistry 2014) 3 74

Products for VANGL1 Gene

Sources for VANGL1 Gene