Human Gene VANGL1 (ENST00000369509.1) Description and Page Index
  Description: 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). (from UniProt Q8TAA9)
RefSeq Summary (NM_001172412): 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].
Gencode Transcript: ENST00000369509.1
Gencode Gene: ENSG00000173218.15
Transcript (Including UTRs)
   Position: hg38 chr1:115,651,402-115,691,854 Size: 40,453 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg38 chr1:115,651,414-115,691,379 Size: 39,966 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:115,651,402-115,691,854)mRNA (may differ from genome)Protein (524 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsHGNCHPRD
LynxMGIneXtProtPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: VANG1_HUMAN
DESCRIPTION: RecName: Full=Vang-like protein 1; AltName: Full=Loop-tail protein 2 homolog; Short=LPP2; AltName: Full=Strabismus 2; AltName: Full=Van Gogh-like protein 1;
SUBUNIT: 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).
INTERACTION: P27701:CD82; NbExp=6; IntAct=EBI-682393, EBI-682379;
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
TISSUE SPECIFICITY: According to PubMed:11956595, ubiquitously expressed. According to PubMed:12011995, expressed specifically in testis and ovary.
DISEASE: Defects in VANGL1 are a cause of neural tube defects (NTD) [MIM:182940]. NTD are congenital malformations. The most common forms of NTD are described as open defects (including anencephaly and myelomeningocele, or spina bifida), which result from the failure of fusion in the cranial and spinal region of the neural tube, respectively. Other open dysraphisms (including myeloschisis, hemimyelomeningocele, and hemimyelocele) are sometimes associated with a Chiari type 2 malformation. A number of skin-covered (closed) NTD are categorized clinically depending on the presence of a subcutaneous mass (lipomyeloschisis, lipomyelomeningocele, meningocele, and myelocystocele) or the absence of such a mass (complex dysraphic states, including split cord malformations, dermal sinus, caudal regression, and segmental spinal dysgenesis).
DISEASE: Defects in VANGL1 are a cause of sacral defect with anterior meningocele (SDAM) [MIM:600145]. SDAM is a 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.
SIMILARITY: Belongs to the Vang family.
SEQUENCE CAUTION: Sequence=AAH32773.1; Type=Erroneous initiation;

-  MalaCards Disease Associations
  MalaCards Gene Search: VANGL1
Diseases sorted by gene-association score: caudal regression syndrome* (925), neural tube defects* (915), vangl1-related neural tube defect* (100), strabismus (18), meningocele (16), upper thoracic spina bifida cystica* (14), cervicothoracic spina bifida cystica* (14), cervical spina bifida cystica* (14), lumbosacral spina bifida cystica* (14), thoracolumbosacral spina bifida cystica* (14), total spina bifida cystica* (14), upper thoracic spina bifida aperta* (14), thoracolumbosacral spina bifida aperta* (14), lumbosacral spina bifida aperta* (14), cervical spina bifida aperta* (14), cervicothoracic spina bifida aperta* (14), total spina bifida aperta* (14), anencephaly (10), myelomeningocele (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.35 RPKM in Cells - Transformed fibroblasts
Total median expression: 85.90 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -118.80475-0.250 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009539 - Strabismus

Pfam Domains:
PF06638 - Strabismus protein

ModBase Predicted Comparative 3D Structure on Q8TAA9
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsemblWormBase 
Protein SequenceProtein Sequence Protein SequenceProtein Sequence 
AlignmentAlignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007275 multicellular organism development
GO:0043473 pigmentation
GO:0060071 Wnt signaling pathway, planar cell polarity pathway

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016328 lateral plasma membrane


-  Descriptions from all associated GenBank mRNAs
  LF205106 - JP 2014500723-A/12609: Polycomb-Associated Non-Coding RNAs.
MA440683 - JP 2018138019-A/12609: Polycomb-Associated Non-Coding RNAs.
BC065272 - Homo sapiens vang-like 1 (van gogh, Drosophila), mRNA (cDNA clone MGC:70584 IMAGE:6165098), complete cds.
AF481859 - Homo sapiens loop-tail protein 2 (LPP2) mRNA, complete cds.
AB057596 - Homo sapiens vangl1 mRNA, complete cds.
AB075805 - Homo sapiens VANGL1 mRNA for four-transmembrane protein associating with Dishevelled, complete cds.
CU688034 - Synthetic construct Homo sapiens gateway clone IMAGE:100021774 5' read VANGL1 mRNA.
KJ894860 - Synthetic construct Homo sapiens clone ccsbBroadEn_04254 VANGL1 gene, encodes complete protein.
KR711140 - Synthetic construct Homo sapiens clone CCSBHm_00020657 VANGL1 (VANGL1) mRNA, encodes complete protein.
KR711141 - Synthetic construct Homo sapiens clone CCSBHm_00020658 VANGL1 (VANGL1) mRNA, encodes complete protein.
KR711142 - Synthetic construct Homo sapiens clone CCSBHm_00020659 VANGL1 (VANGL1) mRNA, encodes complete protein.
KR712222 - Synthetic construct Homo sapiens clone CCSBHm_00900176 VANGL1 (VANGL1) mRNA, encodes complete protein.
AB590612 - Synthetic construct DNA, clone: pFN21AE1961, Homo sapiens VANGL1 gene for vang-like 1, without stop codon, in Flexi system.
BC032773 - Homo sapiens, Similar to vang-like 1 (van gogh, Drosophila), clone IMAGE:4430257, mRNA, partial cds.
JD553752 - Sequence 534776 from Patent EP1572962.
JD505031 - Sequence 486055 from Patent EP1572962.
JD049422 - Sequence 30446 from Patent EP1572962.
JD143120 - Sequence 124144 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04310 - Wnt signaling pathway

-  Other Names for This Gene
  Alternate Gene Symbols: AB075805, Q5T1D3, Q5T1D4, Q86WG8, Q8N559, Q8TAA9, STB2, uc057jri.1, VANG1_HUMAN
UCSC ID: uc057jri.1
RefSeq Accession: NM_001172412
Protein: Q8TAA9 (aka VANG1_HUMAN or VAN1_HUMAN)
CCDS: CCDS883.1, CCDS53350.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.