VANGL2 (VANGL planar cell polarity protein 2) - Chinchilla Research Resource Database
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Gene: VANGL2 (VANGL planar cell polarity protein 2) Homo sapiens
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Symbol: VANGL2
Name: VANGL planar cell polarity protein 2
CRRD ID: 1319787
Description: Predicted to be involved in several processes, including apical protein localization; inner ear development; and morphogenesis of an epithelium. Predicted to localize to several cellular components, including apical cytoplasm; apical plasma membrane; and lateral plasma membrane. Implicated in neural tube defect.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: KIAA1215; loop-tail protein 1 homolog; loop-tail-associated protein; LPP1; LTAP; MGC119403; MGC119404; STB1; STBM; STBM1; strabismus 1; van Gogh-like protein 2; vang, van gogh-like 2; vang-like 2 (van gogh, Drosophila); vang-like protein 2
Orthologs:
Mus musculus (house mouse) : Vangl2 (VANGL planar cell polarity 2)  MGI  Alliance
Rattus norvegicus (Norway rat) : Vangl2 (VANGL planar cell polarity protein 2)  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Vangl2 (VANGL planar cell polarity protein 2)
Pan paniscus (bonobo/pygmy chimpanzee) : VANGL2 (VANGL planar cell polarity protein 2)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Vangl2 (VANGL planar cell polarity protein 2)
Sus scrofa (pig) : VANGL2 (VANGL planar cell polarity protein 2)
Chlorocebus sabaeus (African green monkey) : VANGL2 (VANGL planar cell polarity protein 2)
Heterocephalus glaber (naked mole-rat) : Vangl2 (VANGL planar cell polarity protein 2)
more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1160,400,564 - 160,428,670 (+)EnsemblGRCh38hg38GRCh38
GRCh381160,400,564 - 160,428,674 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371160,370,364 - 160,398,468 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361158,636,988 - 158,665,088 (+)NCBINCBI36hg18NCBI36
Build 341157,198,538 - 157,211,533NCBI
Celera1133,439,094 - 133,467,201 (+)NCBI
Cytogenetic Map1q23.2NCBI
HuRef1131,726,520 - 131,754,628 (+)NCBIHuRef
CHM1_11161,765,749 - 161,793,853 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anterior/posterior pattern specification  (IEA)
apical protein localization  (ISS)
cell migration involved in kidney development  (ISS)
cochlea development  (ISO)
cochlea morphogenesis  (IEA)
convergent extension involved in axis elongation  (IEA)
convergent extension involved in neural plate elongation  (IEA)
convergent extension involved in organogenesis  (ISO)
digestive tract morphogenesis  (IEA)
dopaminergic neuron axon guidance  (IEA)
establishment of body hair planar orientation  (IEA)
establishment of planar polarity  (IBA,ISS)
establishment of planar polarity involved in neural tube closure  (IEA)
establishment or maintenance of epithelial cell apical/basal polarity  (IEA)
glomerulus development  (IEA)
hair follicle development  (IEA)
heart looping  (ISS)
heparan sulfate proteoglycan biosynthetic process  (IEA)
inner ear receptor cell development  (ISO)
inner ear receptor cell stereocilium organization  (IEA)
kidney morphogenesis  (IEA)
lateral sprouting involved in lung morphogenesis  (IEA)
membranous septum morphogenesis  (IEA)
muscular septum morphogenesis  (IEA)
neural tube closure  (ISS)
non-canonical Wnt signaling pathway  (ISO)
non-motile cilium assembly  (ISS)
orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis  (IEA)
planar cell polarity pathway involved in axis elongation  (IEA)
planar cell polarity pathway involved in axon guidance  (IEA)
planar cell polarity pathway involved in heart morphogenesis  (IEA)
planar cell polarity pathway involved in neural tube closure  (IEA)
planar dichotomous subdivision of terminal units involved in lung branching morphogenesis  (IEA)
positive regulation of JUN kinase activity  (IEA)
post-anal tail morphogenesis  (IEA)
regulation of actin cytoskeleton organization  (IEA)
regulation of establishment of planar polarity  (ISO)
regulation of Wnt signaling pathway  (IEA)
Rho protein signal transduction  (IEA)
serotonergic neuron axon guidance  (IEA)
somatic stem cell division  (IEA)
somatic stem cell population maintenance  (IEA)
Wnt signaling pathway, planar cell polarity pathway  (IBA)
wound healing  (IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10574462   PMID:11431695   PMID:12477932   PMID:12490194   PMID:15195140   PMID:15489334   PMID:16710414   PMID:18034999   PMID:18849982   PMID:19577357   PMID:19734545   PMID:20223754  
PMID:20558380   PMID:20738329   PMID:21142127   PMID:21873635   PMID:22610794   PMID:23326640   PMID:23579212   PMID:25068569   PMID:25200836   PMID:25544563   PMID:25627785   PMID:25921289  
PMID:26186194   PMID:26638075   PMID:26754771   PMID:27036398   PMID:28330616   PMID:28481871   PMID:28514442   PMID:28675297   PMID:29097183   PMID:29395067   PMID:29499154   PMID:30125361  
PMID:30126976   PMID:30194290   PMID:30472097   PMID:30639242   PMID:31056421   PMID:31177093   PMID:31678930   PMID:31753913   PMID:32062451   PMID:32877691  


Genomics

Comparative Map Data
VANGL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1160,400,564 - 160,428,670 (+)EnsemblGRCh38hg38GRCh38
GRCh381160,400,564 - 160,428,674 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371160,370,364 - 160,398,468 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361158,636,988 - 158,665,088 (+)NCBINCBI36hg18NCBI36
Build 341157,198,538 - 157,211,533NCBI
Celera1133,439,094 - 133,467,201 (+)NCBI
Cytogenetic Map1q23.2NCBI
HuRef1131,726,520 - 131,754,628 (+)NCBIHuRef
CHM1_11161,765,749 - 161,793,853 (+)NCBICHM1_1
Vangl2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391171,828,527 - 171,856,532 (-)NCBI
GRCm381172,000,960 - 172,027,318 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1172,000,960 - 172,028,444 (-)EnsemblGRCm38mm10GRCm38
MGSCv371173,934,502 - 173,957,399 (-)NCBIGRCm37mm9NCBIm37
MGSCv361173,841,046 - 173,863,943 (-)NCBImm8
Celera1174,856,349 - 174,879,265 (-)NCBICelera
Cytogenetic Map1H3NCBI
cM Map179.54NCBI
Vangl2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01390,379,203 - 90,405,627 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1390,380,632 - 90,405,591 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01394,902,313 - 94,928,719 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41387,964,426 - 87,988,364 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11388,152,106 - 88,178,412 (-)NCBI
Celera1384,077,622 - 84,101,482 (-)NCBICelera
Cytogenetic Map13q24NCBI
Vangl2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546812,161,843 - 12,189,547 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546812,162,084 - 12,189,322 (+)NCBIChiLan1.0ChiLan1.0
VANGL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11139,676,595 - 139,704,281 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1139,683,745 - 139,704,281 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01135,754,897 - 135,783,031 (+)NCBIMhudiblu_PPA_v0panPan3
Vangl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936740228,377 - 242,318 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VANGL2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl490,053,380 - 90,080,656 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1490,051,994 - 90,080,701 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2497,945,552 - 97,971,014 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VANGL2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl203,521,060 - 3,548,718 (-)Ensembl
ChlSab1.1203,521,066 - 3,549,301 (-)NCBI
Vangl2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624794841,302 - 867,717 (-)NCBI

Position Markers
RH92930  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371160,372,984 - 160,373,127UniSTSGRCh37
Build 361158,639,608 - 158,639,751RGDNCBI36
Celera1133,441,713 - 133,441,856RGD
Cytogenetic Map1q22-q23UniSTS
HuRef1131,729,144 - 131,729,287UniSTS
GeneMap99-GB4 RH Map1584.71UniSTS
VANGL2__5059  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371160,397,792 - 160,398,533UniSTSGRCh37
Build 361158,664,416 - 158,665,157RGDNCBI36
Celera1133,466,525 - 133,467,266RGD
HuRef1131,753,953 - 131,754,693UniSTS
AL009375  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371160,368,533 - 160,368,664UniSTSGRCh37
Build 361158,635,157 - 158,635,288RGDNCBI36
Celera1133,437,267 - 133,437,398RGD
Cytogenetic Map1q22-q23UniSTS
HuRef1131,724,689 - 131,724,820UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2185
Count of miRNA genes:971
Interacting mature miRNAs:1135
Transcripts:ENST00000368061, ENST00000483408
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 681 24 772 178 126 20 1771 158 1152 95 937 1115 167 7 899 1
Low 1696 1865 579 146 897 145 2244 1945 2564 278 503 438 7 1 1187 1564 2 2
Below cutoff 35 1072 356 286 836 286 336 86 7 36 14 35 10 325 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000368061   ⟹   ENSP00000357040
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1160,400,564 - 160,428,670 (+)Ensembl
RefSeq Acc Id: ENST00000483408
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1160,419,493 - 160,424,147 (+)Ensembl
RefSeq Acc Id: NM_020335   ⟹   NP_065068
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381160,400,564 - 160,428,670 (+)NCBI
GRCh371160,370,364 - 160,398,468 (+)RGD
Build 361158,636,988 - 158,665,088 (+)NCBI Archive
Celera1133,439,094 - 133,467,201 (+)RGD
HuRef1131,726,520 - 131,754,628 (+)ENTREZGENE
CHM1_11161,765,749 - 161,793,853 (+)NCBI
Sequence:
RefSeq Acc Id: XM_005245357   ⟹   XP_005245414
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381160,408,532 - 160,428,674 (+)NCBI
GRCh371160,370,364 - 160,398,468 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011509804   ⟹   XP_011508106
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381160,401,179 - 160,428,674 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011509805   ⟹   XP_011508107
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381160,415,717 - 160,420,398 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_065068   ⟸   NM_020335
- UniProtKB: Q9ULK5 (UniProtKB/Swiss-Prot),   A8K4L6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005245414   ⟸   XM_005245357
- Peptide Label: isoform X1
- UniProtKB: Q9ULK5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011508106   ⟸   XM_011509804
- Peptide Label: isoform X1
- UniProtKB: Q9ULK5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011508107   ⟸   XM_011509805
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSP00000357040   ⟸   ENST00000368061

Promoters
RGD ID:6787207
Promoter ID:HG_KWN:5772
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562
Transcripts:OTTHUMT00000080677,   UC001FWB.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361158,636,601 - 158,637,101 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_020335.3(VANGL2):c.1057C>T (p.Arg353Cys) single nucleotide variant Neural tube defects, susceptibility to [RCV000009619] Chr1:160421171 [GRCh38]
Chr1:160390961 [GRCh37]
Chr1:1q23.2
pathogenic|risk factor
NM_020335.3(VANGL2):c.1310T>C (p.Phe437Ser) single nucleotide variant Neural tube defects, susceptibility to [RCV000009620] Chr1:160425122 [GRCh38]
Chr1:160394912 [GRCh37]
Chr1:1q23.2
pathogenic|risk factor
GRCh38/hg38 1q23.2-24.1(chr1:159479887-166895086)x1 copy number loss See cases [RCV000051172] Chr1:159479887..166895086 [GRCh38]
Chr1:159449677..166864323 [GRCh37]
Chr1:157716301..165130947 [NCBI36]
Chr1:1q23.2-24.1
pathogenic
GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3 copy number gain See cases [RCV000051854] Chr1:157747246..176021247 [GRCh38]
Chr1:157717036..175990383 [GRCh37]
Chr1:155983660..174257006 [NCBI36]
Chr1:1q23.1-25.1
pathogenic
GRCh38/hg38 1q23.1-23.3(chr1:156664483-160727411)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051851]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051851]|See cases [RCV000051851] Chr1:156664483..160727411 [GRCh38]
Chr1:156634275..160697201 [GRCh37]
Chr1:154900899..158963825 [NCBI36]
Chr1:1q23.1-23.3
pathogenic
NM_020335.2(VANGL2):c.576C>T (p.Leu192=) single nucleotide variant Malignant melanoma [RCV000064256] Chr1:160419385 [GRCh38]
Chr1:160389175 [GRCh37]
Chr1:158655799 [NCBI36]
Chr1:1q23.2
not provided
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2
pathogenic
NM_020335.3(VANGL2):c.971G>A (p.Arg324Gln) single nucleotide variant not provided [RCV000522756] Chr1:160421085 [GRCh38]
Chr1:160390875 [GRCh37]
Chr1:1q23.2
uncertain significance
GRCh37/hg19 1q23.2-25.1(chr1:160369890-175796325) copy number loss not provided [RCV000767779] Chr1:160369890..175796325 [GRCh37]
Chr1:1q23.2-25.1
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
NM_020335.3(VANGL2):c.801-5C>G single nucleotide variant not provided [RCV000578880] Chr1:160420406 [GRCh38]
Chr1:160390196 [GRCh37]
Chr1:1q23.2
uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1q23.2-25.2(chr1:159815642-177026983)x1 copy number loss not provided [RCV000736717] Chr1:159815642..177026983 [GRCh37]
Chr1:1q23.2-25.2
pathogenic
NM_020335.3(VANGL2):c.1328C>T (p.Ala443Val) single nucleotide variant not provided [RCV000904271] Chr1:160425140 [GRCh38]
Chr1:160394930 [GRCh37]
Chr1:1q23.2
benign
NM_020335.3(VANGL2):c.1242C>T (p.Tyr414=) single nucleotide variant not provided [RCV000964376] Chr1:160424220 [GRCh38]
Chr1:160394010 [GRCh37]
Chr1:1q23.2
benign
NM_020335.3(VANGL2):c.91C>T (p.Arg31Cys) single nucleotide variant not provided [RCV000880270] Chr1:160416081 [GRCh38]
Chr1:160385871 [GRCh37]
Chr1:1q23.2
likely benign
GRCh37/hg19 1q23.2-23.3(chr1:159808188-161011163)x3 copy number gain not provided [RCV000846649] Chr1:159808188..161011163 [GRCh37]
Chr1:1q23.2-23.3
uncertain significance
NM_020335.3(VANGL2):c.1005C>T (p.Asp335=) single nucleotide variant not provided [RCV000893267] Chr1:160421119 [GRCh38]
Chr1:160390909 [GRCh37]
Chr1:1q23.2
benign
GRCh37/hg19 1q23.1-24.2(chr1:157321299-167391423)x1 copy number loss not provided [RCV000848773] Chr1:157321299..167391423 [GRCh37]
Chr1:1q23.1-24.2
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:15511 AgrOrtholog
COSMIC VANGL2 COSMIC
Ensembl Genes ENSG00000162738 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000357040 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000368061 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000162738 GTEx
HGNC ID HGNC:15511 ENTREZGENE
Human Proteome Map VANGL2 Human Proteome Map
InterPro VANGL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:57216 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 57216 ENTREZGENE
OMIM 182940 OMIM
  600533 OMIM
PANTHER PTHR20886 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Strabismus UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA37970 PharmGKB
PIRSF Strabismus UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Hs.99477 ENTREZGENE
UniProt A8K4L6 ENTREZGENE, UniProtKB/TrEMBL
  Q9ULK5 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary D3DVE9 UniProtKB/Swiss-Prot
  Q5T212 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-12 VANGL2  VANGL planar cell polarity protein 2    vang-like 2 (van gogh, Drosophila)  Symbol and/or name change 5135510 APPROVED