Incidental Mutation 'R2268:Vangl1'
ID 242210
Institutional Source Beutler Lab
Gene Symbol Vangl1
Ensembl Gene ENSMUSG00000027860
Gene Name VANGL planar cell polarity 1
Synonyms stbm, KITENIN, Lpp2, mStbm
MMRRC Submission 040268-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.304) question?
Stock # R2268 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 102060899-102112009 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 102104160 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Asparagine at position 7 (Y7N)
Ref Sequence ENSEMBL: ENSMUSP00000126254 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029453] [ENSMUST00000159388] [ENSMUST00000159586] [ENSMUST00000161722] [ENSMUST00000168312]
AlphaFold Q80Z96
Predicted Effect probably damaging
Transcript: ENSMUST00000029453
AA Change: Y7N

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000029453
Gene: ENSMUSG00000027860
AA Change: Y7N

DomainStartEndE-ValueType
low complexity region 5 21 N/A INTRINSIC
Pfam:Strabismus 23 360 3.4e-171 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000159388
AA Change: Y7N

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000125043
Gene: ENSMUSG00000027860
AA Change: Y7N

DomainStartEndE-ValueType
low complexity region 5 21 N/A INTRINSIC
Pfam:Strabismus 25 526 8.6e-262 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000159586
AA Change: Y7N

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000124874
Gene: ENSMUSG00000027860
AA Change: Y7N

DomainStartEndE-ValueType
low complexity region 5 21 N/A INTRINSIC
Pfam:Strabismus 23 137 3.5e-41 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000161722
AA Change: Y7N

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
Predicted Effect probably damaging
Transcript: ENSMUST00000168312
AA Change: Y7N

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000126254
Gene: ENSMUSG00000027860
AA Change: Y7N

DomainStartEndE-ValueType
low complexity region 5 21 N/A INTRINSIC
Pfam:Strabismus 23 357 1.2e-170 PFAM
Pfam:Strabismus 354 476 9.5e-67 PFAM
Meta Mutation Damage Score 0.1015 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 94.7%
Validation Efficiency 100% (82/82)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] 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]
PHENOTYPE: Mice homozygous for a gene trapped allele display abnormal orientation of cochlear hair cell stereociliary bundles but do not develop neural tube or cardiac outflow tract abnormalities. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 82 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acox2 A T 14: 8,253,496 (GRCm38) M217K probably damaging Het
Adam34 C T 8: 44,103,647 (GRCm39) R666H probably benign Het
Adap2 G T 11: 80,056,552 (GRCm39) Q188H probably damaging Het
Adgrb3 T C 1: 25,150,898 (GRCm39) T872A possibly damaging Het
Ahnak A G 19: 8,987,938 (GRCm39) K3074R possibly damaging Het
Ano7 A T 1: 93,308,161 (GRCm39) D64V possibly damaging Het
Apob T C 12: 8,065,475 (GRCm39) F4115S possibly damaging Het
Arl13a A G X: 133,106,162 (GRCm39) Q236R possibly damaging Het
Astn1 T C 1: 158,329,669 (GRCm39) Y175H probably damaging Het
Atn1 C G 6: 124,723,203 (GRCm39) probably benign Het
Ccser1 C T 6: 61,547,827 (GRCm39) T118M probably damaging Het
Cenpe A G 3: 134,967,397 (GRCm39) T2180A probably benign Het
Col17a1 G A 19: 47,638,550 (GRCm39) P1173S probably benign Het
Commd8 A G 5: 72,322,765 (GRCm39) W51R probably damaging Het
Cyp4f17 G T 17: 32,736,928 (GRCm39) V87F probably benign Het
D2hgdh C T 1: 93,763,157 (GRCm39) A314V probably damaging Het
Dcun1d4 T A 5: 73,638,618 (GRCm39) probably benign Het
Dhodh A G 8: 110,321,306 (GRCm39) F360S possibly damaging Het
Dipk2b A G X: 18,289,926 (GRCm39) S179P possibly damaging Het
Dynap C T 18: 70,374,218 (GRCm39) A103T probably benign Het
Edem2 G A 2: 155,544,137 (GRCm39) P538S probably benign Het
Egfl8 C T 17: 34,832,832 (GRCm39) V253M probably damaging Het
Erich6 A T 3: 58,526,260 (GRCm39) S581T probably benign Het
Fam117b T C 1: 59,952,789 (GRCm39) L156P probably damaging Het
Fbn1 G T 2: 125,163,661 (GRCm39) A2065E possibly damaging Het
Foxn4 T C 5: 114,393,662 (GRCm39) T486A probably damaging Het
Fzd9 A G 5: 135,279,148 (GRCm39) S246P probably damaging Het
Hdhd2 C T 18: 77,052,866 (GRCm39) T172M probably benign Het
Heatr5a T C 12: 51,940,528 (GRCm39) D1444G possibly damaging Het
Hmcn1 A G 1: 150,500,349 (GRCm39) probably benign Het
Hps3 G A 3: 20,067,099 (GRCm39) probably benign Het
Hr A T 14: 70,795,547 (GRCm39) D393V probably benign Het
Ido2 T C 8: 25,025,268 (GRCm39) Y253C probably damaging Het
Irs2 T C 8: 11,057,586 (GRCm39) E282G probably damaging Het
Itih4 A G 14: 30,614,385 (GRCm39) D445G probably damaging Het
Kif14 T A 1: 136,447,486 (GRCm39) C1430* probably null Het
Kir3dl1 A G X: 135,425,784 (GRCm39) R53G probably benign Het
Lama2 T A 10: 26,868,932 (GRCm39) I2838F probably damaging Het
Lamb1 A T 12: 31,377,644 (GRCm39) I1630F probably damaging Het
Lsmem1 GTACATACATACATACATACATACATACA GTACATACATACATACATACATACATACATACA 12: 40,235,260 (GRCm39) probably null Het
Magi3 G A 3: 103,928,382 (GRCm39) probably benign Het
Mink1 G A 11: 70,492,550 (GRCm39) probably null Het
Mmrn2 A G 14: 34,121,449 (GRCm39) K773R probably benign Het
Mpdz A G 4: 81,301,628 (GRCm39) S266P probably damaging Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Mtbp G A 15: 55,432,556 (GRCm39) probably null Het
Mybphl A G 3: 108,272,317 (GRCm39) E2G probably damaging Het
Myoc C T 1: 162,476,625 (GRCm39) T443M probably damaging Het
Nav1 A T 1: 135,399,974 (GRCm39) L532* probably null Het
Nbeal1 T A 1: 60,370,037 (GRCm39) probably benign Het
Nfix CAAAAA CAAAA 8: 85,442,876 (GRCm39) probably null Het
Opcml T C 9: 28,814,651 (GRCm39) I301T possibly damaging Het
Or10ak16 A T 4: 118,751,071 (GRCm39) R264W probably damaging Het
Or8b1 T A 9: 38,399,504 (GRCm39) Y60N probably damaging Het
Pappa2 A G 1: 158,684,841 (GRCm39) M766T probably damaging Het
Phf8 T C X: 150,355,597 (GRCm39) L520S possibly damaging Het
Phka1 A G X: 101,584,716 (GRCm39) probably benign Het
Ppp2ca G A 11: 52,008,913 (GRCm39) G138R probably damaging Het
Prrc1 G T 18: 57,514,718 (GRCm39) D312Y probably damaging Het
Rdh7 A G 10: 127,720,530 (GRCm39) S281P probably benign Het
Rps17 C T 7: 80,994,746 (GRCm39) R5H probably benign Het
Scgb1b2 T A 7: 30,991,201 (GRCm39) probably benign Het
Skic3 T G 13: 76,260,393 (GRCm39) probably benign Het
Slc35a3 T C 3: 116,467,285 (GRCm39) K325E possibly damaging Het
Snap23 A G 2: 120,429,793 (GRCm39) T213A probably benign Het
Spag17 C A 3: 99,969,182 (GRCm39) probably null Het
Srebf1 A G 11: 60,097,973 (GRCm39) S44P probably damaging Het
St8sia5 T C 18: 77,320,526 (GRCm39) S93P probably damaging Het
Styk1 T C 6: 131,289,539 (GRCm39) E25G probably benign Het
Taar8b T C 10: 23,967,270 (GRCm39) N308S probably damaging Het
Tbc1d14 A G 5: 36,700,561 (GRCm39) L269P possibly damaging Het
Tbc1d22b A G 17: 29,818,828 (GRCm39) H394R probably damaging Het
Tbx5 A T 5: 119,983,174 (GRCm39) probably null Het
Tgfbr3l A G 8: 4,300,506 (GRCm39) E228G probably benign Het
Tlr5 T A 1: 182,802,600 (GRCm39) S635T possibly damaging Het
Tmem233 G C 5: 116,189,517 (GRCm39) probably benign Het
Tymp A T 15: 89,258,011 (GRCm39) V378D probably damaging Het
Vav2 A T 2: 27,182,667 (GRCm39) probably null Het
Vcp G A 4: 42,980,833 (GRCm39) A759V possibly damaging Het
Vmn2r15 A G 5: 109,441,073 (GRCm39) Y262H probably benign Het
Vmn2r76 T C 7: 85,879,707 (GRCm39) M198V probably benign Het
Zfp831 A C 2: 174,486,034 (GRCm39) R236S probably benign Het
Other mutations in Vangl1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00640:Vangl1 APN 3 102,065,545 (GRCm39) utr 3 prime probably benign
IGL00870:Vangl1 APN 3 102,096,756 (GRCm39) missense probably damaging 1.00
IGL01533:Vangl1 APN 3 102,070,667 (GRCm39) missense possibly damaging 0.88
IGL01981:Vangl1 APN 3 102,091,607 (GRCm39) missense probably damaging 1.00
IGL02792:Vangl1 APN 3 102,070,739 (GRCm39) missense probably damaging 0.98
IGL02800:Vangl1 APN 3 102,070,611 (GRCm39) splice site probably benign
IGL02942:Vangl1 APN 3 102,091,347 (GRCm39) missense probably damaging 1.00
IGL03029:Vangl1 APN 3 102,091,400 (GRCm39) missense probably damaging 1.00
R0600:Vangl1 UTSW 3 102,074,253 (GRCm39) missense probably damaging 1.00
R0904:Vangl1 UTSW 3 102,091,310 (GRCm39) missense probably damaging 0.99
R1230:Vangl1 UTSW 3 102,065,609 (GRCm39) missense probably benign 0.00
R1829:Vangl1 UTSW 3 102,070,782 (GRCm39) missense probably benign
R2005:Vangl1 UTSW 3 102,070,782 (GRCm39) missense probably benign
R4181:Vangl1 UTSW 3 102,073,097 (GRCm39) intron probably benign
R4662:Vangl1 UTSW 3 102,074,238 (GRCm39) missense probably benign 0.00
R4724:Vangl1 UTSW 3 102,091,870 (GRCm39) missense probably damaging 1.00
R4755:Vangl1 UTSW 3 102,065,608 (GRCm39) missense probably benign 0.19
R5548:Vangl1 UTSW 3 102,091,762 (GRCm39) missense possibly damaging 0.76
R5740:Vangl1 UTSW 3 102,091,450 (GRCm39) missense probably damaging 0.99
R5758:Vangl1 UTSW 3 102,091,408 (GRCm39) missense probably damaging 1.00
R6150:Vangl1 UTSW 3 102,091,835 (GRCm39) missense probably damaging 1.00
R6373:Vangl1 UTSW 3 102,065,764 (GRCm39) missense probably benign
R6943:Vangl1 UTSW 3 102,073,097 (GRCm39) intron probably benign
R7474:Vangl1 UTSW 3 102,091,565 (GRCm39) missense probably benign 0.22
R7616:Vangl1 UTSW 3 102,091,381 (GRCm39) missense probably damaging 1.00
R8120:Vangl1 UTSW 3 102,070,758 (GRCm39) nonsense probably null
R8827:Vangl1 UTSW 3 102,070,736 (GRCm39) missense probably damaging 0.99
R8859:Vangl1 UTSW 3 102,065,758 (GRCm39) missense
R9494:Vangl1 UTSW 3 102,070,665 (GRCm39) missense probably damaging 0.98
R9745:Vangl1 UTSW 3 102,072,669 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- TGACTGAACCTTCCACGTCC -3'
(R):5'- TCTATAACAGGGACCCCAGAGG -3'

Sequencing Primer
(F):5'- CCTCAGCCTTTCTGGTGGG -3'
(R):5'- CAGAGGAGAGCTGCCTGTTG -3'
Posted On 2014-10-16