Mutagenetix > Incidental Mutation

Incidental Mutation 'R6150:Vangl1'

489174

Institutional Source

Beutler Lab

Gene Symbol

Vangl1

Ensembl Gene

ENSMUSG00000027860

Gene Name

VANGL planar cell polarity 1

Synonyms

stbm, KITENIN, Lpp2, mStbm

MMRRC Submission

044297-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.304) question?

Stock #

R6150 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

102060899-102112009 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 102091835 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 84 (T84A)

Ref Sequence

ENSEMBL: ENSMUSP00000124874 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029453] [ENSMUST00000159388] [ENSMUST00000159586] [ENSMUST00000168312]

AlphaFold

Q80Z96

Predicted Effect

probably damaging
Transcript: ENSMUST00000029453
AA Change: T84A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000029453
Gene: ENSMUSG00000027860
AA Change: T84A

Domain	Start	End	E-Value	Type
low complexity region	5	21	N/A	INTRINSIC
Pfam:Strabismus	23	360	3.4e-171	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000159388
AA Change: T84A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000125043
Gene: ENSMUSG00000027860
AA Change: T84A

Domain	Start	End	E-Value	Type
low complexity region	5	21	N/A	INTRINSIC
Pfam:Strabismus	25	526	8.6e-262	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000159586
AA Change: T84A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000124874
Gene: ENSMUSG00000027860
AA Change: T84A

Domain	Start	End	E-Value	Type
low complexity region	5	21	N/A	INTRINSIC
Pfam:Strabismus	23	137	3.5e-41	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000168312
AA Change: T84A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000126254
Gene: ENSMUSG00000027860
AA Change: T84A

Domain	Start	End	E-Value	Type
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

0.4924

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.9%

Validation Efficiency

97% (56/58)

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aldh3a1	A	G	11: 61,104,334 (GRCm39)	T74A	probably benign	Het
Arhgef1	T	C	7: 24,618,782 (GRCm39)		probably null	Het
Art1	C	G	7: 101,756,294 (GRCm39)	R162G	probably benign	Het
Boll	T	A	1: 55,309,812 (GRCm39)	I280F	possibly damaging	Het
Cep44	T	C	8: 56,992,840 (GRCm39)	E258G	probably benign	Het
Cutc	T	A	19: 43,748,328 (GRCm39)	V75E	probably damaging	Het
Dtx1	T	C	5: 120,819,428 (GRCm39)	K590R	probably damaging	Het
Eps8	A	T	6: 137,494,172 (GRCm39)	D295E	probably damaging	Het
Erc2	C	A	14: 27,863,248 (GRCm39)	S491Y	probably damaging	Het
F2rl3	G	T	8: 73,489,366 (GRCm39)	A198S	probably benign	Het
Fam83b	G	A	9: 76,399,639 (GRCm39)	T488M	probably damaging	Het
Fitm2	A	G	2: 163,311,994 (GRCm39)	L73P	probably damaging	Het
Fxyd1	T	C	7: 30,754,228 (GRCm39)		probably null	Het
Gm17186	T	C	14: 51,918,183 (GRCm39)		noncoding transcript	Het
Hivep3	C	A	4: 119,591,274 (GRCm39)	S94*	probably null	Het
Ifna1	T	A	4: 88,768,349 (GRCm39)	M9K	probably null	Het
Igsf11	G	A	16: 38,843,711 (GRCm39)	E275K	probably damaging	Het
Itga1	G	A	13: 115,104,769 (GRCm39)	L1086F	probably benign	Het
Itgav	T	C	2: 83,606,780 (GRCm39)	S374P	probably benign	Het
Jmy	A	T	13: 93,577,641 (GRCm39)	N842K	probably benign	Het
Kcnh6	G	A	11: 105,911,557 (GRCm39)	V595M	possibly damaging	Het
Kif13b	T	A	14: 64,989,088 (GRCm39)	I823N	probably damaging	Het
Kif26b	T	C	1: 178,743,111 (GRCm39)	L1069P	probably damaging	Het
Kl	T	A	5: 150,912,318 (GRCm39)	M689K	possibly damaging	Het
Kmt2b	G	T	7: 30,287,902 (GRCm39)		probably benign	Het
Map10	G	A	8: 126,398,328 (GRCm39)	D574N	probably damaging	Het
Mau2	A	T	8: 70,472,487 (GRCm39)	H565Q	probably benign	Het
Myb	A	G	10: 21,017,668 (GRCm39)	I641T	probably damaging	Het
Naaladl2	C	A	3: 24,606,214 (GRCm39)	G15V	probably null	Het
Or10k2	G	A	8: 84,267,782 (GRCm39)	C3Y	probably benign	Het
Or3a4	A	C	11: 73,945,145 (GRCm39)	S147A	probably benign	Het
Or6c210	A	G	10: 129,495,803 (GRCm39)	I43V	probably benign	Het
Or7d11	A	T	9: 19,966,170 (GRCm39)	N78K	probably benign	Het
Otog	A	G	7: 45,913,483 (GRCm39)	E772G	possibly damaging	Het
Pla2g4d	T	C	2: 120,100,045 (GRCm39)	D674G	probably damaging	Het
Pmpcb	A	G	5: 21,942,137 (GRCm39)		probably null	Het
Pomk	A	G	8: 26,473,284 (GRCm39)	V223A	possibly damaging	Het
Prpf40a	T	C	2: 53,047,927 (GRCm39)	M197V	probably benign	Het
Serpina1e	A	G	12: 103,917,066 (GRCm39)	V201A	probably benign	Het
Six5	C	T	7: 18,831,446 (GRCm39)	P646S	probably benign	Het
Slc17a9	A	G	2: 180,379,421 (GRCm39)	I298V	probably benign	Het
Slc37a2	G	T	9: 37,149,643 (GRCm39)	T188K	probably damaging	Het
Slc6a11	T	A	6: 114,222,579 (GRCm39)	F525I	probably benign	Het
Slit2	A	T	5: 48,461,516 (GRCm39)	D1504V	probably damaging	Het
Srcap	T	A	7: 127,134,000 (GRCm39)	M907K	probably damaging	Het
Sspo	T	C	6: 48,463,313 (GRCm39)	L3746P	probably benign	Het
Supv3l1	A	T	10: 62,271,501 (GRCm39)	N376K	possibly damaging	Het
Tekt3	A	T	11: 62,985,483 (GRCm39)	T430S	possibly damaging	Het
Tex2	A	T	11: 106,457,906 (GRCm39)	V508D	probably benign	Het
Tmem184c	G	T	8: 78,323,069 (GRCm39)	Q598K	probably benign	Het
Ube2v1	G	A	2: 167,459,874 (GRCm39)	R42*	probably null	Het
Usp45	A	C	4: 21,810,797 (GRCm39)	D331A	probably damaging	Het
Vgll3	T	A	16: 65,625,064 (GRCm39)		probably null	Het
Vmn1r61	T	A	7: 5,613,678 (GRCm39)	H212L	probably benign	Het
Vmn2r114	A	G	17: 23,510,269 (GRCm39)	V737A	probably benign	Het
Vmn2r35	A	T	7: 7,789,555 (GRCm39)	D727E	probably damaging	Het
Vps18	T	A	2: 119,128,073 (GRCm39)	Y965*	probably null	Het
Zfp521	A	T	18: 13,977,135 (GRCm39)	C1093S	probably damaging	Het
Zfp971	A	C	2: 177,675,247 (GRCm39)	H282P	probably benign	Het

Other mutations in Vangl1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
R2268:Vangl1	UTSW	3	102,104,160 (GRCm39)	missense	probably damaging	1.00
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
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'- AAATGGCGCCACAGGGTTTC -3'
(R):5'- TTTCTGGGTTCAAAGGGCAAAC -3'

Sequencing Primer
(F):5'- GCCACAGGGTTTCAGCTC -3'
(R):5'- TGGCGAAAATTTCAATGAAAATAGC -3'

Posted On

2017-10-10