Mutagenetix > Incidental Mutation

Incidental Mutation 'R4662:Vangl1'

352918

Institutional Source

Beutler Lab

Gene Symbol

Vangl1

Ensembl Gene

ENSMUSG00000027860

Gene Name

VANGL planar cell polarity 1

Synonyms

stbm, KITENIN, Lpp2, mStbm

MMRRC Submission

042011-MU

Accession Numbers

Essential gene?

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

Stock #

R4662 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

102060899-102112009 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 102074238 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 290 (T290A)

Ref Sequence

ENSEMBL: ENSMUSP00000125043 (fasta)

Gene Model

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

AlphaFold

Q80Z96

Predicted Effect

probably benign
Transcript: ENSMUST00000029453
AA Change: T290A

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000029453
Gene: ENSMUSG00000027860
AA Change: T290A

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 benign
Transcript: ENSMUST00000159388
AA Change: T290A

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000125043
Gene: ENSMUSG00000027860
AA Change: T290A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160226

Predicted Effect

unknown
Transcript: ENSMUST00000161021
AA Change: T3A

SMART Domains

Protein: ENSMUSP00000125484
Gene: ENSMUSG00000027860
AA Change: T3A

Domain	Start	End	E-Value	Type
Pfam:Strabismus	1	253	3.2e-118	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162361

Predicted Effect

probably benign
Transcript: ENSMUST00000168312
AA Change: T290A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000126254
Gene: ENSMUSG00000027860
AA Change: T290A

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

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.1%

Validation Efficiency

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930590J08Rik	A	T	6: 91,891,939 (GRCm39)	Q67L	probably benign	Het
Adam34l	T	A	8: 44,080,116 (GRCm39)	Y36F	probably benign	Het
Adrb1	A	G	19: 56,711,206 (GRCm39)	T135A	probably damaging	Het
Ark2n	T	A	18: 77,762,186 (GRCm39)	Q42L	probably benign	Het
Asxl2	G	T	12: 3,477,193 (GRCm39)	W13L	probably damaging	Het
Atp4a	G	A	7: 30,419,650 (GRCm39)	R671Q	probably benign	Het
Brsk1	T	C	7: 4,710,298 (GRCm39)	S436P	possibly damaging	Het
Calb2	A	G	8: 110,894,709 (GRCm39)	F21L	probably benign	Het
Camk2a	T	C	18: 61,074,411 (GRCm39)	Y39H	probably damaging	Het
Cavin2	T	C	1: 51,340,510 (GRCm39)	S396P	probably benign	Het
Cfdp1	A	G	8: 112,557,577 (GRCm39)	F188S	probably benign	Het
Chek2	T	A	5: 111,014,908 (GRCm39)	V459D	probably damaging	Het
Cldn8	G	A	16: 88,359,296 (GRCm39)	H210Y	probably benign	Het
Cobl	A	G	11: 12,203,672 (GRCm39)	V1003A	probably benign	Het
Ctsll3	A	G	13: 60,947,416 (GRCm39)	F257L	possibly damaging	Het
Dnajc13	A	C	9: 104,084,957 (GRCm39)	F819V	probably damaging	Het
Dram1	C	A	10: 88,161,246 (GRCm39)	V208L	probably damaging	Het
Dynlt1b	A	G	17: 6,699,279 (GRCm39)	T10A	probably benign	Het
Eml6	A	T	11: 29,727,390 (GRCm39)	V1244E	probably damaging	Het
Ethe1	G	A	7: 24,293,405 (GRCm39)	S17N	probably benign	Het
Foxi1	T	C	11: 34,157,578 (GRCm39)	D149G	probably damaging	Het
Fzd9	T	C	5: 135,278,475 (GRCm39)	E470G	probably damaging	Het
Ggnbp2	A	G	11: 84,753,072 (GRCm39)	F56L	probably damaging	Het
Hao1	G	A	2: 134,364,947 (GRCm39)	R227*	probably null	Het
Hyal1	G	A	9: 107,456,420 (GRCm39)	R369H	probably damaging	Het
Jam2	G	A	16: 84,609,840 (GRCm39)	V151M	probably damaging	Het
Kcna2	T	A	3: 107,012,733 (GRCm39)	I438N	probably benign	Het
Lrp1	A	T	10: 127,388,054 (GRCm39)	C3331*	probably null	Het
Mcm9	T	C	10: 53,424,623 (GRCm39)	I656V	probably benign	Het
Mroh9	C	T	1: 162,883,162 (GRCm39)	C439Y	probably damaging	Het
N4bp2l2	T	C	5: 150,574,160 (GRCm39)	D85G	probably damaging	Het
Nr1h2	A	G	7: 44,199,855 (GRCm39)	Y355H	probably damaging	Het
Nr5a2	T	C	1: 136,868,167 (GRCm39)	I322V	probably benign	Het
Nup153	A	C	13: 46,840,750 (GRCm39)	L273V	possibly damaging	Het
Obscn	A	G	11: 58,890,422 (GRCm39)	L7370P	unknown	Het
Or1a1	T	C	11: 74,086,542 (GRCm39)	I71T	probably damaging	Het
Or4b1	T	A	2: 89,980,222 (GRCm39)	I43F	probably damaging	Het
Or5k15	A	G	16: 58,710,287 (GRCm39)	C99R	probably damaging	Het
Prkdc	G	A	16: 15,551,916 (GRCm39)	D2041N	probably damaging	Het
Ptdss1	A	G	13: 67,081,675 (GRCm39)	D35G	possibly damaging	Het
Ptprs	G	T	17: 56,724,666 (GRCm39)	T1118K	probably damaging	Het
Pygb	C	T	2: 150,657,036 (GRCm39)	T329I	probably benign	Het
Rhoh	T	A	5: 66,050,157 (GRCm39)	D142E	probably benign	Het
Saraf	C	A	8: 34,635,616 (GRCm39)	A306E	probably damaging	Het
Scn1a	T	C	2: 66,181,332 (GRCm39)	I64V	probably benign	Het
Sec16a	A	G	2: 26,320,582 (GRCm39)	W1333R	probably damaging	Het
Shroom1	A	T	11: 53,357,289 (GRCm39)	T651S	possibly damaging	Het
Skint3	C	A	4: 112,134,863 (GRCm39)	Y345*	probably null	Het
Slc1a7	T	A	4: 107,864,751 (GRCm39)	N263K	probably damaging	Het
Sptbn2	C	T	19: 4,789,267 (GRCm39)	R1236C	probably damaging	Het
Tbx21	T	C	11: 96,992,393 (GRCm39)	N226S	probably benign	Het
Thada	A	G	17: 84,743,078 (GRCm39)	L782P	probably damaging	Het
Tle1	T	G	4: 72,055,335 (GRCm39)	I446L	possibly damaging	Het
Trgv1	T	A	13: 19,524,503 (GRCm39)	L76I	possibly damaging	Het
Triobp	A	G	15: 78,877,469 (GRCm39)	D1621G	probably damaging	Het
Trpm2	G	C	10: 77,773,972 (GRCm39)	A481G	probably benign	Het
Unc80	A	T	1: 66,685,595 (GRCm39)	M2240L	probably benign	Het
Usp9x	A	G	X: 12,989,747 (GRCm39)	R776G	possibly damaging	Homo
Vmn1r233	T	A	17: 21,214,393 (GRCm39)	I186F	probably benign	Het
Vmn2r102	G	A	17: 19,901,424 (GRCm39)	C517Y	probably damaging	Het
Vrk2	G	A	11: 26,421,611 (GRCm39)	T449M	possibly damaging	Het
Zfp518a	A	G	19: 40,900,304 (GRCm39)	S78G	probably benign	Het
Zscan25	T	C	5: 145,223,120 (GRCm39)	S131P	unknown	Het
Zscan29	G	A	2: 120,997,096 (GRCm39)	T140I	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
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'- CAGGGTTGAAGCAAACGTACTATG -3'
(R):5'- ATATGGGGAATGCCAGAGCC -3'

Sequencing Primer
(F):5'- TACTATGAGGTTTAAGCCACAGAGCC -3'
(R):5'- GTGTAGGAGCCAGCAGACTTTC -3'

Posted On

2015-10-08