Incidental Mutation 'R5548:Vangl1'
| ID |
434975 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vangl1
|
| Ensembl Gene |
ENSMUSG00000027860 |
| Gene Name |
VANGL planar cell polarity 1 |
| Synonyms |
stbm, KITENIN, Lpp2, mStbm |
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.304)
|
| Stock # |
R5548 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
102060899-102112009 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 102091762 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Valine
at position 108
(D108V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000029453
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029453]
[ENSMUST00000159388]
[ENSMUST00000159586]
[ENSMUST00000168312]
|
| AlphaFold |
Q80Z96 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000029453
AA Change: D108V
PolyPhen 2
Score 0.756 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000029453
Gene: ENSMUSG00000027860
AA Change: D108V
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
5 |
21 |
N/A |
INTRINSIC |
|
Pfam:Strabismus
|
23 |
360 |
3.4e-171 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000159388
AA Change: D108V
PolyPhen 2
Score 0.647 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000125043
Gene: ENSMUSG00000027860
AA Change: D108V
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
5 |
21 |
N/A |
INTRINSIC |
|
Pfam:Strabismus
|
25 |
526 |
8.6e-262 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000159586
AA Change: D108V
PolyPhen 2
Score 0.640 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000124874
Gene: ENSMUSG00000027860
AA Change: D108V
| 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 benign
Transcript: ENSMUST00000168312
AA Change: D108V
PolyPhen 2
Score 0.404 (Sensitivity: 0.89; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000126254
Gene: ENSMUSG00000027860
AA Change: D108V
| 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: 99.9%
- 3x: 99.7%
- 10x: 98.3%
- 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: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2310057J18Rik |
T |
C |
10: 28,849,863 (GRCm39) |
D191G |
probably benign |
Het |
| Ankrd39 |
C |
T |
1: 36,581,062 (GRCm39) |
G96R |
probably damaging |
Het |
| Cdh12 |
C |
T |
15: 21,492,740 (GRCm39) |
T253I |
probably damaging |
Het |
| Cox4i2 |
C |
T |
2: 152,599,011 (GRCm39) |
T56I |
possibly damaging |
Het |
| Cpsf1 |
A |
C |
15: 76,481,527 (GRCm39) |
D1141E |
possibly damaging |
Het |
| Dennd5b |
T |
C |
6: 148,920,847 (GRCm39) |
|
probably null |
Het |
| Dnah6 |
A |
T |
6: 73,128,672 (GRCm39) |
D1194E |
probably damaging |
Het |
| Dst |
C |
A |
1: 34,228,409 (GRCm39) |
H1676N |
probably benign |
Het |
| Eif4a3l1 |
T |
C |
6: 136,306,568 (GRCm39) |
V343A |
probably damaging |
Het |
| Fitm1 |
A |
G |
14: 55,813,154 (GRCm39) |
T6A |
probably benign |
Het |
| Galnt5 |
T |
A |
2: 57,904,922 (GRCm39) |
V495E |
probably damaging |
Het |
| Gtf2h2 |
C |
A |
13: 100,617,544 (GRCm39) |
R206L |
possibly damaging |
Het |
| Heatr5a |
A |
T |
12: 52,005,734 (GRCm39) |
Y80* |
probably null |
Het |
| Il17ra |
A |
G |
6: 120,455,434 (GRCm39) |
R348G |
probably benign |
Het |
| Mmp28 |
A |
T |
11: 83,334,733 (GRCm39) |
Y340* |
probably null |
Het |
| Mrgprb8 |
A |
T |
7: 48,038,778 (GRCm39) |
T150S |
probably benign |
Het |
| Ms4a10 |
A |
T |
19: 10,945,484 (GRCm39) |
|
probably null |
Het |
| Muc5b |
A |
T |
7: 141,417,679 (GRCm39) |
I3542F |
probably benign |
Het |
| Mybbp1a |
T |
C |
11: 72,336,998 (GRCm39) |
L578P |
probably damaging |
Het |
| N4bp2l1 |
G |
A |
5: 150,496,420 (GRCm39) |
R65* |
probably null |
Het |
| Nhsl3 |
GGTG |
GGTGTG |
4: 129,117,773 (GRCm39) |
|
probably null |
Het |
| Nup188 |
T |
A |
2: 30,216,505 (GRCm39) |
Y770N |
probably damaging |
Het |
| Or8b3b |
T |
C |
9: 38,584,600 (GRCm39) |
I60V |
probably benign |
Het |
| Or8s5 |
T |
A |
15: 98,238,253 (GRCm39) |
T206S |
probably benign |
Het |
| Pbrm1 |
T |
A |
14: 30,827,381 (GRCm39) |
C1257S |
probably damaging |
Het |
| Pcdh8 |
T |
C |
14: 80,004,942 (GRCm39) |
T1028A |
probably damaging |
Het |
| Pramel16 |
C |
T |
4: 143,676,550 (GRCm39) |
E185K |
probably benign |
Het |
| Qars1 |
C |
T |
9: 108,390,117 (GRCm39) |
P348S |
possibly damaging |
Het |
| Qrfpr |
T |
A |
3: 36,276,075 (GRCm39) |
Q105L |
possibly damaging |
Het |
| Slc10a5 |
A |
T |
3: 10,399,377 (GRCm39) |
Y428N |
probably benign |
Het |
| Slc16a5 |
A |
T |
11: 115,360,630 (GRCm39) |
Y271F |
probably benign |
Het |
| Slc1a4 |
T |
A |
11: 20,254,429 (GRCm39) |
Q479L |
possibly damaging |
Het |
| Slc38a1 |
C |
T |
15: 96,488,355 (GRCm39) |
G143S |
probably damaging |
Het |
| Susd1 |
G |
A |
4: 59,369,577 (GRCm39) |
T364M |
probably benign |
Het |
| Tmem132c |
T |
A |
5: 127,628,587 (GRCm39) |
Y496* |
probably null |
Het |
| Tmem63b |
A |
G |
17: 45,975,884 (GRCm39) |
I523T |
probably damaging |
Het |
| Tnrc6c |
T |
C |
11: 117,651,669 (GRCm39) |
S1731P |
possibly damaging |
Het |
| Ttll3 |
T |
A |
6: 113,370,078 (GRCm39) |
W139R |
probably damaging |
Het |
| Ubr4 |
C |
T |
4: 139,187,401 (GRCm39) |
T3823M |
probably damaging |
Het |
| Vmn1r120 |
T |
C |
7: 20,787,482 (GRCm39) |
I76M |
probably benign |
Het |
| Wdr17 |
A |
G |
8: 55,156,886 (GRCm39) |
Y17H |
probably damaging |
Het |
| Xkr4 |
C |
T |
1: 3,287,153 (GRCm39) |
A346T |
probably damaging |
Het |
| Zfp267 |
C |
G |
3: 36,219,640 (GRCm39) |
H554Q |
possibly damaging |
Het |
| Zfp600 |
T |
A |
4: 146,133,019 (GRCm39) |
S562R |
possibly damaging |
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 |
|
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'- TTCCGATGAGCAGAATAAGCAG -3'
(R):5'- TCTGGGTTCAAAGGGCAAAC -3'
Sequencing Primer
(F):5'- GCAGAATAAGCAGTTTGAATGATAC -3'
(R):5'- AAAGCTGATTCTATGAACACTTCC -3'
|
| Posted On |
2016-10-24 |
Incidental Mutation