Incidental Mutation 'R6373:Vangl1'
| ID |
513621 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vangl1
|
| Ensembl Gene |
ENSMUSG00000027860 |
| Gene Name |
VANGL planar cell polarity 1 |
| Synonyms |
stbm, KITENIN, Lpp2, mStbm |
| MMRRC Submission |
044523-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.315)
|
| Stock # |
R6373 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
102060899-102112009 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 102065764 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Arginine
at position 407
(K407R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000126254
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000029453]
[ENSMUST00000159388]
[ENSMUST00000168312]
|
| AlphaFold |
Q80Z96 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000029453
AA Change: K457R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000029453
Gene: ENSMUSG00000027860
AA Change: K457R
| 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
|
| SMART Domains |
Protein: ENSMUSP00000125043
Gene: ENSMUSG00000027860
| 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: K183R
|
| SMART Domains |
Protein: ENSMUSP00000125484
Gene: ENSMUSG00000027860
AA Change: K183R
| 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: K407R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000126254
Gene: ENSMUSG00000027860
AA Change: K407R
| 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: 99.6%
- 10x: 98.3%
- 20x: 95.2%
|
| Validation Efficiency |
95% (37/39) |
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abhd13 |
T |
C |
8: 10,038,240 (GRCm39) |
L279P |
probably damaging |
Het |
| Aldh16a1 |
C |
G |
7: 44,795,695 (GRCm39) |
V373L |
probably benign |
Het |
| Btn2a2 |
T |
C |
13: 23,665,999 (GRCm39) |
K278E |
probably benign |
Het |
| Carns1 |
G |
T |
19: 4,216,515 (GRCm39) |
Q556K |
probably benign |
Het |
| Chd1 |
A |
T |
17: 15,958,898 (GRCm39) |
E650V |
probably damaging |
Het |
| Cobl |
A |
G |
11: 12,203,118 (GRCm39) |
S1195P |
probably damaging |
Het |
| Deup1 |
T |
C |
9: 15,472,638 (GRCm39) |
H464R |
probably damaging |
Het |
| Eva1a |
T |
C |
6: 82,068,847 (GRCm39) |
L58S |
probably damaging |
Het |
| Fign |
A |
C |
2: 63,809,989 (GRCm39) |
M427R |
probably benign |
Het |
| Gm6309 |
A |
T |
5: 146,107,085 (GRCm39) |
I87N |
probably damaging |
Het |
| H2ac7 |
A |
G |
13: 23,759,027 (GRCm39) |
K128R |
probably benign |
Het |
| Helz |
A |
G |
11: 107,486,010 (GRCm39) |
T140A |
probably benign |
Het |
| Helz2 |
C |
T |
2: 180,875,260 (GRCm39) |
E1745K |
probably damaging |
Het |
| Kif16b |
A |
T |
2: 142,541,618 (GRCm39) |
H1227Q |
possibly damaging |
Het |
| Mab21l1 |
A |
T |
3: 55,690,505 (GRCm39) |
I31F |
possibly damaging |
Het |
| Mex3c |
T |
C |
18: 73,723,065 (GRCm39) |
M386T |
probably benign |
Het |
| Myh11 |
T |
A |
16: 14,022,994 (GRCm39) |
I1644F |
possibly damaging |
Het |
| Nav2 |
C |
T |
7: 49,102,923 (GRCm39) |
P513S |
probably damaging |
Het |
| Ncoa3 |
C |
T |
2: 165,901,267 (GRCm39) |
S953F |
possibly damaging |
Het |
| Nmt2 |
A |
G |
2: 3,325,988 (GRCm39) |
T462A |
probably benign |
Het |
| Nrxn2 |
T |
C |
19: 6,559,860 (GRCm39) |
I163T |
probably damaging |
Het |
| Nrxn3 |
G |
C |
12: 89,943,237 (GRCm39) |
G122R |
probably damaging |
Het |
| Or1e26 |
A |
G |
11: 73,479,724 (GRCm39) |
V280A |
probably benign |
Het |
| Or5d20-ps1 |
T |
C |
2: 87,932,189 (GRCm39) |
I47M |
possibly damaging |
Het |
| Parg |
T |
G |
14: 31,931,454 (GRCm39) |
|
probably null |
Het |
| Pcdhb7 |
T |
A |
18: 37,475,264 (GRCm39) |
C133* |
probably null |
Het |
| Ppihl |
A |
G |
5: 44,070,893 (GRCm39) |
T127A |
probably damaging |
Het |
| Rigi |
A |
G |
4: 40,216,487 (GRCm39) |
Y504H |
possibly damaging |
Het |
| Rpe |
T |
C |
1: 66,755,139 (GRCm39) |
F174L |
probably benign |
Het |
| Rxrb |
A |
G |
17: 34,252,533 (GRCm39) |
N40S |
probably benign |
Het |
| Ryr3 |
C |
A |
2: 112,486,889 (GRCm39) |
G3840W |
probably damaging |
Het |
| Smurf2 |
A |
G |
11: 106,724,595 (GRCm39) |
L529P |
probably damaging |
Het |
| Sntg2 |
C |
T |
12: 30,308,040 (GRCm39) |
R215H |
probably benign |
Het |
| Spata20 |
A |
G |
11: 94,374,226 (GRCm39) |
V348A |
probably benign |
Het |
| Spink5 |
A |
G |
18: 44,123,739 (GRCm39) |
E342G |
probably damaging |
Het |
| St3gal1 |
A |
G |
15: 66,983,195 (GRCm39) |
V187A |
possibly damaging |
Het |
| Syce1l |
T |
A |
8: 114,376,143 (GRCm39) |
M31K |
probably benign |
Het |
| Ttn |
C |
T |
2: 76,618,960 (GRCm39) |
V14394I |
probably damaging |
Het |
| Twnk |
G |
A |
19: 44,997,820 (GRCm39) |
V450M |
probably damaging |
Het |
| Vmn1r19 |
T |
C |
6: 57,382,317 (GRCm39) |
I290T |
unknown |
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 |
|
R6150:Vangl1
|
UTSW |
3 |
102,091,835 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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'- CTGTAAGCGAAGAACAAACTTGTG -3'
(R):5'- TCCTTCTACAGAGAGGGTCTCG -3'
Sequencing Primer
(F):5'- GAACAAACTTGTGAGATTTAGGGTC -3'
(R):5'- TGGGCCTTCAGCATGAGAG -3'
|
| Posted On |
2018-04-27 |
Incidental Mutation