Incidental Mutation 'R2197:Llgl1'
ID |
238440 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Llgl1
|
Ensembl Gene |
ENSMUSG00000020536 |
Gene Name |
LLGL1 scribble cell polarity complex component |
Synonyms |
Lgl1 |
MMRRC Submission |
040199-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R2197 (G1)
|
Quality Score |
170 |
Status
|
Not validated
|
Chromosome |
11 |
Chromosomal Location |
60590549-60605012 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 60600865 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Proline
at position 654
(S654P)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000104359
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000002889]
[ENSMUST00000052346]
[ENSMUST00000108719]
|
AlphaFold |
Q80Y17 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000002889
|
SMART Domains |
Protein: ENSMUSP00000002889 Gene: ENSMUSG00000002812
Domain | Start | End | E-Value | Type |
LRR
|
55 |
78 |
1.08e-1 |
SMART |
LRR
|
103 |
126 |
4.08e0 |
SMART |
LRR
|
127 |
149 |
2.27e1 |
SMART |
LRR
|
150 |
173 |
1.25e-1 |
SMART |
LRR
|
222 |
244 |
6.78e1 |
SMART |
LRR
|
245 |
268 |
2.86e-1 |
SMART |
LRR
|
269 |
291 |
3.78e-1 |
SMART |
LRR
|
316 |
339 |
2.82e0 |
SMART |
LRR
|
340 |
362 |
2.27e2 |
SMART |
low complexity region
|
403 |
420 |
N/A |
INTRINSIC |
GEL
|
499 |
597 |
4.17e-25 |
SMART |
GEL
|
617 |
709 |
1.72e-26 |
SMART |
low complexity region
|
727 |
740 |
N/A |
INTRINSIC |
GEL
|
745 |
838 |
2.24e-25 |
SMART |
GEL
|
905 |
1039 |
1.13e-3 |
SMART |
GEL
|
1056 |
1152 |
7.28e-16 |
SMART |
GEL
|
1167 |
1263 |
5.51e-25 |
SMART |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000052346
AA Change: S654P
PolyPhen 2
Score 0.621 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000060749 Gene: ENSMUSG00000020536 AA Change: S654P
Domain | Start | End | E-Value | Type |
WD40
|
22 |
62 |
4.42e1 |
SMART |
WD40
|
64 |
103 |
1.65e1 |
SMART |
WD40
|
187 |
223 |
2.74e2 |
SMART |
WD40
|
226 |
264 |
2.06e0 |
SMART |
Pfam:LLGL
|
278 |
379 |
1.2e-43 |
PFAM |
WD40
|
424 |
460 |
3.2e0 |
SMART |
Blast:WD40
|
498 |
541 |
2e-13 |
BLAST |
Blast:WD40
|
585 |
624 |
4e-9 |
BLAST |
Pfam:Lgl_C
|
732 |
978 |
1.2e-7 |
PFAM |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000108719
AA Change: S654P
PolyPhen 2
Score 0.621 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000104359 Gene: ENSMUSG00000020536 AA Change: S654P
Domain | Start | End | E-Value | Type |
WD40
|
22 |
62 |
4.42e1 |
SMART |
WD40
|
64 |
103 |
1.65e1 |
SMART |
WD40
|
187 |
223 |
2.74e2 |
SMART |
WD40
|
226 |
264 |
2.06e0 |
SMART |
Pfam:LLGL
|
275 |
379 |
2e-48 |
PFAM |
WD40
|
424 |
460 |
3.2e0 |
SMART |
Blast:WD40
|
498 |
540 |
2e-13 |
BLAST |
Blast:WD40
|
585 |
624 |
4e-9 |
BLAST |
Pfam:Lgl_C
|
804 |
976 |
1.3e-8 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128749
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000154141
|
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.2%
|
Validation Efficiency |
|
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is similar to a tumor suppressor in Drosophila. The protein is part of a cytoskeletal network and is associated with nonmuscle myosin II heavy chain and a kinase that specifically phosphorylates this protein at serine residues. The gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008] PHENOTYPE: Homozygous mutant mice die neonatally exhibiting hydroencephaly. Neural progenitor cell physiology is abnormal, resulting in a loss of cell polarity and the development of neuroepithelial rosette-like structures throughout the brain. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 63 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adam11 |
A |
T |
11: 102,660,750 (GRCm39) |
I94F |
possibly damaging |
Het |
Ankrd50 |
A |
T |
3: 38,509,741 (GRCm39) |
D875E |
probably damaging |
Het |
Arf3 |
T |
C |
15: 98,639,285 (GRCm39) |
N60S |
probably benign |
Het |
Atxn2 |
T |
G |
5: 121,944,280 (GRCm39) |
|
probably null |
Het |
B3gnt8 |
A |
T |
7: 25,328,373 (GRCm39) |
I268F |
probably benign |
Het |
Bmp1 |
T |
A |
14: 70,723,712 (GRCm39) |
D708V |
possibly damaging |
Het |
C1s2 |
A |
G |
6: 124,609,069 (GRCm39) |
S163P |
probably damaging |
Het |
C3 |
A |
G |
17: 57,526,623 (GRCm39) |
I786T |
probably benign |
Het |
Cacna2d2 |
T |
A |
9: 107,404,602 (GRCm39) |
L1138Q |
probably damaging |
Het |
Cage1 |
T |
A |
13: 38,207,029 (GRCm39) |
Y272F |
probably damaging |
Het |
Cd300ld |
A |
T |
11: 114,875,058 (GRCm39) |
M192K |
possibly damaging |
Het |
Cdc5l |
A |
T |
17: 45,718,745 (GRCm39) |
F624I |
probably benign |
Het |
Cdh8 |
T |
A |
8: 99,922,897 (GRCm39) |
Q333L |
probably damaging |
Het |
Ciapin1 |
T |
A |
8: 95,555,787 (GRCm39) |
K128* |
probably null |
Het |
Col6a3 |
T |
A |
1: 90,731,467 (GRCm39) |
E988D |
probably benign |
Het |
Crip3 |
A |
G |
17: 46,740,338 (GRCm39) |
E46G |
probably damaging |
Het |
D5Ertd579e |
A |
G |
5: 36,772,137 (GRCm39) |
S753P |
possibly damaging |
Het |
Dock6 |
T |
A |
9: 21,744,177 (GRCm39) |
D126V |
probably damaging |
Het |
Duxf4 |
T |
A |
10: 58,072,158 (GRCm39) |
I19F |
possibly damaging |
Het |
Dvl3 |
A |
G |
16: 20,342,506 (GRCm39) |
E153G |
probably damaging |
Het |
Epas1 |
A |
T |
17: 87,136,471 (GRCm39) |
M748L |
probably benign |
Het |
Exoc8 |
A |
G |
8: 125,622,477 (GRCm39) |
L630P |
probably damaging |
Het |
Fam227a |
G |
A |
15: 79,507,668 (GRCm39) |
T454M |
probably damaging |
Het |
Flnc |
A |
T |
6: 29,459,134 (GRCm39) |
D2472V |
probably damaging |
Het |
Galnt4 |
G |
A |
10: 98,944,509 (GRCm39) |
G78E |
probably damaging |
Het |
Ghr |
A |
T |
15: 3,362,956 (GRCm39) |
L172* |
probably null |
Het |
Gjb5 |
A |
T |
4: 127,250,063 (GRCm39) |
|
probably null |
Het |
Hdac5 |
T |
C |
11: 102,095,340 (GRCm39) |
D427G |
probably damaging |
Het |
Hsd17b4 |
G |
A |
18: 50,316,369 (GRCm39) |
|
probably null |
Het |
Kcnab1 |
T |
C |
3: 65,017,368 (GRCm39) |
I59T |
probably benign |
Het |
Kcnh7 |
A |
G |
2: 62,607,950 (GRCm39) |
Y544H |
probably damaging |
Het |
Kdm7a |
A |
G |
6: 39,123,870 (GRCm39) |
S765P |
probably damaging |
Het |
Lama1 |
A |
T |
17: 68,059,936 (GRCm39) |
H675L |
probably benign |
Het |
Lemd3 |
CCCTCCTCCTCCTCCTCCTCC |
CCCTCCTCCTCCTCCTCC |
10: 120,814,432 (GRCm39) |
|
probably benign |
Het |
Lvrn |
G |
T |
18: 47,011,409 (GRCm39) |
M455I |
probably benign |
Het |
Mfsd12 |
T |
A |
10: 81,193,568 (GRCm39) |
L46Q |
probably damaging |
Het |
Mtcl1 |
A |
T |
17: 66,673,427 (GRCm39) |
M783K |
probably benign |
Het |
Mthfd1l |
A |
T |
10: 3,978,399 (GRCm39) |
T420S |
probably damaging |
Het |
Mybphl |
T |
A |
3: 108,284,635 (GRCm39) |
I294N |
probably damaging |
Het |
Or4c52 |
G |
A |
2: 89,845,768 (GRCm39) |
G165S |
probably damaging |
Het |
Or4f14b |
T |
C |
2: 111,775,658 (GRCm39) |
T48A |
possibly damaging |
Het |
Or52ab7 |
T |
A |
7: 102,977,831 (GRCm39) |
L46* |
probably null |
Het |
Oxa1l |
A |
T |
14: 54,598,924 (GRCm39) |
Q70L |
probably benign |
Het |
Pcdhac2 |
A |
T |
18: 37,279,185 (GRCm39) |
I722F |
probably damaging |
Het |
Pde4d |
A |
G |
13: 110,084,924 (GRCm39) |
D460G |
probably damaging |
Het |
Pth1r |
CGGG |
CGGGGGG |
9: 110,556,058 (GRCm39) |
|
probably benign |
Het |
Rab11fip3 |
A |
G |
17: 26,287,152 (GRCm39) |
S334P |
probably benign |
Het |
Ror2 |
C |
T |
13: 53,439,816 (GRCm39) |
|
probably null |
Het |
Scnn1g |
G |
C |
7: 121,366,519 (GRCm39) |
W572S |
probably damaging |
Het |
Skint5 |
G |
A |
4: 113,798,046 (GRCm39) |
S179L |
probably damaging |
Het |
Slc22a2 |
G |
T |
17: 12,817,949 (GRCm39) |
G175V |
probably damaging |
Het |
Spaca6 |
G |
A |
17: 18,056,416 (GRCm39) |
|
probably null |
Het |
Tbc1d30 |
C |
T |
10: 121,140,312 (GRCm39) |
R207H |
probably damaging |
Het |
Tdrd5 |
A |
G |
1: 156,087,435 (GRCm39) |
I829T |
probably benign |
Het |
Tmcc3 |
T |
C |
10: 94,414,780 (GRCm39) |
S161P |
probably damaging |
Het |
Tmem150b |
A |
G |
7: 4,719,353 (GRCm39) |
V189A |
probably benign |
Het |
Tmem248 |
A |
G |
5: 130,260,597 (GRCm39) |
D54G |
probably benign |
Het |
Trmt1 |
T |
A |
8: 85,417,487 (GRCm39) |
S121T |
probably damaging |
Het |
Tyk2 |
C |
T |
9: 21,026,503 (GRCm39) |
V698M |
probably damaging |
Het |
Usp17la |
A |
G |
7: 104,509,919 (GRCm39) |
R175G |
probably damaging |
Het |
Vav1 |
A |
G |
17: 57,610,140 (GRCm39) |
N464S |
probably benign |
Het |
Vmn2r57 |
T |
G |
7: 41,078,249 (GRCm39) |
|
probably null |
Het |
Vmn2r78 |
A |
G |
7: 86,570,535 (GRCm39) |
Y351C |
probably damaging |
Het |
|
Other mutations in Llgl1 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01137:Llgl1
|
APN |
11 |
60,600,825 (GRCm39) |
missense |
probably benign |
0.38 |
IGL01400:Llgl1
|
APN |
11 |
60,597,316 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03066:Llgl1
|
APN |
11 |
60,596,860 (GRCm39) |
missense |
possibly damaging |
0.75 |
IGL03174:Llgl1
|
APN |
11 |
60,597,036 (GRCm39) |
missense |
probably benign |
0.15 |
IGL03306:Llgl1
|
APN |
11 |
60,602,180 (GRCm39) |
missense |
possibly damaging |
0.92 |
R0284:Llgl1
|
UTSW |
11 |
60,602,967 (GRCm39) |
missense |
probably damaging |
0.98 |
R1137:Llgl1
|
UTSW |
11 |
60,595,559 (GRCm39) |
missense |
probably benign |
0.01 |
R1432:Llgl1
|
UTSW |
11 |
60,599,380 (GRCm39) |
missense |
probably damaging |
1.00 |
R1769:Llgl1
|
UTSW |
11 |
60,597,873 (GRCm39) |
missense |
probably damaging |
1.00 |
R1786:Llgl1
|
UTSW |
11 |
60,598,066 (GRCm39) |
missense |
probably benign |
0.19 |
R1835:Llgl1
|
UTSW |
11 |
60,595,556 (GRCm39) |
missense |
probably benign |
0.00 |
R1943:Llgl1
|
UTSW |
11 |
60,596,842 (GRCm39) |
missense |
probably benign |
|
R2510:Llgl1
|
UTSW |
11 |
60,600,862 (GRCm39) |
missense |
probably damaging |
1.00 |
R2568:Llgl1
|
UTSW |
11 |
60,599,638 (GRCm39) |
missense |
probably damaging |
1.00 |
R3690:Llgl1
|
UTSW |
11 |
60,597,828 (GRCm39) |
missense |
probably damaging |
1.00 |
R3853:Llgl1
|
UTSW |
11 |
60,598,075 (GRCm39) |
missense |
probably damaging |
1.00 |
R4079:Llgl1
|
UTSW |
11 |
60,601,110 (GRCm39) |
splice site |
probably null |
|
R4259:Llgl1
|
UTSW |
11 |
60,600,394 (GRCm39) |
missense |
probably benign |
|
R4348:Llgl1
|
UTSW |
11 |
60,600,394 (GRCm39) |
missense |
probably benign |
|
R4349:Llgl1
|
UTSW |
11 |
60,600,394 (GRCm39) |
missense |
probably benign |
|
R4352:Llgl1
|
UTSW |
11 |
60,600,394 (GRCm39) |
missense |
probably benign |
|
R4353:Llgl1
|
UTSW |
11 |
60,600,394 (GRCm39) |
missense |
probably benign |
|
R4396:Llgl1
|
UTSW |
11 |
60,596,834 (GRCm39) |
missense |
probably benign |
|
R4584:Llgl1
|
UTSW |
11 |
60,602,908 (GRCm39) |
missense |
probably damaging |
0.99 |
R4594:Llgl1
|
UTSW |
11 |
60,597,147 (GRCm39) |
missense |
probably benign |
0.15 |
R4628:Llgl1
|
UTSW |
11 |
60,600,811 (GRCm39) |
missense |
probably damaging |
1.00 |
R4651:Llgl1
|
UTSW |
11 |
60,599,477 (GRCm39) |
missense |
possibly damaging |
0.80 |
R4653:Llgl1
|
UTSW |
11 |
60,599,477 (GRCm39) |
missense |
possibly damaging |
0.80 |
R4731:Llgl1
|
UTSW |
11 |
60,597,051 (GRCm39) |
nonsense |
probably null |
|
R4869:Llgl1
|
UTSW |
11 |
60,598,036 (GRCm39) |
nonsense |
probably null |
|
R4898:Llgl1
|
UTSW |
11 |
60,600,394 (GRCm39) |
missense |
probably benign |
|
R4899:Llgl1
|
UTSW |
11 |
60,600,394 (GRCm39) |
missense |
probably benign |
|
R4939:Llgl1
|
UTSW |
11 |
60,600,805 (GRCm39) |
critical splice acceptor site |
probably null |
|
R4941:Llgl1
|
UTSW |
11 |
60,600,394 (GRCm39) |
missense |
probably benign |
|
R4942:Llgl1
|
UTSW |
11 |
60,600,394 (GRCm39) |
missense |
probably benign |
|
R4958:Llgl1
|
UTSW |
11 |
60,602,261 (GRCm39) |
missense |
probably benign |
0.02 |
R4995:Llgl1
|
UTSW |
11 |
60,600,550 (GRCm39) |
missense |
probably benign |
0.00 |
R4997:Llgl1
|
UTSW |
11 |
60,600,394 (GRCm39) |
missense |
probably benign |
|
R5177:Llgl1
|
UTSW |
11 |
60,602,833 (GRCm39) |
missense |
possibly damaging |
0.94 |
R5257:Llgl1
|
UTSW |
11 |
60,602,389 (GRCm39) |
splice site |
probably null |
|
R5258:Llgl1
|
UTSW |
11 |
60,602,389 (GRCm39) |
splice site |
probably null |
|
R5401:Llgl1
|
UTSW |
11 |
60,597,297 (GRCm39) |
missense |
probably benign |
|
R5406:Llgl1
|
UTSW |
11 |
60,604,010 (GRCm39) |
missense |
probably damaging |
0.99 |
R5432:Llgl1
|
UTSW |
11 |
60,598,449 (GRCm39) |
missense |
probably benign |
|
R5587:Llgl1
|
UTSW |
11 |
60,601,168 (GRCm39) |
missense |
probably benign |
0.00 |
R5732:Llgl1
|
UTSW |
11 |
60,600,286 (GRCm39) |
missense |
probably benign |
0.00 |
R5758:Llgl1
|
UTSW |
11 |
60,599,393 (GRCm39) |
missense |
probably damaging |
1.00 |
R5879:Llgl1
|
UTSW |
11 |
60,603,806 (GRCm39) |
missense |
probably benign |
0.00 |
R6268:Llgl1
|
UTSW |
11 |
60,602,989 (GRCm39) |
missense |
probably benign |
0.13 |
R6286:Llgl1
|
UTSW |
11 |
60,600,358 (GRCm39) |
missense |
probably damaging |
1.00 |
R6455:Llgl1
|
UTSW |
11 |
60,600,486 (GRCm39) |
missense |
probably damaging |
0.98 |
R6805:Llgl1
|
UTSW |
11 |
60,593,691 (GRCm39) |
missense |
probably benign |
0.25 |
R6929:Llgl1
|
UTSW |
11 |
60,601,179 (GRCm39) |
nonsense |
probably null |
|
R7274:Llgl1
|
UTSW |
11 |
60,596,812 (GRCm39) |
missense |
possibly damaging |
0.89 |
R7889:Llgl1
|
UTSW |
11 |
60,598,138 (GRCm39) |
missense |
probably damaging |
1.00 |
R7986:Llgl1
|
UTSW |
11 |
60,602,221 (GRCm39) |
missense |
probably benign |
0.16 |
R8141:Llgl1
|
UTSW |
11 |
60,601,142 (GRCm39) |
missense |
probably benign |
0.02 |
R8176:Llgl1
|
UTSW |
11 |
60,597,387 (GRCm39) |
missense |
probably benign |
0.27 |
R8223:Llgl1
|
UTSW |
11 |
60,593,648 (GRCm39) |
missense |
possibly damaging |
0.86 |
R8332:Llgl1
|
UTSW |
11 |
60,601,210 (GRCm39) |
missense |
possibly damaging |
0.90 |
R8350:Llgl1
|
UTSW |
11 |
60,602,947 (GRCm39) |
missense |
probably damaging |
1.00 |
R8500:Llgl1
|
UTSW |
11 |
60,595,809 (GRCm39) |
critical splice donor site |
probably null |
|
R8979:Llgl1
|
UTSW |
11 |
60,601,129 (GRCm39) |
missense |
probably benign |
0.25 |
R9155:Llgl1
|
UTSW |
11 |
60,597,934 (GRCm39) |
missense |
probably benign |
0.00 |
R9163:Llgl1
|
UTSW |
11 |
60,600,402 (GRCm39) |
missense |
probably benign |
0.02 |
R9225:Llgl1
|
UTSW |
11 |
60,600,889 (GRCm39) |
missense |
probably damaging |
1.00 |
R9234:Llgl1
|
UTSW |
11 |
60,600,956 (GRCm39) |
critical splice donor site |
probably null |
|
Z1186:Llgl1
|
UTSW |
11 |
60,603,923 (GRCm39) |
frame shift |
probably null |
|
Z1187:Llgl1
|
UTSW |
11 |
60,603,923 (GRCm39) |
frame shift |
probably null |
|
Z1188:Llgl1
|
UTSW |
11 |
60,603,923 (GRCm39) |
frame shift |
probably null |
|
Z1189:Llgl1
|
UTSW |
11 |
60,603,923 (GRCm39) |
frame shift |
probably null |
|
Z1190:Llgl1
|
UTSW |
11 |
60,603,923 (GRCm39) |
frame shift |
probably null |
|
Z1191:Llgl1
|
UTSW |
11 |
60,603,923 (GRCm39) |
frame shift |
probably null |
|
Z1192:Llgl1
|
UTSW |
11 |
60,603,923 (GRCm39) |
frame shift |
probably null |
|
|
Predicted Primers |
PCR Primer
(F):5'- AGCCCTTGTAAACGCTCTC -3'
(R):5'- TCAGACGTGCTCTTCCAAG -3'
Sequencing Primer
(F):5'- GTAAACGCTCTCCTCCTGC -3'
(R):5'- TCCAGCAGGATCCCTTCAC -3'
|
Posted On |
2014-10-02 |