Incidental Mutation 'R4643:Lgi1'
| ID |
500748 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lgi1
|
| Ensembl Gene |
ENSMUSG00000067242 |
| Gene Name |
leucine-rich repeat LGI family, member 1 |
| Synonyms |
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.772)
|
| Stock # |
R4643 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
19 |
| Chromosomal Location |
38253135-38297387 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 38289158 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Valine
at position 145
(D145V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000143502
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000087252]
[ENSMUST00000196090]
[ENSMUST00000197123]
[ENSMUST00000198045]
[ENSMUST00000198518]
[ENSMUST00000199812]
|
| AlphaFold |
Q9JIA1 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000087252
|
| SMART Domains |
Protein: ENSMUSP00000084507
Gene: ENSMUSG00000067242
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
34 |
N/A |
INTRINSIC |
|
LRRNT
|
41 |
71 |
9.09e0 |
SMART |
|
LRR
|
90 |
113 |
2.61e2 |
SMART |
|
LRR_TYP
|
114 |
137 |
5.14e-3 |
SMART |
|
LRR_TYP
|
138 |
161 |
2.27e-4 |
SMART |
|
LRRCT
|
173 |
222 |
4.63e-6 |
SMART |
|
Pfam:EPTP
|
225 |
266 |
3.8e-9 |
PFAM |
|
Pfam:EPTP
|
271 |
312 |
6.5e-12 |
PFAM |
|
Pfam:EPTP
|
317 |
363 |
7.2e-16 |
PFAM |
|
Pfam:EPTP
|
366 |
414 |
1.4e-7 |
PFAM |
|
Pfam:EPTP
|
419 |
461 |
1.6e-12 |
PFAM |
|
Pfam:EPTP
|
464 |
505 |
7.7e-11 |
PFAM |
|
Pfam:EPTP
|
510 |
550 |
3.4e-13 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130039
|
| SMART Domains |
Protein: ENSMUSP00000117936
Gene: ENSMUSG00000067242
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
11 |
38 |
N/A |
INTRINSIC |
|
LRR
|
51 |
74 |
2.61e2 |
SMART |
|
LRR_TYP
|
75 |
98 |
5.14e-3 |
SMART |
|
LRR_TYP
|
99 |
122 |
2.27e-4 |
SMART |
|
LRRCT
|
131 |
180 |
4.63e-6 |
SMART |
|
Pfam:EPTP
|
182 |
218 |
3e-12 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000196090
AA Change: D121V
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242
AA Change: D121V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
34 |
N/A |
INTRINSIC |
|
LRRNT
|
41 |
71 |
4.4e-2 |
SMART |
|
LRR_TYP
|
90 |
113 |
3.3e-4 |
SMART |
|
LRRCT
|
125 |
174 |
2.3e-8 |
SMART |
|
Pfam:EPTP
|
177 |
218 |
3.1e-6 |
PFAM |
|
Pfam:EPTP
|
223 |
264 |
5.3e-9 |
PFAM |
|
Pfam:EPTP
|
269 |
315 |
5.8e-13 |
PFAM |
|
Pfam:EPTP
|
318 |
366 |
1.1e-4 |
PFAM |
|
Pfam:EPTP
|
371 |
413 |
1.3e-9 |
PFAM |
|
Pfam:EPTP
|
416 |
457 |
6.2e-8 |
PFAM |
|
Pfam:EPTP
|
462 |
502 |
2.7e-10 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000197123
|
| SMART Domains |
Protein: ENSMUSP00000142953
Gene: ENSMUSG00000067242
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
34 |
N/A |
INTRINSIC |
|
LRRNT
|
41 |
71 |
4.3e-2 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000198045
AA Change: D169V
PolyPhen 2
Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000143292
Gene: ENSMUSG00000067242
AA Change: D169V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
34 |
N/A |
INTRINSIC |
|
LRRNT
|
41 |
71 |
4.3e-2 |
SMART |
|
LRR
|
90 |
113 |
1.1e0 |
SMART |
|
LRR_TYP
|
114 |
137 |
2.1e-5 |
SMART |
|
LRR_TYP
|
138 |
161 |
9.2e-7 |
SMART |
|
LRRCT
|
173 |
222 |
2.3e-8 |
SMART |
|
Pfam:EPTP
|
224 |
267 |
2.8e-12 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000198518
AA Change: D169V
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000143128
Gene: ENSMUSG00000067242
AA Change: D169V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
34 |
N/A |
INTRINSIC |
|
LRRNT
|
41 |
71 |
9.09e0 |
SMART |
|
LRR
|
90 |
113 |
2.61e2 |
SMART |
|
LRR_TYP
|
114 |
137 |
5.14e-3 |
SMART |
|
LRR_TYP
|
138 |
161 |
2.27e-4 |
SMART |
|
LRRCT
|
173 |
222 |
4.63e-6 |
SMART |
|
Pfam:EPTP
|
224 |
267 |
8.3e-15 |
PFAM |
|
Pfam:EPTP
|
270 |
313 |
9.4e-16 |
PFAM |
|
Pfam:EPTP
|
316 |
364 |
3.3e-18 |
PFAM |
|
Pfam:EPTP
|
365 |
415 |
5.2e-8 |
PFAM |
|
Pfam:EPTP
|
418 |
462 |
1e-16 |
PFAM |
|
Pfam:EPTP
|
463 |
506 |
1.9e-15 |
PFAM |
|
Pfam:EPTP
|
509 |
550 |
2.8e-17 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000199812
AA Change: D145V
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242
AA Change: D145V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
34 |
N/A |
INTRINSIC |
|
LRRNT
|
41 |
71 |
4.4e-2 |
SMART |
|
LRR_TYP
|
90 |
113 |
2.2e-5 |
SMART |
|
LRR_TYP
|
114 |
137 |
9.4e-7 |
SMART |
|
LRRCT
|
149 |
198 |
2.3e-8 |
SMART |
|
Pfam:EPTP
|
201 |
242 |
3.2e-6 |
PFAM |
|
Pfam:EPTP
|
247 |
288 |
5.6e-9 |
PFAM |
|
Pfam:EPTP
|
293 |
339 |
6.1e-13 |
PFAM |
|
Pfam:EPTP
|
342 |
390 |
1.2e-4 |
PFAM |
|
Pfam:EPTP
|
395 |
437 |
1.4e-9 |
PFAM |
|
Pfam:EPTP
|
440 |
481 |
6.6e-8 |
PFAM |
|
Pfam:EPTP
|
486 |
526 |
2.9e-10 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000200561
|
| 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 secreted leucine-rich repeat (LRR) superfamily and shares homology with members of the SLIT protein family. The encoded protein may regulate the activity of voltage-gated potassium channels and may be involved in neuronal growth regulation and cell survival. This gene is rearranged as a result of translocations in glioblastoma cell lines, and it is frequently down-regulated or rearranged in malignant gliomas. Mutations in this gene result in autosomal dominant lateral temporal epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit growth retardation, seizures, and death by the third week of life. Mice heterozygous for this allele exhibit increased suseptibility to pentylenetetrazole-induced seizures. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 41 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4833420G17Rik |
A |
G |
13: 119,611,396 (GRCm39) |
N398D |
probably damaging |
Het |
| Adamtsl4 |
G |
A |
3: 95,591,929 (GRCm39) |
A58V |
possibly damaging |
Het |
| Anapc2 |
T |
A |
2: 25,166,406 (GRCm39) |
V105E |
probably benign |
Het |
| C3ar1 |
A |
T |
6: 122,827,933 (GRCm39) |
C95S |
probably damaging |
Het |
| Ccdc87 |
G |
A |
19: 4,891,877 (GRCm39) |
G790R |
probably damaging |
Het |
| Cenpf |
A |
T |
1: 189,391,786 (GRCm39) |
M682K |
probably benign |
Het |
| Cyp2j13 |
T |
C |
4: 95,945,161 (GRCm39) |
Q289R |
possibly damaging |
Het |
| Dclk2 |
A |
T |
3: 86,713,487 (GRCm39) |
M453K |
possibly damaging |
Het |
| Dscam |
G |
A |
16: 96,486,501 (GRCm39) |
T1058M |
probably damaging |
Het |
| Gas2l3 |
CACTCGTCATACT |
CACT |
10: 89,266,820 (GRCm39) |
|
probably benign |
Het |
| Grip1 |
A |
G |
10: 119,856,006 (GRCm39) |
N659S |
probably damaging |
Het |
| Hectd4 |
A |
G |
5: 121,487,118 (GRCm39) |
K3371R |
possibly damaging |
Het |
| Il1a |
T |
A |
2: 129,146,623 (GRCm39) |
T157S |
probably benign |
Het |
| Il23r |
A |
G |
6: 67,400,977 (GRCm39) |
V451A |
probably benign |
Het |
| Iqch |
T |
C |
9: 63,502,084 (GRCm39) |
T40A |
probably benign |
Het |
| Irag2 |
A |
T |
6: 145,113,786 (GRCm39) |
D318V |
probably benign |
Het |
| Kazald1 |
G |
T |
19: 45,066,788 (GRCm39) |
V196L |
probably benign |
Het |
| L1td1 |
T |
C |
4: 98,626,120 (GRCm39) |
S772P |
probably damaging |
Het |
| Lrp12 |
A |
T |
15: 39,735,418 (GRCm39) |
L838Q |
probably damaging |
Het |
| Mrgprf |
C |
A |
7: 144,862,242 (GRCm39) |
P268Q |
probably benign |
Het |
| Myef2 |
T |
C |
2: 124,958,731 (GRCm39) |
K66R |
possibly damaging |
Het |
| Myo3b |
A |
G |
2: 70,069,186 (GRCm39) |
D475G |
possibly damaging |
Het |
| Numa1 |
C |
G |
7: 101,649,872 (GRCm39) |
|
probably null |
Het |
| Or6c214 |
T |
C |
10: 129,590,824 (GRCm39) |
E165G |
probably damaging |
Het |
| Prdm8 |
T |
C |
5: 98,332,446 (GRCm39) |
S116P |
possibly damaging |
Het |
| Pyroxd1 |
C |
G |
6: 142,300,467 (GRCm39) |
S199* |
probably null |
Het |
| R3hcc1l |
G |
T |
19: 42,551,239 (GRCm39) |
V79F |
probably benign |
Het |
| Rasal1 |
C |
T |
5: 120,817,029 (GRCm39) |
T779I |
probably benign |
Het |
| Scaper |
A |
C |
9: 55,745,463 (GRCm39) |
F596V |
probably damaging |
Het |
| Slco2b1 |
C |
T |
7: 99,316,214 (GRCm39) |
V439M |
probably benign |
Het |
| Slco6c1 |
A |
T |
1: 96,990,149 (GRCm39) |
D680E |
probably benign |
Het |
| Smurf1 |
A |
T |
5: 144,816,179 (GRCm39) |
F725L |
probably damaging |
Het |
| Snd1 |
A |
G |
6: 28,880,248 (GRCm39) |
E674G |
probably benign |
Het |
| Srcap |
C |
T |
7: 127,140,948 (GRCm39) |
P1515L |
probably damaging |
Het |
| Sycp2l |
A |
G |
13: 41,296,941 (GRCm39) |
M341V |
probably benign |
Het |
| Tmprss6 |
T |
A |
15: 78,329,556 (GRCm39) |
I492F |
probably damaging |
Het |
| Trip10 |
G |
T |
17: 57,568,658 (GRCm39) |
E416* |
probably null |
Het |
| Tstd2 |
T |
C |
4: 46,129,297 (GRCm39) |
D177G |
possibly damaging |
Het |
| Ugt1a5 |
A |
T |
1: 88,094,147 (GRCm39) |
N125I |
possibly damaging |
Het |
| Vmn2r7 |
G |
T |
3: 64,623,825 (GRCm39) |
S165Y |
probably damaging |
Het |
| Zfp663 |
A |
T |
2: 165,194,925 (GRCm39) |
H431Q |
probably benign |
Het |
|
| Other mutations in Lgi1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02882:Lgi1
|
APN |
19 |
38,272,453 (GRCm39) |
missense |
probably benign |
0.24 |
|
IGL03112:Lgi1
|
APN |
19 |
38,272,478 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R0201:Lgi1
|
UTSW |
19 |
38,289,741 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R1573:Lgi1
|
UTSW |
19 |
38,272,629 (GRCm39) |
missense |
probably benign |
0.30 |
|
R1795:Lgi1
|
UTSW |
19 |
38,294,631 (GRCm39) |
missense |
probably benign |
|
|
R2010:Lgi1
|
UTSW |
19 |
38,289,683 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3732:Lgi1
|
UTSW |
19 |
38,294,694 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3732:Lgi1
|
UTSW |
19 |
38,294,694 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3733:Lgi1
|
UTSW |
19 |
38,294,694 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4678:Lgi1
|
UTSW |
19 |
38,289,737 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4814:Lgi1
|
UTSW |
19 |
38,289,326 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4857:Lgi1
|
UTSW |
19 |
38,294,698 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5598:Lgi1
|
UTSW |
19 |
38,294,629 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R6180:Lgi1
|
UTSW |
19 |
38,253,404 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6196:Lgi1
|
UTSW |
19 |
38,294,257 (GRCm39) |
missense |
probably benign |
0.23 |
|
R6847:Lgi1
|
UTSW |
19 |
38,289,738 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7178:Lgi1
|
UTSW |
19 |
38,294,733 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7376:Lgi1
|
UTSW |
19 |
38,272,468 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7448:Lgi1
|
UTSW |
19 |
38,289,713 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8790:Lgi1
|
UTSW |
19 |
38,289,296 (GRCm39) |
missense |
possibly damaging |
0.58 |
|
R8899:Lgi1
|
UTSW |
19 |
38,294,538 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9089:Lgi1
|
UTSW |
19 |
38,294,095 (GRCm39) |
missense |
possibly damaging |
0.56 |
|
R9156:Lgi1
|
UTSW |
19 |
38,289,746 (GRCm39) |
missense |
probably benign |
0.08 |
|
R9484:Lgi1
|
UTSW |
19 |
38,294,757 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- AATAGGTTACTAGGATCTGGGTGGC -3'
(R):5'- CACACATTAAATCGCTCAGATGG -3'
Sequencing Primer
(F):5'- CTTTAGGGGTGCTCTGTGATCACC -3'
(R):5'- AAATCGCTCAGATGGTTCTTAAC -3'
|
| Posted On |
2017-12-01 |
Incidental Mutation