Incidental Mutation 'R3732:Lgi1'
| ID |
271062 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lgi1
|
| Ensembl Gene |
ENSMUSG00000067242 |
| Gene Name |
leucine-rich repeat LGI family, member 1 |
| Synonyms |
|
| MMRRC Submission |
040720-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.772)
|
| Stock # |
R3732 (G1)
|
| Quality Score |
87 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
38253135-38297387 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 38294694 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 465
(Y465H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000143502
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000087252]
[ENSMUST00000196090]
[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: Y441H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242
AA Change: Y441H
| 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: ENSMUST00000198045
|
| SMART Domains |
Protein: ENSMUSP00000143292
Gene: ENSMUSG00000067242
| 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: Y489H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000143128
Gene: ENSMUSG00000067242
AA Change: Y489H
| 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: Y465H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242
AA Change: Y465H
| 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
|
| Meta Mutation Damage Score |
0.5007 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.8%
|
| Validation Efficiency |
100% (44/44) |
| 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: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ablim1 |
A |
T |
19: 57,037,892 (GRCm39) |
|
probably null |
Het |
| Adgrl3 |
C |
A |
5: 81,942,793 (GRCm39) |
H1474Q |
probably benign |
Het |
| Adgrv1 |
T |
C |
13: 81,705,075 (GRCm39) |
I1578M |
probably damaging |
Het |
| Arhgef10l |
AGAGGAGGAGGAGGAGGA |
AGAGGAGGAGGAGGA |
4: 140,308,930 (GRCm39) |
|
probably benign |
Het |
| Bcl7b |
A |
G |
5: 135,209,767 (GRCm39) |
T141A |
probably benign |
Het |
| Cfap97d1 |
C |
T |
11: 101,879,278 (GRCm39) |
Q17* |
probably null |
Het |
| Chrna3 |
T |
C |
9: 54,923,178 (GRCm39) |
K210R |
probably benign |
Het |
| Cpsf2 |
T |
C |
12: 101,953,567 (GRCm39) |
I199T |
probably damaging |
Het |
| Cyp2a4 |
A |
G |
7: 26,012,252 (GRCm39) |
D345G |
probably damaging |
Het |
| Cyp2s1 |
C |
T |
7: 25,503,379 (GRCm39) |
R424Q |
probably null |
Het |
| D1Pas1 |
C |
A |
1: 186,700,294 (GRCm39) |
S74R |
probably benign |
Het |
| Edem1 |
T |
C |
6: 108,818,582 (GRCm39) |
F197L |
probably damaging |
Het |
| Ergic2 |
T |
C |
6: 148,104,020 (GRCm39) |
D79G |
probably damaging |
Het |
| Espl1 |
A |
G |
15: 102,221,424 (GRCm39) |
I944V |
probably damaging |
Het |
| Fat1 |
T |
C |
8: 45,406,306 (GRCm39) |
V1019A |
possibly damaging |
Het |
| Fbxl21 |
T |
A |
13: 56,674,830 (GRCm39) |
H60Q |
probably benign |
Het |
| Fbxw7 |
A |
C |
3: 84,833,014 (GRCm39) |
K19Q |
possibly damaging |
Het |
| Gldn |
A |
G |
9: 54,245,946 (GRCm39) |
K499R |
possibly damaging |
Het |
| Gria4 |
C |
T |
9: 4,513,295 (GRCm39) |
M271I |
probably benign |
Het |
| Herc1 |
C |
T |
9: 66,352,922 (GRCm39) |
T2136I |
probably damaging |
Het |
| Iqcg |
G |
T |
16: 32,873,996 (GRCm39) |
|
probably benign |
Het |
| Itih2 |
A |
T |
2: 10,110,481 (GRCm39) |
F537I |
probably benign |
Het |
| Itpr2 |
T |
C |
6: 146,284,198 (GRCm39) |
D533G |
probably damaging |
Het |
| Kcnk15 |
A |
G |
2: 163,695,733 (GRCm39) |
K22E |
probably benign |
Het |
| Lag3 |
A |
T |
6: 124,887,103 (GRCm39) |
S155T |
probably benign |
Het |
| Lars1 |
T |
C |
18: 42,345,667 (GRCm39) |
E1003G |
probably benign |
Het |
| Layn |
T |
A |
9: 50,970,844 (GRCm39) |
N233I |
probably damaging |
Het |
| Lrig1 |
C |
T |
6: 94,588,557 (GRCm39) |
A531T |
possibly damaging |
Het |
| Mtx2 |
C |
A |
2: 74,677,606 (GRCm39) |
A22E |
probably damaging |
Het |
| Nipal3 |
T |
C |
4: 135,191,157 (GRCm39) |
T325A |
probably damaging |
Het |
| Ola1 |
G |
C |
2: 72,987,204 (GRCm39) |
R143G |
probably damaging |
Het |
| Otog |
A |
G |
7: 45,937,792 (GRCm39) |
T1834A |
probably benign |
Het |
| Panx1 |
GTTCTTCT |
GTTCT |
9: 14,917,467 (GRCm39) |
|
probably benign |
Het |
| Pcdh18 |
T |
C |
3: 49,709,240 (GRCm39) |
S692G |
probably benign |
Het |
| Pkd2 |
G |
A |
5: 104,637,285 (GRCm39) |
|
probably null |
Het |
| Ppp1r9a |
T |
C |
6: 4,906,259 (GRCm39) |
|
probably benign |
Het |
| Robo2 |
A |
C |
16: 73,717,635 (GRCm39) |
L1159W |
possibly damaging |
Het |
| Sfxn5 |
T |
C |
6: 85,276,258 (GRCm39) |
|
probably benign |
Het |
| Shf |
T |
A |
2: 122,175,688 (GRCm39) |
|
probably benign |
Het |
| Siah2 |
A |
G |
3: 58,583,671 (GRCm39) |
V205A |
probably damaging |
Het |
| Slc44a4 |
G |
A |
17: 35,140,537 (GRCm39) |
|
silent |
Het |
| Spindoc |
A |
C |
19: 7,351,666 (GRCm39) |
L202R |
probably damaging |
Het |
| Spock3 |
T |
A |
8: 63,798,733 (GRCm39) |
D251E |
probably damaging |
Het |
| Stk4 |
T |
A |
2: 163,930,828 (GRCm39) |
M143K |
probably benign |
Het |
| Trpc3 |
A |
T |
3: 36,692,708 (GRCm39) |
D761E |
probably benign |
Het |
| Twf1 |
A |
C |
15: 94,482,295 (GRCm39) |
|
probably benign |
Het |
| Ugcg |
C |
T |
4: 59,207,798 (GRCm39) |
P46S |
probably benign |
Het |
| Vps50 |
T |
C |
6: 3,519,243 (GRCm39) |
|
silent |
Het |
| Wapl |
G |
A |
14: 34,458,721 (GRCm39) |
V928I |
probably damaging |
Het |
| Zfand3 |
A |
G |
17: 30,411,630 (GRCm39) |
K130R |
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 |
|
R3733:Lgi1
|
UTSW |
19 |
38,294,694 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4643:Lgi1
|
UTSW |
19 |
38,289,158 (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'- AACATGGAGGACGTATACGC -3'
(R):5'- TGGTGTCTCATGCGCTTAAG -3'
Sequencing Primer
(F):5'- TATACGCGGTGAAGCACTTC -3'
(R):5'- GGTGTCTCATGCGCTTAAGTCAAC -3'
|
| Posted On |
2015-03-18 |
Incidental Mutation