Incidental Mutation 'R6196:Lgi1'
ID |
502954 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Lgi1
|
Ensembl Gene |
ENSMUSG00000067242 |
Gene Name |
leucine-rich repeat LGI family, member 1 |
Synonyms |
|
MMRRC Submission |
044336-MU
|
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.740)
|
Stock # |
R6196 (G1)
|
Quality Score |
105.008 |
Status
|
Validated
|
Chromosome |
19 |
Chromosomal Location |
38253135-38297387 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 38294257 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Asparagine to Serine
at position 295
(N295S)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000143538
(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 benign
Transcript: ENSMUST00000196090
AA Change: N295S
PolyPhen 2
Score 0.228 (Sensitivity: 0.91; Specificity: 0.88)
|
SMART Domains |
Protein: ENSMUSP00000143538 Gene: ENSMUSG00000067242 AA Change: N295S
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 benign
Transcript: ENSMUST00000198518
AA Change: N343S
PolyPhen 2
Score 0.159 (Sensitivity: 0.92; Specificity: 0.87)
|
SMART Domains |
Protein: ENSMUSP00000143128 Gene: ENSMUSG00000067242 AA Change: N343S
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 benign
Transcript: ENSMUST00000199812
AA Change: N319S
PolyPhen 2
Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)
|
SMART Domains |
Protein: ENSMUSP00000143502 Gene: ENSMUSG00000067242 AA Change: N319S
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 |
0.4154 |
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.8%
|
Validation Efficiency |
96% (55/57) |
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: 55 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4933405L10Rik |
A |
T |
8: 106,436,554 (GRCm39) |
H241L |
possibly damaging |
Het |
Acap1 |
T |
C |
11: 69,777,893 (GRCm39) |
D115G |
probably damaging |
Het |
Acvr2b |
T |
C |
9: 119,262,469 (GRCm39) |
V510A |
possibly damaging |
Het |
Acyp2 |
C |
T |
11: 30,456,354 (GRCm39) |
E98K |
possibly damaging |
Het |
Agr2 |
A |
T |
12: 36,045,591 (GRCm39) |
K26* |
probably null |
Het |
Aox4 |
T |
A |
1: 58,256,685 (GRCm39) |
I69N |
probably damaging |
Het |
Asb4 |
G |
A |
6: 5,390,699 (GRCm39) |
G31R |
probably benign |
Het |
Atp6v1c2 |
C |
A |
12: 17,351,187 (GRCm39) |
E105* |
probably null |
Het |
Bend6 |
A |
G |
1: 33,917,509 (GRCm39) |
Y44H |
probably damaging |
Het |
Bltp3b |
T |
G |
10: 89,641,195 (GRCm39) |
S789A |
probably benign |
Het |
Btn2a2 |
C |
T |
13: 23,672,015 (GRCm39) |
V25M |
possibly damaging |
Het |
Cab39l |
T |
A |
14: 59,737,039 (GRCm39) |
L53Q |
probably damaging |
Het |
Cc2d1b |
C |
T |
4: 108,490,422 (GRCm39) |
R825W |
probably damaging |
Het |
Cdc14b |
C |
T |
13: 64,353,338 (GRCm39) |
|
probably benign |
Het |
Cenpu |
A |
G |
8: 47,015,615 (GRCm39) |
R177G |
probably benign |
Het |
Chit1 |
C |
A |
1: 134,074,381 (GRCm39) |
Y229* |
probably null |
Het |
Crybg2 |
C |
A |
4: 133,808,450 (GRCm39) |
S1350R |
probably damaging |
Het |
Ctdspl2 |
A |
G |
2: 121,809,373 (GRCm39) |
|
probably null |
Het |
Ctsr |
A |
T |
13: 61,308,345 (GRCm39) |
H266Q |
probably benign |
Het |
Dynlt5 |
A |
G |
4: 102,849,766 (GRCm39) |
E63G |
possibly damaging |
Het |
Efcab3 |
T |
G |
11: 104,746,386 (GRCm39) |
I2279S |
probably benign |
Het |
Extl3 |
T |
A |
14: 65,313,584 (GRCm39) |
M533L |
probably benign |
Het |
Fam162b |
C |
A |
10: 51,463,506 (GRCm39) |
|
probably null |
Het |
Fbxo28 |
T |
C |
1: 182,157,454 (GRCm39) |
K121R |
probably damaging |
Het |
Fsip2 |
A |
C |
2: 82,820,227 (GRCm39) |
E5320A |
possibly damaging |
Het |
Galc |
A |
T |
12: 98,225,421 (GRCm39) |
D56E |
probably damaging |
Het |
Gm5468 |
A |
G |
15: 25,414,481 (GRCm39) |
|
probably benign |
Het |
Hk1 |
T |
A |
10: 62,135,038 (GRCm39) |
H24L |
probably damaging |
Het |
Igkv5-43 |
A |
G |
6: 69,752,965 (GRCm39) |
V39A |
possibly damaging |
Het |
Lemd2 |
G |
A |
17: 27,411,976 (GRCm39) |
Q439* |
probably null |
Het |
Macc1 |
T |
G |
12: 119,409,785 (GRCm39) |
S184R |
probably damaging |
Het |
Msmo1 |
A |
G |
8: 65,180,918 (GRCm39) |
|
probably benign |
Het |
Muc5b |
C |
A |
7: 141,405,333 (GRCm39) |
R914S |
unknown |
Het |
Or10d1 |
G |
A |
9: 39,483,776 (GRCm39) |
P260S |
possibly damaging |
Het |
Or1e16 |
G |
A |
11: 73,286,299 (GRCm39) |
A183V |
probably benign |
Het |
Or1e17 |
G |
A |
11: 73,831,635 (GRCm39) |
A188T |
possibly damaging |
Het |
Or4k2 |
C |
A |
14: 50,424,135 (GRCm39) |
D180Y |
probably damaging |
Het |
Or5b110-ps1 |
A |
G |
19: 13,260,290 (GRCm39) |
I44T |
probably benign |
Het |
Plekha5 |
T |
C |
6: 140,525,179 (GRCm39) |
S14P |
probably benign |
Het |
Pus10 |
A |
G |
11: 23,622,638 (GRCm39) |
K86R |
probably benign |
Het |
Rab37 |
T |
C |
11: 115,051,132 (GRCm39) |
V147A |
probably benign |
Het |
Sin3a |
T |
A |
9: 57,011,213 (GRCm39) |
I490N |
probably damaging |
Het |
Slc27a4 |
A |
G |
2: 29,695,762 (GRCm39) |
D99G |
probably benign |
Het |
Slc43a2 |
C |
T |
11: 75,459,206 (GRCm39) |
R413* |
probably null |
Het |
Syna |
G |
T |
5: 134,588,466 (GRCm39) |
T161N |
probably benign |
Het |
T |
A |
G |
17: 8,655,996 (GRCm39) |
D86G |
possibly damaging |
Het |
Tanc1 |
G |
A |
2: 59,674,366 (GRCm39) |
E1817K |
possibly damaging |
Het |
Tap2 |
C |
A |
17: 34,433,384 (GRCm39) |
Q516K |
possibly damaging |
Het |
Tcaf1 |
A |
T |
6: 42,653,741 (GRCm39) |
D717E |
probably damaging |
Het |
Tcf20 |
G |
T |
15: 82,736,187 (GRCm39) |
Q1755K |
possibly damaging |
Het |
Top2b |
T |
G |
14: 16,409,189 (GRCm38) |
I777M |
probably damaging |
Het |
Trpm7 |
G |
A |
2: 126,667,559 (GRCm39) |
P811S |
possibly damaging |
Het |
Vmn2r59 |
A |
G |
7: 41,661,679 (GRCm39) |
V712A |
probably benign |
Het |
Vwc2l |
T |
A |
1: 70,768,180 (GRCm39) |
D34E |
probably damaging |
Het |
Wdr35 |
A |
G |
12: 9,077,632 (GRCm39) |
K1091E |
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 |
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 |
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'- GGTGTGCAAGCCCATAGTTATTG -3'
(R):5'- AATAGCTGTGTTGCTTTGCTCC -3'
Sequencing Primer
(F):5'- GTGCAAGCCCATAGTTATTGACACTC -3'
(R):5'- CTTTGCTCCACTGGTAAATAACAGGG -3'
|
Posted On |
2018-02-27 |