Incidental Mutation 'R6847:Lgi1'
| ID |
534836 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lgi1
|
| Ensembl Gene |
ENSMUSG00000067242 |
| Gene Name |
leucine-rich repeat LGI family, member 1 |
| Synonyms |
|
| MMRRC Submission |
045021-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.772)
|
| Stock # |
R6847 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
38253135-38297387 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 38289738 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 268
(V268A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000143128
(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 |
probably damaging
Transcript: ENSMUST00000196090
AA Change: V220A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242
AA Change: V220A
| 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 |
possibly damaging
Transcript: ENSMUST00000198045
AA Change: V268A
PolyPhen 2
Score 0.819 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000143292
Gene: ENSMUSG00000067242
AA Change: V268A
| 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: V268A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000143128
Gene: ENSMUSG00000067242
AA Change: V268A
| 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: V244A
PolyPhen 2
Score 0.159 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242
AA Change: V244A
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.3%
- 20x: 97.8%
|
| Validation Efficiency |
100% (50/50) |
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam26a |
A |
G |
8: 44,021,465 (GRCm39) |
I675T |
probably benign |
Het |
| Adgrb3 |
A |
T |
1: 25,133,003 (GRCm39) |
M1121K |
probably benign |
Het |
| Ak9 |
A |
G |
10: 41,233,797 (GRCm39) |
|
probably null |
Het |
| Akr1c6 |
T |
A |
13: 4,488,497 (GRCm39) |
C34* |
probably null |
Het |
| Akt3 |
G |
A |
1: 176,859,225 (GRCm39) |
P449S |
probably damaging |
Het |
| Atg2b |
A |
T |
12: 105,602,047 (GRCm39) |
V1643E |
probably damaging |
Het |
| Atp2c1 |
T |
C |
9: 105,295,778 (GRCm39) |
I819V |
probably damaging |
Het |
| Casp3 |
C |
T |
8: 47,089,301 (GRCm39) |
A183V |
probably benign |
Het |
| Cdk1 |
A |
T |
10: 69,174,358 (GRCm39) |
D288E |
probably benign |
Het |
| Cep131 |
G |
A |
11: 119,956,517 (GRCm39) |
R944W |
probably damaging |
Het |
| Cep290 |
A |
G |
10: 100,399,281 (GRCm39) |
K2268E |
probably damaging |
Het |
| Crybg2 |
A |
G |
4: 133,792,857 (GRCm39) |
E164G |
probably benign |
Het |
| Cubn |
A |
C |
2: 13,449,064 (GRCm39) |
|
probably null |
Het |
| Dnajc14 |
A |
T |
10: 128,652,656 (GRCm39) |
E571D |
possibly damaging |
Het |
| Dnase1l1 |
C |
T |
X: 73,320,644 (GRCm39) |
|
probably null |
Het |
| Eef1b2 |
A |
G |
1: 63,217,648 (GRCm39) |
E44G |
probably benign |
Het |
| Eml6 |
C |
T |
11: 29,768,447 (GRCm39) |
V747I |
probably benign |
Het |
| Ext1 |
T |
G |
15: 53,208,550 (GRCm39) |
Q70H |
probably benign |
Het |
| Gbp2b |
T |
A |
3: 142,303,940 (GRCm39) |
C12S |
probably damaging |
Het |
| Gbp8 |
A |
C |
5: 105,179,093 (GRCm39) |
D135E |
probably benign |
Het |
| Gm12886 |
A |
T |
4: 121,273,916 (GRCm39) |
L100* |
probably null |
Het |
| Gpatch1 |
A |
T |
7: 34,992,983 (GRCm39) |
|
probably null |
Het |
| Ifit3b |
A |
T |
19: 34,588,925 (GRCm39) |
M34L |
probably benign |
Het |
| Il12a |
G |
T |
3: 68,602,899 (GRCm39) |
D160Y |
probably damaging |
Het |
| Klhl2 |
A |
G |
8: 65,212,816 (GRCm39) |
L241P |
probably damaging |
Het |
| Krt80 |
T |
C |
15: 101,256,610 (GRCm39) |
E195G |
probably benign |
Het |
| Lrrfip1 |
A |
T |
1: 91,032,850 (GRCm39) |
D216V |
probably damaging |
Het |
| Meis3 |
A |
G |
7: 15,917,789 (GRCm39) |
N314S |
probably damaging |
Het |
| Muc5ac |
C |
T |
7: 141,363,481 (GRCm39) |
|
probably benign |
Het |
| Myh15 |
A |
T |
16: 48,965,451 (GRCm39) |
I1119F |
possibly damaging |
Het |
| Nav2 |
A |
T |
7: 49,141,204 (GRCm39) |
Q916H |
probably benign |
Het |
| Ncam2 |
A |
T |
16: 81,229,606 (GRCm39) |
Q22L |
probably damaging |
Het |
| Or5b118 |
A |
T |
19: 13,448,402 (GRCm39) |
I23F |
probably benign |
Het |
| P2rx4 |
G |
A |
5: 122,865,814 (GRCm39) |
V329M |
probably damaging |
Het |
| Peg10 |
A |
G |
6: 4,754,279 (GRCm39) |
|
probably benign |
Het |
| Pgp |
T |
C |
17: 24,690,375 (GRCm39) |
L267P |
probably damaging |
Het |
| Pou2af2 |
G |
A |
9: 51,201,504 (GRCm39) |
T184M |
probably damaging |
Het |
| Prdm2 |
A |
C |
4: 142,859,520 (GRCm39) |
S1257A |
probably benign |
Het |
| Prr12 |
T |
C |
7: 44,695,164 (GRCm39) |
N1434S |
unknown |
Het |
| Psmc3ip |
A |
T |
11: 100,985,999 (GRCm39) |
H40Q |
probably damaging |
Het |
| Ptprc |
A |
T |
1: 138,016,283 (GRCm39) |
N526K |
probably damaging |
Het |
| Sec63 |
T |
A |
10: 42,667,249 (GRCm39) |
D138E |
probably damaging |
Het |
| Serpinb13 |
A |
G |
1: 106,926,663 (GRCm39) |
N220D |
probably benign |
Het |
| Siva1 |
G |
A |
12: 112,611,344 (GRCm39) |
|
probably benign |
Het |
| Slc39a12 |
A |
G |
2: 14,454,728 (GRCm39) |
H546R |
probably damaging |
Het |
| Slc7a1 |
G |
A |
5: 148,271,468 (GRCm39) |
A497V |
probably benign |
Het |
| Smg5 |
G |
T |
3: 88,249,859 (GRCm39) |
K95N |
probably damaging |
Het |
| Speer1a |
G |
A |
5: 11,394,134 (GRCm39) |
V78M |
probably damaging |
Het |
| Traj50 |
T |
A |
14: 54,405,101 (GRCm39) |
|
probably benign |
Het |
| Ubr3 |
T |
C |
2: 69,813,472 (GRCm39) |
V1261A |
probably damaging |
Het |
| Zc3h11a |
A |
T |
1: 133,566,700 (GRCm39) |
|
probably null |
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 |
|
R6196:Lgi1
|
UTSW |
19 |
38,294,257 (GRCm39) |
missense |
probably benign |
0.23 |
|
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'- GGTATTTGGGATCTAGCCAAGAAGTG -3'
(R):5'- GTTTAGCAGGCAATCTCAAGTCAC -3'
Sequencing Primer
(F):5'- AAGTGCGAGGTGTAGTATTAGCTTAC -3'
(R):5'- CCTTGGGCAAAGCAGTT -3'
|
| Posted On |
2018-09-12 |
Incidental Mutation