Incidental Mutation 'IGL02882:Lgi1'
| ID |
362832 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Lgi1
|
| Ensembl Gene |
ENSMUSG00000067242 |
| Gene Name |
leucine-rich repeat LGI family, member 1 |
| Synonyms |
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.740)
|
| Stock # |
IGL02882
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
19 |
| Chromosomal Location |
38253135-38297387 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 38272453 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 84
(D84G)
|
| 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 benign
Transcript: ENSMUST00000196090
|
| SMART Domains |
Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242
| 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 benign
Transcript: ENSMUST00000198045
AA Change: D108G
PolyPhen 2
Score 0.070 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000143292
Gene: ENSMUSG00000067242
AA Change: D108G
| 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: D108G
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000143128
Gene: ENSMUSG00000067242
AA Change: D108G
| 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: D84G
PolyPhen 2
Score 0.238 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242
AA Change: D84G
| 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 |
|
| 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: 33 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcg4 |
A |
T |
9: 44,188,786 (GRCm39) |
L469* |
probably null |
Het |
| Calr3 |
T |
A |
8: 73,188,665 (GRCm39) |
Y46F |
probably damaging |
Het |
| Clcn4 |
A |
G |
7: 7,293,464 (GRCm39) |
C491R |
probably damaging |
Het |
| Col6a5 |
G |
T |
9: 105,811,520 (GRCm39) |
D666E |
unknown |
Het |
| D130052B06Rik |
G |
A |
11: 33,573,780 (GRCm39) |
V126M |
probably damaging |
Het |
| Ddx27 |
A |
G |
2: 166,869,833 (GRCm39) |
I389M |
possibly damaging |
Het |
| Dgka |
T |
C |
10: 128,569,253 (GRCm39) |
I160V |
possibly damaging |
Het |
| Enpp6 |
T |
C |
8: 47,483,567 (GRCm39) |
S120P |
probably damaging |
Het |
| Ezh1 |
A |
G |
11: 101,094,115 (GRCm39) |
I459T |
probably benign |
Het |
| Fam91a1 |
A |
G |
15: 58,324,910 (GRCm39) |
|
probably benign |
Het |
| Foxn2 |
T |
C |
17: 88,770,375 (GRCm39) |
L74P |
probably damaging |
Het |
| Fscn2 |
T |
C |
11: 120,253,325 (GRCm39) |
V264A |
probably benign |
Het |
| Gmeb2 |
G |
A |
2: 180,907,676 (GRCm39) |
T54I |
probably damaging |
Het |
| Hmcn2 |
A |
T |
2: 31,303,379 (GRCm39) |
K3007* |
probably null |
Het |
| Ice1 |
A |
T |
13: 70,772,593 (GRCm39) |
|
probably benign |
Het |
| Mier2 |
T |
C |
10: 79,383,555 (GRCm39) |
I196V |
probably damaging |
Het |
| Nipal2 |
T |
C |
15: 34,600,223 (GRCm39) |
Y198C |
probably damaging |
Het |
| Npas2 |
A |
C |
1: 39,352,077 (GRCm39) |
S176R |
probably benign |
Het |
| Or8b50 |
A |
T |
9: 38,518,234 (GRCm39) |
I158F |
probably benign |
Het |
| Pam |
A |
C |
1: 97,768,092 (GRCm39) |
C713G |
probably damaging |
Het |
| Pcdh17 |
C |
A |
14: 84,684,101 (GRCm39) |
D189E |
probably damaging |
Het |
| Pcdhb8 |
T |
A |
18: 37,489,276 (GRCm39) |
I318N |
possibly damaging |
Het |
| Pcyt2 |
A |
G |
11: 120,502,233 (GRCm39) |
S300P |
possibly damaging |
Het |
| Pkdrej |
A |
G |
15: 85,701,497 (GRCm39) |
S1480P |
probably damaging |
Het |
| Plekhd1 |
G |
A |
12: 80,765,781 (GRCm39) |
|
probably null |
Het |
| Plxna2 |
A |
T |
1: 194,444,878 (GRCm39) |
S757C |
probably damaging |
Het |
| Prkdc |
A |
T |
16: 15,469,383 (GRCm39) |
K163* |
probably null |
Het |
| Serpina3f |
A |
T |
12: 104,183,263 (GRCm39) |
T42S |
probably damaging |
Het |
| Sesn2 |
T |
C |
4: 132,221,104 (GRCm39) |
N456D |
probably benign |
Het |
| Tas2r105 |
A |
T |
6: 131,664,143 (GRCm39) |
L95Q |
possibly damaging |
Het |
| Tln1 |
A |
G |
4: 43,539,522 (GRCm39) |
V1600A |
probably benign |
Het |
| Zfp764l1 |
A |
G |
7: 126,991,424 (GRCm39) |
Y188H |
probably damaging |
Het |
| Zfp808 |
A |
G |
13: 62,320,994 (GRCm39) |
K741R |
probably benign |
Het |
|
| Other mutations in Lgi1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
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 |
|
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 |
|
| Posted On |
2015-12-18 |
Incidental Mutation