Incidental Mutation 'R2278:Lgi4'
| ID |
242897 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lgi4
|
| Ensembl Gene |
ENSMUSG00000036560 |
| Gene Name |
leucine-rich repeat LGI family, member 4 |
| Synonyms |
clp |
| MMRRC Submission |
040277-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2278 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
7 |
| Chromosomal Location |
30758767-30770360 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to G
at 30760037 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Valine
at position 78
(L78V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000041579
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000039775]
[ENSMUST00000039909]
[ENSMUST00000164725]
[ENSMUST00000169785]
[ENSMUST00000205439]
[ENSMUST00000206305]
|
| AlphaFold |
Q8K1S1 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000039775
AA Change: L78V
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000041579
Gene: ENSMUSG00000036560
AA Change: L78V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
19 |
N/A |
INTRINSIC |
|
low complexity region
|
49 |
59 |
N/A |
INTRINSIC |
|
LRR
|
75 |
98 |
7.17e1 |
SMART |
|
LRR
|
99 |
122 |
2.76e1 |
SMART |
|
LRR_TYP
|
123 |
146 |
2.43e-4 |
SMART |
|
LRRCT
|
158 |
207 |
3.97e-5 |
SMART |
|
Pfam:EPTP
|
214 |
251 |
1.1e-7 |
PFAM |
|
Pfam:EPTP
|
396 |
438 |
2.7e-13 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000039909
|
| SMART Domains |
Protein: ENSMUSP00000048460
Gene: ENSMUSG00000036570
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Pfam:ATP1G1_PLM_MAT8
|
23 |
72 |
1.1e-31 |
PFAM |
|
low complexity region
|
81 |
92 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000164725
AA Change: I3S
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000169785
AA Change: L16V
PolyPhen 2
Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000172001
|
| SMART Domains |
Protein: ENSMUSP00000125865
Gene: ENSMUSG00000036560
| Domain | Start | End | E-Value | Type |
|---|
|
LRRCT
|
9 |
58 |
3.97e-5 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000205392
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000205439
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000206305
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000206522
|
| Meta Mutation Damage Score |
0.6467 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.6%
- 20x: 96.0%
|
| Validation Efficiency |
|
| MGI Phenotype |
PHENOTYPE: Homozygous mutant animals have an abnormal posture where the forelimbs are flexed and rotated inwards. The peripheral nervous system is delayed in myelination. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 53 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam3 |
T |
C |
8: 25,201,400 (GRCm39) |
D251G |
probably damaging |
Het |
| Aqp3 |
T |
C |
4: 41,093,836 (GRCm39) |
D219G |
probably damaging |
Het |
| Arhgef15 |
C |
A |
11: 68,842,517 (GRCm39) |
W404C |
probably damaging |
Het |
| Bdp1 |
T |
A |
13: 100,197,847 (GRCm39) |
E846V |
probably damaging |
Het |
| Bdp1 |
C |
A |
13: 100,197,838 (GRCm39) |
S849I |
probably benign |
Het |
| Bmp5 |
T |
A |
9: 75,683,830 (GRCm39) |
N152K |
possibly damaging |
Het |
| Bpifb2 |
C |
T |
2: 153,720,399 (GRCm39) |
Q53* |
probably null |
Het |
| Cep250 |
G |
A |
2: 155,834,552 (GRCm39) |
R2159K |
probably damaging |
Het |
| Chd9 |
C |
T |
8: 91,760,615 (GRCm39) |
P2120L |
probably benign |
Het |
| Clca3a1 |
A |
G |
3: 144,463,785 (GRCm39) |
V164A |
probably damaging |
Het |
| Dnajc28 |
G |
A |
16: 91,413,755 (GRCm39) |
T187M |
probably damaging |
Het |
| Gcn1 |
T |
C |
5: 115,749,234 (GRCm39) |
I1922T |
probably damaging |
Het |
| Gnpat |
A |
G |
8: 125,603,659 (GRCm39) |
D179G |
probably benign |
Het |
| Hook1 |
A |
G |
4: 95,886,957 (GRCm39) |
Q188R |
probably benign |
Het |
| Hsf4 |
G |
A |
8: 105,996,628 (GRCm39) |
D18N |
probably null |
Het |
| Ifi44 |
T |
C |
3: 151,438,025 (GRCm39) |
N421D |
probably benign |
Het |
| Igdcc4 |
C |
T |
9: 65,038,025 (GRCm39) |
T801I |
probably damaging |
Het |
| Itgad |
T |
C |
7: 127,804,342 (GRCm39) |
S107P |
possibly damaging |
Het |
| Kank2 |
C |
A |
9: 21,681,080 (GRCm39) |
M816I |
probably damaging |
Het |
| Kcnk18 |
T |
C |
19: 59,223,926 (GRCm39) |
I357T |
probably damaging |
Het |
| Kcnma1 |
T |
A |
14: 23,593,151 (GRCm39) |
R120* |
probably null |
Het |
| Lypla1 |
T |
G |
1: 4,911,321 (GRCm39) |
|
probably null |
Het |
| Mknk1 |
C |
T |
4: 115,732,690 (GRCm39) |
A306V |
probably damaging |
Het |
| Ncoa6 |
A |
T |
2: 155,249,570 (GRCm39) |
S1245T |
possibly damaging |
Het |
| Npas3 |
T |
A |
12: 53,687,285 (GRCm39) |
V122E |
possibly damaging |
Het |
| Nrxn2 |
G |
C |
19: 6,531,883 (GRCm39) |
Q789H |
probably damaging |
Het |
| Or2h1b |
A |
T |
17: 37,462,145 (GRCm39) |
C239* |
probably null |
Het |
| Or3a1 |
T |
C |
11: 74,225,991 (GRCm39) |
E22G |
probably benign |
Het |
| Or5p69 |
T |
C |
7: 107,967,288 (GRCm39) |
V197A |
probably benign |
Het |
| Or5w12 |
A |
G |
2: 87,502,289 (GRCm39) |
C141R |
possibly damaging |
Het |
| Otog |
G |
A |
7: 45,949,468 (GRCm39) |
V2369M |
probably damaging |
Het |
| Pfkp |
T |
C |
13: 6,669,245 (GRCm39) |
|
probably null |
Het |
| Pja2 |
T |
C |
17: 64,599,865 (GRCm39) |
S478G |
probably damaging |
Het |
| Prune2 |
A |
G |
19: 17,095,919 (GRCm39) |
I474M |
possibly damaging |
Het |
| Psg22 |
C |
A |
7: 18,460,762 (GRCm39) |
Q464K |
possibly damaging |
Het |
| Rp1 |
C |
T |
1: 4,418,250 (GRCm39) |
S954N |
possibly damaging |
Het |
| Rps27l |
T |
A |
9: 66,854,208 (GRCm39) |
D34E |
probably benign |
Het |
| Sae1 |
A |
C |
7: 16,104,291 (GRCm39) |
L106R |
probably damaging |
Het |
| Siglec1 |
T |
A |
2: 130,913,257 (GRCm39) |
Q1553L |
probably benign |
Het |
| Slc11a2 |
A |
G |
15: 100,307,962 (GRCm39) |
|
probably null |
Het |
| Slc14a2 |
A |
T |
18: 78,203,159 (GRCm39) |
M556K |
probably benign |
Het |
| Slk |
T |
G |
19: 47,608,188 (GRCm39) |
I380M |
probably damaging |
Het |
| Spink5 |
A |
G |
18: 44,119,396 (GRCm39) |
N236D |
probably benign |
Het |
| Syne2 |
A |
G |
12: 75,974,240 (GRCm39) |
E1146G |
possibly damaging |
Het |
| Tiam2 |
G |
A |
17: 3,477,495 (GRCm39) |
V573M |
probably damaging |
Het |
| Tmem170 |
C |
A |
8: 112,596,349 (GRCm39) |
V59L |
probably benign |
Het |
| Tmem255b |
C |
T |
8: 13,501,081 (GRCm39) |
A106V |
probably damaging |
Het |
| Ttc23l |
A |
G |
15: 10,523,678 (GRCm39) |
I347T |
possibly damaging |
Het |
| Vps13c |
A |
G |
9: 67,846,354 (GRCm39) |
M2141V |
probably benign |
Het |
| Vwa5a |
T |
C |
9: 38,634,503 (GRCm39) |
Y143H |
probably damaging |
Het |
| Zfp280d |
T |
A |
9: 72,246,055 (GRCm39) |
C707* |
probably null |
Het |
| Zfp668 |
A |
T |
7: 127,465,998 (GRCm39) |
N395K |
probably benign |
Het |
| Znhit6 |
G |
T |
3: 145,281,991 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Lgi4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01288:Lgi4
|
APN |
7 |
30,768,468 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL01624:Lgi4
|
APN |
7 |
30,767,113 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02251:Lgi4
|
APN |
7 |
30,766,688 (GRCm39) |
splice site |
probably null |
|
|
IGL02755:Lgi4
|
APN |
7 |
30,762,530 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03153:Lgi4
|
APN |
7 |
30,759,983 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03392:Lgi4
|
APN |
7 |
30,762,605 (GRCm39) |
splice site |
probably null |
|
|
R0060:Lgi4
|
UTSW |
7 |
30,762,996 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R0575:Lgi4
|
UTSW |
7 |
30,759,518 (GRCm39) |
missense |
probably benign |
0.12 |
|
R2139:Lgi4
|
UTSW |
7 |
30,762,548 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2276:Lgi4
|
UTSW |
7 |
30,760,037 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2277:Lgi4
|
UTSW |
7 |
30,760,037 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2939:Lgi4
|
UTSW |
7 |
30,767,253 (GRCm39) |
nonsense |
probably null |
|
|
R3039:Lgi4
|
UTSW |
7 |
30,759,492 (GRCm39) |
missense |
probably benign |
|
|
R3922:Lgi4
|
UTSW |
7 |
30,766,873 (GRCm39) |
missense |
probably benign |
|
|
R4650:Lgi4
|
UTSW |
7 |
30,768,554 (GRCm39) |
missense |
probably benign |
0.38 |
|
R5184:Lgi4
|
UTSW |
7 |
30,770,182 (GRCm39) |
unclassified |
probably benign |
|
|
R5583:Lgi4
|
UTSW |
7 |
30,760,562 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R5837:Lgi4
|
UTSW |
7 |
30,770,208 (GRCm39) |
unclassified |
probably benign |
|
|
R5917:Lgi4
|
UTSW |
7 |
30,759,603 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
R6198:Lgi4
|
UTSW |
7 |
30,768,547 (GRCm39) |
splice site |
probably null |
|
|
R6454:Lgi4
|
UTSW |
7 |
30,759,557 (GRCm39) |
missense |
probably benign |
|
|
R6845:Lgi4
|
UTSW |
7 |
30,760,510 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6897:Lgi4
|
UTSW |
7 |
30,768,315 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7232:Lgi4
|
UTSW |
7 |
30,766,776 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R7354:Lgi4
|
UTSW |
7 |
30,760,047 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8224:Lgi4
|
UTSW |
7 |
30,763,017 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8257:Lgi4
|
UTSW |
7 |
30,766,766 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R8320:Lgi4
|
UTSW |
7 |
30,768,366 (GRCm39) |
missense |
probably benign |
0.14 |
|
R8440:Lgi4
|
UTSW |
7 |
30,760,049 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8469:Lgi4
|
UTSW |
7 |
30,767,065 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9066:Lgi4
|
UTSW |
7 |
30,759,446 (GRCm39) |
start codon destroyed |
probably benign |
|
|
R9763:Lgi4
|
UTSW |
7 |
30,760,020 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1186:Lgi4
|
UTSW |
7 |
30,768,596 (GRCm39) |
missense |
probably benign |
0.09 |
|
| Predicted Primers |
PCR Primer
(F):5'- ACCTTGGCCACATGTGTAG -3'
(R):5'- AGTGCACGCATATACACACATG -3'
Sequencing Primer
(F):5'- GAATAGGAGACACCCCAGGC -3'
(R):5'- TGCACACACACATGCATGAG -3'
|
| Posted On |
2014-10-16 |
Incidental Mutation