Incidental Mutation 'R6049:Limch1'
ID |
483439 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Limch1
|
Ensembl Gene |
ENSMUSG00000037736 |
Gene Name |
LIM and calponin homology domains 1 |
Synonyms |
3732412D22Rik |
MMRRC Submission |
044217-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.152)
|
Stock # |
R6049 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
5 |
Chromosomal Location |
66903232-67214502 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 67188203 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Glutamic Acid to Valine
at position 878
(E878V)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000112732
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000038188]
[ENSMUST00000101164]
[ENSMUST00000117601]
[ENSMUST00000118242]
|
AlphaFold |
Q3UH68 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000038188
AA Change: E711V
PolyPhen 2
Score 0.265 (Sensitivity: 0.91; Specificity: 0.88)
|
SMART Domains |
Protein: ENSMUSP00000043163 Gene: ENSMUSG00000037736 AA Change: E711V
Domain | Start | End | E-Value | Type |
low complexity region
|
41 |
57 |
N/A |
INTRINSIC |
low complexity region
|
67 |
80 |
N/A |
INTRINSIC |
low complexity region
|
129 |
140 |
N/A |
INTRINSIC |
coiled coil region
|
192 |
241 |
N/A |
INTRINSIC |
low complexity region
|
411 |
430 |
N/A |
INTRINSIC |
coiled coil region
|
615 |
672 |
N/A |
INTRINSIC |
low complexity region
|
679 |
691 |
N/A |
INTRINSIC |
LIM
|
830 |
888 |
5.08e-7 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000101164
AA Change: E867V
PolyPhen 2
Score 0.055 (Sensitivity: 0.94; Specificity: 0.84)
|
SMART Domains |
Protein: ENSMUSP00000098723 Gene: ENSMUSG00000037736 AA Change: E867V
Domain | Start | End | E-Value | Type |
CH
|
23 |
124 |
2.09e-13 |
SMART |
low complexity region
|
197 |
213 |
N/A |
INTRINSIC |
low complexity region
|
223 |
236 |
N/A |
INTRINSIC |
low complexity region
|
285 |
296 |
N/A |
INTRINSIC |
coiled coil region
|
348 |
397 |
N/A |
INTRINSIC |
low complexity region
|
567 |
586 |
N/A |
INTRINSIC |
coiled coil region
|
771 |
828 |
N/A |
INTRINSIC |
low complexity region
|
835 |
847 |
N/A |
INTRINSIC |
LIM
|
986 |
1044 |
5.08e-7 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000117601
AA Change: E708V
PolyPhen 2
Score 0.055 (Sensitivity: 0.94; Specificity: 0.84)
|
SMART Domains |
Protein: ENSMUSP00000113544 Gene: ENSMUSG00000037736 AA Change: E708V
Domain | Start | End | E-Value | Type |
CH
|
23 |
124 |
1e-15 |
SMART |
low complexity region
|
197 |
213 |
N/A |
INTRINSIC |
low complexity region
|
223 |
236 |
N/A |
INTRINSIC |
low complexity region
|
285 |
296 |
N/A |
INTRINSIC |
coiled coil region
|
348 |
397 |
N/A |
INTRINSIC |
low complexity region
|
567 |
586 |
N/A |
INTRINSIC |
coiled coil region
|
704 |
752 |
N/A |
INTRINSIC |
low complexity region
|
759 |
771 |
N/A |
INTRINSIC |
LIM
|
910 |
968 |
2.4e-9 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000118242
AA Change: E878V
PolyPhen 2
Score 0.320 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000112732 Gene: ENSMUSG00000037736 AA Change: E878V
Domain | Start | End | E-Value | Type |
CH
|
23 |
124 |
2.09e-13 |
SMART |
low complexity region
|
197 |
213 |
N/A |
INTRINSIC |
low complexity region
|
223 |
236 |
N/A |
INTRINSIC |
low complexity region
|
285 |
296 |
N/A |
INTRINSIC |
coiled coil region
|
336 |
385 |
N/A |
INTRINSIC |
low complexity region
|
555 |
574 |
N/A |
INTRINSIC |
coiled coil region
|
782 |
839 |
N/A |
INTRINSIC |
low complexity region
|
846 |
858 |
N/A |
INTRINSIC |
LIM
|
997 |
1055 |
5.08e-7 |
SMART |
|
Predicted Effect |
unknown
Transcript: ENSMUST00000119854
AA Change: E583V
|
SMART Domains |
Protein: ENSMUSP00000112651 Gene: ENSMUSG00000037736 AA Change: E583V
Domain | Start | End | E-Value | Type |
CH
|
23 |
124 |
2.09e-13 |
SMART |
low complexity region
|
197 |
213 |
N/A |
INTRINSIC |
low complexity region
|
223 |
236 |
N/A |
INTRINSIC |
Pfam:DUF4757
|
250 |
418 |
5.2e-66 |
PFAM |
low complexity region
|
567 |
586 |
N/A |
INTRINSIC |
coiled coil region
|
771 |
828 |
N/A |
INTRINSIC |
low complexity region
|
835 |
847 |
N/A |
INTRINSIC |
low complexity region
|
989 |
1003 |
N/A |
INTRINSIC |
LIM
|
1012 |
1070 |
5.08e-7 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140428
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000201322
|
Meta Mutation Damage Score |
0.0898 |
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.1%
- 20x: 94.3%
|
Validation Efficiency |
98% (60/61) |
Allele List at MGI |
|
Other mutations in this stock |
Total: 62 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4921539E11Rik |
G |
A |
4: 103,088,520 (GRCm39) |
H229Y |
probably benign |
Het |
Aadacl2fm2 |
A |
C |
3: 59,659,570 (GRCm39) |
D341A |
probably damaging |
Het |
Abcd2 |
A |
G |
15: 91,062,439 (GRCm39) |
F500L |
probably benign |
Het |
Adgb |
A |
G |
10: 10,253,770 (GRCm39) |
L1190P |
probably damaging |
Het |
Adgrv1 |
A |
G |
13: 81,545,473 (GRCm39) |
V5604A |
probably benign |
Het |
Ank2 |
T |
A |
3: 126,736,669 (GRCm39) |
T3072S |
possibly damaging |
Het |
Arhgap39 |
A |
G |
15: 76,611,601 (GRCm39) |
|
probably null |
Het |
C6 |
T |
C |
15: 4,764,654 (GRCm39) |
C117R |
probably damaging |
Het |
Cacna1a |
A |
G |
8: 85,365,475 (GRCm39) |
E2206G |
probably damaging |
Het |
Cd2bp2 |
A |
T |
7: 126,793,007 (GRCm39) |
F338L |
probably damaging |
Het |
Cemip2 |
A |
T |
19: 21,803,490 (GRCm39) |
Q841L |
probably benign |
Het |
Cngb1 |
T |
C |
8: 95,997,470 (GRCm39) |
D575G |
probably damaging |
Het |
Cplane2 |
T |
A |
4: 140,945,473 (GRCm39) |
V108D |
probably benign |
Het |
Crat |
A |
G |
2: 30,293,553 (GRCm39) |
F63S |
probably damaging |
Het |
Crybg3 |
T |
C |
16: 59,364,417 (GRCm39) |
T2402A |
probably benign |
Het |
Ctsq |
A |
G |
13: 61,186,572 (GRCm39) |
|
probably null |
Het |
Cux1 |
T |
C |
5: 136,361,564 (GRCm39) |
R248G |
probably damaging |
Het |
D7Ertd443e |
T |
C |
7: 133,899,961 (GRCm39) |
H420R |
probably benign |
Het |
Deup1 |
A |
G |
9: 15,472,552 (GRCm39) |
F587L |
possibly damaging |
Het |
Dnah6 |
T |
C |
6: 73,063,149 (GRCm39) |
K2651R |
probably benign |
Het |
Dnah7b |
A |
G |
1: 46,124,762 (GRCm39) |
I144V |
probably benign |
Het |
Dnajc1 |
T |
C |
2: 18,236,511 (GRCm39) |
|
probably null |
Het |
Fscb |
T |
C |
12: 64,521,094 (GRCm39) |
N124S |
possibly damaging |
Het |
Gabbr2 |
A |
G |
4: 46,787,641 (GRCm39) |
Y341H |
probably damaging |
Het |
Greb1 |
T |
A |
12: 16,731,395 (GRCm39) |
I1648F |
probably damaging |
Het |
Hace1 |
A |
T |
10: 45,562,758 (GRCm39) |
N758Y |
probably damaging |
Het |
Irs2 |
A |
C |
8: 11,056,805 (GRCm39) |
D542E |
probably benign |
Het |
Kat6a |
T |
A |
8: 23,429,053 (GRCm39) |
H1469Q |
possibly damaging |
Het |
Kif15 |
G |
A |
9: 122,840,687 (GRCm39) |
R36K |
probably damaging |
Het |
Krt42 |
C |
T |
11: 100,157,886 (GRCm39) |
V193M |
probably damaging |
Het |
Med18 |
G |
T |
4: 132,187,024 (GRCm39) |
D158E |
probably benign |
Het |
Med6 |
T |
C |
12: 81,638,097 (GRCm39) |
N38S |
probably damaging |
Het |
Mup13 |
T |
C |
4: 61,183,596 (GRCm39) |
T76A |
probably benign |
Het |
Nlrp4b |
T |
A |
7: 10,448,640 (GRCm39) |
L281* |
probably null |
Het |
Or5h23 |
A |
T |
16: 58,906,509 (GRCm39) |
C112* |
probably null |
Het |
Or7g28 |
C |
A |
9: 19,272,640 (GRCm39) |
G4* |
probably null |
Het |
Or9r3 |
A |
T |
10: 129,948,481 (GRCm39) |
H59Q |
probably benign |
Het |
Pde4d |
A |
T |
13: 109,169,119 (GRCm39) |
R54* |
probably null |
Het |
Pdpk1 |
A |
T |
17: 24,317,109 (GRCm39) |
Y251* |
probably null |
Het |
Pdzk1 |
A |
G |
3: 96,758,979 (GRCm39) |
E128G |
probably benign |
Het |
Phf12 |
A |
G |
11: 77,918,996 (GRCm39) |
|
probably null |
Het |
Pnliprp2 |
A |
G |
19: 58,748,884 (GRCm39) |
E63G |
possibly damaging |
Het |
Prkcd |
T |
C |
14: 30,329,254 (GRCm39) |
E62G |
possibly damaging |
Het |
Prl7b1 |
G |
T |
13: 27,790,161 (GRCm39) |
D77E |
probably benign |
Het |
Rbck1 |
G |
T |
2: 152,165,094 (GRCm39) |
C85* |
probably null |
Het |
Rfx3 |
A |
T |
19: 27,779,795 (GRCm39) |
M481K |
probably damaging |
Het |
Rmdn3 |
A |
G |
2: 118,983,906 (GRCm39) |
F159L |
probably damaging |
Het |
Rpusd3 |
A |
C |
6: 113,394,802 (GRCm39) |
|
probably null |
Het |
Ska1 |
T |
C |
18: 74,335,671 (GRCm39) |
T100A |
probably benign |
Het |
Slc1a3 |
T |
C |
15: 8,675,177 (GRCm39) |
E276G |
probably damaging |
Het |
Slc27a6 |
T |
A |
18: 58,731,732 (GRCm39) |
Y361N |
probably damaging |
Het |
Smc1b |
A |
G |
15: 85,005,896 (GRCm39) |
L336S |
probably damaging |
Het |
St7 |
A |
G |
6: 17,694,347 (GRCm39) |
D46G |
possibly damaging |
Het |
Supt5 |
A |
G |
7: 28,014,622 (GRCm39) |
I1059T |
probably benign |
Het |
Syne1 |
A |
T |
10: 5,297,926 (GRCm39) |
S1124T |
possibly damaging |
Het |
Szt2 |
A |
G |
4: 118,260,185 (GRCm39) |
S54P |
probably damaging |
Het |
Tanc2 |
G |
A |
11: 105,758,543 (GRCm39) |
R768Q |
probably damaging |
Het |
Tbc1d7 |
A |
C |
13: 43,312,836 (GRCm39) |
M19R |
probably damaging |
Het |
Tbpl2 |
T |
C |
2: 23,985,004 (GRCm39) |
N47D |
possibly damaging |
Het |
Tgfbr3 |
C |
T |
5: 107,266,351 (GRCm39) |
A790T |
probably damaging |
Het |
Tnr |
T |
C |
1: 159,740,324 (GRCm39) |
V1166A |
probably damaging |
Het |
Ttn |
G |
A |
2: 76,676,654 (GRCm39) |
|
probably benign |
Het |
|
Other mutations in Limch1 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00583:Limch1
|
APN |
5 |
67,111,022 (GRCm39) |
missense |
probably damaging |
0.99 |
IGL00644:Limch1
|
APN |
5 |
67,173,895 (GRCm39) |
missense |
probably benign |
0.01 |
IGL00705:Limch1
|
APN |
5 |
67,150,496 (GRCm39) |
nonsense |
probably null |
|
IGL01154:Limch1
|
APN |
5 |
66,903,301 (GRCm39) |
nonsense |
probably null |
0.00 |
IGL01865:Limch1
|
APN |
5 |
67,131,923 (GRCm39) |
nonsense |
probably null |
|
IGL02529:Limch1
|
APN |
5 |
67,159,956 (GRCm39) |
missense |
possibly damaging |
0.89 |
IGL03171:Limch1
|
APN |
5 |
67,191,537 (GRCm39) |
missense |
possibly damaging |
0.80 |
IGL03308:Limch1
|
APN |
5 |
67,159,901 (GRCm39) |
missense |
possibly damaging |
0.92 |
IGL03396:Limch1
|
APN |
5 |
67,111,016 (GRCm39) |
missense |
probably damaging |
1.00 |
R0067:Limch1
|
UTSW |
5 |
67,131,965 (GRCm39) |
missense |
probably damaging |
0.99 |
R0067:Limch1
|
UTSW |
5 |
67,131,965 (GRCm39) |
missense |
probably damaging |
0.99 |
R0114:Limch1
|
UTSW |
5 |
67,193,427 (GRCm39) |
intron |
probably benign |
|
R0129:Limch1
|
UTSW |
5 |
67,116,933 (GRCm39) |
missense |
probably damaging |
0.96 |
R0193:Limch1
|
UTSW |
5 |
67,184,882 (GRCm39) |
missense |
probably damaging |
1.00 |
R0194:Limch1
|
UTSW |
5 |
67,156,616 (GRCm39) |
missense |
probably benign |
0.05 |
R0367:Limch1
|
UTSW |
5 |
67,015,297 (GRCm39) |
critical splice donor site |
probably null |
|
R0558:Limch1
|
UTSW |
5 |
67,126,498 (GRCm39) |
missense |
probably damaging |
1.00 |
R0927:Limch1
|
UTSW |
5 |
67,154,576 (GRCm39) |
missense |
probably damaging |
1.00 |
R1190:Limch1
|
UTSW |
5 |
67,126,540 (GRCm39) |
missense |
probably damaging |
1.00 |
R1316:Limch1
|
UTSW |
5 |
67,156,586 (GRCm39) |
missense |
probably damaging |
1.00 |
R1469:Limch1
|
UTSW |
5 |
67,039,323 (GRCm39) |
splice site |
probably benign |
|
R1647:Limch1
|
UTSW |
5 |
67,156,599 (GRCm39) |
missense |
probably damaging |
1.00 |
R1648:Limch1
|
UTSW |
5 |
67,156,599 (GRCm39) |
missense |
probably damaging |
1.00 |
R1944:Limch1
|
UTSW |
5 |
67,156,442 (GRCm39) |
missense |
probably damaging |
1.00 |
R2103:Limch1
|
UTSW |
5 |
67,156,072 (GRCm39) |
missense |
probably benign |
0.05 |
R2126:Limch1
|
UTSW |
5 |
67,187,103 (GRCm39) |
missense |
probably damaging |
1.00 |
R2248:Limch1
|
UTSW |
5 |
67,201,742 (GRCm39) |
missense |
probably damaging |
1.00 |
R2415:Limch1
|
UTSW |
5 |
67,131,977 (GRCm39) |
missense |
probably damaging |
1.00 |
R3762:Limch1
|
UTSW |
5 |
67,186,183 (GRCm39) |
missense |
probably damaging |
1.00 |
R3797:Limch1
|
UTSW |
5 |
67,126,422 (GRCm39) |
missense |
probably damaging |
1.00 |
R4659:Limch1
|
UTSW |
5 |
67,184,900 (GRCm39) |
missense |
probably damaging |
1.00 |
R4773:Limch1
|
UTSW |
5 |
67,184,850 (GRCm39) |
missense |
probably damaging |
0.99 |
R4876:Limch1
|
UTSW |
5 |
67,039,270 (GRCm39) |
missense |
possibly damaging |
0.64 |
R5062:Limch1
|
UTSW |
5 |
67,126,578 (GRCm39) |
missense |
probably damaging |
1.00 |
R5191:Limch1
|
UTSW |
5 |
67,184,904 (GRCm39) |
missense |
probably damaging |
1.00 |
R5202:Limch1
|
UTSW |
5 |
67,150,516 (GRCm39) |
missense |
probably damaging |
1.00 |
R5335:Limch1
|
UTSW |
5 |
67,039,300 (GRCm39) |
missense |
probably damaging |
1.00 |
R5436:Limch1
|
UTSW |
5 |
67,131,909 (GRCm39) |
missense |
possibly damaging |
0.72 |
R5994:Limch1
|
UTSW |
5 |
67,131,965 (GRCm39) |
missense |
probably damaging |
1.00 |
R6228:Limch1
|
UTSW |
5 |
67,173,845 (GRCm39) |
missense |
probably damaging |
1.00 |
R6547:Limch1
|
UTSW |
5 |
67,186,117 (GRCm39) |
missense |
probably damaging |
1.00 |
R6600:Limch1
|
UTSW |
5 |
66,903,281 (GRCm39) |
missense |
probably benign |
|
R6888:Limch1
|
UTSW |
5 |
67,179,269 (GRCm39) |
missense |
probably benign |
0.21 |
R7111:Limch1
|
UTSW |
5 |
67,182,519 (GRCm39) |
splice site |
probably null |
|
R7132:Limch1
|
UTSW |
5 |
67,111,028 (GRCm39) |
missense |
probably damaging |
1.00 |
R7144:Limch1
|
UTSW |
5 |
67,175,001 (GRCm39) |
missense |
probably benign |
0.10 |
R7302:Limch1
|
UTSW |
5 |
67,116,942 (GRCm39) |
missense |
probably benign |
0.02 |
R7341:Limch1
|
UTSW |
5 |
67,191,545 (GRCm39) |
missense |
probably benign |
0.06 |
R7491:Limch1
|
UTSW |
5 |
67,211,580 (GRCm39) |
missense |
probably damaging |
0.99 |
R8079:Limch1
|
UTSW |
5 |
67,204,096 (GRCm39) |
missense |
possibly damaging |
0.73 |
R8229:Limch1
|
UTSW |
5 |
67,186,138 (GRCm39) |
missense |
probably damaging |
1.00 |
R8348:Limch1
|
UTSW |
5 |
67,159,825 (GRCm39) |
missense |
probably damaging |
0.98 |
R8395:Limch1
|
UTSW |
5 |
67,126,394 (GRCm39) |
missense |
probably damaging |
0.96 |
R8416:Limch1
|
UTSW |
5 |
67,156,649 (GRCm39) |
missense |
probably benign |
|
R8448:Limch1
|
UTSW |
5 |
67,159,825 (GRCm39) |
missense |
probably damaging |
0.98 |
R8477:Limch1
|
UTSW |
5 |
67,131,908 (GRCm39) |
missense |
probably benign |
0.01 |
R8924:Limch1
|
UTSW |
5 |
67,190,475 (GRCm39) |
missense |
probably benign |
0.01 |
R9080:Limch1
|
UTSW |
5 |
67,174,992 (GRCm39) |
missense |
probably benign |
0.00 |
R9619:Limch1
|
UTSW |
5 |
67,015,284 (GRCm39) |
missense |
probably damaging |
1.00 |
R9681:Limch1
|
UTSW |
5 |
67,126,422 (GRCm39) |
missense |
probably damaging |
1.00 |
R9715:Limch1
|
UTSW |
5 |
67,156,360 (GRCm39) |
missense |
probably damaging |
1.00 |
X0022:Limch1
|
UTSW |
5 |
67,179,295 (GRCm39) |
missense |
probably benign |
0.00 |
X0027:Limch1
|
UTSW |
5 |
67,159,963 (GRCm39) |
missense |
probably damaging |
1.00 |
Z1177:Limch1
|
UTSW |
5 |
67,186,142 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- AGTGCTCCCATCCACTTGTG -3'
(R):5'- CCATCCTTTTAAAGCAGTGAGAC -3'
Sequencing Primer
(F):5'- TCCACTTGTGCAGAAAACACATG -3'
(R):5'- TTTTAAAGCAGTGAGACCACCCTC -3'
|
Posted On |
2017-07-14 |