Incidental Mutation 'R1647:Limch1'
ID |
173941 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Limch1
|
Ensembl Gene |
ENSMUSG00000037736 |
Gene Name |
LIM and calponin homology domains 1 |
Synonyms |
3732412D22Rik |
MMRRC Submission |
039683-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.121)
|
Stock # |
R1647 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
5 |
Chromosomal Location |
66903232-67214502 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 67156599 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Arginine
at position 511
(S511R)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000098723
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000038188]
[ENSMUST00000101164]
[ENSMUST00000117601]
[ENSMUST00000118242]
[ENSMUST00000127184]
[ENSMUST00000132991]
|
AlphaFold |
Q3UH68 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000038188
AA Change: S355R
PolyPhen 2
Score 0.860 (Sensitivity: 0.83; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000043163 Gene: ENSMUSG00000037736 AA Change: S355R
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 damaging
Transcript: ENSMUST00000101164
AA Change: S511R
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000098723 Gene: ENSMUSG00000037736 AA Change: S511R
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 |
possibly damaging
Transcript: ENSMUST00000117601
AA Change: S352R
PolyPhen 2
Score 0.781 (Sensitivity: 0.85; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000113544 Gene: ENSMUSG00000037736 AA Change: S352R
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 damaging
Transcript: ENSMUST00000118242
AA Change: S499R
PolyPhen 2
Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000112732 Gene: ENSMUSG00000037736 AA Change: S499R
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: S227R
|
SMART Domains |
Protein: ENSMUSP00000112651 Gene: ENSMUSG00000037736 AA Change: S227R
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 |
probably benign
Transcript: ENSMUST00000127184
|
SMART Domains |
Protein: ENSMUSP00000114681 Gene: ENSMUSG00000037736
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
|
180 |
229 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137394
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140428
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000201322
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147050
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000132991
|
SMART Domains |
Protein: ENSMUSP00000123337 Gene: ENSMUSG00000037736
Domain | Start | End | E-Value | Type |
low complexity region
|
50 |
66 |
N/A |
INTRINSIC |
low complexity region
|
76 |
89 |
N/A |
INTRINSIC |
Pfam:DUF4757
|
103 |
269 |
2.6e-63 |
PFAM |
|
Meta Mutation Damage Score |
0.0795 |
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.1%
- 20x: 91.9%
|
Validation Efficiency |
97% (70/72) |
Allele List at MGI |
|
Other mutations in this stock |
Total: 68 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930522H14Rik |
A |
G |
4: 109,362,768 (GRCm39) |
S184P |
probably damaging |
Het |
Adgb |
A |
G |
10: 10,271,115 (GRCm39) |
F817L |
probably damaging |
Het |
Anxa10 |
T |
C |
8: 62,545,618 (GRCm39) |
D38G |
probably damaging |
Het |
Atp8b2 |
G |
A |
3: 89,849,091 (GRCm39) |
A1081V |
probably benign |
Het |
Baz1a |
G |
A |
12: 55,021,983 (GRCm39) |
R100C |
probably damaging |
Het |
Ceacam18 |
A |
C |
7: 43,288,689 (GRCm39) |
T147P |
possibly damaging |
Het |
Cep170b |
C |
T |
12: 112,702,806 (GRCm39) |
T423I |
probably damaging |
Het |
Chd6 |
A |
G |
2: 160,883,978 (GRCm39) |
L89S |
probably damaging |
Het |
Chrm3 |
A |
T |
13: 9,928,461 (GRCm39) |
W192R |
probably damaging |
Het |
Cnn1 |
C |
A |
9: 22,019,150 (GRCm39) |
A202E |
probably damaging |
Het |
Dcaf7 |
T |
A |
11: 105,942,628 (GRCm39) |
F192I |
probably damaging |
Het |
Eif2b5 |
T |
C |
16: 20,321,335 (GRCm39) |
V296A |
possibly damaging |
Het |
Entpd7 |
A |
G |
19: 43,710,184 (GRCm39) |
|
probably benign |
Het |
Esr1 |
A |
G |
10: 4,951,260 (GRCm39) |
E546G |
possibly damaging |
Het |
Etaa1 |
C |
A |
11: 17,896,492 (GRCm39) |
G542C |
probably damaging |
Het |
Exosc8 |
A |
T |
3: 54,641,522 (GRCm39) |
|
probably null |
Het |
Fras1 |
T |
A |
5: 96,874,472 (GRCm39) |
|
probably null |
Het |
G930045G22Rik |
T |
C |
6: 50,823,698 (GRCm39) |
|
noncoding transcript |
Het |
Gm22697+Rbm27 |
AGGTCCAGGCCCAGGCCCTGGTCCTGGCCCTGGCCCTGGTCCCGGCCCAGGCCC |
AGGTCCCGGCCCAGGCCC |
18: 42,434,948 (GRCm39) |
|
probably benign |
Het |
Gpr155 |
T |
C |
2: 73,194,508 (GRCm39) |
|
probably null |
Het |
Has1 |
A |
G |
17: 18,070,247 (GRCm39) |
Y225H |
probably damaging |
Het |
Hk3 |
A |
G |
13: 55,162,274 (GRCm39) |
F110S |
probably damaging |
Het |
Iars1 |
A |
G |
13: 49,876,478 (GRCm39) |
K848E |
possibly damaging |
Het |
Il22ra1 |
C |
A |
4: 135,477,771 (GRCm39) |
H281N |
probably damaging |
Het |
Inpp4b |
G |
T |
8: 82,583,403 (GRCm39) |
|
probably benign |
Het |
Itga11 |
A |
G |
9: 62,667,652 (GRCm39) |
N662D |
probably benign |
Het |
Kif20b |
A |
T |
19: 34,914,190 (GRCm39) |
T355S |
possibly damaging |
Het |
Kif21a |
T |
C |
15: 90,878,570 (GRCm39) |
T237A |
probably damaging |
Het |
Klc1 |
T |
C |
12: 111,743,321 (GRCm39) |
L216P |
probably damaging |
Het |
Krt84 |
G |
A |
15: 101,434,398 (GRCm39) |
S523F |
possibly damaging |
Het |
Lama3 |
A |
G |
18: 12,665,256 (GRCm39) |
D2330G |
possibly damaging |
Het |
Lamb2 |
G |
A |
9: 108,358,622 (GRCm39) |
|
probably null |
Het |
Lnx2 |
C |
A |
5: 146,964,152 (GRCm39) |
V468L |
probably benign |
Het |
Lrriq1 |
A |
T |
10: 103,006,509 (GRCm39) |
C1205* |
probably null |
Het |
Lsm4 |
A |
G |
8: 71,130,456 (GRCm39) |
Y25C |
probably damaging |
Het |
Macc1 |
T |
C |
12: 119,410,156 (GRCm39) |
M308T |
probably benign |
Het |
Miip |
T |
C |
4: 147,949,691 (GRCm39) |
S174G |
probably benign |
Het |
Mroh9 |
T |
G |
1: 162,873,625 (GRCm39) |
E510A |
probably damaging |
Het |
Msh2 |
C |
T |
17: 87,980,064 (GRCm39) |
A14V |
probably benign |
Het |
Nbea |
T |
A |
3: 55,537,650 (GRCm39) |
I2828F |
probably damaging |
Het |
Nkx2-3 |
A |
T |
19: 43,602,895 (GRCm39) |
Q167L |
probably damaging |
Het |
Nup160 |
T |
C |
2: 90,540,432 (GRCm39) |
Y854H |
probably damaging |
Het |
Or10a3n |
A |
G |
7: 108,492,972 (GRCm39) |
I214T |
probably damaging |
Het |
Or51a10 |
A |
G |
7: 103,699,376 (GRCm39) |
Y62H |
probably damaging |
Het |
Or5an10 |
T |
A |
19: 12,276,023 (GRCm39) |
I158L |
probably benign |
Het |
Pate9 |
A |
G |
9: 36,445,736 (GRCm39) |
S72P |
possibly damaging |
Het |
Phldb1 |
G |
A |
9: 44,626,730 (GRCm39) |
P572S |
probably damaging |
Het |
Plcb2 |
A |
T |
2: 118,554,261 (GRCm39) |
M64K |
possibly damaging |
Het |
Prr12 |
T |
A |
7: 44,683,616 (GRCm39) |
N1683Y |
probably benign |
Het |
Prrg4 |
C |
A |
2: 104,663,088 (GRCm39) |
A173S |
probably benign |
Het |
Pygl |
T |
A |
12: 70,243,784 (GRCm39) |
I553F |
possibly damaging |
Het |
Rasd1 |
T |
C |
11: 59,854,920 (GRCm39) |
M187V |
probably benign |
Het |
Rasgrf1 |
A |
G |
9: 89,835,973 (GRCm39) |
I234V |
probably benign |
Het |
Rps6ka4 |
C |
A |
19: 6,816,730 (GRCm39) |
V118L |
probably benign |
Het |
Sbspon |
C |
A |
1: 15,953,983 (GRCm39) |
R99L |
probably damaging |
Het |
Sdhaf3 |
T |
C |
6: 6,956,126 (GRCm39) |
Y34H |
probably damaging |
Het |
Setd2 |
A |
G |
9: 110,378,932 (GRCm39) |
S632G |
probably benign |
Het |
Shc2 |
T |
A |
10: 79,461,945 (GRCm39) |
M367L |
probably benign |
Het |
Slc26a5 |
T |
A |
5: 22,018,974 (GRCm39) |
K590* |
probably null |
Het |
Slc39a12 |
T |
C |
2: 14,456,803 (GRCm39) |
V597A |
probably benign |
Het |
Slc45a3 |
G |
A |
1: 131,905,262 (GRCm39) |
G81D |
probably damaging |
Het |
Spata2l |
T |
C |
8: 123,960,041 (GRCm39) |
N416S |
probably benign |
Het |
Tdrd6 |
A |
C |
17: 43,938,000 (GRCm39) |
V1016G |
possibly damaging |
Het |
Tet2 |
A |
G |
3: 133,191,641 (GRCm39) |
V931A |
probably benign |
Het |
Tmem190 |
A |
G |
7: 4,787,120 (GRCm39) |
D108G |
probably damaging |
Het |
Trip11 |
T |
A |
12: 101,850,651 (GRCm39) |
K853* |
probably null |
Het |
Vmn2r111 |
A |
T |
17: 22,788,042 (GRCm39) |
D436E |
probably benign |
Het |
Zfp704 |
A |
T |
3: 9,536,099 (GRCm39) |
S140R |
probably damaging |
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 |
|
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 |
R6049:Limch1
|
UTSW |
5 |
67,188,203 (GRCm39) |
missense |
probably benign |
0.32 |
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'- TCGAGAGGTTCACCATCAGTGAGG -3'
(R):5'- ACAAGCTACCCACAATTCGGTTTCC -3'
Sequencing Primer
(F):5'- TCACCATCAGTGAGGCTGTC -3'
(R):5'- tcctcctcctcctcctcc -3'
|
Posted On |
2014-04-24 |