Incidental Mutation 'R9080:Limch1'
| ID |
689947 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Limch1
|
| Ensembl Gene |
ENSMUSG00000037736 |
| Gene Name |
LIM and calponin homology domains 1 |
| Synonyms |
3732412D22Rik |
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.121)
|
| Stock # |
R9080 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
5 |
| Chromosomal Location |
66903232-67214502 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 67174992 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Serine
at position 515
(C515S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000043163
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000038188]
[ENSMUST00000101164]
[ENSMUST00000117601]
[ENSMUST00000118242]
|
| AlphaFold |
Q3UH68 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000038188
AA Change: C515S
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: C515S
| 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: C671S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: C671S
| 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: C512S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: C512S
| 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: C659S
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: C659S
| 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 |
|
| SMART Domains |
Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: C387S
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.4%
|
| Validation Efficiency |
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 59 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5730596B20Rik |
T |
C |
6: 52,155,973 (GRCm39) |
I13T |
unknown |
Het |
| Adad1 |
G |
T |
3: 37,119,398 (GRCm39) |
V160L |
probably benign |
Het |
| Adamts6 |
T |
A |
13: 104,449,427 (GRCm39) |
M279K |
probably damaging |
Het |
| Adgra2 |
T |
C |
8: 27,604,529 (GRCm39) |
S535P |
probably benign |
Het |
| Akr1c13 |
C |
T |
13: 4,241,172 (GRCm39) |
|
probably benign |
Het |
| Anapc1 |
A |
G |
2: 128,464,426 (GRCm39) |
I1690T |
possibly damaging |
Het |
| Ccdc138 |
A |
G |
10: 58,397,884 (GRCm39) |
M575V |
probably damaging |
Het |
| Cfap100 |
T |
C |
6: 90,383,183 (GRCm39) |
N330S |
unknown |
Het |
| Col12a1 |
T |
C |
9: 79,517,133 (GRCm39) |
D2849G |
probably benign |
Het |
| Cox11 |
G |
A |
11: 90,535,246 (GRCm39) |
M232I |
probably damaging |
Het |
| Cpne7 |
C |
T |
8: 123,856,951 (GRCm39) |
P402L |
probably damaging |
Het |
| Cspp1 |
G |
A |
1: 10,183,919 (GRCm39) |
S848N |
probably benign |
Het |
| Cxcr5 |
A |
G |
9: 44,424,563 (GRCm39) |
S365P |
probably damaging |
Het |
| Dclre1c |
A |
T |
2: 3,458,589 (GRCm39) |
M389L |
probably benign |
Het |
| Dlc1 |
T |
C |
8: 37,052,006 (GRCm39) |
D124G |
probably benign |
Het |
| Dtx3 |
A |
T |
10: 127,027,137 (GRCm39) |
S346T |
possibly damaging |
Het |
| Exosc10 |
A |
G |
4: 148,649,121 (GRCm39) |
D337G |
probably damaging |
Het |
| Fpr1 |
G |
A |
17: 18,097,212 (GRCm39) |
A259V |
probably benign |
Het |
| Gm11232 |
A |
T |
4: 71,676,070 (GRCm39) |
M25K |
probably benign |
Het |
| Gm4950 |
A |
G |
18: 51,998,922 (GRCm39) |
V11A |
possibly damaging |
Het |
| Gsap |
C |
T |
5: 21,399,410 (GRCm39) |
T37I |
possibly damaging |
Het |
| Igfbp2 |
T |
A |
1: 72,891,157 (GRCm39) |
C252S |
probably damaging |
Het |
| Ing2 |
T |
C |
8: 48,121,808 (GRCm39) |
T247A |
possibly damaging |
Het |
| Ints1 |
C |
T |
5: 139,739,300 (GRCm39) |
V2028M |
probably benign |
Het |
| Itfg1 |
A |
G |
8: 86,466,874 (GRCm39) |
F400L |
possibly damaging |
Het |
| Itga6 |
A |
G |
2: 71,673,633 (GRCm39) |
Y889C |
probably benign |
Het |
| Kcnh3 |
A |
G |
15: 99,139,667 (GRCm39) |
E882G |
probably damaging |
Het |
| Lrrc74a |
G |
T |
12: 86,795,908 (GRCm39) |
V294F |
possibly damaging |
Het |
| Megf8 |
A |
G |
7: 25,041,131 (GRCm39) |
E1120G |
probably damaging |
Het |
| Nbea |
A |
T |
3: 55,912,516 (GRCm39) |
Y1090* |
probably null |
Het |
| Nckap1 |
A |
G |
2: 80,350,726 (GRCm39) |
Y794H |
probably damaging |
Het |
| Nfib |
T |
C |
4: 82,623,754 (GRCm39) |
M25V |
|
Het |
| Ogfod2 |
A |
G |
5: 124,253,007 (GRCm39) |
E339G |
probably damaging |
Het |
| Olah |
T |
A |
2: 3,349,389 (GRCm39) |
E64V |
probably damaging |
Het |
| Or2a14 |
T |
A |
6: 43,130,830 (GRCm39) |
V197D |
possibly damaging |
Het |
| Or9a4 |
T |
A |
6: 40,548,563 (GRCm39) |
L81H |
probably damaging |
Het |
| Pdcd6ip |
T |
A |
9: 113,520,624 (GRCm39) |
K120M |
probably damaging |
Het |
| Pex1 |
A |
G |
5: 3,655,476 (GRCm39) |
I134V |
probably damaging |
Het |
| Plekhm2 |
T |
C |
4: 141,359,039 (GRCm39) |
H576R |
probably damaging |
Het |
| Ptpn13 |
T |
A |
5: 103,637,494 (GRCm39) |
H127Q |
probably damaging |
Het |
| Rmnd5b |
C |
T |
11: 51,515,055 (GRCm39) |
|
probably null |
Het |
| Rsf1 |
A |
AAGGCGACGG |
7: 97,229,111 (GRCm39) |
|
probably null |
Het |
| Sec16b |
C |
A |
1: 157,393,300 (GRCm39) |
Q995K |
probably benign |
Het |
| Serpinb6d |
T |
A |
13: 33,855,107 (GRCm39) |
S260R |
probably benign |
Het |
| Slc47a1 |
C |
T |
11: 61,264,219 (GRCm39) |
G67S |
possibly damaging |
Het |
| Slco6d1 |
T |
C |
1: 98,348,983 (GRCm39) |
V18A |
probably benign |
Het |
| Tfcp2 |
GGTAATCCAAAGAGATGGACTGGTGGCTGTCCTGCTGCTGAGTAATCCAAAGAGATGGACTGGTGGCTGTCCTGCTGCTGAGTAATCCAAAGAGATGGACTGGTGGCTGTCCTGCTGCTGAGTAATCCAAAGAGATGGACTGGTGGCTGTCCTGCTGCTGA |
GGTAATCCAAAGAGATGGACTGGTGGCTGTCCTGCTGCTGAGTAATCCAAAGAGATGGACTGGTGGCTGTCCTGCTGCTGAGTAATCCAAAGAGATGGACTGGTGGCTGTCCTGCTGCTGA |
15: 100,395,968 (GRCm39) |
|
probably null |
Het |
| Tiam2 |
T |
G |
17: 3,464,519 (GRCm39) |
C83G |
probably benign |
Het |
| Tlcd5 |
C |
T |
9: 43,022,664 (GRCm39) |
R230Q |
probably benign |
Het |
| Tln2 |
C |
T |
9: 67,253,843 (GRCm39) |
G743R |
probably damaging |
Het |
| Tnks |
CCCGCCGCCGCCGCCGCCGCCG |
CCCGCCGCCGCCGCCGCCG |
8: 35,432,466 (GRCm39) |
|
probably benign |
Het |
| Ttn |
G |
A |
2: 76,536,843 (GRCm39) |
T34994I |
probably benign |
Het |
| Ube2q2l |
T |
A |
6: 136,377,720 (GRCm39) |
D370V |
probably damaging |
Het |
| Uggt2 |
T |
A |
14: 119,295,017 (GRCm39) |
E536D |
probably benign |
Het |
| Usp54 |
T |
C |
14: 20,612,308 (GRCm39) |
E836G |
probably damaging |
Het |
| Vmn1r41 |
C |
T |
6: 89,724,138 (GRCm39) |
T63M |
unknown |
Het |
| Vmn2r72 |
A |
C |
7: 85,387,464 (GRCm39) |
I700S |
probably damaging |
Het |
| Xrcc4 |
T |
C |
13: 90,149,097 (GRCm39) |
N141S |
probably damaging |
Het |
| Zfp638 |
T |
C |
6: 83,844,155 (GRCm39) |
V6A |
unknown |
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 |
|
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 |
|
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'- TTTCGTAGCAAGGCAGTTTAATGAG -3'
(R):5'- GCTGCCTGAAGCCCTTTAAC -3'
Sequencing Primer
(F):5'- TAATGAGAATCCTGCCATCCTGGG -3'
(R):5'- TGAAGCCCTTTAACCTCTTGG -3'
|
| Posted On |
2021-11-19 |
Incidental Mutation