Incidental Mutation 'R4582:Lima1'
| ID |
343757 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lima1
|
| Ensembl Gene |
ENSMUSG00000023022 |
| Gene Name |
LIM domain and actin binding 1 |
| Synonyms |
3526402A12Rik, EPLIN, epithelial protein lost in neoplasm, 1110021C24Rik |
| MMRRC Submission |
041803-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.123)
|
| Stock # |
R4582 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
15 |
| Chromosomal Location |
99676351-99773292 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 99678873 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 523
(T523A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000073371
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000073691]
[ENSMUST00000109024]
|
| AlphaFold |
Q9ERG0 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000073691
AA Change: T523A
PolyPhen 2
Score 0.655 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000073371
Gene: ENSMUSG00000023022
AA Change: T523A
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
387 |
439 |
5.14e-17 |
SMART |
|
low complexity region
|
534 |
546 |
N/A |
INTRINSIC |
|
low complexity region
|
570 |
587 |
N/A |
INTRINSIC |
|
low complexity region
|
598 |
609 |
N/A |
INTRINSIC |
|
low complexity region
|
613 |
626 |
N/A |
INTRINSIC |
|
low complexity region
|
747 |
753 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000109024
AA Change: T363A
PolyPhen 2
Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
|
| SMART Domains |
Protein: ENSMUSP00000104652
Gene: ENSMUSG00000023022
AA Change: T363A
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
227 |
279 |
5.14e-17 |
SMART |
|
low complexity region
|
374 |
386 |
N/A |
INTRINSIC |
|
low complexity region
|
410 |
427 |
N/A |
INTRINSIC |
|
low complexity region
|
438 |
449 |
N/A |
INTRINSIC |
|
low complexity region
|
453 |
466 |
N/A |
INTRINSIC |
|
low complexity region
|
587 |
593 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000168951
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172119
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 94.7%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a cytoskeleton-associated protein that inhibits actin filament depolymerization and cross-links filaments in bundles. It is downregulated in some cancer cell lines. Alternatively spliced transcript variants encoding different isoforms have been described for this gene, and expression of some of the variants maybe independently regulated. [provided by RefSeq, Aug 2011]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abra |
A |
T |
15: 41,732,681 (GRCm39) |
D128E |
probably benign |
Het |
| Akap11 |
A |
T |
14: 78,749,369 (GRCm39) |
V1006E |
possibly damaging |
Het |
| Ankrd7 |
T |
A |
6: 18,868,020 (GRCm39) |
N95K |
probably damaging |
Het |
| Brd9 |
T |
C |
13: 74,095,852 (GRCm39) |
F366L |
probably benign |
Het |
| Brinp2 |
A |
G |
1: 158,095,508 (GRCm39) |
F118L |
probably damaging |
Het |
| Ccdc138 |
T |
C |
10: 58,343,465 (GRCm39) |
|
probably null |
Het |
| Celsr3 |
T |
C |
9: 108,722,922 (GRCm39) |
F189L |
probably damaging |
Het |
| Cfap45 |
A |
G |
1: 172,357,479 (GRCm39) |
T36A |
probably benign |
Het |
| Clec4a1 |
G |
T |
6: 122,909,150 (GRCm39) |
V173L |
possibly damaging |
Het |
| Col6a5 |
G |
A |
9: 105,739,963 (GRCm39) |
T2552I |
probably benign |
Het |
| Dcaf15 |
A |
G |
8: 84,824,598 (GRCm39) |
V533A |
probably damaging |
Het |
| Dhrs9 |
A |
T |
2: 69,227,997 (GRCm39) |
I204F |
probably damaging |
Het |
| Dock7 |
A |
G |
4: 98,892,153 (GRCm39) |
V811A |
possibly damaging |
Het |
| Eef1akmt1 |
T |
C |
14: 57,787,905 (GRCm39) |
D151G |
probably damaging |
Het |
| Eif4g3 |
G |
A |
4: 137,898,556 (GRCm39) |
R1109H |
probably damaging |
Het |
| Gtpbp10 |
T |
C |
5: 5,592,395 (GRCm39) |
T191A |
possibly damaging |
Het |
| Hectd4 |
A |
G |
5: 121,424,482 (GRCm39) |
N714S |
possibly damaging |
Het |
| Lipe |
A |
G |
7: 25,097,127 (GRCm39) |
L272P |
probably benign |
Het |
| Llgl2 |
A |
G |
11: 115,741,532 (GRCm39) |
E554G |
possibly damaging |
Het |
| Lrrc66 |
T |
C |
5: 73,765,580 (GRCm39) |
S488G |
possibly damaging |
Het |
| Man2a1 |
C |
T |
17: 65,059,494 (GRCm39) |
A1127V |
probably benign |
Het |
| Naglu |
A |
T |
11: 100,962,755 (GRCm39) |
I187F |
probably damaging |
Het |
| Nt5c1b |
T |
A |
12: 10,440,054 (GRCm39) |
M548K |
probably damaging |
Het |
| Or10ak14 |
A |
T |
4: 118,611,090 (GRCm39) |
I217N |
probably damaging |
Het |
| Or6c38 |
A |
T |
10: 128,929,027 (GRCm39) |
V272E |
possibly damaging |
Het |
| Pcdha3 |
T |
C |
18: 37,080,485 (GRCm39) |
V409A |
probably benign |
Het |
| Pde6b |
A |
T |
5: 108,573,097 (GRCm39) |
|
probably null |
Het |
| Pkd2 |
A |
T |
5: 104,650,210 (GRCm39) |
K857* |
probably null |
Het |
| Rfx4 |
T |
A |
10: 84,680,164 (GRCm39) |
S114T |
possibly damaging |
Het |
| Sacs |
G |
A |
14: 61,429,147 (GRCm39) |
G402D |
probably damaging |
Het |
| Slc22a5 |
C |
T |
11: 53,782,035 (GRCm39) |
E111K |
probably damaging |
Het |
| Sptbn1 |
G |
A |
11: 30,169,597 (GRCm39) |
R44C |
probably damaging |
Het |
| Taf1 |
T |
C |
X: 100,637,601 (GRCm39) |
V1696A |
possibly damaging |
Het |
| Tm9sf3 |
C |
A |
19: 41,244,605 (GRCm39) |
G91C |
probably damaging |
Het |
| Tmie |
T |
G |
9: 110,702,865 (GRCm39) |
E32A |
probably benign |
Het |
| Top2b |
T |
G |
14: 16,409,189 (GRCm38) |
I777M |
probably damaging |
Het |
| Tsga13 |
A |
T |
6: 30,879,298 (GRCm39) |
N138K |
probably benign |
Het |
| Ttc7b |
G |
A |
12: 100,466,376 (GRCm39) |
R79C |
probably damaging |
Het |
| Ugt1a10 |
A |
T |
1: 87,983,463 (GRCm39) |
D87V |
possibly damaging |
Het |
| Vdac3-ps1 |
A |
T |
13: 18,206,177 (GRCm39) |
|
noncoding transcript |
Het |
| Vmn1r29 |
A |
C |
6: 58,285,017 (GRCm39) |
I246L |
probably damaging |
Het |
| Zbtb16 |
A |
G |
9: 48,743,382 (GRCm39) |
V310A |
probably benign |
Het |
|
| Other mutations in Lima1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00668:Lima1
|
APN |
15 |
99,700,038 (GRCm39) |
missense |
possibly damaging |
0.47 |
|
IGL01104:Lima1
|
APN |
15 |
99,741,581 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02618:Lima1
|
APN |
15 |
99,700,097 (GRCm39) |
splice site |
probably benign |
|
|
IGL03124:Lima1
|
APN |
15 |
99,694,615 (GRCm39) |
splice site |
probably benign |
|
|
R0312:Lima1
|
UTSW |
15 |
99,678,968 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R0599:Lima1
|
UTSW |
15 |
99,700,040 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0601:Lima1
|
UTSW |
15 |
99,678,353 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1423:Lima1
|
UTSW |
15 |
99,717,626 (GRCm39) |
nonsense |
probably null |
|
|
R1704:Lima1
|
UTSW |
15 |
99,717,617 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1784:Lima1
|
UTSW |
15 |
99,678,344 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R1819:Lima1
|
UTSW |
15 |
99,717,817 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1968:Lima1
|
UTSW |
15 |
99,717,565 (GRCm39) |
missense |
probably benign |
|
|
R2352:Lima1
|
UTSW |
15 |
99,692,396 (GRCm39) |
missense |
probably benign |
0.02 |
|
R2908:Lima1
|
UTSW |
15 |
99,699,991 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4672:Lima1
|
UTSW |
15 |
99,741,590 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4858:Lima1
|
UTSW |
15 |
99,717,457 (GRCm39) |
missense |
probably benign |
0.23 |
|
R6140:Lima1
|
UTSW |
15 |
99,678,939 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6614:Lima1
|
UTSW |
15 |
99,681,461 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6898:Lima1
|
UTSW |
15 |
99,679,148 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
R7598:Lima1
|
UTSW |
15 |
99,717,577 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7601:Lima1
|
UTSW |
15 |
99,717,577 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7878:Lima1
|
UTSW |
15 |
99,717,431 (GRCm39) |
missense |
probably benign |
0.12 |
|
R8219:Lima1
|
UTSW |
15 |
99,678,671 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8348:Lima1
|
UTSW |
15 |
99,678,753 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8733:Lima1
|
UTSW |
15 |
99,678,699 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8821:Lima1
|
UTSW |
15 |
99,704,306 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9285:Lima1
|
UTSW |
15 |
99,678,687 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9300:Lima1
|
UTSW |
15 |
99,704,320 (GRCm39) |
missense |
probably benign |
0.01 |
|
| Predicted Primers |
PCR Primer
(F):5'- TCGAAAGGAAGCTGCTACCG -3'
(R):5'- ATCTGTGGGCAAGCAAGAGC -3'
Sequencing Primer
(F):5'- TCTCCTTCAGGGACGAAGAC -3'
(R):5'- GCGACAATGAGGAGACTTTGG -3'
|
| Posted On |
2015-09-24 |
Incidental Mutation