Incidental Mutation 'R7434:Lims1'
| ID |
576636 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lims1
|
| Ensembl Gene |
ENSMUSG00000019920 |
| Gene Name |
LIM and senescent cell antigen-like domains 1 |
| Synonyms |
Lims1l, 4921524A02Rik, C430041B13Rik, 2310016J22Rik, PINCH1 |
| MMRRC Submission |
045511-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R7434 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
58159288-58260513 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 58230301 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 21
(T21A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000020077
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000020077]
[ENSMUST00000020078]
[ENSMUST00000105468]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000020077
AA Change: T21A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000020077
Gene: ENSMUSG00000019920
AA Change: T21A
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
71 |
124 |
3.78e-15 |
SMART |
|
LIM
|
132 |
183 |
5.35e-15 |
SMART |
|
LIM
|
196 |
246 |
1.01e-10 |
SMART |
|
LIM
|
254 |
305 |
2.84e-19 |
SMART |
|
LIM
|
313 |
365 |
3.84e-16 |
SMART |
|
low complexity region
|
371 |
387 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000020078
|
| SMART Domains |
Protein: ENSMUSP00000020078
Gene: ENSMUSG00000019920
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
21 |
74 |
3.78e-15 |
SMART |
|
LIM
|
82 |
133 |
5.35e-15 |
SMART |
|
LIM
|
146 |
196 |
1.01e-10 |
SMART |
|
LIM
|
204 |
255 |
2.84e-19 |
SMART |
|
LIM
|
263 |
315 |
5.51e-17 |
SMART |
|
low complexity region
|
317 |
334 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000105468
AA Change: T21A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000101108
Gene: ENSMUSG00000019920
AA Change: T21A
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
71 |
124 |
3.78e-15 |
SMART |
|
LIM
|
132 |
183 |
5.35e-15 |
SMART |
|
LIM
|
196 |
246 |
1.01e-10 |
SMART |
|
LIM
|
254 |
305 |
2.84e-19 |
SMART |
|
LIM
|
313 |
365 |
5.51e-17 |
SMART |
|
low complexity region
|
367 |
384 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.0%
|
| Validation Efficiency |
100% (43/43) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an adaptor protein which contains five LIM domains, or double zinc fingers. The protein is likely involved in integrin signaling through its LIM domain-mediated interaction with integrin-linked kinase, found in focal adhesion plaques. It is also thought to act as a bridge linking integrin-linked kinase to NCK adaptor protein 2, which is involved in growth factor receptor kinase signaling pathways. Its localization to the periphery of spreading cells also suggests that this protein may play a role in integrin-mediated cell adhesion or spreading. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
PHENOTYPE: Homozygous null mice die shortly after implantation and have a disorganized egg cylinder by E5.5, which is degenerated by E6.5. E5.5 null embryos exhibit decreased cell proliferation and excessive cell death. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamtsl1 |
T |
C |
4: 86,344,115 (GRCm39) |
V1731A |
probably damaging |
Het |
| Bcat2 |
A |
G |
7: 45,225,429 (GRCm39) |
|
probably null |
Het |
| Bcl6 |
T |
G |
16: 23,788,798 (GRCm39) |
E523D |
possibly damaging |
Het |
| Cdcp3 |
C |
T |
7: 130,881,212 (GRCm39) |
S1828F |
unknown |
Het |
| Col4a2 |
T |
A |
8: 11,471,250 (GRCm39) |
N503K |
probably damaging |
Het |
| Cyb5r1 |
G |
A |
1: 134,335,576 (GRCm39) |
C166Y |
probably benign |
Het |
| Cyp2w1 |
T |
C |
5: 139,342,775 (GRCm39) |
V490A |
possibly damaging |
Het |
| Erich6b |
A |
G |
14: 75,901,024 (GRCm39) |
I113V |
probably benign |
Het |
| Fabp12 |
C |
T |
3: 10,312,738 (GRCm39) |
V95I |
probably benign |
Het |
| Gask1b |
T |
A |
3: 79,848,669 (GRCm39) |
F472I |
probably damaging |
Het |
| Gpr3 |
T |
C |
4: 132,938,448 (GRCm39) |
M75V |
probably benign |
Het |
| Grm5 |
T |
G |
7: 87,779,682 (GRCm39) |
S1073A |
probably benign |
Het |
| Hoxc9 |
A |
G |
15: 102,892,414 (GRCm39) |
K209R |
probably damaging |
Het |
| Irgm2 |
T |
G |
11: 58,110,291 (GRCm39) |
V6G |
probably benign |
Het |
| Jakmip2 |
A |
G |
18: 43,690,444 (GRCm39) |
V627A |
possibly damaging |
Het |
| Kansl1l |
C |
G |
1: 66,801,262 (GRCm39) |
S568T |
probably damaging |
Het |
| Lpar2 |
G |
T |
8: 70,279,165 (GRCm39) |
A320S |
probably benign |
Het |
| Lpcat4 |
A |
G |
2: 112,073,400 (GRCm39) |
N235S |
probably damaging |
Het |
| Ly6g2 |
T |
C |
15: 75,088,567 (GRCm39) |
F12L |
probably benign |
Het |
| Meis1 |
A |
T |
11: 18,835,542 (GRCm39) |
S359T |
unknown |
Het |
| Mtor |
C |
T |
4: 148,549,416 (GRCm39) |
T600I |
probably benign |
Het |
| Ncbp1 |
T |
C |
4: 46,149,910 (GRCm39) |
S144P |
probably damaging |
Het |
| Ncor1 |
T |
C |
11: 62,274,025 (GRCm39) |
E205G |
probably damaging |
Het |
| Nid1 |
T |
C |
13: 13,643,049 (GRCm39) |
I329T |
probably benign |
Het |
| Nos3 |
T |
C |
5: 24,587,633 (GRCm39) |
I1031T |
probably damaging |
Het |
| Nyap1 |
A |
G |
5: 137,734,530 (GRCm39) |
S168P |
probably damaging |
Het |
| Or56a4 |
A |
G |
7: 104,806,106 (GRCm39) |
V261A |
probably damaging |
Het |
| Pam |
T |
A |
1: 97,903,515 (GRCm39) |
K73* |
probably null |
Het |
| Pcdhga11 |
T |
C |
18: 37,891,005 (GRCm39) |
V671A |
probably benign |
Het |
| Ptpn18 |
G |
A |
1: 34,512,445 (GRCm39) |
D417N |
possibly damaging |
Het |
| Ric1 |
A |
G |
19: 29,552,180 (GRCm39) |
D317G |
probably damaging |
Het |
| Scn1a |
T |
C |
2: 66,103,389 (GRCm39) |
E1957G |
probably benign |
Het |
| Srcap |
T |
C |
7: 127,159,414 (GRCm39) |
S3097P |
unknown |
Het |
| Tas2r113 |
C |
T |
6: 132,870,272 (GRCm39) |
T100I |
probably benign |
Het |
| Tnni1 |
A |
G |
1: 135,735,260 (GRCm39) |
D57G |
|
Het |
| Trim29 |
G |
A |
9: 43,246,428 (GRCm39) |
V575I |
probably damaging |
Het |
| Trpv3 |
G |
A |
11: 73,179,087 (GRCm39) |
V499M |
probably damaging |
Het |
| Ubr1 |
C |
T |
2: 120,693,161 (GRCm39) |
M1748I |
probably benign |
Het |
| Upk1a |
A |
T |
7: 30,306,617 (GRCm39) |
M99K |
probably damaging |
Het |
| Usp16 |
T |
A |
16: 87,276,207 (GRCm39) |
L515* |
probably null |
Het |
| Vmn1r103 |
T |
C |
7: 20,244,435 (GRCm39) |
K9E |
probably damaging |
Het |
| Vwde |
A |
G |
6: 13,187,639 (GRCm39) |
V616A |
probably benign |
Het |
| Zfp101 |
A |
T |
17: 33,600,564 (GRCm39) |
S397R |
possibly damaging |
Het |
|
| Other mutations in Lims1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
P0027:Lims1
|
UTSW |
10 |
58,254,277 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4271:Lims1
|
UTSW |
10 |
58,246,026 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4528:Lims1
|
UTSW |
10 |
58,245,882 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4546:Lims1
|
UTSW |
10 |
58,254,612 (GRCm39) |
intron |
probably benign |
|
|
R4992:Lims1
|
UTSW |
10 |
58,246,063 (GRCm39) |
intron |
probably benign |
|
|
R5380:Lims1
|
UTSW |
10 |
58,252,492 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6207:Lims1
|
UTSW |
10 |
58,230,386 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
R6543:Lims1
|
UTSW |
10 |
58,248,273 (GRCm39) |
nonsense |
probably null |
|
|
R6684:Lims1
|
UTSW |
10 |
58,234,835 (GRCm39) |
splice site |
probably null |
|
|
R6762:Lims1
|
UTSW |
10 |
58,248,367 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7373:Lims1
|
UTSW |
10 |
58,245,442 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7597:Lims1
|
UTSW |
10 |
58,248,263 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8035:Lims1
|
UTSW |
10 |
58,246,263 (GRCm39) |
intron |
probably benign |
|
|
R8039:Lims1
|
UTSW |
10 |
58,245,494 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8860:Lims1
|
UTSW |
10 |
58,243,925 (GRCm39) |
nonsense |
probably null |
|
|
R9176:Lims1
|
UTSW |
10 |
58,254,265 (GRCm39) |
missense |
probably damaging |
1.00 |
|
T0722:Lims1
|
UTSW |
10 |
58,254,277 (GRCm39) |
missense |
probably benign |
0.00 |
|
Z1177:Lims1
|
UTSW |
10 |
58,245,478 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GTGCTGCAGAGCTCTTAACATG -3'
(R):5'- ACTGAAGATCTGGAGACTTGAAAGC -3'
Sequencing Primer
(F):5'- CTGCAGAGCTCTTAACATGAAAAGTC -3'
(R):5'- CCTGTATTTTAGGAGGGAAGAGACTC -3'
|
| Posted On |
2019-10-07 |
Incidental Mutation