Incidental Mutation 'R4271:Lims1'
| ID |
322176 |
| 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 |
041076-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4271 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
10 |
| Chromosomal Location |
58159288-58260513 bp(+) (GRCm39) |
| Type of Mutation |
critical splice donor site (2 bp from exon) |
| DNA Base Change (assembly) |
T to C
at 58246026 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000101108
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000020077]
[ENSMUST00000020078]
[ENSMUST00000105468]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably null
Transcript: ENSMUST00000020077
|
| SMART Domains |
Protein: ENSMUSP00000020077
Gene: ENSMUSG00000019920
| 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 null
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 null
Transcript: ENSMUST00000105468
|
| SMART Domains |
Protein: ENSMUSP00000101108
Gene: ENSMUSG00000019920
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124312
|
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.8%
- 10x: 97.6%
- 20x: 95.9%
|
| Validation Efficiency |
|
| 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: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4931422A03Rik |
A |
G |
2: 103,856,549 (GRCm39) |
|
probably benign |
Het |
| Acp6 |
T |
C |
3: 97,073,934 (GRCm39) |
|
probably null |
Het |
| Actr6 |
T |
A |
10: 89,553,101 (GRCm39) |
R252S |
probably benign |
Het |
| Arl6ip1 |
AAAATAAATAAATAAATAAATAAATA |
AAAATAAATAAATAAATAAATAAATAAATA |
7: 117,721,122 (GRCm39) |
|
probably benign |
Het |
| Ash1l |
T |
A |
3: 88,889,347 (GRCm39) |
C409S |
probably benign |
Het |
| Aspg |
T |
C |
12: 112,087,629 (GRCm39) |
S327P |
probably damaging |
Het |
| B430203G13Rik |
CCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT |
CCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT |
12: 17,974,358 (GRCm39) |
|
noncoding transcript |
Het |
| C1galt1 |
T |
C |
6: 7,866,607 (GRCm39) |
F151S |
probably damaging |
Het |
| C1qtnf6 |
G |
A |
15: 78,409,466 (GRCm39) |
T127I |
probably benign |
Het |
| Ccdc88c |
G |
T |
12: 100,913,478 (GRCm39) |
Q516K |
probably damaging |
Het |
| Cdh11 |
T |
A |
8: 103,391,258 (GRCm39) |
D326V |
possibly damaging |
Het |
| Cecr2 |
C |
T |
6: 120,739,436 (GRCm39) |
H1360Y |
probably damaging |
Het |
| Cfap70 |
T |
C |
14: 20,470,793 (GRCm39) |
E484G |
probably benign |
Het |
| Chml |
G |
A |
1: 175,515,360 (GRCm39) |
T187M |
probably benign |
Het |
| Chpt1 |
C |
T |
10: 88,317,214 (GRCm39) |
|
probably benign |
Het |
| Cmtr1 |
T |
C |
17: 29,916,956 (GRCm39) |
S618P |
probably benign |
Het |
| Cspg4b |
G |
T |
13: 113,478,904 (GRCm39) |
V1483L |
possibly damaging |
Het |
| Cyfip1 |
A |
T |
7: 55,528,849 (GRCm39) |
M244L |
probably benign |
Het |
| Dock1 |
T |
C |
7: 134,335,783 (GRCm39) |
I59T |
probably damaging |
Het |
| Duox1 |
T |
C |
2: 122,154,856 (GRCm39) |
F414L |
probably damaging |
Het |
| Gm1110 |
A |
T |
9: 26,806,944 (GRCm39) |
|
probably null |
Het |
| Gsap |
T |
C |
5: 21,431,348 (GRCm39) |
|
probably null |
Het |
| H2-T3 |
T |
C |
17: 36,500,510 (GRCm39) |
Y111C |
probably damaging |
Het |
| Hectd4 |
AGCGGCGGCGGCGGCGGCGGCGG |
AGCGGCGGCGGCGGCGGCGG |
5: 121,358,567 (GRCm39) |
|
probably benign |
Het |
| Kif12 |
T |
C |
4: 63,088,983 (GRCm39) |
Q146R |
probably benign |
Het |
| Kif26a |
C |
T |
12: 112,139,848 (GRCm39) |
S460F |
probably damaging |
Het |
| Klhl15 |
AG |
A |
X: 93,296,718 (GRCm39) |
|
probably null |
Het |
| Nbr1 |
T |
C |
11: 101,458,048 (GRCm39) |
Y276H |
possibly damaging |
Het |
| Nfe2l3 |
A |
G |
6: 51,433,614 (GRCm39) |
D242G |
probably damaging |
Het |
| Oacyl |
T |
A |
18: 65,871,038 (GRCm39) |
L340Q |
probably damaging |
Het |
| Or4n4b |
A |
T |
14: 50,535,908 (GRCm39) |
I286N |
probably damaging |
Het |
| Or5p80 |
T |
A |
7: 108,229,560 (GRCm39) |
Y120* |
probably null |
Het |
| Osbpl5 |
G |
T |
7: 143,249,339 (GRCm39) |
Y543* |
probably null |
Het |
| Polr1a |
G |
A |
6: 71,930,006 (GRCm39) |
E898K |
probably benign |
Het |
| Pramel51 |
A |
T |
12: 88,145,053 (GRCm39) |
I91K |
probably damaging |
Het |
| Rad54l2 |
G |
A |
9: 106,570,825 (GRCm39) |
A1165V |
probably benign |
Het |
| Rimbp2 |
T |
G |
5: 128,896,841 (GRCm39) |
N23T |
probably benign |
Het |
| Scp2 |
T |
C |
4: 107,942,408 (GRCm39) |
D306G |
probably damaging |
Het |
| Slco4a1 |
A |
G |
2: 180,116,003 (GRCm39) |
D713G |
possibly damaging |
Het |
| Smarca2 |
T |
A |
19: 26,698,349 (GRCm39) |
|
probably null |
Het |
| Spem2 |
T |
C |
11: 69,708,251 (GRCm39) |
Y238C |
probably damaging |
Het |
| Srpk2 |
T |
A |
5: 23,753,513 (GRCm39) |
H80L |
possibly damaging |
Het |
| Tmem161a |
T |
C |
8: 70,634,162 (GRCm39) |
L365P |
probably damaging |
Het |
| Tsnax |
T |
C |
8: 125,759,468 (GRCm39) |
L243P |
probably damaging |
Het |
| Ttn |
A |
G |
2: 76,731,979 (GRCm39) |
|
probably benign |
Het |
| V1rd19 |
A |
G |
7: 23,702,839 (GRCm39) |
T102A |
probably benign |
Het |
| Vmn2r94 |
T |
C |
17: 18,463,940 (GRCm39) |
I783M |
probably damaging |
Het |
| Zeb1 |
C |
A |
18: 5,758,985 (GRCm39) |
Q148K |
probably 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 |
|
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 |
|
R7434:Lims1
|
UTSW |
10 |
58,230,301 (GRCm39) |
missense |
probably benign |
|
|
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'- GTGATGAAGTCCATGTGCACC -3'
(R):5'- CCTTCTTCTAACACGAAAAGTTGGG -3'
Sequencing Primer
(F):5'- CTCTACTTTGATTCTAGCACAGGAG -3'
(R):5'- GACCATTTGCCTAGTCTGCACAAG -3'
|
| Posted On |
2015-06-20 |
Incidental Mutation