Incidental Mutation 'R4516:Limk1'
| ID |
332910 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Limk1
|
| Ensembl Gene |
ENSMUSG00000029674 |
| Gene Name |
LIM domain kinase 1 |
| Synonyms |
|
| MMRRC Submission |
041760-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R4516 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
134684893-134717452 bp(-) (GRCm39) |
| Type of Mutation |
intron |
| DNA Base Change (assembly) |
A to G
at 134705640 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000015137]
[ENSMUST00000111233]
|
| AlphaFold |
P53668 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000015137
|
| SMART Domains |
Protein: ENSMUSP00000015137
Gene: ENSMUSG00000029674
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
24 |
75 |
5.3e-19 |
SMART |
|
LIM
|
83 |
137 |
1.73e-9 |
SMART |
|
PDZ
|
176 |
258 |
1.51e-9 |
SMART |
|
low complexity region
|
266 |
277 |
N/A |
INTRINSIC |
|
Pfam:Pkinase
|
339 |
604 |
1.7e-49 |
PFAM |
|
Pfam:Pkinase_Tyr
|
339 |
604 |
1.5e-55 |
PFAM |
|
Pfam:Kdo
|
345 |
509 |
2.5e-10 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000100641
|
| SMART Domains |
Protein: ENSMUSP00000098206
Gene: ENSMUSG00000072573
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
27 |
42 |
N/A |
INTRINSIC |
|
low complexity region
|
48 |
67 |
N/A |
INTRINSIC |
|
low complexity region
|
147 |
158 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111233
|
| SMART Domains |
Protein: ENSMUSP00000106864
Gene: ENSMUSG00000029674
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
23 |
67 |
2.19e-1 |
SMART |
|
LIM
|
75 |
129 |
1.73e-9 |
SMART |
|
PDZ
|
168 |
250 |
1.51e-9 |
SMART |
|
low complexity region
|
258 |
269 |
N/A |
INTRINSIC |
|
Pfam:Pkinase_Tyr
|
331 |
596 |
1.5e-56 |
PFAM |
|
Pfam:Pkinase
|
331 |
597 |
4.7e-50 |
PFAM |
|
Pfam:Kdo
|
339 |
501 |
1.5e-9 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000132027
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000134093
|
| SMART Domains |
Protein: ENSMUSP00000121718
Gene: ENSMUSG00000029674
| Domain | Start | End | E-Value | Type |
|---|
|
LIM
|
16 |
60 |
2.19e-1 |
SMART |
|
LIM
|
68 |
122 |
1.73e-9 |
SMART |
|
PDZ
|
161 |
243 |
1.51e-9 |
SMART |
|
low complexity region
|
251 |
262 |
N/A |
INTRINSIC |
|
Pfam:Pkinase
|
324 |
425 |
3.9e-16 |
PFAM |
|
Pfam:Pkinase_Tyr
|
324 |
434 |
5.4e-14 |
PFAM |
|
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.5%
- 10x: 96.6%
- 20x: 92.9%
|
| Validation Efficiency |
86% (51/59) |
| MGI Phenotype |
FUNCTION: This gene encodes a member of the LIM kinase family of proteins. This protein is a serine/threonine kinase that regulates actin polymerization via phosphorylation and inactivation of the actin binding factor cofilin. This protein also stimulates axon growth and may play a role in brain development. Homozygous knockout mice for this gene exhibit reduced bone mass, abnormal neuronal morphology and altered synaptic function. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
PHENOTYPE: Mice homozygous for disruptions in this gene display an abnormal actin cytoskeleton in neurons of the central nervous system and structural abnormalities of the dendritic spines. Long term potentiation is altered and behavioral anomalies are seen. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 47 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Bean1 |
T |
C |
8: 104,941,786 (GRCm39) |
S211P |
probably damaging |
Het |
| Bltp1 |
T |
C |
3: 36,949,460 (GRCm39) |
S369P |
possibly damaging |
Het |
| Camta1 |
A |
G |
4: 151,229,177 (GRCm39) |
S552P |
possibly damaging |
Het |
| Cdh11 |
T |
C |
8: 103,400,594 (GRCm39) |
T125A |
possibly damaging |
Het |
| Cdk5rap2 |
A |
T |
4: 70,194,952 (GRCm39) |
|
probably null |
Het |
| Cenpc1 |
A |
G |
5: 86,195,446 (GRCm39) |
S108P |
possibly damaging |
Het |
| Cfap20dc |
A |
T |
14: 8,536,609 (GRCm38) |
D199E |
probably damaging |
Het |
| Cfap44 |
T |
A |
16: 44,294,227 (GRCm39) |
Y224* |
probably null |
Het |
| Cfap46 |
G |
A |
7: 139,239,998 (GRCm39) |
|
probably benign |
Het |
| Cntrl |
G |
A |
2: 35,017,993 (GRCm39) |
V468I |
probably benign |
Het |
| Col6a6 |
C |
T |
9: 105,576,148 (GRCm39) |
V2071I |
possibly damaging |
Het |
| Coq7 |
A |
T |
7: 118,109,130 (GRCm39) |
L306Q |
unknown |
Het |
| D7Ertd443e |
C |
G |
7: 133,895,057 (GRCm39) |
Q591H |
probably damaging |
Het |
| Dchs1 |
C |
T |
7: 105,404,059 (GRCm39) |
V2828M |
probably damaging |
Het |
| Dzank1 |
T |
A |
2: 144,352,042 (GRCm39) |
|
probably benign |
Het |
| Elmo1 |
C |
T |
13: 20,467,084 (GRCm39) |
T235I |
probably benign |
Het |
| Elp3 |
A |
T |
14: 65,785,326 (GRCm39) |
F492I |
possibly damaging |
Het |
| Espl1 |
A |
G |
15: 102,231,671 (GRCm39) |
S90G |
probably benign |
Het |
| Fbxl20 |
T |
C |
11: 97,986,061 (GRCm39) |
|
probably benign |
Het |
| Gm10722 |
T |
C |
9: 3,000,937 (GRCm39) |
C6R |
probably benign |
Het |
| Got1 |
T |
C |
19: 43,493,280 (GRCm39) |
Y243C |
probably damaging |
Het |
| Hipk1 |
G |
T |
3: 103,657,688 (GRCm39) |
H799N |
probably damaging |
Het |
| Kif21a |
A |
T |
15: 90,855,345 (GRCm39) |
M673K |
probably benign |
Het |
| Lama3 |
T |
A |
18: 12,628,415 (GRCm39) |
D1502E |
probably damaging |
Het |
| Myo5b |
A |
G |
18: 74,758,745 (GRCm39) |
Y242C |
probably damaging |
Het |
| Naa12 |
G |
A |
18: 80,254,791 (GRCm39) |
M28I |
probably benign |
Het |
| Ncbp1 |
T |
C |
4: 46,157,824 (GRCm39) |
V354A |
probably damaging |
Het |
| Ncoa2 |
T |
C |
1: 13,217,130 (GRCm39) |
D1380G |
probably damaging |
Het |
| Ntng1 |
A |
G |
3: 109,842,329 (GRCm39) |
I148T |
probably damaging |
Het |
| Oas1d |
A |
T |
5: 121,057,233 (GRCm39) |
T280S |
probably damaging |
Het |
| Or1e29 |
C |
T |
11: 73,667,866 (GRCm39) |
G96S |
probably benign |
Het |
| Or4c15b |
T |
A |
2: 89,113,187 (GRCm39) |
M118L |
probably benign |
Het |
| Pax7 |
T |
G |
4: 139,508,104 (GRCm39) |
D307A |
probably benign |
Het |
| Pdxdc1 |
G |
A |
16: 13,656,210 (GRCm39) |
Q621* |
probably null |
Het |
| Rab29 |
A |
T |
1: 131,795,469 (GRCm39) |
Y27F |
possibly damaging |
Het |
| Rab3gap2 |
G |
A |
1: 184,999,265 (GRCm39) |
V991I |
probably benign |
Het |
| Ric1 |
A |
G |
19: 29,548,165 (GRCm39) |
T278A |
probably benign |
Het |
| Rufy4 |
T |
C |
1: 74,186,822 (GRCm39) |
C537R |
probably damaging |
Het |
| Slc47a1 |
T |
C |
11: 61,235,339 (GRCm39) |
H498R |
probably benign |
Het |
| Spmip6 |
T |
C |
4: 41,517,200 (GRCm39) |
|
probably benign |
Het |
| Tas2r116 |
T |
C |
6: 132,833,113 (GRCm39) |
L238P |
probably damaging |
Het |
| Tigd5 |
A |
T |
15: 75,782,364 (GRCm39) |
R252* |
probably null |
Het |
| Tlr6 |
A |
G |
5: 65,112,247 (GRCm39) |
F220S |
possibly damaging |
Het |
| Tmem106b |
C |
T |
6: 13,075,098 (GRCm39) |
T95I |
probably damaging |
Het |
| Ubqlnl |
C |
T |
7: 103,798,925 (GRCm39) |
V191M |
probably benign |
Het |
| Vmn1r174 |
A |
G |
7: 23,453,768 (GRCm39) |
I145V |
probably benign |
Het |
| Vps26a |
T |
C |
10: 62,304,124 (GRCm39) |
M116V |
probably damaging |
Het |
|
| Other mutations in Limk1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01355:Limk1
|
APN |
5 |
134,686,754 (GRCm39) |
unclassified |
probably benign |
|
|
IGL02029:Limk1
|
APN |
5 |
134,686,808 (GRCm39) |
nonsense |
probably null |
|
|
IGL02211:Limk1
|
APN |
5 |
134,686,491 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03000:Limk1
|
APN |
5 |
134,699,355 (GRCm39) |
missense |
probably damaging |
0.99 |
|
extremist
|
UTSW |
5 |
134,699,295 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0046:Limk1
|
UTSW |
5 |
134,701,615 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0046:Limk1
|
UTSW |
5 |
134,701,615 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0058:Limk1
|
UTSW |
5 |
134,688,725 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0058:Limk1
|
UTSW |
5 |
134,688,725 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0071:Limk1
|
UTSW |
5 |
134,690,245 (GRCm39) |
missense |
probably benign |
0.01 |
|
R0180:Limk1
|
UTSW |
5 |
134,698,115 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R1456:Limk1
|
UTSW |
5 |
134,686,364 (GRCm39) |
missense |
probably benign |
0.09 |
|
R2225:Limk1
|
UTSW |
5 |
134,690,410 (GRCm39) |
splice site |
probably null |
|
|
R2379:Limk1
|
UTSW |
5 |
134,708,335 (GRCm39) |
unclassified |
probably benign |
|
|
R2899:Limk1
|
UTSW |
5 |
134,717,154 (GRCm39) |
splice site |
probably null |
|
|
R3423:Limk1
|
UTSW |
5 |
134,701,523 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4235:Limk1
|
UTSW |
5 |
134,699,332 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4566:Limk1
|
UTSW |
5 |
134,715,537 (GRCm39) |
missense |
probably benign |
0.12 |
|
R4752:Limk1
|
UTSW |
5 |
134,699,295 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5682:Limk1
|
UTSW |
5 |
134,694,059 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5917:Limk1
|
UTSW |
5 |
134,686,789 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6163:Limk1
|
UTSW |
5 |
134,686,809 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6479:Limk1
|
UTSW |
5 |
134,690,373 (GRCm39) |
utr 3 prime |
probably benign |
|
|
R6952:Limk1
|
UTSW |
5 |
134,699,332 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
R7009:Limk1
|
UTSW |
5 |
134,701,553 (GRCm39) |
missense |
probably benign |
|
|
R7147:Limk1
|
UTSW |
5 |
134,686,195 (GRCm39) |
missense |
probably benign |
0.14 |
|
R7453:Limk1
|
UTSW |
5 |
134,698,091 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7471:Limk1
|
UTSW |
5 |
134,686,825 (GRCm39) |
splice site |
probably null |
|
|
R9427:Limk1
|
UTSW |
5 |
134,686,358 (GRCm39) |
missense |
probably benign |
0.07 |
|
R9449:Limk1
|
UTSW |
5 |
134,701,864 (GRCm39) |
critical splice donor site |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- ACTCAGGAGCAGCTACATCC -3'
(R):5'- CGTTGCTGATCTAACCAGAGAC -3'
Sequencing Primer
(F):5'- GCAGCTACATCCCACCCTGG -3'
(R):5'- AGGAGTTCAAGGCCATCTTC -3'
|
| Posted On |
2015-08-18 |
Incidental Mutation