Incidental Mutation 'R1456:Limk1'
ID 161770
Institutional Source Beutler Lab
Gene Symbol Limk1
Ensembl Gene ENSMUSG00000029674
Gene Name LIM domain kinase 1
Synonyms
MMRRC Submission 039511-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1456 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 134684893-134717452 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 134686364 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 580 (D580E)
Ref Sequence ENSEMBL: ENSMUSP00000106864 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000015137] [ENSMUST00000111233] [ENSMUST00000138590]
AlphaFold P53668
Predicted Effect probably benign
Transcript: ENSMUST00000015137
AA Change: D588E

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000015137
Gene: ENSMUSG00000029674
AA Change: D588E

DomainStartEndE-ValueType
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 probably benign
Transcript: ENSMUST00000111233
AA Change: D580E

PolyPhen 2 Score 0.094 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000106864
Gene: ENSMUSG00000029674
AA Change: D580E

DomainStartEndE-ValueType
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 probably benign
Transcript: ENSMUST00000134093
SMART Domains Protein: ENSMUSP00000121718
Gene: ENSMUSG00000029674

DomainStartEndE-ValueType
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
Predicted Effect probably benign
Transcript: ENSMUST00000138590
SMART Domains Protein: ENSMUSP00000118268
Gene: ENSMUSG00000029674

DomainStartEndE-ValueType
Pfam:Pkinase 3 59 3.6e-9 PFAM
Pfam:Pkinase_Tyr 3 80 2.6e-13 PFAM
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.9%
  • 10x: 95.1%
  • 20x: 88.9%
Validation Efficiency 98% (90/92)
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: 88 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921504E06Rik C T 2: 19,485,731 (GRCm39) probably null Het
4932414N04Rik A T 2: 68,546,558 (GRCm39) E80V possibly damaging Het
Alkbh3 A G 2: 93,831,764 (GRCm39) probably null Het
Ankar A T 1: 72,704,277 (GRCm39) Y664N probably benign Het
Arhgap18 T C 10: 26,792,436 (GRCm39) I629T probably benign Het
Arhgef28 C T 13: 98,211,510 (GRCm39) E158K probably benign Het
Asxl2 C T 12: 3,551,872 (GRCm39) H1205Y possibly damaging Het
Birc6 A G 17: 74,916,285 (GRCm39) I427V probably benign Het
Camk4 A G 18: 33,262,896 (GRCm39) probably benign Het
Ccdc178 A T 18: 22,283,481 (GRCm39) D16E possibly damaging Het
Cct6b G T 11: 82,644,446 (GRCm39) probably benign Het
Ccz1 A G 5: 143,947,836 (GRCm39) probably benign Het
Cdh23 T C 10: 60,322,899 (GRCm39) N335S possibly damaging Het
Cemip T A 7: 83,647,718 (GRCm39) S121C possibly damaging Het
Cers1 A G 8: 70,783,838 (GRCm39) E262G probably damaging Het
Clec11a G T 7: 43,955,874 (GRCm39) P58T possibly damaging Het
Clec16a T C 16: 10,509,419 (GRCm39) I797T probably damaging Het
Col4a1 A C 8: 11,292,829 (GRCm39) probably benign Het
Colgalt2 G A 1: 152,360,655 (GRCm39) V231I probably damaging Het
D430041D05Rik G T 2: 104,038,428 (GRCm39) N1580K probably damaging Het
Dcdc5 A G 2: 106,181,910 (GRCm39) noncoding transcript Het
Ddx17 T C 15: 79,414,577 (GRCm39) D530G probably benign Het
Dhx9 A T 1: 153,341,441 (GRCm39) D601E probably benign Het
Dnah3 A G 7: 119,646,853 (GRCm39) Y1059H probably damaging Het
Dtx1 C A 5: 120,848,569 (GRCm39) probably benign Het
Egfr A G 11: 16,813,065 (GRCm39) S182G probably benign Het
Fads1 A G 19: 10,163,116 (GRCm39) N131S probably benign Het
Fam243 T A 16: 92,117,553 (GRCm39) Y245F probably damaging Het
Fancm C T 12: 65,165,125 (GRCm39) A1490V possibly damaging Het
Fsd2 C A 7: 81,209,339 (GRCm39) E168* probably null Het
Galnt2l T C 8: 123,568,687 (GRCm39) probably benign Het
Gm9772 A T 17: 22,226,099 (GRCm39) C62S probably damaging Het
H60c C T 10: 3,210,307 (GRCm39) A81T possibly damaging Het
Hira T G 16: 18,744,413 (GRCm39) S377A probably benign Het
Iffo1 T C 6: 125,122,877 (GRCm39) S220P possibly damaging Het
Itih4 A G 14: 30,614,610 (GRCm39) M491V probably benign Het
Khdrbs2 T C 1: 32,559,777 (GRCm39) R102G possibly damaging Het
Klhdc7a T G 4: 139,692,835 (GRCm39) Y704S possibly damaging Het
Klk1b21 G A 7: 43,754,923 (GRCm39) V73I probably benign Het
Krt42 G A 11: 100,160,435 (GRCm39) A88V probably benign Het
Krt42 C T 11: 100,160,436 (GRCm39) A88T probably benign Het
Lipk C T 19: 34,024,185 (GRCm39) P323S probably damaging Het
Lipo5 T A 19: 33,443,273 (GRCm39) probably benign Het
Llgl2 A G 11: 115,736,325 (GRCm39) D166G probably benign Het
Mapk8ip3 A T 17: 25,125,923 (GRCm39) N439K probably damaging Het
Mapkbp1 C T 2: 119,803,626 (GRCm39) R32W probably damaging Het
Med23 T A 10: 24,779,550 (GRCm39) probably benign Het
Mrgprb1 A T 7: 48,097,777 (GRCm39) M45K probably damaging Het
Mroh7 G A 4: 106,552,338 (GRCm39) probably benign Het
Mrpl27 G A 11: 94,544,659 (GRCm39) probably benign Het
Ms4a10 T A 19: 10,942,097 (GRCm39) T175S possibly damaging Het
Muc17 T C 5: 137,166,799 (GRCm39) H330R probably benign Het
Myo15a A T 11: 60,399,028 (GRCm39) I2787F probably damaging Het
Ndst1 A G 18: 60,846,277 (GRCm39) C11R possibly damaging Het
Obsl1 C A 1: 75,464,300 (GRCm39) G1669* probably null Het
Or5p56 A G 7: 107,589,605 (GRCm39) E11G probably benign Het
Or6c208 A T 10: 129,223,652 (GRCm39) D50V probably damaging Het
Or7e177 T C 9: 20,212,134 (GRCm39) Y214H probably benign Het
Pafah2 T A 4: 134,131,468 (GRCm39) I52N probably damaging Het
Pcsk6 A T 7: 65,693,283 (GRCm39) I693F possibly damaging Het
Pde4c G T 8: 71,199,262 (GRCm39) R228L probably benign Het
Pdzd8 T C 19: 59,288,904 (GRCm39) N832S probably benign Het
Plbd1 T A 6: 136,590,814 (GRCm39) M451L probably benign Het
Pramel14 G T 4: 143,719,851 (GRCm39) D171E probably benign Het
Prom1 T C 5: 44,194,965 (GRCm39) D260G probably damaging Het
Ranbp17 A G 11: 33,216,310 (GRCm39) S813P probably damaging Het
Scn10a T C 9: 119,520,544 (GRCm39) I119V probably benign Het
Sh3pxd2b A G 11: 32,365,967 (GRCm39) T353A probably damaging Het
Shq1 A T 6: 100,646,659 (GRCm39) probably null Het
Slc22a28 T A 19: 8,049,223 (GRCm39) H342L possibly damaging Het
Slco2b1 C T 7: 99,314,114 (GRCm39) E9K probably null Het
Specc1l T C 10: 75,082,118 (GRCm39) F505L probably damaging Het
Sptan1 G T 2: 29,870,215 (GRCm39) probably null Het
St6gal2 A G 17: 55,797,932 (GRCm39) probably benign Het
Taok2 T C 7: 126,479,313 (GRCm39) I73V probably benign Het
Tax1bp1 C T 6: 52,721,229 (GRCm39) T478I probably benign Het
Tbc1d4 A T 14: 101,744,542 (GRCm39) N361K probably damaging Het
Tph1 A T 7: 46,296,907 (GRCm39) Y429* probably null Het
Tprkb A T 6: 85,901,403 (GRCm39) R14W probably damaging Het
Trio A T 15: 27,753,890 (GRCm39) probably benign Het
Ttc23 T C 7: 67,316,902 (GRCm39) probably benign Het
Vmn1r211 T C 13: 23,036,415 (GRCm39) Y84C probably damaging Het
Vmn2r22 C G 6: 123,614,624 (GRCm39) G322A possibly damaging Het
Wdr74 A G 19: 8,717,776 (GRCm39) Q330R probably benign Het
Wdtc1 C A 4: 133,024,739 (GRCm39) S486I possibly damaging Het
Zbtb24 T C 10: 41,340,989 (GRCm39) V673A possibly damaging Het
Zfpm2 A T 15: 40,965,877 (GRCm39) R655S probably damaging Het
Zkscan5 A G 5: 145,157,798 (GRCm39) N694D probably benign Het
Other mutations in Limk1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
R4516:Limk1 UTSW 5 134,705,640 (GRCm39) intron probably benign
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'- TCGTCTCCAAAGGTAGGGATGCAG -3'
(R):5'- GCATTTGGCAGGCTTCCAGAAC -3'

Sequencing Primer
(F):5'- AGCTCAGTCAGGGACCTC -3'
(R):5'- GGCTTCCAGAACCCCCAAG -3'
Posted On 2014-03-14