Incidental Mutation 'R5682:Limk1'
ID 443101
Institutional Source Beutler Lab
Gene Symbol Limk1
Ensembl Gene ENSMUSG00000029674
Gene Name LIM domain kinase 1
Synonyms
MMRRC Submission 043318-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5682 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 134684893-134717452 bp(-) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) A to C at 134694059 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000106864 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000015137] [ENSMUST00000015137] [ENSMUST00000111233] [ENSMUST00000111233] [ENSMUST00000138590]
AlphaFold P53668
Predicted Effect probably null
Transcript: ENSMUST00000015137
SMART Domains Protein: ENSMUSP00000015137
Gene: ENSMUSG00000029674

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 null
Transcript: ENSMUST00000015137
SMART Domains Protein: ENSMUSP00000015137
Gene: ENSMUSG00000029674

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 null
Transcript: ENSMUST00000111233
SMART Domains Protein: ENSMUSP00000106864
Gene: ENSMUSG00000029674

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 null
Transcript: ENSMUST00000111233
SMART Domains Protein: ENSMUSP00000106864
Gene: ENSMUSG00000029674

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 noncoding transcript
Transcript: ENSMUST00000132027
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: 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 noncoding transcript
Transcript: ENSMUST00000137897
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
Coding Region Coverage
  • 1x: 99.7%
  • 3x: 99.0%
  • 10x: 97.4%
  • 20x: 95.3%
Validation Efficiency
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: 81 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc3 A T 11: 94,283,723 (GRCm39) S7T probably benign Het
Acot4 G A 12: 84,085,576 (GRCm39) V98M probably damaging Het
Acsm2 A T 7: 119,162,774 (GRCm39) N41I probably benign Het
Adamtsl3 A T 7: 82,255,758 (GRCm39) N1590I probably damaging Het
Ank3 G A 10: 69,729,347 (GRCm39) G714R probably damaging Het
Armh4 T C 14: 49,989,043 (GRCm39) D642G probably damaging Het
Ash1l G A 3: 88,914,914 (GRCm39) R1848Q probably damaging Het
Atp1a4 A T 1: 172,081,730 (GRCm39) Y141N probably damaging Het
Atxn3 A T 12: 101,924,406 (GRCm39) I1N probably damaging Het
Avil A C 10: 126,849,973 (GRCm39) Q608P probably damaging Het
Axin1 T C 17: 26,406,775 (GRCm39) V456A probably benign Het
Cacna1g A G 11: 94,349,940 (GRCm39) L635P probably damaging Het
Card11 G A 5: 140,888,666 (GRCm39) Q231* probably null Het
Ccdc162 G A 10: 41,432,799 (GRCm39) R500* probably null Het
Cdh24 T C 14: 54,874,805 (GRCm39) D400G probably damaging Het
Cep112 T C 11: 108,361,138 (GRCm39) L164P probably damaging Het
Corin A G 5: 72,579,497 (GRCm39) S224P possibly damaging Het
Csgalnact2 T C 6: 118,097,953 (GRCm39) Y371C probably damaging Het
Cspg4 A T 9: 56,793,480 (GRCm39) E405V probably benign Het
Ctnna3 T A 10: 64,709,085 (GRCm39) M708K probably damaging Het
Cyp7a1 T A 4: 6,268,429 (GRCm39) Y432F probably benign Het
Dcaf11 T A 14: 55,800,883 (GRCm39) V113E probably damaging Het
Dhx29 T C 13: 113,067,383 (GRCm39) I88T probably damaging Het
Dnhd1 G A 7: 105,352,416 (GRCm39) R2523Q probably damaging Het
Elmo2 A G 2: 165,139,330 (GRCm39) F406L probably damaging Het
Eps15l1 G A 8: 73,125,592 (GRCm39) Q648* probably null Het
Fam171a1 G A 2: 3,227,126 (GRCm39) R753Q probably damaging Het
Figla T A 6: 85,995,604 (GRCm39) V86E probably damaging Het
Galnt7 C A 8: 58,036,967 (GRCm39) E141* probably null Het
Garnl3 A G 2: 32,944,185 (GRCm39) Y125H probably damaging Het
Gnb5 A G 9: 75,234,523 (GRCm39) D74G probably damaging Het
Grk1 A T 8: 13,464,351 (GRCm39) I408F possibly damaging Het
Has1 A T 17: 18,064,425 (GRCm39) W405R possibly damaging Het
Hdac5 A G 11: 102,104,749 (GRCm39) probably benign Het
Helq T A 5: 100,933,170 (GRCm39) M555L probably benign Het
Hipk2 T C 6: 38,714,408 (GRCm39) N556S possibly damaging Het
Htr7 C A 19: 35,947,271 (GRCm39) A248S probably damaging Het
Ing3 T C 6: 21,968,949 (GRCm39) S144P probably damaging Het
Itgb1 G A 8: 129,453,549 (GRCm39) probably null Het
Kcnh4 A T 11: 100,640,628 (GRCm39) M466K possibly damaging Het
Krit1 T A 5: 3,880,737 (GRCm39) N565K probably damaging Het
Lrif1 T C 3: 106,639,884 (GRCm39) I323T possibly damaging Het
Macf1 T C 4: 123,328,552 (GRCm39) E1811G probably damaging Het
Mctp2 A C 7: 71,895,207 (GRCm39) probably null Het
Mmp21 A G 7: 133,276,358 (GRCm39) I495T probably benign Het
Mpz A T 1: 170,986,463 (GRCm39) T126S possibly damaging Het
Napsa A G 7: 44,234,768 (GRCm39) Y301C possibly damaging Het
Ncbp1 T A 4: 46,170,474 (GRCm39) probably benign Het
Nup160 A G 2: 90,510,155 (GRCm39) E47G probably benign Het
Or8b56 A G 9: 38,739,424 (GRCm39) I146V probably benign Het
Pcdha11 A G 18: 37,144,502 (GRCm39) K198E probably damaging Het
Pcdha3 A G 18: 37,081,040 (GRCm39) D594G probably damaging Het
Pdcd5 G A 7: 35,346,613 (GRCm39) probably benign Het
Pdhx A T 2: 102,865,685 (GRCm39) S166T probably benign Het
Pigc A G 1: 161,798,516 (GRCm39) Y166C probably damaging Het
Prkch C T 12: 73,744,724 (GRCm39) H246Y probably damaging Het
Ptk2 A T 15: 73,134,413 (GRCm39) L562* probably null Het
Rab3ip C T 10: 116,743,008 (GRCm39) W439* probably null Het
Rasef T A 4: 73,659,208 (GRCm39) R435* probably null Het
Rnf103 C T 6: 71,485,708 (GRCm39) probably benign Het
Rtel1 T C 2: 180,991,765 (GRCm39) F388L probably benign Het
Sds A C 5: 120,621,784 (GRCm39) S309R possibly damaging Het
Sgip1 T A 4: 102,824,847 (GRCm39) D736E possibly damaging Het
Sgms2 A G 3: 131,118,611 (GRCm39) Y291H probably damaging Het
Sgsm3 A G 15: 80,895,661 (GRCm39) probably null Het
Siglec1 T A 2: 130,925,930 (GRCm39) I259F probably damaging Het
Sik2 G A 9: 50,828,382 (GRCm39) P220L probably damaging Het
Slc29a3 A G 10: 60,551,991 (GRCm39) V351A probably benign Het
Slc36a3 A G 11: 55,016,489 (GRCm39) S369P probably benign Het
Srgap1 A T 10: 121,640,919 (GRCm39) M649K probably damaging Het
Thnsl1 A G 2: 21,216,879 (GRCm39) E211G possibly damaging Het
Tmprss9 A G 10: 80,733,207 (GRCm39) probably null Het
Tpgs1 G A 10: 79,511,421 (GRCm39) V188M probably damaging Het
Vmn1r201 G T 13: 22,659,355 (GRCm39) V190F probably damaging Het
Vmn1r64 A T 7: 5,886,622 (GRCm39) L307Q possibly damaging Het
Wbp11 T C 6: 136,791,252 (GRCm39) probably benign Het
Wdr35 A G 12: 9,031,125 (GRCm39) Y134C probably damaging Het
Zan G T 5: 137,412,521 (GRCm39) C3263* probably null Het
Zc3h12c G T 9: 52,037,876 (GRCm39) D301E probably damaging Het
Zfp365 A C 10: 67,745,637 (GRCm39) L47R probably damaging Het
Zmym6 C T 4: 126,998,200 (GRCm39) P412L probably damaging 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
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
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
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'- TCTGAGTCCTCTAGCAGGGT -3'
(R):5'- TGGACAGATTGAGAACTTTGTGG -3'

Sequencing Primer
(F):5'- TCCTCTAGCAGGGTAGGCAAC -3'
(R):5'- GTAAACCTCTCAAGTACTGGGGTC -3'
Posted On 2016-11-09