Incidental Mutation 'P0027:Lims1'
ID 8052
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 038280-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # P0027 (G1)
Quality Score
Status Validated
Chromosome 10
Chromosomal Location 58159288-58260513 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 58254277 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Aspartic acid at position 344 (N344D)
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 benign
Transcript: ENSMUST00000020077
AA Change: N344D

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000020077
Gene: ENSMUSG00000019920
AA Change: N344D

DomainStartEndE-ValueType
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
AA Change: N294D

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000020078
Gene: ENSMUSG00000019920
AA Change: N294D

DomainStartEndE-ValueType
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: N344D

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000101108
Gene: ENSMUSG00000019920
AA Change: N344D

DomainStartEndE-ValueType
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: ENSMUST00000148799
Meta Mutation Damage Score 0.0600 question?
Coding Region Coverage
  • 1x: 82.6%
  • 3x: 72.9%
  • 10x: 45.3%
  • 20x: 23.4%
Validation Efficiency 93% (53/57)
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: 20 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Bicd2 C A 13: 49,533,127 (GRCm39) P571Q probably benign Het
Camta2 A G 11: 70,574,831 (GRCm39) I75T probably damaging Het
Casp1 A T 9: 5,299,851 (GRCm39) H108L probably benign Het
Copa A G 1: 171,939,515 (GRCm39) E593G possibly damaging Het
Ftsj3 C A 11: 106,145,634 (GRCm39) M66I possibly damaging Het
Kdm2a C T 19: 4,393,273 (GRCm39) probably benign Het
Klhl14 T C 18: 21,691,192 (GRCm39) Y446C probably damaging Het
Marco A T 1: 120,402,441 (GRCm39) W502R probably damaging Het
Ms4a10 T C 19: 10,941,492 (GRCm39) D159G probably damaging Het
Msi2 A T 11: 88,285,423 (GRCm39) M207K probably damaging Het
Myh15 C T 16: 48,901,571 (GRCm39) T249I possibly damaging Het
Nap1l5 T A 6: 58,883,810 (GRCm39) N48I probably damaging Het
Nup188 A G 2: 30,212,693 (GRCm39) D632G probably damaging Het
Or1n2 T C 2: 36,797,582 (GRCm39) V208A probably benign Het
Phactr4 G C 4: 132,098,401 (GRCm39) T252R probably damaging Het
Sec14l2 C T 11: 4,053,673 (GRCm39) probably null Het
Sim2 C A 16: 93,910,281 (GRCm39) H228N probably benign Het
Tent4a G A 13: 69,655,074 (GRCm39) R224* probably null Het
Tmem26 A G 10: 68,614,548 (GRCm39) E321G probably benign Het
Yif1b T C 7: 28,938,038 (GRCm39) probably null Het
Other mutations in Lims1
AlleleSourceChrCoordTypePredicted EffectPPH Score
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
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
Posted On 2012-11-20