Incidental Mutation 'R7597:Lims1'
ID 587794
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 045672-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7597 (G1)
Quality Score 225.009
Status Not validated
Chromosome 10
Chromosomal Location 58159288-58260513 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 58248263 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 240 (E240G)
Ref Sequence ENSEMBL: ENSMUSP00000020077 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020077] [ENSMUST00000020078] [ENSMUST00000105468]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000020077
AA Change: E240G

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000020077
Gene: ENSMUSG00000019920
AA Change: E240G

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 damaging
Transcript: ENSMUST00000020078
AA Change: E190G

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000020078
Gene: ENSMUSG00000019920
AA Change: E190G

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 possibly damaging
Transcript: ENSMUST00000105468
AA Change: E240G

PolyPhen 2 Score 0.913 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000101108
Gene: ENSMUSG00000019920
AA Change: E240G

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
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: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc6 A G 7: 45,644,661 (GRCm39) L838P probably damaging Het
Adam34l T G 8: 44,078,281 (GRCm39) N648H probably damaging Het
Adgrl4 T A 3: 151,248,895 (GRCm39) F728I probably damaging Het
Asap1 A G 15: 64,184,304 (GRCm39) V7A probably benign Het
B230104I21Rik A G 4: 154,434,050 (GRCm39) probably benign Het
C4b A T 17: 34,958,649 (GRCm39) S562T probably benign Het
Carmil2 A G 8: 106,422,121 (GRCm39) Y1130C probably damaging Het
Cit A T 5: 116,024,740 (GRCm39) K328* probably null Het
Col18a1 T C 10: 76,949,137 (GRCm39) D125G unknown Het
Cxadr T C 16: 78,125,996 (GRCm39) V122A probably damaging Het
Cyp2d22 G A 15: 82,260,053 (GRCm39) P44S probably damaging Het
Elapor1 A G 3: 108,378,745 (GRCm39) V351A possibly damaging Het
Gabrr1 A G 4: 33,148,964 (GRCm39) T74A probably benign Het
Gfm2 C A 13: 97,309,086 (GRCm39) A597E probably benign Het
H2-T22 T C 17: 36,351,408 (GRCm39) Y274C probably damaging Het
Has2 C A 15: 56,531,817 (GRCm39) W299C probably damaging Het
Hsd17b6 A G 10: 127,827,227 (GRCm39) S282P probably benign Het
Itga1 T C 13: 115,110,676 (GRCm39) I972V probably benign Het
Itih5 T A 2: 10,254,187 (GRCm39) Y813N probably damaging Het
Kctd16 A G 18: 40,663,848 (GRCm39) T326A possibly damaging Het
Klhdc1 T C 12: 69,316,642 (GRCm39) S342P probably damaging Het
Kmt2a T C 9: 44,742,650 (GRCm39) I1682M unknown Het
Lamc1 T C 1: 153,116,200 (GRCm39) K994E possibly damaging Het
Lig1 T G 7: 13,030,270 (GRCm39) S416A probably benign Het
Lnpk T C 2: 74,399,316 (GRCm39) M76V probably benign Het
Lrrtm4 T A 6: 79,999,428 (GRCm39) L280* probably null Het
Mfap3l A T 8: 61,124,315 (GRCm39) I186F possibly damaging Het
Mta3 T C 17: 84,083,011 (GRCm39) F234L probably benign Het
Muc4 C G 16: 32,575,221 (GRCm39) Q1269E probably benign Het
Mybpc2 C T 7: 44,159,223 (GRCm39) G609D probably damaging Het
Naga A T 15: 82,219,035 (GRCm39) D237E probably benign Het
Naip6 C T 13: 100,437,108 (GRCm39) A472T probably benign Het
Nbn G A 4: 15,963,911 (GRCm39) S104N probably damaging Het
Nipsnap2 T C 5: 129,816,637 (GRCm39) L60P probably damaging Het
Or4f47 T A 2: 111,972,925 (GRCm39) F212I probably benign Het
Or8b1b G A 9: 38,375,802 (GRCm39) G155D probably benign Het
Pclo C T 5: 14,727,601 (GRCm39) T2153I unknown Het
Pclo A C 5: 14,908,869 (GRCm39) K5059T unknown Het
Pdlim2 C A 14: 70,403,645 (GRCm39) A256S possibly damaging Het
Pira2 T C 7: 3,845,460 (GRCm39) D308G probably damaging Het
Proc G T 18: 32,256,689 (GRCm39) A326E probably damaging Het
Rab40b T C 11: 121,248,709 (GRCm39) D182G probably benign Het
Rai14 A G 15: 10,574,937 (GRCm39) S703P possibly damaging Het
Rdx C T 9: 51,972,196 (GRCm39) P2L possibly damaging Het
Recql5 T C 11: 115,819,207 (GRCm39) K120E probably benign Het
Rev3l C T 10: 39,698,880 (GRCm39) R1126C probably damaging Het
Slc2a6 G T 2: 26,917,195 (GRCm39) D70E possibly damaging Het
Slc6a17 A T 3: 107,378,668 (GRCm39) D671E possibly damaging Het
Slc7a8 G A 14: 55,018,857 (GRCm39) probably benign Het
Srpk2 A G 5: 23,753,517 (GRCm39) Y79H possibly damaging Het
Traf3ip1 T A 1: 91,439,167 (GRCm39) I361K probably damaging Het
Trpm8 A G 1: 88,255,918 (GRCm39) Y191C probably damaging Het
Ubr3 T C 2: 69,803,812 (GRCm39) V1135A possibly damaging Het
Usp12 C A 5: 146,691,179 (GRCm39) probably null Het
Vmn1r44 C A 6: 89,870,818 (GRCm39) P188Q probably benign Het
Xirp2 T A 2: 67,356,099 (GRCm39) V3620D possibly damaging Het
Zcchc14 A T 8: 122,335,239 (GRCm39) S294T unknown Het
Zfp800 T C 6: 28,260,764 (GRCm39) D5G probably damaging Het
Zfp87 C T 13: 67,665,412 (GRCm39) R350Q probably benign Het
Other mutations in Lims1
AlleleSourceChrCoordTypePredicted EffectPPH Score
P0027:Lims1 UTSW 10 58,254,277 (GRCm39) missense probably benign 0.00
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
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'- ACCCAGCCAAGTCTCTTAATTC -3'
(R):5'- TCTTGCTAGCACACTTGAGGC -3'

Sequencing Primer
(F):5'- CTCAGATCACCTTTAATGAGGGG -3'
(R):5'- CACACTTGAGGCATGGAGATTG -3'
Posted On 2019-10-24