Incidental Mutation 'R0312:Lima1'
ID 25312
Institutional Source Beutler Lab
Gene Symbol Lima1
Ensembl Gene ENSMUSG00000023022
Gene Name LIM domain and actin binding 1
Synonyms 3526402A12Rik, EPLIN, epithelial protein lost in neoplasm, 1110021C24Rik
MMRRC Submission 038522-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.123) question?
Stock # R0312 (G1)
Quality Score 225
Status Validated
Chromosome 15
Chromosomal Location 99676351-99773292 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 99678968 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 491 (V491A)
Ref Sequence ENSEMBL: ENSMUSP00000073371 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000073691] [ENSMUST00000109024]
AlphaFold Q9ERG0
Predicted Effect possibly damaging
Transcript: ENSMUST00000073691
AA Change: V491A

PolyPhen 2 Score 0.685 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000073371
Gene: ENSMUSG00000023022
AA Change: V491A

DomainStartEndE-ValueType
LIM 387 439 5.14e-17 SMART
low complexity region 534 546 N/A INTRINSIC
low complexity region 570 587 N/A INTRINSIC
low complexity region 598 609 N/A INTRINSIC
low complexity region 613 626 N/A INTRINSIC
low complexity region 747 753 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000109024
AA Change: V331A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000104652
Gene: ENSMUSG00000023022
AA Change: V331A

DomainStartEndE-ValueType
LIM 227 279 5.14e-17 SMART
low complexity region 374 386 N/A INTRINSIC
low complexity region 410 427 N/A INTRINSIC
low complexity region 438 449 N/A INTRINSIC
low complexity region 453 466 N/A INTRINSIC
low complexity region 587 593 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000168951
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172119
Meta Mutation Damage Score 0.0761 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.9%
  • 10x: 95.3%
  • 20x: 90.3%
Validation Efficiency 100% (60/60)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a cytoskeleton-associated protein that inhibits actin filament depolymerization and cross-links filaments in bundles. It is downregulated in some cancer cell lines. Alternatively spliced transcript variants encoding different isoforms have been described for this gene, and expression of some of the variants maybe independently regulated. [provided by RefSeq, Aug 2011]
Allele List at MGI
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb5 G T 12: 118,836,572 (GRCm39) A1113D probably damaging Het
Adcy1 G T 11: 7,099,538 (GRCm39) A673S probably benign Het
Apob T A 12: 8,059,034 (GRCm39) H2505Q probably benign Het
Arhgap12 A G 18: 6,061,982 (GRCm39) probably benign Het
Bcl9 C T 3: 97,116,727 (GRCm39) E656K probably benign Het
Bnc1 C T 7: 81,627,072 (GRCm39) R106H possibly damaging Het
Ccdc54 T C 16: 50,411,165 (GRCm39) K34E possibly damaging Het
Cfap65 G A 1: 74,943,226 (GRCm39) R1600W probably damaging Het
Csmd1 A T 8: 16,034,760 (GRCm39) N2470K probably damaging Het
Cspp1 T C 1: 10,129,054 (GRCm39) probably benign Het
Dgkz A T 2: 91,768,684 (GRCm39) I699N probably damaging Het
Dhx40 G A 11: 86,662,775 (GRCm39) T639I probably damaging Het
Dlg1 A G 16: 31,609,085 (GRCm39) T227A probably benign Het
Dnah10 G A 5: 124,873,433 (GRCm39) probably benign Het
Dnah3 T A 7: 119,644,882 (GRCm39) K1133M probably damaging Het
Dock5 G C 14: 68,033,440 (GRCm39) F976L possibly damaging Het
Evc C T 5: 37,485,885 (GRCm39) C97Y possibly damaging Het
Fbxw7 T C 3: 84,874,876 (GRCm39) probably benign Het
Fggy A C 4: 95,732,422 (GRCm39) D112A probably damaging Het
Fpgs A G 2: 32,574,813 (GRCm39) Y435H probably damaging Het
Fryl T A 5: 73,230,231 (GRCm39) H1642L probably damaging Het
G3bp1 T C 11: 55,389,452 (GRCm39) F383L probably damaging Het
Gda T A 19: 21,394,369 (GRCm39) I237F probably damaging Het
Glt1d1 A G 5: 127,768,134 (GRCm39) N247S probably damaging Het
Gm7647 T C 5: 95,110,839 (GRCm39) S7P probably benign Het
Gpr31b C T 17: 13,270,498 (GRCm39) V224I probably damaging Het
Hlf G A 11: 90,278,701 (GRCm39) P121L possibly damaging Het
Hsh2d G A 8: 72,954,304 (GRCm39) D229N probably benign Het
Ism1 G T 2: 139,520,592 (GRCm39) M1I probably null Het
Kansl1l T C 1: 66,817,265 (GRCm39) N365S probably null Het
Lama1 T C 17: 68,082,846 (GRCm39) L1368P possibly damaging Het
Lrch1 G T 14: 75,185,034 (GRCm39) H23N possibly damaging Het
Lrp1b A G 2: 41,172,183 (GRCm39) V1488A probably damaging Het
Lrp8 T C 4: 107,664,052 (GRCm39) probably benign Het
Lrrc8e A G 8: 4,285,733 (GRCm39) S653G probably benign Het
Mnat1 A G 12: 73,228,558 (GRCm39) T141A possibly damaging Het
Mpeg1 C A 19: 12,439,767 (GRCm39) N408K probably damaging Het
Myo7b T C 18: 32,147,390 (GRCm39) E51G possibly damaging Het
Myrf G C 19: 10,195,526 (GRCm39) T428S probably benign Het
Naa35 A G 13: 59,757,395 (GRCm39) T257A probably benign Het
Obox5 T A 7: 15,491,485 (GRCm39) H8Q probably damaging Het
Or1j4 A T 2: 36,740,372 (GRCm39) I105L probably benign Het
Or51q1c T C 7: 103,653,232 (GRCm39) V250A probably damaging Het
Or5h26 A T 16: 58,988,202 (GRCm39) F101L probably benign Het
Phldb2 G T 16: 45,609,410 (GRCm39) T732N probably damaging Het
Phyhip G T 14: 70,704,410 (GRCm39) A210S possibly damaging Het
Pik3r4 A G 9: 105,563,409 (GRCm39) D1262G probably damaging Het
Pip G A 6: 41,826,798 (GRCm39) E48K possibly damaging Het
Plk4 C T 3: 40,767,982 (GRCm39) L74F probably damaging Het
Prdm14 G A 1: 13,189,031 (GRCm39) R438W probably damaging Het
Rab19 G A 6: 39,361,023 (GRCm39) R57H probably benign Het
Rtl1 G T 12: 109,556,661 (GRCm39) P1726Q probably damaging Het
Sema6a G A 18: 47,423,112 (GRCm39) probably null Het
Skint6 A T 4: 112,666,297 (GRCm39) V1176D possibly damaging Het
Slc12a1 A G 2: 125,067,948 (GRCm39) I1012V probably damaging Het
Slc1a3 C T 15: 8,665,721 (GRCm39) M509I probably benign Het
Spata18 G A 5: 73,824,224 (GRCm39) G35E probably benign Het
Spata31h1 A T 10: 82,120,203 (GRCm39) I4269N probably damaging Het
Sspo C T 6: 48,432,335 (GRCm39) P801L possibly damaging Het
Ugt2b37 C T 5: 87,398,524 (GRCm39) G304D probably damaging Het
Vmn2r25 A T 6: 123,805,539 (GRCm39) probably benign Het
Xrcc6 C A 15: 81,911,423 (GRCm39) probably null Het
Other mutations in Lima1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00668:Lima1 APN 15 99,700,038 (GRCm39) missense possibly damaging 0.47
IGL01104:Lima1 APN 15 99,741,581 (GRCm39) missense probably damaging 1.00
IGL02618:Lima1 APN 15 99,700,097 (GRCm39) splice site probably benign
IGL03124:Lima1 APN 15 99,694,615 (GRCm39) splice site probably benign
R0599:Lima1 UTSW 15 99,700,040 (GRCm39) missense probably damaging 1.00
R0601:Lima1 UTSW 15 99,678,353 (GRCm39) missense probably damaging 0.98
R1423:Lima1 UTSW 15 99,717,626 (GRCm39) nonsense probably null
R1704:Lima1 UTSW 15 99,717,617 (GRCm39) missense probably benign 0.00
R1784:Lima1 UTSW 15 99,678,344 (GRCm39) missense possibly damaging 0.93
R1819:Lima1 UTSW 15 99,717,817 (GRCm39) missense probably benign 0.01
R1968:Lima1 UTSW 15 99,717,565 (GRCm39) missense probably benign
R2352:Lima1 UTSW 15 99,692,396 (GRCm39) missense probably benign 0.02
R2908:Lima1 UTSW 15 99,699,991 (GRCm39) critical splice donor site probably null
R4582:Lima1 UTSW 15 99,678,873 (GRCm39) missense possibly damaging 0.65
R4672:Lima1 UTSW 15 99,741,590 (GRCm39) missense probably damaging 1.00
R4858:Lima1 UTSW 15 99,717,457 (GRCm39) missense probably benign 0.23
R6140:Lima1 UTSW 15 99,678,939 (GRCm39) missense probably damaging 1.00
R6614:Lima1 UTSW 15 99,681,461 (GRCm39) missense probably damaging 1.00
R6898:Lima1 UTSW 15 99,679,148 (GRCm39) missense possibly damaging 0.61
R7598:Lima1 UTSW 15 99,717,577 (GRCm39) missense probably benign 0.01
R7601:Lima1 UTSW 15 99,717,577 (GRCm39) missense probably benign 0.01
R7878:Lima1 UTSW 15 99,717,431 (GRCm39) missense probably benign 0.12
R8219:Lima1 UTSW 15 99,678,671 (GRCm39) missense probably damaging 1.00
R8348:Lima1 UTSW 15 99,678,753 (GRCm39) missense probably benign 0.00
R8733:Lima1 UTSW 15 99,678,699 (GRCm39) missense probably damaging 1.00
R8821:Lima1 UTSW 15 99,704,306 (GRCm39) missense probably benign 0.00
R9285:Lima1 UTSW 15 99,678,687 (GRCm39) missense probably damaging 1.00
R9300:Lima1 UTSW 15 99,704,320 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- TCGAAAGGAAGCTGCTACCGTAAAC -3'
(R):5'- TTACAGCCTGCCGCAGTAACTGAG -3'

Sequencing Primer
(F):5'- TCTCCTTCAGGGACGAAGAC -3'
(R):5'- TGCATCCTTACATGGACGAATC -3'
Posted On 2013-04-16