Incidental Mutation 'R4672:Lima1'
ID 348573
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 041927-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.123) question?
Stock # R4672 (G1)
Quality Score 225
Status Validated
Chromosome 15
Chromosomal Location 99676351-99773292 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 99741590 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Aspartic acid at position 29 (N29D)
Ref Sequence ENSEMBL: ENSMUSP00000155772 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000073691] [ENSMUST00000231121]
AlphaFold Q9ERG0
Predicted Effect probably damaging
Transcript: ENSMUST00000073691
AA Change: N29D

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000073371
Gene: ENSMUSG00000023022
AA Change: N29D

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 noncoding transcript
Transcript: ENSMUST00000171450
Predicted Effect probably damaging
Transcript: ENSMUST00000231121
AA Change: N29D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Meta Mutation Damage Score 0.0613 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.8%
Validation Efficiency 98% (113/115)
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: 105 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca8a G A 11: 109,962,702 (GRCm39) L483F possibly damaging Het
Abca8b A G 11: 109,827,274 (GRCm39) F1507L possibly damaging Het
Adamdec1 C A 14: 68,815,353 (GRCm39) E104* probably null Het
Adamts16 G A 13: 70,927,637 (GRCm39) probably benign Het
Alppl2 T C 1: 87,017,187 (GRCm39) probably benign Het
Aplnr A G 2: 84,967,524 (GRCm39) Y183C probably damaging Het
Atm G A 9: 53,433,501 (GRCm39) R250W probably damaging Het
B4galt7 T C 13: 55,757,132 (GRCm39) L275P probably damaging Het
Bltp1 A G 3: 36,944,139 (GRCm39) *330W probably null Het
Ccdc178 G A 18: 22,283,501 (GRCm39) Q10* probably null Het
Ccr9 T C 9: 123,608,752 (GRCm39) Y145H probably damaging Het
Cd209f C T 8: 4,153,685 (GRCm39) G188D probably damaging Het
Cep70 T A 9: 99,136,365 (GRCm39) S23T possibly damaging Het
Cpped1 C A 16: 11,623,238 (GRCm39) E294* probably null Het
Crisp1 T A 17: 40,605,404 (GRCm39) probably null Het
Disp1 T C 1: 182,880,215 (GRCm39) probably null Het
Dlg2 A T 7: 91,935,743 (GRCm39) M624L probably damaging Het
Elf2 A G 3: 51,163,855 (GRCm39) V558A probably damaging Het
Eno2 T C 6: 124,743,109 (GRCm39) D209G probably damaging Het
Fam187b G A 7: 30,676,968 (GRCm39) R159H probably damaging Het
Fh1 G A 1: 175,431,617 (GRCm39) A423V probably benign Het
Frg1 C T 8: 41,853,846 (GRCm39) D164N probably benign Het
Fsbp T G 4: 11,579,841 (GRCm39) N36K probably benign Het
Gcn1 A G 5: 115,744,579 (GRCm39) T1592A probably damaging Het
Gimap3 A G 6: 48,742,687 (GRCm39) I81T probably damaging Het
Gjb6 C T 14: 57,362,235 (GRCm39) V9I probably benign Het
Gkap1 T C 13: 58,411,770 (GRCm39) S68G possibly damaging Het
Gpatch8 A T 11: 102,369,784 (GRCm39) S1251R probably damaging Het
Gria4 A G 9: 4,664,981 (GRCm39) F92L possibly damaging Het
H2-Q1 C A 17: 35,539,906 (GRCm39) D58E probably damaging Het
Hs1bp3 G T 12: 8,391,983 (GRCm39) G362* probably null Het
Igfn1 T A 1: 135,893,107 (GRCm39) H2114L possibly damaging Het
Igkv12-98 A G 6: 68,547,940 (GRCm39) Q22R probably benign Het
Ing3 A G 6: 21,965,729 (GRCm39) probably null Het
Insr C T 8: 3,217,501 (GRCm39) probably null Het
Kdm3b T C 18: 34,941,630 (GRCm39) S374P probably benign Het
Kif14 A C 1: 136,449,016 (GRCm39) Q1472P probably benign Het
Kif14 G T 1: 136,449,017 (GRCm39) Q1472H probably benign Het
Knstrn A G 2: 118,664,512 (GRCm39) E202G probably damaging Het
Knstrn G T 2: 118,664,513 (GRCm39) E202D possibly damaging Het
Krt12 A G 11: 99,309,509 (GRCm39) probably benign Het
Lgi3 A T 14: 70,771,897 (GRCm39) I195F possibly damaging Het
Liph T C 16: 21,802,806 (GRCm39) I88V probably benign Het
Lrrk1 A G 7: 65,929,120 (GRCm39) S86P probably benign Het
Lsamp A G 16: 41,775,697 (GRCm39) R166G probably damaging Het
Mamdc2 T A 19: 23,328,148 (GRCm39) N407Y probably damaging Het
Mast3 CATA CA 8: 71,237,441 (GRCm39) probably null Het
Megf6 T A 4: 154,333,909 (GRCm39) N212K probably damaging Het
Met A C 6: 17,571,803 (GRCm39) D1374A probably benign Het
Mrc2 A G 11: 105,233,923 (GRCm39) T902A probably benign Het
Mroh3 T A 1: 136,118,713 (GRCm39) T535S probably benign Het
Muc1 G T 3: 89,139,384 (GRCm39) V595L probably damaging Het
Myh2 T A 11: 67,079,303 (GRCm39) L957Q probably damaging Het
Myorg T A 4: 41,499,061 (GRCm39) M190L probably benign Het
Ncl A T 1: 86,284,324 (GRCm39) D257E probably benign Het
Nipbl T A 15: 8,332,468 (GRCm39) D2263V probably damaging Het
Optc C A 1: 133,825,555 (GRCm39) V324L possibly damaging Het
Or4k15 A G 14: 50,364,714 (GRCm39) N227D probably benign Het
Or4k42 A T 2: 111,319,902 (GRCm39) N200K possibly damaging Het
Or7g35 A G 9: 19,496,726 (GRCm39) K298E possibly damaging Het
Osbpl9 A G 4: 108,921,806 (GRCm39) I604T possibly damaging Het
Otog C A 7: 45,939,210 (GRCm39) A2080D probably damaging Het
Parp6 G C 9: 59,547,393 (GRCm39) R460P probably damaging Het
Phactr4 G T 4: 132,098,017 (GRCm39) P417Q probably damaging Het
Pigt T C 2: 164,339,498 (GRCm39) probably benign Het
Plekha5 A G 6: 140,470,655 (GRCm39) I99V probably damaging Het
Plxna3 T G X: 73,382,554 (GRCm39) probably null Het
Ppp2r1b G A 9: 50,779,019 (GRCm39) M362I probably damaging Het
Pramel34 T A 5: 93,784,182 (GRCm39) R230S probably damaging Het
Rad51 A G 2: 118,954,327 (GRCm39) I136V probably benign Het
Rad54b T A 4: 11,609,449 (GRCm39) H633Q probably benign Het
Rasal2 A G 1: 157,071,231 (GRCm39) F41S probably benign Het
Reep3 T A 10: 66,857,629 (GRCm39) H154L probably benign Het
Rp1l1 T G 14: 64,268,719 (GRCm39) V1435G probably damaging Het
Rps6ka5 C A 12: 100,620,546 (GRCm39) K125N possibly damaging Het
Rsad1 A T 11: 94,434,444 (GRCm39) M330K probably damaging Het
Scand1 A G 2: 156,153,850 (GRCm39) probably null Het
Setd6 A G 8: 96,444,640 (GRCm39) H111R probably null Het
Slc27a3 T C 3: 90,294,953 (GRCm39) N368S possibly damaging Het
Slc38a2 T C 15: 96,596,518 (GRCm39) T32A probably benign Het
Smg7 A G 1: 152,721,164 (GRCm39) S683P probably damaging Het
Smyd2 A T 1: 189,642,101 (GRCm39) L62M probably damaging Het
Sox5 T C 6: 143,779,075 (GRCm39) Y687C probably damaging Het
Spaca6 T A 17: 18,057,005 (GRCm39) C53* probably null Het
Spata31e4 T C 13: 50,857,208 (GRCm39) Y949H probably benign Het
Spire2 T C 8: 124,084,850 (GRCm39) V230A probably benign Het
Sptbn2 G T 19: 4,782,524 (GRCm39) V487L probably benign Het
Stk3 T A 15: 35,099,603 (GRCm39) I110L probably benign Het
Stox2 T A 8: 47,645,141 (GRCm39) Y773F probably damaging Het
Tbrg1 C A 9: 37,562,632 (GRCm39) A259S probably damaging Het
Tnfsf18 C A 1: 161,331,307 (GRCm39) D152E probably benign Het
Tpr G A 1: 150,299,318 (GRCm39) A1173T probably benign Het
Trrap T C 5: 144,722,290 (GRCm39) L271P probably damaging Het
Ttn G T 2: 76,657,419 (GRCm39) probably benign Het
U2surp A G 9: 95,375,198 (GRCm39) S192P possibly damaging Het
Ubr4 C T 4: 139,138,027 (GRCm39) S1128L probably damaging Het
Ucma G A 2: 4,981,465 (GRCm39) probably null Het
Urb1 A T 16: 90,569,522 (GRCm39) D1401E probably benign Het
Usp54 A T 14: 20,631,597 (GRCm39) probably benign Het
Vmn1r31 A G 6: 58,449,056 (GRCm39) Y270H probably damaging Het
Vmn1r90 T A 7: 14,295,493 (GRCm39) T202S probably benign Het
Vmn2r88 A G 14: 51,655,612 (GRCm39) Y616C probably damaging Het
Vmn2r95 T A 17: 18,672,413 (GRCm39) W717R probably damaging Het
Zcchc4 C A 5: 52,953,947 (GRCm39) T209K probably benign Het
Zfp955b T A 17: 33,524,233 (GRCm39) probably benign 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
R0312:Lima1 UTSW 15 99,678,968 (GRCm39) missense possibly damaging 0.69
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
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'- TCCTCTCCAGTGACCTGTAG -3'
(R):5'- TTTGCACAGTAGGGTCAGTG -3'

Sequencing Primer
(F):5'- CTGTAGGGTGCATAAAGCCC -3'
(R):5'- AGGATCCTGACTCCTCTGACAGAG -3'
Posted On 2015-10-08