Incidental Mutation 'R5979:Limd1'
ID 481320
Institutional Source Beutler Lab
Gene Symbol Limd1
Ensembl Gene ENSMUSG00000025239
Gene Name LIM domains containing 1
Synonyms D9Ertd192e
MMRRC Submission 044161-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.382) question?
Stock # R5979 (G1)
Quality Score 197.009
Status Validated
Chromosome 9
Chromosomal Location 123307771-123350617 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 123308479 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Histidine at position 59 (Q59H)
Ref Sequence ENSEMBL: ENSMUSP00000026269 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026269]
AlphaFold Q9QXD8
Predicted Effect possibly damaging
Transcript: ENSMUST00000026269
AA Change: Q59H

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000026269
Gene: ENSMUSG00000025239
AA Change: Q59H

DomainStartEndE-ValueType
low complexity region 57 67 N/A INTRINSIC
low complexity region 238 252 N/A INTRINSIC
LIM 463 516 2.17e-15 SMART
LIM 528 580 9.6e-17 SMART
LIM 588 649 2.26e-13 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000216352
Predicted Effect probably benign
Transcript: ENSMUST00000217639
Meta Mutation Damage Score 0.0587 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.4%
  • 20x: 95.4%
Validation Efficiency 100% (87/87)
MGI Phenotype PHENOTYPE: Mice homozygous for a knock-out allele exhibit normal basal bone osteoclast numbers and bone density but are resistant to physiological and pathologic osteoclastogenic stimuli. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 85 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acss2 A G 2: 155,364,029 (GRCm39) I103V possibly damaging Het
Adam3 T C 8: 25,167,383 (GRCm39) N36S probably benign Het
Adamts3 A G 5: 90,009,528 (GRCm39) V45A probably damaging Het
Afg3l2 G T 18: 67,554,329 (GRCm39) L458M probably damaging Het
Agtpbp1 A T 13: 59,681,860 (GRCm39) L69* probably null Het
Alkbh5 T A 11: 60,429,517 (GRCm39) I90N probably damaging Het
Alx1 T C 10: 102,858,120 (GRCm39) Y193C probably damaging Het
Ankrd11 T G 8: 123,619,139 (GRCm39) D1571A probably damaging Het
Brd4 T C 17: 32,417,700 (GRCm39) D124G probably benign Het
C2cd2 G A 16: 97,676,418 (GRCm39) T443I probably benign Het
Casp8 A T 1: 58,868,071 (GRCm39) M171L probably benign Het
Cd200r4 G A 16: 44,653,295 (GRCm39) V22I probably benign Het
Cdcp2 A G 4: 106,962,478 (GRCm39) Y217C probably damaging Het
Cfh C A 1: 140,046,409 (GRCm39) V556F possibly damaging Het
Chka T G 19: 3,934,513 (GRCm39) I182M probably damaging Het
Cope T C 8: 70,755,193 (GRCm39) probably null Het
Coq10b T C 1: 55,092,077 (GRCm39) V15A probably benign Het
Cpne9 T A 6: 113,270,710 (GRCm39) S309T probably benign Het
Daam2 T A 17: 49,766,232 (GRCm39) H992L possibly damaging Het
Dctn3 T C 4: 41,715,393 (GRCm39) probably null Het
Dhx35 G T 2: 158,684,789 (GRCm39) R536L probably benign Het
Dnah8 G T 17: 31,034,638 (GRCm39) E4186* probably null Het
Dnah9 A G 11: 65,725,307 (GRCm39) L4282P probably damaging Het
Dpp10 A G 1: 123,312,012 (GRCm39) probably null Het
Dst T A 1: 34,199,453 (GRCm39) probably benign Het
Ehbp1 C A 11: 22,101,887 (GRCm39) V214L probably benign Het
Fam131b T C 6: 42,298,905 (GRCm39) D25G probably damaging Het
Fbxl13 T A 5: 21,787,089 (GRCm39) I283F probably damaging Het
Gabrr3 T G 16: 59,254,931 (GRCm39) N205K possibly damaging Het
Got1l1 C T 8: 27,687,951 (GRCm39) probably null Het
Gprin1 G A 13: 54,887,791 (GRCm39) A161V probably benign Het
Hepacam2 A T 6: 3,476,149 (GRCm39) F183I probably damaging Het
Hmx2 A G 7: 131,156,279 (GRCm39) T82A probably benign Het
Igsf10 C T 3: 59,243,894 (GRCm39) E147K probably damaging Het
Kndc1 G A 7: 139,519,740 (GRCm39) A1700T probably benign Het
Knl1 T C 2: 118,899,841 (GRCm39) V514A possibly damaging Het
Lama2 T C 10: 27,111,728 (GRCm39) D764G probably damaging Het
Lgi3 G A 14: 70,773,900 (GRCm39) R358H probably damaging Het
Lrrk2 A G 15: 91,657,148 (GRCm39) Y1814C possibly damaging Het
Lysmd3 G A 13: 81,813,393 (GRCm39) probably null Het
Mroh7 T C 4: 106,578,123 (GRCm39) N185S probably benign Het
Muc2 G A 7: 141,305,143 (GRCm39) G149D probably damaging Het
Muc2 A G 7: 141,283,493 (GRCm39) probably null Het
Nlrp3 T C 11: 59,439,797 (GRCm39) F458S probably benign Het
Nop58 A T 1: 59,741,990 (GRCm39) D173V probably damaging Het
Nrxn1 C T 17: 91,395,631 (GRCm39) R175H possibly damaging Het
Nxpe4 A G 9: 48,307,862 (GRCm39) N322S probably benign Het
Ocstamp A G 2: 165,239,467 (GRCm39) S240P probably damaging Het
Or10a5 G A 7: 106,635,543 (GRCm39) M60I probably damaging Het
Or2j3 T C 17: 38,616,083 (GRCm39) K90E probably benign Het
Or8b36 ATTGCTGTTT ATTGCTGTTTGCTGTTT 9: 37,937,836 (GRCm39) probably null Het
Or9e1 A G 11: 58,732,666 (GRCm39) H242R probably damaging Het
Ovch2 G A 7: 107,393,595 (GRCm39) T177I possibly damaging Het
Parn A C 16: 13,424,035 (GRCm39) L454R probably damaging Het
Pcdhb12 T A 18: 37,571,044 (GRCm39) L730Q possibly damaging Het
Phf3 G T 1: 30,844,827 (GRCm39) F1377L probably damaging Het
Pign G T 1: 105,516,999 (GRCm39) S542R probably benign Het
Prex2 G T 1: 11,202,596 (GRCm39) V502F probably damaging Het
Psmd1 A T 1: 86,017,775 (GRCm39) I529F possibly damaging Het
Ptafr A G 4: 132,306,616 (GRCm39) E2G probably benign Het
R3hdm1 A G 1: 128,138,960 (GRCm39) N380S probably benign Het
Rbm12 A C 2: 155,939,679 (GRCm39) probably benign Het
Rgl1 A G 1: 152,433,244 (GRCm39) Y174H probably damaging Het
Rps6kc1 A G 1: 190,532,632 (GRCm39) S457P probably damaging Het
Sall4 A T 2: 168,592,263 (GRCm39) S964T probably benign Het
Sart1 T A 19: 5,431,251 (GRCm39) I681F probably damaging Het
Serinc5 T C 13: 92,797,644 (GRCm39) L49P probably benign Het
Serpinb9e T C 13: 33,439,036 (GRCm39) V154A probably benign Het
Skic2 A T 17: 35,060,439 (GRCm39) N851K probably benign Het
Smox G A 2: 131,358,334 (GRCm39) V136I probably damaging Het
Sspo C T 6: 48,440,627 (GRCm39) T1747I probably benign Het
Swt1 A T 1: 151,283,339 (GRCm39) D339E possibly damaging Het
Synpo2 A G 3: 122,911,060 (GRCm39) L195P probably damaging Het
Syt7 G T 19: 10,420,843 (GRCm39) G414W probably damaging Het
Tmem186 G A 16: 8,454,024 (GRCm39) T79I probably damaging Het
Tmem39a A T 16: 38,396,106 (GRCm39) N113I probably damaging Het
Trim14 C T 4: 46,507,239 (GRCm39) V326M probably damaging Het
Trim58 A G 11: 58,536,909 (GRCm39) E234G probably damaging Het
Ttr T C 18: 20,803,059 (GRCm39) L75P probably damaging Het
Ubr1 C T 2: 120,776,863 (GRCm39) V293I probably benign Het
Vmn1r91 T A 7: 19,835,990 (GRCm39) V303E probably benign Het
Vmn2r30 A C 7: 7,315,334 (GRCm39) I833S probably damaging Het
Zfp131 G T 13: 120,237,982 (GRCm39) N125K probably benign Het
Zfp169 A T 13: 48,644,516 (GRCm39) probably benign Het
Zfp213 C A 17: 23,776,885 (GRCm39) E386* probably null Het
Other mutations in Limd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00953:Limd1 APN 9 123,308,948 (GRCm39) missense probably benign 0.31
IGL00972:Limd1 APN 9 123,309,141 (GRCm39) missense probably benign 0.06
IGL01815:Limd1 APN 9 123,308,801 (GRCm39) missense probably benign 0.01
IGL02598:Limd1 APN 9 123,309,236 (GRCm39) missense probably benign
IGL02598:Limd1 APN 9 123,345,933 (GRCm39) missense probably benign 0.11
IGL02633:Limd1 APN 9 123,308,987 (GRCm39) unclassified probably benign
IGL02999:Limd1 APN 9 123,345,864 (GRCm39) missense probably damaging 1.00
R0314:Limd1 UTSW 9 123,345,892 (GRCm39) missense probably benign 0.04
R1612:Limd1 UTSW 9 123,347,219 (GRCm39) missense probably damaging 1.00
R2009:Limd1 UTSW 9 123,308,564 (GRCm39) missense probably benign
R2299:Limd1 UTSW 9 123,345,942 (GRCm39) nonsense probably null
R3791:Limd1 UTSW 9 123,309,439 (GRCm39) missense possibly damaging 0.92
R4453:Limd1 UTSW 9 123,309,359 (GRCm39) missense possibly damaging 0.52
R7493:Limd1 UTSW 9 123,308,748 (GRCm39) missense probably benign 0.00
R8101:Limd1 UTSW 9 123,329,216 (GRCm39) nonsense probably null
R8332:Limd1 UTSW 9 123,308,319 (GRCm39) missense probably damaging 1.00
R9060:Limd1 UTSW 9 123,309,514 (GRCm39) missense probably benign 0.08
R9679:Limd1 UTSW 9 123,308,457 (GRCm39) missense probably damaging 1.00
R9681:Limd1 UTSW 9 123,345,903 (GRCm39) missense possibly damaging 0.48
R9726:Limd1 UTSW 9 123,308,984 (GRCm39) missense probably benign 0.00
X0028:Limd1 UTSW 9 123,345,927 (GRCm39) missense probably damaging 0.99
Z1177:Limd1 UTSW 9 123,309,086 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- ACACCTTGAACCAGGGCTAG -3'
(R):5'- TCTGCTCCTGAGATGGGTAC -3'

Sequencing Primer
(F):5'- CGGACACTGATCTACAACATGG -3'
(R):5'- CTCCTGAGATGGGTACGAGGG -3'
Posted On 2017-06-26