Incidental Mutation 'R1612:Limd1'
ID176875
Institutional Source Beutler Lab
Gene Symbol Limd1
Ensembl Gene ENSMUSG00000025239
Gene NameLIM domains containing 1
SynonymsD9Ertd192e
MMRRC Submission 039649-MU
Accession Numbers
Is this an essential gene? Possibly non essential (E-score: 0.401) question?
Stock #R1612 (G1)
Quality Score225
Status Validated
Chromosome9
Chromosomal Location123478706-123521552 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to G at 123518154 bp
ZygosityHeterozygous
Amino Acid Change Tyrosine to Cysteine at position 620 (Y620C)
Ref Sequence ENSEMBL: ENSMUSP00000026269 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026269]
Predicted Effect probably damaging
Transcript: ENSMUST00000026269
AA Change: Y620C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000026269
Gene: ENSMUSG00000025239
AA Change: Y620C

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: ENSMUST00000213278
Predicted Effect noncoding transcript
Transcript: ENSMUST00000214309
Predicted Effect noncoding transcript
Transcript: ENSMUST00000216352
Predicted Effect probably benign
Transcript: ENSMUST00000217639
Meta Mutation Damage Score 0.362 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.6%
Validation Efficiency 97% (69/71)
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930579G24Rik A G 3: 79,631,144 T66A probably benign Het
9930021J03Rik A G 19: 29,717,845 V1483A possibly damaging Het
Actb A G 5: 142,905,595 F31S probably damaging Het
Adamts7 T C 9: 90,188,697 S624P possibly damaging Het
Adh7 T C 3: 138,228,881 I355T possibly damaging Het
Arhgef40 A G 14: 52,004,081 E106G probably damaging Het
Cabp7 T C 11: 4,739,198 D149G probably damaging Het
Cass4 A T 2: 172,427,078 Q362L possibly damaging Het
Cd14 G A 18: 36,725,665 Q246* probably null Het
Cdr2l A C 11: 115,393,406 E189D probably benign Het
Col6a6 A G 9: 105,777,549 V991A probably damaging Het
Coq7 A G 7: 118,509,911 W305R unknown Het
Cracr2a G T 6: 127,603,929 G23* probably null Het
Dclk2 C T 3: 86,805,639 R503Q possibly damaging Het
Epcam T C 17: 87,639,938 L40P possibly damaging Het
Eps8 G A 6: 137,500,618 P531S probably benign Het
Faap100 C A 11: 120,377,088 L286F probably damaging Het
Fabp3 C T 4: 130,312,387 T57I probably benign Het
Fbn2 A T 18: 58,061,752 C1446S probably damaging Het
Fmo3 A G 1: 162,967,885 V127A probably damaging Het
Frem3 A G 8: 80,614,861 D1261G probably damaging Het
Gabbr1 A G 17: 37,070,669 Y775C probably damaging Het
Gbp11 G T 5: 105,326,596 Q405K possibly damaging Het
Gdi2 T A 13: 3,560,051 V260E probably benign Het
Glp2r C T 11: 67,742,207 V98M possibly damaging Het
Gm13741 T C 2: 87,656,087 Y278C probably damaging Het
Gm7732 G A 17: 21,129,915 noncoding transcript Het
Gnptab T A 10: 88,428,482 probably null Het
Hbs1l T G 10: 21,358,835 F596V probably damaging Het
Krt78 A T 15: 101,951,844 probably null Het
Krt83 A T 15: 101,488,211 L223Q probably benign Het
Lcmt2 T C 2: 121,139,120 Y274C probably damaging Het
Lvrn G T 18: 46,894,703 A862S probably damaging Het
Map4k2 A G 19: 6,343,341 E206G probably damaging Het
Med16 A G 10: 79,899,245 S461P probably damaging Het
Mrfap1 C A 5: 36,796,362 A78S probably damaging Het
Mum1 T A 10: 80,233,055 probably benign Het
Nav2 T A 7: 49,571,211 N1715K probably damaging Het
Ndc1 A G 4: 107,395,068 probably benign Het
Ngly1 G T 14: 16,290,867 G450* probably null Het
Olfr195 T C 16: 59,149,624 M258T probably benign Het
Olfr272 T A 4: 52,911,501 M98L probably benign Het
Pde3b T A 7: 114,519,556 Y643* probably null Het
Pdilt T G 7: 119,486,975 N506H possibly damaging Het
Pear1 C T 3: 87,751,853 probably null Het
Pfkp A T 13: 6,588,589 M582K probably damaging Het
Pigl T A 11: 62,512,994 F251I probably benign Het
Plk3 A G 4: 117,131,807 Y252H probably damaging Het
Prdx3 A G 19: 60,874,434 S12P possibly damaging Het
Prkag2 T C 5: 24,877,028 I96V probably benign Het
Rgs3 G A 4: 62,625,935 V146M probably damaging Het
Serpinh1 T C 7: 99,348,931 D164G probably damaging Het
Slc35d2 T C 13: 64,111,510 probably benign Het
Slc6a6 A G 6: 91,741,027 N316D probably damaging Het
Snx14 A T 9: 88,376,905 M973K possibly damaging Het
Sptan1 C G 2: 30,003,336 R1126G probably damaging Het
Stpg3 T C 2: 25,213,854 T157A probably benign Het
Tmem39b A T 4: 129,686,922 M259K possibly damaging Het
Tomm40l A T 1: 171,221,902 probably null Het
Tsen34 G T 7: 3,695,396 G180W probably damaging Het
Ube2l6 C T 2: 84,806,373 R54W probably damaging Het
Vdac1 A T 11: 52,384,070 T182S probably benign Het
Wdr3 T C 3: 100,151,199 probably benign Het
Wsb1 T A 11: 79,248,585 Q95L probably benign Het
Other mutations in Limd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00953:Limd1 APN 9 123479883 missense probably benign 0.31
IGL00972:Limd1 APN 9 123480076 missense probably benign 0.06
IGL01815:Limd1 APN 9 123479736 missense probably benign 0.01
IGL02598:Limd1 APN 9 123516868 missense probably benign 0.11
IGL02598:Limd1 APN 9 123480171 missense probably benign
IGL02633:Limd1 APN 9 123479922 unclassified probably benign
IGL02999:Limd1 APN 9 123516799 missense probably damaging 1.00
R0314:Limd1 UTSW 9 123516827 missense probably benign 0.04
R2009:Limd1 UTSW 9 123479499 missense probably benign
R2299:Limd1 UTSW 9 123516877 nonsense probably null
R3791:Limd1 UTSW 9 123480374 missense possibly damaging 0.92
R4453:Limd1 UTSW 9 123480294 missense possibly damaging 0.52
R5979:Limd1 UTSW 9 123479414 missense possibly damaging 0.96
X0028:Limd1 UTSW 9 123516862 missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- TCTGACATCCTAGAAGACCACATGGC -3'
(R):5'- TCTTTACCCAGGAGGGAACGACAC -3'

Sequencing Primer
(F):5'- ACTCTCACATCCACTGAATCTGG -3'
(R):5'- TATGTAAGTGACAGTGTAGCCCC -3'
Posted On2014-04-24