Incidental Mutation 'R2248:Limch1'
ID 240942
Institutional Source Beutler Lab
Gene Symbol Limch1
Ensembl Gene ENSMUSG00000037736
Gene Name LIM and calponin homology domains 1
Synonyms 3732412D22Rik
MMRRC Submission 040248-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.121) question?
Stock # R2248 (G1)
Quality Score 217
Status Validated
Chromosome 5
Chromosomal Location 66903232-67214502 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 67201742 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glycine to Valine at position 838 (G838V)
Ref Sequence ENSEMBL: ENSMUSP00000113544 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038188] [ENSMUST00000101164] [ENSMUST00000117601] [ENSMUST00000118242] [ENSMUST00000153174]
AlphaFold Q3UH68
Predicted Effect probably damaging
Transcript: ENSMUST00000038188
AA Change: G841V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: G841V

DomainStartEndE-ValueType
low complexity region 41 57 N/A INTRINSIC
low complexity region 67 80 N/A INTRINSIC
low complexity region 129 140 N/A INTRINSIC
coiled coil region 192 241 N/A INTRINSIC
low complexity region 411 430 N/A INTRINSIC
coiled coil region 615 672 N/A INTRINSIC
low complexity region 679 691 N/A INTRINSIC
LIM 830 888 5.08e-7 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000101164
AA Change: G997V

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: G997V

DomainStartEndE-ValueType
CH 23 124 2.09e-13 SMART
low complexity region 197 213 N/A INTRINSIC
low complexity region 223 236 N/A INTRINSIC
low complexity region 285 296 N/A INTRINSIC
coiled coil region 348 397 N/A INTRINSIC
low complexity region 567 586 N/A INTRINSIC
coiled coil region 771 828 N/A INTRINSIC
low complexity region 835 847 N/A INTRINSIC
LIM 986 1044 5.08e-7 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000117601
AA Change: G838V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: G838V

DomainStartEndE-ValueType
CH 23 124 1e-15 SMART
low complexity region 197 213 N/A INTRINSIC
low complexity region 223 236 N/A INTRINSIC
low complexity region 285 296 N/A INTRINSIC
coiled coil region 348 397 N/A INTRINSIC
low complexity region 567 586 N/A INTRINSIC
coiled coil region 704 752 N/A INTRINSIC
low complexity region 759 771 N/A INTRINSIC
LIM 910 968 2.4e-9 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000118242
AA Change: G1008V

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: G1008V

DomainStartEndE-ValueType
CH 23 124 2.09e-13 SMART
low complexity region 197 213 N/A INTRINSIC
low complexity region 223 236 N/A INTRINSIC
low complexity region 285 296 N/A INTRINSIC
coiled coil region 336 385 N/A INTRINSIC
low complexity region 555 574 N/A INTRINSIC
coiled coil region 782 839 N/A INTRINSIC
low complexity region 846 858 N/A INTRINSIC
LIM 997 1055 5.08e-7 SMART
Predicted Effect unknown
Transcript: ENSMUST00000119854
AA Change: G713V
SMART Domains Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: G713V

DomainStartEndE-ValueType
CH 23 124 2.09e-13 SMART
low complexity region 197 213 N/A INTRINSIC
low complexity region 223 236 N/A INTRINSIC
Pfam:DUF4757 250 418 5.2e-66 PFAM
low complexity region 567 586 N/A INTRINSIC
coiled coil region 771 828 N/A INTRINSIC
low complexity region 835 847 N/A INTRINSIC
low complexity region 989 1003 N/A INTRINSIC
LIM 1012 1070 5.08e-7 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135334
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201322
Predicted Effect probably benign
Transcript: ENSMUST00000153174
SMART Domains Protein: ENSMUSP00000118979
Gene: ENSMUSG00000037736

DomainStartEndE-ValueType
Pfam:LIM 1 52 2e-9 PFAM
Meta Mutation Damage Score 0.6027 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 94.8%
Validation Efficiency 100% (67/67)
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca2 A G 2: 25,323,476 (GRCm39) probably benign Het
Afp A G 5: 90,649,429 (GRCm39) D332G probably damaging Het
AI593442 TGAGGAGGAGGAGGAGGA TGAGGAGGAGGAGGA 9: 52,589,114 (GRCm39) probably benign Het
Aldh1a2 A T 9: 71,123,144 (GRCm39) I6F possibly damaging Het
Alg6 C T 4: 99,626,444 (GRCm39) A84V probably damaging Het
Ank T A 15: 27,562,797 (GRCm39) probably null Het
Ano5 A T 7: 51,243,537 (GRCm39) M837L probably benign Het
Arl8b A G 6: 108,760,304 (GRCm39) Y30C probably benign Het
Bfsp1 A T 2: 143,669,572 (GRCm39) probably null Het
Cdhr1 C G 14: 36,803,334 (GRCm39) V581L probably benign Het
Chst8 G T 7: 34,447,597 (GRCm39) T7K probably damaging Het
Clca3b T C 3: 144,530,980 (GRCm39) K790R probably benign Het
Clta A G 4: 44,012,852 (GRCm39) N21D probably damaging Het
Col6a4 T G 9: 105,957,158 (GRCm39) E222A probably benign Het
Dcc G T 18: 71,959,239 (GRCm39) Q178K probably benign Het
Dpysl3 T C 18: 43,491,358 (GRCm39) D140G possibly damaging Het
Dthd1 A T 5: 63,007,243 (GRCm39) D648V probably damaging Het
Eva1c A G 16: 90,628,213 (GRCm39) N18S probably benign Het
Flnc A G 6: 29,451,400 (GRCm39) H1538R probably damaging Het
Foxn3 T C 12: 99,162,815 (GRCm39) E362G probably benign Het
Frk C A 10: 34,484,527 (GRCm39) T500K probably benign Het
Glipr1l1 A G 10: 111,898,192 (GRCm39) E99G probably benign Het
Gphn T C 12: 78,501,595 (GRCm39) L120P probably damaging Het
Gpr152 T C 19: 4,193,805 (GRCm39) S449P probably benign Het
Greb1 T A 12: 16,730,379 (GRCm39) I1655F possibly damaging Het
Hectd1 G T 12: 51,853,254 (GRCm39) T89N probably damaging Het
Helz2 A C 2: 180,875,226 (GRCm39) I1756S probably benign Het
Hydin G T 8: 111,304,835 (GRCm39) R3825L probably benign Het
Ifi207 G A 1: 173,564,036 (GRCm39) probably benign Het
Itpr3 A T 17: 27,334,033 (GRCm39) E2035V probably damaging Het
Khnyn T A 14: 56,124,195 (GRCm39) S150T probably benign Het
Kif21b T C 1: 136,100,704 (GRCm39) I1595T probably damaging Het
Lgsn A T 1: 31,242,607 (GRCm39) T230S possibly damaging Het
Lrp2 T A 2: 69,341,354 (GRCm39) D942V probably damaging Het
Lrrc31 T A 3: 30,744,050 (GRCm39) T153S possibly damaging Het
Mal2 T A 15: 54,451,732 (GRCm39) I51N probably damaging Het
Matcap2 A G 9: 22,355,410 (GRCm39) T482A probably benign Het
Mroh2a T C 1: 88,184,476 (GRCm39) V1453A probably benign Het
Mycbp2 T A 14: 103,407,295 (GRCm39) Q385L possibly damaging Het
Nav3 T A 10: 109,532,088 (GRCm39) D2117V probably damaging Het
Ntn1 T C 11: 68,168,398 (GRCm39) N353S possibly damaging Het
Oas1c T C 5: 120,940,926 (GRCm39) E289G possibly damaging Het
Or2m13 A G 16: 19,225,944 (GRCm39) V274A probably damaging Het
Or4a81 C A 2: 89,619,524 (GRCm39) M57I possibly damaging Het
Or5w17 T C 2: 87,584,287 (GRCm39) I17V probably null Het
Plk1 A G 7: 121,768,044 (GRCm39) probably benign Het
Pms2 G A 5: 143,853,324 (GRCm39) V230M probably damaging Het
Pole3 C A 4: 62,443,250 (GRCm39) probably benign Het
Ppp2r5c T C 12: 110,452,357 (GRCm39) F22S probably benign Het
Prp2rt C A 13: 97,235,406 (GRCm39) V114F possibly damaging Het
Ptcd3 A T 6: 71,871,269 (GRCm39) probably null Het
Ptprq A T 10: 107,478,931 (GRCm39) probably null Het
Rab18 T A 18: 6,788,629 (GRCm39) C199S probably damaging Het
Rbp3 C T 14: 33,677,975 (GRCm39) T641M probably damaging Het
Sacs A G 14: 61,450,251 (GRCm39) N4099S probably damaging Het
Sh3yl1 T A 12: 30,992,869 (GRCm39) probably null Het
Slco1c1 T A 6: 141,492,415 (GRCm39) I217N probably damaging Het
Syne2 C T 12: 76,143,678 (GRCm39) T6241I probably damaging Het
Tas2r119 T C 15: 32,178,297 (GRCm39) F288L possibly damaging Het
Tmod2 G T 9: 75,499,931 (GRCm39) T107N probably benign Het
Trappc6b T C 12: 59,097,167 (GRCm39) T52A probably damaging Het
Tsen54 A G 11: 115,706,232 (GRCm39) E122G probably damaging Het
Tspear A G 10: 77,709,103 (GRCm39) N443S probably damaging Het
Unc80 A G 1: 66,662,365 (GRCm39) probably benign Het
Virma T A 4: 11,518,927 (GRCm39) Y725N probably damaging Het
Vwa7 G A 17: 35,238,019 (GRCm39) D207N probably benign Het
Other mutations in Limch1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00583:Limch1 APN 5 67,111,022 (GRCm39) missense probably damaging 0.99
IGL00644:Limch1 APN 5 67,173,895 (GRCm39) missense probably benign 0.01
IGL00705:Limch1 APN 5 67,150,496 (GRCm39) nonsense probably null
IGL01154:Limch1 APN 5 66,903,301 (GRCm39) nonsense probably null 0.00
IGL01865:Limch1 APN 5 67,131,923 (GRCm39) nonsense probably null
IGL02529:Limch1 APN 5 67,159,956 (GRCm39) missense possibly damaging 0.89
IGL03171:Limch1 APN 5 67,191,537 (GRCm39) missense possibly damaging 0.80
IGL03308:Limch1 APN 5 67,159,901 (GRCm39) missense possibly damaging 0.92
IGL03396:Limch1 APN 5 67,111,016 (GRCm39) missense probably damaging 1.00
R0067:Limch1 UTSW 5 67,131,965 (GRCm39) missense probably damaging 0.99
R0067:Limch1 UTSW 5 67,131,965 (GRCm39) missense probably damaging 0.99
R0114:Limch1 UTSW 5 67,193,427 (GRCm39) intron probably benign
R0129:Limch1 UTSW 5 67,116,933 (GRCm39) missense probably damaging 0.96
R0193:Limch1 UTSW 5 67,184,882 (GRCm39) missense probably damaging 1.00
R0194:Limch1 UTSW 5 67,156,616 (GRCm39) missense probably benign 0.05
R0367:Limch1 UTSW 5 67,015,297 (GRCm39) critical splice donor site probably null
R0558:Limch1 UTSW 5 67,126,498 (GRCm39) missense probably damaging 1.00
R0927:Limch1 UTSW 5 67,154,576 (GRCm39) missense probably damaging 1.00
R1190:Limch1 UTSW 5 67,126,540 (GRCm39) missense probably damaging 1.00
R1316:Limch1 UTSW 5 67,156,586 (GRCm39) missense probably damaging 1.00
R1469:Limch1 UTSW 5 67,039,323 (GRCm39) splice site probably benign
R1647:Limch1 UTSW 5 67,156,599 (GRCm39) missense probably damaging 1.00
R1648:Limch1 UTSW 5 67,156,599 (GRCm39) missense probably damaging 1.00
R1944:Limch1 UTSW 5 67,156,442 (GRCm39) missense probably damaging 1.00
R2103:Limch1 UTSW 5 67,156,072 (GRCm39) missense probably benign 0.05
R2126:Limch1 UTSW 5 67,187,103 (GRCm39) missense probably damaging 1.00
R2415:Limch1 UTSW 5 67,131,977 (GRCm39) missense probably damaging 1.00
R3762:Limch1 UTSW 5 67,186,183 (GRCm39) missense probably damaging 1.00
R3797:Limch1 UTSW 5 67,126,422 (GRCm39) missense probably damaging 1.00
R4659:Limch1 UTSW 5 67,184,900 (GRCm39) missense probably damaging 1.00
R4773:Limch1 UTSW 5 67,184,850 (GRCm39) missense probably damaging 0.99
R4876:Limch1 UTSW 5 67,039,270 (GRCm39) missense possibly damaging 0.64
R5062:Limch1 UTSW 5 67,126,578 (GRCm39) missense probably damaging 1.00
R5191:Limch1 UTSW 5 67,184,904 (GRCm39) missense probably damaging 1.00
R5202:Limch1 UTSW 5 67,150,516 (GRCm39) missense probably damaging 1.00
R5335:Limch1 UTSW 5 67,039,300 (GRCm39) missense probably damaging 1.00
R5436:Limch1 UTSW 5 67,131,909 (GRCm39) missense possibly damaging 0.72
R5994:Limch1 UTSW 5 67,131,965 (GRCm39) missense probably damaging 1.00
R6049:Limch1 UTSW 5 67,188,203 (GRCm39) missense probably benign 0.32
R6228:Limch1 UTSW 5 67,173,845 (GRCm39) missense probably damaging 1.00
R6547:Limch1 UTSW 5 67,186,117 (GRCm39) missense probably damaging 1.00
R6600:Limch1 UTSW 5 66,903,281 (GRCm39) missense probably benign
R6888:Limch1 UTSW 5 67,179,269 (GRCm39) missense probably benign 0.21
R7111:Limch1 UTSW 5 67,182,519 (GRCm39) splice site probably null
R7132:Limch1 UTSW 5 67,111,028 (GRCm39) missense probably damaging 1.00
R7144:Limch1 UTSW 5 67,175,001 (GRCm39) missense probably benign 0.10
R7302:Limch1 UTSW 5 67,116,942 (GRCm39) missense probably benign 0.02
R7341:Limch1 UTSW 5 67,191,545 (GRCm39) missense probably benign 0.06
R7491:Limch1 UTSW 5 67,211,580 (GRCm39) missense probably damaging 0.99
R8079:Limch1 UTSW 5 67,204,096 (GRCm39) missense possibly damaging 0.73
R8229:Limch1 UTSW 5 67,186,138 (GRCm39) missense probably damaging 1.00
R8348:Limch1 UTSW 5 67,159,825 (GRCm39) missense probably damaging 0.98
R8395:Limch1 UTSW 5 67,126,394 (GRCm39) missense probably damaging 0.96
R8416:Limch1 UTSW 5 67,156,649 (GRCm39) missense probably benign
R8448:Limch1 UTSW 5 67,159,825 (GRCm39) missense probably damaging 0.98
R8477:Limch1 UTSW 5 67,131,908 (GRCm39) missense probably benign 0.01
R8924:Limch1 UTSW 5 67,190,475 (GRCm39) missense probably benign 0.01
R9080:Limch1 UTSW 5 67,174,992 (GRCm39) missense probably benign 0.00
R9619:Limch1 UTSW 5 67,015,284 (GRCm39) missense probably damaging 1.00
R9681:Limch1 UTSW 5 67,126,422 (GRCm39) missense probably damaging 1.00
R9715:Limch1 UTSW 5 67,156,360 (GRCm39) missense probably damaging 1.00
X0022:Limch1 UTSW 5 67,179,295 (GRCm39) missense probably benign 0.00
X0027:Limch1 UTSW 5 67,159,963 (GRCm39) missense probably damaging 1.00
Z1177:Limch1 UTSW 5 67,186,142 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCACTGTCAGTTCGATGGTTC -3'
(R):5'- GAGCTGCATCTTTAAAGCTGGAC -3'

Sequencing Primer
(F):5'- AGCCAAGGCTCTCATTTC -3'
(R):5'- GCATCTTTAAAGCTGGACTTGACC -3'
Posted On 2014-10-15