Incidental Mutation 'R1648:Limch1'
ID 174010
Institutional Source Beutler Lab
Gene Symbol Limch1
Ensembl Gene ENSMUSG00000037736
Gene Name LIM and calponin homology domains 1
Synonyms 3732412D22Rik
MMRRC Submission 039684-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.121) question?
Stock # R1648 (G1)
Quality Score 201
Status Validated
Chromosome 5
Chromosomal Location 66903232-67214502 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 67156599 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 511 (S511R)
Ref Sequence ENSEMBL: ENSMUSP00000098723 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038188] [ENSMUST00000101164] [ENSMUST00000117601] [ENSMUST00000118242] [ENSMUST00000127184] [ENSMUST00000132991]
AlphaFold Q3UH68
Predicted Effect possibly damaging
Transcript: ENSMUST00000038188
AA Change: S355R

PolyPhen 2 Score 0.860 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: S355R

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: S511R

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: S511R

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 possibly damaging
Transcript: ENSMUST00000117601
AA Change: S352R

PolyPhen 2 Score 0.781 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: S352R

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: S499R

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: S499R

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: S227R
SMART Domains Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: S227R

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 probably benign
Transcript: ENSMUST00000127184
SMART Domains Protein: ENSMUSP00000114681
Gene: ENSMUSG00000037736

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 180 229 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137394
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140428
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201322
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147050
Predicted Effect probably benign
Transcript: ENSMUST00000132991
SMART Domains Protein: ENSMUSP00000123337
Gene: ENSMUSG00000037736

DomainStartEndE-ValueType
low complexity region 50 66 N/A INTRINSIC
low complexity region 76 89 N/A INTRINSIC
Pfam:DUF4757 103 269 2.6e-63 PFAM
Meta Mutation Damage Score 0.0795 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 95.9%
  • 20x: 91.4%
Validation Efficiency 95% (73/77)
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik A G 3: 137,775,181 (GRCm39) N1457D probably benign Het
Adgb A G 10: 10,271,115 (GRCm39) F817L probably damaging Het
Akap6 A T 12: 53,188,789 (GRCm39) K2068* probably null Het
Alms1 T C 6: 85,655,384 (GRCm39) L3310P probably damaging Het
Ankrd27 T A 7: 35,303,278 (GRCm39) D219E probably benign Het
Atp10a T C 7: 58,434,575 (GRCm39) V283A probably damaging Het
Atp11a C T 8: 12,897,495 (GRCm39) S270L probably damaging Het
Casp3 T C 8: 47,091,109 (GRCm39) S254P probably benign Het
Cep104 G A 4: 154,063,553 (GRCm39) probably null Het
Cep170b C T 12: 112,702,806 (GRCm39) T423I probably damaging Het
Cfap58 A G 19: 47,943,844 (GRCm39) E348G probably benign Het
Chd6 A G 2: 160,883,978 (GRCm39) L89S probably damaging Het
Cyp2a22 T C 7: 26,631,793 (GRCm39) S488G probably damaging Het
D130040H23Rik C A 8: 69,755,633 (GRCm39) H363Q probably benign Het
Dcaf7 T A 11: 105,942,628 (GRCm39) F192I probably damaging Het
Ddx20 T C 3: 105,586,504 (GRCm39) I614V probably benign Het
Ehbp1 G A 11: 22,046,000 (GRCm39) T558I probably damaging Het
Eif2ak3 T A 6: 70,860,615 (GRCm39) V397D possibly damaging Het
Eif2b5 T C 16: 20,321,335 (GRCm39) V296A possibly damaging Het
Esr1 A G 10: 4,951,260 (GRCm39) E546G possibly damaging Het
Fras1 T A 5: 96,874,472 (GRCm39) probably null Het
G930045G22Rik T C 6: 50,823,698 (GRCm39) noncoding transcript Het
Gemin5 A T 11: 58,038,805 (GRCm39) L568* probably null Het
Gm22697+Rbm27 AGGTCCAGGCCCAGGCCCTGGTCCTGGCCCTGGCCCTGGTCCCGGCCCAGGCCC AGGTCCCGGCCCAGGCCC 18: 42,434,948 (GRCm39) probably benign Het
Gpr155 T C 2: 73,194,508 (GRCm39) probably null Het
Has1 A G 17: 18,070,247 (GRCm39) Y225H probably damaging Het
Hk3 A G 13: 55,162,274 (GRCm39) F110S probably damaging Het
Iars1 A G 13: 49,876,478 (GRCm39) K848E possibly damaging Het
Kif17 A G 4: 137,997,206 (GRCm39) Y43C probably damaging Het
Kif20b A T 19: 34,914,190 (GRCm39) T355S possibly damaging Het
Kif21a T C 15: 90,878,570 (GRCm39) T237A probably damaging Het
Klc1 T C 12: 111,743,321 (GRCm39) L216P probably damaging Het
Krt7 A C 15: 101,310,448 (GRCm39) S32R probably damaging Het
Lama3 A G 18: 12,665,256 (GRCm39) D2330G possibly damaging Het
Luzp2 T A 7: 54,914,018 (GRCm39) probably null Het
Macc1 T C 12: 119,410,156 (GRCm39) M308T probably benign Het
Mroh9 T G 1: 162,873,625 (GRCm39) E510A probably damaging Het
Myo1h G T 5: 114,474,336 (GRCm39) L458F probably damaging Het
Neto1 A T 18: 86,518,179 (GRCm39) Y528F probably damaging Het
Nlrp9b T A 7: 19,760,469 (GRCm39) C187S possibly damaging Het
Nup160 T C 2: 90,540,432 (GRCm39) Y854H probably damaging Het
Odc1 T C 12: 17,598,538 (GRCm39) probably benign Het
Or10a3n A G 7: 108,492,972 (GRCm39) I214T probably damaging Het
Or51a10 A G 7: 103,699,376 (GRCm39) Y62H probably damaging Het
Or5an10 T A 19: 12,276,023 (GRCm39) I158L probably benign Het
Plcb2 A T 2: 118,554,261 (GRCm39) M64K possibly damaging Het
Plcxd3 A T 15: 4,405,291 (GRCm39) I33F probably benign Het
Postn A G 3: 54,283,522 (GRCm39) T534A probably damaging Het
Prkd2 T A 7: 16,591,732 (GRCm39) F588I possibly damaging Het
Prrg4 C A 2: 104,663,088 (GRCm39) A173S probably benign Het
Rinl C T 7: 28,497,057 (GRCm39) A519V probably damaging Het
Rpgrip1l A C 8: 91,979,517 (GRCm39) V975G probably damaging Het
Rps6ka4 C A 19: 6,816,730 (GRCm39) V118L probably benign Het
Rtkn T C 6: 83,112,975 (GRCm39) S16P probably damaging Het
Sbspon C A 1: 15,953,983 (GRCm39) R99L probably damaging Het
Sdf4 G A 4: 156,083,886 (GRCm39) A119T probably damaging Het
Sgpp1 T A 12: 75,762,990 (GRCm39) H397L possibly damaging Het
Shc2 T A 10: 79,461,945 (GRCm39) M367L probably benign Het
Slc26a5 T A 5: 22,018,974 (GRCm39) K590* probably null Het
Slc39a12 T C 2: 14,456,803 (GRCm39) V597A probably benign Het
Smcp A T 3: 92,491,788 (GRCm39) C20S unknown Het
Tdrd6 A C 17: 43,938,000 (GRCm39) V1016G possibly damaging Het
Tmem132c T A 5: 127,540,120 (GRCm39) probably benign Het
Tmem170b A T 13: 41,759,738 (GRCm39) Q16L probably null Het
Tmem30a A G 9: 79,700,311 (GRCm39) F61S probably damaging Het
Tnfsf13b T C 8: 10,081,534 (GRCm39) M232T probably damaging Het
Trip11 T A 12: 101,850,651 (GRCm39) K853* probably null Het
Tusc3 C A 8: 39,513,721 (GRCm39) S64* probably null Het
Vmn2r111 A T 17: 22,788,042 (GRCm39) D436E probably benign Het
Zfp607a T C 7: 27,578,493 (GRCm39) V521A probably benign Het
Zfp704 A T 3: 9,536,099 (GRCm39) S140R probably damaging 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
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
R2248:Limch1 UTSW 5 67,201,742 (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'- GCAGTACATCGAGAGGTTCACCATC -3'
(R):5'- ACAAGCTACCCACAATTCGGTTTCC -3'

Sequencing Primer
(F):5'- AGGTTCACCATCAGTGAGGC -3'
(R):5'- tcctcctcctcctcctcc -3'
Posted On 2014-04-24