Incidental Mutation 'R0558:Limch1'
ID 45712
Institutional Source Beutler Lab
Gene Symbol Limch1
Ensembl Gene ENSMUSG00000037736
Gene Name LIM and calponin homology domains 1
Synonyms 3732412D22Rik
MMRRC Submission 038750-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.121) question?
Stock # R0558 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 66903232-67214502 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 67126498 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 42 (D42G)
Ref Sequence ENSEMBL: ENSMUSP00000123337 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038188] [ENSMUST00000101164] [ENSMUST00000117601] [ENSMUST00000118242] [ENSMUST00000122812] [ENSMUST00000127184] [ENSMUST00000132991]
AlphaFold Q3UH68
Predicted Effect probably damaging
Transcript: ENSMUST00000038188
AA Change: D33G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: D33G

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: D189G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: D189G

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: D30G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: D30G

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: D189G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: D189G

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 probably damaging
Transcript: ENSMUST00000119854
AA Change: D189G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: D189G

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: ENSMUST00000122812
Predicted Effect probably damaging
Transcript: ENSMUST00000127184
AA Change: D33G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000114681
Gene: ENSMUSG00000037736
AA Change: D33G

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 probably damaging
Transcript: ENSMUST00000132991
AA Change: D42G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000123337
Gene: ENSMUSG00000037736
AA Change: D42G

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140428
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201322
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201848
Predicted Effect noncoding transcript
Transcript: ENSMUST00000202048
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201852
Meta Mutation Damage Score 0.1195 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.7%
  • 20x: 93.8%
Validation Efficiency 100% (80/80)
Allele List at MGI
Other mutations in this stock
Total: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc2 G A 19: 43,789,163 (GRCm39) G273R probably benign Het
Adamts10 T C 17: 33,769,583 (GRCm39) V935A probably benign Het
Anapc15-ps T C 10: 95,508,983 (GRCm39) D90G probably damaging Het
Atic T A 1: 71,602,947 (GRCm39) V107E probably benign Het
Atp4b T C 8: 13,443,523 (GRCm39) T52A possibly damaging Het
Cacna1h C T 17: 25,600,524 (GRCm39) A1606T probably damaging Het
Cacng6 T A 7: 3,483,324 (GRCm39) Y217* probably null Het
Cc2d2a T G 5: 43,881,729 (GRCm39) probably benign Het
Cd226 T A 18: 89,225,338 (GRCm39) H78Q probably benign Het
Cers3 A G 7: 66,433,166 (GRCm39) D161G probably damaging Het
Ces1f T C 8: 94,002,017 (GRCm39) H37R probably benign Het
Cfhr4 A G 1: 139,667,230 (GRCm39) V376A probably damaging Het
Chek1 T A 9: 36,623,411 (GRCm39) N421I possibly damaging Het
Cibar1 T C 4: 12,164,095 (GRCm39) D248G probably damaging Het
Cma2 T C 14: 56,210,249 (GRCm39) Y45H probably damaging Het
Cmas C A 6: 142,720,970 (GRCm39) Y401* probably null Het
Cyp2j8 A T 4: 96,332,871 (GRCm39) S492T probably benign Het
Dnah12 T C 14: 26,430,465 (GRCm39) S358P probably benign Het
Dnajc13 T C 9: 104,079,151 (GRCm39) probably null Het
Ep400 A C 5: 110,832,933 (GRCm39) probably benign Het
Fam209 T A 2: 172,314,758 (GRCm39) N82K probably benign Het
G3bp2 A T 5: 92,221,056 (GRCm39) Y20N probably damaging Het
Gli2 T C 1: 118,765,379 (GRCm39) D924G probably benign Het
Gm10787 T C 10: 76,857,850 (GRCm39) noncoding transcript Het
Gm11568 A G 11: 99,748,872 (GRCm39) R26G unknown Het
Hivep3 T G 4: 119,953,763 (GRCm39) L693R probably damaging Het
Hook1 A G 4: 95,881,449 (GRCm39) probably benign Het
Ibtk A C 9: 85,619,591 (GRCm39) D116E probably damaging Het
Insrr C T 3: 87,718,288 (GRCm39) T927I possibly damaging Het
Irx1 T G 13: 72,107,747 (GRCm39) S312R probably benign Het
Itga11 T C 9: 62,659,570 (GRCm39) Y441H probably benign Het
Itsn1 A G 16: 91,696,511 (GRCm39) D38G possibly damaging Het
Kat6b G T 14: 21,719,489 (GRCm39) E1280D probably benign Het
Kcnk10 T A 12: 98,402,560 (GRCm39) Y293F possibly damaging Het
Krt74 T A 15: 101,669,398 (GRCm39) noncoding transcript Het
Lars1 T G 18: 42,347,902 (GRCm39) I974L probably benign Het
Mau2 G C 8: 70,495,082 (GRCm39) T85R probably damaging Het
Mkrn3 A G 7: 62,068,612 (GRCm39) I393T probably benign Het
Mpl A C 4: 118,301,217 (GRCm39) S541R probably damaging Het
Nfrkb T C 9: 31,321,564 (GRCm39) S754P possibly damaging Het
Or4c125 A G 2: 89,170,580 (GRCm39) L22P probably benign Het
Or5bw2 T C 7: 6,573,652 (GRCm39) Y221H possibly damaging Het
Or5d41 A G 2: 88,054,818 (GRCm39) V186A possibly damaging Het
Or8g18 T A 9: 39,149,496 (GRCm39) T75S probably damaging Het
P2rx7 A T 5: 122,811,861 (GRCm39) I391F possibly damaging Het
Pbrm1 T A 14: 30,807,016 (GRCm39) probably null Het
Pcdh8 T C 14: 80,007,516 (GRCm39) D349G probably damaging Het
Pias1 A G 9: 62,789,291 (GRCm39) S639P possibly damaging Het
Pkhd1l1 A T 15: 44,347,820 (GRCm39) I232F probably damaging Het
Plxnc1 C T 10: 94,673,797 (GRCm39) R995Q probably damaging Het
Pnliprp2 T A 19: 58,762,519 (GRCm39) S375T probably benign Het
Prkar1b C T 5: 139,005,847 (GRCm39) V313M probably benign Het
Prr35 T C 17: 26,166,523 (GRCm39) N338S probably benign Het
Ptpn13 T C 5: 103,677,583 (GRCm39) S734P probably damaging Het
Rdh1 T C 10: 127,595,810 (GRCm39) W2R possibly damaging Het
Rsph10b A T 5: 143,886,156 (GRCm39) I285L probably benign Het
Rubcnl T C 14: 75,284,987 (GRCm39) F502S probably damaging Het
Ryr2 T A 13: 11,653,329 (GRCm39) I3693F probably damaging Het
Ryr2 T C 13: 11,814,747 (GRCm39) Y675C probably damaging Het
Scaper T C 9: 55,593,207 (GRCm39) T477A probably benign Het
Scn2a G T 2: 65,542,269 (GRCm39) V791L probably benign Het
Sdk1 A T 5: 142,117,820 (GRCm39) T1573S probably damaging Het
Sema3c A T 5: 17,919,413 (GRCm39) H483L probably benign Het
Sema6c T C 3: 95,076,002 (GRCm39) S219P probably damaging Het
Slc10a5 T G 3: 10,400,177 (GRCm39) E161A probably damaging Het
Slc22a23 C T 13: 34,528,366 (GRCm39) G139S possibly damaging Het
Slc34a3 C T 2: 25,123,077 (GRCm39) probably benign Het
Slc38a9 A T 13: 112,865,730 (GRCm39) probably null Het
Taok1 A C 11: 77,450,670 (GRCm39) S367R possibly damaging Het
Tlr6 G A 5: 65,112,203 (GRCm39) Q235* probably null Het
Top2a A G 11: 98,887,665 (GRCm39) V1281A probably benign Het
Tpgs1 T C 10: 79,511,616 (GRCm39) Y253H probably damaging Het
Tubgcp3 T C 8: 12,703,462 (GRCm39) T288A probably benign Het
Ubr4 A G 4: 139,154,213 (GRCm39) E2140G probably benign Het
Uso1 A G 5: 92,321,878 (GRCm39) Q257R probably benign Het
Zfp106 A G 2: 120,362,677 (GRCm39) V48A probably damaging Het
Zfp174 T A 16: 3,666,118 (GRCm39) S128T possibly damaging Het
Zscan26 T A 13: 21,629,225 (GRCm39) D426V 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
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
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'- TTTCCACACAGATCCTCCATGCAAG -3'
(R):5'- TAGAATTACCAGGCTCCAGCCAGG -3'

Sequencing Primer
(F):5'- GATCCTCCATGCAAGTGTCTTTG -3'
(R):5'- GAGTTTGCCTTTCCAAGGAC -3'
Posted On 2013-06-11