Incidental Mutation 'IGL03308:Limch1'
ID416466
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Limch1
Ensembl Gene ENSMUSG00000037736
Gene NameLIM and calponin homology domains 1
Synonyms3732412D22Rik
Accession Numbers
Is this an essential gene? Probably non essential (E-score: 0.185) question?
Stock #IGL03308
Quality Score
Status
Chromosome5
Chromosomal Location66745827-67057158 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) C to T at 67002558 bp
ZygosityHeterozygous
Amino Acid Change Threonine to Methionine at position 443 (T443M)
Ref Sequence ENSEMBL: ENSMUSP00000043163 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038188] [ENSMUST00000101164] [ENSMUST00000117601] [ENSMUST00000118242] [ENSMUST00000127184] [ENSMUST00000132991]
Predicted Effect possibly damaging
Transcript: ENSMUST00000038188
AA Change: T443M

PolyPhen 2 Score 0.921 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: T443M

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 possibly damaging
Transcript: ENSMUST00000101164
AA Change: T599M

PolyPhen 2 Score 0.920 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: T599M

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: T440M

PolyPhen 2 Score 0.871 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: T440M

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 possibly damaging
Transcript: ENSMUST00000118242
AA Change: T587M

PolyPhen 2 Score 0.920 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: T587M

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: T315M
SMART Domains Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: T315M

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 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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137394
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140428
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147050
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201322
Coding Region Coverage
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aadacl3 T C 4: 144,456,251 I216V probably damaging Het
Abcc1 A G 16: 14,470,611 I1367V possibly damaging Het
Ap1g2 T A 14: 55,104,876 I175F probably benign Het
Atad2 A G 15: 58,102,523 V671A probably benign Het
Ccdc134 A G 15: 82,131,520 D67G probably damaging Het
Cdk17 G A 10: 93,221,644 probably null Het
Col3a1 A G 1: 45,330,617 probably benign Het
Col5a3 A G 9: 20,808,379 L228P unknown Het
Eef1a2 A G 2: 181,148,836 probably benign Het
Fars2 T G 13: 36,204,687 I53R possibly damaging Het
Frmd4a G T 2: 4,498,026 A98S possibly damaging Het
Gprin1 T A 13: 54,740,144 M106L probably benign Het
Hspb8 T C 5: 116,409,342 T194A possibly damaging Het
Ift27 A G 15: 78,166,015 S65P probably damaging Het
Inpp5d A C 1: 87,703,197 Y430S probably damaging Het
Kat6b T C 14: 21,624,834 S356P probably damaging Het
Mcf2l C T 8: 13,009,512 R708C probably damaging Het
Mlf1 T C 3: 67,397,807 W214R probably damaging Het
Naga A T 15: 82,335,887 L153Q probably damaging Het
Nbas A G 12: 13,324,348 Q559R possibly damaging Het
Olfr324 T C 11: 58,597,699 F101S probably damaging Het
Olfr720 T A 14: 14,175,161 H307L probably benign Het
Prex2 A G 1: 11,185,175 D1148G possibly damaging Het
Prss23 A C 7: 89,509,730 L377R probably benign Het
Ptprc G T 1: 138,126,320 T27K possibly damaging Het
Rnf213 A G 11: 119,474,172 T4553A probably benign Het
Scgb2b7 A T 7: 31,705,081 C65S probably damaging Het
Skint3 T C 4: 112,254,067 F130L probably damaging Het
Slc8a1 A G 17: 81,442,195 probably benign Het
Stau1 T C 2: 166,950,320 N433D probably damaging Het
Tapbpl G A 6: 125,228,179 A268V possibly damaging Het
Tmem131l T C 3: 83,940,902 I314V probably benign Het
Tmem44 A G 16: 30,543,748 W151R probably damaging Het
Tnnc1 T C 14: 31,209,841 probably benign Het
Traf5 T G 1: 191,997,500 N530T probably damaging Het
Ttn A G 2: 76,746,563 I24662T probably damaging Het
Vmn1r49 A T 6: 90,072,359 H220Q possibly damaging Het
Vmn2r106 A T 17: 20,278,523 C375* probably null Het
Vps26b T C 9: 27,029,500 Y41C probably damaging Het
Wdr64 T C 1: 175,766,996 probably benign Het
Xylt1 C T 7: 117,637,751 Q576* probably null Het
Zfp106 T C 2: 120,524,024 D1422G probably benign Het
Other mutations in Limch1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00583:Limch1 APN 5 66953679 missense probably damaging 0.99
IGL00644:Limch1 APN 5 67016552 missense probably benign 0.01
IGL00705:Limch1 APN 5 66993153 nonsense probably null
IGL01154:Limch1 APN 5 66745958 nonsense probably null 0.00
IGL01865:Limch1 APN 5 66974580 nonsense probably null
IGL02529:Limch1 APN 5 67002613 missense possibly damaging 0.89
IGL03171:Limch1 APN 5 67034194 missense possibly damaging 0.80
IGL03396:Limch1 APN 5 66953673 missense probably damaging 1.00
R0067:Limch1 UTSW 5 66974622 missense probably damaging 0.99
R0067:Limch1 UTSW 5 66974622 missense probably damaging 0.99
R0114:Limch1 UTSW 5 67036084 intron probably benign
R0129:Limch1 UTSW 5 66959590 missense probably damaging 0.96
R0193:Limch1 UTSW 5 67027539 missense probably damaging 1.00
R0194:Limch1 UTSW 5 66999273 missense probably benign 0.05
R0367:Limch1 UTSW 5 66857954 critical splice donor site probably null
R0558:Limch1 UTSW 5 66969155 missense probably damaging 1.00
R0927:Limch1 UTSW 5 66997233 missense probably damaging 1.00
R1190:Limch1 UTSW 5 66969197 missense probably damaging 1.00
R1316:Limch1 UTSW 5 66999243 missense probably damaging 1.00
R1469:Limch1 UTSW 5 66881980 splice site probably benign
R1647:Limch1 UTSW 5 66999256 missense probably damaging 1.00
R1648:Limch1 UTSW 5 66999256 missense probably damaging 1.00
R1944:Limch1 UTSW 5 66999099 missense probably damaging 1.00
R2103:Limch1 UTSW 5 66998729 missense probably benign 0.05
R2126:Limch1 UTSW 5 67029760 missense probably damaging 1.00
R2248:Limch1 UTSW 5 67044399 missense probably damaging 1.00
R2415:Limch1 UTSW 5 66974634 missense probably damaging 1.00
R3762:Limch1 UTSW 5 67028840 missense probably damaging 1.00
R3797:Limch1 UTSW 5 66969079 missense probably damaging 1.00
R4659:Limch1 UTSW 5 67027557 missense probably damaging 1.00
R4773:Limch1 UTSW 5 67027507 missense probably damaging 0.99
R4876:Limch1 UTSW 5 66881927 missense possibly damaging 0.64
R5062:Limch1 UTSW 5 66969235 missense probably damaging 1.00
R5191:Limch1 UTSW 5 67027561 missense probably damaging 1.00
R5202:Limch1 UTSW 5 66993173 missense probably damaging 1.00
R5335:Limch1 UTSW 5 66881957 missense probably damaging 1.00
R5436:Limch1 UTSW 5 66974566 missense possibly damaging 0.72
R5994:Limch1 UTSW 5 66974622 missense probably damaging 1.00
R6049:Limch1 UTSW 5 67030860 missense probably benign 0.32
R6228:Limch1 UTSW 5 67016502 missense probably damaging 1.00
R6547:Limch1 UTSW 5 67028774 missense probably damaging 1.00
R6600:Limch1 UTSW 5 66745938 missense probably benign
R6888:Limch1 UTSW 5 67021926 missense probably benign 0.21
R7111:Limch1 UTSW 5 67025176 intron probably null
R7132:Limch1 UTSW 5 66953685 missense probably damaging 1.00
R7144:Limch1 UTSW 5 67017658 missense probably benign 0.10
R7302:Limch1 UTSW 5 66959599 missense probably benign 0.02
R7341:Limch1 UTSW 5 67034202 missense probably benign 0.06
R7491:Limch1 UTSW 5 67054237 missense probably damaging 0.99
X0022:Limch1 UTSW 5 67021952 missense probably benign 0.00
X0027:Limch1 UTSW 5 67002620 missense probably damaging 1.00
Posted On2016-08-02