Incidental Mutation 'R5994:Limch1'
ID 480991
Institutional Source Beutler Lab
Gene Symbol Limch1
Ensembl Gene ENSMUSG00000037736
Gene Name LIM and calponin homology domains 1
Synonyms 3732412D22Rik
MMRRC Submission 044173-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.175) question?
Stock # R5994 (G1)
Quality Score 190.009
Status Not validated
Chromosome 5
Chromosomal Location 66745827-67057158 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to T at 66974622 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Serine to Cysteine at position 152 (S152C)
Ref Sequence ENSEMBL: ENSMUSP00000123337 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038188] [ENSMUST00000101164] [ENSMUST00000117601] [ENSMUST00000118242] [ENSMUST00000127184] [ENSMUST00000132991]
AlphaFold Q3UH68
Predicted Effect probably damaging
Transcript: ENSMUST00000038188
AA Change: S143C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000043163
Gene: ENSMUSG00000037736
AA Change: S143C

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: S299C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000098723
Gene: ENSMUSG00000037736
AA Change: S299C

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: S140C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000113544
Gene: ENSMUSG00000037736
AA Change: S140C

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: S299C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000112732
Gene: ENSMUSG00000037736
AA Change: S299C

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: S27C
SMART Domains Protein: ENSMUSP00000112651
Gene: ENSMUSG00000037736
AA Change: S27C

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 damaging
Transcript: ENSMUST00000127184
AA Change: S143C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000114681
Gene: ENSMUSG00000037736
AA Change: S143C

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: S152C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000123337
Gene: ENSMUSG00000037736
AA Change: S152C

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: ENSMUST00000147050
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201322
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201848
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201852
Predicted Effect noncoding transcript
Transcript: ENSMUST00000202048
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.4%
  • 20x: 91.7%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2m A T 6: 121,670,903 (GRCm38) H1118L probably benign Het
Abca8b A G 11: 109,949,766 (GRCm38) probably null Het
Abcb5 A T 12: 118,965,260 (GRCm38) probably null Het
Adcy6 A T 15: 98,593,664 (GRCm38) I1016N probably damaging Het
Afg3l2 A T 18: 67,429,070 (GRCm38) C312S probably damaging Het
Ano8 C T 8: 71,484,834 (GRCm38) V89M probably damaging Het
Arhgap21 C T 2: 20,881,376 (GRCm38) G330D possibly damaging Het
Caskin1 T C 17: 24,496,961 (GRCm38) L195P probably damaging Het
Cfap54 A G 10: 93,039,081 (GRCm38) I514T probably damaging Het
Ctdsp2 G A 10: 126,995,820 (GRCm38) probably benign Het
Cyp4x1 T C 4: 115,121,945 (GRCm38) I152V probably benign Het
Dglucy G A 12: 100,842,700 (GRCm38) R219Q probably benign Het
Disp3 G T 4: 148,254,284 (GRCm38) A810E possibly damaging Het
Dtx4 T C 19: 12,501,153 (GRCm38) Y22C probably damaging Het
Edaradd A T 13: 12,478,496 (GRCm38) I105N probably damaging Het
Eepd1 C T 9: 25,603,453 (GRCm38) P519S probably damaging Het
Fscn3 A T 6: 28,430,295 (GRCm38) S155C probably benign Het
Gm10134 A T 2: 28,506,246 (GRCm38) E51V probably damaging Het
Gm7247 C T 14: 51,364,348 (GRCm38) S26F probably benign Het
Golga7 T C 8: 23,250,265 (GRCm38) E83G probably benign Het
Gpr12 T C 5: 146,583,431 (GRCm38) H227R probably damaging Het
Hoxa2 T G 6: 52,164,392 (GRCm38) S85R possibly damaging Het
Hrnr T C 3: 93,332,300 (GRCm38) S3282P unknown Het
Ift74 C A 4: 94,691,724 (GRCm38) T543K possibly damaging Het
Klf10 C A 15: 38,296,041 (GRCm38) R420L probably damaging Het
Krt77 T A 15: 101,862,855 (GRCm38) I338F probably damaging Het
Mgat4e T A 1: 134,541,496 (GRCm38) H270L probably benign Het
Myrf A T 19: 10,219,117 (GRCm38) L504Q probably null Het
Nckipsd A G 9: 108,813,977 (GRCm38) Q366R probably benign Het
Npy5r A T 8: 66,682,099 (GRCm38) V14D probably benign Het
Nrap T A 19: 56,351,599 (GRCm38) R830* probably null Het
Ogfrl1 A T 1: 23,378,989 (GRCm38) Y103N probably damaging Het
Olfr978 A T 9: 39,994,223 (GRCm38) R138* probably null Het
P2rx4 T A 5: 122,725,079 (GRCm38) L232H probably damaging Het
Pabpc2 A T 18: 39,773,894 (GRCm38) T71S probably benign Het
Paip2b C A 6: 83,808,885 (GRCm38) S121I probably damaging Het
Pofut1 C T 2: 153,261,229 (GRCm38) T261I possibly damaging Het
Ppp6c G T 2: 39,210,992 (GRCm38) T46K possibly damaging Het
Prkd2 C A 7: 16,850,336 (GRCm38) H371Q probably benign Het
Prrc2c A T 1: 162,674,156 (GRCm38) probably null Het
Psd3 C T 8: 67,719,968 (GRCm38) A894T probably damaging Het
Pygm A T 19: 6,398,043 (GRCm38) probably null Het
Pzp A T 6: 128,491,597 (GRCm38) M989K probably damaging Het
Ralgapa2 A T 2: 146,361,453 (GRCm38) S1159T probably benign Het
Rapgefl1 T C 11: 98,850,160 (GRCm38) F575L probably benign Het
Rassf6 A G 5: 90,617,768 (GRCm38) L28S probably damaging Het
Rbp3 G T 14: 33,954,900 (GRCm38) K268N probably damaging Het
Rela C T 19: 5,647,064 (GRCm38) T433M possibly damaging Het
Rnf103 T A 6: 71,496,910 (GRCm38) S102R probably damaging Het
Scarf2 A G 16: 17,806,379 (GRCm38) N516S probably damaging Het
Sdcbp2 T C 2: 151,587,483 (GRCm38) I241T probably damaging Het
Sept7 T C 9: 25,288,198 (GRCm38) I131T possibly damaging Het
Sh3pxd2b T C 11: 32,407,570 (GRCm38) F191L probably damaging Het
Siglec15 C A 18: 78,047,375 (GRCm38) C236F probably damaging Het
Slc11a2 T C 15: 100,397,681 (GRCm38) T520A probably benign Het
Slc26a11 C A 11: 119,379,912 (GRCm38) F553L probably benign Het
Smchd1 G A 17: 71,365,409 (GRCm38) P1596S possibly damaging Het
Taar7b A G 10: 24,000,348 (GRCm38) H137R probably damaging Het
Thap12 T A 7: 98,716,030 (GRCm38) C468* probably null Het
Timp4 C T 6: 115,247,354 (GRCm38) G118D probably damaging Het
Tnnt3 A G 7: 142,511,266 (GRCm38) K48E probably damaging Het
Trmt10a T A 3: 138,156,714 (GRCm38) I255N probably damaging Het
Ttll10 T C 4: 156,048,732 (GRCm38) probably null Het
Ube4b A G 4: 149,372,932 (GRCm38) Y283H probably damaging Het
Ucp1 G T 8: 83,293,938 (GRCm38) V126L possibly damaging Het
Unc13b T A 4: 43,172,596 (GRCm38) probably benign Het
Vps13b T C 15: 35,875,772 (GRCm38) S2768P probably damaging Het
Zcchc6 T G 13: 59,789,209 (GRCm38) Y806S probably damaging Het
Zfp101 T A 17: 33,380,962 (GRCm38) M607L probably benign Het
Zfp292 C T 4: 34,805,464 (GRCm38) V2527M possibly damaging Het
Zfp503 T A 14: 21,985,562 (GRCm38) T429S possibly damaging Het
Other mutations in Limch1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00583:Limch1 APN 5 66,953,679 (GRCm38) missense probably damaging 0.99
IGL00644:Limch1 APN 5 67,016,552 (GRCm38) missense probably benign 0.01
IGL00705:Limch1 APN 5 66,993,153 (GRCm38) nonsense probably null
IGL01154:Limch1 APN 5 66,745,958 (GRCm38) nonsense probably null 0.00
IGL01865:Limch1 APN 5 66,974,580 (GRCm38) nonsense probably null
IGL02529:Limch1 APN 5 67,002,613 (GRCm38) missense possibly damaging 0.89
IGL03171:Limch1 APN 5 67,034,194 (GRCm38) missense possibly damaging 0.80
IGL03308:Limch1 APN 5 67,002,558 (GRCm38) missense possibly damaging 0.92
IGL03396:Limch1 APN 5 66,953,673 (GRCm38) missense probably damaging 1.00
R0067:Limch1 UTSW 5 66,974,622 (GRCm38) missense probably damaging 0.99
R0067:Limch1 UTSW 5 66,974,622 (GRCm38) missense probably damaging 0.99
R0114:Limch1 UTSW 5 67,036,084 (GRCm38) intron probably benign
R0129:Limch1 UTSW 5 66,959,590 (GRCm38) missense probably damaging 0.96
R0193:Limch1 UTSW 5 67,027,539 (GRCm38) missense probably damaging 1.00
R0194:Limch1 UTSW 5 66,999,273 (GRCm38) missense probably benign 0.05
R0367:Limch1 UTSW 5 66,857,954 (GRCm38) critical splice donor site probably null
R0558:Limch1 UTSW 5 66,969,155 (GRCm38) missense probably damaging 1.00
R0927:Limch1 UTSW 5 66,997,233 (GRCm38) missense probably damaging 1.00
R1190:Limch1 UTSW 5 66,969,197 (GRCm38) missense probably damaging 1.00
R1316:Limch1 UTSW 5 66,999,243 (GRCm38) missense probably damaging 1.00
R1469:Limch1 UTSW 5 66,881,980 (GRCm38) splice site probably benign
R1647:Limch1 UTSW 5 66,999,256 (GRCm38) missense probably damaging 1.00
R1648:Limch1 UTSW 5 66,999,256 (GRCm38) missense probably damaging 1.00
R1944:Limch1 UTSW 5 66,999,099 (GRCm38) missense probably damaging 1.00
R2103:Limch1 UTSW 5 66,998,729 (GRCm38) missense probably benign 0.05
R2126:Limch1 UTSW 5 67,029,760 (GRCm38) missense probably damaging 1.00
R2248:Limch1 UTSW 5 67,044,399 (GRCm38) missense probably damaging 1.00
R2415:Limch1 UTSW 5 66,974,634 (GRCm38) missense probably damaging 1.00
R3762:Limch1 UTSW 5 67,028,840 (GRCm38) missense probably damaging 1.00
R3797:Limch1 UTSW 5 66,969,079 (GRCm38) missense probably damaging 1.00
R4659:Limch1 UTSW 5 67,027,557 (GRCm38) missense probably damaging 1.00
R4773:Limch1 UTSW 5 67,027,507 (GRCm38) missense probably damaging 0.99
R4876:Limch1 UTSW 5 66,881,927 (GRCm38) missense possibly damaging 0.64
R5062:Limch1 UTSW 5 66,969,235 (GRCm38) missense probably damaging 1.00
R5191:Limch1 UTSW 5 67,027,561 (GRCm38) missense probably damaging 1.00
R5202:Limch1 UTSW 5 66,993,173 (GRCm38) missense probably damaging 1.00
R5335:Limch1 UTSW 5 66,881,957 (GRCm38) missense probably damaging 1.00
R5436:Limch1 UTSW 5 66,974,566 (GRCm38) missense possibly damaging 0.72
R6049:Limch1 UTSW 5 67,030,860 (GRCm38) missense probably benign 0.32
R6228:Limch1 UTSW 5 67,016,502 (GRCm38) missense probably damaging 1.00
R6547:Limch1 UTSW 5 67,028,774 (GRCm38) missense probably damaging 1.00
R6600:Limch1 UTSW 5 66,745,938 (GRCm38) missense probably benign
R6888:Limch1 UTSW 5 67,021,926 (GRCm38) missense probably benign 0.21
R7111:Limch1 UTSW 5 67,025,176 (GRCm38) splice site probably null
R7132:Limch1 UTSW 5 66,953,685 (GRCm38) missense probably damaging 1.00
R7144:Limch1 UTSW 5 67,017,658 (GRCm38) missense probably benign 0.10
R7302:Limch1 UTSW 5 66,959,599 (GRCm38) missense probably benign 0.02
R7341:Limch1 UTSW 5 67,034,202 (GRCm38) missense probably benign 0.06
R7491:Limch1 UTSW 5 67,054,237 (GRCm38) missense probably damaging 0.99
R8079:Limch1 UTSW 5 67,046,753 (GRCm38) missense possibly damaging 0.73
R8229:Limch1 UTSW 5 67,028,795 (GRCm38) missense probably damaging 1.00
R8348:Limch1 UTSW 5 67,002,482 (GRCm38) missense probably damaging 0.98
R8395:Limch1 UTSW 5 66,969,051 (GRCm38) missense probably damaging 0.96
R8416:Limch1 UTSW 5 66,999,306 (GRCm38) missense probably benign
R8448:Limch1 UTSW 5 67,002,482 (GRCm38) missense probably damaging 0.98
R8477:Limch1 UTSW 5 66,974,565 (GRCm38) missense probably benign 0.01
R8924:Limch1 UTSW 5 67,033,132 (GRCm38) missense probably benign 0.01
R9080:Limch1 UTSW 5 67,017,649 (GRCm38) missense probably benign 0.00
R9619:Limch1 UTSW 5 66,857,941 (GRCm38) missense probably damaging 1.00
R9681:Limch1 UTSW 5 66,969,079 (GRCm38) missense probably damaging 1.00
R9715:Limch1 UTSW 5 66,999,017 (GRCm38) missense probably damaging 1.00
X0022:Limch1 UTSW 5 67,021,952 (GRCm38) missense probably benign 0.00
X0027:Limch1 UTSW 5 67,002,620 (GRCm38) missense probably damaging 1.00
Z1177:Limch1 UTSW 5 67,028,799 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCGGAAGTTGCCAGATGTGAAG -3'
(R):5'- CATGGTCAACAGAACTGGCC -3'

Sequencing Primer
(F):5'- TGTGAAGAAAGATGATATGTCCGCAC -3'
(R):5'- GCTCCTCAGCAAAGTATATGTTG -3'
Posted On 2017-06-26