Incidental Mutation 'R5843:Lrch3'
ID 450562
Institutional Source Beutler Lab
Gene Symbol Lrch3
Ensembl Gene ENSMUSG00000022801
Gene Name leucine-rich repeats and calponin homology (CH) domain containing 3
Synonyms LOC385628, 2210409B11Rik
MMRRC Submission 043224-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.115) question?
Stock # R5843 (G1)
Quality Score 225
Status Not validated
Chromosome 16
Chromosomal Location 32734470-32836017 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 32818896 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 629 (V629A)
Ref Sequence ENSEMBL: ENSMUSP00000126964 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023491] [ENSMUST00000135193] [ENSMUST00000165616] [ENSMUST00000165826] [ENSMUST00000170201] [ENSMUST00000170899]
AlphaFold Q8BVU0
Predicted Effect probably damaging
Transcript: ENSMUST00000023491
AA Change: V665A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000023491
Gene: ENSMUSG00000022801
AA Change: V665A

DomainStartEndE-ValueType
low complexity region 2 13 N/A INTRINSIC
low complexity region 31 44 N/A INTRINSIC
LRR 104 126 2.54e1 SMART
LRR 127 150 2.86e-1 SMART
LRR 172 194 4.44e0 SMART
LRR 195 218 4.33e1 SMART
LRR 240 263 2.76e1 SMART
low complexity region 482 493 N/A INTRINSIC
low complexity region 539 554 N/A INTRINSIC
CH 651 754 9.24e-15 SMART
low complexity region 759 774 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000093713
Predicted Effect noncoding transcript
Transcript: ENSMUST00000105610
Predicted Effect probably damaging
Transcript: ENSMUST00000135193
AA Change: V665A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000130708
Gene: ENSMUSG00000022801
AA Change: V665A

DomainStartEndE-ValueType
low complexity region 2 13 N/A INTRINSIC
low complexity region 31 44 N/A INTRINSIC
LRR 104 126 2.54e1 SMART
LRR 127 150 2.86e-1 SMART
LRR 172 194 4.44e0 SMART
LRR 195 218 4.33e1 SMART
LRR 240 263 2.76e1 SMART
low complexity region 482 493 N/A INTRINSIC
low complexity region 539 554 N/A INTRINSIC
CH 651 755 6.79e-13 SMART
transmembrane domain 771 793 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000142290
AA Change: V218A
SMART Domains Protein: ENSMUSP00000117302
Gene: ENSMUSG00000022801
AA Change: V218A

DomainStartEndE-ValueType
low complexity region 31 42 N/A INTRINSIC
low complexity region 88 103 N/A INTRINSIC
SCOP:d1h67a_ 201 253 1e-11 SMART
Blast:CH 205 253 6e-27 BLAST
Predicted Effect unknown
Transcript: ENSMUST00000163428
AA Change: V247A
SMART Domains Protein: ENSMUSP00000133034
Gene: ENSMUSG00000022801
AA Change: V247A

DomainStartEndE-ValueType
low complexity region 122 137 N/A INTRINSIC
SCOP:d1h67a_ 230 265 9e-5 SMART
Blast:CH 234 265 7e-14 BLAST
Predicted Effect probably damaging
Transcript: ENSMUST00000165616
AA Change: V511A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000130009
Gene: ENSMUSG00000022801
AA Change: V511A

DomainStartEndE-ValueType
low complexity region 2 13 N/A INTRINSIC
low complexity region 31 44 N/A INTRINSIC
Blast:LRR 89 113 1e-6 BLAST
Blast:LRR 114 137 3e-7 BLAST
low complexity region 328 339 N/A INTRINSIC
low complexity region 385 400 N/A INTRINSIC
CH 497 600 9.24e-15 SMART
low complexity region 605 620 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000165826
SMART Domains Protein: ENSMUSP00000126308
Gene: ENSMUSG00000022801

DomainStartEndE-ValueType
low complexity region 105 116 N/A INTRINSIC
low complexity region 162 177 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000170201
AA Change: V629A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000126964
Gene: ENSMUSG00000022801
AA Change: V629A

DomainStartEndE-ValueType
low complexity region 2 13 N/A INTRINSIC
low complexity region 31 44 N/A INTRINSIC
LRR 104 126 2.54e1 SMART
LRR 127 150 2.86e-1 SMART
LRR 172 194 4.44e0 SMART
LRR 195 218 4.33e1 SMART
LRR 240 263 2.76e1 SMART
low complexity region 482 493 N/A INTRINSIC
low complexity region 539 554 N/A INTRINSIC
CH 615 718 9.24e-15 SMART
low complexity region 723 738 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000170899
AA Change: V579A

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000127547
Gene: ENSMUSG00000022801
AA Change: V579A

DomainStartEndE-ValueType
low complexity region 2 13 N/A INTRINSIC
low complexity region 31 44 N/A INTRINSIC
LRR 104 126 2.54e1 SMART
LRR 127 150 2.86e-1 SMART
LRR 172 194 4.44e0 SMART
LRR 195 218 4.33e1 SMART
LRR 240 263 2.76e1 SMART
low complexity region 489 504 N/A INTRINSIC
CH 565 668 9.24e-15 SMART
low complexity region 673 688 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.7%
  • 20x: 96.5%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agap1 A G 1: 89,537,272 (GRCm39) T93A probably damaging Het
Atp6v1h T A 1: 5,232,312 (GRCm39) probably null Het
Ccnk T C 12: 108,159,989 (GRCm39) V157A probably damaging Het
Cdh10 T C 15: 18,985,286 (GRCm39) F317L possibly damaging Het
Chn1 A G 2: 73,510,092 (GRCm39) I139T probably benign Het
Creld2 A T 15: 88,710,632 (GRCm39) D349V probably damaging Het
Dnah3 TTCCTC TTC 7: 119,550,244 (GRCm39) probably benign Het
Eml2 G A 7: 18,935,088 (GRCm39) V432I probably damaging Het
Frem1 T C 4: 82,854,289 (GRCm39) D1660G probably damaging Het
Hipk3 A C 2: 104,270,569 (GRCm39) S470R possibly damaging Het
Hook2 T A 8: 85,717,912 (GRCm39) I37K probably damaging Het
Hpcal1 T C 12: 17,841,200 (GRCm39) F193L probably benign Het
Hps4 T C 5: 112,497,296 (GRCm39) probably null Het
Iqgap1 T C 7: 80,375,828 (GRCm39) N1349S probably benign Het
Khk A G 5: 31,079,275 (GRCm39) I6V possibly damaging Het
Kmt2d G A 15: 98,749,990 (GRCm39) probably benign Het
Mtpn C T 6: 35,489,225 (GRCm39) D100N probably benign Het
Muc13 A G 16: 33,626,421 (GRCm39) Y320C probably damaging Het
Or2aj4 T A 16: 19,385,333 (GRCm39) Q100L probably damaging Het
Or2y1b A T 11: 49,209,076 (GRCm39) R234S probably benign Het
Or5ac21 T A 16: 59,123,724 (GRCm39) D69E probably damaging Het
Parpbp A G 10: 87,969,053 (GRCm39) L131P probably damaging Het
Prl3a1 T C 13: 27,454,093 (GRCm39) W24R probably damaging Het
Ptprk T A 10: 28,369,060 (GRCm39) N677K probably damaging Het
Rbm39 A T 2: 156,004,793 (GRCm39) D181E possibly damaging Het
Ros1 T C 10: 52,042,293 (GRCm39) T220A possibly damaging Het
Slc46a3 T C 5: 147,823,021 (GRCm39) I274V probably benign Het
Tas2r104 T A 6: 131,661,938 (GRCm39) N257I probably damaging Het
Timeless A G 10: 128,080,113 (GRCm39) probably null Het
Tmem63a T C 1: 180,800,398 (GRCm39) probably null Het
Traf5 T C 1: 191,729,446 (GRCm39) D535G possibly damaging Het
Trank1 C T 9: 111,194,928 (GRCm39) S984L possibly damaging Het
Trpm6 A G 19: 18,833,539 (GRCm39) T1573A probably benign Het
Ube3b T A 5: 114,550,360 (GRCm39) I835N probably damaging Het
Wnt16 T A 6: 22,290,947 (GRCm39) I125N probably damaging Het
Xirp2 G T 2: 67,307,129 (GRCm39) probably benign Het
Zbtb47 T C 9: 121,596,405 (GRCm39) F624S possibly damaging Het
Zc3h12c G T 9: 52,027,982 (GRCm39) T460K probably benign Het
Zfp865 C A 7: 5,033,416 (GRCm39) T467K probably benign Het
Zim1 A G 7: 6,680,697 (GRCm39) V322A possibly damaging Het
Other mutations in Lrch3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01129:Lrch3 APN 16 32,815,335 (GRCm39) missense probably benign 0.10
IGL01400:Lrch3 APN 16 32,799,911 (GRCm39) missense probably damaging 1.00
IGL02565:Lrch3 APN 16 32,826,084 (GRCm39) missense probably benign 0.00
IGL03076:Lrch3 APN 16 32,802,223 (GRCm39) missense possibly damaging 0.52
IGL03103:Lrch3 APN 16 32,772,507 (GRCm39) missense probably damaging 1.00
IGL03125:Lrch3 APN 16 32,734,647 (GRCm39) missense possibly damaging 0.83
IGL03349:Lrch3 APN 16 32,775,694 (GRCm39) missense probably damaging 1.00
eluted UTSW 16 32,806,377 (GRCm39) missense probably null
leached UTSW 16 32,779,833 (GRCm39) missense probably damaging 1.00
R0054:Lrch3 UTSW 16 32,816,222 (GRCm39) intron probably benign
R0123:Lrch3 UTSW 16 32,782,124 (GRCm39) splice site probably benign
R0225:Lrch3 UTSW 16 32,782,124 (GRCm39) splice site probably benign
R0326:Lrch3 UTSW 16 32,799,870 (GRCm39) missense probably damaging 1.00
R0455:Lrch3 UTSW 16 32,807,250 (GRCm39) missense probably damaging 0.99
R0734:Lrch3 UTSW 16 32,817,853 (GRCm39) nonsense probably null
R1204:Lrch3 UTSW 16 32,829,584 (GRCm39) missense probably damaging 1.00
R1470:Lrch3 UTSW 16 32,808,865 (GRCm39) splice site probably benign
R1526:Lrch3 UTSW 16 32,770,746 (GRCm39) missense probably damaging 1.00
R1597:Lrch3 UTSW 16 32,770,781 (GRCm39) nonsense probably null
R1850:Lrch3 UTSW 16 32,807,163 (GRCm39) missense probably benign 0.01
R1966:Lrch3 UTSW 16 32,734,755 (GRCm39) missense possibly damaging 0.94
R2241:Lrch3 UTSW 16 32,816,211 (GRCm39) missense probably damaging 0.99
R2313:Lrch3 UTSW 16 32,782,045 (GRCm39) missense probably damaging 1.00
R2902:Lrch3 UTSW 16 32,770,766 (GRCm39) missense probably damaging 1.00
R4723:Lrch3 UTSW 16 32,808,854 (GRCm39) splice site probably null
R4795:Lrch3 UTSW 16 32,826,074 (GRCm39) missense probably damaging 1.00
R4970:Lrch3 UTSW 16 32,818,883 (GRCm39) missense probably damaging 1.00
R5223:Lrch3 UTSW 16 32,734,767 (GRCm39) missense probably damaging 0.99
R5292:Lrch3 UTSW 16 32,796,177 (GRCm39) missense probably damaging 1.00
R5414:Lrch3 UTSW 16 32,806,335 (GRCm39) splice site probably null
R5470:Lrch3 UTSW 16 32,818,960 (GRCm39) missense probably damaging 1.00
R5594:Lrch3 UTSW 16 32,734,554 (GRCm39) missense probably damaging 0.99
R5862:Lrch3 UTSW 16 32,816,179 (GRCm39) missense probably damaging 1.00
R5911:Lrch3 UTSW 16 32,779,833 (GRCm39) missense probably damaging 1.00
R5932:Lrch3 UTSW 16 32,796,106 (GRCm39) missense probably damaging 1.00
R6519:Lrch3 UTSW 16 32,815,367 (GRCm39) critical splice donor site probably benign
R6731:Lrch3 UTSW 16 32,770,790 (GRCm39) missense probably damaging 1.00
R7182:Lrch3 UTSW 16 32,814,149 (GRCm39) missense probably benign 0.05
R7197:Lrch3 UTSW 16 32,810,665 (GRCm39) missense probably damaging 1.00
R7319:Lrch3 UTSW 16 32,815,363 (GRCm39) missense probably benign 0.19
R7392:Lrch3 UTSW 16 32,807,125 (GRCm39) nonsense probably null
R7408:Lrch3 UTSW 16 32,807,113 (GRCm39) nonsense probably null
R7414:Lrch3 UTSW 16 32,818,883 (GRCm39) missense probably damaging 1.00
R7425:Lrch3 UTSW 16 32,826,077 (GRCm39) missense probably damaging 1.00
R7909:Lrch3 UTSW 16 32,829,663 (GRCm39) missense probably benign 0.00
R7956:Lrch3 UTSW 16 32,806,377 (GRCm39) missense probably null
R8009:Lrch3 UTSW 16 32,826,083 (GRCm39) missense possibly damaging 0.72
R8247:Lrch3 UTSW 16 32,829,713 (GRCm39) nonsense probably null
R8408:Lrch3 UTSW 16 32,775,750 (GRCm39) missense probably damaging 1.00
R8686:Lrch3 UTSW 16 32,802,223 (GRCm39) missense possibly damaging 0.52
R8756:Lrch3 UTSW 16 32,808,810 (GRCm39) missense probably benign 0.33
R8947:Lrch3 UTSW 16 32,802,199 (GRCm39) missense possibly damaging 0.66
R9459:Lrch3 UTSW 16 32,799,775 (GRCm39) missense probably damaging 0.99
R9710:Lrch3 UTSW 16 32,796,108 (GRCm39) nonsense probably null
Z1176:Lrch3 UTSW 16 32,734,686 (GRCm39) missense possibly damaging 0.89
Predicted Primers PCR Primer
(F):5'- TGACTCTGAAGTTACTGACCTG -3'
(R):5'- GCACAATGACTCCACTGAGC -3'

Sequencing Primer
(F):5'- GAGACAAGGTCTTTATAGCCCTGC -3'
(R):5'- TGACTCCACTGAGCTGAAAC -3'
Posted On 2016-12-20