Incidental Mutation 'R8756:Lrch3'
ID 664186
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 068597-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.115) question?
Stock # R8756 (G1)
Quality Score 225.009
Status Not validated
Chromosome 16
Chromosomal Location 32734470-32836017 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 32808810 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 514 (S514T)
Ref Sequence ENSEMBL: ENSMUSP00000023491 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023491] [ENSMUST00000135193] [ENSMUST00000165616] [ENSMUST00000165826] [ENSMUST00000170201] [ENSMUST00000170899]
AlphaFold Q8BVU0
Predicted Effect probably benign
Transcript: ENSMUST00000023491
AA Change: S514T

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000023491
Gene: ENSMUSG00000022801
AA Change: S514T

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 possibly damaging
Transcript: ENSMUST00000135193
AA Change: S514T

PolyPhen 2 Score 0.680 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000130708
Gene: ENSMUSG00000022801
AA Change: S514T

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
SMART Domains Protein: ENSMUSP00000117302
Gene: ENSMUSG00000022801
AA Change: S62T

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
SMART Domains Protein: ENSMUSP00000133034
Gene: ENSMUSG00000022801
AA Change: S96T

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 possibly damaging
Transcript: ENSMUST00000165616
AA Change: S360T

PolyPhen 2 Score 0.680 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000130009
Gene: ENSMUSG00000022801
AA Change: S360T

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
AA Change: S137T

PolyPhen 2 Score 0.390 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000126308
Gene: ENSMUSG00000022801
AA Change: S137T

DomainStartEndE-ValueType
low complexity region 105 116 N/A INTRINSIC
low complexity region 162 177 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000170201
AA Change: S514T

PolyPhen 2 Score 0.390 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000126964
Gene: ENSMUSG00000022801
AA Change: S514T

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 possibly damaging
Transcript: ENSMUST00000170899
AA Change: S464T

PolyPhen 2 Score 0.532 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000127547
Gene: ENSMUSG00000022801
AA Change: S464T

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: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Antxr1 A T 6: 87,165,235 (GRCm39) S401T probably damaging Het
Armh1 T A 4: 117,094,861 (GRCm39) I60L probably benign Het
Atp8b5 T C 4: 43,342,439 (GRCm39) V370A probably damaging Het
Atraid T A 5: 31,211,385 (GRCm39) Y184N probably damaging Het
Cp G C 3: 20,059,736 (GRCm39) probably null Het
Crebbp A G 16: 3,903,767 (GRCm39) I1824T probably benign Het
Cyp2c65 A T 19: 39,049,552 (GRCm39) R27* probably null Het
Dtl T C 1: 191,271,371 (GRCm39) H725R probably benign Het
Dync1h1 G T 12: 110,583,261 (GRCm39) A453S probably benign Het
Fat3 T A 9: 16,287,885 (GRCm39) D546V probably damaging Het
Flt1 T C 5: 147,576,224 (GRCm39) T595A probably benign Het
Gtf2ird2 C T 5: 134,226,090 (GRCm39) P179S possibly damaging Het
Hoga1 A G 19: 42,048,716 (GRCm39) I145V probably benign Het
Igfn1 G T 1: 135,895,698 (GRCm39) Q1623K probably benign Het
Jsrp1 T A 10: 80,647,940 (GRCm39) probably null Het
Krt90 A C 15: 101,470,779 (GRCm39) probably null Het
Mad2l1 T C 6: 66,512,569 (GRCm39) V20A probably damaging Het
Malrd1 T C 2: 15,757,706 (GRCm39) probably null Het
Matn2 A C 15: 34,423,876 (GRCm39) E578A possibly damaging Het
Myof A T 19: 37,928,400 (GRCm39) W1050R probably benign Het
Nemp1 T A 10: 127,528,845 (GRCm39) I183N probably benign Het
Nid1 A G 13: 13,683,386 (GRCm39) T1155A probably benign Het
Nsd1 T C 13: 55,461,506 (GRCm39) S2681P probably benign Het
Onecut3 C A 10: 80,349,750 (GRCm39) R415S probably damaging Het
Or2d2 T C 7: 106,728,019 (GRCm39) T194A probably benign Het
Or4s2 T A 2: 88,473,183 (GRCm39) V24E possibly damaging Het
Pclo T A 5: 14,764,398 (GRCm39) S1005R Het
Ppp1r16b G A 2: 158,593,098 (GRCm39) D226N probably damaging Het
R3hcc1l G A 19: 42,552,073 (GRCm39) V357M probably damaging Het
Sec63 C T 10: 42,686,905 (GRCm39) T475M possibly damaging Het
Serpinh1 A G 7: 98,996,359 (GRCm39) Y242H probably damaging Het
Slit2 G T 5: 48,459,829 (GRCm39) E1370* probably null Het
Sos2 C A 12: 69,695,310 (GRCm39) L142F probably damaging Het
Spag4 T C 2: 155,908,493 (GRCm39) L141P possibly damaging Het
Sun1 T C 5: 139,222,444 (GRCm39) L570P probably damaging Het
Tars2 A G 3: 95,648,672 (GRCm39) V662A probably benign Het
Tmem245 C A 4: 56,899,025 (GRCm39) probably null Het
Tpp2 T A 1: 43,999,295 (GRCm39) Y356* probably null Het
Trafd1 T C 5: 121,513,878 (GRCm39) E303G probably damaging Het
Trim71 T C 9: 114,342,605 (GRCm39) E559G possibly damaging Het
Ush2a T A 1: 188,644,141 (GRCm39) V4501E possibly damaging Het
Vegfa T C 17: 46,342,465 (GRCm39) T118A probably damaging Het
Vmn2r124 A T 17: 18,294,094 (GRCm39) H727L probably benign Het
Zdhhc2 T A 8: 40,920,551 (GRCm39) V270E probably damaging Het
Zfp112 T C 7: 23,824,997 (GRCm39) S326P probably benign Het
Zfp37 T C 4: 62,110,371 (GRCm39) D272G 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
R5843:Lrch3 UTSW 16 32,818,896 (GRCm39) missense probably damaging 1.00
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
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'- GTATAGCTCGTTGCAGTTCTTC -3'
(R):5'- TGACTCAAGCTGCAGACCAG -3'

Sequencing Primer
(F):5'- AGCTCGTTGCAGTTCTTCATTTAAG -3'
(R):5'- GGCTATCCCAGAATTCACTATGTAGC -3'
Posted On 2021-03-08