Incidental Mutation 'R5937:Lrtm1'
ID 462342
Institutional Source Beutler Lab
Gene Symbol Lrtm1
Ensembl Gene ENSMUSG00000045776
Gene Name leucine-rich repeats and transmembrane domains 1
Synonyms A930016D02Rik
MMRRC Submission 043242-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.088) question?
Stock # R5937 (G1)
Quality Score 225
Status Not validated
Chromosome 14
Chromosomal Location 28740165-28755599 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 28743787 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 85 (V85A)
Ref Sequence ENSEMBL: ENSMUSP00000061828 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000022567] [ENSMUST00000055662] [ENSMUST00000224708] [ENSMUST00000224760]
AlphaFold Q8BXQ3
Predicted Effect probably benign
Transcript: ENSMUST00000022567
SMART Domains Protein: ENSMUSP00000022567
Gene: ENSMUSG00000021991

DomainStartEndE-ValueType
low complexity region 14 27 N/A INTRINSIC
Blast:WNT1 28 103 2e-33 BLAST
Pfam:VWA_N 113 229 6.8e-40 PFAM
VWA 254 439 4.13e-24 SMART
Pfam:Cache_1 452 548 3e-32 PFAM
low complexity region 1070 1088 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000055662
AA Change: V85A

PolyPhen 2 Score 0.901 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000061828
Gene: ENSMUSG00000045776
AA Change: V85A

DomainStartEndE-ValueType
LRRNT 32 66 4.41e-6 SMART
LRR 65 84 2.33e2 SMART
LRR 85 108 2.67e-1 SMART
LRR 109 131 1.15e1 SMART
LRR_TYP 133 156 3.89e-3 SMART
LRRCT 192 245 8.63e-6 SMART
transmembrane domain 297 319 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000224708
AA Change: V112A

PolyPhen 2 Score 0.247 (Sensitivity: 0.91; Specificity: 0.88)
Predicted Effect probably benign
Transcript: ENSMUST00000224760
AA Change: V85A

PolyPhen 2 Score 0.247 (Sensitivity: 0.91; Specificity: 0.88)
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.4%
  • 10x: 97.3%
  • 20x: 91.5%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A1bg A T 15: 60,791,495 (GRCm39) W314R probably benign Het
Adgrv1 A T 13: 81,255,194 (GRCm39) V6143E probably damaging Het
Agap3 C T 5: 24,682,815 (GRCm39) T261I probably damaging Het
Ano6 T C 15: 95,811,838 (GRCm39) I241T probably damaging Het
Arhgef28 T C 13: 98,076,051 (GRCm39) T1328A probably benign Het
Capn10 C T 1: 92,867,105 (GRCm39) R112W probably damaging Het
Car5a A T 8: 122,666,560 (GRCm39) W46R probably damaging Het
Cntn6 C A 6: 104,810,064 (GRCm39) T582K possibly damaging Het
Ctsh T C 9: 89,943,509 (GRCm39) V60A probably benign Het
Ctsll3 A G 13: 60,947,410 (GRCm39) F259L probably damaging Het
Dennd2b A T 7: 109,156,478 (GRCm39) C91S possibly damaging Het
Fam228a T C 12: 4,787,725 (GRCm39) E16G probably damaging Het
G3bp2 A G 5: 92,203,256 (GRCm39) I388T probably damaging Het
Galnt5 A T 2: 57,928,949 (GRCm39) K926N probably benign Het
Gm10097 G A 10: 5,019,485 (GRCm39) probably benign Het
Gm9978 T A 10: 78,322,675 (GRCm39) noncoding transcript Het
Gria1 A G 11: 57,080,559 (GRCm39) T112A probably benign Het
Hnrnpk A C 13: 58,543,016 (GRCm39) V134G probably damaging Het
Insr A G 8: 3,224,808 (GRCm39) V220A probably benign Het
Lhx4 A G 1: 155,586,023 (GRCm39) I96T probably damaging Het
Lrp1 T C 10: 127,419,745 (GRCm39) T955A possibly damaging Het
Man2a2 T C 7: 80,013,251 (GRCm39) Y514C probably damaging Het
Npas1 T A 7: 16,197,187 (GRCm39) D226V probably benign Het
Nrcam G A 12: 44,619,074 (GRCm39) V858I probably benign Het
Or14c40 G T 7: 86,313,684 (GRCm39) L271F probably benign Het
Or5b108 T A 19: 13,168,675 (GRCm39) S215T probably damaging Het
Pde6b G T 5: 108,572,193 (GRCm39) A478S probably benign Het
Pex1 T A 5: 3,674,487 (GRCm39) N789K possibly damaging Het
Plekha6 A G 1: 133,187,839 (GRCm39) D120G possibly damaging Het
Pomgnt1 A G 4: 116,011,110 (GRCm39) T220A probably benign Het
Sdr39u1 A T 14: 56,135,364 (GRCm39) I193K probably damaging Het
Sec61a2 C A 2: 5,891,368 (GRCm39) M54I probably benign Het
Sema5a A G 15: 32,574,987 (GRCm39) Y365C probably damaging Het
Sra1 C T 18: 36,804,652 (GRCm39) probably null Het
Taf5 C T 19: 47,070,334 (GRCm39) S640L probably damaging Het
Tas2r140 T A 6: 133,032,236 (GRCm39) H174L probably benign Het
Tmem63a T A 1: 180,788,716 (GRCm39) V351D probably damaging Het
Ttll7 C T 3: 146,649,847 (GRCm39) Q626* probably null Het
Ubn2 T A 6: 38,440,917 (GRCm39) V263E possibly damaging Het
Vmn2r106 C T 17: 20,505,667 (GRCm39) W9* probably null Het
Xrcc3 C G 12: 111,774,406 (GRCm39) C141S probably null Het
Zfp516 T A 18: 82,974,958 (GRCm39) D385E probably damaging Het
Other mutations in Lrtm1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02191:Lrtm1 APN 14 28,743,906 (GRCm39) missense probably benign 0.00
R0102:Lrtm1 UTSW 14 28,744,184 (GRCm39) splice site probably benign
R0102:Lrtm1 UTSW 14 28,744,184 (GRCm39) splice site probably benign
R0602:Lrtm1 UTSW 14 28,744,179 (GRCm39) splice site probably benign
R5214:Lrtm1 UTSW 14 28,743,651 (GRCm39) missense possibly damaging 0.58
R5253:Lrtm1 UTSW 14 28,743,801 (GRCm39) missense probably benign 0.13
R5787:Lrtm1 UTSW 14 28,743,947 (GRCm39) missense possibly damaging 0.89
R6238:Lrtm1 UTSW 14 28,749,628 (GRCm39) missense probably benign 0.02
R6850:Lrtm1 UTSW 14 28,749,407 (GRCm39) missense probably benign 0.00
R7304:Lrtm1 UTSW 14 28,744,075 (GRCm39) missense probably damaging 0.97
R7363:Lrtm1 UTSW 14 28,743,850 (GRCm39) missense probably damaging 1.00
R7385:Lrtm1 UTSW 14 28,749,673 (GRCm39) missense probably benign 0.00
R8181:Lrtm1 UTSW 14 28,743,894 (GRCm39) missense probably damaging 1.00
R9299:Lrtm1 UTSW 14 28,743,714 (GRCm39) missense probably damaging 1.00
RF036:Lrtm1 UTSW 14 28,743,400 (GRCm39) frame shift probably null
RF063:Lrtm1 UTSW 14 28,743,400 (GRCm39) frame shift probably null
Predicted Primers PCR Primer
(F):5'- TGCTTTAGGTACTCTGCTGC -3'
(R):5'- AGGCTGTTGGATGAAAGATCTAGC -3'

Sequencing Primer
(F):5'- AGGTACTCTGCTGCTGGTCTC -3'
(R):5'- TGGATGAAAGATCTAGCTCCCTG -3'
Posted On 2017-02-28