Incidental Mutation 'R0077:Lrrtm1'
ID 19475
Institutional Source Beutler Lab
Gene Symbol Lrrtm1
Ensembl Gene ENSMUSG00000060780
Gene Name leucine rich repeat transmembrane neuronal 1
Synonyms 4632401D06Rik
MMRRC Submission 038364-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0077 (G1)
Quality Score 216
Status Validated
Chromosome 6
Chromosomal Location 77219672-77234774 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 77220855 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 104 (V104E)
Ref Sequence ENSEMBL: ENSMUSP00000124373 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020400] [ENSMUST00000075340] [ENSMUST00000159616] [ENSMUST00000159626] [ENSMUST00000160894] [ENSMUST00000161677] [ENSMUST00000161811] [ENSMUST00000161846]
AlphaFold Q8K377
Predicted Effect probably damaging
Transcript: ENSMUST00000020400
AA Change: V104E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000020400
Gene: ENSMUSG00000060780
AA Change: V104E

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
LRRNT 38 70 1.06e0 SMART
LRR 64 87 5.56e0 SMART
LRR 88 111 1.03e1 SMART
LRR_TYP 112 135 2.71e-2 SMART
LRR_TYP 136 159 1.98e-4 SMART
LRR_TYP 160 183 9.44e-2 SMART
LRR 184 207 6.96e0 SMART
LRR 208 236 1.76e2 SMART
LRR 255 278 4.71e1 SMART
LRR 279 302 1.03e1 SMART
Blast:LRRCT 314 364 4e-13 BLAST
transmembrane domain 428 450 N/A INTRINSIC
low complexity region 467 475 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000075340
SMART Domains Protein: ENSMUSP00000074809
Gene: ENSMUSG00000063063

DomainStartEndE-ValueType
Pfam:Vinculin 18 337 2e-104 PFAM
Pfam:Vinculin 331 866 7.7e-222 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000159616
AA Change: V104E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000125207
Gene: ENSMUSG00000060780
AA Change: V104E

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
LRRNT 38 70 1.06e0 SMART
LRR 64 87 5.56e0 SMART
LRR 88 111 1.03e1 SMART
LRR_TYP 112 135 2.71e-2 SMART
LRR_TYP 136 159 1.98e-4 SMART
LRR_TYP 160 183 9.44e-2 SMART
LRR 184 207 6.96e0 SMART
LRR 208 236 1.76e2 SMART
LRR 255 278 4.71e1 SMART
LRR 279 302 1.03e1 SMART
Blast:LRRCT 314 364 4e-13 BLAST
transmembrane domain 428 450 N/A INTRINSIC
low complexity region 467 475 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000159626
SMART Domains Protein: ENSMUSP00000124376
Gene: ENSMUSG00000063063

DomainStartEndE-ValueType
Pfam:Vinculin 18 337 3.4e-105 PFAM
Pfam:Vinculin 330 914 6.6e-214 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000160894
SMART Domains Protein: ENSMUSP00000124764
Gene: ENSMUSG00000063063

DomainStartEndE-ValueType
Pfam:Vinculin 31 352 2.1e-104 PFAM
Pfam:Vinculin 343 927 4.6e-213 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000161677
AA Change: V104E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000124373
Gene: ENSMUSG00000060780
AA Change: V104E

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
LRRNT 38 70 1.06e0 SMART
LRR 64 87 5.56e0 SMART
LRR 88 111 1.03e1 SMART
LRR_TYP 112 135 2.71e-2 SMART
LRR_TYP 136 159 1.98e-4 SMART
LRR_TYP 160 183 9.44e-2 SMART
LRR 184 207 6.96e0 SMART
LRR 208 236 1.76e2 SMART
LRR 255 278 4.71e1 SMART
LRR 279 302 1.03e1 SMART
Blast:LRRCT 314 364 4e-13 BLAST
transmembrane domain 428 450 N/A INTRINSIC
low complexity region 467 475 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000161811
AA Change: V104E

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000124948
Gene: ENSMUSG00000060780
AA Change: V104E

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
LRRNT 38 70 1.06e0 SMART
LRR 64 87 5.56e0 SMART
LRR 88 111 1.03e1 SMART
LRR_TYP 112 135 2.71e-2 SMART
LRR_TYP 136 159 1.98e-4 SMART
LRR_TYP 160 183 9.44e-2 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000161846
SMART Domains Protein: ENSMUSP00000123714
Gene: ENSMUSG00000063063

DomainStartEndE-ValueType
Pfam:Vinculin 31 350 5.3e-105 PFAM
Pfam:Vinculin 344 879 2.1e-222 PFAM
Meta Mutation Damage Score 0.9239 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.9%
  • 10x: 95.4%
  • 20x: 90.5%
Validation Efficiency 83% (159/192)
MGI Phenotype PHENOTYPE: Mice homozygous for a null mutation are viable and fertile with grossly normal brain morphology. Mice homozygous for another knock-out allele exhibit impaired cognitive function and altered hippocampal synapse morphology. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrl3 T C 5: 81,919,532 (GRCm39) probably benign Het
Adgrl4 A G 3: 151,223,418 (GRCm39) I624V probably damaging Het
AI661453 A G 17: 47,780,287 (GRCm39) probably benign Het
Alg12 C T 15: 88,700,181 (GRCm39) E60K probably damaging Het
Angel2 A T 1: 190,665,284 (GRCm39) N72Y possibly damaging Het
Ank1 C A 8: 23,630,183 (GRCm39) P81Q probably damaging Het
Atp6v1c2 A T 12: 17,371,613 (GRCm39) D61E probably damaging Het
Bpi T A 2: 158,103,254 (GRCm39) M83K probably damaging Het
Capn7 A G 14: 31,090,072 (GRCm39) I642V probably benign Het
Ccdc134 T C 15: 82,015,938 (GRCm39) probably benign Het
Ccr3 C T 9: 123,829,061 (GRCm39) T132I probably damaging Het
Cfap65 C A 1: 74,971,077 (GRCm39) W80C probably damaging Het
Chaf1a T A 17: 56,354,384 (GRCm39) I218K unknown Het
Ddx23 A G 15: 98,554,481 (GRCm39) probably null Het
Dmkn A G 7: 30,464,719 (GRCm39) S231G probably benign Het
Ep300 T C 15: 81,525,514 (GRCm39) I1446T unknown Het
Fmnl1 T C 11: 103,080,795 (GRCm39) F318S probably damaging Het
Grik5 A T 7: 24,722,805 (GRCm39) V497E probably damaging Het
Gtf2ird2 T C 5: 134,242,925 (GRCm39) Y380H probably damaging Het
Hecw2 C T 1: 53,907,990 (GRCm39) probably benign Het
Hspb7 A G 4: 141,151,358 (GRCm39) I167V probably damaging Het
Kcnh2 T A 5: 24,527,700 (GRCm39) N884I probably benign Het
Krba1 T C 6: 48,382,159 (GRCm39) probably benign Het
Krt18 G T 15: 101,939,409 (GRCm39) R294L probably benign Het
Lctl T A 9: 64,029,389 (GRCm39) M1K probably null Het
Lingo2 G A 4: 35,708,375 (GRCm39) S535F possibly damaging Het
Lrba A C 3: 86,449,995 (GRCm39) N2105H probably damaging Het
Lrrc10 A G 10: 116,881,419 (GRCm39) D31G probably damaging Het
Mgat3 C T 15: 80,096,778 (GRCm39) T535I probably benign Het
Nav3 T C 10: 109,552,503 (GRCm39) I1780V possibly damaging Het
Nlrc4 A G 17: 74,753,826 (GRCm39) W186R probably damaging Het
Nr2c1 T A 10: 94,024,117 (GRCm39) F441I probably benign Het
Obscn A G 11: 58,942,347 (GRCm39) probably benign Het
Or1p1 T C 11: 74,179,501 (GRCm39) F10L probably benign Het
Or2a56 T C 6: 42,932,707 (GRCm39) S92P probably benign Het
Or56b34 T C 7: 104,937,726 (GRCm39) V142A probably damaging Het
Or5au1 T C 14: 52,273,442 (GRCm39) N42S possibly damaging Het
Osr1 A T 12: 9,629,691 (GRCm39) Y188F probably damaging Het
Pak2 A T 16: 31,852,661 (GRCm39) N293K possibly damaging Het
Pappa A T 4: 65,226,049 (GRCm39) T1301S probably damaging Het
Pde4dip G A 3: 97,660,442 (GRCm39) Q679* probably null Het
Pik3r5 T A 11: 68,377,448 (GRCm39) probably null Het
Plbd2 C T 5: 120,624,104 (GRCm39) probably null Het
Ppp1r3a G T 6: 14,754,516 (GRCm39) P244T possibly damaging Het
Pum1 C A 4: 130,499,985 (GRCm39) R960S probably benign Het
Ralgapb T C 2: 158,315,169 (GRCm39) Y845H probably damaging Het
Rbms1 A T 2: 60,589,179 (GRCm39) M287K possibly damaging Het
Rdh1 A T 10: 127,595,906 (GRCm39) I34F probably damaging Het
Rgl3 T A 9: 21,885,398 (GRCm39) Q644L probably benign Het
Rpap2 T C 5: 107,768,340 (GRCm39) S393P probably damaging Het
Rsad2 T C 12: 26,506,376 (GRCm39) S15G probably damaging Het
Rspo1 G A 4: 124,885,190 (GRCm39) R22Q probably benign Het
S100a11 A C 3: 93,431,509 (GRCm39) probably null Het
Septin4 T C 11: 87,472,022 (GRCm39) S11P probably benign Het
Serpina1c T C 12: 103,862,350 (GRCm39) S322G probably benign Het
Setdb1 A T 3: 95,248,762 (GRCm39) C385S probably damaging Het
Shank2 A T 7: 143,746,204 (GRCm39) I193F possibly damaging Het
Slc4a11 G T 2: 130,528,221 (GRCm39) probably benign Het
Snrnp40 C G 4: 130,271,836 (GRCm39) probably null Het
Tbcd C A 11: 121,485,100 (GRCm39) Q761K probably benign Het
Tmed6 C T 8: 107,792,198 (GRCm39) V16M probably damaging Het
Tmem229a T C 6: 24,955,701 (GRCm39) T18A probably benign Het
Tsc1 T A 2: 28,568,955 (GRCm39) probably benign Het
Ube2m T C 7: 12,769,657 (GRCm39) N49D probably damaging Het
Ubqlnl T C 7: 103,799,254 (GRCm39) D81G probably damaging Het
Vmn2r56 A G 7: 12,449,332 (GRCm39) V302A probably benign Het
Vmn2r73 T A 7: 85,525,075 (GRCm39) R24S probably benign Het
Wfs1 C A 5: 37,130,538 (GRCm39) S236I probably damaging Het
Xpot A T 10: 121,441,544 (GRCm39) N560K probably benign Het
Yipf3 A G 17: 46,562,503 (GRCm39) T303A probably benign Het
Zfp790 T C 7: 29,524,300 (GRCm39) W19R probably damaging Het
Zfp846 T C 9: 20,505,303 (GRCm39) C388R probably benign Het
Zpr1 T A 9: 46,184,634 (GRCm39) I47N probably damaging Het
Other mutations in Lrrtm1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00927:Lrrtm1 APN 6 77,221,046 (GRCm39) missense probably benign 0.00
IGL01011:Lrrtm1 APN 6 77,221,218 (GRCm39) splice site probably null
IGL01125:Lrrtm1 APN 6 77,221,436 (GRCm39) missense probably damaging 1.00
IGL01924:Lrrtm1 APN 6 77,221,169 (GRCm39) missense possibly damaging 0.81
IGL02508:Lrrtm1 APN 6 77,221,574 (GRCm39) missense probably damaging 1.00
IGL03005:Lrrtm1 APN 6 77,221,139 (GRCm39) missense probably damaging 1.00
IGL03076:Lrrtm1 APN 6 77,221,568 (GRCm39) missense probably damaging 1.00
R0540:Lrrtm1 UTSW 6 77,221,611 (GRCm39) missense probably damaging 1.00
R0607:Lrrtm1 UTSW 6 77,221,611 (GRCm39) missense probably damaging 1.00
R0927:Lrrtm1 UTSW 6 77,221,843 (GRCm39) missense probably damaging 1.00
R1742:Lrrtm1 UTSW 6 77,221,074 (GRCm39) missense probably damaging 1.00
R1762:Lrrtm1 UTSW 6 77,221,680 (GRCm39) missense probably benign
R1933:Lrrtm1 UTSW 6 77,221,949 (GRCm39) splice site probably null
R1934:Lrrtm1 UTSW 6 77,221,949 (GRCm39) splice site probably null
R2180:Lrrtm1 UTSW 6 77,221,329 (GRCm39) missense probably damaging 1.00
R2267:Lrrtm1 UTSW 6 77,220,996 (GRCm39) missense probably damaging 0.97
R2914:Lrrtm1 UTSW 6 77,221,962 (GRCm39) missense probably damaging 0.99
R2937:Lrrtm1 UTSW 6 77,220,635 (GRCm39) missense probably benign 0.03
R2938:Lrrtm1 UTSW 6 77,220,635 (GRCm39) missense probably benign 0.03
R4604:Lrrtm1 UTSW 6 77,221,127 (GRCm39) missense probably damaging 1.00
R4908:Lrrtm1 UTSW 6 77,221,661 (GRCm39) missense probably benign 0.01
R4910:Lrrtm1 UTSW 6 77,221,884 (GRCm39) missense probably damaging 1.00
R5739:Lrrtm1 UTSW 6 77,221,872 (GRCm39) missense probably damaging 0.99
R6604:Lrrtm1 UTSW 6 77,221,221 (GRCm39) missense possibly damaging 0.70
R6845:Lrrtm1 UTSW 6 77,220,864 (GRCm39) missense probably benign 0.02
R7048:Lrrtm1 UTSW 6 77,221,152 (GRCm39) missense probably damaging 1.00
R7203:Lrrtm1 UTSW 6 77,220,584 (GRCm39) missense probably damaging 1.00
R7783:Lrrtm1 UTSW 6 77,221,236 (GRCm39) missense probably damaging 1.00
R7826:Lrrtm1 UTSW 6 77,221,095 (GRCm39) splice site probably null
R8164:Lrrtm1 UTSW 6 77,221,199 (GRCm39) missense probably damaging 1.00
R8303:Lrrtm1 UTSW 6 77,221,662 (GRCm39) missense probably benign 0.03
R8856:Lrrtm1 UTSW 6 77,221,807 (GRCm39) missense possibly damaging 0.85
R9221:Lrrtm1 UTSW 6 77,221,596 (GRCm39) missense probably damaging 1.00
R9564:Lrrtm1 UTSW 6 77,221,536 (GRCm39) missense probably benign 0.00
R9749:Lrrtm1 UTSW 6 77,220,855 (GRCm39) missense probably damaging 1.00
RF018:Lrrtm1 UTSW 6 77,221,334 (GRCm39) missense possibly damaging 0.63
Predicted Primers PCR Primer
(F):5'- CGCTAATGGATTTCCTGCTACTCGG -3'
(R):5'- AGCTCTGTGAGCTTGAACAAGCC -3'

Sequencing Primer
(F):5'- CTGTCTACACTGGCTGCTGAG -3'
(R):5'- AGACTCTTGAGCTGATTGTATCC -3'
Posted On 2013-04-11