Incidental Mutation 'IGL02043:Lrrtm4'
ID 184817
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Lrrtm4
Ensembl Gene ENSMUSG00000052581
Gene Name leucine rich repeat transmembrane neuronal 4
Synonyms 7530419J18Rik
Accession Numbers
Essential gene? Probably non essential (E-score: 0.100) question?
Stock # IGL02043
Quality Score
Status
Chromosome 6
Chromosomal Location 79995860-80787124 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 79998845 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Aspartic acid at position 86 (N86D)
Ref Sequence ENSEMBL: ENSMUSP00000117263 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000074662] [ENSMUST00000126005] [ENSMUST00000126399] [ENSMUST00000128718] [ENSMUST00000133918] [ENSMUST00000147663] [ENSMUST00000145407] [ENSMUST00000136421]
AlphaFold Q80XG9
Predicted Effect possibly damaging
Transcript: ENSMUST00000074662
AA Change: N85D

PolyPhen 2 Score 0.895 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000074232
Gene: ENSMUSG00000052581
AA Change: N85D

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
LRRNT 33 65 1.66e0 SMART
LRR_TYP 84 107 6.67e-2 SMART
LRR 108 131 3.52e-1 SMART
LRR_TYP 132 155 2.53e-2 SMART
LRR 156 179 1.16e-1 SMART
LRR 180 203 4.34e-1 SMART
LRR 204 224 2.4e1 SMART
LRR 228 251 4.97e0 SMART
LRR 252 275 1.07e0 SMART
LRR 276 299 1.64e-1 SMART
Blast:LRRCT 311 361 4e-25 BLAST
low complexity region 375 392 N/A INTRINSIC
transmembrane domain 425 447 N/A INTRINSIC
low complexity region 464 469 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000126005
AA Change: N85D

PolyPhen 2 Score 0.895 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000117445
Gene: ENSMUSG00000052581
AA Change: N85D

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
LRRNT 33 65 1.66e0 SMART
LRR_TYP 84 107 6.67e-2 SMART
LRR 108 131 3.52e-1 SMART
LRR_TYP 132 155 2.53e-2 SMART
LRR 156 179 1.16e-1 SMART
LRR 180 203 4.34e-1 SMART
LRR 204 224 2.4e1 SMART
LRR 228 251 4.97e0 SMART
LRR 252 275 1.07e0 SMART
LRR 276 299 1.64e-1 SMART
Blast:LRRCT 311 361 4e-25 BLAST
low complexity region 375 392 N/A INTRINSIC
transmembrane domain 425 447 N/A INTRINSIC
low complexity region 464 469 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000126399
AA Change: N85D

PolyPhen 2 Score 0.895 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000121124
Gene: ENSMUSG00000052581
AA Change: N85D

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
LRRNT 33 65 1.66e0 SMART
LRR_TYP 84 107 6.67e-2 SMART
LRR 108 131 3.52e-1 SMART
LRR_TYP 132 155 2.53e-2 SMART
LRR 156 179 1.16e-1 SMART
LRR 180 203 4.34e-1 SMART
LRR 204 224 2.4e1 SMART
LRR 228 251 4.97e0 SMART
LRR 252 275 1.07e0 SMART
LRR 276 299 1.64e-1 SMART
Blast:LRRCT 311 361 2e-25 BLAST
low complexity region 375 392 N/A INTRINSIC
transmembrane domain 425 447 N/A INTRINSIC
low complexity region 464 469 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000128718
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130734
Predicted Effect possibly damaging
Transcript: ENSMUST00000133918
AA Change: N85D

PolyPhen 2 Score 0.895 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000115016
Gene: ENSMUSG00000052581
AA Change: N85D

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
LRRNT 33 65 1.66e0 SMART
LRR_TYP 84 107 6.67e-2 SMART
LRR 108 131 3.52e-1 SMART
LRR_TYP 132 155 2.53e-2 SMART
LRR 156 179 1.16e-1 SMART
LRR 180 203 4.34e-1 SMART
LRR 204 224 2.4e1 SMART
LRR 228 251 4.97e0 SMART
LRR 252 275 1.07e0 SMART
LRR 276 299 1.64e-1 SMART
Blast:LRRCT 311 361 2e-25 BLAST
low complexity region 375 392 N/A INTRINSIC
transmembrane domain 425 447 N/A INTRINSIC
low complexity region 464 469 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000147663
AA Change: N86D

PolyPhen 2 Score 0.895 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000117263
Gene: ENSMUSG00000052581
AA Change: N86D

DomainStartEndE-ValueType
signal peptide 1 31 N/A INTRINSIC
LRRNT 34 66 1.66e0 SMART
LRR_TYP 85 108 6.67e-2 SMART
LRR 109 132 3.52e-1 SMART
LRR_TYP 133 156 2.53e-2 SMART
LRR 157 180 1.16e-1 SMART
LRR 181 204 4.34e-1 SMART
LRR 205 225 2.4e1 SMART
LRR 229 252 4.97e0 SMART
LRR 253 276 1.07e0 SMART
LRR 277 300 1.64e-1 SMART
Blast:LRRCT 312 362 2e-25 BLAST
low complexity region 376 393 N/A INTRINSIC
transmembrane domain 426 448 N/A INTRINSIC
low complexity region 465 470 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000145407
AA Change: N85D

PolyPhen 2 Score 0.821 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000114465
Gene: ENSMUSG00000052581
AA Change: N85D

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
LRRNT 33 65 1.66e0 SMART
Blast:LRR_TYP 84 104 3e-7 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000136421
AA Change: N86D

PolyPhen 2 Score 0.721 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000121621
Gene: ENSMUSG00000052581
AA Change: N86D

DomainStartEndE-ValueType
signal peptide 1 31 N/A INTRINSIC
LRRNT 34 66 1.66e0 SMART
LRR_TYP 85 108 6.67e-2 SMART
LRR 109 132 3.52e-1 SMART
LRR_TYP 133 156 2.53e-2 SMART
LRR 157 180 1.16e-1 SMART
LRR 181 204 4.34e-1 SMART
LRR 205 225 2.4e1 SMART
LRR 229 252 4.97e0 SMART
LRR 253 276 1.07e0 SMART
LRR 277 300 1.64e-1 SMART
Blast:LRRCT 312 362 4e-25 BLAST
low complexity region 376 393 N/A INTRINSIC
transmembrane domain 426 448 N/A INTRINSIC
low complexity region 465 470 N/A INTRINSIC
Coding Region Coverage
Validation Efficiency
MGI Phenotype PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired excitatory synapse development and excitatory transmission in dentate gyrus granule cells. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Atp1b2 T C 11: 69,496,102 (GRCm39) T33A probably benign Het
Brd2 A T 17: 34,331,590 (GRCm39) probably benign Het
Carmil1 T C 13: 24,208,299 (GRCm39) probably benign Het
Cdh9 A T 15: 16,856,318 (GRCm39) D786V probably damaging Het
Cep128 A C 12: 91,233,504 (GRCm39) probably benign Het
Cep85 T C 4: 133,883,038 (GRCm39) T284A probably benign Het
Chrna1 C T 2: 73,398,450 (GRCm39) E330K probably benign Het
Clec2l T C 6: 38,653,785 (GRCm39) Y104H probably damaging Het
Clybl G T 14: 122,616,664 (GRCm39) K226N probably damaging Het
Cmip T A 8: 118,172,067 (GRCm39) D467E probably benign Het
Cpne3 A T 4: 19,543,340 (GRCm39) probably null Het
Crisp4 A G 1: 18,204,324 (GRCm39) V46A probably damaging Het
Csnk2a1 T C 2: 152,116,070 (GRCm39) Y261H probably damaging Het
Cul5 C A 9: 53,569,973 (GRCm39) G86V probably benign Het
Czib T G 4: 107,752,065 (GRCm39) probably benign Het
Depdc7 T C 2: 104,560,626 (GRCm39) T123A probably benign Het
Edem2 T C 2: 155,547,661 (GRCm39) T384A probably damaging Het
F8 C T X: 74,376,247 (GRCm39) M377I probably benign Het
Fan1 T A 7: 64,021,367 (GRCm39) probably null Het
Fez2 T C 17: 78,689,051 (GRCm39) D366G probably damaging Het
Gm4841 A C 18: 60,404,037 (GRCm39) S19A probably benign Het
Gm4862 T A 3: 138,834,396 (GRCm39) noncoding transcript Het
Hk3 T A 13: 55,162,908 (GRCm39) Q44L probably damaging Het
Irgm1 C A 11: 48,757,642 (GRCm39) L56F probably damaging Het
Ldlr A G 9: 21,644,795 (GRCm39) T108A probably benign Het
Lgr4 T A 2: 109,841,635 (GRCm39) M516K probably damaging Het
Lrp1b T C 2: 40,587,537 (GRCm39) N3906S probably null Het
Map3k2 A G 18: 32,340,587 (GRCm39) D198G probably damaging Het
Mapkapk3 C T 9: 107,139,621 (GRCm39) probably null Het
Mvp A T 7: 126,592,790 (GRCm39) Y374N probably damaging Het
Myo3a T C 2: 22,404,776 (GRCm39) S711P probably benign Het
Myom3 A G 4: 135,497,986 (GRCm39) K189E probably damaging Het
Naip1 T A 13: 100,563,304 (GRCm39) K620N probably benign Het
Nlrp10 T C 7: 108,524,709 (GRCm39) E257G probably damaging Het
Nptn T G 9: 58,548,012 (GRCm39) M139R possibly damaging Het
Nrk T G X: 137,889,544 (GRCm39) M1105R possibly damaging Het
Or10a3n A T 7: 108,493,046 (GRCm39) C189* probably null Het
Or10d4 T G 9: 39,580,374 (GRCm39) V7G probably damaging Het
Or1q1 T A 2: 36,887,477 (GRCm39) Y218* probably null Het
Pcdhb16 A G 18: 37,612,248 (GRCm39) T403A probably benign Het
Pcyt1b A G X: 92,745,722 (GRCm39) E50G possibly damaging Het
Pigg C T 5: 108,492,190 (GRCm39) T892I probably damaging Het
Ppig T G 2: 69,566,327 (GRCm39) probably null Het
Prr12 A G 7: 44,699,429 (GRCm39) probably benign Het
Slc5a5 G T 8: 71,345,073 (GRCm39) A78E possibly damaging Het
Slc7a2 T G 8: 41,364,095 (GRCm39) M436R probably benign Het
Sp7 T A 15: 102,267,690 (GRCm39) M39L probably benign Het
Spag8 T A 4: 43,653,134 (GRCm39) probably benign Het
Svep1 A G 4: 58,068,556 (GRCm39) S3077P probably benign Het
Tmem30a A T 9: 79,681,371 (GRCm39) probably benign Het
Tmem63a C T 1: 180,800,353 (GRCm39) T714I probably benign Het
Trank1 T C 9: 111,193,028 (GRCm39) L535P probably damaging Het
Tuba8 A C 6: 121,197,470 (GRCm39) N44T probably benign Het
Wnk1 A G 6: 119,926,039 (GRCm39) probably benign Het
Zfp654 A T 16: 64,605,391 (GRCm39) I396K probably benign Het
Other mutations in Lrrtm4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00498:Lrrtm4 APN 6 79,999,529 (GRCm39) missense probably damaging 1.00
IGL02603:Lrrtm4 APN 6 79,999,967 (GRCm39) missense possibly damaging 0.92
IGL02614:Lrrtm4 APN 6 79,998,827 (GRCm39) missense probably benign 0.01
IGL02735:Lrrtm4 APN 6 80,786,031 (GRCm39) missense probably benign
IGL02812:Lrrtm4 APN 6 79,998,947 (GRCm39) missense probably damaging 1.00
IGL02885:Lrrtm4 APN 6 79,998,786 (GRCm39) missense probably damaging 1.00
IGL02956:Lrrtm4 APN 6 79,998,633 (GRCm39) missense probably benign 0.04
IGL03242:Lrrtm4 APN 6 79,999,071 (GRCm39) missense probably benign 0.22
R0504:Lrrtm4 UTSW 6 79,999,029 (GRCm39) missense probably damaging 1.00
R0537:Lrrtm4 UTSW 6 79,999,103 (GRCm39) missense probably benign 0.02
R0656:Lrrtm4 UTSW 6 79,998,953 (GRCm39) missense possibly damaging 0.87
R0698:Lrrtm4 UTSW 6 79,999,911 (GRCm39) missense probably damaging 1.00
R1651:Lrrtm4 UTSW 6 79,999,511 (GRCm39) missense probably benign 0.06
R2126:Lrrtm4 UTSW 6 79,998,722 (GRCm39) missense probably damaging 1.00
R2211:Lrrtm4 UTSW 6 79,999,623 (GRCm39) missense probably benign 0.00
R2363:Lrrtm4 UTSW 6 79,998,857 (GRCm39) missense probably damaging 1.00
R3732:Lrrtm4 UTSW 6 79,996,638 (GRCm39) intron probably benign
R3817:Lrrtm4 UTSW 6 79,999,044 (GRCm39) missense probably benign 0.00
R4814:Lrrtm4 UTSW 6 80,000,117 (GRCm39) missense possibly damaging 0.69
R5304:Lrrtm4 UTSW 6 79,999,683 (GRCm39) missense probably benign 0.01
R5318:Lrrtm4 UTSW 6 79,999,495 (GRCm39) missense probably damaging 1.00
R5327:Lrrtm4 UTSW 6 79,999,620 (GRCm39) missense probably damaging 1.00
R5931:Lrrtm4 UTSW 6 79,998,722 (GRCm39) missense probably damaging 0.99
R6195:Lrrtm4 UTSW 6 79,998,939 (GRCm39) missense probably damaging 1.00
R7597:Lrrtm4 UTSW 6 79,999,428 (GRCm39) nonsense probably null
R7793:Lrrtm4 UTSW 6 79,999,841 (GRCm39) missense probably damaging 0.97
R7875:Lrrtm4 UTSW 6 79,999,343 (GRCm39) missense possibly damaging 0.89
R8058:Lrrtm4 UTSW 6 79,999,528 (GRCm39) missense probably benign
R8238:Lrrtm4 UTSW 6 79,999,668 (GRCm39) missense probably damaging 0.97
R8324:Lrrtm4 UTSW 6 79,998,974 (GRCm39) missense probably damaging 1.00
R8751:Lrrtm4 UTSW 6 79,999,092 (GRCm39) missense probably damaging 1.00
R8859:Lrrtm4 UTSW 6 79,998,870 (GRCm39) missense probably damaging 1.00
R9142:Lrrtm4 UTSW 6 79,999,426 (GRCm39) missense probably damaging 1.00
R9633:Lrrtm4 UTSW 6 80,000,064 (GRCm39) missense probably damaging 1.00
R9709:Lrrtm4 UTSW 6 80,786,154 (GRCm39) missense probably damaging 0.96
Z1177:Lrrtm4 UTSW 6 79,999,700 (GRCm39) missense probably benign
Posted On 2014-05-07