Incidental Mutation 'IGL02508:Lrrtm1'
ID296439
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Lrrtm1
Ensembl Gene ENSMUSG00000060780
Gene Nameleucine rich repeat transmembrane neuronal 1
Synonyms4632401D06Rik
Accession Numbers
Is this an essential gene? Non essential (E-score: 0.000) question?
Stock #IGL02508
Quality Score
Status
Chromosome6
Chromosomal Location77242689-77257791 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to T at 77244591 bp
ZygosityHeterozygous
Amino Acid Change Serine to Cysteine at position 344 (S344C)
Ref Sequence ENSEMBL: ENSMUSP00000124373 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020400] [ENSMUST00000075340] [ENSMUST00000159616] [ENSMUST00000159626] [ENSMUST00000160894] [ENSMUST00000161677] [ENSMUST00000161811] [ENSMUST00000161846]
Predicted Effect probably damaging
Transcript: ENSMUST00000020400
AA Change: S344C

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000020400
Gene: ENSMUSG00000060780
AA Change: S344C

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: S344C

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000125207
Gene: ENSMUSG00000060780
AA Change: S344C

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: S344C

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000124373
Gene: ENSMUSG00000060780
AA Change: S344C

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: ENSMUST00000161811
SMART Domains Protein: ENSMUSP00000124948
Gene: ENSMUSG00000060780

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
Coding Region Coverage
Validation Efficiency
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700061I17Rik T A 3: 117,077,115 noncoding transcript Het
5430419D17Rik A G 7: 131,222,830 E91G probably damaging Het
Adgrv1 A T 13: 81,435,556 probably benign Het
AI429214 T G 8: 36,994,086 D129E probably benign Het
Alx1 G A 10: 103,022,193 T215M probably damaging Het
Arhgap39 A G 15: 76,724,984 *1079Q probably null Het
Brca2 T C 5: 150,543,308 V2179A possibly damaging Het
Celsr1 G A 15: 86,030,617 Q1052* probably null Het
Chd5 A G 4: 152,363,024 E510G probably damaging Het
Cntnap2 A G 6: 46,234,320 D556G probably damaging Het
Cux2 G A 5: 121,860,822 P1352S possibly damaging Het
Cyp4a31 A T 4: 115,571,064 Y319F probably damaging Het
Dcaf12 C T 4: 41,296,310 probably null Het
Dcc C A 18: 71,370,702 A942S probably benign Het
Dyrk1a A T 16: 94,685,183 D463V probably damaging Het
Eln T A 5: 134,704,568 probably benign Het
Fbxl13 A G 5: 21,556,805 probably null Het
Fndc3b T C 3: 27,458,751 Y742C probably damaging Het
Furin G A 7: 80,392,521 T442I probably benign Het
Gli1 T C 10: 127,337,092 Q155R probably benign Het
Glra3 A G 8: 56,085,144 E218G probably benign Het
Gm13101 T C 4: 143,965,020 N378D probably benign Het
Grb10 C T 11: 11,946,767 V236M probably damaging Het
Grhl2 T C 15: 37,309,765 probably benign Het
Hgfac A T 5: 35,047,220 M579L probably damaging Het
Ifi202b A T 1: 173,974,772 D165E probably benign Het
Klhl26 A T 8: 70,452,731 D95E probably damaging Het
Klk12 T C 7: 43,769,689 V26A probably benign Het
Lrp2 C T 2: 69,503,430 G1489D probably benign Het
Lzts1 G A 8: 69,140,848 R36* probably null Het
Mapkap1 T C 2: 34,518,669 probably benign Het
Meis3 T A 7: 16,178,797 probably null Het
Mtmr14 T A 6: 113,240,306 C60S probably damaging Het
Nfkb1 T A 3: 135,590,818 Y789F probably damaging Het
Nup54 G A 5: 92,417,539 Q440* probably null Het
Ogdhl T G 14: 32,345,174 M861R probably damaging Het
Olfr1290 C T 2: 111,489,835 A108T probably damaging Het
Olfr1425 G T 19: 12,073,887 H248Q possibly damaging Het
Olfr156 T C 4: 43,821,289 E24G possibly damaging Het
Olfr692 A T 7: 105,368,536 H61L possibly damaging Het
Olfr810 A G 10: 129,790,791 V266A probably benign Het
Pde6c A G 19: 38,157,500 K412R probably benign Het
Pex5l T C 3: 32,992,902 probably benign Het
Pigr A T 1: 130,850,858 I760L probably benign Het
Prr14l G A 5: 32,830,942 A403V probably benign Het
Prrt3 T C 6: 113,494,307 D968G probably damaging Het
Psmc5 T C 11: 106,263,043 I401T possibly damaging Het
Ralyl T A 3: 14,107,272 probably benign Het
Samd9l T C 6: 3,374,798 E821G probably damaging Het
Serpinb3a T A 1: 107,046,072 I370F probably damaging Het
Setd1a A G 7: 127,797,698 probably benign Het
Slco2a1 T A 9: 103,074,416 F381L probably benign Het
Strada A G 11: 106,168,356 Y199H probably benign Het
Stxbp2 T C 8: 3,632,531 I40T probably damaging Het
Tbx3 T C 5: 119,678,812 V358A possibly damaging Het
Tenm3 A G 8: 48,299,639 L896S probably benign Het
Tmem132a A G 19: 10,858,518 S883P probably damaging Het
Trio A G 15: 27,818,104 I496T possibly damaging Het
Unc79 C T 12: 103,112,276 R1548W probably damaging Het
Unc79 T C 12: 103,112,018 probably benign Het
Vmn2r9 T C 5: 108,848,201 M194V possibly damaging Het
Other mutations in Lrrtm1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00927:Lrrtm1 APN 6 77244063 missense probably benign 0.00
IGL01011:Lrrtm1 APN 6 77244235 unclassified probably null
IGL01125:Lrrtm1 APN 6 77244453 missense probably damaging 1.00
IGL01924:Lrrtm1 APN 6 77244186 missense possibly damaging 0.81
IGL03005:Lrrtm1 APN 6 77244156 missense probably damaging 1.00
IGL03076:Lrrtm1 APN 6 77244585 missense probably damaging 1.00
R0077:Lrrtm1 UTSW 6 77243872 missense probably damaging 1.00
R0540:Lrrtm1 UTSW 6 77244628 missense probably damaging 1.00
R0607:Lrrtm1 UTSW 6 77244628 missense probably damaging 1.00
R0927:Lrrtm1 UTSW 6 77244860 missense probably damaging 1.00
R1742:Lrrtm1 UTSW 6 77244091 missense probably damaging 1.00
R1762:Lrrtm1 UTSW 6 77244697 missense probably benign
R1933:Lrrtm1 UTSW 6 77244966 intron probably null
R1934:Lrrtm1 UTSW 6 77244966 intron probably null
R2180:Lrrtm1 UTSW 6 77244346 missense probably damaging 1.00
R2267:Lrrtm1 UTSW 6 77244013 missense probably damaging 0.97
R2914:Lrrtm1 UTSW 6 77244979 missense probably damaging 0.99
R2937:Lrrtm1 UTSW 6 77243652 missense probably benign 0.03
R2938:Lrrtm1 UTSW 6 77243652 missense probably benign 0.03
R4604:Lrrtm1 UTSW 6 77244144 missense probably damaging 1.00
R4908:Lrrtm1 UTSW 6 77244678 missense probably benign 0.01
R4910:Lrrtm1 UTSW 6 77244901 missense probably damaging 1.00
R5739:Lrrtm1 UTSW 6 77244889 missense probably damaging 0.99
R6604:Lrrtm1 UTSW 6 77244238 missense possibly damaging 0.70
R6845:Lrrtm1 UTSW 6 77243881 missense probably benign 0.02
R7048:Lrrtm1 UTSW 6 77244169 missense probably damaging 1.00
R7203:Lrrtm1 UTSW 6 77243601 missense probably damaging 1.00
R7783:Lrrtm1 UTSW 6 77244253 missense probably damaging 1.00
R7826:Lrrtm1 UTSW 6 77244112 splice site probably null
RF018:Lrrtm1 UTSW 6 77244351 missense possibly damaging 0.63
Posted On2015-04-16