Incidental Mutation 'R0077:Lingo2'
ID 19459
Institutional Source Beutler Lab
Gene Symbol Lingo2
Ensembl Gene ENSMUSG00000045083
Gene Name leucine rich repeat and Ig domain containing 2
Synonyms Lrrn6c, LERN3, B230217C06Rik
MMRRC Submission 038364-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.109) question?
Stock # R0077 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 35706647-36951747 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 35708375 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Phenylalanine at position 535 (S535F)
Ref Sequence ENSEMBL: ENSMUSP00000130423 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000065173] [ENSMUST00000098151] [ENSMUST00000108122] [ENSMUST00000108124] [ENSMUST00000164772]
AlphaFold Q3URE9
Predicted Effect possibly damaging
Transcript: ENSMUST00000065173
AA Change: S535F

PolyPhen 2 Score 0.508 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000069772
Gene: ENSMUSG00000045083
AA Change: S535F

DomainStartEndE-ValueType
LRRNT 27 61 1.86e-4 SMART
LRR 80 103 5.89e1 SMART
LRR_TYP 104 127 8.22e-2 SMART
LRR 128 151 6.57e-1 SMART
LRR 152 175 1.31e0 SMART
LRR 176 199 4.83e0 SMART
LRR 200 223 1.62e2 SMART
low complexity region 249 263 N/A INTRINSIC
LRR 272 295 2.17e-1 SMART
LRR 296 319 8.01e0 SMART
LRR_TYP 320 343 7.15e-2 SMART
LRRCT 355 408 3.7e-2 SMART
IGc2 423 490 9.99e-13 SMART
transmembrane domain 543 565 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000098151
AA Change: S535F

PolyPhen 2 Score 0.508 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000095754
Gene: ENSMUSG00000045083
AA Change: S535F

DomainStartEndE-ValueType
LRRNT 27 61 1.86e-4 SMART
LRR 80 103 5.89e1 SMART
LRR_TYP 104 127 8.22e-2 SMART
LRR 128 151 6.57e-1 SMART
LRR 152 175 1.31e0 SMART
LRR 176 199 4.83e0 SMART
LRR 200 223 1.62e2 SMART
low complexity region 249 263 N/A INTRINSIC
LRR 272 295 2.17e-1 SMART
LRR 296 319 8.01e0 SMART
LRR_TYP 320 343 7.15e-2 SMART
LRRCT 355 408 3.7e-2 SMART
IGc2 423 490 9.99e-13 SMART
transmembrane domain 543 565 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000108122
AA Change: S535F

PolyPhen 2 Score 0.508 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000103757
Gene: ENSMUSG00000045083
AA Change: S535F

DomainStartEndE-ValueType
LRRNT 27 61 1.86e-4 SMART
LRR 80 103 5.89e1 SMART
LRR_TYP 104 127 8.22e-2 SMART
LRR 128 151 6.57e-1 SMART
LRR 152 175 1.31e0 SMART
LRR 176 199 4.83e0 SMART
LRR 200 223 1.62e2 SMART
low complexity region 249 263 N/A INTRINSIC
LRR 272 295 2.17e-1 SMART
LRR 296 319 8.01e0 SMART
LRR_TYP 320 343 7.15e-2 SMART
LRRCT 355 408 3.7e-2 SMART
IGc2 423 490 9.99e-13 SMART
transmembrane domain 543 565 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000108124
AA Change: S535F

PolyPhen 2 Score 0.508 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000103759
Gene: ENSMUSG00000045083
AA Change: S535F

DomainStartEndE-ValueType
LRRNT 27 61 1.86e-4 SMART
LRR 80 103 5.89e1 SMART
LRR_TYP 104 127 8.22e-2 SMART
LRR 128 151 6.57e-1 SMART
LRR 152 175 1.31e0 SMART
LRR 176 199 4.83e0 SMART
LRR 200 223 1.62e2 SMART
low complexity region 249 263 N/A INTRINSIC
LRR 272 295 2.17e-1 SMART
LRR 296 319 8.01e0 SMART
LRR_TYP 320 343 7.15e-2 SMART
LRRCT 355 408 3.7e-2 SMART
IGc2 423 490 9.99e-13 SMART
transmembrane domain 543 565 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000164772
AA Change: S535F

PolyPhen 2 Score 0.508 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000130423
Gene: ENSMUSG00000045083
AA Change: S535F

DomainStartEndE-ValueType
LRRNT 27 61 1.86e-4 SMART
LRR 80 103 5.89e1 SMART
LRR_TYP 104 127 8.22e-2 SMART
LRR 128 151 6.57e-1 SMART
LRR 152 175 1.31e0 SMART
LRR 176 199 4.83e0 SMART
LRR 200 223 1.62e2 SMART
low complexity region 249 263 N/A INTRINSIC
LRR 272 295 2.17e-1 SMART
LRR 296 319 8.01e0 SMART
LRR_TYP 320 343 7.15e-2 SMART
LRRCT 355 408 3.7e-2 SMART
IGc2 423 490 9.99e-13 SMART
transmembrane domain 543 565 N/A INTRINSIC
Meta Mutation Damage Score 0.0705 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.9%
  • 10x: 95.4%
  • 20x: 90.5%
Validation Efficiency 83% (159/192)
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
Lrba A C 3: 86,449,995 (GRCm39) N2105H probably damaging Het
Lrrc10 A G 10: 116,881,419 (GRCm39) D31G probably damaging Het
Lrrtm1 T A 6: 77,220,855 (GRCm39) V104E 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 Lingo2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01861:Lingo2 APN 4 35,709,526 (GRCm39) missense probably benign 0.31
IGL02532:Lingo2 APN 4 35,709,171 (GRCm39) missense possibly damaging 0.69
IGL02999:Lingo2 APN 4 35,708,744 (GRCm39) missense probably damaging 1.00
R0669:Lingo2 UTSW 4 35,709,120 (GRCm39) missense probably benign 0.00
R1195:Lingo2 UTSW 4 35,708,538 (GRCm39) missense probably damaging 1.00
R1195:Lingo2 UTSW 4 35,708,538 (GRCm39) missense probably damaging 1.00
R1195:Lingo2 UTSW 4 35,708,538 (GRCm39) missense probably damaging 1.00
R1403:Lingo2 UTSW 4 35,709,420 (GRCm39) missense possibly damaging 0.83
R1403:Lingo2 UTSW 4 35,709,420 (GRCm39) missense possibly damaging 0.83
R1552:Lingo2 UTSW 4 35,708,315 (GRCm39) missense probably damaging 0.99
R2066:Lingo2 UTSW 4 35,709,179 (GRCm39) missense probably benign
R4207:Lingo2 UTSW 4 35,709,810 (GRCm39) missense probably benign 0.01
R4208:Lingo2 UTSW 4 35,709,810 (GRCm39) missense probably benign 0.01
R4326:Lingo2 UTSW 4 35,708,462 (GRCm39) missense probably damaging 1.00
R4327:Lingo2 UTSW 4 35,708,462 (GRCm39) missense probably damaging 1.00
R4328:Lingo2 UTSW 4 35,708,462 (GRCm39) missense probably damaging 1.00
R4474:Lingo2 UTSW 4 35,708,810 (GRCm39) missense probably benign
R6801:Lingo2 UTSW 4 35,709,566 (GRCm39) missense probably damaging 0.97
R7343:Lingo2 UTSW 4 35,709,450 (GRCm39) missense possibly damaging 0.88
R7629:Lingo2 UTSW 4 35,708,675 (GRCm39) missense possibly damaging 0.88
R7740:Lingo2 UTSW 4 35,709,248 (GRCm39) missense probably damaging 0.98
R7867:Lingo2 UTSW 4 35,709,302 (GRCm39) missense probably benign
R7995:Lingo2 UTSW 4 35,709,425 (GRCm39) missense probably damaging 1.00
R8909:Lingo2 UTSW 4 35,708,349 (GRCm39) missense probably damaging 0.99
R9418:Lingo2 UTSW 4 35,709,035 (GRCm39) missense probably benign 0.38
R9612:Lingo2 UTSW 4 35,708,450 (GRCm39) missense probably damaging 0.99
R9633:Lingo2 UTSW 4 35,709,885 (GRCm39) missense
R9764:Lingo2 UTSW 4 35,709,750 (GRCm39) missense possibly damaging 0.55
R9775:Lingo2 UTSW 4 35,708,781 (GRCm39) missense probably benign 0.16
Z1177:Lingo2 UTSW 4 35,709,656 (GRCm39) missense probably benign 0.17
Predicted Primers PCR Primer
(F):5'- CGGGGCACATACTCAAGGTCAATG -3'
(R):5'- TCTCCTCGTGGATGAAGGGCAAAC -3'

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