Incidental Mutation 'R0645:Lingo3'
ID 57081
Institutional Source Beutler Lab
Gene Symbol Lingo3
Ensembl Gene ENSMUSG00000051067
Gene Name leucine rich repeat and Ig domain containing 3
Synonyms LERN2
MMRRC Submission 038830-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.072) question?
Stock # R0645 (G1)
Quality Score 130
Status Validated
Chromosome 10
Chromosomal Location 80668635-80679873 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 80671169 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Asparagine at position 254 (H254N)
Ref Sequence ENSEMBL: ENSMUSP00000054960 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000053986] [ENSMUST00000219924]
AlphaFold Q6GQU6
Predicted Effect probably benign
Transcript: ENSMUST00000053986
AA Change: H254N

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000054960
Gene: ENSMUSG00000051067
AA Change: H254N

DomainStartEndE-ValueType
LRRNT 23 57 1.54e-5 SMART
LRR_TYP 76 99 1.38e-3 SMART
LRR_TYP 100 123 4.94e-5 SMART
LRR 124 147 3.86e0 SMART
LRR 148 171 4.98e-1 SMART
LRR 172 195 1.62e1 SMART
LRR 246 267 3.46e2 SMART
LRR 269 291 3.86e0 SMART
LRR 292 315 3.24e0 SMART
LRR 316 339 4.34e-1 SMART
LRRCT 351 404 7.18e-3 SMART
IGc2 419 486 3.12e-14 SMART
transmembrane domain 526 548 N/A INTRINSIC
low complexity region 571 581 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000219924
Meta Mutation Damage Score 0.0593 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency 99% (94/95)
Allele List at MGI
Other mutations in this stock
Total: 92 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam18 G T 8: 25,162,136 (GRCm39) Y46* probably null Het
Adam26b A C 8: 43,973,524 (GRCm39) C493G probably damaging Het
Ak5 A T 3: 152,359,252 (GRCm39) L182Q probably damaging Het
Akt1s1 T C 7: 44,498,645 (GRCm39) probably benign Het
Amhr2 G T 15: 102,354,863 (GRCm39) G133C probably damaging Het
Btbd9 A T 17: 30,743,941 (GRCm39) L187Q probably damaging Het
Ccdc117 A T 11: 5,484,385 (GRCm39) probably benign Het
Ccdc138 A T 10: 58,411,542 (GRCm39) I637F probably damaging Het
Ccdc162 A G 10: 41,462,407 (GRCm39) probably benign Het
Cdc25b C A 2: 131,033,533 (GRCm39) H157Q probably benign Het
Cdon A G 9: 35,388,379 (GRCm39) probably null Het
Cdt1 G A 8: 123,298,884 (GRCm39) probably benign Het
Cep350 C T 1: 155,816,458 (GRCm39) probably null Het
Cfb T C 17: 35,078,992 (GRCm39) K831R probably benign Het
Cldn4 C A 5: 134,975,645 (GRCm39) probably benign Het
Cntnap5b T C 1: 99,999,767 (GRCm39) probably benign Het
Cyp27b1 T G 10: 126,884,967 (GRCm39) S77A probably benign Het
Dlc1 T C 8: 37,041,203 (GRCm39) D1342G possibly damaging Het
Dlgap4 A G 2: 156,603,799 (GRCm39) H887R probably damaging Het
Duox2 A G 2: 122,123,139 (GRCm39) I503T probably damaging Het
Eml4 T C 17: 83,770,922 (GRCm39) probably benign Het
Ermap A G 4: 119,042,888 (GRCm39) S212P probably benign Het
Esrrg T A 1: 187,775,538 (GRCm39) C22S probably benign Het
Evx2 T A 2: 74,488,238 (GRCm39) Y194F possibly damaging Het
Fbn2 T G 18: 58,191,461 (GRCm39) D1554A probably damaging Het
Flrt1 G A 19: 7,074,508 (GRCm39) probably benign Het
Fndc5 A G 4: 129,033,630 (GRCm39) probably benign Het
Frem1 A T 4: 82,907,403 (GRCm39) I837N probably damaging Het
Fzd10 G T 5: 128,679,662 (GRCm39) A461S possibly damaging Het
Ganab T A 19: 8,888,477 (GRCm39) Y511N probably damaging Het
Gbp7 A G 3: 142,243,926 (GRCm39) probably null Het
Gm5919 T A 9: 83,765,436 (GRCm39) C91S unknown Het
Gpr31b A T 17: 13,271,093 (GRCm39) C25* probably null Het
Grb10 A G 11: 11,886,755 (GRCm39) S505P probably damaging Het
Grm4 A T 17: 27,654,183 (GRCm39) V542E probably damaging Het
Gsta5 T C 9: 78,206,303 (GRCm39) I75T possibly damaging Het
Hivep3 G A 4: 119,954,531 (GRCm39) R949H possibly damaging Het
Hycc1 C T 5: 24,184,506 (GRCm39) G242D probably damaging Het
Invs A T 4: 48,407,653 (GRCm39) M543L probably benign Het
Kcnk2 T C 1: 188,988,927 (GRCm39) probably null Het
Kdm6b A T 11: 69,295,844 (GRCm39) S808T unknown Het
Klhl30 C T 1: 91,283,228 (GRCm39) R277W probably damaging Het
Lama1 A G 17: 68,080,707 (GRCm39) Q1245R probably benign Het
Lzts1 A T 8: 69,588,392 (GRCm39) H521Q possibly damaging Het
Map3k19 A C 1: 127,749,919 (GRCm39) I1144S possibly damaging Het
Mast2 T C 4: 116,170,043 (GRCm39) probably benign Het
Mast2 A G 4: 116,165,184 (GRCm39) S1411P probably damaging Het
Mesp1 G T 7: 79,442,328 (GRCm39) S225R possibly damaging Het
Micu1 A G 10: 59,675,503 (GRCm39) T366A possibly damaging Het
Mideas G T 12: 84,205,077 (GRCm39) N834K possibly damaging Het
Mknk2 T C 10: 80,507,742 (GRCm39) probably null Het
Msh5 A G 17: 35,258,199 (GRCm39) L309P probably damaging Het
Myo7b T C 18: 32,127,962 (GRCm39) I577V probably benign Het
Myom2 T A 8: 15,167,698 (GRCm39) D1094E probably damaging Het
Nedd1 T C 10: 92,527,693 (GRCm39) probably null Het
Neu4 T C 1: 93,950,191 (GRCm39) L50S probably damaging Het
Noa1 T C 5: 77,457,722 (GRCm39) Y61C probably benign Het
Nr1h4 A T 10: 89,342,390 (GRCm39) M30K probably benign Het
Nsd3 A G 8: 26,199,096 (GRCm39) I1219V probably benign Het
Nup188 T A 2: 30,233,478 (GRCm39) probably null Het
Or10ag2 T A 2: 87,248,612 (GRCm39) Y71* probably null Het
Or5al5 A G 2: 85,961,378 (GRCm39) S210P probably damaging Het
Or6c208 T A 10: 129,224,162 (GRCm39) I220N possibly damaging Het
Or6k2 A T 1: 173,986,920 (GRCm39) T194S probably benign Het
Pbk G A 14: 66,051,245 (GRCm39) probably benign Het
Pcnx2 G A 8: 126,487,459 (GRCm39) T1848M possibly damaging Het
Pdzd7 C T 19: 45,033,914 (GRCm39) G57R possibly damaging Het
Pik3r4 C A 9: 105,546,386 (GRCm39) probably benign Het
Plce1 A G 19: 38,766,433 (GRCm39) S2153G probably damaging Het
Potefam1 C T 2: 111,044,928 (GRCm39) probably null Het
Pphln1 G A 15: 93,318,192 (GRCm39) V34M possibly damaging Het
Prrc2a T C 17: 35,375,308 (GRCm39) D1114G probably damaging Het
Prss16 T C 13: 22,193,546 (GRCm39) probably benign Het
Rtp3 T C 9: 110,816,168 (GRCm39) K128E probably damaging Het
Scn3a T A 2: 65,355,194 (GRCm39) I241F possibly damaging Het
Setd1a G A 7: 127,386,382 (GRCm39) V336I probably damaging Het
Sfpq A G 4: 126,916,762 (GRCm39) I320V possibly damaging Het
Skint5 A T 4: 113,620,679 (GRCm39) D678E unknown Het
Slc12a9 G A 5: 137,313,638 (GRCm39) P774S probably benign Het
Slc25a54 C G 3: 109,019,481 (GRCm39) L362V possibly damaging Het
Smarcd1 A G 15: 99,605,267 (GRCm39) probably null Het
Spata31e5 T A 1: 28,816,011 (GRCm39) N674Y probably damaging Het
Suco A T 1: 161,661,683 (GRCm39) M916K probably damaging Het
Tiam2 T C 17: 3,564,973 (GRCm39) S1404P possibly damaging Het
Topors T C 4: 40,260,333 (GRCm39) T984A unknown Het
Trabd2b A T 4: 114,443,767 (GRCm39) K308M probably damaging Het
Trmo A T 4: 46,377,083 (GRCm39) probably benign Het
Trpc3 A T 3: 36,725,654 (GRCm39) D107E probably benign Het
Ugcg C T 4: 59,207,798 (GRCm39) P46S probably benign Het
Uggt2 A C 14: 119,295,010 (GRCm39) Y539D probably benign Het
Wwc2 T G 8: 48,353,674 (GRCm39) probably benign Het
Zdbf2 T A 1: 63,344,109 (GRCm39) D829E possibly damaging Het
Other mutations in Lingo3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01141:Lingo3 APN 10 80,671,147 (GRCm39) missense probably damaging 1.00
IGL02120:Lingo3 APN 10 80,671,693 (GRCm39) missense probably damaging 1.00
IGL02755:Lingo3 APN 10 80,671,843 (GRCm39) missense possibly damaging 0.49
IGL02938:Lingo3 APN 10 80,670,988 (GRCm39) missense probably benign 0.00
IGL02945:Lingo3 APN 10 80,670,532 (GRCm39) missense probably damaging 1.00
IGL03167:Lingo3 APN 10 80,671,178 (GRCm39) missense probably damaging 1.00
R0639:Lingo3 UTSW 10 80,671,618 (GRCm39) missense probably benign 0.11
R0673:Lingo3 UTSW 10 80,671,618 (GRCm39) missense probably benign 0.11
R1250:Lingo3 UTSW 10 80,670,605 (GRCm39) missense probably benign 0.05
R1521:Lingo3 UTSW 10 80,671,555 (GRCm39) missense probably benign
R1794:Lingo3 UTSW 10 80,671,432 (GRCm39) missense probably benign 0.19
R4665:Lingo3 UTSW 10 80,671,372 (GRCm39) missense probably damaging 1.00
R5587:Lingo3 UTSW 10 80,671,364 (GRCm39) missense probably damaging 0.98
R6458:Lingo3 UTSW 10 80,671,150 (GRCm39) missense probably damaging 1.00
R7082:Lingo3 UTSW 10 80,671,625 (GRCm39) missense probably benign
R7231:Lingo3 UTSW 10 80,670,938 (GRCm39) missense possibly damaging 0.86
R7314:Lingo3 UTSW 10 80,670,707 (GRCm39) missense possibly damaging 0.92
R7390:Lingo3 UTSW 10 80,670,463 (GRCm39) missense probably damaging 1.00
R7450:Lingo3 UTSW 10 80,670,671 (GRCm39) nonsense probably null
R7650:Lingo3 UTSW 10 80,671,597 (GRCm39) missense probably damaging 1.00
R7894:Lingo3 UTSW 10 80,670,610 (GRCm39) nonsense probably null
R7920:Lingo3 UTSW 10 80,670,382 (GRCm39) missense probably benign 0.09
R8070:Lingo3 UTSW 10 80,671,955 (GRCm39) start gained probably benign
R8095:Lingo3 UTSW 10 80,671,255 (GRCm39) missense probably benign 0.01
R8171:Lingo3 UTSW 10 80,670,595 (GRCm39) missense probably benign
R8178:Lingo3 UTSW 10 80,670,464 (GRCm39) missense possibly damaging 0.80
R8425:Lingo3 UTSW 10 80,670,816 (GRCm39) missense probably benign 0.04
R9053:Lingo3 UTSW 10 80,670,821 (GRCm39) missense probably benign 0.00
R9059:Lingo3 UTSW 10 80,670,523 (GRCm39) missense probably benign 0.12
R9706:Lingo3 UTSW 10 80,670,288 (GRCm39) missense probably damaging 0.99
R9794:Lingo3 UTSW 10 80,670,707 (GRCm39) missense possibly damaging 0.92
Z1176:Lingo3 UTSW 10 80,670,689 (GRCm39) missense possibly damaging 0.95
Predicted Primers PCR Primer
(F):5'- TTGTCCGAAAGGTTGAGCAGGC -3'
(R):5'- GCGCTGCAATCTCACATCACTGTC -3'

Sequencing Primer
(F):5'- ATCTGTCGCAGCCCCAC -3'
(R):5'- ACATCACTGTCCCCGGAG -3'
Posted On 2013-07-11