Incidental Mutation 'R6196:Lgi1'
ID 502954
Institutional Source Beutler Lab
Gene Symbol Lgi1
Ensembl Gene ENSMUSG00000067242
Gene Name leucine-rich repeat LGI family, member 1
Synonyms
MMRRC Submission 044336-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.740) question?
Stock # R6196 (G1)
Quality Score 105.008
Status Validated
Chromosome 19
Chromosomal Location 38253135-38297387 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 38294257 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 295 (N295S)
Ref Sequence ENSEMBL: ENSMUSP00000143538 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000087252] [ENSMUST00000196090] [ENSMUST00000198045] [ENSMUST00000198518] [ENSMUST00000199812]
AlphaFold Q9JIA1
Predicted Effect probably benign
Transcript: ENSMUST00000087252
SMART Domains Protein: ENSMUSP00000084507
Gene: ENSMUSG00000067242

DomainStartEndE-ValueType
signal peptide 1 34 N/A INTRINSIC
LRRNT 41 71 9.09e0 SMART
LRR 90 113 2.61e2 SMART
LRR_TYP 114 137 5.14e-3 SMART
LRR_TYP 138 161 2.27e-4 SMART
LRRCT 173 222 4.63e-6 SMART
Pfam:EPTP 225 266 3.8e-9 PFAM
Pfam:EPTP 271 312 6.5e-12 PFAM
Pfam:EPTP 317 363 7.2e-16 PFAM
Pfam:EPTP 366 414 1.4e-7 PFAM
Pfam:EPTP 419 461 1.6e-12 PFAM
Pfam:EPTP 464 505 7.7e-11 PFAM
Pfam:EPTP 510 550 3.4e-13 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130039
SMART Domains Protein: ENSMUSP00000117936
Gene: ENSMUSG00000067242

DomainStartEndE-ValueType
low complexity region 11 38 N/A INTRINSIC
LRR 51 74 2.61e2 SMART
LRR_TYP 75 98 5.14e-3 SMART
LRR_TYP 99 122 2.27e-4 SMART
LRRCT 131 180 4.63e-6 SMART
Pfam:EPTP 182 218 3e-12 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000196090
AA Change: N295S

PolyPhen 2 Score 0.228 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000143538
Gene: ENSMUSG00000067242
AA Change: N295S

DomainStartEndE-ValueType
signal peptide 1 34 N/A INTRINSIC
LRRNT 41 71 4.4e-2 SMART
LRR_TYP 90 113 3.3e-4 SMART
LRRCT 125 174 2.3e-8 SMART
Pfam:EPTP 177 218 3.1e-6 PFAM
Pfam:EPTP 223 264 5.3e-9 PFAM
Pfam:EPTP 269 315 5.8e-13 PFAM
Pfam:EPTP 318 366 1.1e-4 PFAM
Pfam:EPTP 371 413 1.3e-9 PFAM
Pfam:EPTP 416 457 6.2e-8 PFAM
Pfam:EPTP 462 502 2.7e-10 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000198045
SMART Domains Protein: ENSMUSP00000143292
Gene: ENSMUSG00000067242

DomainStartEndE-ValueType
signal peptide 1 34 N/A INTRINSIC
LRRNT 41 71 4.3e-2 SMART
LRR 90 113 1.1e0 SMART
LRR_TYP 114 137 2.1e-5 SMART
LRR_TYP 138 161 9.2e-7 SMART
LRRCT 173 222 2.3e-8 SMART
Pfam:EPTP 224 267 2.8e-12 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000198518
AA Change: N343S

PolyPhen 2 Score 0.159 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000143128
Gene: ENSMUSG00000067242
AA Change: N343S

DomainStartEndE-ValueType
signal peptide 1 34 N/A INTRINSIC
LRRNT 41 71 9.09e0 SMART
LRR 90 113 2.61e2 SMART
LRR_TYP 114 137 5.14e-3 SMART
LRR_TYP 138 161 2.27e-4 SMART
LRRCT 173 222 4.63e-6 SMART
Pfam:EPTP 224 267 8.3e-15 PFAM
Pfam:EPTP 270 313 9.4e-16 PFAM
Pfam:EPTP 316 364 3.3e-18 PFAM
Pfam:EPTP 365 415 5.2e-8 PFAM
Pfam:EPTP 418 462 1e-16 PFAM
Pfam:EPTP 463 506 1.9e-15 PFAM
Pfam:EPTP 509 550 2.8e-17 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000199812
AA Change: N319S

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000143502
Gene: ENSMUSG00000067242
AA Change: N319S

DomainStartEndE-ValueType
signal peptide 1 34 N/A INTRINSIC
LRRNT 41 71 4.4e-2 SMART
LRR_TYP 90 113 2.2e-5 SMART
LRR_TYP 114 137 9.4e-7 SMART
LRRCT 149 198 2.3e-8 SMART
Pfam:EPTP 201 242 3.2e-6 PFAM
Pfam:EPTP 247 288 5.6e-9 PFAM
Pfam:EPTP 293 339 6.1e-13 PFAM
Pfam:EPTP 342 390 1.2e-4 PFAM
Pfam:EPTP 395 437 1.4e-9 PFAM
Pfam:EPTP 440 481 6.6e-8 PFAM
Pfam:EPTP 486 526 2.9e-10 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200561
Meta Mutation Damage Score 0.4154 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.8%
Validation Efficiency 96% (55/57)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the secreted leucine-rich repeat (LRR) superfamily and shares homology with members of the SLIT protein family. The encoded protein may regulate the activity of voltage-gated potassium channels and may be involved in neuronal growth regulation and cell survival. This gene is rearranged as a result of translocations in glioblastoma cell lines, and it is frequently down-regulated or rearranged in malignant gliomas. Mutations in this gene result in autosomal dominant lateral temporal epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit growth retardation, seizures, and death by the third week of life. Mice heterozygous for this allele exhibit increased suseptibility to pentylenetetrazole-induced seizures. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933405L10Rik A T 8: 106,436,554 (GRCm39) H241L possibly damaging Het
Acap1 T C 11: 69,777,893 (GRCm39) D115G probably damaging Het
Acvr2b T C 9: 119,262,469 (GRCm39) V510A possibly damaging Het
Acyp2 C T 11: 30,456,354 (GRCm39) E98K possibly damaging Het
Agr2 A T 12: 36,045,591 (GRCm39) K26* probably null Het
Aox4 T A 1: 58,256,685 (GRCm39) I69N probably damaging Het
Asb4 G A 6: 5,390,699 (GRCm39) G31R probably benign Het
Atp6v1c2 C A 12: 17,351,187 (GRCm39) E105* probably null Het
Bend6 A G 1: 33,917,509 (GRCm39) Y44H probably damaging Het
Bltp3b T G 10: 89,641,195 (GRCm39) S789A probably benign Het
Btn2a2 C T 13: 23,672,015 (GRCm39) V25M possibly damaging Het
Cab39l T A 14: 59,737,039 (GRCm39) L53Q probably damaging Het
Cc2d1b C T 4: 108,490,422 (GRCm39) R825W probably damaging Het
Cdc14b C T 13: 64,353,338 (GRCm39) probably benign Het
Cenpu A G 8: 47,015,615 (GRCm39) R177G probably benign Het
Chit1 C A 1: 134,074,381 (GRCm39) Y229* probably null Het
Crybg2 C A 4: 133,808,450 (GRCm39) S1350R probably damaging Het
Ctdspl2 A G 2: 121,809,373 (GRCm39) probably null Het
Ctsr A T 13: 61,308,345 (GRCm39) H266Q probably benign Het
Dynlt5 A G 4: 102,849,766 (GRCm39) E63G possibly damaging Het
Efcab3 T G 11: 104,746,386 (GRCm39) I2279S probably benign Het
Extl3 T A 14: 65,313,584 (GRCm39) M533L probably benign Het
Fam162b C A 10: 51,463,506 (GRCm39) probably null Het
Fbxo28 T C 1: 182,157,454 (GRCm39) K121R probably damaging Het
Fsip2 A C 2: 82,820,227 (GRCm39) E5320A possibly damaging Het
Galc A T 12: 98,225,421 (GRCm39) D56E probably damaging Het
Gm5468 A G 15: 25,414,481 (GRCm39) probably benign Het
Hk1 T A 10: 62,135,038 (GRCm39) H24L probably damaging Het
Igkv5-43 A G 6: 69,752,965 (GRCm39) V39A possibly damaging Het
Lemd2 G A 17: 27,411,976 (GRCm39) Q439* probably null Het
Macc1 T G 12: 119,409,785 (GRCm39) S184R probably damaging Het
Msmo1 A G 8: 65,180,918 (GRCm39) probably benign Het
Muc5b C A 7: 141,405,333 (GRCm39) R914S unknown Het
Or10d1 G A 9: 39,483,776 (GRCm39) P260S possibly damaging Het
Or1e16 G A 11: 73,286,299 (GRCm39) A183V probably benign Het
Or1e17 G A 11: 73,831,635 (GRCm39) A188T possibly damaging Het
Or4k2 C A 14: 50,424,135 (GRCm39) D180Y probably damaging Het
Or5b110-ps1 A G 19: 13,260,290 (GRCm39) I44T probably benign Het
Plekha5 T C 6: 140,525,179 (GRCm39) S14P probably benign Het
Pus10 A G 11: 23,622,638 (GRCm39) K86R probably benign Het
Rab37 T C 11: 115,051,132 (GRCm39) V147A probably benign Het
Sin3a T A 9: 57,011,213 (GRCm39) I490N probably damaging Het
Slc27a4 A G 2: 29,695,762 (GRCm39) D99G probably benign Het
Slc43a2 C T 11: 75,459,206 (GRCm39) R413* probably null Het
Syna G T 5: 134,588,466 (GRCm39) T161N probably benign Het
T A G 17: 8,655,996 (GRCm39) D86G possibly damaging Het
Tanc1 G A 2: 59,674,366 (GRCm39) E1817K possibly damaging Het
Tap2 C A 17: 34,433,384 (GRCm39) Q516K possibly damaging Het
Tcaf1 A T 6: 42,653,741 (GRCm39) D717E probably damaging Het
Tcf20 G T 15: 82,736,187 (GRCm39) Q1755K possibly damaging Het
Top2b T G 14: 16,409,189 (GRCm38) I777M probably damaging Het
Trpm7 G A 2: 126,667,559 (GRCm39) P811S possibly damaging Het
Vmn2r59 A G 7: 41,661,679 (GRCm39) V712A probably benign Het
Vwc2l T A 1: 70,768,180 (GRCm39) D34E probably damaging Het
Wdr35 A G 12: 9,077,632 (GRCm39) K1091E probably benign Het
Other mutations in Lgi1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02882:Lgi1 APN 19 38,272,453 (GRCm39) missense probably benign 0.24
IGL03112:Lgi1 APN 19 38,272,478 (GRCm39) missense possibly damaging 0.84
R0201:Lgi1 UTSW 19 38,289,741 (GRCm39) missense possibly damaging 0.92
R1573:Lgi1 UTSW 19 38,272,629 (GRCm39) missense probably benign 0.30
R1795:Lgi1 UTSW 19 38,294,631 (GRCm39) missense probably benign
R2010:Lgi1 UTSW 19 38,289,683 (GRCm39) missense probably damaging 1.00
R3732:Lgi1 UTSW 19 38,294,694 (GRCm39) missense probably damaging 1.00
R3732:Lgi1 UTSW 19 38,294,694 (GRCm39) missense probably damaging 1.00
R3733:Lgi1 UTSW 19 38,294,694 (GRCm39) missense probably damaging 1.00
R4643:Lgi1 UTSW 19 38,289,158 (GRCm39) missense probably damaging 1.00
R4678:Lgi1 UTSW 19 38,289,737 (GRCm39) missense probably damaging 1.00
R4814:Lgi1 UTSW 19 38,289,326 (GRCm39) critical splice donor site probably null
R4857:Lgi1 UTSW 19 38,294,698 (GRCm39) missense probably damaging 1.00
R5598:Lgi1 UTSW 19 38,294,629 (GRCm39) missense possibly damaging 0.94
R6180:Lgi1 UTSW 19 38,253,404 (GRCm39) missense probably damaging 1.00
R6847:Lgi1 UTSW 19 38,289,738 (GRCm39) missense probably damaging 1.00
R7178:Lgi1 UTSW 19 38,294,733 (GRCm39) missense probably damaging 1.00
R7376:Lgi1 UTSW 19 38,272,468 (GRCm39) missense probably damaging 1.00
R7448:Lgi1 UTSW 19 38,289,713 (GRCm39) missense probably damaging 1.00
R8790:Lgi1 UTSW 19 38,289,296 (GRCm39) missense possibly damaging 0.58
R8899:Lgi1 UTSW 19 38,294,538 (GRCm39) missense probably damaging 1.00
R9089:Lgi1 UTSW 19 38,294,095 (GRCm39) missense possibly damaging 0.56
R9156:Lgi1 UTSW 19 38,289,746 (GRCm39) missense probably benign 0.08
R9484:Lgi1 UTSW 19 38,294,757 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- GGTGTGCAAGCCCATAGTTATTG -3'
(R):5'- AATAGCTGTGTTGCTTTGCTCC -3'

Sequencing Primer
(F):5'- GTGCAAGCCCATAGTTATTGACACTC -3'
(R):5'- CTTTGCTCCACTGGTAAATAACAGGG -3'
Posted On 2018-02-27