Incidental Mutation 'R4899:Llgl1'
ID 376026
Institutional Source Beutler Lab
Gene Symbol Llgl1
Ensembl Gene ENSMUSG00000020536
Gene Name LLGL1 scribble cell polarity complex component
Synonyms Lgl1
MMRRC Submission 042503-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4899 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 60590549-60605012 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 60600394 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Leucine at position 581 (P581L)
Ref Sequence ENSEMBL: ENSMUSP00000104359 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002889] [ENSMUST00000052346] [ENSMUST00000108719]
AlphaFold Q80Y17
Predicted Effect probably benign
Transcript: ENSMUST00000002889
SMART Domains Protein: ENSMUSP00000002889
Gene: ENSMUSG00000002812

DomainStartEndE-ValueType
LRR 55 78 1.08e-1 SMART
LRR 103 126 4.08e0 SMART
LRR 127 149 2.27e1 SMART
LRR 150 173 1.25e-1 SMART
LRR 222 244 6.78e1 SMART
LRR 245 268 2.86e-1 SMART
LRR 269 291 3.78e-1 SMART
LRR 316 339 2.82e0 SMART
LRR 340 362 2.27e2 SMART
low complexity region 403 420 N/A INTRINSIC
GEL 499 597 4.17e-25 SMART
GEL 617 709 1.72e-26 SMART
low complexity region 727 740 N/A INTRINSIC
GEL 745 838 2.24e-25 SMART
GEL 905 1039 1.13e-3 SMART
GEL 1056 1152 7.28e-16 SMART
GEL 1167 1263 5.51e-25 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000052346
AA Change: P581L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000060749
Gene: ENSMUSG00000020536
AA Change: P581L

DomainStartEndE-ValueType
WD40 22 62 4.42e1 SMART
WD40 64 103 1.65e1 SMART
WD40 187 223 2.74e2 SMART
WD40 226 264 2.06e0 SMART
Pfam:LLGL 278 379 1.2e-43 PFAM
WD40 424 460 3.2e0 SMART
Blast:WD40 498 541 2e-13 BLAST
Blast:WD40 585 624 4e-9 BLAST
Pfam:Lgl_C 732 978 1.2e-7 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000108719
AA Change: P581L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000104359
Gene: ENSMUSG00000020536
AA Change: P581L

DomainStartEndE-ValueType
WD40 22 62 4.42e1 SMART
WD40 64 103 1.65e1 SMART
WD40 187 223 2.74e2 SMART
WD40 226 264 2.06e0 SMART
Pfam:LLGL 275 379 2e-48 PFAM
WD40 424 460 3.2e0 SMART
Blast:WD40 498 540 2e-13 BLAST
Blast:WD40 585 624 4e-9 BLAST
Pfam:Lgl_C 804 976 1.3e-8 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128749
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154141
Meta Mutation Damage Score 0.0616 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.7%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is similar to a tumor suppressor in Drosophila. The protein is part of a cytoskeletal network and is associated with nonmuscle myosin II heavy chain and a kinase that specifically phosphorylates this protein at serine residues. The gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutant mice die neonatally exhibiting hydroencephaly. Neural progenitor cell physiology is abnormal, resulting in a loss of cell polarity and the development of neuroepithelial rosette-like structures throughout the brain. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd18 C G 3: 40,860,304 (GRCm39) probably null Het
Adra2c A T 5: 35,437,705 (GRCm39) Y159F probably damaging Het
Alkal2 T A 12: 30,934,972 (GRCm39) S64T probably benign Het
Apbb1ip T C 2: 22,713,361 (GRCm39) V72A unknown Het
Atp13a5 A G 16: 29,197,318 (GRCm39) L13P probably damaging Het
Azin2 G A 4: 128,828,446 (GRCm39) P254S probably benign Het
Bmpr1b T C 3: 141,546,444 (GRCm39) R481G probably damaging Het
Cacna2d4 G A 6: 119,245,157 (GRCm39) W288* probably null Het
Cass4 A G 2: 172,269,789 (GRCm39) T626A probably benign Het
Cep112 T A 11: 108,497,110 (GRCm39) D683E probably damaging Het
Cfap300 A T 9: 8,022,494 (GRCm39) S243T possibly damaging Het
Chat G T 14: 32,170,934 (GRCm39) S188R possibly damaging Het
Cit A G 5: 116,001,087 (GRCm39) Y162C possibly damaging Het
Clca3a1 T A 3: 144,443,722 (GRCm39) Y676F probably damaging Het
Clec2h A G 6: 128,652,787 (GRCm39) N185D probably benign Het
Cnbd2 G T 2: 156,181,141 (GRCm39) V192F probably benign Het
Col6a3 C A 1: 90,730,149 (GRCm39) G1112V probably damaging Het
Csta2 A T 16: 36,077,731 (GRCm39) Y96F possibly damaging Het
Cyp3a25 A G 5: 145,914,481 (GRCm39) F483S possibly damaging Het
Dscam T C 16: 96,485,018 (GRCm39) E1103G probably benign Het
Dync2h1 G A 9: 7,131,921 (GRCm39) Q1629* probably null Het
Enpp6 A G 8: 47,440,118 (GRCm39) Y38C probably damaging Het
Epg5 T A 18: 78,028,272 (GRCm39) L1271Q probably damaging Het
Fam47e G A 5: 92,722,528 (GRCm39) V75I probably benign Het
Fat3 T C 9: 15,881,095 (GRCm39) D3259G probably damaging Het
Fbxw28 T C 9: 109,159,921 (GRCm39) D211G probably damaging Het
Flnc A G 6: 29,446,842 (GRCm39) N990D probably benign Het
Frat1 T G 19: 41,818,761 (GRCm39) L52R probably damaging Het
Ftmt C G 18: 52,464,658 (GRCm39) probably benign Het
H2-M1 C T 17: 36,982,112 (GRCm39) G163D probably benign Het
Hapln1 A G 13: 89,749,769 (GRCm39) K105E possibly damaging Het
Igkv17-127 G T 6: 67,838,381 (GRCm39) A31S probably benign Het
Il6st T C 13: 112,637,695 (GRCm39) L628P probably damaging Het
Kcnj6 A G 16: 94,633,472 (GRCm39) I213T probably damaging Het
Kidins220 T C 12: 25,063,442 (GRCm39) probably null Het
Lama2 TTTGCGCATT TTT 10: 26,919,639 (GRCm39) probably null Het
Mertk C A 2: 128,625,845 (GRCm39) P660Q probably damaging Het
Mrtfa A G 15: 80,902,587 (GRCm39) Y241H probably damaging Het
Mtarc2 A T 1: 184,577,821 (GRCm39) I65N probably damaging Het
Napepld A G 5: 21,888,438 (GRCm39) Y4H probably benign Het
Ncam1 T A 9: 49,456,551 (GRCm39) probably null Het
Nuak2 A T 1: 132,252,724 (GRCm39) K93* probably null Het
Oat A T 7: 132,165,951 (GRCm39) D211E probably benign Het
Or1j19 A G 2: 36,676,810 (GRCm39) Q91R probably benign Het
Or2aj6 G A 16: 19,442,950 (GRCm39) A300V probably benign Het
Or4c109 A C 2: 88,818,454 (GRCm39) L31V probably null Het
Or51b17 A G 7: 103,542,672 (GRCm39) I90T possibly damaging Het
Or7a39 A T 10: 78,715,041 (GRCm39) S12C probably benign Het
Pde4dip C A 3: 97,616,874 (GRCm39) K1789N probably damaging Het
Piezo2 T C 18: 63,211,862 (GRCm39) I1322V possibly damaging Het
Pih1d1 A G 7: 44,803,951 (GRCm39) probably benign Het
Plekhd1 T C 12: 80,769,101 (GRCm39) S454P probably damaging Het
Polr2h G A 16: 20,539,303 (GRCm39) V89M probably damaging Het
Pptc7 G A 5: 122,422,780 (GRCm39) G17S possibly damaging Het
Pramel55 T C 5: 95,949,586 (GRCm39) V111A probably benign Het
Ptpra T C 2: 130,386,356 (GRCm39) V602A probably damaging Het
Rnf123 C T 9: 107,940,879 (GRCm39) R654H probably damaging Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Samsn1 A G 16: 75,675,991 (GRCm39) S135P probably damaging Het
Sgsm3 A G 15: 80,890,980 (GRCm39) N147S probably benign Het
Shoc1 T C 4: 59,062,640 (GRCm39) Y872C probably damaging Het
Slc22a29 T C 19: 8,138,933 (GRCm39) T510A probably benign Het
Smc4 T A 3: 68,939,144 (GRCm39) H978Q probably damaging Het
Sox7 G A 14: 64,185,927 (GRCm39) R321H probably damaging Het
Spred3 T C 7: 28,861,258 (GRCm39) D307G probably damaging Het
Syne2 T A 12: 75,900,875 (GRCm39) D11E probably benign Het
Tob1 ACAGCAGCAGCAGCAGCAGCAGCAGCA ACAGCAGCAGCAGCAGCAGCAGCA 11: 94,105,278 (GRCm39) probably benign Het
Top2b A T 14: 16,387,313 (GRCm38) I134F probably damaging Het
Tspan1 T A 4: 116,020,563 (GRCm39) R206* probably null Het
Ttc3 A T 16: 94,230,314 (GRCm39) N837I probably damaging Het
Vmn1r36 T C 6: 66,693,549 (GRCm39) T72A possibly damaging Het
Vmn2r10 A G 5: 109,151,324 (GRCm39) S97P probably damaging Het
Zfp2 T A 11: 50,790,841 (GRCm39) I401F probably damaging Het
Zfp629 T C 7: 127,210,190 (GRCm39) T540A possibly damaging Het
Zfr G A 15: 12,166,231 (GRCm39) V834I probably benign Het
Other mutations in Llgl1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01137:Llgl1 APN 11 60,600,825 (GRCm39) missense probably benign 0.38
IGL01400:Llgl1 APN 11 60,597,316 (GRCm39) missense probably damaging 1.00
IGL03066:Llgl1 APN 11 60,596,860 (GRCm39) missense possibly damaging 0.75
IGL03174:Llgl1 APN 11 60,597,036 (GRCm39) missense probably benign 0.15
IGL03306:Llgl1 APN 11 60,602,180 (GRCm39) missense possibly damaging 0.92
R0284:Llgl1 UTSW 11 60,602,967 (GRCm39) missense probably damaging 0.98
R1137:Llgl1 UTSW 11 60,595,559 (GRCm39) missense probably benign 0.01
R1432:Llgl1 UTSW 11 60,599,380 (GRCm39) missense probably damaging 1.00
R1769:Llgl1 UTSW 11 60,597,873 (GRCm39) missense probably damaging 1.00
R1786:Llgl1 UTSW 11 60,598,066 (GRCm39) missense probably benign 0.19
R1835:Llgl1 UTSW 11 60,595,556 (GRCm39) missense probably benign 0.00
R1943:Llgl1 UTSW 11 60,596,842 (GRCm39) missense probably benign
R2197:Llgl1 UTSW 11 60,600,865 (GRCm39) missense possibly damaging 0.62
R2510:Llgl1 UTSW 11 60,600,862 (GRCm39) missense probably damaging 1.00
R2568:Llgl1 UTSW 11 60,599,638 (GRCm39) missense probably damaging 1.00
R3690:Llgl1 UTSW 11 60,597,828 (GRCm39) missense probably damaging 1.00
R3853:Llgl1 UTSW 11 60,598,075 (GRCm39) missense probably damaging 1.00
R4079:Llgl1 UTSW 11 60,601,110 (GRCm39) splice site probably null
R4259:Llgl1 UTSW 11 60,600,394 (GRCm39) missense probably benign
R4348:Llgl1 UTSW 11 60,600,394 (GRCm39) missense probably benign
R4349:Llgl1 UTSW 11 60,600,394 (GRCm39) missense probably benign
R4352:Llgl1 UTSW 11 60,600,394 (GRCm39) missense probably benign
R4353:Llgl1 UTSW 11 60,600,394 (GRCm39) missense probably benign
R4396:Llgl1 UTSW 11 60,596,834 (GRCm39) missense probably benign
R4584:Llgl1 UTSW 11 60,602,908 (GRCm39) missense probably damaging 0.99
R4594:Llgl1 UTSW 11 60,597,147 (GRCm39) missense probably benign 0.15
R4628:Llgl1 UTSW 11 60,600,811 (GRCm39) missense probably damaging 1.00
R4651:Llgl1 UTSW 11 60,599,477 (GRCm39) missense possibly damaging 0.80
R4653:Llgl1 UTSW 11 60,599,477 (GRCm39) missense possibly damaging 0.80
R4731:Llgl1 UTSW 11 60,597,051 (GRCm39) nonsense probably null
R4869:Llgl1 UTSW 11 60,598,036 (GRCm39) nonsense probably null
R4898:Llgl1 UTSW 11 60,600,394 (GRCm39) missense probably benign
R4939:Llgl1 UTSW 11 60,600,805 (GRCm39) critical splice acceptor site probably null
R4941:Llgl1 UTSW 11 60,600,394 (GRCm39) missense probably benign
R4942:Llgl1 UTSW 11 60,600,394 (GRCm39) missense probably benign
R4958:Llgl1 UTSW 11 60,602,261 (GRCm39) missense probably benign 0.02
R4995:Llgl1 UTSW 11 60,600,550 (GRCm39) missense probably benign 0.00
R4997:Llgl1 UTSW 11 60,600,394 (GRCm39) missense probably benign
R5177:Llgl1 UTSW 11 60,602,833 (GRCm39) missense possibly damaging 0.94
R5257:Llgl1 UTSW 11 60,602,389 (GRCm39) splice site probably null
R5258:Llgl1 UTSW 11 60,602,389 (GRCm39) splice site probably null
R5401:Llgl1 UTSW 11 60,597,297 (GRCm39) missense probably benign
R5406:Llgl1 UTSW 11 60,604,010 (GRCm39) missense probably damaging 0.99
R5432:Llgl1 UTSW 11 60,598,449 (GRCm39) missense probably benign
R5587:Llgl1 UTSW 11 60,601,168 (GRCm39) missense probably benign 0.00
R5732:Llgl1 UTSW 11 60,600,286 (GRCm39) missense probably benign 0.00
R5758:Llgl1 UTSW 11 60,599,393 (GRCm39) missense probably damaging 1.00
R5879:Llgl1 UTSW 11 60,603,806 (GRCm39) missense probably benign 0.00
R6268:Llgl1 UTSW 11 60,602,989 (GRCm39) missense probably benign 0.13
R6286:Llgl1 UTSW 11 60,600,358 (GRCm39) missense probably damaging 1.00
R6455:Llgl1 UTSW 11 60,600,486 (GRCm39) missense probably damaging 0.98
R6805:Llgl1 UTSW 11 60,593,691 (GRCm39) missense probably benign 0.25
R6929:Llgl1 UTSW 11 60,601,179 (GRCm39) nonsense probably null
R7274:Llgl1 UTSW 11 60,596,812 (GRCm39) missense possibly damaging 0.89
R7889:Llgl1 UTSW 11 60,598,138 (GRCm39) missense probably damaging 1.00
R7986:Llgl1 UTSW 11 60,602,221 (GRCm39) missense probably benign 0.16
R8141:Llgl1 UTSW 11 60,601,142 (GRCm39) missense probably benign 0.02
R8176:Llgl1 UTSW 11 60,597,387 (GRCm39) missense probably benign 0.27
R8223:Llgl1 UTSW 11 60,593,648 (GRCm39) missense possibly damaging 0.86
R8332:Llgl1 UTSW 11 60,601,210 (GRCm39) missense possibly damaging 0.90
R8350:Llgl1 UTSW 11 60,602,947 (GRCm39) missense probably damaging 1.00
R8500:Llgl1 UTSW 11 60,595,809 (GRCm39) critical splice donor site probably null
R8979:Llgl1 UTSW 11 60,601,129 (GRCm39) missense probably benign 0.25
R9155:Llgl1 UTSW 11 60,597,934 (GRCm39) missense probably benign 0.00
R9163:Llgl1 UTSW 11 60,600,402 (GRCm39) missense probably benign 0.02
R9225:Llgl1 UTSW 11 60,600,889 (GRCm39) missense probably damaging 1.00
R9234:Llgl1 UTSW 11 60,600,956 (GRCm39) critical splice donor site probably null
Z1186:Llgl1 UTSW 11 60,603,923 (GRCm39) frame shift probably null
Z1187:Llgl1 UTSW 11 60,603,923 (GRCm39) frame shift probably null
Z1188:Llgl1 UTSW 11 60,603,923 (GRCm39) frame shift probably null
Z1189:Llgl1 UTSW 11 60,603,923 (GRCm39) frame shift probably null
Z1190:Llgl1 UTSW 11 60,603,923 (GRCm39) frame shift probably null
Z1191:Llgl1 UTSW 11 60,603,923 (GRCm39) frame shift probably null
Z1192:Llgl1 UTSW 11 60,603,923 (GRCm39) frame shift probably null
Predicted Primers PCR Primer
(F):5'- GCTCAGTGAAGGCTTTGGTAC -3'
(R):5'- ACCTCGTGCCACATACCTAG -3'

Sequencing Primer
(F):5'- ACATTGTAGGTATTCAGGGGCC -3'
(R):5'- TACCTAGCCAGCACAGGG -3'
Posted On 2016-03-17