Incidental Mutation 'R7652:Lef1'
ID 590896
Institutional Source Beutler Lab
Gene Symbol Lef1
Ensembl Gene ENSMUSG00000027985
Gene Name lymphoid enhancer binding factor 1
Synonyms lymphoid enhancer factor 1, Lef-1
MMRRC Submission 045729-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7652 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 130904120-131018005 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 130994003 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Serine at position 354 (R354S)
Ref Sequence ENSEMBL: ENSMUSP00000029611 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029611] [ENSMUST00000066849] [ENSMUST00000098611] [ENSMUST00000106341]
AlphaFold P27782
PDB Structure LEF1 HMG DOMAIN (FROM MOUSE), COMPLEXED WITH DNA (15BP), NMR, 12 STRUCTURES [SOLUTION NMR]
Structure of beta-catenin with Lef-1 [X-RAY DIFFRACTION]
Structure of beta-catenin with phosphorylated Lef-1 [X-RAY DIFFRACTION]
Predicted Effect probably damaging
Transcript: ENSMUST00000029611
AA Change: R354S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000029611
Gene: ENSMUSG00000027985
AA Change: R354S

DomainStartEndE-ValueType
Pfam:CTNNB1_binding 1 211 5e-88 PFAM
low complexity region 245 259 N/A INTRINSIC
HMG 296 366 7.68e-23 SMART
low complexity region 372 380 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000066849
AA Change: R326S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000067808
Gene: ENSMUSG00000027985
AA Change: R326S

DomainStartEndE-ValueType
Pfam:CTNNB1_binding 1 211 1e-75 PFAM
low complexity region 217 231 N/A INTRINSIC
HMG 268 338 7.68e-23 SMART
low complexity region 344 352 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000098611
AA Change: R288S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000096211
Gene: ENSMUSG00000027985
AA Change: R288S

DomainStartEndE-ValueType
Pfam:CTNNB1_binding 1 145 2.8e-54 PFAM
low complexity region 179 193 N/A INTRINSIC
HMG 230 300 7.68e-23 SMART
low complexity region 306 314 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000106341
AA Change: R326S

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000101948
Gene: ENSMUSG00000027985
AA Change: R326S

DomainStartEndE-ValueType
Pfam:CTNNB1_binding 1 211 1.3e-75 PFAM
low complexity region 217 231 N/A INTRINSIC
HMG 268 338 7.68e-23 SMART
low complexity region 344 352 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency 100% (66/66)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a transcription factor belonging to a family of proteins that share homology with the high mobility group protein-1. The protein encoded by this gene can bind to a functionally important site in the T-cell receptor-alpha enhancer, thereby conferring maximal enhancer activity. This transcription factor is involved in the Wnt signaling pathway, and it may function in hair cell differentiation and follicle morphogenesis. Mutations in this gene have been found in somatic sebaceous tumors. This gene has also been linked to other cancers, including androgen-independent prostate cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
PHENOTYPE: Mice homozygous for a null allele are small and die postnatally showing lack of teeth, mammary and uterine glands, whiskers, body hair, dermal-associated fat, and a dentate gyrus, as well as defects in hippocampus morphology, hair follicle development, retinal vasculature, and vascular regression. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agrn A G 4: 156,253,675 (GRCm39) probably null Het
Alb G C 5: 90,615,214 (GRCm39) R242P probably damaging Het
Anxa2r2 A T 13: 120,488,529 (GRCm39) S7T possibly damaging Het
Aph1b T C 9: 66,691,823 (GRCm39) T195A probably benign Het
Apoe G T 7: 19,430,535 (GRCm39) R236S possibly damaging Het
Arap3 G T 18: 38,111,505 (GRCm39) T1137K probably damaging Het
Arhgap45 C T 10: 79,864,672 (GRCm39) A908V probably benign Het
Atp13a1 T C 8: 70,258,209 (GRCm39) C965R probably damaging Het
C7 A G 15: 5,041,587 (GRCm39) Y440H probably damaging Het
Cacna2d2 T C 9: 107,401,397 (GRCm39) probably null Het
Ddah2 C A 17: 35,280,026 (GRCm39) R173S possibly damaging Het
Dnajc11 T C 4: 152,058,682 (GRCm39) Y337H probably damaging Het
Dnajc25 A G 4: 59,020,483 (GRCm39) K302R probably benign Het
Dnajc6 A T 4: 101,463,874 (GRCm39) Q209L probably damaging Het
Drosha G A 15: 12,859,522 (GRCm39) V577I probably benign Het
Ebf2 G T 14: 67,628,016 (GRCm39) probably null Het
Epx A G 11: 87,766,160 (GRCm39) probably null Het
Eqtn T C 4: 94,816,574 (GRCm39) Y73C probably damaging Het
Fam107b A G 2: 3,773,884 (GRCm39) N21S probably benign Het
Fasn G A 11: 120,707,154 (GRCm39) S857F probably damaging Het
Fat1 A G 8: 45,406,336 (GRCm39) N1029S probably damaging Het
Gas8 A G 8: 124,253,275 (GRCm39) I208V probably benign Het
Gm3269 T C 14: 16,026,209 (GRCm39) I88T probably benign Het
Gm8005 C A 14: 42,258,919 (GRCm39) L136F Het
Grid2ip C A 5: 143,368,393 (GRCm39) P743Q probably damaging Het
H2-T15 A T 17: 36,367,675 (GRCm39) V221D probably damaging Het
Hbs1l C T 10: 21,240,659 (GRCm39) T626I probably benign Het
Hdac3 T A 18: 38,087,972 (GRCm39) probably benign Het
Hnrnpab T C 11: 51,496,400 (GRCm39) Y94C probably damaging Het
Homer2 T C 7: 81,299,414 (GRCm39) D17G probably damaging Het
Ikbke C T 1: 131,199,569 (GRCm39) R308Q probably damaging Het
Ints10 A G 8: 69,277,771 (GRCm39) T682A possibly damaging Het
Klhl3 G A 13: 58,261,146 (GRCm39) probably benign Het
Klk1b9 A T 7: 43,445,514 (GRCm39) T235S probably benign Het
Kmt2c T C 5: 25,520,717 (GRCm39) T1798A probably benign Het
Kri1 TTCCTCCTCCTCCTCCTCCTCCTCCTCCTC TTCCTCCTCCTCCTCCTCCTCCTCCTC 9: 21,192,352 (GRCm39) probably benign Het
Krtap4-6 T C 11: 99,556,440 (GRCm39) I96V unknown Het
Lrp6 A T 6: 134,488,208 (GRCm39) L296* probably null Het
Maml2 T C 9: 13,532,945 (GRCm39) Y720H Het
Mmrn1 A G 6: 60,954,490 (GRCm39) N924D probably benign Het
Myh7b A G 2: 155,474,156 (GRCm39) K1624E probably damaging Het
Nos3 T A 5: 24,588,610 (GRCm39) V1112D probably damaging Het
Or2y14 T C 11: 49,404,512 (GRCm39) F16L probably damaging Het
Or4c111 C T 2: 88,843,893 (GRCm39) V172I probably benign Het
Or5an1b C A 19: 12,299,651 (GRCm39) C180F probably damaging Het
Or5w13 A G 2: 87,523,704 (GRCm39) I174T probably damaging Het
Or6c70 A T 10: 129,710,346 (GRCm39) N93K probably damaging Het
Phospho1 T C 11: 95,721,645 (GRCm39) L105S probably damaging Het
Prss35 T A 9: 86,638,023 (GRCm39) N264K probably benign Het
Ptpn13 A G 5: 103,677,578 (GRCm39) D732G probably benign Het
Rab18 A T 18: 6,783,123 (GRCm39) T64S possibly damaging Het
Rft1 A G 14: 30,399,773 (GRCm39) Q319R probably benign Het
Rgs7 T A 1: 174,921,396 (GRCm39) M220L probably benign Het
Rnf13 A G 3: 57,671,772 (GRCm39) N28S probably benign Het
Setd3 A T 12: 108,078,548 (GRCm39) I311N probably damaging Het
Setd5 G A 6: 113,098,725 (GRCm39) R786H probably damaging Het
Slc26a6 T C 9: 108,733,143 (GRCm39) probably null Het
Slc26a9 A T 1: 131,691,634 (GRCm39) T626S probably benign Het
Stambp A T 6: 83,540,910 (GRCm39) probably null Het
Stom A T 2: 35,206,041 (GRCm39) N229K probably benign Het
Tlr1 A T 5: 65,084,130 (GRCm39) L149* probably null Het
Trpc3 C A 3: 36,692,677 (GRCm39) V772F probably benign Het
Ube3a A G 7: 58,893,102 (GRCm39) probably benign Het
Ugt2b35 T A 5: 87,149,369 (GRCm39) F207I probably damaging Het
Usp53 A T 3: 122,746,884 (GRCm39) D360E possibly damaging Het
Vmn2r96 T G 17: 18,793,832 (GRCm39) S59A probably benign Het
Wdr70 A G 15: 8,108,700 (GRCm39) C149R probably benign Het
Wnt3 A G 11: 103,703,290 (GRCm39) T258A possibly damaging Het
Zfp729b T C 13: 67,739,371 (GRCm39) T965A probably benign Het
Zfp764l1 C T 7: 126,992,496 (GRCm39) C38Y probably null Het
Other mutations in Lef1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00096:Lef1 APN 3 130,907,499 (GRCm39) splice site probably benign
IGL00515:Lef1 APN 3 130,997,926 (GRCm39) missense probably damaging 1.00
IGL00780:Lef1 APN 3 130,986,779 (GRCm39) missense possibly damaging 0.69
IGL02057:Lef1 APN 3 130,994,051 (GRCm39) nonsense probably null
IGL02556:Lef1 APN 3 130,988,442 (GRCm39) splice site probably null
IGL02804:Lef1 APN 3 130,988,338 (GRCm39) missense probably damaging 1.00
IGL03143:Lef1 APN 3 130,993,965 (GRCm39) nonsense probably null
IGL03169:Lef1 APN 3 130,988,312 (GRCm39) missense probably damaging 1.00
R0470:Lef1 UTSW 3 130,906,475 (GRCm39) intron probably benign
R1354:Lef1 UTSW 3 130,988,317 (GRCm39) missense probably damaging 1.00
R1677:Lef1 UTSW 3 130,993,938 (GRCm39) splice site probably benign
R1860:Lef1 UTSW 3 130,905,290 (GRCm39) missense probably damaging 0.99
R2013:Lef1 UTSW 3 130,905,236 (GRCm39) missense probably damaging 0.98
R2015:Lef1 UTSW 3 130,905,236 (GRCm39) missense probably damaging 0.98
R3440:Lef1 UTSW 3 130,978,407 (GRCm39) missense probably damaging 1.00
R3736:Lef1 UTSW 3 130,984,715 (GRCm39) missense possibly damaging 0.51
R3918:Lef1 UTSW 3 130,905,290 (GRCm39) missense probably damaging 0.99
R4052:Lef1 UTSW 3 130,988,338 (GRCm39) missense probably damaging 1.00
R4346:Lef1 UTSW 3 130,988,357 (GRCm39) missense probably damaging 1.00
R4608:Lef1 UTSW 3 130,978,382 (GRCm39) missense probably benign 0.00
R4764:Lef1 UTSW 3 130,978,382 (GRCm39) missense probably benign 0.00
R4786:Lef1 UTSW 3 130,905,173 (GRCm39) missense probably damaging 0.99
R5298:Lef1 UTSW 3 130,988,316 (GRCm39) missense possibly damaging 0.80
R5394:Lef1 UTSW 3 130,988,308 (GRCm39) missense probably damaging 1.00
R6827:Lef1 UTSW 3 130,994,053 (GRCm39) critical splice donor site probably null
R6893:Lef1 UTSW 3 130,909,149 (GRCm39) missense possibly damaging 0.77
R6974:Lef1 UTSW 3 130,905,223 (GRCm39) missense probably damaging 1.00
R7541:Lef1 UTSW 3 130,984,748 (GRCm39) missense probably benign 0.00
R7544:Lef1 UTSW 3 130,988,414 (GRCm39) missense probably damaging 1.00
R8074:Lef1 UTSW 3 130,997,954 (GRCm39) critical splice donor site probably null
R8348:Lef1 UTSW 3 130,906,461 (GRCm39) start codon destroyed probably benign 0.02
R8543:Lef1 UTSW 3 130,909,138 (GRCm39) missense possibly damaging 0.92
R8762:Lef1 UTSW 3 130,988,366 (GRCm39) missense probably damaging 1.00
Z1176:Lef1 UTSW 3 130,993,972 (GRCm39) missense probably damaging 1.00
Z1177:Lef1 UTSW 3 130,986,830 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GTAAGTTTCACCCCAGCCTC -3'
(R):5'- CAGTACAGACACGTGCATCCTC -3'

Sequencing Primer
(F):5'- TAGCCGGCAGCCATCCTTTAAC -3'
(R):5'- TCCTCCAAAGATCCCCTCTGAG -3'
Posted On 2019-10-24