Incidental Mutation 'R4764:Lef1'
ID 357082
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 042405-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4764 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 130904120-131018005 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 130978382 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 167 (S167P)
Ref Sequence ENSEMBL: ENSMUSP00000101948 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029611] [ENSMUST00000066849] [ENSMUST00000098611] [ENSMUST00000106341]
AlphaFold P27782
Predicted Effect probably benign
Transcript: ENSMUST00000029611
AA Change: S167P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000029611
Gene: ENSMUSG00000027985
AA Change: S167P

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 benign
Transcript: ENSMUST00000066849
AA Change: S167P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000067808
Gene: ENSMUSG00000027985
AA Change: S167P

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 benign
Transcript: ENSMUST00000098611
AA Change: S101P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000096211
Gene: ENSMUSG00000027985
AA Change: S101P

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 benign
Transcript: ENSMUST00000106341
AA Change: S167P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000101948
Gene: ENSMUSG00000027985
AA Change: S167P

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132737
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198624
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200166
Meta Mutation Damage Score 0.0696 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency 99% (78/79)
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700001J03Rik T G 5: 146,122,029 (GRCm39) S18R probably benign Het
2010315B03Rik A C 9: 124,056,396 (GRCm39) V176G probably benign Het
Abcb1a T A 5: 8,765,732 (GRCm39) probably null Het
Acad11 C A 9: 103,953,076 (GRCm39) P102T probably damaging Het
Aggf1 T A 13: 95,501,221 (GRCm39) D387V probably damaging Het
Akr1c13 G A 13: 4,248,496 (GRCm39) V234I probably benign Het
Alg5 A G 3: 54,653,894 (GRCm39) Y210C possibly damaging Het
Arl8a C A 1: 135,074,837 (GRCm39) A41E probably benign Het
Axin1 C A 17: 26,392,730 (GRCm39) T337K possibly damaging Het
Bdp1 A G 13: 100,192,775 (GRCm39) L1353P probably damaging Het
Bptf A T 11: 106,934,520 (GRCm39) V2851E probably damaging Het
C9 A T 15: 6,489,124 (GRCm39) E160D probably damaging Het
Cbx6 T C 15: 79,712,881 (GRCm39) D182G probably damaging Het
Cep57l1 T C 10: 41,597,678 (GRCm39) R242G possibly damaging Het
Chst8 T C 7: 34,375,149 (GRCm39) D230G probably damaging Het
Col3a1 A C 1: 45,385,270 (GRCm39) D129A probably damaging Het
Cst12 A G 2: 148,631,393 (GRCm39) E38G possibly damaging Het
Disp1 G T 1: 182,869,660 (GRCm39) A920E probably damaging Het
Dtna T G 18: 23,668,206 (GRCm39) probably null Het
Elp3 T A 14: 65,820,378 (GRCm39) H97L probably damaging Het
Exoc8 A G 8: 125,624,314 (GRCm39) F18L possibly damaging Het
Extl3 T C 14: 65,314,769 (GRCm39) T138A probably benign Het
Foxi2 G T 7: 135,012,396 (GRCm39) G95C probably damaging Het
Foxj2 G T 6: 122,810,230 (GRCm39) Q196H probably benign Het
Frem1 A T 4: 82,907,426 (GRCm39) D811E probably damaging Het
Frmd4a A T 2: 4,608,259 (GRCm39) E709V probably damaging Het
Fscn3 T A 6: 28,436,200 (GRCm39) *499K probably null Het
Galc C T 12: 98,209,003 (GRCm39) G217D possibly damaging Het
Gm5592 G T 7: 40,865,542 (GRCm39) probably benign Het
Gm57858 T G 3: 36,064,809 (GRCm39) *521C probably null Het
Hnrnpul1 A G 7: 25,442,436 (GRCm39) S269P probably benign Het
Hrh1 T C 6: 114,457,496 (GRCm39) V259A probably benign Het
Mtf2 T C 5: 108,241,218 (GRCm39) I248T probably benign Het
Muc2 C T 7: 141,299,345 (GRCm39) T130M possibly damaging Het
Myo16 T C 8: 10,485,880 (GRCm39) F653S probably damaging Het
Myo1e T C 9: 70,250,417 (GRCm39) probably null Het
Myo5a G T 9: 75,023,618 (GRCm39) probably benign Het
Nlrp1b T A 11: 71,073,489 (GRCm39) D118V probably damaging Het
Npat T C 9: 53,483,920 (GRCm39) F1412S probably damaging Het
Onecut3 G T 10: 80,331,541 (GRCm39) A234S unknown Het
Or1ad1 G A 11: 50,875,602 (GRCm39) E25K probably benign Het
Or8b37 T G 9: 37,959,436 (GRCm39) L306R probably benign Het
Osbpl6 T A 2: 76,376,344 (GRCm39) I73K probably damaging Het
Otog C T 7: 45,937,943 (GRCm39) T1884I probably benign Het
Pax6 C A 2: 105,526,847 (GRCm39) P251Q probably benign Het
Pias4 A G 10: 80,999,868 (GRCm39) Y62H possibly damaging Het
Pknox1 T A 17: 31,809,687 (GRCm39) V97D possibly damaging Het
Plekhf1 A G 7: 37,921,022 (GRCm39) V182A probably damaging Het
Plscr4 T C 9: 92,366,833 (GRCm39) V149A probably damaging Het
Polr2l A T 7: 141,053,309 (GRCm39) L35Q probably damaging Het
Ppp3ca T C 3: 136,596,250 (GRCm39) I305T probably damaging Het
Ptprg G A 14: 12,122,068 (GRCm38) A311T probably benign Het
Raet1e T G 10: 22,057,231 (GRCm39) I185R probably damaging Het
Rims1 A C 1: 22,518,543 (GRCm39) V520G probably damaging Het
Rp1 A T 1: 4,416,101 (GRCm39) D1670E probably damaging Het
Rps6ka1 A T 4: 133,587,868 (GRCm39) I352N probably damaging Het
Rtp3 T C 9: 110,816,418 (GRCm39) probably benign Het
Ryr3 T A 2: 112,563,376 (GRCm39) probably null Het
Sall3 A G 18: 81,017,691 (GRCm39) V79A probably damaging Het
Sdsl C T 5: 120,600,119 (GRCm39) V93M probably damaging Het
Slc7a13 A G 4: 19,819,390 (GRCm39) N197D probably benign Het
Slit1 T A 19: 41,709,483 (GRCm39) R137* probably null Het
Stxbp5 C A 10: 9,646,367 (GRCm39) R115L probably damaging Het
Tcea1 G A 1: 4,965,167 (GRCm39) R290H probably damaging Het
Tmem132e A T 11: 82,325,338 (GRCm39) T113S probably damaging Het
Tpp1 A T 7: 105,398,458 (GRCm39) I286N probably damaging Het
Trio G A 15: 27,732,624 (GRCm39) R3086* probably null Het
Usp22 T A 11: 61,051,462 (GRCm39) N294Y probably damaging Het
Usp44 T A 10: 93,681,933 (GRCm39) S128T probably benign Het
Zc3h7b T C 15: 81,653,384 (GRCm39) probably null Het
Zfhx2 T C 14: 55,304,372 (GRCm39) Y1204C possibly damaging 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
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
R7652:Lef1 UTSW 3 130,994,003 (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'- TAATGACTGCCTACTGCTCCTG -3'
(R):5'- TTCTGAAGAACTGCCAGCC -3'

Sequencing Primer
(F):5'- ACTGCTCCTGCGTGACATC -3'
(R):5'- TGCCAGCCAACTGTACG -3'
Posted On 2015-11-11