Incidental Mutation 'R6974:Lef1'
ID 542333
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 045084-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6974 (G1)
Quality Score 225.009
Status Not validated
Chromosome 3
Chromosomal Location 130904120-131018005 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 130905223 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 35 (I35F)
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: I35F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000029611
Gene: ENSMUSG00000027985
AA Change: I35F

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: I35F

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000067808
Gene: ENSMUSG00000027985
AA Change: I35F

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
SMART Domains Protein: ENSMUSP00000096211
Gene: ENSMUSG00000027985

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: I35F

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000101948
Gene: ENSMUSG00000027985
AA Change: I35F

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: 99.2%
  • 20x: 97.2%
Validation Efficiency
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: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd12b T A 12: 70,206,221 (GRCm39) N67K probably benign Het
Amotl1 C A 9: 14,556,216 (GRCm39) E37* probably null Het
Ap4b1 C A 3: 103,720,601 (GRCm39) Y90* probably null Het
Apc A G 18: 34,431,480 (GRCm39) E277G possibly damaging Het
Atl1 T A 12: 69,972,813 (GRCm39) H44Q probably damaging Het
Atp6v0b G A 4: 117,742,864 (GRCm39) T74M probably benign Het
Auts2 T C 5: 131,469,437 (GRCm39) T627A probably benign Het
B4galnt4 T A 7: 140,647,449 (GRCm39) I372N possibly damaging Het
B4galt2 A G 4: 117,731,148 (GRCm39) S338P probably damaging Het
Cfap43 A C 19: 47,773,717 (GRCm39) probably null Het
Col4a1 T C 8: 11,362,538 (GRCm39) probably benign Het
Col7a1 A C 9: 108,798,494 (GRCm39) I1741L possibly damaging Het
Coprs A T 8: 13,935,750 (GRCm39) S90T probably benign Het
Csrnp3 T C 2: 65,779,408 (GRCm39) V40A possibly damaging Het
Ephx1 C A 1: 180,827,287 (GRCm39) probably null Het
Erich6 C A 3: 58,526,220 (GRCm39) R594L probably benign Het
F2rl2 A T 13: 95,837,038 (GRCm39) N28Y probably damaging Het
Fbxo38 A T 18: 62,639,740 (GRCm39) N1041K possibly damaging Het
Fcgr2b C T 1: 170,790,977 (GRCm39) probably null Het
Fsip2 T A 2: 82,809,061 (GRCm39) N1793K probably damaging Het
Gatad1 T C 5: 3,693,540 (GRCm39) R210G probably benign Het
Gcnt3 A G 9: 69,942,169 (GRCm39) I133T probably damaging Het
Gm57859 A G 11: 113,578,818 (GRCm39) D71G probably benign Het
Hoxa1 T A 6: 52,135,021 (GRCm39) I61F probably damaging Het
Impact C T 18: 13,115,169 (GRCm39) L102F probably damaging Het
Ist1 A T 8: 110,404,284 (GRCm39) I196N probably damaging Het
Kcnv2 T A 19: 27,311,282 (GRCm39) S550T probably benign Het
Krt1c A T 15: 101,726,314 (GRCm39) S75T unknown Het
Krtap21-1 A G 16: 89,200,466 (GRCm39) S59P unknown Het
Lpcat2 A C 8: 93,599,707 (GRCm39) N225T probably damaging Het
Lztfl1 A T 9: 123,538,649 (GRCm39) N142K probably benign Het
Mdh1b G A 1: 63,760,975 (GRCm39) H88Y probably benign Het
Mettl26 A G 17: 26,095,658 (GRCm39) D171G probably damaging Het
Mrps24 A T 11: 5,654,663 (GRCm39) M97K probably benign Het
Ms4a14 A T 19: 11,279,499 (GRCm39) C1020S probably benign Het
Mterf1a A T 5: 3,940,854 (GRCm39) I338K probably benign Het
Odad2 A T 18: 7,294,479 (GRCm39) Y45N probably benign Het
Or1e22 A G 11: 73,377,299 (GRCm39) I117T probably benign Het
Or4p20 T C 2: 88,254,156 (GRCm39) Y71C possibly damaging Het
Or52s1b T A 7: 102,822,442 (GRCm39) H134L probably damaging Het
Or7g12 T A 9: 18,899,689 (GRCm39) I135N probably damaging Het
Paqr3 T A 5: 97,256,146 (GRCm39) H76L probably damaging Het
Parp1 T A 1: 180,417,071 (GRCm39) Y618* probably null Het
Pilrb2 C T 5: 137,870,049 (GRCm39) probably benign Het
Pkm A G 9: 59,575,853 (GRCm39) N90D probably damaging Het
Pla2g4c T G 7: 13,078,459 (GRCm39) probably null Het
Plppr4 C T 3: 117,116,667 (GRCm39) V339I probably damaging Het
Pnkp T A 7: 44,510,462 (GRCm39) D304E probably damaging Het
Pnlip T C 19: 58,668,067 (GRCm39) probably null Het
Polr2a A G 11: 69,638,026 (GRCm39) C148R probably damaging Het
Ppp1r10 G A 17: 36,240,443 (GRCm39) G578S probably benign Het
Ptges2 C T 2: 32,287,683 (GRCm39) T137I possibly damaging Het
Ptpre T C 7: 135,270,877 (GRCm39) V344A possibly damaging Het
Rag1 A G 2: 101,472,137 (GRCm39) F1002L probably damaging Het
Rcn2 T A 9: 55,960,298 (GRCm39) Y188* probably null Het
Rest A G 5: 77,416,046 (GRCm39) S87G probably damaging Het
Rgsl1 C T 1: 153,675,568 (GRCm39) D913N probably damaging Het
Scp2 A G 4: 107,928,475 (GRCm39) M1T probably null Het
Slamf8 T A 1: 172,415,590 (GRCm39) N83Y probably damaging Het
Slc26a11 T A 11: 119,248,844 (GRCm39) F75Y possibly damaging Het
Slc26a5 A G 5: 22,045,570 (GRCm39) S133P probably damaging Het
Sncb A T 13: 54,910,487 (GRCm39) V83E probably damaging Het
Tmem243 A G 5: 9,151,348 (GRCm39) T11A probably damaging Het
Trim38 A G 13: 23,973,502 (GRCm39) N277D probably benign Het
Vmn1r189 C T 13: 22,286,628 (GRCm39) G70S probably damaging Het
Vmn2r-ps117 A G 17: 19,058,495 (GRCm39) R684G probably benign Het
Wdr59 T C 8: 112,187,420 (GRCm39) N792D possibly damaging Het
Wnt5a A G 14: 28,244,527 (GRCm39) D238G possibly damaging Het
Zbtb42 C A 12: 112,646,824 (GRCm39) T333K probably damaging Het
Zfp119b A G 17: 56,245,564 (GRCm39) S509P probably benign Het
Zfp365 T A 10: 67,745,594 (GRCm39) K61N probably damaging Het
Zfp553 T C 7: 126,835,825 (GRCm39) F460S probably damaging Het
Zfp788 C T 7: 41,299,301 (GRCm39) Q594* probably null Het
Zfp984 T A 4: 147,845,707 (GRCm39) M1L possibly damaging Het
Zmiz2 T A 11: 6,347,566 (GRCm39) Y291* 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
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'- TTCTAAGTGGGAAAGCGCG -3'
(R):5'- TGGACTAGGGGCCGTTATTC -3'

Sequencing Primer
(F):5'- CAATCGCAGAGGCTCCTG -3'
(R):5'- TCAATGGCCACCGTGGTC -3'
Posted On 2018-11-28