Incidental Mutation 'R0470:Lef1'
ID 41783
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 038670-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0470 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 130904120-131018005 bp(+) (GRCm39)
Type of Mutation intron
DNA Base Change (assembly) T to C at 130906475 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
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
SMART Domains Protein: ENSMUSP00000029611
Gene: ENSMUSG00000027985

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
SMART Domains Protein: ENSMUSP00000067808
Gene: ENSMUSG00000027985

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 benign
Transcript: ENSMUST00000106341
SMART Domains Protein: ENSMUSP00000101948
Gene: ENSMUSG00000027985

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: ENSMUST00000136147
Predicted Effect noncoding transcript
Transcript: ENSMUST00000196419
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200166
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198624
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.3%
  • 20x: 93.0%
Validation Efficiency 98% (55/56)
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ahnak T G 19: 8,986,331 (GRCm39) D2538E probably benign Het
Akr1c13 T A 13: 4,248,500 (GRCm39) L235H probably damaging Het
Ank G A 15: 27,571,721 (GRCm39) C331Y probably damaging Het
Ankrd12 T C 17: 66,293,129 (GRCm39) E768G probably benign Het
Atm A T 9: 53,372,266 (GRCm39) V2172E probably damaging Het
Atp10b T A 11: 43,093,866 (GRCm39) L470Q possibly damaging Het
Bcl2 G A 1: 106,640,292 (GRCm39) R107C probably damaging Het
Ccn4 A G 15: 66,789,227 (GRCm39) I238V probably benign Het
Cdadc1 A T 14: 59,811,290 (GRCm39) probably benign Het
Cfhr2 A T 1: 139,749,517 (GRCm39) V155E probably damaging Het
Chp1 C T 2: 119,391,244 (GRCm39) R34C probably damaging Het
Cilp2 A T 8: 70,338,055 (GRCm39) V192E possibly damaging Het
Cyth1 T C 11: 118,023,074 (GRCm39) probably benign Het
Dnah8 T A 17: 30,927,514 (GRCm39) probably benign Het
Gja3 T C 14: 57,273,884 (GRCm39) T163A probably damaging Het
Gsdmcl1 C T 15: 63,722,280 (GRCm39) noncoding transcript Het
Herc6 C T 6: 57,596,437 (GRCm39) T459M probably damaging Het
Hexb A G 13: 97,314,507 (GRCm39) L412P probably damaging Het
Il17ra T G 6: 120,458,767 (GRCm39) D639E probably benign Het
Kcnh5 G A 12: 75,161,188 (GRCm39) T240I probably benign Het
Lilrb4a T A 10: 51,370,923 (GRCm39) N282K possibly damaging Het
Mbnl2 A T 14: 120,642,062 (GRCm39) H342L probably damaging Het
Minar2 C T 18: 59,208,711 (GRCm39) R120C probably damaging Het
Nipal3 A G 4: 135,174,683 (GRCm39) V356A probably damaging Het
Or2a54 C G 6: 43,093,558 (GRCm39) A294G probably null Het
Or51i1 A T 7: 103,670,877 (GRCm39) I216N probably damaging Het
Plekha6 G A 1: 133,200,045 (GRCm39) R208Q probably benign Het
Prkar1b A G 5: 139,036,504 (GRCm39) I82T probably damaging Het
Prrc1 C T 18: 57,496,469 (GRCm39) T140M probably damaging Het
Psg22 A C 7: 18,453,589 (GRCm39) S95R probably damaging Het
Ptk6 T C 2: 180,837,732 (GRCm39) T396A probably benign Het
Ptov1 A G 7: 44,514,235 (GRCm39) S9P probably damaging Het
Scin A C 12: 40,123,291 (GRCm39) probably benign Het
Sec13 T C 6: 113,717,593 (GRCm39) probably benign Het
Setd1a G A 7: 127,384,229 (GRCm39) probably benign Het
Sf3a2 G A 10: 80,640,388 (GRCm39) probably benign Het
Shmt1 T C 11: 60,683,789 (GRCm39) Y341C possibly damaging Het
Slc27a4 T A 2: 29,694,197 (GRCm39) L7Q probably benign Het
Slc41a2 T C 10: 83,152,086 (GRCm39) M130V possibly damaging Het
Sorcs3 T C 19: 48,785,956 (GRCm39) probably null Het
Tex24 C T 8: 27,834,936 (GRCm39) R155* probably null Het
Tgfb1 T A 7: 25,387,355 (GRCm39) probably benign Het
Tmc5 A G 7: 118,239,154 (GRCm39) D349G possibly damaging Het
Trappc13 C T 13: 104,297,512 (GRCm39) V131I possibly damaging Het
Trim66 A G 7: 109,056,749 (GRCm39) probably benign Het
Tspoap1 T C 11: 87,666,988 (GRCm39) S1027P probably damaging Het
Usp34 C T 11: 23,386,001 (GRCm39) H2143Y possibly damaging Het
Vmn1r179 A C 7: 23,627,818 (GRCm39) Y3S probably benign Het
Vmn1r231 G A 17: 21,110,265 (GRCm39) Q217* probably null Het
Vmn1r62 T A 7: 5,679,066 (GRCm39) L249* probably null Het
Vmn1r71 G C 7: 10,482,019 (GRCm39) S223C possibly damaging Het
Vmn2r109 T C 17: 20,773,148 (GRCm39) Q491R probably benign Het
Vwf G A 6: 125,605,391 (GRCm39) V925M possibly damaging Het
Zbtb6 A C 2: 37,319,505 (GRCm39) L141W probably damaging Het
Zranb1 G T 7: 132,584,500 (GRCm39) L615F probably 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
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
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'- TGATACCCAAATGATGTGCCCAACG -3'
(R):5'- CAGTGGGCTAAGCCTTACATCTTCC -3'

Sequencing Primer
(F):5'- CAAATGATGTGCCCAACGTTTTTTC -3'
(R):5'- CCGGTAGTTGACAGTCTCCTAAG -3'
Posted On 2013-05-23