Incidental Mutation 'R2013:Lef1'
ID 222318
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 040022-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2013 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 130904120-131018005 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 130905236 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 39 (I39N)
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: I39N

PolyPhen 2 Score 0.305 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000029611
Gene: ENSMUSG00000027985
AA Change: I39N

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: I39N

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000067808
Gene: ENSMUSG00000027985
AA Change: I39N

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: I39N

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000101948
Gene: ENSMUSG00000027985
AA Change: I39N

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: ENSMUST00000198624
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200166
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.8%
  • 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 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: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700122O11Rik T G 17: 48,347,723 (GRCm39) T194P possibly damaging Het
4921504E06Rik T A 2: 19,545,124 (GRCm39) M110L probably benign Het
Acad9 T G 3: 36,127,737 (GRCm39) I113R probably damaging Het
Adam34l T C 8: 44,079,442 (GRCm39) S261G possibly damaging Het
Adamts6 A T 13: 104,450,812 (GRCm39) I332F probably damaging Het
Adcy8 C T 15: 64,639,727 (GRCm39) G678S probably benign Het
Afg3l2 C T 18: 67,564,842 (GRCm39) V211I probably damaging Het
Ahnak T C 19: 8,991,937 (GRCm39) I4407T probably damaging Het
Alpl G T 4: 137,482,458 (GRCm39) H79N probably benign Het
Apc A G 18: 34,448,644 (GRCm39) I1813V probably damaging Het
Ascc3 T C 10: 50,525,908 (GRCm39) M540T probably damaging Het
Blm T C 7: 80,152,147 (GRCm39) E600G probably damaging Het
Btbd8 T C 5: 107,658,655 (GRCm39) W1742R probably damaging Het
Cadps T A 14: 12,522,337 (GRCm38) D609V probably damaging Het
Ccdc69 C T 11: 54,941,983 (GRCm39) M174I probably benign Het
Cdk13 A T 13: 17,913,748 (GRCm39) L877* probably null Het
Cdk14 T C 5: 5,143,047 (GRCm39) Y228C probably damaging Het
Dip2c C T 13: 9,617,882 (GRCm39) Q426* probably null Het
Dsp A G 13: 38,375,434 (GRCm39) N1073S probably damaging Het
Epyc T C 10: 97,511,655 (GRCm39) I216T probably damaging Het
Erbin A G 13: 103,994,041 (GRCm39) S300P probably damaging Het
Ercc3 A G 18: 32,381,482 (GRCm39) T433A probably benign Het
Exoc4 A G 6: 33,243,026 (GRCm39) T80A probably damaging Het
Foxm1 T A 6: 128,352,465 (GRCm39) probably null Het
Gaa A G 11: 119,175,409 (GRCm39) probably null Het
H2-Q4 A G 17: 35,599,526 (GRCm39) E203G probably damaging Het
Helt T C 8: 46,745,355 (GRCm39) D214G probably damaging Het
Hlcs A G 16: 94,063,599 (GRCm39) V487A probably benign Het
Hmmr A T 11: 40,619,259 (GRCm39) S74T possibly damaging Het
Hspa9 A T 18: 35,079,701 (GRCm39) Y243N probably damaging Het
Htt T G 5: 35,010,215 (GRCm39) L1556R probably damaging Het
Ift80 T C 3: 68,898,117 (GRCm39) K73E possibly damaging Het
Il6st G A 13: 112,635,423 (GRCm39) A551T probably null Het
Kdm5a T C 6: 120,408,951 (GRCm39) S1545P probably benign Het
Lmo2 T C 2: 103,811,407 (GRCm39) Y147H probably damaging Het
Lrp6 A G 6: 134,457,337 (GRCm39) probably null Het
Macf1 T C 4: 123,577,807 (GRCm39) D59G probably damaging Het
Maged1 T C X: 93,580,523 (GRCm39) Y636C possibly damaging Het
Mamdc4 T A 2: 25,453,584 (GRCm39) D1195V probably damaging Het
Mob3b A G 4: 35,083,922 (GRCm39) V89A probably benign Het
Mogs C T 6: 83,094,631 (GRCm39) R483* probably null Het
Mybphl A C 3: 108,282,718 (GRCm39) T203P probably benign Het
Myo15a A G 11: 60,385,057 (GRCm39) T1720A probably damaging Het
Myo16 T A 8: 10,552,796 (GRCm39) F945I probably damaging Het
Nbeal2 G A 9: 110,463,139 (GRCm39) L1309F probably benign Het
Nes A G 3: 87,883,985 (GRCm39) Q748R possibly damaging Het
Nhsl1 A T 10: 18,387,340 (GRCm39) R205W probably damaging Het
Nlrc3 A C 16: 3,782,974 (GRCm39) L161R probably damaging Het
Npy2r T A 3: 82,448,487 (GRCm39) D96V probably damaging Het
Or4d11 T A 19: 12,013,518 (GRCm39) E196V probably damaging Het
Or5w18 T G 2: 87,632,847 (GRCm39) V38G probably damaging Het
Pappa2 C T 1: 158,662,498 (GRCm39) C1159Y probably damaging Het
Phf21a T C 2: 92,058,828 (GRCm39) probably null Het
Pik3c2a T A 7: 115,950,166 (GRCm39) probably null Het
Psg22 A T 7: 18,453,560 (GRCm39) Y85F possibly damaging Het
Pttg1ip2 T A 5: 5,505,964 (GRCm39) I106L probably benign Het
Qtrt2 A G 16: 43,689,455 (GRCm39) I181T probably damaging Het
Sash1 A T 10: 8,605,177 (GRCm39) V1071D probably benign Het
Scn10a A T 9: 119,442,802 (GRCm39) I1481N probably damaging Het
Slc15a1 G A 14: 121,713,399 (GRCm39) A376V possibly damaging Het
Slc25a46 A T 18: 31,742,778 (GRCm39) H29Q probably benign Het
Slit2 T C 5: 48,459,832 (GRCm39) C1354R probably damaging Het
Ssu2 C T 6: 112,360,902 (GRCm39) E52K possibly damaging Het
Taar7e A T 10: 23,913,732 (GRCm39) H74L possibly damaging Het
Tcte1 A T 17: 45,852,237 (GRCm39) N490I probably benign Het
Tent4b T A 8: 88,972,223 (GRCm39) probably null Het
Tpst2 G T 5: 112,455,880 (GRCm39) G140C probably damaging Het
Trip11 A T 12: 101,803,981 (GRCm39) F1634I probably damaging Het
Trpm2 A G 10: 77,761,600 (GRCm39) F1017L probably damaging Het
Utp18 A G 11: 93,766,948 (GRCm39) V253A possibly damaging Het
Vmn2r102 A G 17: 19,897,006 (GRCm39) T118A probably benign Het
Vmn2r14 T C 5: 109,369,109 (GRCm39) T155A probably benign Het
Vmn2r19 T A 6: 123,292,954 (GRCm39) M332K probably benign Het
Vmn2r71 T A 7: 85,269,845 (GRCm39) M452K probably benign Het
Vmn2r79 T G 7: 86,653,289 (GRCm39) L518R possibly damaging Het
Vps13b T C 15: 35,607,288 (GRCm39) S1074P probably damaging Het
Vps13d A G 4: 144,835,078 (GRCm39) S2757P probably damaging Het
Wdr33 C A 18: 32,022,029 (GRCm39) Q860K unknown Het
Zfp423 T A 8: 88,509,025 (GRCm39) I440F probably benign Het
Zup1 A G 10: 33,805,820 (GRCm39) V437A 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
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'- TTCTAAGTGGGAAAGCGCGG -3'
(R):5'- ATGGACTAGGGGCCGTTATTC -3'

Sequencing Primer
(F):5'- CAATCGCAGAGGCTCCTG -3'
(R):5'- GGGCCGTTATTCCCCAC -3'
Posted On 2014-08-25