Incidental Mutation 'R3918:Lef1'
ID 307493
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 040816-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3918 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 130904120-131018005 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 130905290 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 57 (N57S)
Ref Sequence ENSEMBL: ENSMUSP00000101948 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029611] [ENSMUST00000066849] [ENSMUST00000098611] [ENSMUST00000106341]
AlphaFold P27782
Predicted Effect probably damaging
Transcript: ENSMUST00000029611
AA Change: N57S

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000029611
Gene: ENSMUSG00000027985
AA Change: N57S

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 possibly damaging
Transcript: ENSMUST00000066849
AA Change: N57S

PolyPhen 2 Score 0.944 (Sensitivity: 0.80; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000067808
Gene: ENSMUSG00000027985
AA Change: N57S

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: N57S

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000101948
Gene: ENSMUSG00000027985
AA Change: N57S

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: ENSMUST00000200166
Predicted Effect noncoding transcript
Transcript: ENSMUST00000196419
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198624
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.8%
  • 10x: 97.5%
  • 20x: 95.7%
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: 35 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aars1 T C 8: 111,766,774 (GRCm39) I52T probably damaging Het
Adhfe1 G A 1: 9,646,441 (GRCm39) R447H probably damaging Het
Ak7 A G 12: 105,676,515 (GRCm39) K72E probably benign Het
Best2 T G 8: 85,736,353 (GRCm39) D270A probably damaging Het
Brinp3 C A 1: 146,627,599 (GRCm39) D277E probably damaging Het
Col18a1 T C 10: 76,889,192 (GRCm39) M1721V probably benign Het
Ctnnal1 T C 4: 56,865,000 (GRCm39) T39A possibly damaging Het
Dnah9 T A 11: 65,761,800 (GRCm39) M3897L possibly damaging Het
Dysf G A 6: 84,163,491 (GRCm39) probably null Het
Egf T C 3: 129,490,509 (GRCm39) I395V probably null Het
Fbln5 C T 12: 101,717,050 (GRCm39) G446D probably damaging Het
Gprc6a CAAA CA 10: 51,491,776 (GRCm39) probably null Het
Hmcn1 G C 1: 150,566,361 (GRCm39) T2214S probably benign Het
Lpin1 A G 12: 16,621,190 (GRCm39) S266P probably benign Het
Marveld2 T C 13: 100,748,401 (GRCm39) Q226R probably benign Het
Mest G A 6: 30,742,749 (GRCm39) S132N probably benign Het
Mras T A 9: 99,293,473 (GRCm39) I56F probably damaging Het
Myh13 G A 11: 67,220,064 (GRCm39) E138K probably benign Het
Nsun2 A G 13: 69,778,799 (GRCm39) T516A probably damaging Het
Ola1 A G 2: 72,972,683 (GRCm39) V200A probably benign Het
Or5ak24 A T 2: 85,261,074 (GRCm39) V33D possibly damaging Het
Patj C A 4: 98,344,455 (GRCm39) P20H probably damaging Het
Pcdhb12 T A 18: 37,570,101 (GRCm39) W416R probably benign Het
Pcdhga9 G A 18: 37,871,995 (GRCm39) R608H probably benign Het
Pola1 C A X: 92,505,078 (GRCm39) R1313L probably benign Het
Ppp1r36 G A 12: 76,464,431 (GRCm39) V10I probably benign Het
Rnf150 C T 8: 83,591,090 (GRCm39) T151I probably benign Het
Tank G T 2: 61,474,130 (GRCm39) probably null Het
Tmprss4 C T 9: 45,091,964 (GRCm39) V174M probably benign Het
Trappc13 T C 13: 104,297,590 (GRCm39) T105A probably damaging Het
Tut7 A G 13: 59,929,838 (GRCm39) S1066P probably damaging Het
Txndc9 G A 1: 38,033,131 (GRCm39) Q84* probably null Het
Ubr3 A T 2: 69,846,474 (GRCm39) probably null Het
Wfs1 C A 5: 37,125,968 (GRCm39) V308L probably benign Het
Zfp51 A G 17: 21,683,702 (GRCm39) K106E probably benign 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
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'- CTTCTAAGTGGGAAAGCGCG -3'
(R):5'- CATGGACTAGGGGCCGTTATTC -3'

Sequencing Primer
(F):5'- AGATTACACAGCCGCCGG -3'
(R):5'- GGGCCGTTATTCCCCAC -3'
Posted On 2015-04-17