Mutagenetix > Incidental Mutation

Incidental Mutation 'R5394:Lef1'

426014

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

042966-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5394 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

130904120-131018005 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 130988308 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 264 (P264S)

Ref Sequence

ENSEMBL: ENSMUSP00000101948 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029611] [ENSMUST00000066849] [ENSMUST00000098611] [ENSMUST00000106341]

AlphaFold

P27782

Predicted Effect

possibly damaging
Transcript: ENSMUST00000029611
AA Change: P292S

PolyPhen 2 Score 0.920 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000029611
Gene: ENSMUSG00000027985
AA Change: P292S

Domain	Start	End	E-Value	Type
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: P264S

PolyPhen 2 Score 0.668 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000067808
Gene: ENSMUSG00000027985
AA Change: P264S

Domain	Start	End	E-Value	Type
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

possibly damaging
Transcript: ENSMUST00000098611
AA Change: P226S

PolyPhen 2 Score 0.895 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000096211
Gene: ENSMUSG00000027985
AA Change: P226S

Domain	Start	End	E-Value	Type
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: P264S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000101948
Gene: ENSMUSG00000027985
AA Change: P264S

Domain	Start	End	E-Value	Type
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: ENSMUST00000198624

Meta Mutation Damage Score

0.1031

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.8%

Validation Efficiency

97% (96/99)

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930503B20Rik	A	G	3: 146,356,363 (GRCm39)	F182L	probably damaging	Het
4930503B20Rik	T	C	3: 146,356,713 (GRCm39)	Y65C	probably damaging	Het
4930590J08Rik	A	G	6: 91,896,174 (GRCm39)	T341A	probably benign	Het
Adamts13	G	A	2: 26,876,570 (GRCm39)	V495I	probably benign	Het
Alms1	C	A	6: 85,600,070 (GRCm39)	T2101K	probably benign	Het
Als2	T	C	1: 59,214,105 (GRCm39)	D1361G	probably benign	Het
Ankdd1a	A	T	9: 65,412,496 (GRCm39)	M275K	probably benign	Het
Arfip2	A	T	7: 105,286,183 (GRCm39)	Y161*	probably null	Het
Asap3	A	T	4: 135,968,570 (GRCm39)	E707D	probably benign	Het
Atm	C	T	9: 53,419,077 (GRCm39)		probably null	Het
Atp9b	A	T	18: 80,820,052 (GRCm39)	S577R	probably benign	Het
Bltp1	G	T	3: 36,971,817 (GRCm39)	V517F	probably damaging	Het
Camk1d	G	C	2: 5,308,177 (GRCm39)	D274E	probably benign	Het
Cebpz	C	T	17: 79,229,634 (GRCm39)	D907N	probably benign	Het
Cmtm1	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	8: 105,036,102 (GRCm39)		probably benign	Het
Cnst	T	A	1: 179,429,301 (GRCm39)		probably benign	Het
Cog2	G	T	8: 125,259,268 (GRCm39)	V196L	probably benign	Het
Col11a1	A	G	3: 113,987,833 (GRCm39)		probably null	Het
Cops6	T	A	5: 138,161,762 (GRCm39)		probably null	Het
Cspg4	A	G	9: 56,797,484 (GRCm39)	E1316G	probably damaging	Het
Cwc22	G	C	2: 77,759,683 (GRCm39)	D122E	possibly damaging	Het
Dapk2	G	A	9: 66,176,000 (GRCm39)	V300M	probably benign	Het
Dcp1b	C	A	6: 119,152,328 (GRCm39)	D25E	probably damaging	Het
Ddx10	A	T	9: 53,145,157 (GRCm39)	Y273*	probably null	Het
Dhx58	T	C	11: 100,589,034 (GRCm39)	E504G	probably benign	Het
Dync2h1	C	T	9: 7,120,899 (GRCm39)	W2129*	probably null	Het
Egr4	A	T	6: 85,489,442 (GRCm39)	L206Q	probably damaging	Het
Eif4g3	A	G	4: 137,830,709 (GRCm39)		probably null	Het
Fbxo46	A	G	7: 18,870,541 (GRCm39)	N387D	possibly damaging	Het
Fpr-rs3	T	G	17: 20,844,470 (GRCm39)	M224L	probably benign	Het
Gm14325	G	A	2: 177,474,777 (GRCm39)	H102Y	possibly damaging	Het
Gxylt2	A	G	6: 100,682,075 (GRCm39)	K91E	probably benign	Het
Hecw1	A	T	13: 14,497,174 (GRCm39)	V278E	probably damaging	Het
Hydin	A	G	8: 111,266,474 (GRCm39)		probably null	Het
Iars1	T	C	13: 49,875,641 (GRCm39)	L776P	probably damaging	Het
Kcnh2	T	A	5: 24,537,039 (GRCm39)	T182S	probably benign	Het
Kplce	T	C	3: 92,776,005 (GRCm39)	E226G	probably damaging	Het
Lats2	T	G	14: 57,928,810 (GRCm39)	S1022R	probably benign	Het
Lyrm1	A	C	7: 119,513,471 (GRCm39)	I79L	possibly damaging	Het
Macroh2a2	G	A	10: 61,587,466 (GRCm39)	T156M	possibly damaging	Het
Man2b2	T	G	5: 36,971,862 (GRCm39)	Q618P	probably benign	Het
Mei1	T	C	15: 81,976,957 (GRCm39)	V180A	possibly damaging	Het
Mmp15	A	T	8: 96,093,032 (GRCm39)	N137I	probably damaging	Het
Mms22l	A	G	4: 24,517,115 (GRCm39)	D222G	possibly damaging	Het
Mmut	T	A	17: 41,258,075 (GRCm39)	S414T	probably benign	Het
Myo18a	T	C	11: 77,744,176 (GRCm39)	M1846T	probably benign	Het
Neo1	A	T	9: 58,897,517 (GRCm39)	N146K	probably benign	Het
Nos3	A	G	5: 24,588,888 (GRCm39)	T1174A	probably benign	Het
Or10d4b	A	T	9: 39,534,430 (GRCm39)	T4S	probably benign	Het
Or10x1	T	C	1: 174,196,836 (GRCm39)	Y118H	probably damaging	Het
Or4c125	A	T	2: 89,169,806 (GRCm39)	I280N	probably damaging	Het
Or51f1	A	T	7: 102,505,686 (GRCm39)	S268T	probably damaging	Het
Pax8	A	T	2: 24,332,922 (GRCm39)		probably benign	Het
Pde5a	G	A	3: 122,611,658 (GRCm39)	C532Y	probably damaging	Het
Pigq	T	C	17: 26,150,446 (GRCm39)	D442G	possibly damaging	Het
Pik3c2g	T	C	6: 139,665,808 (GRCm39)	V43A	probably benign	Het
Pik3cb	T	C	9: 98,970,716 (GRCm39)	N325S	probably benign	Het
Pot1b	T	C	17: 56,007,063 (GRCm39)	K18R	probably benign	Het
Ppp1r42	A	T	1: 10,069,630 (GRCm39)	L144Q	probably damaging	Het
Prdm13	T	A	4: 21,679,455 (GRCm39)	Q345L	unknown	Het
Pyroxd2	T	A	19: 42,728,898 (GRCm39)	K167N	probably benign	Het
Rnf123	T	C	9: 107,947,930 (GRCm39)	Y131C	probably damaging	Het
Rnf25	T	C	1: 74,634,411 (GRCm39)	D204G	probably damaging	Het
Rpf2	G	A	10: 40,109,181 (GRCm39)	T60I	possibly damaging	Het
Scaf11	T	C	15: 96,317,339 (GRCm39)	N742D	probably benign	Het
Shank1	G	A	7: 44,002,075 (GRCm39)	D1257N	possibly damaging	Het
Shc2	A	G	10: 79,465,933 (GRCm39)	V168A	probably damaging	Het
Slc16a4	G	A	3: 107,199,758 (GRCm39)	V2M	probably benign	Het
Slc24a3	T	C	2: 145,455,494 (GRCm39)	V461A	probably benign	Het
Slc45a2	C	T	15: 11,027,871 (GRCm39)	T480I	probably damaging	Het
Slc4a4	T	A	5: 89,345,623 (GRCm39)		probably null	Het
Snx30	T	A	4: 59,879,329 (GRCm39)	D189E	probably benign	Het
Sspo	A	G	6: 48,472,194 (GRCm39)	Q4653R	possibly damaging	Het
Tpte	G	T	8: 22,817,806 (GRCm39)	R264I	probably damaging	Het
Tsc22d4	T	A	5: 137,757,036 (GRCm39)		probably benign	Het
Ubn1	T	C	16: 4,892,233 (GRCm39)	L585P	possibly damaging	Het
Usp24	A	T	4: 106,265,210 (GRCm39)	D1781V	probably damaging	Het
Utp20	A	T	10: 88,608,777 (GRCm39)	Y1514*	probably null	Het
Vmn1r55	A	T	7: 5,149,995 (GRCm39)	Y143N	probably damaging	Het
Vmn2r65	A	G	7: 84,595,862 (GRCm39)	V274A	probably benign	Het
Wdr17	A	G	8: 55,092,524 (GRCm39)	S1087P	possibly damaging	Het
Wnt5b	C	A	6: 119,417,283 (GRCm39)	R156L	probably damaging	Het
Zan	T	C	5: 137,433,896 (GRCm39)	D2279G	unknown	Het
Zan	T	C	5: 137,462,336 (GRCm39)	T948A	unknown	Het
Zfp758	T	C	17: 22,591,049 (GRCm39)	S4P	probably damaging	Het
Zfp839	A	G	12: 110,822,020 (GRCm39)	E278G	probably benign	Het
Zfp994	T	A	17: 22,419,506 (GRCm39)	H481L	probably damaging	Het
Zswim9	G	A	7: 12,994,909 (GRCm39)	R416C	probably damaging	Het

Other mutations in Lef1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- CACTGTGGAAATGAAGGGGTTC -3'
(R):5'- TCAACATCATCCGCGCATCG -3'

Sequencing Primer
(F):5'- TTTCATCGGGTGAGCCACAG -3'
(R):5'- GTTATTACGTGCGCACCG -3'

Posted On

2016-08-04