Mutagenetix > Incidental Mutation

Incidental Mutation 'R2015:Lef1'

222742

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

040024-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2015 (G1)

Quality Score

225

Status

Not validated

Chromosome

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

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

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

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

probably benign
Transcript: ENSMUST00000098611

SMART Domains

Protein: ENSMUSP00000096211
Gene: ENSMUSG00000027985

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: I39N

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000101948
Gene: ENSMUSG00000027985
AA Change: I39N

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: 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: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.7%

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: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	A	T	11: 110,022,672 (GRCm39)	M1022K	probably benign	Het
Abhd4	T	A	14: 54,500,289 (GRCm39)	H74Q	probably damaging	Het
Actg1	A	G	11: 120,237,636 (GRCm39)	S49P	possibly damaging	Het
Adcy8	C	T	15: 64,639,727 (GRCm39)	G678S	probably benign	Het
Aire	T	C	10: 77,878,792 (GRCm39)	D85G	probably damaging	Het
Akr1c18	T	A	13: 4,195,308 (GRCm39)	D50V	probably damaging	Het
Ankrd13a	C	A	5: 114,930,170 (GRCm39)	A185E	probably damaging	Het
Apc	A	G	18: 34,448,644 (GRCm39)	I1813V	probably damaging	Het
Armc8	A	T	9: 99,365,158 (GRCm39)	C661*	probably null	Het
Bbs10	C	T	10: 111,136,716 (GRCm39)	Q610*	probably null	Het
Blm	T	C	7: 80,152,147 (GRCm39)	E600G	probably damaging	Het
Bpifb9a	T	C	2: 154,110,120 (GRCm39)		probably null	Het
Cdk14	T	C	5: 5,430,082 (GRCm39)	K15R	probably benign	Het
Cdr1	A	G	X: 60,228,420 (GRCm39)	F249L	probably benign	Het
Cep250	A	C	2: 155,823,373 (GRCm39)	H1009P	probably damaging	Het
Cfap97d1	C	A	11: 101,878,044 (GRCm39)	H35Q	probably damaging	Het
Clasp2	A	G	9: 113,740,568 (GRCm39)	T495A	possibly damaging	Het
Col19a1	C	G	1: 24,598,834 (GRCm39)	G53A	unknown	Het
Cpne1	G	A	2: 155,920,308 (GRCm39)	R166C	probably damaging	Het
Dtx3l	G	A	16: 35,756,797 (GRCm39)	H129Y	probably benign	Het
Ercc3	A	G	18: 32,381,482 (GRCm39)	T433A	probably benign	Het
Gm9936	T	A	5: 114,995,482 (GRCm39)		probably benign	Het
Grina	T	C	15: 76,132,734 (GRCm39)	V167A	probably damaging	Het
H2ac25	T	A	11: 58,845,754 (GRCm39)	L64Q	probably damaging	Het
Hcfc2	A	G	10: 82,574,814 (GRCm39)	N618D	probably benign	Het
Herpud1	T	C	8: 95,118,834 (GRCm39)	V196A	probably benign	Het
Hlcs	A	G	16: 94,063,599 (GRCm39)	V487A	probably benign	Het
Hspa9	A	T	18: 35,079,701 (GRCm39)	Y243N	probably damaging	Het
Igll1	A	G	16: 16,681,639 (GRCm39)	S39P	probably benign	Het
Kdm5a	T	C	6: 120,408,951 (GRCm39)	S1545P	probably benign	Het
Klra8	C	A	6: 130,092,536 (GRCm39)	C255F	probably damaging	Het
Krtap4-6	A	T	11: 99,556,398 (GRCm39)	C110S	unknown	Het
Lnpep	G	A	17: 17,799,325 (GRCm39)	T110I	probably damaging	Het
Lrp1	T	A	10: 127,376,563 (GRCm39)	T4282S	probably benign	Het
Lrp6	A	G	6: 134,457,337 (GRCm39)		probably null	Het
Ly6g5b	A	C	17: 35,333,654 (GRCm39)	S53A	possibly damaging	Het
M6pr	T	G	6: 122,290,332 (GRCm39)	N98K	probably damaging	Het
Mal2	T	C	15: 54,464,136 (GRCm39)	*176Q	probably null	Het
Mansc1	T	C	6: 134,587,274 (GRCm39)	D301G	possibly damaging	Het
Marchf1	C	A	8: 66,574,473 (GRCm39)	N11K	probably damaging	Het
Mast3	T	A	8: 71,240,007 (GRCm39)	I338F	probably benign	Het
Mcm3	A	G	1: 20,873,804 (GRCm39)	L772P	probably damaging	Het
Mib2	C	T	4: 155,742,337 (GRCm39)	G176D	probably damaging	Het
Mier2	A	T	10: 79,377,036 (GRCm39)		probably null	Het
Mogs	C	T	6: 83,094,631 (GRCm39)	R483*	probably null	Het
Msl2	G	T	9: 100,957,304 (GRCm39)		probably benign	Het
Naa16	A	T	14: 79,582,499 (GRCm39)	M530K	probably damaging	Het
Nde1	A	T	16: 13,987,321 (GRCm39)		probably benign	Het
Ndufb10	T	C	17: 24,941,503 (GRCm39)		probably null	Het
Nhsl1	A	T	10: 18,387,340 (GRCm39)	R205W	probably damaging	Het
Npffr2	T	A	5: 89,730,751 (GRCm39)	I227N	probably damaging	Het
Nup210l	T	A	3: 90,092,739 (GRCm39)	L1231Q	probably damaging	Het
Or2f1	A	G	6: 42,721,784 (GRCm39)	E271G	probably damaging	Het
Or7a39	T	C	10: 78,715,222 (GRCm39)	I72T	possibly damaging	Het
Pclo	C	A	5: 14,571,515 (GRCm39)	P300Q	probably damaging	Het
Pik3c2a	T	A	7: 115,950,166 (GRCm39)		probably null	Het
Plekha5	T	A	6: 140,480,290 (GRCm39)		probably null	Het
Pls1	A	G	9: 95,643,418 (GRCm39)	V527A	possibly damaging	Het
Ppfia2	T	C	10: 106,310,538 (GRCm39)	M15T	probably benign	Het
Prkd2	T	A	7: 16,581,602 (GRCm39)	C152*	probably null	Het
Ptprq	T	G	10: 107,503,283 (GRCm39)	K792Q	probably damaging	Het
Pttg1ip2	T	A	5: 5,505,964 (GRCm39)	I106L	probably benign	Het
Rbbp8	T	C	18: 11,853,681 (GRCm39)	M296T	probably benign	Het
Rfc3	T	C	5: 151,571,003 (GRCm39)		probably null	Het
Rnf17	A	G	14: 56,724,426 (GRCm39)	N1090S	probably benign	Het
Sash1	A	T	10: 8,605,177 (GRCm39)	V1071D	probably benign	Het
Sdsl	G	A	5: 120,601,218 (GRCm39)	T18M	probably damaging	Het
Sepsecs	T	A	5: 52,804,966 (GRCm39)	Q365L	probably benign	Het
Sgta	A	T	10: 80,887,130 (GRCm39)	V45E	probably damaging	Het
Slc25a46	A	T	18: 31,742,778 (GRCm39)	H29Q	probably benign	Het
Slc2a8	A	C	2: 32,871,392 (GRCm39)	V136G	probably benign	Het
Smg7	A	T	1: 152,736,259 (GRCm39)	N166K	probably damaging	Het
Spata21	C	T	4: 140,834,640 (GRCm39)	Q505*	probably null	Het
Strn4	T	C	7: 16,566,953 (GRCm39)	S458P	possibly damaging	Het
Tbc1d22a	C	T	15: 86,183,885 (GRCm39)	T248M	probably damaging	Het
Trabd	T	A	15: 88,968,929 (GRCm39)	M149K	possibly damaging	Het
Trpv3	A	T	11: 73,170,653 (GRCm39)	N178Y	probably damaging	Het
Try5	C	T	6: 41,291,585 (GRCm39)		probably null	Het
Tsg101	C	T	7: 46,558,652 (GRCm39)		probably null	Het
Ube3b	A	G	5: 114,549,210 (GRCm39)	E738G	probably damaging	Het
Unc13d	A	G	11: 115,959,581 (GRCm39)	S631P	probably damaging	Het
Unc5d	T	C	8: 29,249,007 (GRCm39)	T297A	probably damaging	Het
Usp18	A	T	6: 121,245,509 (GRCm39)	E1V	probably damaging	Het
Vapb	C	A	2: 173,613,391 (GRCm39)	P97T	probably benign	Het
Vmn1r33	T	A	6: 66,589,356 (GRCm39)	D66V	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
Vps13b	T	C	15: 35,607,288 (GRCm39)	S1074P	probably damaging	Het
Vwde	C	A	6: 13,208,337 (GRCm39)	G182C	possibly damaging	Het
Wdfy3	A	C	5: 102,008,352 (GRCm39)	S2778A	probably null	Het
Zbtb2	T	A	10: 4,319,757 (GRCm39)	I90F	possibly damaging	Het
Zfp518b	C	A	5: 38,829,345 (GRCm39)	V887F	probably benign	Het
Zfp790	A	G	7: 29,528,286 (GRCm39)	T324A	probably benign	Het
Zup1	A	G	10: 33,805,820 (GRCm39)	V437A	possibly 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
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'- CTTCTAAGTGGGAAAGCGCG -3'
(R):5'- CATGGACTAGGGGCCGTTATTC -3'

Sequencing Primer
(F):5'- CAATCGCAGAGGCTCCTG -3'
(R):5'- GGGCCGTTATTCCCCAC -3'

Posted On

2014-08-25