Mutagenetix > Incidental Mutation

Incidental Mutation 'R4718:Ltb'

354261

Institutional Source

Beutler Lab

Gene Symbol

Ltb

Ensembl Gene

ENSMUSG00000024399

Gene Name

lymphotoxin B

Synonyms

p33, Tnfc, lymphotoxin beta, LTbeta, Tnfsf3

MMRRC Submission

041985-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.097) question?

Stock #

R4718 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

35413483-35415281 bp(+) (GRCm39)

Type of Mutation

splice site (4170 bp from exon)

DNA Base Change (assembly)

C to A at 35414313 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000126122 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025262] [ENSMUST00000025263] [ENSMUST00000167924] [ENSMUST00000173600]

AlphaFold

P41155

Predicted Effect

probably benign
Transcript: ENSMUST00000025262
AA Change: N150K

PolyPhen 2 Score 0.047 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000025262
Gene: ENSMUSG00000024399
AA Change: N150K

Domain	Start	End	E-Value	Type
transmembrane domain	21	43	N/A	INTRINSIC
low complexity region	72	85	N/A	INTRINSIC
TNF	154	305	8.76e-42	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000025263

SMART Domains

Protein: ENSMUSP00000025263
Gene: ENSMUSG00000024401

Domain	Start	End	E-Value	Type
transmembrane domain	35	57	N/A	INTRINSIC
TNF	91	235	1.59e-53	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000167924

SMART Domains

Protein: ENSMUSP00000126122
Gene: ENSMUSG00000024401

Domain	Start	End	E-Value	Type
transmembrane domain	35	57	N/A	INTRINSIC
TNF	74	219	2.8e-49	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173510

Predicted Effect

probably benign
Transcript: ENSMUST00000173600
AA Change: N29K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000134706
Gene: ENSMUSG00000024399
AA Change: N29K

Domain	Start	End	E-Value	Type
TNF	33	184	8.76e-42	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000183646

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.5%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Lymphotoxin beta is a type II membrane protein of the TNF family. It anchors lymphotoxin-alpha to the cell surface through heterotrimer formation. The predominant form on the lymphocyte surface is the lymphotoxin-alpha 1/beta 2 complex (e.g. 1 molecule alpha/2 molecules beta) and this complex is the primary ligand for the lymphotoxin-beta receptor. The minor complex is lymphotoxin-alpha 2/beta 1. LTB is an inducer of the inflammatory response system and involved in normal development of lymphoid tissue. Lymphotoxin-beta isoform b is unable to complex with lymphotoxin-alpha suggesting a function for lymphotoxin-beta which is independent of lympyhotoxin-alpha. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations lack peripheral lymph nodes, Peyer's patches, splenic germinal centers and follicular dendritic cells. Mutants exhibit lymphocytosis in the circulation and peritoneal cavity with infiltrations of the lung and liver. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930519G04Rik	G	A	5: 115,001,615 (GRCm39)		probably null	Het
Acsm2	A	T	7: 119,172,826 (GRCm39)	Y147F	probably damaging	Het
Alg12	A	T	15: 88,690,256 (GRCm39)	Y413N	probably damaging	Het
Arrdc3	A	T	13: 81,031,986 (GRCm39)	Q73L	possibly damaging	Het
Atp13a5	T	C	16: 29,066,922 (GRCm39)	K1017E	probably damaging	Het
Bmal1	A	T	7: 112,902,568 (GRCm39)	I399F	probably damaging	Het
Bms1	T	C	6: 118,380,196 (GRCm39)	N704D	possibly damaging	Het
Bsph1	T	A	7: 13,206,107 (GRCm39)	Y47*	probably null	Het
Crat	A	T	2: 30,298,176 (GRCm39)	Y174*	probably null	Het
Csmd3	G	T	15: 47,561,546 (GRCm39)	Y2254*	probably null	Het
Cyld	T	A	8: 89,468,933 (GRCm39)	I568N	probably damaging	Het
Dapl1	T	C	2: 59,315,072 (GRCm39)	V7A	probably benign	Het
Dhx29	G	A	13: 113,083,469 (GRCm39)	R508H	unknown	Het
Dnah9	A	G	11: 65,976,299 (GRCm39)	I1250T	probably benign	Het
Dnajb3	C	T	1: 88,133,061 (GRCm39)	D114N	probably benign	Het
Dsg1b	A	G	18: 20,530,986 (GRCm39)	N446D	probably damaging	Het
Dthd1	T	A	5: 62,976,136 (GRCm39)	V270E	probably damaging	Het
F2rl3	A	C	8: 73,489,536 (GRCm39)	R254S	possibly damaging	Het
Fgfr2	A	G	7: 129,863,518 (GRCm39)	S24P	probably damaging	Het
Fpr2	T	C	17: 18,113,598 (GRCm39)	V198A	probably benign	Het
Gbp2b	G	A	3: 142,304,756 (GRCm39)	G64D	probably damaging	Het
Gbp9	T	G	5: 105,231,624 (GRCm39)	N321H	probably damaging	Het
Gk2	T	A	5: 97,603,725 (GRCm39)	Y371F	probably benign	Het
Gm10382	T	C	5: 125,466,462 (GRCm39)		probably benign	Het
Gpatch3	A	G	4: 133,309,855 (GRCm39)	D396G	probably benign	Het
Heatr5a	A	C	12: 51,962,946 (GRCm39)	L985V	possibly damaging	Het
Homer1	T	A	13: 93,528,272 (GRCm39)	V269E	probably damaging	Het
Hspbap1	T	C	16: 35,607,692 (GRCm39)	V66A	probably benign	Het
Ighv7-2	A	C	12: 113,876,089 (GRCm39)	I5M	possibly damaging	Het
Ints7	T	A	1: 191,315,389 (GRCm39)	F108Y	possibly damaging	Het
Itga7	CT	CTGGGGATT	10: 128,776,603 (GRCm39)		probably null	Het
Junb	G	A	8: 85,705,061 (GRCm39)		probably benign	Het
Lcp2	A	G	11: 34,020,992 (GRCm39)	N116S	probably benign	Het
Lrguk	A	G	6: 34,006,431 (GRCm39)	T14A	probably benign	Het
Lrrcc1	T	A	3: 14,601,092 (GRCm39)	H41Q	probably damaging	Het
Mapk7	A	G	11: 61,380,080 (GRCm39)	S693P	possibly damaging	Het
Mbd5	A	T	2: 49,146,414 (GRCm39)	H208L	possibly damaging	Het
Megf9	A	T	4: 70,367,015 (GRCm39)	S322R	possibly damaging	Het
Mgat4c	T	C	10: 102,224,467 (GRCm39)	V227A	probably damaging	Het
Mospd3	G	A	5: 137,597,915 (GRCm39)	T151M	probably benign	Het
Mpl	A	G	4: 118,313,921 (GRCm39)	S115P	probably benign	Het
Myo6	C	A	9: 80,153,799 (GRCm39)	D258E	probably benign	Het
N4bp2	G	A	5: 65,960,806 (GRCm39)	M492I	probably damaging	Het
Ndst3	G	A	3: 123,465,915 (GRCm39)	A19V	probably benign	Het
Nkx2-3	C	A	19: 43,601,082 (GRCm39)	T48K	probably benign	Het
Nlrp4f	T	C	13: 65,342,803 (GRCm39)	T281A	probably benign	Het
Nmur1	A	G	1: 86,315,463 (GRCm39)	V157A	probably damaging	Het
Obscn	A	T	11: 58,912,780 (GRCm39)	F6992L	probably damaging	Het
Ocm	G	T	5: 143,961,375 (GRCm39)	P22Q	possibly damaging	Het
Or5be3	T	C	2: 86,864,239 (GRCm39)	T109A	probably damaging	Het
Osbp2	C	A	11: 3,661,793 (GRCm39)	C753F	probably damaging	Het
Pabpc2	A	G	18: 39,907,556 (GRCm39)	T274A	probably benign	Het
Pamr1	T	A	2: 102,472,681 (GRCm39)	I660N	probably damaging	Het
Papola	C	T	12: 105,786,707 (GRCm39)	T466I	possibly damaging	Het
Pask	T	C	1: 93,249,918 (GRCm39)	E494G	possibly damaging	Het
Pck1	A	T	2: 172,997,014 (GRCm39)	I219F	probably damaging	Het
Pgm3	T	C	9: 86,452,448 (GRCm39)	E4G	probably benign	Het
Pgs1	A	G	11: 117,896,709 (GRCm39)	H462R	probably damaging	Het
Phlpp2	T	A	8: 110,667,452 (GRCm39)	M1327K	probably benign	Het
Pkhd1	C	A	1: 20,151,452 (GRCm39)	G3815W	probably damaging	Het
Plin4	T	A	17: 56,413,981 (GRCm39)	I215F	possibly damaging	Het
Plod1	T	G	4: 148,000,701 (GRCm39)		probably benign	Het
Ppfia2	T	C	10: 106,694,146 (GRCm39)	S707P	probably damaging	Het
Psmd12	A	G	11: 107,377,259 (GRCm39)	Q86R	probably benign	Het
Rasgrf2	C	A	13: 92,138,716 (GRCm39)		probably null	Het
Rictor	T	C	15: 6,812,641 (GRCm39)	S926P	possibly damaging	Het
Rras2	A	T	7: 113,649,584 (GRCm39)	I160N	probably benign	Het
Slc27a6	A	T	18: 58,738,138 (GRCm39)	Y398F	probably benign	Het
Speer4f1	A	G	5: 17,685,422 (GRCm39)	E239G	unknown	Het
Sppl2c	T	C	11: 104,079,141 (GRCm39)	I647T	probably benign	Het
Sptan1	A	G	2: 29,921,074 (GRCm39)	Y2467C	probably damaging	Het
Sptbn1	G	T	11: 30,104,297 (GRCm39)	H136N	probably damaging	Het
Stau2	T	C	1: 16,416,269 (GRCm39)		probably null	Het
Tasor2	A	T	13: 3,624,495 (GRCm39)	D1818E	probably benign	Het
Tet1	T	A	10: 62,649,591 (GRCm39)	I40F	probably damaging	Het
Tnfaip2	A	G	12: 111,412,463 (GRCm39)	E288G	possibly damaging	Het
Trav7-5	T	A	14: 53,768,610 (GRCm39)	H59Q	probably benign	Het
Usp53	T	C	3: 122,727,631 (GRCm39)	I984V	probably benign	Het
Wdfy4	A	G	14: 32,867,273 (GRCm39)	I403T	probably benign	Het
Yars2	T	A	16: 16,127,204 (GRCm39)	M423K	probably benign	Het
Zfp292	A	T	4: 34,819,521 (GRCm39)	V272D	possibly damaging	Het
Zmynd11	A	T	13: 9,739,603 (GRCm39)	V478D	possibly damaging	Het

Other mutations in Ltb

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00944:Ltb	APN	17	35,413,642 (GRCm39)	missense	possibly damaging	0.78
IGL01112:Ltb	APN	17	35,413,576 (GRCm39)	missense	probably benign	0.04
IGL02263:Ltb	APN	17	35,414,977 (GRCm39)	missense	probably damaging	1.00
IGL02983:Ltb	APN	17	35,413,646 (GRCm39)	missense	probably benign	0.15
IGL02995:Ltb	APN	17	35,414,348 (GRCm39)	splice site	probably benign
IGL03389:Ltb	APN	17	35,414,044 (GRCm39)	missense	probably benign	0.00
R0103:Ltb	UTSW	17	35,414,016 (GRCm39)	intron	probably benign
R0103:Ltb	UTSW	17	35,414,016 (GRCm39)	intron	probably benign
R2060:Ltb	UTSW	17	35,414,739 (GRCm39)	missense	probably damaging	0.97
R4823:Ltb	UTSW	17	35,414,206 (GRCm39)	missense	probably benign
R4884:Ltb	UTSW	17	35,414,234 (GRCm39)	missense	probably benign
R5231:Ltb	UTSW	17	35,414,802 (GRCm39)	missense	probably damaging	1.00
R5327:Ltb	UTSW	17	35,414,935 (GRCm39)	missense	probably damaging	1.00
R8297:Ltb	UTSW	17	35,413,655 (GRCm39)	missense	probably benign	0.00
R8344:Ltb	UTSW	17	35,414,169 (GRCm39)	missense	probably benign	0.41
R9778:Ltb	UTSW	17	35,414,906 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- TAGCCTCTCAGAGACTCCTGAC -3'
(R):5'- TAAAGTGGCGAGATCCCTGC -3'

Sequencing Primer
(F):5'- CCCGTCTGCATCCTCAGAG -3'
(R):5'- GAGATCCCTGCCGGTTTTTAC -3'

Posted On

2015-10-21