Mutagenetix > Incidental Mutation

Incidental Mutation 'R4823:Ltb'

371335

Institutional Source

Beutler Lab

Gene Symbol

Ltb

Ensembl Gene

ENSMUSG00000024399

Gene Name

lymphotoxin B

Synonyms

p33, Tnfc, lymphotoxin beta, LTbeta, Tnfsf3

MMRRC Submission

042439-MU

Accession Numbers

Essential gene?

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

Stock #

R4823 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

35413483-35415281 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 35414206 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 115 (S115P)

Ref Sequence

ENSEMBL: ENSMUSP00000025262 (fasta)

Gene Model

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

AlphaFold

P41155

Predicted Effect

probably benign
Transcript: ENSMUST00000025262
AA Change: S115P

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

SMART Domains

Protein: ENSMUSP00000025262
Gene: ENSMUSG00000024399
AA Change: S115P

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 benign
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 benign
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

SMART Domains

Protein: ENSMUSP00000134706
Gene: ENSMUSG00000024399

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000183646

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.8%
20x: 94.1%

Validation Efficiency

98% (96/98)

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310003L06Rik	G	A	5: 88,120,457 (GRCm39)	D405N	probably benign	Het
4921517D22Rik	T	G	13: 59,838,718 (GRCm39)	E38A	probably damaging	Het
4930433I11Rik	A	T	7: 40,642,786 (GRCm39)	I152F	probably benign	Het
Aass	A	T	6: 23,107,690 (GRCm39)	D364E	probably benign	Het
Adamts2	A	G	11: 50,628,014 (GRCm39)	D238G	probably benign	Het
Albfm1	T	A	5: 90,714,362 (GRCm39)	L124H	probably benign	Het
Aoc1l1	A	G	6: 48,952,195 (GRCm39)	D40G	probably damaging	Het
Aplf	G	A	6: 87,623,237 (GRCm39)	L302F	probably damaging	Het
Apol7b	G	T	15: 77,311,982 (GRCm39)		probably benign	Het
Arhgef12	A	G	9: 42,931,992 (GRCm39)	V165A	probably benign	Het
Ascc3	T	C	10: 50,589,329 (GRCm39)	S1017P	probably damaging	Het
B230104I21Rik	T	A	4: 154,434,204 (GRCm39)		probably benign	Het
Bfsp2	C	A	9: 103,357,082 (GRCm39)	C115F	probably damaging	Het
Bhmt2	A	T	13: 93,799,798 (GRCm39)	W213R	probably benign	Het
Capn5	A	T	7: 97,775,648 (GRCm39)	V431E	probably damaging	Het
Ccdc88c	A	G	12: 100,896,802 (GRCm39)	Y1390H	probably damaging	Het
Ccr3	A	G	9: 123,828,718 (GRCm39)	T18A	probably damaging	Het
Cdh5	T	C	8: 104,869,301 (GRCm39)	S676P	probably benign	Het
Ceacam5	A	G	7: 17,491,669 (GRCm39)	T680A	possibly damaging	Het
Cebpd	G	A	16: 15,705,978 (GRCm39)	G264S	probably benign	Het
Cfd	T	C	10: 79,726,782 (GRCm39)	V8A	probably benign	Het
Cops9	C	T	1: 92,569,588 (GRCm39)		probably benign	Het
Cpne6	T	C	14: 55,754,467 (GRCm39)	Y533H	probably damaging	Het
Cyp2c67	T	A	19: 39,604,168 (GRCm39)	H396L	probably benign	Het
Cyp2j9	G	A	4: 96,456,972 (GRCm39)	P500S	possibly damaging	Het
Cyp4a12a	A	T	4: 115,184,610 (GRCm39)		probably null	Het
Dbt	G	A	3: 116,317,036 (GRCm39)	D71N	probably damaging	Het
Ddx41	G	T	13: 55,679,868 (GRCm39)	Q440K	probably benign	Het
Elovl4	A	G	9: 83,662,738 (GRCm39)	F174S	probably damaging	Het
Emcn	C	G	3: 137,129,187 (GRCm39)	P193R	probably damaging	Het
Etnk1	T	C	6: 143,113,364 (GRCm39)		probably null	Het
Fads3	A	C	19: 10,019,252 (GRCm39)	S53R	probably damaging	Het
Fam193a	A	G	5: 34,616,372 (GRCm39)	E849G	probably damaging	Het
Fat3	A	G	9: 15,907,803 (GRCm39)	V2733A	probably benign	Het
Frem3	T	A	8: 81,340,587 (GRCm39)	M960K	probably benign	Het
Frmd6	A	T	12: 70,919,349 (GRCm39)	I62L	probably benign	Het
Glmp	T	C	3: 88,232,530 (GRCm39)		probably benign	Het
Gm17421	T	C	12: 113,333,161 (GRCm39)		noncoding transcript	Het
Gm27013	T	A	6: 130,499,186 (GRCm39)		noncoding transcript	Het
Gtf2ird1	A	G	5: 134,424,576 (GRCm39)	V390A	probably damaging	Het
Hps3	A	G	3: 20,066,890 (GRCm39)	Y559H	probably benign	Het
Hsh2d	G	A	8: 72,954,304 (GRCm39)	D229N	probably benign	Het
Itpr3	A	G	17: 27,304,121 (GRCm39)	D114G	probably benign	Het
Jmjd4	G	A	11: 59,346,406 (GRCm39)	A408T	probably benign	Het
Kcnh4	G	T	11: 100,646,000 (GRCm39)	A316D	probably damaging	Het
Klrg1	T	A	6: 122,250,492 (GRCm39)		probably null	Het
Lancl2	T	A	6: 57,709,262 (GRCm39)	Y355N	probably damaging	Het
Mccc2	T	G	13: 100,136,762 (GRCm39)	R64S	probably benign	Het
Mgam2-ps	T	A	6: 40,809,596 (GRCm39)		noncoding transcript	Het
Mrrf	T	G	2: 36,038,042 (GRCm39)	N104K	possibly damaging	Het
Nipa1	C	A	7: 55,629,436 (GRCm39)	V226L	possibly damaging	Het
Numa1	T	A	7: 101,645,244 (GRCm39)	L290Q	probably damaging	Het
Ofcc1	T	A	13: 40,433,949 (GRCm39)	H52L	probably damaging	Het
Ogfod3	G	A	11: 121,086,027 (GRCm39)	A189V	probably benign	Het
Or14c39	T	A	7: 86,343,796 (GRCm39)	I44N	probably damaging	Het
Or5b21	A	T	19: 12,839,180 (GRCm39)	I14F	probably benign	Het
Or5d46	A	G	2: 88,170,179 (GRCm39)	D90G	probably damaging	Het
Or9i1b	G	A	19: 13,897,022 (GRCm39)	V213I	probably benign	Het
P2ry12	G	A	3: 59,125,318 (GRCm39)	S119L	probably benign	Het
Pde7b	T	A	10: 20,314,531 (GRCm39)	N192Y	probably damaging	Het
Pfkl	T	C	10: 77,833,428 (GRCm39)	N258S	probably damaging	Het
Phykpl	G	A	11: 51,477,420 (GRCm39)	A71T	probably damaging	Het
Ppp1r16a	T	C	15: 76,577,393 (GRCm39)		probably benign	Het
Pramel15	T	C	4: 144,099,781 (GRCm39)	N328S	possibly damaging	Het
Pramel32	T	C	4: 88,547,452 (GRCm39)	K160R	probably damaging	Het
Prune2	C	T	19: 17,097,868 (GRCm39)	T1124M	probably damaging	Het
Rapgef6	A	G	11: 54,585,326 (GRCm39)	I1570V	probably benign	Het
Rbm34	T	C	8: 127,697,655 (GRCm39)	S19G	probably benign	Het
Rnf10	T	C	5: 115,393,501 (GRCm39)		probably null	Het
Rnf34	A	G	5: 122,988,365 (GRCm39)		probably null	Het
Setd4	A	G	16: 93,386,838 (GRCm39)	S287P	probably benign	Het
Shc3	C	T	13: 51,605,606 (GRCm39)	V225I	probably benign	Het
Sipa1l3	C	T	7: 29,070,427 (GRCm39)	V1030I	probably damaging	Het
Siva1	G	T	12: 112,611,498 (GRCm39)	R33L	probably damaging	Het
Slc4a5	C	T	6: 83,249,115 (GRCm39)	T573I	probably damaging	Het
Sorcs1	C	T	19: 50,666,578 (GRCm39)	R110Q	possibly damaging	Het
Sorcs1	T	C	19: 50,218,740 (GRCm39)	I581V	possibly damaging	Het
Sorl1	T	C	9: 41,903,617 (GRCm39)	D1545G	probably damaging	Het
Tas2r124	T	G	6: 132,732,509 (GRCm39)	S273A	probably damaging	Het
Tcf15	T	C	2: 151,985,813 (GRCm39)	F90L	probably damaging	Het
Trim59	G	A	3: 68,944,453 (GRCm39)	R296C	probably benign	Het
Tulp1	A	T	17: 28,572,546 (GRCm39)	D229E	probably benign	Het
Ush1c	T	A	7: 45,845,157 (GRCm39)	N886I	probably benign	Het
Usp9y	A	T	Y: 1,444,559 (GRCm39)	S127T	probably damaging	Het
Vmn1r19	T	A	6: 57,382,219 (GRCm39)	Y257*	probably null	Het
Vmn2r109	A	T	17: 20,774,153 (GRCm39)	Y401N	probably damaging	Het
Vmn2r69	A	C	7: 85,060,508 (GRCm39)	S359A	probably benign	Het
Zfp37	A	T	4: 62,109,740 (GRCm39)	N479K	probably benign	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
R4718:Ltb	UTSW	17	35,414,313 (GRCm39)	splice site	probably null
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'- ATTAGCCAAATCTGACCTCTGGG -3'
(R):5'- ACATAGCCAGCACTCTTCGG -3'

Sequencing Primer
(F):5'- CCCATCCAGGTTGAGAAGATCATTG -3'
(R):5'- GGTCTACCAGATGCTTACCTATGAG -3'

Posted On

2016-03-01