Mutagenetix > Incidental Mutation

Incidental Mutation 'R6128:Lta'

487545

Institutional Source

Beutler Lab

Gene Symbol

Lta

Ensembl Gene

ENSMUSG00000024402

Gene Name

lymphotoxin A

Synonyms

LT-[a], LTalpha, hlb382, lymphotoxin alpha, lymphotoxin, TNF beta, Tnfsf1b, Ltx, LT, TNF-beta, Tnfb, LT-alpha, LT[a]

MMRRC Submission

044275-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6128 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

35422141-35424327 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 35422817 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Leucine at position 169 (V169L)

Ref Sequence

ENSEMBL: ENSMUSP00000025266 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025263] [ENSMUST00000025266] [ENSMUST00000167924]

AlphaFold

P09225

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

possibly damaging
Transcript: ENSMUST00000025266
AA Change: V169L

PolyPhen 2 Score 0.945 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000025266
Gene: ENSMUSG00000024402
AA Change: V169L

Domain	Start	End	E-Value	Type
transmembrane domain	7	29	N/A	INTRINSIC
TNF	60	202	5.38e-51	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: ENSMUST00000184381

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.5%
20x: 95.9%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The encoded protein, a member of the tumor necrosis factor family, is a cytokine produced by lymphocytes. The protein is highly inducible, secreted, and forms heterotrimers with lymphotoxin-beta which anchor lymphotoxin-alpha to the cell surface. This protein also mediates a large variety of inflammatory, immunostimulatory, and antiviral responses, is involved in the formation of secondary lymphoid organs during development and plays a role in apoptosis. Genetic variations in this gene are associated with susceptibility to leprosy type 4, myocardial infarction, non-Hodgkin's lymphoma, and psoriatic arthritis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]
PHENOTYPE: Homozygotes for targeted null mutations exhibit absence of lymph nodes, Peyer's patches, and splenic germinal centers, impaired class switching and NK cell recruitment, and greater susceptibility to Mycobacterium bovis, influenza A, and Toxoplasma gondii. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930553M12Rik	T	C	4: 88,786,596 (GRCm39)	I7M	unknown	Het
A430033K04Rik	A	G	5: 138,646,038 (GRCm39)	H641R	probably damaging	Het
Acyp2	C	T	11: 30,456,354 (GRCm39)	E98K	possibly damaging	Het
Asah1	C	T	8: 41,807,092 (GRCm39)	V111M	probably damaging	Het
Ascc3	T	C	10: 50,526,734 (GRCm39)	L611P	probably damaging	Het
Atl2	C	A	17: 80,172,470 (GRCm39)		probably null	Het
Bhlhe22	A	T	3: 18,109,987 (GRCm39)	S346C	probably damaging	Het
Bicc1	T	C	10: 70,776,313 (GRCm39)		probably null	Het
Bptf	G	T	11: 106,965,516 (GRCm39)	A1163D	possibly damaging	Het
Bub1b	T	A	2: 118,448,293 (GRCm39)	C382S	probably benign	Het
Carmil1	A	T	13: 24,197,177 (GRCm39)	Y158*	probably null	Het
Ccdc175	A	T	12: 72,175,933 (GRCm39)	I473K	probably benign	Het
Ccdc18	A	G	5: 108,311,625 (GRCm39)	I444V	possibly damaging	Het
Cep131	T	A	11: 119,956,801 (GRCm39)	I880F	probably damaging	Het
Ces2e	T	A	8: 105,655,428 (GRCm39)	I117N	probably benign	Het
Clk2	C	T	3: 89,081,531 (GRCm39)	T289M	probably damaging	Het
Crocc2	A	T	1: 93,122,123 (GRCm39)	D672V	probably benign	Het
Cul7	T	A	17: 46,962,588 (GRCm39)	I73N	probably damaging	Het
Cyp2d12	C	A	15: 82,443,166 (GRCm39)	D358E	probably benign	Het
Cyp7a1	A	G	4: 6,272,788 (GRCm39)	S142P	possibly damaging	Het
Daw1	T	A	1: 83,183,647 (GRCm39)	C232*	probably null	Het
Dhx9	T	C	1: 153,353,835 (GRCm39)	K195R	probably damaging	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Het
Dpp3	A	G	19: 4,972,420 (GRCm39)	V168A	probably benign	Het
Eml2	G	A	7: 18,935,088 (GRCm39)	V432I	probably damaging	Het
Ercc6l2	T	C	13: 64,001,563 (GRCm39)	V459A	probably damaging	Het
Erp44	A	T	4: 48,243,493 (GRCm39)	N38K	probably damaging	Het
Fam135a	A	G	1: 24,069,821 (GRCm39)		probably null	Het
Fblim1	G	A	4: 141,312,033 (GRCm39)	R231C	probably damaging	Het
Fdps	T	C	3: 89,006,740 (GRCm39)	E117G	possibly damaging	Het
Gbp4	A	C	5: 105,283,030 (GRCm39)	V80G	possibly damaging	Het
Glt1d1	A	T	5: 127,754,335 (GRCm39)	D179V	probably damaging	Het
Gtf2a1l	T	A	17: 89,002,086 (GRCm39)	V314E	probably null	Het
Gzmf	G	T	14: 56,443,443 (GRCm39)	Y178*	probably null	Het
Hira	C	T	16: 18,751,727 (GRCm39)	P509S	probably benign	Het
Ifi44	T	C	3: 151,454,823 (GRCm39)	N134S	probably benign	Het
Igfbp2	T	A	1: 72,863,958 (GRCm39)	C74S	probably damaging	Het
Il24	A	G	1: 130,813,435 (GRCm39)	L54P	probably damaging	Het
Ints10	T	C	8: 69,274,904 (GRCm39)		probably null	Het
Ipo9	A	G	1: 135,318,311 (GRCm39)	C700R	possibly damaging	Het
Kalrn	T	A	16: 34,033,255 (GRCm39)	Q469L	probably damaging	Het
Lrp1b	T	G	2: 40,750,667 (GRCm39)	I2966L	probably benign	Het
Lyst	T	C	13: 13,933,964 (GRCm39)	V3554A	possibly damaging	Het
Mobp	A	G	9: 119,997,392 (GRCm39)		probably benign	Het
Myorg	T	A	4: 41,498,445 (GRCm39)	N395I	probably damaging	Het
Or10d1	C	G	9: 39,484,549 (GRCm39)	R2T	probably benign	Het
Or4b1d	A	T	2: 89,968,954 (GRCm39)	C176*	probably null	Het
Or8c14-ps1	T	C	9: 38,101,299 (GRCm39)	S93P	probably benign	Het
Pacs1	A	T	19: 5,202,400 (GRCm39)		probably null	Het
Phf21a	G	T	2: 92,181,953 (GRCm39)		probably null	Het
Pick1	T	A	15: 79,123,896 (GRCm39)	M89K	probably damaging	Het
Pik3cb	T	C	9: 98,946,152 (GRCm39)	D558G	possibly damaging	Het
Pnma8a	A	G	7: 16,694,661 (GRCm39)	D172G	probably benign	Het
Polr2a	A	C	11: 69,627,803 (GRCm39)	V1368G	probably damaging	Het
Pomt2	A	G	12: 87,158,109 (GRCm39)		probably null	Het
Pou2f1	T	C	1: 165,703,056 (GRCm39)		probably benign	Het
Rnf145	T	C	11: 44,446,018 (GRCm39)	V284A	probably damaging	Het
Robo1	A	T	16: 72,809,956 (GRCm39)	M1235L	probably benign	Het
Rsf1	ATGGCG	ATGGCGACGGTGGCG	7: 97,229,111 (GRCm39)		probably benign	Het
Ryr3	C	T	2: 112,784,639 (GRCm39)		probably null	Het
Scamp1	A	C	13: 94,344,735 (GRCm39)	L202R	possibly damaging	Het
Snx25	C	T	8: 46,558,240 (GRCm39)	V110I	probably benign	Het
Spata31e2	G	A	1: 26,724,506 (GRCm39)	P225S	probably benign	Het
Susd6	T	A	12: 80,915,388 (GRCm39)	H124Q	possibly damaging	Het
Tarm1	T	C	7: 3,537,720 (GRCm39)	T248A	probably benign	Het
Tc2n	A	G	12: 101,675,748 (GRCm39)	M1T	probably null	Het
Tcerg1	C	A	18: 42,644,563 (GRCm39)		probably null	Het
Ticrr	C	A	7: 79,343,716 (GRCm39)	P1194T	probably damaging	Het
Trim31	T	G	17: 37,220,491 (GRCm39)	V469G	probably benign	Het
Vcp	T	C	4: 42,980,941 (GRCm39)	E723G	probably benign	Het
Vmn1r177	C	A	7: 23,565,267 (GRCm39)	S203I	probably damaging	Het
Vmn1r177	T	A	7: 23,565,268 (GRCm39)	S203C	probably damaging	Het
Vmn1r210	A	T	13: 23,012,277 (GRCm39)	L3*	probably null	Het
Wdr27	T	A	17: 15,152,796 (GRCm39)	R104*	probably null	Het
Wnk1	A	C	6: 119,940,747 (GRCm39)		probably null	Het
Zfp157	A	G	5: 138,453,281 (GRCm39)	E88G	possibly damaging	Het
Zfp708	A	T	13: 67,222,965 (GRCm39)	L22Q	probably damaging	Het
Zfp788	T	C	7: 41,299,785 (GRCm39)	F787S	probably damaging	Het

Other mutations in Lta

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01396:Lta	APN	17	35,423,061 (GRCm39)	splice site	probably null
R4730:Lta	UTSW	17	35,423,065 (GRCm39)	missense	probably benign	0.05
R7422:Lta	UTSW	17	35,422,805 (GRCm39)	missense	probably benign	0.14
R8047:Lta	UTSW	17	35,423,011 (GRCm39)	missense	probably damaging	1.00
R8732:Lta	UTSW	17	35,423,045 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GATGTGACCCTTGAAACAACG -3'
(R):5'- TGAGCAACAACTCCCTCCTG -3'

Sequencing Primer
(F):5'- CCCTTGAAACAACGGTCAGGATG -3'
(R):5'- ACTTTGTCTACTCCCAGGTGG -3'

Posted On

2017-10-10