Mutagenetix > Incidental Mutation

Incidental Mutation 'R7319:Tnf'

568093

Institutional Source

Beutler Lab

Gene Symbol

Tnf

Ensembl Gene

ENSMUSG00000024401

Gene Name

tumor necrosis factor

Synonyms

DIF, TNF alpha, TNFalpha, Tnfsf1a, Tnfa, tumor necrosis factor-alpha, TNF-alpha

MMRRC Submission

045415-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7319 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

35418357-35420983 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 35419347 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 161 (F161S)

Ref Sequence

ENSEMBL: ENSMUSP00000025263 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025262] [ENSMUST00000025263] [ENSMUST00000025266] [ENSMUST00000167924] [ENSMUST00000173600]

AlphaFold

P06804

PDB Structure

1.4 A RESOLUTION STRUCTURE OF MOUSE TUMOR NECROSIS FACTOR, TOWARDS MODULATION OF ITS SELCTIVITY AND TRIMERISATION [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000025262

SMART Domains

Protein: ENSMUSP00000025262
Gene: ENSMUSG00000024399

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

possibly damaging
Transcript: ENSMUST00000025263
AA Change: F161S

PolyPhen 2 Score 0.580 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000025263
Gene: ENSMUSG00000024401
AA Change: F161S

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: ENSMUST00000025266

SMART Domains

Protein: ENSMUSP00000025266
Gene: ENSMUSG00000024402

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000167924
AA Change: F145S

PolyPhen 2 Score 0.580 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000126122
Gene: ENSMUSG00000024401
AA Change: F145S

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

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

96% (79/82)

MGI Phenotype

FUNCTION: This gene encodes a multifunctional proinflammatory cytokine that belongs to the tumor necrosis factor (TNF) superfamily. Members of this family are classified based on primary sequence, function, and structure. This protein is synthesized as a type-II transmembrane protein and is reported to be cleaved into products that exert distinct biological functions. It plays an important role in the innate immune response as well as regulating homeostasis but is also implicated in diseases of chronic inflammation. In mouse deficiency of this gene is associated with defects in response to bacterial infection, with defects in forming organized follicular dendritic cell networks and germinal centers, and with a lack of primary B cell follicles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2013]
PHENOTYPE: Mutations at this locus primarily affect the immune system, causing increased susceptibility to infection, failure to form splenic B-cell follicles, increased inflammation and impaired contact hypersensitivity. Homozygotes also may show metabolic defects. [provided by MGI curators]

Allele List at MGI

All alleles(23) : Targeted(20) Spontaneous(2) Chemically induced(1)

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9930012K11Rik	A	T	14: 70,393,635 (GRCm39)	I287N	probably benign	Het
Aco2	G	T	15: 81,787,820 (GRCm39)	E223D	probably damaging	Het
Acsf3	T	A	8: 123,539,770 (GRCm39)	I466N	probably damaging	Het
Albfm1	G	A	5: 90,719,625 (GRCm39)		probably null	Het
Aox3	T	A	1: 58,191,761 (GRCm39)	F438I	probably benign	Het
Arhgap33	T	C	7: 30,225,794 (GRCm39)	T591A	probably benign	Het
Ash1l	C	T	3: 88,888,694 (GRCm39)	A191V	probably benign	Het
Btg2	T	C	1: 134,006,779 (GRCm39)	K5E	probably benign	Het
C1galt1	T	A	6: 7,871,150 (GRCm39)	Y329N	probably damaging	Het
Cacna1h	A	G	17: 25,608,435 (GRCm39)	I824T	possibly damaging	Het
Carmil3	A	G	14: 55,731,817 (GRCm39)	I182V	probably benign	Het
Ccdc150	T	A	1: 54,302,496 (GRCm39)		probably null	Het
Chek1	T	A	9: 36,633,939 (GRCm39)	R129W	probably damaging	Het
Chrna6	A	G	8: 27,896,815 (GRCm39)	M354T	possibly damaging	Het
Cpq	A	G	15: 33,250,185 (GRCm39)	T181A	probably benign	Het
Csmd2	A	T	4: 128,287,472 (GRCm39)	Y1069F		Het
Defb28	T	A	2: 152,361,974 (GRCm39)	C45S	possibly damaging	Het
Dnah1	A	G	14: 31,018,551 (GRCm39)	Y1360H	probably benign	Het
Dnah7c	T	C	1: 46,823,608 (GRCm39)	V3749A	possibly damaging	Het
Dnah7c	T	A	1: 46,819,935 (GRCm39)	D3728E	probably benign	Het
Dym	G	A	18: 75,196,245 (GRCm39)		probably null	Het
Dync2i2	G	A	2: 29,928,341 (GRCm39)	P95L	probably benign	Het
Dzip3	A	G	16: 48,747,903 (GRCm39)		probably null	Het
Eef1akmt4	A	G	16: 20,436,666 (GRCm39)	K163E	probably benign	Het
Fbrs	A	G	7: 127,081,985 (GRCm39)	T242A	possibly damaging	Het
Fgfr3	G	A	5: 33,885,146 (GRCm39)	V87M	possibly damaging	Het
Fst	A	T	13: 114,595,068 (GRCm39)	C19S	probably benign	Het
Gm7276	G	A	18: 77,273,216 (GRCm39)	R173W	unknown	Het
Gm9195	G	A	14: 72,697,929 (GRCm39)	H1284Y	probably benign	Het
Herc6	C	A	6: 57,581,074 (GRCm39)	T258K	probably damaging	Het
Hip1r	A	G	5: 124,137,174 (GRCm39)	Y678C	probably damaging	Het
Ifne	A	T	4: 88,798,243 (GRCm39)	N58K	probably damaging	Het
Ighv1-26	A	T	12: 114,752,163 (GRCm39)	H60Q	possibly damaging	Het
Ints1	A	G	5: 139,746,520 (GRCm39)	F1276L	probably damaging	Het
Itprid2	A	T	2: 79,466,416 (GRCm39)	D82V	probably damaging	Het
Kcnc4	T	A	3: 107,366,100 (GRCm39)	E36V	probably benign	Het
Kcnq2	C	T	2: 180,750,895 (GRCm39)	G315S	probably damaging	Het
Kdm4c	G	A	4: 74,255,200 (GRCm39)	V585M	probably damaging	Het
Klhl26	C	T	8: 70,905,592 (GRCm39)	R106H	probably damaging	Het
Kmo	T	C	1: 175,481,221 (GRCm39)	F313S	probably damaging	Het
Lmtk3	T	A	7: 45,443,740 (GRCm39)	S808T	unknown	Het
Lrch3	A	G	16: 32,815,363 (GRCm39)	T585A	probably benign	Het
Lrch4	T	A	5: 137,637,977 (GRCm39)	H86Q		Het
Map3k20	A	G	2: 72,195,062 (GRCm39)	D113G	probably damaging	Het
Mbd3l1	T	C	9: 18,396,417 (GRCm39)	S181P	probably benign	Het
Mccc2	T	C	13: 100,104,241 (GRCm39)	T303A	probably benign	Het
Med27	A	G	2: 29,303,490 (GRCm39)	R147G	possibly damaging	Het
Mrps5	T	A	2: 127,437,762 (GRCm39)	S196R	possibly damaging	Het
Muc21	GGGGTGGGCATAGATCCTGAGGCAGAGCTGGATGCAGTGGTGGTCAGGGTGGG	GGGGTGGG	17: 35,932,935 (GRCm39)		probably benign	Het
Myo16	A	T	8: 10,526,185 (GRCm39)		probably null	Het
Nudt2	A	T	4: 41,477,575 (GRCm39)	M19L	probably benign	Het
Pcdha11	C	T	18: 37,146,245 (GRCm39)	P779S	probably benign	Het
Phykpl	A	G	11: 51,489,530 (GRCm39)	T379A	probably benign	Het
Plekha8	A	C	6: 54,601,206 (GRCm39)	M270L	probably benign	Het
Plekhg5	A	G	4: 152,192,885 (GRCm39)	H593R	probably benign	Het
Polr2a	T	C	11: 69,637,196 (GRCm39)	N293S	possibly damaging	Het
Pramel32	G	A	4: 88,548,184 (GRCm39)	P74S	probably benign	Het
Prex2	T	A	1: 11,232,532 (GRCm39)	N866K	probably benign	Het
Psme4	A	T	11: 30,757,790 (GRCm39)	I308L	probably benign	Het
Ptprb	T	C	10: 116,177,309 (GRCm39)	V1003A	probably benign	Het
Rbbp8	T	A	18: 11,865,269 (GRCm39)	D719E	probably damaging	Het
Rnaset2b	A	T	17: 7,259,166 (GRCm39)	D144V	probably benign	Het
Senp6	T	G	9: 80,033,481 (GRCm39)	D662E	probably damaging	Het
Serpinb3c	T	C	1: 107,200,817 (GRCm39)	N200S	possibly damaging	Het
Serpinb9g	C	G	13: 33,672,543 (GRCm39)	Y113*	probably null	Het
Sgf29	T	C	7: 126,270,821 (GRCm39)	I134T	probably benign	Het
Sh3bp4	T	G	1: 89,080,824 (GRCm39)		probably null	Het
Stab1	G	A	14: 30,862,783 (GRCm39)	L2243F	probably damaging	Het
Sympk	T	C	7: 18,769,770 (GRCm39)	V149A	probably benign	Het
Syt3	C	T	7: 44,041,953 (GRCm39)	Q271*	probably null	Het
Tas2r109	A	G	6: 132,957,663 (GRCm39)	I89T	probably benign	Het
Tgif1	A	G	17: 71,151,847 (GRCm39)	S255P	probably damaging	Het
Tm9sf1	G	A	14: 55,875,432 (GRCm39)		probably benign	Het
Topaz1	T	A	9: 122,579,428 (GRCm39)	S779R	possibly damaging	Het
Topors	A	G	4: 40,260,540 (GRCm39)	S915P	unknown	Het
Tpm4	C	T	8: 72,900,321 (GRCm39)	L161F	probably damaging	Het
Trim38	C	T	13: 23,975,384 (GRCm39)	T441I	probably damaging	Het
Trpv1	A	G	11: 73,141,620 (GRCm39)	M548V	probably benign	Het
Vmn2r68	T	A	7: 84,883,042 (GRCm39)	T237S	probably benign	Het
Zc3hav1	A	G	6: 38,309,209 (GRCm39)	S538P	probably benign	Het
Zfp541	C	T	7: 15,813,294 (GRCm39)	T649I	probably benign	Het

Other mutations in Tnf

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
Dome	UTSW	17	35,420,650 (GRCm39)	missense	probably damaging	0.99
Panr1	UTSW	17	35,419,180 (GRCm39)	missense	probably damaging	1.00
R0783:Tnf	UTSW	17	35,420,650 (GRCm39)	missense	probably damaging	0.99
R0815:Tnf	UTSW	17	35,420,120 (GRCm39)	unclassified	probably benign
R0863:Tnf	UTSW	17	35,420,120 (GRCm39)	unclassified	probably benign
R2195:Tnf	UTSW	17	35,420,089 (GRCm39)	splice site	probably null
R2570:Tnf	UTSW	17	35,419,476 (GRCm39)	missense	probably damaging	0.99
R4660:Tnf	UTSW	17	35,419,156 (GRCm39)	missense	probably benign	0.00
R6670:Tnf	UTSW	17	35,420,800 (GRCm39)	missense	possibly damaging	0.73
R7708:Tnf	UTSW	17	35,419,134 (GRCm39)	missense	possibly damaging	0.63
R8093:Tnf	UTSW	17	35,420,072 (GRCm39)	missense	probably benign	0.11

Predicted Primers

PCR Primer
(F):5'- CCGCAAAGTCTAAGTACTTGGG -3'
(R):5'- GGTGACACTGACTCAATCCTC -3'

Sequencing Primer
(F):5'- AGTCTAAGTACTTGGGCAGATTGAC -3'
(R):5'- CCAAGTGGAGGAGCAGCTG -3'

Posted On

2019-06-26