Mutagenetix > Incidental Mutation

Incidental Mutation 'R4660:Tnf'

352808

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

041920-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4660 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

35418357-35420983 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 35419156 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 209 (S209P)

Ref Sequence

ENSEMBL: ENSMUSP00000126122 (fasta)

Gene Model

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

AlphaFold

P06804

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

probably benign
Transcript: ENSMUST00000025263
AA Change: S225P

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000025263
Gene: ENSMUSG00000024401
AA Change: S225P

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

probably benign
Transcript: ENSMUST00000167924
AA Change: S209P

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000126122
Gene: ENSMUSG00000024401
AA Change: S209P

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: ENSMUST00000184381

Meta Mutation Damage Score

0.2928

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 95.0%

Validation Efficiency

96% (102/106)

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adra1d	T	C	2: 131,403,062 (GRCm39)	T343A	probably damaging	Het
Angptl4	A	T	17: 33,996,249 (GRCm39)		probably benign	Het
Antxr2	A	T	5: 98,151,913 (GRCm39)		probably null	Het
Ap1b1	T	A	11: 4,966,760 (GRCm39)	V145E	probably damaging	Het
Asns	G	T	6: 7,678,012 (GRCm39)	N355K	probably benign	Het
Asxl3	A	G	18: 22,649,534 (GRCm39)	T508A	probably benign	Het
B4galt7	T	A	13: 55,752,111 (GRCm39)	V54D	possibly damaging	Het
Bach2	C	T	4: 32,562,777 (GRCm39)	P415S	probably benign	Het
Bbs9	G	A	9: 22,490,063 (GRCm39)	R278Q	probably benign	Het
Blzf1	C	T	1: 164,134,062 (GRCm39)		probably benign	Het
Btd	A	T	14: 31,389,760 (GRCm39)	T494S	probably benign	Het
Casp9	C	T	4: 141,540,934 (GRCm39)	T434I	probably benign	Het
Cavin2	T	C	1: 51,340,510 (GRCm39)	S396P	probably benign	Het
Ccnk	C	T	12: 108,168,575 (GRCm39)		probably benign	Het
Cldn8	G	A	16: 88,359,296 (GRCm39)	H210Y	probably benign	Het
Clip1	G	A	5: 123,717,437 (GRCm39)	T1284I	probably damaging	Het
Coch	T	C	12: 51,642,268 (GRCm39)	V80A	probably benign	Het
Cttnbp2	A	G	6: 18,406,536 (GRCm39)	S1052P	probably benign	Het
Cyp2j7	C	T	4: 96,083,579 (GRCm39)	R457K	probably benign	Het
Dalrd3	T	C	9: 108,447,568 (GRCm39)	S129P	probably benign	Het
Ddx10	A	G	9: 53,147,698 (GRCm39)		probably null	Het
Dnah7b	A	T	1: 46,328,696 (GRCm39)	T3143S	probably damaging	Het
Dynlt1b	A	G	17: 6,699,279 (GRCm39)	T10A	probably benign	Het
Eif2s2	G	A	2: 154,730,189 (GRCm39)	T36I	probably benign	Het
Fam118b	A	T	9: 35,146,551 (GRCm39)	H105Q	possibly damaging	Het
Galntl5	T	A	5: 25,408,377 (GRCm39)	I250N	probably damaging	Het
Gm11544	C	T	11: 94,736,306 (GRCm39)		noncoding transcript	Het
Gm5709	C	T	3: 59,526,124 (GRCm39)		noncoding transcript	Het
Golgb1	T	A	16: 36,707,980 (GRCm39)	I107N	probably damaging	Het
Gpld1	T	C	13: 25,166,586 (GRCm39)		probably null	Het
Grik1	T	A	16: 87,720,019 (GRCm39)	T768S	probably damaging	Het
H2-T23	T	G	17: 36,341,108 (GRCm39)	Q349P	probably damaging	Het
Ing3	A	T	6: 21,973,710 (GRCm39)		probably benign	Het
Iqgap3	T	G	3: 88,027,483 (GRCm39)	L702R	probably damaging	Het
Itga8	A	G	2: 12,270,069 (GRCm39)	V139A	probably damaging	Het
Jam2	G	A	16: 84,609,840 (GRCm39)	V151M	probably damaging	Het
Kbtbd12	T	C	6: 88,594,772 (GRCm39)	I353V	probably benign	Het
Kif27	T	C	13: 58,471,730 (GRCm39)	E786G	probably damaging	Het
Lingo4	T	A	3: 94,310,672 (GRCm39)	S537T	probably benign	Het
Lipo3	C	T	19: 33,598,360 (GRCm39)		probably benign	Het
Lrrc3	G	T	10: 77,729,866 (GRCm39)		probably benign	Het
Ltbp3	T	A	19: 5,798,814 (GRCm39)		probably null	Het
Lyg1	T	A	1: 37,985,942 (GRCm39)		probably benign	Het
Mcm9	T	C	10: 53,424,623 (GRCm39)	I656V	probably benign	Het
Mfsd8	T	A	3: 40,776,372 (GRCm39)	I427F	probably benign	Het
Mga	T	A	2: 119,769,104 (GRCm39)		probably benign	Het
Miga1	A	G	3: 151,993,155 (GRCm39)	L422P	probably damaging	Het
Msantd3	A	G	4: 48,552,536 (GRCm39)	I42V	probably benign	Het
Mybbp1a	T	C	11: 72,336,538 (GRCm39)	V510A	probably benign	Het
Nccrp1	G	T	7: 28,245,760 (GRCm39)	P135T	probably damaging	Het
Neb	T	A	2: 52,145,600 (GRCm39)	M2975L	possibly damaging	Het
Nfxl1	A	T	5: 72,710,011 (GRCm39)	I171N	probably damaging	Het
Odad2	A	G	18: 7,211,609 (GRCm39)	V755A	possibly damaging	Het
Or10q3	T	C	19: 11,848,412 (GRCm39)	H56R	possibly damaging	Het
Or12j5	A	T	7: 140,083,933 (GRCm39)	F146L	probably benign	Het
Or13a19	T	C	7: 139,903,325 (GRCm39)	F238L	possibly damaging	Het
Otop1	T	G	5: 38,457,368 (GRCm39)	S376A	possibly damaging	Het
Pdgfra	T	C	5: 75,322,932 (GRCm39)	V10A	possibly damaging	Het
Pgs1	T	C	11: 117,910,503 (GRCm39)	V538A	probably damaging	Het
Ppa2	A	T	3: 133,032,445 (GRCm39)	T97S	probably damaging	Het
Pramel22	T	A	4: 143,380,847 (GRCm39)	Y392F	probably benign	Het
Pramel26	A	G	4: 143,538,435 (GRCm39)	S179P	probably benign	Het
Prdm10	G	A	9: 31,238,624 (GRCm39)	C172Y	probably damaging	Het
Prrc2c	G	A	1: 162,508,464 (GRCm39)	P1091L	probably damaging	Het
Pthlh	G	A	6: 147,158,796 (GRCm39)	R55C	probably damaging	Het
Ptpn9	A	T	9: 56,943,782 (GRCm39)	T105S	probably benign	Het
Rundc1	T	A	11: 101,324,830 (GRCm39)	V512E	possibly damaging	Het
Scrib	G	A	15: 75,937,185 (GRCm39)	S307L	probably damaging	Het
Sec23ip	A	G	7: 128,352,010 (GRCm39)	S26G	probably null	Het
Sec61a2	A	G	2: 5,878,504 (GRCm39)		probably benign	Het
Sema3c	T	C	5: 17,877,511 (GRCm39)	V206A	probably damaging	Het
Sgk2	C	T	2: 162,839,763 (GRCm39)	H124Y	possibly damaging	Het
Slc26a6	C	T	9: 108,738,540 (GRCm39)	T592I	probably damaging	Het
Slc5a11	T	C	7: 122,864,486 (GRCm39)	Y361H	probably damaging	Het
Smc6	T	C	12: 11,324,008 (GRCm39)	V51A	probably damaging	Het
Stab1	A	T	14: 30,876,872 (GRCm39)	N817K	possibly damaging	Het
Swt1	A	T	1: 151,283,348 (GRCm39)	D336E	probably benign	Het
Taf13	T	A	3: 108,480,293 (GRCm39)		probably benign	Het
Tmub2	T	C	11: 102,175,845 (GRCm39)		probably benign	Het
Try10	A	G	6: 41,334,761 (GRCm39)	Y229C	probably damaging	Het
Ttbk1	G	T	17: 46,788,714 (GRCm39)	Y183*	probably null	Het
Ttc17	A	T	2: 94,194,774 (GRCm39)	I533N	possibly damaging	Het
Tubb6	C	T	18: 67,535,016 (GRCm39)	P305L	probably damaging	Het
Tulp3	G	A	6: 128,300,017 (GRCm39)		probably benign	Het
Usp9x	A	G	X: 12,989,747 (GRCm39)	R776G	possibly damaging	Het
Virma	T	C	4: 11,513,505 (GRCm39)	V453A	probably damaging	Het
Vmn2r103	A	T	17: 20,032,077 (GRCm39)	N617I	probably damaging	Het
Xirp1	G	T	9: 119,846,058 (GRCm39)	L942M	probably damaging	Het
Zc3h7b	T	G	15: 81,676,451 (GRCm39)	V731G	probably benign	Het
Zfp534	C	T	4: 147,759,175 (GRCm39)	G498D	probably benign	Het
Zfp639	T	C	3: 32,574,679 (GRCm39)	Y435H	probably damaging	Het
Zxdc	A	G	6: 90,355,820 (GRCm39)	H443R	probably damaging	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
R6670:Tnf	UTSW	17	35,420,800 (GRCm39)	missense	possibly damaging	0.73
R7319:Tnf	UTSW	17	35,419,347 (GRCm39)	missense	possibly damaging	0.58
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'- GTCACTGTCCCAGCATCTTG -3'
(R):5'- AAAGTCAACCTCCTCTCTGC -3'

Sequencing Primer
(F):5'- TCTGAGCACAGAGTTGGACC -3'
(R):5'- TCTCTGCCGTCAAGAGCC -3'

Posted On

2015-10-08