Mutagenetix > Incidental Mutation

Incidental Mutation 'R7440:Tnfrsf9'

576881

Institutional Source

Beutler Lab

Gene Symbol

Tnfrsf9

Ensembl Gene

ENSMUSG00000028965

Gene Name

tumor necrosis factor receptor superfamily, member 9

Synonyms

Cd137, CDw137, 4-1BB, ILA, Ly63, A930040I11Rik

MMRRC Submission

045516-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.089) question?

Stock #

R7440 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

151004612-151030561 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 151014331 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 10 (V10A)

Ref Sequence

ENSEMBL: ENSMUSP00000111961 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030808] [ENSMUST00000060901] [ENSMUST00000105671] [ENSMUST00000105672] [ENSMUST00000116257] [ENSMUST00000126707] [ENSMUST00000135169] [ENSMUST00000139826] [ENSMUST00000169423]

AlphaFold

P20334

Predicted Effect

probably benign
Transcript: ENSMUST00000030808
AA Change: V10A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000030808
Gene: ENSMUSG00000028965
AA Change: V10A

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TNFR	47	85	2.36e-6	SMART
TNFR	119	158	1.11e-2	SMART
transmembrane domain	189	211	N/A	INTRINSIC
low complexity region	246	253	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000060901
AA Change: V10A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000059684
Gene: ENSMUSG00000028965
AA Change: V10A

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TNFR	47	85	1.1e-8	SMART
TNFR	119	158	5.4e-5	SMART
low complexity region	201	208	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000105671
AA Change: V10A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000101296
Gene: ENSMUSG00000028965
AA Change: V10A

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TNFR	47	85	2.36e-6	SMART
TNFR	119	158	1.11e-2	SMART
transmembrane domain	189	211	N/A	INTRINSIC
low complexity region	246	253	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000105672
AA Change: V10A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000101297
Gene: ENSMUSG00000028965
AA Change: V10A

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TNFR	47	85	1.1e-8	SMART
TNFR	119	158	5.4e-5	SMART
low complexity region	201	208	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000116257
AA Change: V10A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000111961
Gene: ENSMUSG00000028965
AA Change: V10A

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TNFR	47	85	2.36e-6	SMART
TNFR	119	158	1.11e-2	SMART
transmembrane domain	189	211	N/A	INTRINSIC
low complexity region	246	253	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000126707
AA Change: V10A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000122917
Gene: ENSMUSG00000028965
AA Change: V10A

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TNFR	47	85	2.36e-6	SMART
TNFR	119	158	1.11e-2	SMART
transmembrane domain	189	211	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000135169
AA Change: V10A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000120761
Gene: ENSMUSG00000028965
AA Change: V10A

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TNFR	47	85	2.36e-6	SMART
TNFR	119	158	1.11e-2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000139826
AA Change: V10A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000117860
Gene: ENSMUSG00000028965
AA Change: V10A

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TNFR	47	85	2.36e-6	SMART
TNFR	119	158	1.11e-2	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146133

Predicted Effect

probably benign
Transcript: ENSMUST00000169423

SMART Domains

Protein: ENSMUSP00000127916
Gene: ENSMUSG00000014592

Domain	Start	End	E-Value	Type
CG-1	67	183	1.39e-91	SMART
low complexity region	550	583	N/A	INTRINSIC
low complexity region	677	688	N/A	INTRINSIC
Pfam:TIG	874	954	3.1e-11	PFAM
low complexity region	997	1030	N/A	INTRINSIC
ANK	1066	1095	1.7e2	SMART
ANK	1111	1141	4.73e2	SMART
low complexity region	1301	1319	N/A	INTRINSIC
IQ	1548	1564	2.38e2	SMART
IQ	1578	1600	5.42e0	SMART

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (69/69)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor contributes to the clonal expansion, survival, and development of T cells. It can also induce proliferation in peripheral monocytes, enhance T cell apoptosis induced by TCR/CD3 triggered activation, and regulate CD28 co-stimulation to promote Th1 cell responses. The expression of this receptor is induced by lymphocyte activation. TRAF adaptor proteins have been shown to bind to this receptor and transduce the signals leading to activation of NF-kappaB. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutation of this gene results in enhanced T cell proliferation, decreased B cell IgG production, decreased cytotoxic T cell activity, and increased numbers of erythrocytes, granulocyte macrophages, and multipotential progenitor cells in the bone marrow, blood, and spleen. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acadm	G	A	3: 153,628,626 (GRCm39)	T403I	probably damaging	Het
Adat1	A	T	8: 112,716,530 (GRCm39)	M64K	probably damaging	Het
Adcy2	C	T	13: 68,944,786 (GRCm39)	V199M	probably damaging	Het
Ankrd13a	T	C	5: 114,941,636 (GRCm39)	S508P	possibly damaging	Het
Ap1g1	T	A	8: 110,529,356 (GRCm39)		probably null	Het
Bicral	C	T	17: 47,136,710 (GRCm39)	G167R	probably damaging	Het
Ccser2	T	C	14: 36,620,174 (GRCm39)	K727E	possibly damaging	Het
Cep350	T	G	1: 155,816,518 (GRCm39)	K332N	probably damaging	Het
Cfap68	A	G	9: 50,676,213 (GRCm39)	V35A	probably benign	Het
Chd5	A	G	4: 152,469,108 (GRCm39)	N1811S	probably benign	Het
Chpf	A	T	1: 75,452,245 (GRCm39)	V565D	probably damaging	Het
Clcn6	A	T	4: 148,098,652 (GRCm39)	L489H	probably damaging	Het
Cntln	C	A	4: 84,981,453 (GRCm39)	T877K	possibly damaging	Het
Cog4	T	C	8: 111,606,338 (GRCm39)	V630A	probably benign	Het
Col6a5	G	T	9: 105,758,630 (GRCm39)	S2192*	probably null	Het
Cry2	G	A	2: 92,243,983 (GRCm39)	R397W	probably damaging	Het
Cstdc2	A	C	2: 148,688,911 (GRCm39)	C109W	probably damaging	Het
Cyp1b1	T	C	17: 80,020,986 (GRCm39)	N252S	probably damaging	Het
Dhx9	T	C	1: 153,356,977 (GRCm39)	I91V	probably benign	Het
Dnajb6	G	A	5: 29,962,857 (GRCm39)	A256T	possibly damaging	Het
Epm2a	T	G	10: 11,266,619 (GRCm39)	Y121*	probably null	Het
Erlec1	T	C	11: 30,900,818 (GRCm39)	I117V	possibly damaging	Het
Exoc8	T	C	8: 125,622,520 (GRCm39)	M616V	probably benign	Het
Fmn1	A	T	2: 113,271,956 (GRCm39)	Q108L	unknown	Het
Fuz	T	C	7: 44,545,996 (GRCm39)	L46P	probably damaging	Het
Insc	T	C	7: 114,444,278 (GRCm39)	S422P	possibly damaging	Het
Intu	A	G	3: 40,651,981 (GRCm39)	I813V	probably benign	Het
Jak3	T	A	8: 72,133,362 (GRCm39)	S352T	probably benign	Het
Klf11	T	C	12: 24,705,490 (GRCm39)	S315P	probably benign	Het
Lrrc63	T	C	14: 75,358,453 (GRCm39)	N400D	possibly damaging	Het
Lrrk1	T	C	7: 65,940,602 (GRCm39)	D760G	probably damaging	Het
Macf1	A	T	4: 123,349,239 (GRCm39)	L3976*	probably null	Het
Map7	C	T	10: 20,137,605 (GRCm39)	A259V	probably damaging	Het
Meioc	T	A	11: 102,565,063 (GRCm39)	D170E	possibly damaging	Het
Mgat5b	T	A	11: 116,859,271 (GRCm39)	Y34*	probably null	Het
Mgst1	A	G	6: 138,127,842 (GRCm39)	K68R	probably benign	Het
Miga1	T	A	3: 152,043,683 (GRCm39)		probably null	Het
Mrps33	G	A	6: 39,779,413 (GRCm39)	P94L	probably damaging	Het
Ncapg2	G	T	12: 116,414,033 (GRCm39)	G1068C	possibly damaging	Het
Ndufaf7	C	T	17: 79,249,546 (GRCm39)	H148Y	probably damaging	Het
Nkx6-3	A	T	8: 23,643,770 (GRCm39)	D57V	probably damaging	Het
Nlrp1a	T	C	11: 70,983,150 (GRCm39)	D1272G	probably damaging	Het
Oit3	T	C	10: 59,265,392 (GRCm39)	N291S	probably damaging	Het
Or1b1	A	T	2: 36,995,181 (GRCm39)	H160Q	possibly damaging	Het
Pld1	T	G	3: 28,095,419 (GRCm39)	S251A	probably benign	Het
Polr1h	T	A	17: 37,268,736 (GRCm39)	L75F	probably benign	Het
Potefam3a	C	T	8: 20,356,948 (GRCm38)	S254N	unknown	Het
Ppfibp1	T	C	6: 146,921,001 (GRCm39)	S580P	probably benign	Het
Prdx6b	A	T	2: 80,123,560 (GRCm39)	D123V	probably damaging	Het
Ptprs	A	G	17: 56,731,256 (GRCm39)	L1050P	possibly damaging	Het
Rcc1	A	C	4: 132,065,110 (GRCm39)	S138A	probably damaging	Het
Rimbp3	G	T	16: 17,031,065 (GRCm39)	R1496S	possibly damaging	Het
Sacs	T	C	14: 61,429,054 (GRCm39)	V371A	probably benign	Het
Sfxn4	A	G	19: 60,830,642 (GRCm39)	L260P	possibly damaging	Het
Slc17a1	G	A	13: 24,062,466 (GRCm39)	S211N	possibly damaging	Het
Slc39a11	C	T	11: 113,452,918 (GRCm39)	V8M	probably damaging	Het
Smpd2	A	G	10: 41,365,012 (GRCm39)	I78T	probably benign	Het
Steap3	A	C	1: 120,169,248 (GRCm39)	F350V	probably benign	Het
Syt17	A	T	7: 117,981,107 (GRCm39)	V462E	probably damaging	Het
Tlr11	T	A	14: 50,598,801 (GRCm39)	D262E	probably benign	Het
Trpv3	C	A	11: 73,168,800 (GRCm39)	Q87K	probably benign	Het
Ugt1a5	T	C	1: 88,094,281 (GRCm39)	Y170H	probably benign	Het
Urb1	A	G	16: 90,584,296 (GRCm39)	L562P	probably damaging	Het
Usp3	G	T	9: 66,437,537 (GRCm39)	N299K	probably benign	Het
Vmn1r83	T	C	7: 12,055,556 (GRCm39)	Y167C	probably damaging	Het
Vmn2r117	T	A	17: 23,694,539 (GRCm39)	Y436F	probably benign	Het
Vps13d	A	G	4: 144,854,981 (GRCm39)	I2220T		Het
Zfp936	T	A	7: 42,836,685 (GRCm39)	V32D	probably damaging	Het
Zswim2	A	G	2: 83,751,063 (GRCm39)	C259R	probably damaging	Het

Other mutations in Tnfrsf9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
asilomar	UTSW	4	151,014,331 (GRCm39)	missense	probably benign	0.01
Monterey	UTSW	4	151,018,804 (GRCm39)	nonsense	probably null
FR4304:Tnfrsf9	UTSW	4	151,018,852 (GRCm39)	intron	probably benign
FR4342:Tnfrsf9	UTSW	4	151,018,851 (GRCm39)	intron	probably benign
R1496:Tnfrsf9	UTSW	4	151,017,561 (GRCm39)	critical splice donor site	probably null
R1870:Tnfrsf9	UTSW	4	151,018,804 (GRCm39)	nonsense	probably null
R5596:Tnfrsf9	UTSW	4	151,014,331 (GRCm39)	missense	probably benign	0.01
R7219:Tnfrsf9	UTSW	4	151,019,991 (GRCm39)	missense	probably damaging	1.00
R7322:Tnfrsf9	UTSW	4	151,018,794 (GRCm39)	missense	probably damaging	1.00
R7680:Tnfrsf9	UTSW	4	151,014,395 (GRCm39)	missense	probably damaging	1.00
R8300:Tnfrsf9	UTSW	4	151,017,556 (GRCm39)	missense	probably damaging	1.00
R9684:Tnfrsf9	UTSW	4	151,018,865 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AATGACACTTGTGAGATATCCCC -3'
(R):5'- GTCCTCATGGCTGCTTTGTT -3'

Sequencing Primer
(F):5'- TGGGGTTACAGCATCCACTAC -3'
(R):5'- AGTCGGTGCTCTTAACCAAAGTC -3'

Posted On

2019-10-07