Mutagenetix > Incidental Mutation

Incidental Mutation 'R5596:Tnfrsf9'

437823

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

043148-MU

Accession Numbers

Essential gene?

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

Stock #

R5596 (G1)

Quality Score

225

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: 99.9%
3x: 99.7%
10x: 98.8%
20x: 96.9%

Validation Efficiency

100% (40/40)

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: 39 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca15	A	G	7: 120,000,972 (GRCm39)	M1503V	possibly damaging	Het
Abraxas1	A	T	5: 100,966,403 (GRCm39)	V53D	probably damaging	Het
Bub1b	T	C	2: 118,461,463 (GRCm39)	S672P	probably damaging	Het
C1qtnf7	A	T	5: 43,673,313 (GRCm39)		probably benign	Het
Cacng7	A	T	7: 3,415,420 (GRCm39)	I262F	probably benign	Het
Capzb	T	G	4: 139,006,738 (GRCm39)		probably benign	Het
Ccdc149	A	G	5: 52,561,493 (GRCm39)	V229A	probably damaging	Het
Cfap69	A	G	5: 5,676,020 (GRCm39)	L225P	probably damaging	Het
Cftr	A	G	6: 18,268,095 (GRCm39)	T685A	probably benign	Het
Col12a1	G	A	9: 79,611,041 (GRCm39)	T177M	probably damaging	Het
Creb3l3	T	G	10: 80,920,881 (GRCm39)	D383A	probably benign	Het
Cyp2j8	T	A	4: 96,395,578 (GRCm39)	I16F	probably benign	Het
Dnah5	G	T	15: 28,343,754 (GRCm39)	A2385S	probably damaging	Het
Enox1	A	G	14: 77,816,493 (GRCm39)	I158V	probably benign	Het
Erich3	A	T	3: 154,433,033 (GRCm39)	T139S	probably damaging	Het
Fam186b	A	T	15: 99,169,170 (GRCm39)	S926T	possibly damaging	Het
Gjd2	C	A	2: 113,841,965 (GRCm39)	V171F	possibly damaging	Het
Helz2	A	T	2: 180,879,082 (GRCm39)		probably benign	Het
Herc1	T	TTN	9: 66,341,345 (GRCm39)		probably benign	Het
Impg1	A	T	9: 80,252,500 (GRCm39)	V483E	probably benign	Het
Irx4	A	G	13: 73,415,799 (GRCm39)	N196S	probably damaging	Het
Kcnip1	T	C	11: 33,580,597 (GRCm39)	D213G	probably damaging	Het
Lmntd1	T	A	6: 145,359,140 (GRCm39)	T191S	probably benign	Het
Med12l	T	A	3: 59,159,771 (GRCm39)	N1273K	probably benign	Het
Musk	T	C	4: 58,373,036 (GRCm39)	C654R	probably damaging	Het
Nlrp4d	A	T	7: 10,115,951 (GRCm39)	S274T	noncoding transcript	Het
Omd	A	G	13: 49,745,814 (GRCm39)	H408R	probably benign	Het
Pbld2	C	T	10: 62,907,791 (GRCm39)	A219V	probably damaging	Het
Pramel22	T	A	4: 143,381,025 (GRCm39)	T333S	probably damaging	Het
Pramel32	C	T	4: 88,548,292 (GRCm39)	E38K	probably damaging	Het
Ptpn1	T	C	2: 167,816,683 (GRCm39)	I246T	probably damaging	Het
Sap18b	G	T	8: 96,551,998 (GRCm39)	A3S	unknown	Het
Sptbn5	G	A	2: 119,876,965 (GRCm39)		probably benign	Het
Sstr4	G	T	2: 148,237,652 (GRCm39)	V88F	possibly damaging	Het
Tdpoz4	A	T	3: 93,704,806 (GRCm39)	T368S	probably benign	Het
Tmcc2	T	C	1: 132,288,221 (GRCm39)	N489D	probably damaging	Het
Tnxb	T	A	17: 34,907,778 (GRCm39)	V1274E	probably damaging	Het
Ube3b	T	A	5: 114,544,221 (GRCm39)		probably null	Het
Vwa5a	A	T	9: 38,633,874 (GRCm39)	I26F	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
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
R7440:Tnfrsf9	UTSW	4	151,014,331 (GRCm39)	missense	probably benign	0.01
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'- AGAATGACACTTGTGAGATATCCC -3'
(R):5'- GGCTGCTTTGTTGGATTCAA -3'

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

Posted On

2016-10-26