Mutagenetix > Incidental Mutation

Incidental Mutation 'R9052:Tnfrsf11a'

688424

Institutional Source

Beutler Lab

Gene Symbol

Tnfrsf11a

Ensembl Gene

ENSMUSG00000026321

Gene Name

tumor necrosis factor receptor superfamily, member 11a, NFKB activator

Synonyms

TRANCE-R, Rank

MMRRC Submission

068878-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.181) question?

Stock #

R9052 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

105708443-105775709 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 105754854 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 309 (A309T)

Ref Sequence

ENSEMBL: ENSMUSP00000027559 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027559]

AlphaFold

O35305

PDB Structure

Crystal structure of mouse RANKL-RANK complex [X-RAY DIFFRACTION]
Crystal structure of mouse RANK [X-RAY DIFFRACTION]
Crystal structure of extracellular domains of mouse RANK-RANKL complex [X-RAY DIFFRACTION]
Crystal Structure of mouse RANK bound to RANKL [X-RAY DIFFRACTION]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000027559
AA Change: A309T

PolyPhen 2 Score 0.917 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000027559
Gene: ENSMUSG00000026321
AA Change: A309T

Domain	Start	End	E-Value	Type
signal peptide	1	30	N/A	INTRINSIC
TNFR	35	69	1.48e-7	SMART
TNFR	72	113	2.59e-3	SMART
TNFR	115	152	4.28e-4	SMART
TNFR	155	195	5.27e-4	SMART
transmembrane domain	212	234	N/A	INTRINSIC
low complexity region	300	313	N/A	INTRINSIC
low complexity region	495	511	N/A	INTRINSIC
low complexity region	543	558	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

99% (69/70)

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 receptors can interact with various TRAF family proteins, through which this receptor induces the activation of NF-kappa B and MAPK8/JNK. This receptor and its ligand are important regulators of the interaction between T cells and dendritic cells. This receptor is also an essential mediator for osteoclast and lymph node development. Mutations at this locus have been associated with familial expansile osteolysis, autosomal recessive osteopetrosis, and Paget disease of bone. Alternatively spliced transcript variants have been described for this locus. [provided by RefSeq, Aug 2012]
PHENOTYPE: Mice homozygous for a knock-out or spontaneous allele exhibit a failure of tooth eruption, osteopetrosis, and abnormal immune system morphology. [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
1110059G10Rik	T	C	9: 122,778,031 (GRCm39)	E71G	probably damaging	Het
2610021A01Rik	G	T	7: 41,275,449 (GRCm39)	G384V	probably benign	Het
4931406B18Rik	T	A	7: 43,147,631 (GRCm39)	R247*	probably null	Het
Abca4	G	T	3: 121,940,908 (GRCm39)	V1576F	possibly damaging	Het
Acsl6	A	T	11: 54,232,615 (GRCm39)	T489S	possibly damaging	Het
Adcy8	C	T	15: 64,792,764 (GRCm39)	R64H	probably benign	Het
Atad2b	C	A	12: 5,015,982 (GRCm39)	F569L	probably damaging	Het
Atp2c1	A	T	9: 105,330,032 (GRCm39)	I266N	probably damaging	Het
Atp8a1	A	G	5: 67,936,301 (GRCm39)		probably null	Het
Coch	T	C	12: 51,640,408 (GRCm39)	M1T	probably null	Het
Col5a3	C	A	9: 20,710,733 (GRCm39)	R537L	unknown	Het
Crb1	C	T	1: 139,171,161 (GRCm39)	R743Q	possibly damaging	Het
Crybg2	T	C	4: 133,803,035 (GRCm39)	F889L	probably damaging	Het
Cyp4f15	C	T	17: 32,911,589 (GRCm39)	T157I	probably damaging	Het
D630045J12Rik	G	T	6: 38,154,544 (GRCm39)	Q1212K	probably damaging	Het
Dennd1a	A	G	2: 37,911,463 (GRCm39)	Y175H	probably damaging	Het
Dhcr7	C	A	7: 143,395,060 (GRCm39)	T192K	possibly damaging	Het
Dlg1	T	A	16: 31,656,942 (GRCm39)	I612N	probably damaging	Het
Dmpk	G	A	7: 18,821,614 (GRCm39)	V291M	probably damaging	Het
Dnajc6	T	C	4: 101,496,617 (GRCm39)	V928A	probably damaging	Het
Dst	A	G	1: 34,206,045 (GRCm39)	Y859C	probably damaging	Het
Dst	C	T	1: 34,236,411 (GRCm39)	Q1592*	probably null	Het
Gm10226	T	A	17: 21,910,959 (GRCm39)	C65S	possibly damaging	Het
Helz2	T	C	2: 180,881,968 (GRCm39)	K275R	possibly damaging	Het
Hltf	A	G	3: 20,152,246 (GRCm39)	T581A	probably damaging	Het
Ighv1-24	C	T	12: 114,736,555 (GRCm39)	C115Y	probably damaging	Het
Il18	C	T	9: 50,489,090 (GRCm39)	L40F	possibly damaging	Het
Isg20	A	G	7: 78,566,390 (GRCm39)	D113G	probably damaging	Het
Itgb3	A	T	11: 104,524,413 (GRCm39)	D183V	probably damaging	Het
Kif12	C	T	4: 63,090,068 (GRCm39)	V28M	probably damaging	Het
Manbal	T	C	2: 157,221,107 (GRCm39)	L28P	probably damaging	Het
Masp1	T	A	16: 23,339,350 (GRCm39)		probably benign	Het
Mfap5	A	G	6: 122,501,463 (GRCm39)	T72A	probably benign	Het
Mier2	G	A	10: 79,384,274 (GRCm39)	R166W	probably damaging	Het
Mrps5	G	A	2: 127,433,876 (GRCm39)		probably benign	Het
Ms4a1	T	A	19: 11,233,954 (GRCm39)	T101S	probably benign	Het
Myo3b	A	G	2: 70,062,747 (GRCm39)	M344V	probably benign	Het
Naaladl1	T	G	19: 6,158,716 (GRCm39)	F283V	probably benign	Het
Nacc1	A	C	8: 85,403,377 (GRCm39)	V166G	probably damaging	Het
Nwd2	A	T	5: 63,961,773 (GRCm39)	R452S	probably damaging	Het
Or1n1b	T	C	2: 36,780,105 (GRCm39)	T252A	probably damaging	Het
Or1x6	G	A	11: 50,938,938 (GRCm39)	M1I	probably null	Het
Or5k16	T	C	16: 58,736,561 (GRCm39)	T148A	probably benign	Het
Or6c214	C	G	10: 129,591,094 (GRCm39)	C75S	possibly damaging	Het
Pik3cg	T	C	12: 32,245,708 (GRCm39)	I847V	possibly damaging	Het
Plcz1	G	A	6: 139,968,905 (GRCm39)	H178Y	probably damaging	Het
Prkdc	T	A	16: 15,508,160 (GRCm39)	M937K	probably benign	Het
Prr14l	A	T	5: 32,987,478 (GRCm39)	C672*	probably null	Het
Rasl11a	C	A	5: 146,782,107 (GRCm39)	D27E	probably benign	Het
Rbm27	T	C	18: 42,465,893 (GRCm39)	S860P	probably damaging	Het
Rfxap	G	A	3: 54,715,155 (GRCm39)		probably benign	Het
Rhbdf2	A	C	11: 116,494,758 (GRCm39)	L306R	probably benign	Het
Rigi	C	A	4: 40,208,459 (GRCm39)	V826L	probably benign	Het
Rnf123	A	T	9: 107,936,930 (GRCm39)	V875E	probably damaging	Het
Sh3bp2	A	G	5: 34,709,164 (GRCm39)		probably benign	Het
Slc7a9	A	G	7: 35,153,017 (GRCm39)	K145R	probably benign	Het
Slco5a1	A	T	1: 13,060,397 (GRCm39)	V108E	possibly damaging	Het
Stat2	A	G	10: 128,117,538 (GRCm39)	E352G	probably damaging	Het
Synj1	A	T	16: 90,735,728 (GRCm39)	S1408R	probably benign	Het
Tent5c	A	T	3: 100,380,618 (GRCm39)	I46K	probably benign	Het
Tgs1	T	A	4: 3,585,166 (GRCm39)	M102K	probably benign	Het
Ttc23	C	A	7: 67,342,687 (GRCm39)	C268*	probably null	Het
Uhrf2	T	C	19: 30,070,236 (GRCm39)	F795S	probably damaging	Het
Urgcp	A	G	11: 5,673,153 (GRCm39)	W41R	probably damaging	Het
Uso1	G	T	5: 92,328,422 (GRCm39)	V340F	probably damaging	Het
Vta1	A	C	10: 14,551,692 (GRCm39)	I169R	probably benign	Het
Zfp317	A	G	9: 19,556,568 (GRCm39)	I59V	probably benign	Het
Zfp799	G	A	17: 33,039,786 (GRCm39)	T160I	probably benign	Het
Zfp955a	G	T	17: 33,461,279 (GRCm39)	H284Q	possibly damaging	Het

Other mutations in Tnfrsf11a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01137:Tnfrsf11a	APN	1	105,737,147 (GRCm39)	missense	possibly damaging	0.80
IGL02429:Tnfrsf11a	APN	1	105,755,443 (GRCm39)	missense	probably benign	0.14
IGL03222:Tnfrsf11a	APN	1	105,749,215 (GRCm39)	missense	probably damaging	1.00
IGL03276:Tnfrsf11a	APN	1	105,749,215 (GRCm39)	missense	probably damaging	1.00
PIT4354001:Tnfrsf11a	UTSW	1	105,749,242 (GRCm39)	missense	probably damaging	1.00
R0321:Tnfrsf11a	UTSW	1	105,772,583 (GRCm39)	nonsense	probably null
R0514:Tnfrsf11a	UTSW	1	105,754,717 (GRCm39)	missense	probably damaging	1.00
R0655:Tnfrsf11a	UTSW	1	105,735,880 (GRCm39)	missense	unknown
R1470:Tnfrsf11a	UTSW	1	105,752,773 (GRCm39)	missense	probably damaging	0.96
R1470:Tnfrsf11a	UTSW	1	105,752,773 (GRCm39)	missense	probably damaging	0.96
R1868:Tnfrsf11a	UTSW	1	105,772,431 (GRCm39)	missense	probably damaging	1.00
R2900:Tnfrsf11a	UTSW	1	105,754,786 (GRCm39)	missense	probably benign	0.03
R3418:Tnfrsf11a	UTSW	1	105,737,130 (GRCm39)	missense	possibly damaging	0.84
R3816:Tnfrsf11a	UTSW	1	105,737,085 (GRCm39)	missense	probably damaging	0.96
R3817:Tnfrsf11a	UTSW	1	105,737,085 (GRCm39)	missense	probably damaging	0.96
R3818:Tnfrsf11a	UTSW	1	105,737,085 (GRCm39)	missense	probably damaging	0.96
R3819:Tnfrsf11a	UTSW	1	105,737,085 (GRCm39)	missense	probably damaging	0.96
R3879:Tnfrsf11a	UTSW	1	105,737,085 (GRCm39)	missense	probably damaging	0.96
R4037:Tnfrsf11a	UTSW	1	105,755,464 (GRCm39)	splice site	probably null
R4039:Tnfrsf11a	UTSW	1	105,755,464 (GRCm39)	splice site	probably null
R4238:Tnfrsf11a	UTSW	1	105,754,962 (GRCm39)	missense	probably damaging	1.00
R5708:Tnfrsf11a	UTSW	1	105,741,545 (GRCm39)	splice site	probably null
R6102:Tnfrsf11a	UTSW	1	105,747,671 (GRCm39)	missense	possibly damaging	0.62
R6910:Tnfrsf11a	UTSW	1	105,772,272 (GRCm39)	missense	probably damaging	1.00
R7169:Tnfrsf11a	UTSW	1	105,772,421 (GRCm39)	missense	possibly damaging	0.95
R7178:Tnfrsf11a	UTSW	1	105,755,264 (GRCm39)	missense	probably benign	0.04
R7293:Tnfrsf11a	UTSW	1	105,735,866 (GRCm39)	critical splice acceptor site	probably null
R7323:Tnfrsf11a	UTSW	1	105,772,456 (GRCm39)	missense	probably damaging	1.00
R7334:Tnfrsf11a	UTSW	1	105,754,854 (GRCm39)	missense	possibly damaging	0.92
R7607:Tnfrsf11a	UTSW	1	105,772,458 (GRCm39)	missense	probably benign	0.02
R7614:Tnfrsf11a	UTSW	1	105,755,094 (GRCm39)	missense	probably damaging	1.00
R7651:Tnfrsf11a	UTSW	1	105,737,171 (GRCm39)	missense	probably damaging	1.00
R7908:Tnfrsf11a	UTSW	1	105,737,099 (GRCm39)	missense	probably damaging	1.00
R8078:Tnfrsf11a	UTSW	1	105,745,409 (GRCm39)	missense	probably damaging	1.00
R8364:Tnfrsf11a	UTSW	1	105,745,412 (GRCm39)	missense	probably damaging	0.99
R8859:Tnfrsf11a	UTSW	1	105,772,244 (GRCm39)	critical splice acceptor site	probably null
R8979:Tnfrsf11a	UTSW	1	105,754,825 (GRCm39)	missense	possibly damaging	0.78
R9008:Tnfrsf11a	UTSW	1	105,754,854 (GRCm39)	missense	possibly damaging	0.92
R9016:Tnfrsf11a	UTSW	1	105,754,854 (GRCm39)	missense	possibly damaging	0.92
R9017:Tnfrsf11a	UTSW	1	105,754,854 (GRCm39)	missense	possibly damaging	0.92
Z1177:Tnfrsf11a	UTSW	1	105,754,724 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- CAGGGTGGAAACAGTTCATATTTTC -3'
(R):5'- TGCTTCCCTGCTGGATTAGG -3'

Sequencing Primer
(F):5'- GTGAACATGTTGCACTAATTCTGG -3'
(R):5'- CTGGATTAGGAGCAGTGAACCAGTC -3'

Posted On

2021-11-19