Incidental Mutation 'R3879:Tnfrsf11a'
| ID |
308663 |
| 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 |
040793-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.181)
|
| Stock # |
R3879 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
105708443-105775709 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 105737085 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Isoleucine
at position 64
(T64I)
|
| 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 |
probably damaging
Transcript: ENSMUST00000027559
AA Change: T64I
PolyPhen 2
Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000027559
Gene: ENSMUSG00000026321
AA Change: T64I
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000187812
|
| Meta Mutation Damage Score |
0.0899 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.5%
|
| Validation Efficiency |
95% (38/40) |
| 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 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: 33 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4933434E20Rik |
T |
C |
3: 89,970,561 (GRCm39) |
|
probably benign |
Het |
| Aass |
G |
A |
6: 23,122,520 (GRCm39) |
H68Y |
probably damaging |
Het |
| Abcc8 |
T |
A |
7: 45,754,051 (GRCm39) |
K1588N |
possibly damaging |
Het |
| Calcoco1 |
T |
C |
15: 102,615,823 (GRCm39) |
D601G |
probably damaging |
Het |
| Ccdc175 |
C |
A |
12: 72,182,792 (GRCm39) |
R409I |
probably damaging |
Het |
| Ccnl1 |
A |
G |
3: 65,856,179 (GRCm39) |
V242A |
possibly damaging |
Het |
| Clasp2 |
T |
C |
9: 113,719,029 (GRCm39) |
F705L |
probably damaging |
Het |
| Cyp46a1 |
A |
G |
12: 108,324,389 (GRCm39) |
T389A |
probably benign |
Het |
| Eps8 |
A |
G |
6: 137,504,360 (GRCm39) |
|
probably benign |
Het |
| Gm9894 |
T |
C |
13: 67,912,916 (GRCm39) |
|
noncoding transcript |
Het |
| Kcnd3 |
C |
T |
3: 105,566,082 (GRCm39) |
A421V |
probably damaging |
Het |
| Nup153 |
A |
T |
13: 46,837,436 (GRCm39) |
V1262E |
probably damaging |
Het |
| Nup210l |
A |
G |
3: 90,092,780 (GRCm39) |
T1245A |
probably damaging |
Het |
| Or10ad1b |
C |
T |
15: 98,125,085 (GRCm39) |
C147Y |
probably damaging |
Het |
| Or5b121 |
A |
G |
19: 13,507,613 (GRCm39) |
Y236C |
probably damaging |
Het |
| Pcif1 |
G |
A |
2: 164,727,878 (GRCm39) |
G189D |
probably benign |
Het |
| Pdzd2 |
A |
G |
15: 12,375,594 (GRCm39) |
S1514P |
probably damaging |
Het |
| Pigu |
A |
T |
2: 155,141,063 (GRCm39) |
F276I |
probably damaging |
Het |
| Pramex1 |
T |
C |
X: 134,514,194 (GRCm39) |
H365R |
probably benign |
Het |
| Psmd9 |
C |
T |
5: 123,372,653 (GRCm39) |
|
probably benign |
Het |
| Rasgrp2 |
A |
T |
19: 6,463,920 (GRCm39) |
Q539H |
probably benign |
Het |
| Rgs22 |
T |
G |
15: 36,107,051 (GRCm39) |
I112L |
possibly damaging |
Het |
| Slc26a9 |
A |
T |
1: 131,696,969 (GRCm39) |
T786S |
probably benign |
Het |
| Sned1 |
A |
G |
1: 93,192,752 (GRCm39) |
|
probably benign |
Het |
| St7l |
G |
A |
3: 104,833,763 (GRCm39) |
V475I |
probably damaging |
Het |
| Top3a |
A |
G |
11: 60,634,765 (GRCm39) |
V713A |
possibly damaging |
Het |
| Trim16 |
G |
A |
11: 62,731,433 (GRCm39) |
G348S |
probably damaging |
Het |
| Tshz3 |
C |
T |
7: 36,470,962 (GRCm39) |
Q984* |
probably null |
Het |
| Ttn |
A |
G |
2: 76,566,406 (GRCm39) |
|
probably null |
Het |
| Ubfd1 |
T |
A |
7: 121,667,999 (GRCm39) |
|
probably benign |
Het |
| Zfp37 |
A |
T |
4: 62,109,572 (GRCm39) |
Y497* |
probably null |
Het |
| Zfp462 |
G |
A |
4: 55,060,095 (GRCm39) |
C1207Y |
probably damaging |
Het |
| Zfp607b |
A |
G |
7: 27,403,476 (GRCm39) |
E644G |
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 |
|
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 |
|
R9052: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'- GCTTCCTGGATGAATGGTCC -3'
(R):5'- TGAGGAGAACCACTCAAAGC -3'
Sequencing Primer
(F):5'- GTCCTGTGAGTCAAATCTATAGGC -3'
(R):5'- GGGCATATTTAACAAGATCCTGTGG -3'
|
| Posted On |
2015-04-17 |
Incidental Mutation