Incidental Mutation 'R5441:Ltbr'
| ID |
427174 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ltbr
|
| Ensembl Gene |
ENSMUSG00000030339 |
| Gene Name |
lymphotoxin B receptor |
| Synonyms |
Ltar, TNF-R-III, Tnfrsf3, TNFR2-RP, LT-beta receptor, LT beta-R, TNF receptor-related protein, Tnfbr, LTbetaR, TNFCR, TNFRrp |
| MMRRC Submission |
043006-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5441 (G1)
|
| Quality Score |
209 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
125283534-125290848 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 125289757 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Tryptophan
at position 146
(R146W)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000032489
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000032489]
|
| AlphaFold |
P50284 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000032489
AA Change: R146W
PolyPhen 2
Score 0.973 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000032489
Gene: ENSMUSG00000030339
AA Change: R146W
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
27 |
N/A |
INTRINSIC |
|
TNFR
|
43 |
80 |
5.73e-5 |
SMART |
|
TNFR
|
83 |
124 |
3.96e-8 |
SMART |
|
Blast:TNFR
|
126 |
169 |
3e-7 |
BLAST |
|
TNFR
|
172 |
212 |
1.95e-7 |
SMART |
|
transmembrane domain
|
222 |
244 |
N/A |
INTRINSIC |
|
low complexity region
|
294 |
305 |
N/A |
INTRINSIC |
|
low complexity region
|
362 |
388 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160901
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161891
|
| Meta Mutation Damage Score |
0.6467 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 95.1%
|
| Validation Efficiency |
98% (56/57) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the tumor necrosis factor receptor superfamily. The major ligands of this receptor include lymphotoxin alpha/beta and tumor necrosis factor ligand superfamily member 14. The encoded protein plays a role in signalling during the development of lymphoid and other organs, lipid metabolism, immune response, and programmed cell death. Activity of this receptor has also been linked to carcinogenesis. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Aug 2012]
PHENOTYPE: Homozygotes for a targeted null mutation lack Peyer's patches, colon-associated lymphoid tissues, and lymph nodes. Mutants also exhibit severely reduced numbers of NK cells and increased susceptibility to Theiler's murine encephalomyelitis virus. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 55 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca12 |
A |
G |
1: 71,334,215 (GRCm39) |
Y1096H |
probably damaging |
Het |
| Aspa |
A |
T |
11: 73,196,420 (GRCm39) |
F261I |
probably damaging |
Het |
| Atm |
C |
A |
9: 53,427,767 (GRCm39) |
G448* |
probably null |
Het |
| Atmin |
T |
A |
8: 117,684,696 (GRCm39) |
D785E |
probably damaging |
Het |
| Car1 |
G |
C |
3: 14,841,364 (GRCm39) |
R90G |
probably damaging |
Het |
| Cdh11 |
T |
C |
8: 103,374,178 (GRCm39) |
D520G |
probably benign |
Het |
| Cers5 |
T |
A |
15: 99,649,119 (GRCm39) |
K50* |
probably null |
Het |
| Chad |
A |
T |
11: 94,459,118 (GRCm39) |
D340V |
probably benign |
Het |
| Cspg5 |
T |
C |
9: 110,075,711 (GRCm39) |
I68T |
probably benign |
Het |
| Fcgbpl1 |
C |
T |
7: 27,856,339 (GRCm39) |
T2042M |
probably damaging |
Het |
| Fcrla |
T |
A |
1: 170,752,991 (GRCm39) |
|
probably benign |
Het |
| Fer1l4 |
T |
A |
2: 155,865,177 (GRCm39) |
D1608V |
probably benign |
Het |
| Fzd5 |
T |
A |
1: 64,774,576 (GRCm39) |
Q395L |
probably benign |
Het |
| Gm7664 |
T |
A |
13: 62,676,464 (GRCm39) |
|
probably benign |
Het |
| Hk3 |
T |
C |
13: 55,162,869 (GRCm39) |
E2G |
probably damaging |
Het |
| Hmcn2 |
G |
A |
2: 31,296,428 (GRCm39) |
E2677K |
possibly damaging |
Het |
| Hydin |
T |
C |
8: 111,291,741 (GRCm39) |
L3411P |
possibly damaging |
Het |
| Lysmd2 |
C |
T |
9: 75,533,254 (GRCm39) |
H70Y |
possibly damaging |
Het |
| Msi2 |
A |
G |
11: 88,370,818 (GRCm39) |
|
probably benign |
Het |
| Msi2 |
G |
A |
11: 88,608,921 (GRCm39) |
|
probably benign |
Het |
| Napsa |
T |
A |
7: 44,230,817 (GRCm39) |
|
probably benign |
Het |
| Nlrp4a |
T |
A |
7: 26,153,578 (GRCm39) |
L710M |
probably damaging |
Het |
| Or10g1 |
T |
A |
14: 52,647,414 (GRCm39) |
K305M |
probably benign |
Het |
| Or12d13 |
T |
C |
17: 37,647,159 (GRCm39) |
|
probably null |
Het |
| Or5m13 |
T |
A |
2: 85,748,934 (GRCm39) |
F222I |
probably benign |
Het |
| Or6ae1 |
T |
C |
7: 139,742,564 (GRCm39) |
T100A |
probably benign |
Het |
| Or9a2 |
C |
T |
6: 41,748,782 (GRCm39) |
M150I |
probably benign |
Het |
| Plbd2 |
T |
A |
5: 120,637,147 (GRCm39) |
Y105F |
probably benign |
Het |
| Plppr5 |
A |
T |
3: 117,456,120 (GRCm39) |
I214F |
possibly damaging |
Het |
| Pramel34 |
A |
T |
5: 93,784,456 (GRCm39) |
M139K |
possibly damaging |
Het |
| Ptcd3 |
A |
G |
6: 71,858,505 (GRCm39) |
V655A |
possibly damaging |
Het |
| Ptpn14 |
T |
C |
1: 189,530,767 (GRCm39) |
L78P |
probably damaging |
Het |
| Ralgapa1 |
A |
C |
12: 55,766,408 (GRCm39) |
D1295E |
probably damaging |
Het |
| Rnf213 |
G |
A |
11: 119,299,846 (GRCm39) |
D192N |
probably damaging |
Het |
| Ropn1 |
A |
G |
16: 34,487,167 (GRCm39) |
I34M |
probably damaging |
Het |
| Rpe65 |
G |
T |
3: 159,310,038 (GRCm39) |
G104C |
probably damaging |
Het |
| Scgb2b27 |
T |
C |
7: 33,712,582 (GRCm39) |
|
probably benign |
Het |
| Sh3bgr |
T |
C |
16: 96,007,117 (GRCm39) |
I29T |
possibly damaging |
Het |
| Smg1 |
T |
C |
7: 117,794,304 (GRCm39) |
|
probably benign |
Het |
| Stim2 |
T |
A |
5: 54,232,712 (GRCm39) |
C68* |
probably null |
Het |
| Syne2 |
G |
A |
12: 76,035,917 (GRCm39) |
V3736I |
possibly damaging |
Het |
| Tbx19 |
T |
C |
1: 164,981,249 (GRCm39) |
N82D |
probably damaging |
Het |
| Tdp1 |
T |
A |
12: 99,876,544 (GRCm39) |
V353D |
probably damaging |
Het |
| Tg |
T |
A |
15: 66,568,369 (GRCm39) |
I1352K |
possibly damaging |
Het |
| Thsd4 |
T |
C |
9: 59,887,066 (GRCm39) |
T919A |
probably damaging |
Het |
| Tmprss11f |
A |
T |
5: 86,676,062 (GRCm39) |
M373K |
probably damaging |
Het |
| Tmprss15 |
T |
A |
16: 78,868,335 (GRCm39) |
|
probably null |
Het |
| Tpd52 |
A |
T |
3: 9,068,466 (GRCm39) |
Y16* |
probably null |
Het |
| Ube2o |
G |
A |
11: 116,435,268 (GRCm39) |
R507C |
probably damaging |
Het |
| Unc93b1 |
T |
C |
19: 3,993,703 (GRCm39) |
F382L |
probably benign |
Het |
| Vav2 |
A |
T |
2: 27,160,122 (GRCm39) |
|
probably benign |
Het |
| Vmn1r207 |
T |
C |
13: 22,910,686 (GRCm39) |
|
noncoding transcript |
Het |
| Zan |
T |
A |
5: 137,435,013 (GRCm39) |
I2127F |
unknown |
Het |
| Zfp748 |
C |
A |
13: 67,688,737 (GRCm39) |
C841F |
probably damaging |
Het |
| Zic4 |
C |
A |
9: 91,266,253 (GRCm39) |
P299Q |
probably damaging |
Het |
|
| Other mutations in Ltbr |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL03349:Ltbr
|
APN |
6 |
125,289,329 (GRCm39) |
missense |
probably damaging |
0.96 |
|
Armitage
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
bonsai
|
UTSW |
6 |
125,289,733 (GRCm39) |
missense |
probably damaging |
1.00 |
|
kama
|
UTSW |
6 |
125,290,351 (GRCm39) |
critical splice donor site |
probably null |
|
|
marine_blue
|
UTSW |
6 |
125,289,771 (GRCm39) |
missense |
probably damaging |
0.98 |
|
moksha
|
UTSW |
6 |
125,285,031 (GRCm39) |
missense |
probably benign |
0.00 |
|
Questionable
|
UTSW |
6 |
125,290,338 (GRCm39) |
splice site |
probably benign |
|
|
R0090:Ltbr
|
UTSW |
6 |
125,286,412 (GRCm39) |
splice site |
probably benign |
|
|
R0234:Ltbr
|
UTSW |
6 |
125,289,836 (GRCm39) |
missense |
probably benign |
0.16 |
|
R0234:Ltbr
|
UTSW |
6 |
125,289,836 (GRCm39) |
missense |
probably benign |
0.16 |
|
R0553:Ltbr
|
UTSW |
6 |
125,290,351 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0686:Ltbr
|
UTSW |
6 |
125,285,024 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R0879:Ltbr
|
UTSW |
6 |
125,290,338 (GRCm39) |
splice site |
probably benign |
|
|
R1086:Ltbr
|
UTSW |
6 |
125,289,703 (GRCm39) |
splice site |
probably benign |
|
|
R2118:Ltbr
|
UTSW |
6 |
125,286,440 (GRCm39) |
missense |
probably benign |
0.34 |
|
R2120:Ltbr
|
UTSW |
6 |
125,286,440 (GRCm39) |
missense |
probably benign |
0.34 |
|
R2122:Ltbr
|
UTSW |
6 |
125,286,440 (GRCm39) |
missense |
probably benign |
0.34 |
|
R2124:Ltbr
|
UTSW |
6 |
125,286,440 (GRCm39) |
missense |
probably benign |
0.34 |
|
R2199:Ltbr
|
UTSW |
6 |
125,289,024 (GRCm39) |
missense |
probably benign |
0.25 |
|
R4931:Ltbr
|
UTSW |
6 |
125,284,437 (GRCm39) |
splice site |
probably null |
|
|
R5051:Ltbr
|
UTSW |
6 |
125,289,733 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5174:Ltbr
|
UTSW |
6 |
125,286,500 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5268:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5269:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5357:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5358:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5360:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5361:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5363:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5434:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5436:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5442:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5533:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5534:Ltbr
|
UTSW |
6 |
125,289,757 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5859:Ltbr
|
UTSW |
6 |
125,289,771 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6217:Ltbr
|
UTSW |
6 |
125,284,417 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6702:Ltbr
|
UTSW |
6 |
125,285,031 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7101:Ltbr
|
UTSW |
6 |
125,289,763 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7584:Ltbr
|
UTSW |
6 |
125,284,204 (GRCm39) |
missense |
probably benign |
0.09 |
|
R7587:Ltbr
|
UTSW |
6 |
125,289,315 (GRCm39) |
missense |
probably benign |
|
|
R8798:Ltbr
|
UTSW |
6 |
125,284,258 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9720:Ltbr
|
UTSW |
6 |
125,284,348 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9721:Ltbr
|
UTSW |
6 |
125,284,348 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9723:Ltbr
|
UTSW |
6 |
125,284,348 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9746:Ltbr
|
UTSW |
6 |
125,290,064 (GRCm39) |
missense |
probably benign |
|
|
R9750:Ltbr
|
UTSW |
6 |
125,284,348 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9753:Ltbr
|
UTSW |
6 |
125,284,348 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- ATACCAGTTCATGTCTTGGCAG -3'
(R):5'- CTGCATGATGGGTACGACTG -3'
Sequencing Primer
(F):5'- GACTGATAGATTCTTTATGGTTCTCC -3'
(R):5'- TACGACTGGGAGGGCCAG -3'
|
| Posted On |
2016-09-01 |
Incidental Mutation