Incidental Mutation 'R2363:Lrrtm4'
ID |
247216 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Lrrtm4
|
Ensembl Gene |
ENSMUSG00000052581 |
Gene Name |
leucine rich repeat transmembrane neuronal 4 |
Synonyms |
7530419J18Rik |
MMRRC Submission |
040344-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.100)
|
Stock # |
R2363 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
6 |
Chromosomal Location |
79995860-80787124 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 79998857 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Tryptophan to Arginine
at position 90
(W90R)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000117263
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000074662]
[ENSMUST00000126005]
[ENSMUST00000126399]
[ENSMUST00000128718]
[ENSMUST00000133918]
[ENSMUST00000136421]
[ENSMUST00000147663]
[ENSMUST00000145407]
|
AlphaFold |
Q80XG9 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000074662
AA Change: W89R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000074232 Gene: ENSMUSG00000052581 AA Change: W89R
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
30 |
N/A |
INTRINSIC |
LRRNT
|
33 |
65 |
1.66e0 |
SMART |
LRR_TYP
|
84 |
107 |
6.67e-2 |
SMART |
LRR
|
108 |
131 |
3.52e-1 |
SMART |
LRR_TYP
|
132 |
155 |
2.53e-2 |
SMART |
LRR
|
156 |
179 |
1.16e-1 |
SMART |
LRR
|
180 |
203 |
4.34e-1 |
SMART |
LRR
|
204 |
224 |
2.4e1 |
SMART |
LRR
|
228 |
251 |
4.97e0 |
SMART |
LRR
|
252 |
275 |
1.07e0 |
SMART |
LRR
|
276 |
299 |
1.64e-1 |
SMART |
Blast:LRRCT
|
311 |
361 |
4e-25 |
BLAST |
low complexity region
|
375 |
392 |
N/A |
INTRINSIC |
transmembrane domain
|
425 |
447 |
N/A |
INTRINSIC |
low complexity region
|
464 |
469 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000126005
AA Change: W89R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000117445 Gene: ENSMUSG00000052581 AA Change: W89R
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
30 |
N/A |
INTRINSIC |
LRRNT
|
33 |
65 |
1.66e0 |
SMART |
LRR_TYP
|
84 |
107 |
6.67e-2 |
SMART |
LRR
|
108 |
131 |
3.52e-1 |
SMART |
LRR_TYP
|
132 |
155 |
2.53e-2 |
SMART |
LRR
|
156 |
179 |
1.16e-1 |
SMART |
LRR
|
180 |
203 |
4.34e-1 |
SMART |
LRR
|
204 |
224 |
2.4e1 |
SMART |
LRR
|
228 |
251 |
4.97e0 |
SMART |
LRR
|
252 |
275 |
1.07e0 |
SMART |
LRR
|
276 |
299 |
1.64e-1 |
SMART |
Blast:LRRCT
|
311 |
361 |
4e-25 |
BLAST |
low complexity region
|
375 |
392 |
N/A |
INTRINSIC |
transmembrane domain
|
425 |
447 |
N/A |
INTRINSIC |
low complexity region
|
464 |
469 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000126399
AA Change: W89R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000121124 Gene: ENSMUSG00000052581 AA Change: W89R
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
30 |
N/A |
INTRINSIC |
LRRNT
|
33 |
65 |
1.66e0 |
SMART |
LRR_TYP
|
84 |
107 |
6.67e-2 |
SMART |
LRR
|
108 |
131 |
3.52e-1 |
SMART |
LRR_TYP
|
132 |
155 |
2.53e-2 |
SMART |
LRR
|
156 |
179 |
1.16e-1 |
SMART |
LRR
|
180 |
203 |
4.34e-1 |
SMART |
LRR
|
204 |
224 |
2.4e1 |
SMART |
LRR
|
228 |
251 |
4.97e0 |
SMART |
LRR
|
252 |
275 |
1.07e0 |
SMART |
LRR
|
276 |
299 |
1.64e-1 |
SMART |
Blast:LRRCT
|
311 |
361 |
2e-25 |
BLAST |
low complexity region
|
375 |
392 |
N/A |
INTRINSIC |
transmembrane domain
|
425 |
447 |
N/A |
INTRINSIC |
low complexity region
|
464 |
469 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000128718
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130734
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000133918
AA Change: W89R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000115016 Gene: ENSMUSG00000052581 AA Change: W89R
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
30 |
N/A |
INTRINSIC |
LRRNT
|
33 |
65 |
1.66e0 |
SMART |
LRR_TYP
|
84 |
107 |
6.67e-2 |
SMART |
LRR
|
108 |
131 |
3.52e-1 |
SMART |
LRR_TYP
|
132 |
155 |
2.53e-2 |
SMART |
LRR
|
156 |
179 |
1.16e-1 |
SMART |
LRR
|
180 |
203 |
4.34e-1 |
SMART |
LRR
|
204 |
224 |
2.4e1 |
SMART |
LRR
|
228 |
251 |
4.97e0 |
SMART |
LRR
|
252 |
275 |
1.07e0 |
SMART |
LRR
|
276 |
299 |
1.64e-1 |
SMART |
Blast:LRRCT
|
311 |
361 |
2e-25 |
BLAST |
low complexity region
|
375 |
392 |
N/A |
INTRINSIC |
transmembrane domain
|
425 |
447 |
N/A |
INTRINSIC |
low complexity region
|
464 |
469 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000136421
AA Change: W90R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000121621 Gene: ENSMUSG00000052581 AA Change: W90R
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
31 |
N/A |
INTRINSIC |
LRRNT
|
34 |
66 |
1.66e0 |
SMART |
LRR_TYP
|
85 |
108 |
6.67e-2 |
SMART |
LRR
|
109 |
132 |
3.52e-1 |
SMART |
LRR_TYP
|
133 |
156 |
2.53e-2 |
SMART |
LRR
|
157 |
180 |
1.16e-1 |
SMART |
LRR
|
181 |
204 |
4.34e-1 |
SMART |
LRR
|
205 |
225 |
2.4e1 |
SMART |
LRR
|
229 |
252 |
4.97e0 |
SMART |
LRR
|
253 |
276 |
1.07e0 |
SMART |
LRR
|
277 |
300 |
1.64e-1 |
SMART |
Blast:LRRCT
|
312 |
362 |
4e-25 |
BLAST |
low complexity region
|
376 |
393 |
N/A |
INTRINSIC |
transmembrane domain
|
426 |
448 |
N/A |
INTRINSIC |
low complexity region
|
465 |
470 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000147663
AA Change: W90R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000117263 Gene: ENSMUSG00000052581 AA Change: W90R
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
31 |
N/A |
INTRINSIC |
LRRNT
|
34 |
66 |
1.66e0 |
SMART |
LRR_TYP
|
85 |
108 |
6.67e-2 |
SMART |
LRR
|
109 |
132 |
3.52e-1 |
SMART |
LRR_TYP
|
133 |
156 |
2.53e-2 |
SMART |
LRR
|
157 |
180 |
1.16e-1 |
SMART |
LRR
|
181 |
204 |
4.34e-1 |
SMART |
LRR
|
205 |
225 |
2.4e1 |
SMART |
LRR
|
229 |
252 |
4.97e0 |
SMART |
LRR
|
253 |
276 |
1.07e0 |
SMART |
LRR
|
277 |
300 |
1.64e-1 |
SMART |
Blast:LRRCT
|
312 |
362 |
2e-25 |
BLAST |
low complexity region
|
376 |
393 |
N/A |
INTRINSIC |
transmembrane domain
|
426 |
448 |
N/A |
INTRINSIC |
low complexity region
|
465 |
470 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000145407
AA Change: W89R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000114465 Gene: ENSMUSG00000052581 AA Change: W89R
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
30 |
N/A |
INTRINSIC |
LRRNT
|
33 |
65 |
1.66e0 |
SMART |
Blast:LRR_TYP
|
84 |
104 |
3e-7 |
BLAST |
|
Meta Mutation Damage Score |
0.3630 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.3%
|
Validation Efficiency |
98% (51/52) |
MGI Phenotype |
PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired excitatory synapse development and excitatory transmission in dentate gyrus granule cells. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 48 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abtb2 |
T |
C |
2: 103,397,528 (GRCm39) |
C153R |
probably damaging |
Het |
Adam23 |
A |
G |
1: 63,596,650 (GRCm39) |
|
probably null |
Het |
Adpgk |
G |
T |
9: 59,222,136 (GRCm39) |
M354I |
probably benign |
Het |
Atmin |
G |
T |
8: 117,681,653 (GRCm39) |
|
probably null |
Het |
C1rl |
G |
A |
6: 124,486,069 (GRCm39) |
G480D |
probably benign |
Het |
C4b |
G |
A |
17: 34,955,032 (GRCm39) |
|
probably benign |
Het |
Cacnb1 |
G |
A |
11: 97,903,672 (GRCm39) |
T127I |
possibly damaging |
Het |
Cmya5 |
A |
T |
13: 93,230,210 (GRCm39) |
V1626E |
probably benign |
Het |
Cndp2 |
C |
T |
18: 84,686,694 (GRCm39) |
G443S |
probably damaging |
Het |
Crb1 |
A |
G |
1: 139,265,016 (GRCm39) |
I134T |
possibly damaging |
Het |
Dnaaf3 |
T |
C |
7: 4,535,276 (GRCm39) |
|
probably null |
Het |
Enam |
C |
T |
5: 88,651,008 (GRCm39) |
P764L |
probably benign |
Het |
Fat3 |
G |
A |
9: 15,909,567 (GRCm39) |
S2145F |
probably damaging |
Het |
Fbln1 |
G |
A |
15: 85,111,341 (GRCm39) |
|
probably null |
Het |
Flnb |
A |
G |
14: 7,945,950 (GRCm38) |
I2452V |
possibly damaging |
Het |
Fmo3 |
A |
T |
1: 162,781,884 (GRCm39) |
W490R |
probably damaging |
Het |
Gabrb1 |
C |
T |
5: 72,026,916 (GRCm39) |
R106* |
probably null |
Het |
Galnt4 |
C |
T |
10: 98,944,923 (GRCm39) |
T216I |
probably damaging |
Het |
Gkn3 |
C |
T |
6: 87,360,507 (GRCm39) |
A163T |
probably damaging |
Het |
Golph3 |
A |
G |
15: 12,349,649 (GRCm39) |
D223G |
probably benign |
Het |
Herc4 |
T |
A |
10: 63,151,473 (GRCm39) |
F905I |
possibly damaging |
Het |
Il23r |
T |
C |
6: 67,429,401 (GRCm39) |
T314A |
probably benign |
Het |
Maml2 |
C |
T |
9: 13,532,541 (GRCm39) |
T585I |
probably damaging |
Het |
Mpp3 |
G |
A |
11: 101,911,312 (GRCm39) |
A170V |
probably damaging |
Het |
Naip6 |
T |
A |
13: 100,452,928 (GRCm39) |
K44N |
possibly damaging |
Het |
Or10aa3 |
C |
T |
1: 173,878,814 (GRCm39) |
R292C |
probably damaging |
Het |
Or10ak7 |
C |
T |
4: 118,791,230 (GRCm39) |
E272K |
probably benign |
Het |
Or1e17 |
A |
G |
11: 73,831,182 (GRCm39) |
T37A |
possibly damaging |
Het |
Or4k51 |
C |
T |
2: 111,585,139 (GRCm39) |
P182S |
probably damaging |
Het |
Or51b6 |
T |
A |
7: 103,556,267 (GRCm39) |
M207K |
probably benign |
Het |
Or6f2 |
A |
G |
7: 139,756,878 (GRCm39) |
T282A |
probably damaging |
Het |
Or7e165 |
T |
G |
9: 19,694,892 (GRCm39) |
I154M |
probably benign |
Het |
Or8c10 |
T |
C |
9: 38,279,394 (GRCm39) |
I174T |
probably damaging |
Het |
Pak1 |
T |
A |
7: 97,535,521 (GRCm39) |
V204E |
probably benign |
Het |
Pcdhb10 |
T |
A |
18: 37,547,190 (GRCm39) |
C755* |
probably null |
Het |
Pcdhb20 |
A |
G |
18: 37,638,725 (GRCm39) |
Y417C |
probably damaging |
Het |
Pkd1l3 |
G |
T |
8: 110,355,341 (GRCm39) |
W723L |
probably benign |
Het |
Plin1 |
C |
T |
7: 79,376,139 (GRCm39) |
|
probably null |
Het |
Polr3a |
A |
T |
14: 24,525,960 (GRCm39) |
|
probably null |
Het |
Ranbp2 |
A |
T |
10: 58,314,758 (GRCm39) |
K1826I |
possibly damaging |
Het |
Rapgef1 |
A |
G |
2: 29,626,608 (GRCm39) |
I970V |
possibly damaging |
Het |
Rdx |
C |
A |
9: 51,980,173 (GRCm39) |
F255L |
probably damaging |
Het |
Rp1l1 |
A |
T |
14: 64,267,447 (GRCm39) |
H1011L |
possibly damaging |
Het |
Serpina6 |
T |
C |
12: 103,614,868 (GRCm39) |
D326G |
probably benign |
Het |
Sh3tc2 |
A |
G |
18: 62,123,966 (GRCm39) |
E909G |
probably benign |
Het |
Shprh |
T |
A |
10: 11,047,697 (GRCm39) |
V1015D |
probably damaging |
Het |
Slfn8 |
A |
T |
11: 82,894,920 (GRCm39) |
Y629N |
probably damaging |
Het |
Triml1 |
A |
G |
8: 43,594,408 (GRCm39) |
S8P |
probably damaging |
Het |
|
Other mutations in Lrrtm4 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00498:Lrrtm4
|
APN |
6 |
79,999,529 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02043:Lrrtm4
|
APN |
6 |
79,998,845 (GRCm39) |
missense |
possibly damaging |
0.89 |
IGL02603:Lrrtm4
|
APN |
6 |
79,999,967 (GRCm39) |
missense |
possibly damaging |
0.92 |
IGL02614:Lrrtm4
|
APN |
6 |
79,998,827 (GRCm39) |
missense |
probably benign |
0.01 |
IGL02735:Lrrtm4
|
APN |
6 |
80,786,031 (GRCm39) |
missense |
probably benign |
|
IGL02812:Lrrtm4
|
APN |
6 |
79,998,947 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02885:Lrrtm4
|
APN |
6 |
79,998,786 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02956:Lrrtm4
|
APN |
6 |
79,998,633 (GRCm39) |
missense |
probably benign |
0.04 |
IGL03242:Lrrtm4
|
APN |
6 |
79,999,071 (GRCm39) |
missense |
probably benign |
0.22 |
R0504:Lrrtm4
|
UTSW |
6 |
79,999,029 (GRCm39) |
missense |
probably damaging |
1.00 |
R0537:Lrrtm4
|
UTSW |
6 |
79,999,103 (GRCm39) |
missense |
probably benign |
0.02 |
R0656:Lrrtm4
|
UTSW |
6 |
79,998,953 (GRCm39) |
missense |
possibly damaging |
0.87 |
R0698:Lrrtm4
|
UTSW |
6 |
79,999,911 (GRCm39) |
missense |
probably damaging |
1.00 |
R1651:Lrrtm4
|
UTSW |
6 |
79,999,511 (GRCm39) |
missense |
probably benign |
0.06 |
R2126:Lrrtm4
|
UTSW |
6 |
79,998,722 (GRCm39) |
missense |
probably damaging |
1.00 |
R2211:Lrrtm4
|
UTSW |
6 |
79,999,623 (GRCm39) |
missense |
probably benign |
0.00 |
R3732:Lrrtm4
|
UTSW |
6 |
79,996,638 (GRCm39) |
intron |
probably benign |
|
R3817:Lrrtm4
|
UTSW |
6 |
79,999,044 (GRCm39) |
missense |
probably benign |
0.00 |
R4814:Lrrtm4
|
UTSW |
6 |
80,000,117 (GRCm39) |
missense |
possibly damaging |
0.69 |
R5304:Lrrtm4
|
UTSW |
6 |
79,999,683 (GRCm39) |
missense |
probably benign |
0.01 |
R5318:Lrrtm4
|
UTSW |
6 |
79,999,495 (GRCm39) |
missense |
probably damaging |
1.00 |
R5327:Lrrtm4
|
UTSW |
6 |
79,999,620 (GRCm39) |
missense |
probably damaging |
1.00 |
R5931:Lrrtm4
|
UTSW |
6 |
79,998,722 (GRCm39) |
missense |
probably damaging |
0.99 |
R6195:Lrrtm4
|
UTSW |
6 |
79,998,939 (GRCm39) |
missense |
probably damaging |
1.00 |
R7597:Lrrtm4
|
UTSW |
6 |
79,999,428 (GRCm39) |
nonsense |
probably null |
|
R7793:Lrrtm4
|
UTSW |
6 |
79,999,841 (GRCm39) |
missense |
probably damaging |
0.97 |
R7875:Lrrtm4
|
UTSW |
6 |
79,999,343 (GRCm39) |
missense |
possibly damaging |
0.89 |
R8058:Lrrtm4
|
UTSW |
6 |
79,999,528 (GRCm39) |
missense |
probably benign |
|
R8238:Lrrtm4
|
UTSW |
6 |
79,999,668 (GRCm39) |
missense |
probably damaging |
0.97 |
R8324:Lrrtm4
|
UTSW |
6 |
79,998,974 (GRCm39) |
missense |
probably damaging |
1.00 |
R8751:Lrrtm4
|
UTSW |
6 |
79,999,092 (GRCm39) |
missense |
probably damaging |
1.00 |
R8859:Lrrtm4
|
UTSW |
6 |
79,998,870 (GRCm39) |
missense |
probably damaging |
1.00 |
R9142:Lrrtm4
|
UTSW |
6 |
79,999,426 (GRCm39) |
missense |
probably damaging |
1.00 |
R9633:Lrrtm4
|
UTSW |
6 |
80,000,064 (GRCm39) |
missense |
probably damaging |
1.00 |
R9709:Lrrtm4
|
UTSW |
6 |
80,786,154 (GRCm39) |
missense |
probably damaging |
0.96 |
Z1177:Lrrtm4
|
UTSW |
6 |
79,999,700 (GRCm39) |
missense |
probably benign |
|
|
Predicted Primers |
PCR Primer
(F):5'- CTCAGAGAGCTTGCCCAAAG -3'
(R):5'- TGCAAAATGATGAGTTTCCGGAG -3'
Sequencing Primer
(F):5'- TTGCCCAAAGAACTGCAGATG -3'
(R):5'- GAGGCCTTTAAACTGCTCAGACTG -3'
|
Posted On |
2014-10-30 |