Incidental Mutation 'R0537:Lrrtm4'
ID |
49496 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Lrrtm4
|
Ensembl Gene |
ENSMUSG00000052581 |
Gene Name |
leucine rich repeat transmembrane neuronal 4 |
Synonyms |
7530419J18Rik |
MMRRC Submission |
038729-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.100)
|
Stock # |
R0537 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
6 |
Chromosomal Location |
79995860-80787124 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 79999103 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Serine
at position 172
(T172S)
|
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 benign
Transcript: ENSMUST00000074662
AA Change: T171S
PolyPhen 2
Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
|
SMART Domains |
Protein: ENSMUSP00000074232 Gene: ENSMUSG00000052581 AA Change: T171S
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 benign
Transcript: ENSMUST00000126005
AA Change: T171S
PolyPhen 2
Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
|
SMART Domains |
Protein: ENSMUSP00000117445 Gene: ENSMUSG00000052581 AA Change: T171S
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 benign
Transcript: ENSMUST00000126399
AA Change: T171S
PolyPhen 2
Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
|
SMART Domains |
Protein: ENSMUSP00000121124 Gene: ENSMUSG00000052581 AA Change: T171S
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 benign
Transcript: ENSMUST00000133918
AA Change: T171S
PolyPhen 2
Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
|
SMART Domains |
Protein: ENSMUSP00000115016 Gene: ENSMUSG00000052581 AA Change: T171S
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: ENSMUST00000136421
AA Change: T172S
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
SMART Domains |
Protein: ENSMUSP00000121621 Gene: ENSMUSG00000052581 AA Change: T172S
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 benign
Transcript: ENSMUST00000147663
AA Change: T172S
PolyPhen 2
Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
|
SMART Domains |
Protein: ENSMUSP00000117263 Gene: ENSMUSG00000052581 AA Change: T172S
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 benign
Transcript: ENSMUST00000145407
|
SMART Domains |
Protein: ENSMUSP00000114465 Gene: ENSMUSG00000052581
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 |
0.0878 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.7%
- 20x: 93.9%
|
Validation Efficiency |
100% (53/53) |
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: 51 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930474N05Rik |
A |
T |
14: 35,818,657 (GRCm39) |
K218N |
probably benign |
Het |
Acot11 |
T |
C |
4: 106,619,652 (GRCm39) |
E156G |
probably benign |
Het |
Arhgef28 |
A |
T |
13: 98,094,224 (GRCm39) |
N973K |
probably damaging |
Het |
B4galt3 |
T |
C |
1: 171,101,821 (GRCm39) |
|
probably benign |
Het |
Bmpr1a |
T |
C |
14: 34,165,769 (GRCm39) |
|
probably benign |
Het |
Camkmt |
A |
T |
17: 85,702,087 (GRCm39) |
I184F |
probably benign |
Het |
Ccdc33 |
T |
C |
9: 58,024,737 (GRCm39) |
Y163C |
probably damaging |
Het |
Ccdc9 |
A |
G |
7: 16,014,701 (GRCm39) |
|
probably benign |
Het |
Dars2 |
A |
T |
1: 160,888,318 (GRCm39) |
C201S |
possibly damaging |
Het |
Dnajc1 |
A |
T |
2: 18,312,767 (GRCm39) |
S194R |
possibly damaging |
Het |
Dock8 |
A |
G |
19: 25,148,941 (GRCm39) |
D1473G |
probably benign |
Het |
Dpm2 |
T |
A |
2: 32,462,961 (GRCm39) |
|
probably null |
Het |
Dsg4 |
T |
C |
18: 20,591,628 (GRCm39) |
S456P |
probably damaging |
Het |
Gys1 |
T |
C |
7: 45,089,425 (GRCm39) |
S195P |
probably damaging |
Het |
Heatr6 |
G |
T |
11: 83,670,290 (GRCm39) |
E948* |
probably null |
Het |
Itgal |
G |
A |
7: 126,910,445 (GRCm39) |
R518Q |
possibly damaging |
Het |
Klhdc8b |
G |
C |
9: 108,326,422 (GRCm39) |
R158G |
possibly damaging |
Het |
Klhl41 |
G |
A |
2: 69,500,554 (GRCm39) |
R5Q |
probably benign |
Het |
Lypd1 |
A |
G |
1: 125,840,604 (GRCm39) |
|
probably benign |
Het |
Mei1 |
T |
C |
15: 81,975,562 (GRCm39) |
F121S |
possibly damaging |
Het |
Mtor |
C |
T |
4: 148,622,817 (GRCm39) |
R1966W |
probably damaging |
Het |
Myh7 |
A |
G |
14: 55,228,256 (GRCm39) |
F247L |
possibly damaging |
Het |
Nebl |
G |
T |
2: 17,409,026 (GRCm39) |
D392E |
possibly damaging |
Het |
Notch2 |
C |
A |
3: 98,024,057 (GRCm39) |
N840K |
possibly damaging |
Het |
Nubp1 |
T |
C |
16: 10,240,678 (GRCm39) |
|
probably benign |
Het |
Or5w16 |
A |
T |
2: 87,577,017 (GRCm39) |
Q159L |
probably benign |
Het |
Or7g19 |
T |
C |
9: 18,856,444 (GRCm39) |
S167P |
probably damaging |
Het |
Pcdh17 |
T |
A |
14: 84,684,897 (GRCm39) |
S455T |
probably damaging |
Het |
Picalm |
C |
A |
7: 89,779,876 (GRCm39) |
H32Q |
probably benign |
Het |
Pold1 |
T |
C |
7: 44,184,516 (GRCm39) |
E828G |
probably damaging |
Het |
Ptpro |
T |
A |
6: 137,420,592 (GRCm39) |
V1007D |
probably damaging |
Het |
Rala |
A |
T |
13: 18,063,233 (GRCm39) |
N119K |
probably benign |
Het |
Rasal2 |
A |
T |
1: 156,975,362 (GRCm39) |
V1149E |
possibly damaging |
Het |
Rd3 |
A |
G |
1: 191,715,501 (GRCm39) |
Y92C |
probably damaging |
Het |
Rps18-ps6 |
A |
T |
13: 97,897,071 (GRCm39) |
F9Y |
probably benign |
Het |
Sart1 |
A |
T |
19: 5,431,752 (GRCm39) |
D635E |
probably damaging |
Het |
Sec16b |
A |
G |
1: 157,365,116 (GRCm39) |
T335A |
possibly damaging |
Het |
Slc11a2 |
C |
T |
15: 100,303,679 (GRCm39) |
G185R |
probably damaging |
Het |
Slc2a12 |
G |
A |
10: 22,540,967 (GRCm39) |
R274H |
probably damaging |
Het |
Spag17 |
T |
C |
3: 100,032,618 (GRCm39) |
V2276A |
probably damaging |
Het |
Tcam1 |
G |
A |
11: 106,174,904 (GRCm39) |
E120K |
probably benign |
Het |
Tenm2 |
T |
C |
11: 36,054,557 (GRCm39) |
D601G |
probably damaging |
Het |
Tmem168 |
C |
A |
6: 13,603,360 (GRCm39) |
C2F |
probably damaging |
Het |
Tmem80 |
A |
G |
7: 140,913,609 (GRCm39) |
Y13C |
probably damaging |
Het |
Try4 |
T |
A |
6: 41,281,296 (GRCm39) |
N79K |
probably benign |
Het |
Vldlr |
C |
A |
19: 27,225,318 (GRCm39) |
N798K |
probably damaging |
Het |
Wdr41 |
A |
G |
13: 95,131,813 (GRCm39) |
|
probably benign |
Het |
Zfp30 |
A |
T |
7: 29,492,160 (GRCm39) |
E138V |
probably damaging |
Het |
Zfp366 |
A |
C |
13: 99,365,786 (GRCm39) |
T316P |
probably damaging |
Het |
Zfp563 |
A |
T |
17: 33,323,659 (GRCm39) |
S85C |
possibly damaging |
Het |
Znfx1 |
T |
C |
2: 166,883,621 (GRCm39) |
H162R |
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 |
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 |
R2363:Lrrtm4
|
UTSW |
6 |
79,998,857 (GRCm39) |
missense |
probably damaging |
1.00 |
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'- TCAGTGGACGAAGATGCCTTTCAAG -3'
(R):5'- GCAAGGAACTCCAGGTCCATGTTAG -3'
Sequencing Primer
(F):5'- GGATCCGCAGACTGAAAGAA -3'
(R):5'- CCATTGCAGGTAGATGGATCG -3'
|
Posted On |
2013-06-12 |