Incidental Mutation 'R9633:Lrrtm4'
| ID |
725661 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lrrtm4
|
| Ensembl Gene |
ENSMUSG00000052581 |
| Gene Name |
leucine rich repeat transmembrane neuronal 4 |
| Synonyms |
7530419J18Rik |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.100)
|
| Stock # |
R9633 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
6 |
| Chromosomal Location |
79995860-80787124 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 80000064 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Methionine
at position 492
(T492M)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000117263
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000074662]
[ENSMUST00000126005]
[ENSMUST00000126399]
[ENSMUST00000128718]
[ENSMUST00000133918]
[ENSMUST00000136421]
[ENSMUST00000145407]
[ENSMUST00000147663]
|
| AlphaFold |
Q80XG9 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000074662
AA Change: T491M
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000074232
Gene: ENSMUSG00000052581
AA Change: T491M
| 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: T491M
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000117445
Gene: ENSMUSG00000052581
AA Change: T491M
| 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: T491M
PolyPhen 2
Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000121124
Gene: ENSMUSG00000052581
AA Change: T491M
| 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 |
probably damaging
Transcript: ENSMUST00000133918
AA Change: T491M
PolyPhen 2
Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000115016
Gene: ENSMUSG00000052581
AA Change: T491M
| 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: T492M
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000121621
Gene: ENSMUSG00000052581
AA Change: T492M
| 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: 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 |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000147663
AA Change: T492M
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000117263
Gene: ENSMUSG00000052581
AA Change: T492M
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.2%
|
| Validation Efficiency |
|
| 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 |
|---|
| Acot11 |
A |
G |
4: 106,613,178 (GRCm39) |
V319A |
probably damaging |
Het |
| Afap1l1 |
A |
C |
18: 61,890,795 (GRCm39) |
S53A |
possibly damaging |
Het |
| Alms1 |
T |
A |
6: 85,600,125 (GRCm39) |
N1650K |
probably damaging |
Het |
| Atf6b |
T |
A |
17: 34,872,507 (GRCm39) |
V553E |
possibly damaging |
Het |
| Avl9 |
T |
A |
6: 56,707,634 (GRCm39) |
I193N |
probably damaging |
Het |
| Ceacam3 |
A |
G |
7: 16,895,688 (GRCm39) |
N553D |
|
Het |
| Dnah3 |
C |
A |
7: 119,550,216 (GRCm39) |
V389L |
probably benign |
Het |
| Erich6 |
T |
C |
3: 58,537,277 (GRCm39) |
M246V |
probably benign |
Het |
| F830016B08Rik |
A |
T |
18: 60,432,965 (GRCm39) |
D16V |
probably damaging |
Het |
| Fgfr1 |
T |
A |
8: 26,060,776 (GRCm39) |
Y483N |
probably damaging |
Het |
| Fmo4 |
T |
A |
1: 162,631,191 (GRCm39) |
M259L |
probably benign |
Het |
| Gnat2 |
T |
A |
3: 108,002,770 (GRCm39) |
D59E |
probably benign |
Het |
| Izumo3 |
T |
A |
4: 92,034,795 (GRCm39) |
Y94F |
probably damaging |
Het |
| Kcnb2 |
A |
T |
1: 15,781,444 (GRCm39) |
H772L |
probably benign |
Het |
| Kcnrg |
CACAACAA |
CACAA |
14: 61,845,009 (GRCm39) |
|
probably benign |
Het |
| Krt6b |
C |
T |
15: 101,586,996 (GRCm39) |
V259M |
probably benign |
Het |
| Lingo2 |
A |
G |
4: 35,709,885 (GRCm39) |
C32R |
|
Het |
| Maea |
T |
A |
5: 33,526,050 (GRCm39) |
M242K |
possibly damaging |
Het |
| Mdga2 |
T |
C |
12: 66,736,206 (GRCm39) |
T341A |
probably benign |
Het |
| Mfsd14b |
C |
A |
13: 65,221,414 (GRCm39) |
V293L |
probably benign |
Het |
| Mmadhc |
A |
T |
2: 50,178,988 (GRCm39) |
S143R |
probably benign |
Het |
| Ms4a8a |
A |
G |
19: 11,056,956 (GRCm39) |
V42A |
probably benign |
Het |
| N4bp2l2 |
A |
T |
5: 150,585,103 (GRCm39) |
H292Q |
probably benign |
Het |
| Nkx2-2 |
A |
G |
2: 147,027,686 (GRCm39) |
Y85H |
possibly damaging |
Het |
| Pramel14 |
T |
C |
4: 143,720,818 (GRCm39) |
K41R |
possibly damaging |
Het |
| Psmb9 |
T |
A |
17: 34,402,119 (GRCm39) |
D159V |
probably damaging |
Het |
| Rgs4 |
T |
A |
1: 169,572,843 (GRCm39) |
D31V |
possibly damaging |
Het |
| Shank1 |
G |
A |
7: 43,962,342 (GRCm39) |
S71N |
unknown |
Het |
| Slc22a14 |
A |
G |
9: 119,008,528 (GRCm39) |
S247P |
probably benign |
Het |
| Slc26a7 |
G |
A |
4: 14,524,540 (GRCm39) |
T448I |
possibly damaging |
Het |
| Slc7a14 |
T |
A |
3: 31,278,166 (GRCm39) |
T480S |
probably benign |
Het |
| Spocd1 |
T |
C |
4: 129,850,463 (GRCm39) |
S830P |
unknown |
Het |
| Sycp2 |
A |
G |
2: 177,998,254 (GRCm39) |
S1089P |
probably damaging |
Het |
| Tcf4 |
A |
T |
18: 69,726,382 (GRCm39) |
|
probably benign |
Het |
| Tktl2 |
T |
C |
8: 66,965,813 (GRCm39) |
V457A |
probably benign |
Het |
| Tmem131 |
A |
T |
1: 36,847,069 (GRCm39) |
I1343N |
probably damaging |
Het |
| Tnrc6c |
G |
A |
11: 117,638,009 (GRCm39) |
A1164T |
probably damaging |
Het |
| Tomm5 |
G |
A |
4: 45,107,982 (GRCm39) |
R18W |
probably damaging |
Het |
| Ubxn7 |
T |
C |
16: 32,200,248 (GRCm39) |
S335P |
probably benign |
Het |
| Unc5c |
A |
C |
3: 141,495,654 (GRCm39) |
T508P |
probably damaging |
Het |
| Upp1 |
G |
A |
11: 9,084,909 (GRCm39) |
M209I |
|
Het |
| Vmn1r213 |
A |
G |
13: 23,195,519 (GRCm39) |
D34G |
unknown |
Het |
| Vmn1r235 |
G |
T |
17: 21,482,330 (GRCm39) |
W218C |
possibly damaging |
Het |
| Vmn1r235 |
G |
T |
17: 21,482,329 (GRCm39) |
W218L |
probably benign |
Het |
| Vmn2r57 |
T |
C |
7: 41,076,006 (GRCm39) |
E502G |
probably benign |
Het |
| Wwc2 |
GCC |
GCCC |
8: 48,304,959 (GRCm39) |
|
probably null |
Het |
| Zfc3h1 |
T |
A |
10: 115,247,852 (GRCm39) |
H1018Q |
probably damaging |
Het |
| Zfp318 |
T |
A |
17: 46,710,421 (GRCm39) |
S715T |
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 |
|
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 |
|
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'- ACGGATCATGAGTACGAGCAC -3'
(R):5'- TCTAGTGATTAGCCACACCAC -3'
Sequencing Primer
(F):5'- GTCGTTTCACAAAATCATCGCAGG -3'
(R):5'- TCTAGTGATTAGCCACACCACTAGAG -3'
|
| Posted On |
2022-09-12 |
Incidental Mutation