Incidental Mutation 'R0656:Lrrtm4'
| ID |
226142 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lrrtm4
|
| Ensembl Gene |
ENSMUSG00000052581 |
| Gene Name |
leucine rich repeat transmembrane neuronal 4 |
| Synonyms |
7530419J18Rik |
| MMRRC Submission |
038841-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.100)
|
| Stock # |
R0656 (G1)
|
| Quality Score |
21 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
79995860-80787124 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 79998953 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 122
(I122V)
|
| 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 |
possibly damaging
Transcript: ENSMUST00000074662
AA Change: I121V
PolyPhen 2
Score 0.715 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000074232
Gene: ENSMUSG00000052581
AA Change: I121V
| 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 |
possibly damaging
Transcript: ENSMUST00000126005
AA Change: I121V
PolyPhen 2
Score 0.733 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000117445
Gene: ENSMUSG00000052581
AA Change: I121V
| 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 |
possibly damaging
Transcript: ENSMUST00000126399
AA Change: I121V
PolyPhen 2
Score 0.715 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000121124
Gene: ENSMUSG00000052581
AA Change: I121V
| 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 |
possibly damaging
Transcript: ENSMUST00000133918
AA Change: I121V
PolyPhen 2
Score 0.715 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000115016
Gene: ENSMUSG00000052581
AA Change: I121V
| 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 |
possibly damaging
Transcript: ENSMUST00000136421
AA Change: I122V
PolyPhen 2
Score 0.775 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000121621
Gene: ENSMUSG00000052581
AA Change: I122V
| 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 |
possibly damaging
Transcript: ENSMUST00000147663
AA Change: I122V
PolyPhen 2
Score 0.874 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000117263
Gene: ENSMUSG00000052581
AA Change: I122V
| 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 |
0.1148 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.8%
- 10x: 97.3%
- 20x: 94.2%
|
| Validation Efficiency |
98% (92/94) |
| 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: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930533K18Rik |
T |
A |
10: 70,704,630 (GRCm39) |
|
noncoding transcript |
Het |
| Alox5 |
A |
G |
6: 116,400,291 (GRCm39) |
|
probably benign |
Het |
| Anxa11 |
T |
A |
14: 25,874,421 (GRCm39) |
D203E |
probably damaging |
Het |
| Atp12a |
A |
T |
14: 56,611,938 (GRCm39) |
N371Y |
probably damaging |
Het |
| Bloc1s6 |
A |
G |
2: 122,584,543 (GRCm39) |
I39M |
probably benign |
Het |
| Celsr3 |
A |
C |
9: 108,711,854 (GRCm39) |
I1688L |
possibly damaging |
Het |
| Cgn |
T |
C |
3: 94,682,204 (GRCm39) |
|
probably benign |
Het |
| Chd4 |
A |
T |
6: 125,079,930 (GRCm39) |
I453F |
probably damaging |
Het |
| Dbnl |
A |
G |
11: 5,747,321 (GRCm39) |
T247A |
probably benign |
Het |
| Dpysl3 |
T |
C |
18: 43,571,136 (GRCm39) |
E46G |
possibly damaging |
Het |
| Dsg1a |
T |
C |
18: 20,468,949 (GRCm39) |
|
probably benign |
Het |
| Fbp1 |
C |
T |
13: 63,019,099 (GRCm39) |
E150K |
probably benign |
Het |
| Flnb |
T |
A |
14: 7,927,352 (GRCm38) |
L1854Q |
probably damaging |
Het |
| Gcn1 |
C |
T |
5: 115,727,362 (GRCm39) |
T714M |
probably benign |
Het |
| Gm12216 |
A |
T |
11: 53,704,162 (GRCm39) |
|
probably benign |
Het |
| Gpr82 |
T |
C |
X: 13,531,829 (GRCm39) |
S126P |
probably benign |
Het |
| Hmbs |
T |
A |
9: 44,248,657 (GRCm39) |
H256L |
probably benign |
Het |
| Ibsp |
A |
T |
5: 104,457,886 (GRCm39) |
|
probably null |
Het |
| Ints13 |
A |
G |
6: 146,453,959 (GRCm39) |
V240A |
probably benign |
Het |
| Iqca1l |
C |
T |
5: 24,754,760 (GRCm39) |
V337M |
possibly damaging |
Het |
| Kalrn |
T |
C |
16: 33,852,837 (GRCm39) |
D343G |
probably damaging |
Het |
| Kin |
T |
C |
2: 10,090,531 (GRCm39) |
|
probably benign |
Het |
| Klhdc1 |
T |
C |
12: 69,304,804 (GRCm39) |
V192A |
probably benign |
Het |
| Lpar3 |
T |
A |
3: 145,946,426 (GRCm39) |
C35S |
possibly damaging |
Het |
| Mfsd13a |
C |
T |
19: 46,354,943 (GRCm39) |
T40I |
probably benign |
Het |
| Mgat4c |
T |
C |
10: 102,224,452 (GRCm39) |
M222T |
probably damaging |
Het |
| Muc4 |
C |
A |
16: 32,570,488 (GRCm39) |
S516Y |
possibly damaging |
Het |
| Myo1e |
A |
T |
9: 70,274,956 (GRCm39) |
Q703L |
probably damaging |
Het |
| Neb |
A |
G |
2: 52,115,570 (GRCm39) |
|
probably benign |
Het |
| Necab3 |
T |
G |
2: 154,388,223 (GRCm39) |
E239A |
probably null |
Het |
| Npr1 |
G |
T |
3: 90,368,676 (GRCm39) |
N461K |
probably benign |
Het |
| Or4k44 |
T |
C |
2: 111,367,972 (GRCm39) |
I221V |
probably damaging |
Het |
| Pcdhb2 |
A |
G |
18: 37,428,543 (GRCm39) |
Y172C |
probably damaging |
Het |
| Pcdhb7 |
A |
G |
18: 37,474,954 (GRCm39) |
D30G |
probably benign |
Het |
| Phf12 |
A |
C |
11: 77,920,158 (GRCm39) |
Q898P |
probably benign |
Het |
| Plekhn1 |
T |
C |
4: 156,309,821 (GRCm39) |
E132G |
possibly damaging |
Het |
| Ptpn3 |
A |
G |
4: 57,270,075 (GRCm39) |
V29A |
probably benign |
Het |
| Rundc3b |
T |
A |
5: 8,619,529 (GRCm39) |
I143F |
probably damaging |
Het |
| Ryr3 |
T |
G |
2: 112,478,651 (GRCm39) |
|
probably benign |
Het |
| Sash1 |
A |
G |
10: 8,626,901 (GRCm39) |
|
probably null |
Het |
| Slc4a2 |
A |
G |
5: 24,636,257 (GRCm39) |
D201G |
probably benign |
Het |
| Tecpr1 |
T |
A |
5: 144,150,871 (GRCm39) |
|
probably null |
Het |
| Timm21 |
T |
C |
18: 84,967,326 (GRCm39) |
H150R |
probably damaging |
Het |
| Tmem79 |
T |
C |
3: 88,240,241 (GRCm39) |
T236A |
probably damaging |
Het |
| Usp34 |
G |
T |
11: 23,422,967 (GRCm39) |
V3095F |
probably damaging |
Het |
| Vmn1r8 |
A |
T |
6: 57,013,573 (GRCm39) |
Q208L |
probably benign |
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 |
|
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'- AGGTTTCCGTCTAATCACGCAGC -3'
(R):5'- TCCAGAAAGTCAAGGTTCCGGCAG -3'
Sequencing Primer
(F):5'- GACATCCCTGAGAACATTTCTGG -3'
(R):5'- GTTCCGGCAGTCTTGAAAAAC -3'
|
| Posted On |
2014-09-17 |
Incidental Mutation