Incidental Mutation 'R2180:Lrrtm1'
| ID |
237117 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lrrtm1
|
| Ensembl Gene |
ENSMUSG00000060780 |
| Gene Name |
leucine rich repeat transmembrane neuronal 1 |
| Synonyms |
4632401D06Rik |
| MMRRC Submission |
040182-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2180 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
6 |
| Chromosomal Location |
77219672-77234774 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 77221329 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 262
(D262G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000124373
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000020400]
[ENSMUST00000075340]
[ENSMUST00000159616]
[ENSMUST00000159626]
[ENSMUST00000160894]
[ENSMUST00000161677]
[ENSMUST00000161811]
[ENSMUST00000161846]
|
| AlphaFold |
Q8K377 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000020400
AA Change: D262G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000020400
Gene: ENSMUSG00000060780
AA Change: D262G
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
19 |
N/A |
INTRINSIC |
|
LRRNT
|
38 |
70 |
1.06e0 |
SMART |
|
LRR
|
64 |
87 |
5.56e0 |
SMART |
|
LRR
|
88 |
111 |
1.03e1 |
SMART |
|
LRR_TYP
|
112 |
135 |
2.71e-2 |
SMART |
|
LRR_TYP
|
136 |
159 |
1.98e-4 |
SMART |
|
LRR_TYP
|
160 |
183 |
9.44e-2 |
SMART |
|
LRR
|
184 |
207 |
6.96e0 |
SMART |
|
LRR
|
208 |
236 |
1.76e2 |
SMART |
|
LRR
|
255 |
278 |
4.71e1 |
SMART |
|
LRR
|
279 |
302 |
1.03e1 |
SMART |
|
Blast:LRRCT
|
314 |
364 |
4e-13 |
BLAST |
|
transmembrane domain
|
428 |
450 |
N/A |
INTRINSIC |
|
low complexity region
|
467 |
475 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000075340
|
| SMART Domains |
Protein: ENSMUSP00000074809
Gene: ENSMUSG00000063063
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Vinculin
|
18 |
337 |
2e-104 |
PFAM |
|
Pfam:Vinculin
|
331 |
866 |
7.7e-222 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000159616
AA Change: D262G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000125207
Gene: ENSMUSG00000060780
AA Change: D262G
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
19 |
N/A |
INTRINSIC |
|
LRRNT
|
38 |
70 |
1.06e0 |
SMART |
|
LRR
|
64 |
87 |
5.56e0 |
SMART |
|
LRR
|
88 |
111 |
1.03e1 |
SMART |
|
LRR_TYP
|
112 |
135 |
2.71e-2 |
SMART |
|
LRR_TYP
|
136 |
159 |
1.98e-4 |
SMART |
|
LRR_TYP
|
160 |
183 |
9.44e-2 |
SMART |
|
LRR
|
184 |
207 |
6.96e0 |
SMART |
|
LRR
|
208 |
236 |
1.76e2 |
SMART |
|
LRR
|
255 |
278 |
4.71e1 |
SMART |
|
LRR
|
279 |
302 |
1.03e1 |
SMART |
|
Blast:LRRCT
|
314 |
364 |
4e-13 |
BLAST |
|
transmembrane domain
|
428 |
450 |
N/A |
INTRINSIC |
|
low complexity region
|
467 |
475 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000159626
|
| SMART Domains |
Protein: ENSMUSP00000124376
Gene: ENSMUSG00000063063
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Vinculin
|
18 |
337 |
3.4e-105 |
PFAM |
|
Pfam:Vinculin
|
330 |
914 |
6.6e-214 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160894
|
| SMART Domains |
Protein: ENSMUSP00000124764
Gene: ENSMUSG00000063063
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Vinculin
|
31 |
352 |
2.1e-104 |
PFAM |
|
Pfam:Vinculin
|
343 |
927 |
4.6e-213 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000161677
AA Change: D262G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000124373
Gene: ENSMUSG00000060780
AA Change: D262G
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
19 |
N/A |
INTRINSIC |
|
LRRNT
|
38 |
70 |
1.06e0 |
SMART |
|
LRR
|
64 |
87 |
5.56e0 |
SMART |
|
LRR
|
88 |
111 |
1.03e1 |
SMART |
|
LRR_TYP
|
112 |
135 |
2.71e-2 |
SMART |
|
LRR_TYP
|
136 |
159 |
1.98e-4 |
SMART |
|
LRR_TYP
|
160 |
183 |
9.44e-2 |
SMART |
|
LRR
|
184 |
207 |
6.96e0 |
SMART |
|
LRR
|
208 |
236 |
1.76e2 |
SMART |
|
LRR
|
255 |
278 |
4.71e1 |
SMART |
|
LRR
|
279 |
302 |
1.03e1 |
SMART |
|
Blast:LRRCT
|
314 |
364 |
4e-13 |
BLAST |
|
transmembrane domain
|
428 |
450 |
N/A |
INTRINSIC |
|
low complexity region
|
467 |
475 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161811
|
| SMART Domains |
Protein: ENSMUSP00000124948
Gene: ENSMUSG00000060780
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
19 |
N/A |
INTRINSIC |
|
LRRNT
|
38 |
70 |
1.06e0 |
SMART |
|
LRR
|
64 |
87 |
5.56e0 |
SMART |
|
LRR
|
88 |
111 |
1.03e1 |
SMART |
|
LRR_TYP
|
112 |
135 |
2.71e-2 |
SMART |
|
LRR_TYP
|
136 |
159 |
1.98e-4 |
SMART |
|
LRR_TYP
|
160 |
183 |
9.44e-2 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161846
|
| SMART Domains |
Protein: ENSMUSP00000123714
Gene: ENSMUSG00000063063
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Vinculin
|
31 |
350 |
5.3e-105 |
PFAM |
|
Pfam:Vinculin
|
344 |
879 |
2.1e-222 |
PFAM |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.1%
|
| Validation Efficiency |
|
| MGI Phenotype |
PHENOTYPE: Mice homozygous for a null mutation are viable and fertile with grossly normal brain morphology. Mice homozygous for another knock-out allele exhibit impaired cognitive function and altered hippocampal synapse morphology. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamts5 |
T |
C |
16: 85,684,812 (GRCm39) |
D377G |
probably damaging |
Het |
| Adgrl4 |
A |
T |
3: 151,205,779 (GRCm39) |
I164F |
probably damaging |
Het |
| Anxa9 |
T |
C |
3: 95,213,735 (GRCm39) |
|
probably null |
Het |
| Aox4 |
A |
T |
1: 58,252,226 (GRCm39) |
T34S |
probably benign |
Het |
| Asic1 |
G |
T |
15: 99,569,846 (GRCm39) |
V56F |
probably benign |
Het |
| Atpaf1 |
T |
C |
4: 115,645,557 (GRCm39) |
M1T |
probably null |
Het |
| Axin1 |
A |
G |
17: 26,362,309 (GRCm39) |
T218A |
probably benign |
Het |
| Bdp1 |
ATTCTTCTTCTTCTTCTTC |
ATTCTTCTTCTTCTTCTTCTTC |
13: 100,197,913 (GRCm39) |
|
probably benign |
Het |
| Birc6 |
T |
C |
17: 74,919,146 (GRCm39) |
I1988T |
probably benign |
Het |
| Btbd7 |
A |
T |
12: 102,752,156 (GRCm39) |
D869E |
probably damaging |
Het |
| Caln1 |
T |
C |
5: 130,868,249 (GRCm39) |
*220Q |
probably null |
Het |
| Ccdc150 |
G |
A |
1: 54,311,706 (GRCm39) |
|
probably null |
Het |
| Ccnt1 |
A |
T |
15: 98,441,481 (GRCm39) |
S596T |
possibly damaging |
Het |
| Cd44 |
C |
T |
2: 102,658,955 (GRCm39) |
G640E |
possibly damaging |
Het |
| Cep192 |
A |
G |
18: 67,957,813 (GRCm39) |
E582G |
possibly damaging |
Het |
| Clcnkb |
G |
T |
4: 141,136,819 (GRCm39) |
|
probably null |
Het |
| Dhx29 |
T |
C |
13: 113,099,406 (GRCm39) |
|
probably null |
Het |
| Dnah8 |
T |
C |
17: 31,059,621 (GRCm39) |
F4407S |
probably benign |
Het |
| Enah |
A |
T |
1: 181,746,024 (GRCm39) |
M419K |
probably damaging |
Het |
| Fancd2 |
A |
T |
6: 113,551,598 (GRCm39) |
T1055S |
probably benign |
Het |
| Gigyf2 |
G |
A |
1: 87,344,642 (GRCm39) |
G525D |
probably damaging |
Het |
| Gm5800 |
T |
A |
14: 51,953,451 (GRCm39) |
K55* |
probably null |
Het |
| Gpr149 |
A |
G |
3: 62,511,489 (GRCm39) |
L170P |
probably damaging |
Het |
| Grik4 |
A |
T |
9: 42,453,301 (GRCm39) |
Y695N |
probably benign |
Het |
| Gsg1 |
A |
T |
6: 135,217,143 (GRCm39) |
V228D |
probably damaging |
Het |
| Helb |
G |
A |
10: 119,941,353 (GRCm39) |
T445M |
probably benign |
Het |
| Helz2 |
A |
T |
2: 180,875,525 (GRCm39) |
D1656E |
probably damaging |
Het |
| Hyou1 |
A |
T |
9: 44,299,316 (GRCm39) |
K669M |
probably benign |
Het |
| Itga2 |
T |
C |
13: 114,985,917 (GRCm39) |
N953D |
possibly damaging |
Het |
| Ldhd |
T |
C |
8: 112,356,018 (GRCm39) |
I122V |
probably benign |
Het |
| Mapkapk5 |
T |
C |
5: 121,673,927 (GRCm39) |
|
probably null |
Het |
| Msantd5l |
C |
A |
11: 51,145,437 (GRCm39) |
W50L |
probably damaging |
Het |
| Niban1 |
A |
T |
1: 151,593,829 (GRCm39) |
H838L |
probably benign |
Het |
| Numa1 |
T |
C |
7: 101,649,197 (GRCm39) |
I976T |
probably benign |
Het |
| Or10x1 |
A |
G |
1: 174,196,967 (GRCm39) |
I161M |
probably damaging |
Het |
| Or2a12 |
C |
T |
6: 42,904,459 (GRCm39) |
T98I |
probably benign |
Het |
| Or4f14b |
A |
G |
2: 111,775,348 (GRCm39) |
V151A |
probably benign |
Het |
| Or52e4 |
T |
C |
7: 104,706,092 (GRCm39) |
I213T |
probably benign |
Het |
| Patj |
G |
A |
4: 98,411,739 (GRCm39) |
|
probably null |
Het |
| Pfas |
T |
C |
11: 68,883,013 (GRCm39) |
D757G |
possibly damaging |
Het |
| Pom121l2 |
A |
G |
13: 22,166,145 (GRCm39) |
N139D |
probably benign |
Het |
| Ppp2r3d |
A |
T |
9: 101,004,214 (GRCm39) |
Y994* |
probably null |
Het |
| Ppp6c |
T |
C |
2: 39,087,525 (GRCm39) |
D227G |
probably benign |
Het |
| Ptpn13 |
T |
G |
5: 103,717,424 (GRCm39) |
H1855Q |
probably damaging |
Het |
| Ptprh |
T |
A |
7: 4,604,867 (GRCm39) |
Q59L |
probably benign |
Het |
| Rap1gap2 |
T |
C |
11: 74,283,972 (GRCm39) |
K669E |
probably benign |
Het |
| Rbl2 |
T |
C |
8: 91,816,683 (GRCm39) |
S348P |
possibly damaging |
Het |
| Rptor |
T |
A |
11: 119,615,970 (GRCm39) |
N161K |
probably damaging |
Het |
| Satb1 |
C |
T |
17: 52,110,524 (GRCm39) |
A192T |
probably damaging |
Het |
| Scn5a |
A |
G |
9: 119,345,117 (GRCm39) |
V1083A |
probably benign |
Het |
| Sec14l2 |
C |
T |
11: 4,058,964 (GRCm39) |
A194T |
probably damaging |
Het |
| Sema4b |
A |
G |
7: 79,862,583 (GRCm39) |
N53S |
probably benign |
Het |
| Sin3b |
T |
A |
8: 73,479,923 (GRCm39) |
Y876* |
probably null |
Het |
| Smchd1 |
C |
A |
17: 71,770,794 (GRCm39) |
M129I |
probably benign |
Het |
| Spmip6 |
T |
A |
4: 41,507,170 (GRCm39) |
M209L |
probably benign |
Het |
| Tmc1 |
T |
C |
19: 20,801,448 (GRCm39) |
Y484C |
probably damaging |
Het |
| Utp20 |
A |
G |
10: 88,656,801 (GRCm39) |
S135P |
probably damaging |
Het |
| Zfp266 |
A |
T |
9: 20,410,975 (GRCm39) |
C401S |
probably damaging |
Het |
| Zfp738 |
G |
A |
13: 67,819,313 (GRCm39) |
T226I |
probably damaging |
Het |
| Zfp871 |
G |
A |
17: 32,994,275 (GRCm39) |
T300M |
probably damaging |
Het |
|
| Other mutations in Lrrtm1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00927:Lrrtm1
|
APN |
6 |
77,221,046 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01011:Lrrtm1
|
APN |
6 |
77,221,218 (GRCm39) |
splice site |
probably null |
|
|
IGL01125:Lrrtm1
|
APN |
6 |
77,221,436 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01924:Lrrtm1
|
APN |
6 |
77,221,169 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
IGL02508:Lrrtm1
|
APN |
6 |
77,221,574 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03005:Lrrtm1
|
APN |
6 |
77,221,139 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03076:Lrrtm1
|
APN |
6 |
77,221,568 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0077:Lrrtm1
|
UTSW |
6 |
77,220,855 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0540:Lrrtm1
|
UTSW |
6 |
77,221,611 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0607:Lrrtm1
|
UTSW |
6 |
77,221,611 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0927:Lrrtm1
|
UTSW |
6 |
77,221,843 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1742:Lrrtm1
|
UTSW |
6 |
77,221,074 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1762:Lrrtm1
|
UTSW |
6 |
77,221,680 (GRCm39) |
missense |
probably benign |
|
|
R1933:Lrrtm1
|
UTSW |
6 |
77,221,949 (GRCm39) |
splice site |
probably null |
|
|
R1934:Lrrtm1
|
UTSW |
6 |
77,221,949 (GRCm39) |
splice site |
probably null |
|
|
R2267:Lrrtm1
|
UTSW |
6 |
77,220,996 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R2914:Lrrtm1
|
UTSW |
6 |
77,221,962 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2937:Lrrtm1
|
UTSW |
6 |
77,220,635 (GRCm39) |
missense |
probably benign |
0.03 |
|
R2938:Lrrtm1
|
UTSW |
6 |
77,220,635 (GRCm39) |
missense |
probably benign |
0.03 |
|
R4604:Lrrtm1
|
UTSW |
6 |
77,221,127 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4908:Lrrtm1
|
UTSW |
6 |
77,221,661 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4910:Lrrtm1
|
UTSW |
6 |
77,221,884 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5739:Lrrtm1
|
UTSW |
6 |
77,221,872 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6604:Lrrtm1
|
UTSW |
6 |
77,221,221 (GRCm39) |
missense |
possibly damaging |
0.70 |
|
R6845:Lrrtm1
|
UTSW |
6 |
77,220,864 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7048:Lrrtm1
|
UTSW |
6 |
77,221,152 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7203:Lrrtm1
|
UTSW |
6 |
77,220,584 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7783:Lrrtm1
|
UTSW |
6 |
77,221,236 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7826:Lrrtm1
|
UTSW |
6 |
77,221,095 (GRCm39) |
splice site |
probably null |
|
|
R8164:Lrrtm1
|
UTSW |
6 |
77,221,199 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8303:Lrrtm1
|
UTSW |
6 |
77,221,662 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8856:Lrrtm1
|
UTSW |
6 |
77,221,807 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R9221:Lrrtm1
|
UTSW |
6 |
77,221,596 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9564:Lrrtm1
|
UTSW |
6 |
77,221,536 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9749:Lrrtm1
|
UTSW |
6 |
77,220,855 (GRCm39) |
missense |
probably damaging |
1.00 |
|
RF018:Lrrtm1
|
UTSW |
6 |
77,221,334 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
| Predicted Primers |
PCR Primer
(F):5'- CGGCTTGTTCAAGCTCACAG -3'
(R):5'- CAAGTTAGCATCGTAACGTCC -3'
Sequencing Primer
(F):5'- GAGCTACACCTGGAGCATAATGAC -3'
(R):5'- TTAGCATCGTAACGTCCCTGGAAG -3'
|
| Posted On |
2014-10-02 |
Incidental Mutation