Incidental Mutation 'R0455:Lrch3'
| ID |
39978 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lrch3
|
| Ensembl Gene |
ENSMUSG00000022801 |
| Gene Name |
leucine-rich repeats and calponin homology (CH) domain containing 3 |
| Synonyms |
LOC385628, 2210409B11Rik |
| MMRRC Submission |
038655-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.100)
|
| Stock # |
R0455 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
16 |
| Chromosomal Location |
32734470-32836017 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 32807250 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Leucine
at position 508
(F508L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000126964
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000023491]
[ENSMUST00000135193]
[ENSMUST00000165616]
[ENSMUST00000165826]
[ENSMUST00000170201]
[ENSMUST00000170899]
|
| AlphaFold |
Q8BVU0 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000023491
AA Change: F508L
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000023491
Gene: ENSMUSG00000022801
AA Change: F508L
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
13 |
N/A |
INTRINSIC |
|
low complexity region
|
31 |
44 |
N/A |
INTRINSIC |
|
LRR
|
104 |
126 |
2.54e1 |
SMART |
|
LRR
|
127 |
150 |
2.86e-1 |
SMART |
|
LRR
|
172 |
194 |
4.44e0 |
SMART |
|
LRR
|
195 |
218 |
4.33e1 |
SMART |
|
LRR
|
240 |
263 |
2.76e1 |
SMART |
|
low complexity region
|
482 |
493 |
N/A |
INTRINSIC |
|
low complexity region
|
539 |
554 |
N/A |
INTRINSIC |
|
CH
|
651 |
754 |
9.24e-15 |
SMART |
|
low complexity region
|
759 |
774 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000105610
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000135193
AA Change: F508L
PolyPhen 2
Score 0.716 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000130708
Gene: ENSMUSG00000022801
AA Change: F508L
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
13 |
N/A |
INTRINSIC |
|
low complexity region
|
31 |
44 |
N/A |
INTRINSIC |
|
LRR
|
104 |
126 |
2.54e1 |
SMART |
|
LRR
|
127 |
150 |
2.86e-1 |
SMART |
|
LRR
|
172 |
194 |
4.44e0 |
SMART |
|
LRR
|
195 |
218 |
4.33e1 |
SMART |
|
LRR
|
240 |
263 |
2.76e1 |
SMART |
|
low complexity region
|
482 |
493 |
N/A |
INTRINSIC |
|
low complexity region
|
539 |
554 |
N/A |
INTRINSIC |
|
CH
|
651 |
755 |
6.79e-13 |
SMART |
|
transmembrane domain
|
771 |
793 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000142290
AA Change: F56L
|
| SMART Domains |
Protein: ENSMUSP00000117302
Gene: ENSMUSG00000022801
AA Change: F56L
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
31 |
42 |
N/A |
INTRINSIC |
|
low complexity region
|
88 |
103 |
N/A |
INTRINSIC |
|
SCOP:d1h67a_
|
201 |
253 |
1e-11 |
SMART |
|
Blast:CH
|
205 |
253 |
6e-27 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156928
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000163428
|
| SMART Domains |
Protein: ENSMUSP00000133034
Gene: ENSMUSG00000022801
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
122 |
137 |
N/A |
INTRINSIC |
|
SCOP:d1h67a_
|
230 |
265 |
9e-5 |
SMART |
|
Blast:CH
|
234 |
265 |
7e-14 |
BLAST |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000165616
AA Change: F354L
PolyPhen 2
Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000130009
Gene: ENSMUSG00000022801
AA Change: F354L
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
13 |
N/A |
INTRINSIC |
|
low complexity region
|
31 |
44 |
N/A |
INTRINSIC |
|
Blast:LRR
|
89 |
113 |
1e-6 |
BLAST |
|
Blast:LRR
|
114 |
137 |
3e-7 |
BLAST |
|
low complexity region
|
328 |
339 |
N/A |
INTRINSIC |
|
low complexity region
|
385 |
400 |
N/A |
INTRINSIC |
|
CH
|
497 |
600 |
9.24e-15 |
SMART |
|
low complexity region
|
605 |
620 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000165826
AA Change: F131L
PolyPhen 2
Score 0.904 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000126308
Gene: ENSMUSG00000022801
AA Change: F131L
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
105 |
116 |
N/A |
INTRINSIC |
|
low complexity region
|
162 |
177 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000170201
AA Change: F508L
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000126964
Gene: ENSMUSG00000022801
AA Change: F508L
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
13 |
N/A |
INTRINSIC |
|
low complexity region
|
31 |
44 |
N/A |
INTRINSIC |
|
LRR
|
104 |
126 |
2.54e1 |
SMART |
|
LRR
|
127 |
150 |
2.86e-1 |
SMART |
|
LRR
|
172 |
194 |
4.44e0 |
SMART |
|
LRR
|
195 |
218 |
4.33e1 |
SMART |
|
LRR
|
240 |
263 |
2.76e1 |
SMART |
|
low complexity region
|
482 |
493 |
N/A |
INTRINSIC |
|
low complexity region
|
539 |
554 |
N/A |
INTRINSIC |
|
CH
|
615 |
718 |
9.24e-15 |
SMART |
|
low complexity region
|
723 |
738 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000170899
|
| SMART Domains |
Protein: ENSMUSP00000127547
Gene: ENSMUSG00000022801
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
13 |
N/A |
INTRINSIC |
|
low complexity region
|
31 |
44 |
N/A |
INTRINSIC |
|
LRR
|
104 |
126 |
2.54e1 |
SMART |
|
LRR
|
127 |
150 |
2.86e-1 |
SMART |
|
LRR
|
172 |
194 |
4.44e0 |
SMART |
|
LRR
|
195 |
218 |
4.33e1 |
SMART |
|
LRR
|
240 |
263 |
2.76e1 |
SMART |
|
low complexity region
|
489 |
504 |
N/A |
INTRINSIC |
|
CH
|
565 |
668 |
9.24e-15 |
SMART |
|
low complexity region
|
673 |
688 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.0791 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.1%
- 10x: 95.7%
- 20x: 90.8%
|
| Validation Efficiency |
100% (56/56) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4921539E11Rik |
C |
T |
4: 103,088,180 (GRCm39) |
G342D |
possibly damaging |
Het |
| Acvr2b |
C |
T |
9: 119,261,675 (GRCm39) |
R399W |
probably damaging |
Het |
| Arb2a |
T |
A |
13: 77,982,832 (GRCm39) |
|
probably benign |
Het |
| Atf6 |
A |
G |
1: 170,662,492 (GRCm39) |
V256A |
probably benign |
Het |
| Atp2b4 |
A |
T |
1: 133,656,454 (GRCm39) |
I732N |
probably damaging |
Het |
| C1qtnf9 |
A |
C |
14: 61,009,820 (GRCm39) |
Q25H |
probably damaging |
Het |
| Ccdc6 |
T |
A |
10: 69,978,401 (GRCm39) |
|
probably benign |
Het |
| Cds2 |
T |
C |
2: 132,127,887 (GRCm39) |
|
probably null |
Het |
| Chdh |
A |
G |
14: 29,756,603 (GRCm39) |
Y343C |
probably damaging |
Het |
| Col5a2 |
T |
C |
1: 45,421,262 (GRCm39) |
|
probably benign |
Het |
| Cts3 |
G |
A |
13: 61,716,024 (GRCm39) |
|
probably benign |
Het |
| Cyfip1 |
T |
A |
7: 55,541,802 (GRCm39) |
D362E |
probably benign |
Het |
| Dsg1b |
T |
A |
18: 20,529,082 (GRCm39) |
S273T |
probably benign |
Het |
| Dysf |
A |
T |
6: 84,117,649 (GRCm39) |
H1274L |
probably benign |
Het |
| Eva1c |
T |
C |
16: 90,672,986 (GRCm39) |
S187P |
probably benign |
Het |
| Fam13b |
G |
A |
18: 34,578,581 (GRCm39) |
|
probably benign |
Het |
| Fbn2 |
C |
T |
18: 58,168,408 (GRCm39) |
G2310S |
probably damaging |
Het |
| Fcna |
T |
C |
2: 25,515,520 (GRCm39) |
Y183C |
probably damaging |
Het |
| Fnta |
T |
C |
8: 26,491,056 (GRCm39) |
T263A |
probably benign |
Het |
| Gm94 |
T |
C |
18: 43,914,309 (GRCm39) |
D83G |
possibly damaging |
Het |
| Gnal |
C |
T |
18: 67,268,720 (GRCm39) |
|
probably benign |
Het |
| Grb7 |
T |
G |
11: 98,343,014 (GRCm39) |
S244A |
probably benign |
Het |
| Grm3 |
T |
C |
5: 9,562,477 (GRCm39) |
T458A |
probably benign |
Het |
| Hdac2 |
C |
T |
10: 36,867,832 (GRCm39) |
R193C |
probably damaging |
Het |
| Hycc2 |
T |
C |
1: 58,573,638 (GRCm39) |
|
probably benign |
Het |
| Ighmbp2 |
T |
C |
19: 3,315,072 (GRCm39) |
R783G |
probably benign |
Het |
| Inpp5j |
G |
T |
11: 3,453,122 (GRCm39) |
L43I |
possibly damaging |
Het |
| Itga11 |
A |
T |
9: 62,604,243 (GRCm39) |
T44S |
probably damaging |
Het |
| Itsn1 |
C |
T |
16: 91,665,036 (GRCm39) |
|
probably benign |
Het |
| Kdm6b |
G |
T |
11: 69,297,822 (GRCm39) |
C233* |
probably null |
Het |
| Lamb3 |
T |
C |
1: 193,025,700 (GRCm39) |
L1130P |
probably damaging |
Het |
| Lrrd1 |
T |
A |
5: 3,916,425 (GRCm39) |
V814E |
probably benign |
Het |
| Megf10 |
C |
T |
18: 57,386,054 (GRCm39) |
P356S |
probably benign |
Het |
| Myorg |
G |
A |
4: 41,499,538 (GRCm39) |
R31* |
probably null |
Het |
| Naip1 |
A |
T |
13: 100,559,727 (GRCm39) |
D1092E |
probably benign |
Het |
| Nus1 |
T |
A |
10: 52,306,190 (GRCm39) |
V42E |
probably damaging |
Het |
| Or11g24 |
A |
G |
14: 50,662,359 (GRCm39) |
I128V |
possibly damaging |
Het |
| Or2a51 |
A |
C |
6: 43,179,006 (GRCm39) |
M143L |
probably benign |
Het |
| Padi3 |
T |
C |
4: 140,523,024 (GRCm39) |
N306S |
probably damaging |
Het |
| Pex13 |
T |
C |
11: 23,605,949 (GRCm39) |
S94G |
probably benign |
Het |
| Ppm1h |
G |
T |
10: 122,638,229 (GRCm39) |
Q166H |
probably benign |
Het |
| Ptafr |
A |
T |
4: 132,307,396 (GRCm39) |
Y262F |
probably benign |
Het |
| Rabgap1 |
T |
A |
2: 37,377,132 (GRCm39) |
D321E |
probably damaging |
Het |
| Samsn1 |
C |
T |
16: 75,742,113 (GRCm39) |
|
noncoding transcript |
Het |
| Scarb1 |
T |
C |
5: 125,366,745 (GRCm39) |
N63D |
probably damaging |
Het |
| Serpinb7 |
T |
C |
1: 107,379,340 (GRCm39) |
I249T |
possibly damaging |
Het |
| Srpra |
A |
G |
9: 35,126,277 (GRCm39) |
K490R |
probably benign |
Het |
| Sycn |
A |
G |
7: 28,240,398 (GRCm39) |
N22D |
probably benign |
Het |
| Tarbp1 |
C |
T |
8: 127,167,612 (GRCm39) |
A1067T |
probably benign |
Het |
| Tex14 |
A |
G |
11: 87,405,131 (GRCm39) |
D681G |
possibly damaging |
Het |
| Usp34 |
C |
T |
11: 23,396,741 (GRCm39) |
|
probably benign |
Het |
| Vmn2r107 |
T |
C |
17: 20,595,085 (GRCm39) |
|
probably benign |
Het |
| Vwde |
A |
T |
6: 13,187,528 (GRCm39) |
M653K |
probably benign |
Het |
| Wrap73 |
T |
A |
4: 154,233,200 (GRCm39) |
S125T |
possibly damaging |
Het |
|
| Other mutations in Lrch3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01129:Lrch3
|
APN |
16 |
32,815,335 (GRCm39) |
missense |
probably benign |
0.10 |
|
IGL01400:Lrch3
|
APN |
16 |
32,799,911 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02565:Lrch3
|
APN |
16 |
32,826,084 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL03076:Lrch3
|
APN |
16 |
32,802,223 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
IGL03103:Lrch3
|
APN |
16 |
32,772,507 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03125:Lrch3
|
APN |
16 |
32,734,647 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
IGL03349:Lrch3
|
APN |
16 |
32,775,694 (GRCm39) |
missense |
probably damaging |
1.00 |
|
eluted
|
UTSW |
16 |
32,806,377 (GRCm39) |
missense |
probably null |
|
|
leached
|
UTSW |
16 |
32,779,833 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0054:Lrch3
|
UTSW |
16 |
32,816,222 (GRCm39) |
intron |
probably benign |
|
|
R0123:Lrch3
|
UTSW |
16 |
32,782,124 (GRCm39) |
splice site |
probably benign |
|
|
R0225:Lrch3
|
UTSW |
16 |
32,782,124 (GRCm39) |
splice site |
probably benign |
|
|
R0326:Lrch3
|
UTSW |
16 |
32,799,870 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0734:Lrch3
|
UTSW |
16 |
32,817,853 (GRCm39) |
nonsense |
probably null |
|
|
R1204:Lrch3
|
UTSW |
16 |
32,829,584 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1470:Lrch3
|
UTSW |
16 |
32,808,865 (GRCm39) |
splice site |
probably benign |
|
|
R1526:Lrch3
|
UTSW |
16 |
32,770,746 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1597:Lrch3
|
UTSW |
16 |
32,770,781 (GRCm39) |
nonsense |
probably null |
|
|
R1850:Lrch3
|
UTSW |
16 |
32,807,163 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1966:Lrch3
|
UTSW |
16 |
32,734,755 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R2241:Lrch3
|
UTSW |
16 |
32,816,211 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2313:Lrch3
|
UTSW |
16 |
32,782,045 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2902:Lrch3
|
UTSW |
16 |
32,770,766 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4723:Lrch3
|
UTSW |
16 |
32,808,854 (GRCm39) |
splice site |
probably null |
|
|
R4795:Lrch3
|
UTSW |
16 |
32,826,074 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4970:Lrch3
|
UTSW |
16 |
32,818,883 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5223:Lrch3
|
UTSW |
16 |
32,734,767 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5292:Lrch3
|
UTSW |
16 |
32,796,177 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5414:Lrch3
|
UTSW |
16 |
32,806,335 (GRCm39) |
splice site |
probably null |
|
|
R5470:Lrch3
|
UTSW |
16 |
32,818,960 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5594:Lrch3
|
UTSW |
16 |
32,734,554 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5843:Lrch3
|
UTSW |
16 |
32,818,896 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5862:Lrch3
|
UTSW |
16 |
32,816,179 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5911:Lrch3
|
UTSW |
16 |
32,779,833 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5932:Lrch3
|
UTSW |
16 |
32,796,106 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6519:Lrch3
|
UTSW |
16 |
32,815,367 (GRCm39) |
critical splice donor site |
probably benign |
|
|
R6731:Lrch3
|
UTSW |
16 |
32,770,790 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7182:Lrch3
|
UTSW |
16 |
32,814,149 (GRCm39) |
missense |
probably benign |
0.05 |
|
R7197:Lrch3
|
UTSW |
16 |
32,810,665 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7319:Lrch3
|
UTSW |
16 |
32,815,363 (GRCm39) |
missense |
probably benign |
0.19 |
|
R7392:Lrch3
|
UTSW |
16 |
32,807,125 (GRCm39) |
nonsense |
probably null |
|
|
R7408:Lrch3
|
UTSW |
16 |
32,807,113 (GRCm39) |
nonsense |
probably null |
|
|
R7414:Lrch3
|
UTSW |
16 |
32,818,883 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7425:Lrch3
|
UTSW |
16 |
32,826,077 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7909:Lrch3
|
UTSW |
16 |
32,829,663 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7956:Lrch3
|
UTSW |
16 |
32,806,377 (GRCm39) |
missense |
probably null |
|
|
R8009:Lrch3
|
UTSW |
16 |
32,826,083 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
R8247:Lrch3
|
UTSW |
16 |
32,829,713 (GRCm39) |
nonsense |
probably null |
|
|
R8408:Lrch3
|
UTSW |
16 |
32,775,750 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8686:Lrch3
|
UTSW |
16 |
32,802,223 (GRCm39) |
missense |
possibly damaging |
0.52 |
|
R8756:Lrch3
|
UTSW |
16 |
32,808,810 (GRCm39) |
missense |
probably benign |
0.33 |
|
R8947:Lrch3
|
UTSW |
16 |
32,802,199 (GRCm39) |
missense |
possibly damaging |
0.66 |
|
R9459:Lrch3
|
UTSW |
16 |
32,799,775 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9710:Lrch3
|
UTSW |
16 |
32,796,108 (GRCm39) |
nonsense |
probably null |
|
|
Z1176:Lrch3
|
UTSW |
16 |
32,734,686 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
| Predicted Primers |
PCR Primer
(F):5'- ATGAGACCTCTCTTGCAGCTTTCAC -3'
(R):5'- CAGATGCTTCTGAGTCTCCTTGGC -3'
Sequencing Primer
(F):5'- GCAGCTTTCACATTCAGACTTGG -3'
(R):5'- CTGCTCTACAATGCATAGATGGG -3'
|
| Posted On |
2013-05-23 |
Incidental Mutation