Incidental Mutation 'R2241:Lrch3'
| ID |
240677 |
| 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 |
040241-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.115)
|
| Stock # |
R2241 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
16 |
| Chromosomal Location |
32734470-32836017 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 32816211 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 151
(T151A)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000023491]
[ENSMUST00000135193]
[ENSMUST00000165616]
[ENSMUST00000165826]
[ENSMUST00000170899]
[ENSMUST00000170201]
|
| AlphaFold |
Q8BVU0 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000023491
AA Change: T598A
PolyPhen 2
Score 0.097 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000023491
Gene: ENSMUSG00000022801
AA Change: T598A
| 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 |
probably benign
Transcript: ENSMUST00000135193
AA Change: T598A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000130708
Gene: ENSMUSG00000022801
AA Change: T598A
| 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 |
probably damaging
Transcript: ENSMUST00000142290
AA Change: T151A
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000117302
Gene: ENSMUSG00000022801
AA Change: T151A
| 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 |
possibly damaging
Transcript: ENSMUST00000163428
AA Change: T180A
PolyPhen 2
Score 0.741 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000133034
Gene: ENSMUSG00000022801
AA Change: T180A
| 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 benign
Transcript: ENSMUST00000165616
AA Change: T444A
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000130009
Gene: ENSMUSG00000022801
AA Change: T444A
| 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 |
probably benign
Transcript: ENSMUST00000165826
|
| SMART Domains |
Protein: ENSMUSP00000126308
Gene: ENSMUSG00000022801
| 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 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 |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000170201
|
| SMART Domains |
Protein: ENSMUSP00000126964
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
|
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 |
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 94.7%
|
| Validation Efficiency |
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 27 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adcy8 |
G |
T |
15: 64,571,230 (GRCm39) |
L1138I |
possibly damaging |
Het |
| Aftph |
T |
C |
11: 20,676,328 (GRCm39) |
D427G |
possibly damaging |
Het |
| Cep350 |
C |
T |
1: 155,834,302 (GRCm39) |
|
probably null |
Het |
| Clca4b |
A |
T |
3: 144,616,987 (GRCm39) |
S888T |
probably benign |
Het |
| Cyb5b |
A |
G |
8: 107,897,045 (GRCm39) |
D105G |
probably benign |
Het |
| Ddx20 |
A |
C |
3: 105,590,521 (GRCm39) |
Y258* |
probably null |
Het |
| Farp2 |
C |
T |
1: 93,507,625 (GRCm39) |
T441I |
probably benign |
Het |
| Fzd6 |
G |
T |
15: 38,894,931 (GRCm39) |
A366S |
probably damaging |
Het |
| Gpr149 |
A |
G |
3: 62,511,474 (GRCm39) |
V175A |
probably benign |
Het |
| Hivep2 |
C |
A |
10: 14,004,713 (GRCm39) |
T437K |
probably benign |
Het |
| Itga4 |
T |
A |
2: 79,131,357 (GRCm39) |
I575N |
probably damaging |
Het |
| Kcnj14 |
C |
T |
7: 45,469,325 (GRCm39) |
R60H |
probably benign |
Het |
| Mslnl |
G |
A |
17: 25,961,908 (GRCm39) |
V128M |
probably damaging |
Het |
| Mterf2 |
T |
C |
10: 84,956,180 (GRCm39) |
N148S |
possibly damaging |
Het |
| Nae1 |
A |
C |
8: 105,246,420 (GRCm39) |
D268E |
probably benign |
Het |
| Or5p5 |
T |
C |
7: 107,414,040 (GRCm39) |
V83A |
possibly damaging |
Het |
| Or6c211 |
G |
A |
10: 129,505,764 (GRCm39) |
T208I |
probably damaging |
Het |
| Or8b48 |
A |
G |
9: 38,493,101 (GRCm39) |
H176R |
probably damaging |
Het |
| Pcnx4 |
T |
C |
12: 72,620,928 (GRCm39) |
L916P |
probably damaging |
Het |
| Prune2 |
T |
A |
19: 17,100,456 (GRCm39) |
Y1987N |
probably damaging |
Het |
| Rsf1 |
ATGGCG |
ATGGCGACGGTGGCG |
7: 97,229,111 (GRCm39) |
|
probably benign |
Het |
| Ryr3 |
A |
G |
2: 112,631,737 (GRCm39) |
L2096P |
probably damaging |
Het |
| Serpina3m |
G |
A |
12: 104,355,708 (GRCm39) |
S125N |
probably benign |
Het |
| Tep1 |
G |
C |
14: 51,091,667 (GRCm39) |
R625G |
probably benign |
Het |
| Vmn2r102 |
T |
C |
17: 19,897,003 (GRCm39) |
Y117H |
probably benign |
Het |
| Wdfy4 |
A |
T |
14: 32,795,468 (GRCm39) |
N2091K |
possibly damaging |
Het |
| Yme1l1 |
C |
T |
2: 23,086,912 (GRCm39) |
R673* |
probably null |
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 |
|
R0455:Lrch3
|
UTSW |
16 |
32,807,250 (GRCm39) |
missense |
probably damaging |
0.99 |
|
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 |
|
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'- AAGCAGCTTTACTGTTTACATACGC -3'
(R):5'- TTAATGTTAGCGAGGTCACAGACAC -3'
Sequencing Primer
(F):5'- CGCTTTTCATTAACGAGTAGACTC -3'
(R):5'- GTCACAGACACCTGCAGAGTTAG -3'
|
| Posted On |
2014-10-15 |
Incidental Mutation