Incidental Mutation 'R5470:Lrch3'
ID |
433497 |
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 |
043031-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.100)
|
Stock # |
R5470 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
16 |
Chromosomal Location |
32734470-32836017 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 32818960 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Asparagine to Lysine
at position 650
(N650K)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000126964
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000023491]
[ENSMUST00000135193]
[ENSMUST00000165616]
[ENSMUST00000170201]
[ENSMUST00000170899]
[ENSMUST00000165826]
|
AlphaFold |
Q8BVU0 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000023491
AA Change: N686K
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000023491 Gene: ENSMUSG00000022801 AA Change: N686K
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: ENSMUST00000093713
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000105610
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000135193
AA Change: N686K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000130708 Gene: ENSMUSG00000022801 AA Change: N686K
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: N239K
|
SMART Domains |
Protein: ENSMUSP00000117302 Gene: ENSMUSG00000022801 AA Change: N239K
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 |
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: N532K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000130009 Gene: ENSMUSG00000022801 AA Change: N532K
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 damaging
Transcript: ENSMUST00000170201
AA Change: N650K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000126964 Gene: ENSMUSG00000022801 AA Change: N650K
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 damaging
Transcript: ENSMUST00000170899
AA Change: N600K
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000127547 Gene: ENSMUSG00000022801 AA Change: N600K
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: 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 |
|
Meta Mutation Damage Score |
0.8467 |
Coding Region Coverage |
- 1x: 98.3%
- 3x: 97.3%
- 10x: 95.1%
- 20x: 90.4%
|
Validation Efficiency |
99% (79/80) |
Allele List at MGI |
|
Other mutations in this stock |
Total: 69 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Actn1 |
T |
A |
12: 80,215,715 (GRCm39) |
I813F |
probably damaging |
Het |
Aqr |
G |
A |
2: 113,988,056 (GRCm39) |
L169F |
probably damaging |
Het |
Atp6v1d |
G |
A |
12: 78,892,058 (GRCm39) |
R182C |
probably benign |
Het |
Bcl2l13 |
G |
T |
6: 120,839,833 (GRCm39) |
A44S |
probably benign |
Het |
Brip1 |
T |
C |
11: 86,039,368 (GRCm39) |
K389E |
possibly damaging |
Het |
C530025M09Rik |
G |
A |
2: 149,673,045 (GRCm39) |
|
probably benign |
Het |
Ccdc7b |
T |
A |
8: 129,799,081 (GRCm39) |
S53T |
possibly damaging |
Het |
Chd8 |
A |
G |
14: 52,450,066 (GRCm39) |
F154L |
probably damaging |
Het |
Cop1 |
A |
T |
1: 159,094,430 (GRCm39) |
|
probably benign |
Het |
Cyp2c39 |
A |
G |
19: 39,501,974 (GRCm39) |
K121R |
possibly damaging |
Het |
Cyp3a57 |
A |
G |
5: 145,309,429 (GRCm39) |
M256V |
probably benign |
Het |
Deup1 |
T |
C |
9: 15,493,916 (GRCm39) |
|
probably null |
Het |
Dnah10 |
A |
G |
5: 124,830,232 (GRCm39) |
N709D |
probably benign |
Het |
Dthd1 |
A |
G |
5: 62,976,109 (GRCm39) |
Y261C |
probably damaging |
Het |
Ear-ps2 |
G |
A |
14: 44,284,517 (GRCm39) |
|
noncoding transcript |
Het |
En2 |
C |
T |
5: 28,371,922 (GRCm39) |
T133M |
probably benign |
Het |
Endou |
A |
G |
15: 97,616,836 (GRCm39) |
F229S |
probably damaging |
Het |
Etl4 |
A |
T |
2: 20,534,791 (GRCm39) |
H79L |
probably damaging |
Het |
Fah |
C |
T |
7: 84,242,393 (GRCm39) |
|
probably null |
Het |
Fetub |
C |
T |
16: 22,751,081 (GRCm39) |
R143C |
probably damaging |
Het |
Fignl1 |
T |
A |
11: 11,752,640 (GRCm39) |
E138D |
probably benign |
Het |
Fndc3a |
A |
G |
14: 72,812,008 (GRCm39) |
L311P |
possibly damaging |
Het |
Gdf9 |
T |
A |
11: 53,327,581 (GRCm39) |
V179E |
probably benign |
Het |
Gm14129 |
G |
T |
2: 148,769,737 (GRCm39) |
|
noncoding transcript |
Het |
Gorab |
A |
G |
1: 163,220,078 (GRCm39) |
I188T |
probably damaging |
Het |
Gpr152 |
G |
A |
19: 4,193,128 (GRCm39) |
C223Y |
probably damaging |
Het |
Heatr5b |
A |
T |
17: 79,129,008 (GRCm39) |
|
probably null |
Het |
Hsd17b3 |
G |
T |
13: 64,221,713 (GRCm39) |
T104N |
probably damaging |
Het |
Il6ra |
C |
T |
3: 89,793,302 (GRCm39) |
V283M |
probably benign |
Het |
Klk1b16 |
A |
T |
7: 43,786,755 (GRCm39) |
I5F |
probably damaging |
Het |
Krt74 |
G |
A |
15: 101,662,900 (GRCm39) |
|
noncoding transcript |
Het |
Ly96 |
A |
T |
1: 16,779,710 (GRCm39) |
E126D |
probably benign |
Het |
Mgarp |
C |
A |
3: 51,298,706 (GRCm39) |
R66L |
possibly damaging |
Het |
Naalad2 |
T |
A |
9: 18,242,147 (GRCm39) |
T586S |
probably damaging |
Het |
Ndufaf3 |
T |
C |
9: 108,443,643 (GRCm39) |
|
probably benign |
Het |
Neb |
A |
G |
2: 52,139,450 (GRCm39) |
M3055T |
possibly damaging |
Het |
Neo1 |
G |
T |
9: 58,838,350 (GRCm39) |
A478D |
probably damaging |
Het |
Nmrk1 |
A |
T |
19: 18,617,248 (GRCm39) |
|
probably null |
Het |
Nsl1 |
T |
C |
1: 190,812,737 (GRCm39) |
M184T |
probably benign |
Het |
Nup133 |
T |
C |
8: 124,657,705 (GRCm39) |
N410S |
probably benign |
Het |
Opalin |
A |
G |
19: 41,054,970 (GRCm39) |
S75P |
probably benign |
Het |
Or1e17 |
T |
C |
11: 73,831,696 (GRCm39) |
I208T |
probably benign |
Het |
Or3a4 |
A |
G |
11: 73,944,733 (GRCm39) |
I284T |
possibly damaging |
Het |
Or51ag1 |
T |
G |
7: 103,155,716 (GRCm39) |
I146L |
probably benign |
Het |
Palb2 |
C |
A |
7: 121,713,574 (GRCm39) |
C903F |
probably damaging |
Het |
Pcm1 |
T |
A |
8: 41,740,720 (GRCm39) |
W989R |
probably damaging |
Het |
Pfkfb4 |
T |
A |
9: 108,856,661 (GRCm39) |
I389N |
probably damaging |
Het |
Pitrm1 |
T |
C |
13: 6,603,306 (GRCm39) |
C119R |
probably benign |
Het |
Plekha1 |
T |
C |
7: 130,510,106 (GRCm39) |
V45A |
probably damaging |
Het |
Pold2 |
G |
A |
11: 5,823,048 (GRCm39) |
P376S |
probably damaging |
Het |
Rcan2 |
A |
G |
17: 44,147,174 (GRCm39) |
D4G |
probably benign |
Het |
Slc12a1 |
A |
T |
2: 125,012,634 (GRCm39) |
T299S |
probably damaging |
Het |
Slc22a29 |
A |
T |
19: 8,138,880 (GRCm39) |
H527Q |
probably benign |
Het |
Slc22a8 |
G |
A |
19: 8,585,234 (GRCm39) |
R261H |
probably damaging |
Het |
Slc35e2 |
C |
T |
4: 155,694,483 (GRCm39) |
P10L |
probably benign |
Het |
Slco4a1 |
T |
C |
2: 180,115,907 (GRCm39) |
F681S |
probably benign |
Het |
Sorcs2 |
A |
T |
5: 36,188,527 (GRCm39) |
H860Q |
probably benign |
Het |
Strn |
A |
T |
17: 78,964,374 (GRCm39) |
H530Q |
probably benign |
Het |
Tex14 |
A |
G |
11: 87,442,430 (GRCm39) |
R179G |
probably damaging |
Het |
Tjp3 |
T |
C |
10: 81,115,381 (GRCm39) |
D350G |
probably benign |
Het |
Tnrc6b |
G |
T |
15: 80,800,912 (GRCm39) |
R1406L |
possibly damaging |
Het |
Tnxb |
A |
G |
17: 34,935,947 (GRCm39) |
D2666G |
probably null |
Het |
Ttn |
A |
T |
2: 76,560,208 (GRCm39) |
Y27652N |
probably benign |
Het |
Utp20 |
T |
A |
10: 88,653,758 (GRCm39) |
E287D |
probably benign |
Het |
Vmn1r45 |
T |
C |
6: 89,910,698 (GRCm39) |
I91V |
probably benign |
Het |
Wdr72 |
A |
T |
9: 74,046,981 (GRCm39) |
K76* |
probably null |
Het |
Zfp689 |
C |
T |
7: 127,043,425 (GRCm39) |
A402T |
probably damaging |
Het |
Zfpm1 |
A |
G |
8: 123,060,532 (GRCm39) |
E207G |
probably damaging |
Het |
Zhx2 |
G |
T |
15: 57,686,470 (GRCm39) |
R613L |
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 |
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 |
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 |
|
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'- TGCCCAGCTTTCTGTCTGAG -3'
(R):5'- CCTACAATATTCCATACATGCTGTAGC -3'
Sequencing Primer
(F):5'- CCAGCTTTCTGTCTGAGTTTCTGG -3'
(R):5'- ACATGCTGTAGCTTATTGTTCATG -3'
|
Posted On |
2016-10-06 |