Incidental Mutation 'IGL01124:Lrch1'
ID |
52708 |
Institutional Source |
Australian Phenomics Network
(link to record)
|
Gene Symbol |
Lrch1
|
Ensembl Gene |
ENSMUSG00000068015 |
Gene Name |
leucine-rich repeats and calponin homology (CH) domain containing 1 |
Synonyms |
4832412D13Rik, Chdc1 |
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
IGL01124
|
Quality Score |
|
Status
|
|
Chromosome |
14 |
Chromosomal Location |
74992115-75185316 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 74994503 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Glutamic Acid
at position 673
(D673E)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000154004
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000088970]
[ENSMUST00000228252]
|
AlphaFold |
P62046 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000088970
AA Change: D700E
PolyPhen 2
Score 0.155 (Sensitivity: 0.92; Specificity: 0.87)
|
SMART Domains |
Protein: ENSMUSP00000086363 Gene: ENSMUSG00000068015 AA Change: D700E
Domain | Start | End | E-Value | Type |
low complexity region
|
25 |
44 |
N/A |
INTRINSIC |
LRR
|
109 |
131 |
1.86e1 |
SMART |
LRR_TYP
|
132 |
155 |
3.39e-3 |
SMART |
LRR
|
177 |
199 |
1.41e1 |
SMART |
LRR
|
200 |
223 |
4.34e-1 |
SMART |
LRR
|
245 |
268 |
1.66e1 |
SMART |
low complexity region
|
306 |
322 |
N/A |
INTRINSIC |
CH
|
591 |
698 |
1.71e-18 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000228134
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000228252
AA Change: D673E
PolyPhen 2
Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)
|
Coding Region Coverage |
|
Validation Efficiency |
|
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with a leucine-rich repeat and a calponin homology domain. Polymorphism in this gene may be associated with susceptibililty to knee osteoarthritis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2010] PHENOTYPE: Homozygous knockout leads to increased susceptibility to experimental autoimmune encephalomyelitis as a result of increased migration of T cells into the central nervous system. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 42 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Ascc3 |
T |
C |
10: 50,608,569 (GRCm39) |
I1477T |
probably damaging |
Het |
Baat |
A |
G |
4: 49,490,391 (GRCm39) |
I231T |
possibly damaging |
Het |
Cactin |
T |
C |
10: 81,160,184 (GRCm39) |
S426P |
possibly damaging |
Het |
Cfh |
A |
T |
1: 140,110,999 (GRCm39) |
F6I |
probably benign |
Het |
Clec4a2 |
C |
T |
6: 123,116,037 (GRCm39) |
|
probably benign |
Het |
Col12a1 |
A |
G |
9: 79,611,129 (GRCm39) |
S148P |
probably damaging |
Het |
Cubn |
G |
T |
2: 13,482,904 (GRCm39) |
Q281K |
possibly damaging |
Het |
Cyp2c65 |
T |
A |
19: 39,081,954 (GRCm39) |
|
probably benign |
Het |
Dennd4b |
A |
T |
3: 90,176,381 (GRCm39) |
T243S |
possibly damaging |
Het |
Epha8 |
C |
T |
4: 136,663,394 (GRCm39) |
G518D |
probably damaging |
Het |
Fmo3 |
G |
A |
1: 162,785,830 (GRCm39) |
R387C |
probably damaging |
Het |
Foxo6 |
T |
C |
4: 120,126,349 (GRCm39) |
T149A |
probably benign |
Het |
Fthl17d |
T |
C |
X: 8,852,827 (GRCm39) |
E3G |
probably benign |
Het |
Gm10521 |
A |
G |
1: 171,724,010 (GRCm39) |
Y107C |
unknown |
Het |
Ipo8 |
T |
A |
6: 148,678,874 (GRCm39) |
E908V |
probably benign |
Het |
Kcnd2 |
T |
C |
6: 21,217,216 (GRCm39) |
S307P |
probably damaging |
Het |
Klf3 |
A |
G |
5: 64,974,123 (GRCm39) |
M3V |
possibly damaging |
Het |
Ldb3 |
T |
A |
14: 34,266,157 (GRCm39) |
E417D |
probably damaging |
Het |
Map3k4 |
T |
C |
17: 12,474,087 (GRCm39) |
K865E |
probably benign |
Het |
Muc4 |
G |
A |
16: 32,589,104 (GRCm39) |
V754I |
possibly damaging |
Het |
Nek4 |
A |
G |
14: 30,692,219 (GRCm39) |
N223D |
probably benign |
Het |
Nell2 |
G |
A |
15: 95,194,060 (GRCm39) |
T551M |
probably damaging |
Het |
Nup155 |
T |
A |
15: 8,183,163 (GRCm39) |
M1241K |
probably damaging |
Het |
Or2t49 |
A |
T |
11: 58,393,020 (GRCm39) |
S121T |
possibly damaging |
Het |
Or5i1 |
T |
C |
2: 87,613,720 (GRCm39) |
F279L |
probably benign |
Het |
Orc1 |
T |
C |
4: 108,445,984 (GRCm39) |
|
probably benign |
Het |
Pclo |
T |
C |
5: 14,764,343 (GRCm39) |
I4272T |
unknown |
Het |
Ppp1r12c |
A |
G |
7: 4,500,344 (GRCm39) |
|
probably benign |
Het |
Prcp |
A |
G |
7: 92,559,416 (GRCm39) |
E160G |
probably benign |
Het |
Prl3d3 |
G |
A |
13: 27,343,090 (GRCm39) |
R92Q |
possibly damaging |
Het |
Prl6a1 |
T |
A |
13: 27,500,347 (GRCm39) |
M106K |
possibly damaging |
Het |
Slc22a1 |
T |
A |
17: 12,869,749 (GRCm39) |
|
probably benign |
Het |
Slco3a1 |
A |
G |
7: 73,934,295 (GRCm39) |
Y626H |
probably damaging |
Het |
Smtn |
A |
G |
11: 3,476,326 (GRCm39) |
|
probably null |
Het |
Snx30 |
T |
C |
4: 59,886,404 (GRCm39) |
|
probably benign |
Het |
Spock2 |
A |
G |
10: 59,967,209 (GRCm39) |
D393G |
unknown |
Het |
Trem3 |
T |
G |
17: 48,556,829 (GRCm39) |
L100R |
probably damaging |
Het |
Trpm2 |
A |
T |
10: 77,781,659 (GRCm39) |
|
probably benign |
Het |
Ubr1 |
T |
C |
2: 120,745,386 (GRCm39) |
M901V |
probably benign |
Het |
Usp28 |
T |
A |
9: 48,948,513 (GRCm39) |
S873T |
probably damaging |
Het |
Vmn1r86 |
T |
C |
7: 12,836,856 (GRCm39) |
I7V |
probably benign |
Het |
Xirp2 |
T |
C |
2: 67,338,959 (GRCm39) |
L400P |
probably damaging |
Het |
|
Other mutations in Lrch1 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01137:Lrch1
|
APN |
14 |
74,994,532 (GRCm39) |
missense |
probably damaging |
0.98 |
IGL01978:Lrch1
|
APN |
14 |
75,023,782 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01988:Lrch1
|
APN |
14 |
75,032,813 (GRCm39) |
splice site |
probably benign |
|
IGL02036:Lrch1
|
APN |
14 |
75,032,733 (GRCm39) |
splice site |
probably benign |
|
IGL02650:Lrch1
|
APN |
14 |
75,051,138 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03006:Lrch1
|
APN |
14 |
75,051,060 (GRCm39) |
missense |
probably damaging |
0.99 |
IGL03106:Lrch1
|
APN |
14 |
75,073,202 (GRCm39) |
missense |
possibly damaging |
0.84 |
IGL03353:Lrch1
|
APN |
14 |
75,095,482 (GRCm39) |
missense |
probably damaging |
1.00 |
FR4304:Lrch1
|
UTSW |
14 |
75,057,005 (GRCm39) |
missense |
possibly damaging |
0.81 |
LCD18:Lrch1
|
UTSW |
14 |
75,142,461 (GRCm39) |
intron |
probably benign |
|
R0129:Lrch1
|
UTSW |
14 |
75,073,186 (GRCm39) |
missense |
probably benign |
0.13 |
R0312:Lrch1
|
UTSW |
14 |
75,185,034 (GRCm39) |
missense |
possibly damaging |
0.82 |
R0441:Lrch1
|
UTSW |
14 |
75,184,985 (GRCm39) |
missense |
possibly damaging |
0.95 |
R0622:Lrch1
|
UTSW |
14 |
75,033,491 (GRCm39) |
missense |
probably benign |
0.00 |
R1418:Lrch1
|
UTSW |
14 |
75,041,709 (GRCm39) |
splice site |
probably benign |
|
R1618:Lrch1
|
UTSW |
14 |
75,051,144 (GRCm39) |
missense |
probably damaging |
1.00 |
R2116:Lrch1
|
UTSW |
14 |
75,022,971 (GRCm39) |
missense |
probably damaging |
1.00 |
R2428:Lrch1
|
UTSW |
14 |
75,044,985 (GRCm39) |
splice site |
probably benign |
|
R3707:Lrch1
|
UTSW |
14 |
75,095,437 (GRCm39) |
missense |
probably damaging |
0.99 |
R4352:Lrch1
|
UTSW |
14 |
75,056,018 (GRCm39) |
missense |
probably damaging |
0.98 |
R5689:Lrch1
|
UTSW |
14 |
75,023,764 (GRCm39) |
missense |
probably damaging |
1.00 |
R5754:Lrch1
|
UTSW |
14 |
75,054,558 (GRCm39) |
missense |
probably damaging |
1.00 |
R6142:Lrch1
|
UTSW |
14 |
75,184,940 (GRCm39) |
missense |
probably damaging |
1.00 |
R6469:Lrch1
|
UTSW |
14 |
75,054,525 (GRCm39) |
missense |
probably damaging |
1.00 |
R6740:Lrch1
|
UTSW |
14 |
75,049,063 (GRCm39) |
missense |
probably benign |
|
R6871:Lrch1
|
UTSW |
14 |
75,049,063 (GRCm39) |
missense |
probably benign |
|
R7051:Lrch1
|
UTSW |
14 |
75,022,962 (GRCm39) |
missense |
probably damaging |
1.00 |
R7438:Lrch1
|
UTSW |
14 |
74,994,477 (GRCm39) |
missense |
possibly damaging |
0.88 |
R7509:Lrch1
|
UTSW |
14 |
75,185,048 (GRCm39) |
missense |
probably benign |
0.25 |
R8037:Lrch1
|
UTSW |
14 |
75,023,794 (GRCm39) |
missense |
probably damaging |
1.00 |
R8262:Lrch1
|
UTSW |
14 |
75,055,935 (GRCm39) |
missense |
probably damaging |
0.97 |
R8302:Lrch1
|
UTSW |
14 |
75,032,772 (GRCm39) |
missense |
probably benign |
0.01 |
R8943:Lrch1
|
UTSW |
14 |
75,032,808 (GRCm39) |
missense |
probably benign |
0.06 |
R9427:Lrch1
|
UTSW |
14 |
75,032,787 (GRCm39) |
missense |
probably benign |
|
RF002:Lrch1
|
UTSW |
14 |
75,185,014 (GRCm39) |
small deletion |
probably benign |
|
RF009:Lrch1
|
UTSW |
14 |
75,185,014 (GRCm39) |
small deletion |
probably benign |
|
RF018:Lrch1
|
UTSW |
14 |
75,184,995 (GRCm39) |
frame shift |
probably null |
|
RF022:Lrch1
|
UTSW |
14 |
75,185,014 (GRCm39) |
small deletion |
probably benign |
|
RF023:Lrch1
|
UTSW |
14 |
75,185,006 (GRCm39) |
frame shift |
probably null |
|
RF037:Lrch1
|
UTSW |
14 |
75,184,989 (GRCm39) |
small deletion |
probably benign |
|
RF039:Lrch1
|
UTSW |
14 |
75,184,989 (GRCm39) |
small deletion |
probably benign |
|
RF043:Lrch1
|
UTSW |
14 |
75,185,015 (GRCm39) |
frame shift |
probably null |
|
RF061:Lrch1
|
UTSW |
14 |
75,185,007 (GRCm39) |
frame shift |
probably null |
|
RF061:Lrch1
|
UTSW |
14 |
75,184,995 (GRCm39) |
frame shift |
probably null |
|
|
Posted On |
2013-06-21 |