Incidental Mutation 'IGL03106:Lrch1'
ID |
418978 |
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 # |
IGL03106
|
Quality Score |
|
Status
|
|
Chromosome |
14 |
Chromosomal Location |
74992115-75185316 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 75073202 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Threonine
at position 146
(S146T)
|
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: S146T
PolyPhen 2
Score 0.174 (Sensitivity: 0.92; Specificity: 0.87)
|
SMART Domains |
Protein: ENSMUSP00000086363 Gene: ENSMUSG00000068015 AA Change: S146T
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: ENSMUST00000227433
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000228134
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000228252
AA Change: S146T
PolyPhen 2
Score 0.842 (Sensitivity: 0.83; Specificity: 0.93)
|
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: 52 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adam3 |
G |
T |
8: 25,205,135 (GRCm39) |
|
probably benign |
Het |
Adgrv1 |
T |
C |
13: 81,621,018 (GRCm39) |
N3911S |
probably benign |
Het |
Alox12b |
C |
T |
11: 69,059,702 (GRCm39) |
Q585* |
probably null |
Het |
Amtn |
A |
G |
5: 88,525,944 (GRCm39) |
Q36R |
probably benign |
Het |
Arg2 |
G |
A |
12: 79,196,665 (GRCm39) |
G129S |
probably damaging |
Het |
Arhgef28 |
A |
C |
13: 98,094,301 (GRCm39) |
Y948D |
probably damaging |
Het |
Atp10b |
T |
C |
11: 43,138,304 (GRCm39) |
V1195A |
probably benign |
Het |
Bet1l |
G |
T |
7: 140,434,523 (GRCm39) |
T42K |
probably benign |
Het |
Cabin1 |
G |
A |
10: 75,569,462 (GRCm39) |
T875I |
probably benign |
Het |
Ccdc17 |
A |
G |
4: 116,454,033 (GRCm39) |
|
probably null |
Het |
Crebrf |
A |
G |
17: 26,990,293 (GRCm39) |
E612G |
probably damaging |
Het |
Cyp2c67 |
A |
T |
19: 39,632,119 (GRCm39) |
M83K |
probably benign |
Het |
Dgkz |
A |
G |
2: 91,771,204 (GRCm39) |
S414P |
probably damaging |
Het |
Dock10 |
G |
T |
1: 80,546,551 (GRCm39) |
H411N |
probably damaging |
Het |
Dpyd |
A |
T |
3: 118,988,783 (GRCm39) |
T749S |
probably benign |
Het |
Dsc1 |
C |
T |
18: 20,219,701 (GRCm39) |
|
probably null |
Het |
Echdc1 |
A |
T |
10: 29,198,276 (GRCm39) |
M74L |
probably damaging |
Het |
Edn1 |
C |
A |
13: 42,458,499 (GRCm39) |
T104K |
possibly damaging |
Het |
Fat2 |
T |
A |
11: 55,202,727 (GRCm39) |
T116S |
probably benign |
Het |
Fcrl5 |
A |
T |
3: 87,343,190 (GRCm39) |
|
probably null |
Het |
Fpgt |
C |
T |
3: 154,792,759 (GRCm39) |
G423R |
probably damaging |
Het |
Gprc5b |
A |
T |
7: 118,583,416 (GRCm39) |
V151E |
probably damaging |
Het |
Grm5 |
A |
G |
7: 87,685,278 (GRCm39) |
Y465C |
probably damaging |
Het |
Idh3b |
T |
A |
2: 130,126,321 (GRCm39) |
N6I |
probably benign |
Het |
Ighmbp2 |
T |
C |
19: 3,323,022 (GRCm39) |
K308R |
possibly damaging |
Het |
Lyl1 |
C |
T |
8: 85,429,300 (GRCm39) |
P3L |
possibly damaging |
Het |
Mterf3 |
T |
C |
13: 67,078,221 (GRCm39) |
K16R |
probably damaging |
Het |
Ncapg |
T |
A |
5: 45,853,010 (GRCm39) |
H825Q |
probably damaging |
Het |
Or2t1 |
G |
A |
14: 14,328,851 (GRCm38) |
V247I |
probably damaging |
Het |
Or2y1f |
T |
A |
11: 49,184,988 (GRCm39) |
I280N |
probably damaging |
Het |
Or4d5 |
A |
G |
9: 40,012,030 (GRCm39) |
V252A |
probably damaging |
Het |
Or5b95 |
G |
A |
19: 12,658,287 (GRCm39) |
V272M |
possibly damaging |
Het |
Or5t15 |
A |
C |
2: 86,681,958 (GRCm39) |
L28R |
possibly damaging |
Het |
Or5w15 |
A |
T |
2: 87,568,462 (GRCm39) |
S69T |
probably benign |
Het |
Pald1 |
A |
T |
10: 61,182,884 (GRCm39) |
M355K |
probably benign |
Het |
Phc1 |
A |
G |
6: 122,300,428 (GRCm39) |
|
probably benign |
Het |
Phkb |
T |
A |
8: 86,745,095 (GRCm39) |
|
probably benign |
Het |
Pkn3 |
G |
T |
2: 29,975,257 (GRCm39) |
R506L |
probably damaging |
Het |
Plod2 |
T |
C |
9: 92,455,620 (GRCm39) |
Y100H |
probably damaging |
Het |
Prl7b1 |
G |
T |
13: 27,790,918 (GRCm39) |
Q56K |
probably benign |
Het |
Rhot1 |
T |
A |
11: 80,133,407 (GRCm39) |
C229* |
probably null |
Het |
Sema3a |
G |
A |
5: 13,649,456 (GRCm39) |
R735Q |
probably damaging |
Het |
Slc18b1 |
A |
G |
10: 23,702,557 (GRCm39) |
*460W |
probably null |
Het |
Slco6c1 |
T |
A |
1: 96,993,748 (GRCm39) |
|
probably benign |
Het |
Slu7 |
T |
A |
11: 43,333,457 (GRCm39) |
V359D |
possibly damaging |
Het |
Suco |
T |
C |
1: 161,662,049 (GRCm39) |
Y794C |
possibly damaging |
Het |
Sult3a2 |
T |
C |
10: 33,655,769 (GRCm39) |
N70S |
probably benign |
Het |
Taar2 |
A |
T |
10: 23,817,195 (GRCm39) |
D245V |
probably damaging |
Het |
Taf1d |
A |
G |
9: 15,221,237 (GRCm39) |
H181R |
possibly damaging |
Het |
Tmem33 |
T |
C |
5: 67,421,139 (GRCm39) |
S38P |
probably damaging |
Het |
Traf3ip1 |
T |
C |
1: 91,450,609 (GRCm39) |
S519P |
probably benign |
Het |
Ttc12 |
T |
C |
9: 49,369,362 (GRCm39) |
K253E |
possibly damaging |
Het |
|
Other mutations in Lrch1 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01124:Lrch1
|
APN |
14 |
74,994,503 (GRCm39) |
missense |
probably benign |
0.22 |
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 |
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 |
2016-08-02 |