Incidental Mutation 'R5754:Lrch1'
| ID |
444968 |
| Institutional Source |
Beutler Lab
|
| 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 # |
R5754 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
14 |
| Chromosomal Location |
74992115-75185316 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 75054558 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 312
(D312G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000154004
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000088970]
[ENSMUST00000228252]
|
| AlphaFold |
P62046 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000088970
AA Change: D312G
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000086363
Gene: ENSMUSG00000068015
AA Change: D312G
| 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 |
probably damaging
Transcript: ENSMUST00000228252
AA Change: D312G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| Meta Mutation Damage Score |
0.4455 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.8%
|
| Validation Efficiency |
98% (61/62) |
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb4 |
T |
A |
5: 8,984,320 (GRCm39) |
N683K |
probably benign |
Het |
| Atad2b |
T |
A |
12: 5,060,351 (GRCm39) |
H915Q |
probably benign |
Het |
| Bltp2 |
T |
C |
11: 78,160,367 (GRCm39) |
S609P |
probably damaging |
Het |
| Camk1d |
G |
T |
2: 5,449,908 (GRCm39) |
P91Q |
probably benign |
Het |
| Camk1d |
G |
C |
2: 5,449,910 (GRCm39) |
S90R |
probably damaging |
Het |
| Card11 |
T |
C |
5: 140,885,524 (GRCm39) |
E345G |
probably damaging |
Het |
| Ccpg1 |
G |
T |
9: 72,920,526 (GRCm39) |
V714L |
possibly damaging |
Het |
| Chst9 |
T |
C |
18: 15,586,254 (GRCm39) |
E103G |
possibly damaging |
Het |
| Cnga1 |
C |
T |
5: 72,762,615 (GRCm39) |
V300I |
probably benign |
Het |
| Crb1 |
T |
C |
1: 139,159,337 (GRCm39) |
Y1295C |
probably damaging |
Het |
| Dnah5 |
A |
G |
15: 28,402,014 (GRCm39) |
T3392A |
probably benign |
Het |
| Elp3 |
C |
A |
14: 65,785,439 (GRCm39) |
R473L |
probably damaging |
Het |
| Epgn |
T |
A |
5: 91,181,807 (GRCm39) |
I145N |
probably benign |
Het |
| Fam107b |
G |
A |
2: 3,779,457 (GRCm39) |
G220D |
probably damaging |
Het |
| Fbn2 |
A |
G |
18: 58,257,383 (GRCm39) |
V328A |
probably benign |
Het |
| Fn1 |
A |
T |
1: 71,639,481 (GRCm39) |
I1770N |
probably damaging |
Het |
| Fndc1 |
T |
A |
17: 7,988,585 (GRCm39) |
Y1159F |
unknown |
Het |
| Frem2 |
A |
G |
3: 53,444,679 (GRCm39) |
L2484P |
probably damaging |
Het |
| Grk2 |
C |
T |
19: 4,340,496 (GRCm39) |
R295H |
probably damaging |
Het |
| Gtf3c1 |
A |
T |
7: 125,243,237 (GRCm39) |
V1789D |
possibly damaging |
Het |
| Hmgcl |
T |
C |
4: 135,677,898 (GRCm39) |
V33A |
probably damaging |
Het |
| Ighv7-1 |
A |
G |
12: 113,860,239 (GRCm39) |
F51S |
probably damaging |
Het |
| Kcna6 |
A |
G |
6: 126,716,688 (GRCm39) |
L67P |
probably damaging |
Het |
| Lamc1 |
A |
T |
1: 153,123,030 (GRCm39) |
V720E |
probably benign |
Het |
| Mix23 |
A |
G |
16: 35,905,427 (GRCm39) |
N63S |
probably benign |
Het |
| Nav2 |
A |
G |
7: 49,206,794 (GRCm39) |
T1540A |
probably damaging |
Het |
| Nisch |
A |
T |
14: 30,913,373 (GRCm39) |
|
probably benign |
Het |
| Nos1ap |
T |
A |
1: 170,176,968 (GRCm39) |
K145M |
probably damaging |
Het |
| Npc1l1 |
A |
G |
11: 6,177,839 (GRCm39) |
Y524H |
probably damaging |
Het |
| Nrap |
T |
C |
19: 56,377,916 (GRCm39) |
T25A |
possibly damaging |
Het |
| Nusap1 |
A |
G |
2: 119,477,580 (GRCm39) |
K363R |
probably damaging |
Het |
| Or5ar1 |
T |
C |
2: 85,671,656 (GRCm39) |
T160A |
probably damaging |
Het |
| Or5b124 |
A |
G |
19: 13,611,357 (GRCm39) |
E294G |
probably damaging |
Het |
| Or7e177 |
T |
A |
9: 20,212,390 (GRCm39) |
L298Q |
probably damaging |
Het |
| Pde4d |
T |
C |
13: 110,074,547 (GRCm39) |
I384T |
probably damaging |
Het |
| Pkhd1 |
T |
A |
1: 20,593,875 (GRCm39) |
R1413* |
probably null |
Het |
| Plcd3 |
T |
A |
11: 102,964,592 (GRCm39) |
Y593F |
possibly damaging |
Het |
| Plxna1 |
A |
T |
6: 89,310,087 (GRCm39) |
I1026N |
possibly damaging |
Het |
| Podxl |
T |
A |
6: 31,501,329 (GRCm39) |
I409F |
probably damaging |
Het |
| Polq |
A |
C |
16: 36,837,625 (GRCm39) |
Q179P |
probably benign |
Het |
| Pomt1 |
T |
C |
2: 32,137,602 (GRCm39) |
V401A |
probably damaging |
Het |
| Qdpr |
C |
T |
5: 45,596,727 (GRCm39) |
G146S |
probably damaging |
Het |
| Shc4 |
T |
A |
2: 125,512,218 (GRCm39) |
Q2L |
probably damaging |
Het |
| Skint8 |
T |
A |
4: 111,807,387 (GRCm39) |
C358S |
probably benign |
Het |
| Smc5 |
T |
C |
19: 23,221,467 (GRCm39) |
E354G |
possibly damaging |
Het |
| Snx30 |
T |
C |
4: 59,868,275 (GRCm39) |
V129A |
probably damaging |
Het |
| Sp110 |
G |
C |
1: 85,504,923 (GRCm39) |
|
probably benign |
Het |
| Spag6 |
T |
A |
2: 18,703,613 (GRCm39) |
|
probably benign |
Het |
| Trim28 |
T |
A |
7: 12,763,036 (GRCm39) |
Y450N |
probably benign |
Het |
| Trip11 |
C |
T |
12: 101,851,924 (GRCm39) |
W428* |
probably null |
Het |
| Umodl1 |
T |
A |
17: 31,213,761 (GRCm39) |
V966E |
probably damaging |
Het |
| Utf1 |
A |
G |
7: 139,524,704 (GRCm39) |
|
probably benign |
Het |
| Vmn1r72 |
T |
C |
7: 11,403,776 (GRCm39) |
Y224C |
probably damaging |
Het |
| Whrn |
A |
G |
4: 63,334,825 (GRCm39) |
S748P |
probably damaging |
Het |
| Zbtb41 |
T |
A |
1: 139,359,816 (GRCm39) |
|
probably null |
Het |
| Zfhx3 |
T |
C |
8: 109,526,964 (GRCm39) |
F954L |
probably damaging |
Het |
| Zfp456 |
A |
T |
13: 67,514,359 (GRCm39) |
I449K |
probably benign |
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 |
|
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 |
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GCTCTTAGGAACACTGAGCG -3'
(R):5'- CAGCCTGTTGCCATATATCAATAAC -3'
Sequencing Primer
(F):5'- GCTGCTTTCACACATGATTGAACTG -3'
(R):5'- ATCGATGTACTTTGGTGTC -3'
|
| Posted On |
2016-11-21 |
Incidental Mutation