Incidental Mutation 'R0622:Lrch1'
| ID |
58749 |
| 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 |
| MMRRC Submission |
038811-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R0622 (G1)
|
| Quality Score |
221 |
|
Status
|
Not validated
|
| Chromosome |
14 |
| Chromosomal Location |
74992115-75185316 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 75033491 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 509
(Y509C)
|
| 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: Y509C
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000086363
Gene: ENSMUSG00000068015
AA Change: Y509C
| 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: ENSMUST00000226799
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000228134
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000228252
AA Change: Y509C
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000229311
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000230218
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000230381
|
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.9%
- 10x: 97.7%
- 20x: 95.9%
|
| 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: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Agtr1a |
T |
A |
13: 30,565,664 (GRCm39) |
M243K |
probably benign |
Het |
| Ap1b1 |
A |
G |
11: 4,987,707 (GRCm39) |
M744V |
probably damaging |
Het |
| Ccdc152 |
T |
C |
15: 3,327,660 (GRCm39) |
N39S |
probably damaging |
Het |
| Cd163 |
G |
A |
6: 124,294,311 (GRCm39) |
V490M |
probably damaging |
Het |
| Col6a5 |
G |
T |
9: 105,803,051 (GRCm39) |
H1305N |
unknown |
Het |
| Cpb1 |
C |
A |
3: 20,303,982 (GRCm39) |
D361Y |
probably damaging |
Het |
| Dchs1 |
T |
A |
7: 105,412,656 (GRCm39) |
Y1248F |
probably damaging |
Het |
| Dhdds |
G |
C |
4: 133,721,547 (GRCm39) |
F83L |
probably damaging |
Het |
| Dsg4 |
T |
A |
18: 20,582,845 (GRCm39) |
V161E |
possibly damaging |
Het |
| Exosc4 |
A |
G |
15: 76,211,736 (GRCm39) |
D15G |
probably damaging |
Het |
| F3 |
A |
T |
3: 121,518,668 (GRCm39) |
D44V |
probably damaging |
Het |
| Fat2 |
A |
T |
11: 55,173,954 (GRCm39) |
F2253Y |
probably damaging |
Het |
| Fbn1 |
T |
C |
2: 125,220,944 (GRCm39) |
D650G |
possibly damaging |
Het |
| Gramd4 |
T |
A |
15: 85,975,590 (GRCm39) |
F36I |
probably damaging |
Het |
| Grm7 |
G |
A |
6: 111,335,457 (GRCm39) |
A623T |
probably damaging |
Het |
| Gys1 |
A |
T |
7: 45,089,419 (GRCm39) |
T193S |
probably damaging |
Het |
| Hectd4 |
A |
G |
5: 121,486,688 (GRCm39) |
T3228A |
possibly damaging |
Het |
| Itpk1 |
G |
T |
12: 102,540,239 (GRCm39) |
D281E |
probably damaging |
Het |
| Kcnh7 |
A |
C |
2: 62,667,633 (GRCm39) |
|
probably null |
Het |
| Klhl29 |
A |
G |
12: 5,131,224 (GRCm39) |
L852P |
probably damaging |
Het |
| Lrp1b |
A |
G |
2: 41,618,563 (GRCm39) |
|
probably null |
Het |
| Mcpt4 |
C |
A |
14: 56,298,119 (GRCm39) |
R144L |
probably benign |
Het |
| Mia2 |
C |
T |
12: 59,178,364 (GRCm39) |
R12W |
probably damaging |
Het |
| Mrps5 |
A |
G |
2: 127,436,451 (GRCm39) |
K116R |
probably benign |
Het |
| Myrf |
G |
A |
19: 10,200,816 (GRCm39) |
P286S |
probably damaging |
Het |
| Nanp |
A |
G |
2: 150,881,164 (GRCm39) |
M28T |
probably benign |
Het |
| Neb |
T |
C |
2: 52,102,963 (GRCm39) |
I4472V |
probably benign |
Het |
| Nfix |
A |
C |
8: 85,453,111 (GRCm39) |
N314K |
probably damaging |
Het |
| Nlrc3 |
C |
T |
16: 3,771,832 (GRCm39) |
R849Q |
probably benign |
Het |
| Nup210l |
G |
A |
3: 90,075,047 (GRCm39) |
V786M |
probably damaging |
Het |
| Or2t44 |
T |
C |
11: 58,677,167 (GRCm39) |
S36P |
probably damaging |
Het |
| Or52ad1 |
A |
G |
7: 102,996,064 (GRCm39) |
S24P |
probably damaging |
Het |
| Or6z5 |
T |
C |
7: 6,477,598 (GRCm39) |
I163T |
possibly damaging |
Het |
| Or8c20 |
A |
G |
9: 38,260,667 (GRCm39) |
N96S |
possibly damaging |
Het |
| Pdia4 |
A |
T |
6: 47,783,452 (GRCm39) |
F197Y |
probably damaging |
Het |
| Phldb1 |
T |
C |
9: 44,627,149 (GRCm39) |
D432G |
probably damaging |
Het |
| Pik3ca |
A |
G |
3: 32,490,701 (GRCm39) |
E116G |
probably damaging |
Het |
| Polq |
T |
C |
16: 36,881,355 (GRCm39) |
V1173A |
probably benign |
Het |
| Pou2f3 |
C |
T |
9: 43,036,414 (GRCm39) |
R423H |
probably damaging |
Het |
| Pramel29 |
T |
C |
4: 143,939,583 (GRCm39) |
|
probably benign |
Het |
| Prkag2 |
T |
C |
5: 25,074,247 (GRCm39) |
N246S |
probably damaging |
Het |
| Proser1 |
A |
G |
3: 53,385,281 (GRCm39) |
S388G |
probably benign |
Het |
| Ralgps1 |
G |
A |
2: 33,064,459 (GRCm39) |
R238* |
probably null |
Het |
| Rfx2 |
T |
C |
17: 57,084,071 (GRCm39) |
D657G |
probably damaging |
Het |
| Ryr3 |
A |
G |
2: 112,492,900 (GRCm39) |
F3724S |
probably damaging |
Het |
| Sh2d5 |
T |
C |
4: 137,986,539 (GRCm39) |
S421P |
probably damaging |
Het |
| Slc34a1 |
C |
A |
13: 23,996,594 (GRCm39) |
T33K |
probably damaging |
Het |
| St8sia5 |
A |
G |
18: 77,333,809 (GRCm39) |
T156A |
probably damaging |
Het |
| Stk32c |
T |
C |
7: 138,768,026 (GRCm39) |
D85G |
probably benign |
Het |
| Tnks |
A |
G |
8: 35,407,976 (GRCm39) |
S251P |
probably damaging |
Het |
| Tnxb |
T |
A |
17: 34,937,703 (GRCm39) |
L3864Q |
probably damaging |
Het |
| Trim9 |
A |
G |
12: 70,393,378 (GRCm39) |
Y189H |
probably damaging |
Het |
| Vmn1r77 |
T |
G |
7: 11,775,315 (GRCm39) |
F30L |
probably benign |
Het |
| Wasf3 |
A |
G |
5: 146,403,602 (GRCm39) |
|
probably null |
Het |
| Wdr90 |
C |
T |
17: 26,074,632 (GRCm39) |
C603Y |
probably damaging |
Het |
| Zdhhc25 |
T |
C |
15: 88,485,310 (GRCm39) |
L215P |
probably damaging |
Het |
| Zeb1 |
C |
T |
18: 5,759,123 (GRCm39) |
Q140* |
probably null |
Het |
| Zfp677 |
C |
T |
17: 21,617,962 (GRCm39) |
L340F |
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 |
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TGACAACTATCGAGAGACCCCAGAG -3'
(R):5'- GGAGCCAGGAGACAGTTTGGTTAC -3'
Sequencing Primer
(F):5'- AGACAGTCCCATTAACTCTTTAATCC -3'
(R):5'- AGATGCGCTCATAGCTACTG -3'
|
| Posted On |
2013-07-11 |
Incidental Mutation