Incidental Mutation 'R5056:Lrch4'
| ID |
390837 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lrch4
|
| Ensembl Gene |
ENSMUSG00000093445 |
| Gene Name |
leucine-rich repeats and calponin homology (CH) domain containing 4 |
| Synonyms |
LRRN4, LRN, 2810008P14Rik, 2900069C24Rik |
| MMRRC Submission |
042646-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.173)
|
| Stock # |
R5056 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
137627385-137639361 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to G
at 137635113 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Lysine
at position 237
(N237K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000135832
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000031734]
[ENSMUST00000166099]
[ENSMUST00000175968]
[ENSMUST00000176011]
[ENSMUST00000176667]
[ENSMUST00000177545]
[ENSMUST00000177477]
[ENSMUST00000177466]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000031734
AA Change: N237K
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000031734
Gene: ENSMUSG00000093445
AA Change: N237K
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
22 |
N/A |
INTRINSIC |
|
LRR
|
90 |
112 |
4.84e1 |
SMART |
|
LRR_TYP
|
113 |
136 |
4.61e-5 |
SMART |
|
LRR
|
158 |
180 |
2.63e0 |
SMART |
|
LRR_TYP
|
181 |
204 |
1.1e-2 |
SMART |
|
LRR
|
226 |
249 |
3.98e1 |
SMART |
|
low complexity region
|
389 |
405 |
N/A |
INTRINSIC |
|
low complexity region
|
440 |
453 |
N/A |
INTRINSIC |
|
low complexity region
|
474 |
479 |
N/A |
INTRINSIC |
|
low complexity region
|
510 |
530 |
N/A |
INTRINSIC |
|
CH
|
533 |
642 |
9.24e-15 |
SMART |
|
transmembrane domain
|
656 |
678 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000166099
|
| SMART Domains |
Protein: ENSMUSP00000127076
Gene: ENSMUSG00000079165
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SAP25
|
76 |
261 |
1.8e-77 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000175968
AA Change: N183K
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000134767
Gene: ENSMUSG00000093445
AA Change: N183K
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
14 |
N/A |
INTRINSIC |
|
LRR
|
36 |
58 |
4.84e1 |
SMART |
|
LRR_TYP
|
59 |
82 |
4.61e-5 |
SMART |
|
LRR
|
104 |
126 |
2.63e0 |
SMART |
|
LRR_TYP
|
127 |
150 |
1.1e-2 |
SMART |
|
LRR
|
172 |
195 |
3.98e1 |
SMART |
|
low complexity region
|
335 |
351 |
N/A |
INTRINSIC |
|
low complexity region
|
386 |
399 |
N/A |
INTRINSIC |
|
low complexity region
|
420 |
425 |
N/A |
INTRINSIC |
|
low complexity region
|
456 |
476 |
N/A |
INTRINSIC |
|
CH
|
479 |
588 |
9.24e-15 |
SMART |
|
transmembrane domain
|
602 |
624 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000176011
|
| SMART Domains |
Protein: ENSMUSP00000135133
Gene: ENSMUSG00000093445
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
22 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000176667
AA Change: N237K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000135832
Gene: ENSMUSG00000093445
AA Change: N237K
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
22 |
N/A |
INTRINSIC |
|
LRR
|
90 |
112 |
4.84e1 |
SMART |
|
LRR_TYP
|
113 |
136 |
4.61e-5 |
SMART |
|
LRR
|
158 |
180 |
2.63e0 |
SMART |
|
LRR_TYP
|
181 |
204 |
1.1e-2 |
SMART |
|
LRR
|
226 |
249 |
3.98e1 |
SMART |
|
low complexity region
|
389 |
405 |
N/A |
INTRINSIC |
|
low complexity region
|
440 |
453 |
N/A |
INTRINSIC |
|
low complexity region
|
474 |
479 |
N/A |
INTRINSIC |
|
low complexity region
|
510 |
530 |
N/A |
INTRINSIC |
|
CH
|
533 |
648 |
4.73e-12 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000176768
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000176871
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000177545
AA Change: N237K
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000135286
Gene: ENSMUSG00000029720
AA Change: N237K
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
22 |
N/A |
INTRINSIC |
|
LRR
|
90 |
112 |
4.84e1 |
SMART |
|
LRR_TYP
|
113 |
136 |
4.61e-5 |
SMART |
|
LRR
|
158 |
180 |
2.63e0 |
SMART |
|
LRR_TYP
|
181 |
204 |
1.1e-2 |
SMART |
|
LRR
|
226 |
249 |
3.98e1 |
SMART |
|
low complexity region
|
389 |
405 |
N/A |
INTRINSIC |
|
low complexity region
|
440 |
453 |
N/A |
INTRINSIC |
|
low complexity region
|
474 |
479 |
N/A |
INTRINSIC |
|
low complexity region
|
510 |
530 |
N/A |
INTRINSIC |
|
CH
|
533 |
642 |
9.24e-15 |
SMART |
|
transmembrane domain
|
656 |
678 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000176988
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000177354
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000177477
|
| SMART Domains |
Protein: ENSMUSP00000135724
Gene: ENSMUSG00000093445
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
22 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000177466
|
| Meta Mutation Damage Score |
0.9052 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.0%
- 20x: 91.2%
|
| Validation Efficiency |
99% (73/74) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that contains leucine-rich repeats (LRR) at its amino terminus and that is known to be involved in ligand binding. The carboxyl terminus may act as a membrane anchor. Identified structural elements suggest that the encoded protein resembles a receptor. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 66 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700030J22Rik |
T |
A |
8: 117,698,421 (GRCm39) |
K229* |
probably null |
Het |
| Adora2a |
T |
A |
10: 75,161,992 (GRCm39) |
S44T |
probably damaging |
Het |
| Agap3 |
T |
C |
5: 24,682,860 (GRCm39) |
V459A |
probably damaging |
Het |
| Apc2 |
T |
C |
10: 80,137,148 (GRCm39) |
V31A |
probably benign |
Het |
| Asic2 |
T |
A |
11: 80,862,429 (GRCm39) |
K189N |
possibly damaging |
Het |
| Bbs10 |
C |
T |
10: 111,136,401 (GRCm39) |
P505S |
probably benign |
Het |
| Brd10 |
A |
T |
19: 29,694,759 (GRCm39) |
I1578K |
probably benign |
Het |
| Cdh20 |
G |
T |
1: 104,881,722 (GRCm39) |
V396L |
probably benign |
Het |
| Cenpb |
C |
T |
2: 131,020,091 (GRCm39) |
|
probably benign |
Het |
| Chil6 |
T |
A |
3: 106,301,659 (GRCm39) |
Y147F |
probably damaging |
Het |
| Cluh |
C |
T |
11: 74,552,772 (GRCm39) |
R606C |
probably damaging |
Het |
| Cmtr1 |
A |
G |
17: 29,909,302 (GRCm39) |
T404A |
possibly damaging |
Het |
| Cnot1 |
T |
C |
8: 96,467,636 (GRCm39) |
N1499S |
probably damaging |
Het |
| Dmkn |
T |
C |
7: 30,463,529 (GRCm39) |
S61P |
probably damaging |
Het |
| Dmxl1 |
T |
C |
18: 50,003,990 (GRCm39) |
C872R |
probably benign |
Het |
| Dnah3 |
A |
G |
7: 119,620,169 (GRCm39) |
Y1587H |
probably damaging |
Het |
| Dsc2 |
A |
T |
18: 20,183,199 (GRCm39) |
V73D |
probably damaging |
Het |
| F5 |
A |
T |
1: 164,019,601 (GRCm39) |
Y692F |
possibly damaging |
Het |
| Fam184a |
A |
T |
10: 53,550,670 (GRCm39) |
L80I |
probably damaging |
Het |
| Foxj2 |
A |
G |
6: 122,810,833 (GRCm39) |
H271R |
probably benign |
Het |
| Grm7 |
A |
G |
6: 111,057,404 (GRCm39) |
T335A |
probably damaging |
Het |
| Hspa9 |
A |
G |
18: 35,071,734 (GRCm39) |
L622P |
probably damaging |
Het |
| Kcna7 |
G |
A |
7: 45,056,015 (GRCm39) |
R77H |
probably damaging |
Het |
| Kcnd3 |
T |
A |
3: 105,574,244 (GRCm39) |
|
probably benign |
Het |
| Klhdc8b |
ACACGCACGCACGCACGCACGCACGCACGCACGCACGCAC |
ACACGCACGCACGCACGCACGCACGCACGCACGCACGCACGCAC |
9: 108,326,184 (GRCm39) |
|
probably benign |
Het |
| Klk14 |
G |
A |
7: 43,341,501 (GRCm39) |
C51Y |
probably damaging |
Het |
| Lss |
T |
G |
10: 76,388,760 (GRCm39) |
|
probably null |
Het |
| Map6 |
T |
C |
7: 98,985,859 (GRCm39) |
F588L |
probably benign |
Het |
| Mbd6 |
C |
T |
10: 127,122,310 (GRCm39) |
V173I |
probably benign |
Het |
| Med13 |
A |
T |
11: 86,219,391 (GRCm39) |
S352T |
probably benign |
Het |
| Mettl16 |
T |
A |
11: 74,707,766 (GRCm39) |
V320E |
probably benign |
Het |
| Myh7b |
G |
C |
2: 155,474,293 (GRCm39) |
R1669S |
possibly damaging |
Het |
| Nup188 |
T |
A |
2: 30,194,143 (GRCm39) |
D149E |
probably damaging |
Het |
| Ogfrl1 |
A |
G |
1: 23,418,130 (GRCm39) |
S83P |
probably damaging |
Het |
| Or52l1 |
T |
A |
7: 104,829,779 (GRCm39) |
H262L |
probably damaging |
Het |
| Or5m13 |
T |
A |
2: 85,748,480 (GRCm39) |
D70E |
probably damaging |
Het |
| Or8k36-ps1 |
T |
A |
2: 86,437,364 (GRCm39) |
I184F |
unknown |
Het |
| Or9m1 |
T |
C |
2: 87,733,915 (GRCm39) |
Y35C |
probably damaging |
Het |
| Pafah1b3 |
C |
T |
7: 24,994,764 (GRCm39) |
R98Q |
probably damaging |
Het |
| Pde6b |
A |
T |
5: 108,571,357 (GRCm39) |
K437* |
probably null |
Het |
| Ppp1r12b |
A |
T |
1: 134,762,130 (GRCm39) |
|
probably benign |
Het |
| Ppp1r12b |
G |
T |
1: 134,883,471 (GRCm39) |
A17E |
probably benign |
Het |
| Pramel34 |
T |
C |
5: 93,786,784 (GRCm39) |
|
probably benign |
Het |
| Prdm9 |
T |
C |
17: 15,782,679 (GRCm39) |
Q104R |
possibly damaging |
Het |
| Rgs22 |
A |
T |
15: 36,050,391 (GRCm39) |
|
probably null |
Het |
| Rnf14 |
C |
T |
18: 38,441,441 (GRCm39) |
P277L |
probably damaging |
Het |
| Robo4 |
T |
C |
9: 37,316,102 (GRCm39) |
S258P |
probably benign |
Het |
| Sfrp1 |
T |
A |
8: 23,907,420 (GRCm39) |
F207I |
probably damaging |
Het |
| Sgms1 |
A |
G |
19: 32,137,087 (GRCm39) |
S160P |
probably damaging |
Het |
| Sil1 |
T |
C |
18: 35,402,755 (GRCm39) |
K263R |
probably benign |
Het |
| St14 |
A |
G |
9: 31,008,847 (GRCm39) |
|
probably null |
Het |
| Syne2 |
A |
G |
12: 75,955,905 (GRCm39) |
|
probably benign |
Het |
| Tbc1d9 |
T |
C |
8: 83,995,835 (GRCm39) |
S1013P |
probably benign |
Het |
| Tent5b |
C |
T |
4: 133,207,749 (GRCm39) |
R47W |
possibly damaging |
Het |
| Tmem67 |
T |
C |
4: 12,070,471 (GRCm39) |
S352G |
probably benign |
Het |
| Trib2 |
C |
A |
12: 15,843,795 (GRCm39) |
K282N |
possibly damaging |
Het |
| Trnau1ap |
T |
C |
4: 132,054,482 (GRCm39) |
|
probably benign |
Het |
| Trpm4 |
T |
C |
7: 44,958,054 (GRCm39) |
D952G |
probably damaging |
Het |
| Unc93b1 |
A |
G |
19: 3,992,762 (GRCm39) |
N305D |
possibly damaging |
Het |
| Usp32 |
A |
G |
11: 84,917,621 (GRCm39) |
V802A |
probably benign |
Het |
| Vmn2r48 |
T |
A |
7: 9,676,251 (GRCm39) |
H410L |
probably damaging |
Het |
| Wfs1 |
T |
C |
5: 37,132,931 (GRCm39) |
N116S |
probably benign |
Het |
| Wif1 |
A |
T |
10: 120,935,684 (GRCm39) |
H333L |
probably benign |
Het |
| Zfp109 |
T |
C |
7: 23,928,162 (GRCm39) |
T416A |
possibly damaging |
Het |
| Zfp808 |
T |
A |
13: 62,320,444 (GRCm39) |
C558S |
probably damaging |
Het |
| Zpbp |
T |
C |
11: 11,409,734 (GRCm39) |
D116G |
possibly damaging |
Het |
|
| Other mutations in Lrch4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00340:Lrch4
|
APN |
5 |
137,636,009 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
IGL01862:Lrch4
|
APN |
5 |
137,635,271 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03289:Lrch4
|
APN |
5 |
137,631,839 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0144:Lrch4
|
UTSW |
5 |
137,636,805 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0724:Lrch4
|
UTSW |
5 |
137,635,570 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1330:Lrch4
|
UTSW |
5 |
137,636,051 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1557:Lrch4
|
UTSW |
5 |
137,635,818 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1694:Lrch4
|
UTSW |
5 |
137,636,723 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2358:Lrch4
|
UTSW |
5 |
137,636,810 (GRCm39) |
unclassified |
probably benign |
|
|
R3755:Lrch4
|
UTSW |
5 |
137,635,992 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3756:Lrch4
|
UTSW |
5 |
137,635,992 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4608:Lrch4
|
UTSW |
5 |
137,637,408 (GRCm39) |
nonsense |
probably null |
|
|
R5114:Lrch4
|
UTSW |
5 |
137,636,179 (GRCm39) |
missense |
probably benign |
|
|
R5181:Lrch4
|
UTSW |
5 |
137,627,665 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5325:Lrch4
|
UTSW |
5 |
137,636,168 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5430:Lrch4
|
UTSW |
5 |
137,636,795 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R5712:Lrch4
|
UTSW |
5 |
137,636,188 (GRCm39) |
missense |
possibly damaging |
0.57 |
|
R5846:Lrch4
|
UTSW |
5 |
137,631,919 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5909:Lrch4
|
UTSW |
5 |
137,632,127 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R7319:Lrch4
|
UTSW |
5 |
137,637,977 (GRCm39) |
missense |
|
|
|
R7525:Lrch4
|
UTSW |
5 |
137,637,727 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7761:Lrch4
|
UTSW |
5 |
137,638,025 (GRCm39) |
missense |
|
|
|
R7848:Lrch4
|
UTSW |
5 |
137,632,116 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8209:Lrch4
|
UTSW |
5 |
137,637,997 (GRCm39) |
missense |
|
|
|
R8226:Lrch4
|
UTSW |
5 |
137,637,997 (GRCm39) |
missense |
|
|
|
R8713:Lrch4
|
UTSW |
5 |
137,638,125 (GRCm39) |
nonsense |
probably null |
|
|
R9361:Lrch4
|
UTSW |
5 |
137,635,076 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9372:Lrch4
|
UTSW |
5 |
137,631,953 (GRCm39) |
missense |
possibly damaging |
0.70 |
|
R9440:Lrch4
|
UTSW |
5 |
137,636,051 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9752:Lrch4
|
UTSW |
5 |
137,636,218 (GRCm39) |
missense |
probably benign |
|
|
R9796:Lrch4
|
UTSW |
5 |
137,635,269 (GRCm39) |
missense |
probably damaging |
0.99 |
|
RF009:Lrch4
|
UTSW |
5 |
137,635,805 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- CTATGATGGAGCTAGGGGTGAC -3'
(R):5'- GCTTCCATTGTTAGGTACTTGAAG -3'
Sequencing Primer
(F):5'- CTGCCCAGAGCCAAGTTAAAGG -3'
(R):5'- CTTGAAGATGTGAAGTTTCCCC -3'
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| Posted On |
2016-06-06 |
Incidental Mutation