Incidental Mutation 'R1330:Lrch4'
| ID |
156141 |
| 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 |
039395-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.173)
|
| Stock # |
R1330 (G1)
|
| Quality Score |
171 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
137627385-137639361 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 137636051 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Glutamine
at position 368
(R368Q)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000135286
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000031734]
[ENSMUST00000166099]
[ENSMUST00000175968]
[ENSMUST00000176011]
[ENSMUST00000176667]
[ENSMUST00000177545]
[ENSMUST00000177466]
[ENSMUST00000177477]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000031734
AA Change: R368Q
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000031734
Gene: ENSMUSG00000093445
AA Change: R368Q
| 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 benign
Transcript: ENSMUST00000175968
AA Change: R314Q
PolyPhen 2
Score 0.385 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000134767
Gene: ENSMUSG00000093445
AA Change: R314Q
| 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 |
noncoding transcript
Transcript: ENSMUST00000176075
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000176256
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000176667
AA Change: R368Q
PolyPhen 2
Score 0.615 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000135832
Gene: ENSMUSG00000093445
AA Change: R368Q
| 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 damaging
Transcript: ENSMUST00000177545
AA Change: R368Q
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000135286
Gene: ENSMUSG00000029720
AA Change: R368Q
| 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: ENSMUST00000177038
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000177354
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000176988
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000176871
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000177466
|
| 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: ENSMUST00000176768
|
| Meta Mutation Damage Score |
0.1594 |
| Coding Region Coverage |
- 1x: 98.5%
- 3x: 97.2%
- 10x: 92.6%
- 20x: 82.0%
|
| Validation Efficiency |
100% (40/40) |
| 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: 34 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4933421I07Rik |
T |
C |
7: 42,097,018 (GRCm39) |
T98A |
probably benign |
Het |
| Adgre4 |
T |
A |
17: 56,085,814 (GRCm39) |
C38S |
probably benign |
Het |
| Adgrf3 |
T |
A |
5: 30,400,093 (GRCm39) |
T83S |
probably benign |
Het |
| Arhgef40 |
T |
C |
14: 52,227,613 (GRCm39) |
V453A |
probably benign |
Het |
| Art4 |
A |
T |
6: 136,831,339 (GRCm39) |
|
probably benign |
Het |
| Cdhr2 |
A |
G |
13: 54,882,081 (GRCm39) |
K1177R |
possibly damaging |
Het |
| Ddx41 |
G |
A |
13: 55,682,293 (GRCm39) |
R205W |
possibly damaging |
Het |
| Ddx6 |
T |
C |
9: 44,539,070 (GRCm39) |
|
probably benign |
Het |
| Dolk |
A |
T |
2: 30,175,112 (GRCm39) |
V311E |
probably damaging |
Het |
| Dstyk |
A |
G |
1: 132,377,618 (GRCm39) |
N408S |
probably benign |
Het |
| Efcab3 |
A |
G |
11: 104,637,116 (GRCm39) |
Y1049C |
possibly damaging |
Het |
| Eva1c |
A |
C |
16: 90,701,284 (GRCm39) |
E318D |
probably damaging |
Het |
| Frem3 |
T |
A |
8: 81,395,468 (GRCm39) |
W1832R |
probably damaging |
Het |
| Jup |
A |
T |
11: 100,263,502 (GRCm39) |
I689N |
probably benign |
Het |
| Kcnh7 |
A |
G |
2: 62,607,755 (GRCm39) |
S609P |
possibly damaging |
Het |
| Ncbp1 |
G |
A |
4: 46,167,354 (GRCm39) |
V586M |
probably benign |
Het |
| Ncstn |
C |
T |
1: 171,899,092 (GRCm39) |
M346I |
probably damaging |
Het |
| Osbpl1a |
A |
G |
18: 13,015,251 (GRCm39) |
|
probably null |
Het |
| Pcdh12 |
A |
G |
18: 38,414,914 (GRCm39) |
V737A |
probably benign |
Het |
| Pds5b |
T |
A |
5: 150,684,542 (GRCm39) |
M600K |
probably damaging |
Het |
| Rbm25 |
A |
G |
12: 83,724,666 (GRCm39) |
D805G |
probably damaging |
Het |
| Rfx7 |
C |
T |
9: 72,524,547 (GRCm39) |
T579I |
probably benign |
Het |
| Rhod |
C |
A |
19: 4,476,182 (GRCm39) |
A190S |
probably damaging |
Het |
| Rin2 |
C |
T |
2: 145,702,366 (GRCm39) |
T354I |
probably benign |
Het |
| Slc22a2 |
A |
C |
17: 12,805,699 (GRCm39) |
D150A |
possibly damaging |
Het |
| Spink11 |
A |
G |
18: 44,329,195 (GRCm39) |
I17T |
unknown |
Het |
| Tas1r2 |
A |
G |
4: 139,396,640 (GRCm39) |
I660V |
probably benign |
Het |
| Utp20 |
G |
A |
10: 88,637,051 (GRCm39) |
P720L |
probably damaging |
Het |
| Vmn1r1 |
A |
T |
1: 181,985,572 (GRCm39) |
L31H |
probably damaging |
Het |
| Vmn2r23 |
T |
C |
6: 123,718,963 (GRCm39) |
L772P |
probably damaging |
Het |
| Wap |
T |
C |
11: 6,586,818 (GRCm39) |
T94A |
unknown |
Het |
| Wdr47 |
T |
C |
3: 108,537,069 (GRCm39) |
S586P |
probably benign |
Het |
| Zfp318 |
A |
G |
17: 46,724,684 (GRCm39) |
Y2229C |
possibly damaging |
Het |
| Zfp429 |
T |
C |
13: 67,544,262 (GRCm39) |
|
probably null |
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 |
|
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 |
|
|
R5056:Lrch4
|
UTSW |
5 |
137,635,113 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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'- GCAAGGGAGTTTGCCCAGGAAATC -3'
(R):5'- TCCTGCCACAACTGCAAAGTGTC -3'
Sequencing Primer
(F):5'- GCCCAGGAAATCATGGGTG -3'
(R):5'- CGGAATACCTGCTGCTAGATG -3'
|
| Posted On |
2014-02-11 |
Incidental Mutation