Incidental Mutation 'R5430:Lrch4'
ID |
427122 |
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 |
042996-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.179)
|
Stock # |
R5430 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
5 |
Chromosomal Location |
137627385-137639361 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 137636795 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Proline
at position 433
(S433P)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000134767
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000031734]
[ENSMUST00000057314]
[ENSMUST00000166099]
[ENSMUST00000175968]
[ENSMUST00000176011]
[ENSMUST00000176667]
[ENSMUST00000177545]
[ENSMUST00000177477]
[ENSMUST00000196511]
[ENSMUST00000177466]
|
AlphaFold |
no structure available at present |
Predicted Effect |
probably benign
Transcript: ENSMUST00000031734
AA Change: S487P
PolyPhen 2
Score 0.403 (Sensitivity: 0.89; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000031734 Gene: ENSMUSG00000093445 AA Change: S487P
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: ENSMUST00000057314
|
SMART Domains |
Protein: ENSMUSP00000060844 Gene: ENSMUSG00000047182
Domain | Start | End | E-Value | Type |
PH
|
33 |
135 |
4.46e-11 |
SMART |
IRS
|
159 |
272 |
1.18e-30 |
SMART |
PTBI
|
159 |
272 |
7.23e-55 |
SMART |
|
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 |
possibly damaging
Transcript: ENSMUST00000175968
AA Change: S433P
PolyPhen 2
Score 0.462 (Sensitivity: 0.89; Specificity: 0.90)
|
SMART Domains |
Protein: ENSMUSP00000134767 Gene: ENSMUSG00000093445 AA Change: S433P
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 |
unknown
Transcript: ENSMUST00000176871
AA Change: S46P
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000176667
AA Change: S487P
PolyPhen 2
Score 0.335 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000135832 Gene: ENSMUSG00000093445 AA Change: S487P
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: ENSMUST00000177545
AA Change: S487P
PolyPhen 2
Score 0.403 (Sensitivity: 0.89; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000135286 Gene: ENSMUSG00000029720 AA Change: S487P
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: ENSMUST00000177354
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000176988
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000177038
|
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: ENSMUST00000196511
|
SMART Domains |
Protein: ENSMUSP00000142730 Gene: ENSMUSG00000047182
Domain | Start | End | E-Value | Type |
PH
|
33 |
135 |
4.46e-11 |
SMART |
IRS
|
159 |
272 |
1.18e-30 |
SMART |
PTBI
|
159 |
272 |
7.23e-55 |
SMART |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000177466
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000176768
|
Meta Mutation Damage Score |
0.1795 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.7%
|
Validation Efficiency |
96% (54/56) |
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: 49 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700001J11Rik |
T |
A |
9: 39,963,587 (GRCm39) |
|
noncoding transcript |
Het |
Acot11 |
C |
T |
4: 106,617,327 (GRCm39) |
G240R |
probably damaging |
Het |
Ankrd34a |
G |
A |
3: 96,504,837 (GRCm39) |
G14R |
probably damaging |
Het |
Arhgef1 |
C |
A |
7: 24,611,732 (GRCm39) |
|
probably null |
Het |
Brsk1 |
T |
C |
7: 4,713,435 (GRCm39) |
F702L |
probably benign |
Het |
Chrna3 |
C |
T |
9: 54,920,192 (GRCm39) |
V470I |
probably damaging |
Het |
Cpm |
A |
G |
10: 117,511,986 (GRCm39) |
Q310R |
possibly damaging |
Het |
Dennd5a |
T |
C |
7: 109,533,447 (GRCm39) |
T108A |
probably damaging |
Het |
Dvl3 |
C |
T |
16: 20,342,481 (GRCm39) |
R145W |
probably damaging |
Het |
E4f1 |
G |
A |
17: 24,663,944 (GRCm39) |
A532V |
probably damaging |
Het |
Eid1 |
A |
G |
2: 125,515,550 (GRCm39) |
T147A |
probably damaging |
Het |
Eipr1 |
A |
T |
12: 28,913,015 (GRCm39) |
N239Y |
probably damaging |
Het |
Eml5 |
T |
C |
12: 98,760,417 (GRCm39) |
I1777M |
probably damaging |
Het |
Gm11787 |
A |
T |
4: 3,512,786 (GRCm39) |
|
noncoding transcript |
Het |
Gnat2 |
T |
C |
3: 108,005,716 (GRCm39) |
L227P |
probably damaging |
Het |
H2-T15 |
C |
T |
17: 36,366,967 (GRCm39) |
V359I |
probably benign |
Het |
Jag1 |
T |
C |
2: 136,943,626 (GRCm39) |
H190R |
possibly damaging |
Het |
Kdm7a |
A |
G |
6: 39,126,276 (GRCm39) |
W570R |
possibly damaging |
Het |
Lmbrd1 |
A |
G |
1: 24,732,061 (GRCm39) |
T93A |
possibly damaging |
Het |
Lrp1 |
G |
A |
10: 127,376,930 (GRCm39) |
R4216W |
probably damaging |
Het |
Magohb |
A |
G |
6: 131,266,381 (GRCm39) |
Y42H |
probably damaging |
Het |
Melk |
A |
G |
4: 44,309,033 (GRCm39) |
H130R |
probably damaging |
Het |
Mettl24 |
G |
T |
10: 40,613,780 (GRCm39) |
R173L |
probably benign |
Het |
Mup4 |
A |
T |
4: 59,960,044 (GRCm39) |
H73Q |
probably damaging |
Het |
Mylk2 |
A |
T |
2: 152,759,468 (GRCm39) |
E386V |
probably damaging |
Het |
Nppb |
C |
T |
4: 148,070,838 (GRCm39) |
P71L |
probably benign |
Het |
Oca2 |
T |
C |
7: 55,945,208 (GRCm39) |
V272A |
probably damaging |
Het |
Or14j6 |
T |
A |
17: 38,215,304 (GRCm39) |
I289N |
probably damaging |
Het |
Or2t6 |
C |
T |
14: 14,175,692 (GRCm38) |
R130H |
probably benign |
Het |
Or4c10 |
A |
T |
2: 89,760,257 (GRCm39) |
I35F |
probably benign |
Het |
Osbpl6 |
T |
C |
2: 76,416,482 (GRCm39) |
S628P |
probably damaging |
Het |
Papola |
T |
C |
12: 105,775,843 (GRCm39) |
V253A |
probably damaging |
Het |
Pex12 |
T |
C |
11: 83,188,572 (GRCm39) |
D141G |
probably damaging |
Het |
Ppm1k |
A |
T |
6: 57,501,871 (GRCm39) |
C97* |
probably null |
Het |
Ptprh |
T |
A |
7: 4,554,046 (GRCm39) |
E807V |
probably damaging |
Het |
Sema3a |
A |
T |
5: 13,615,730 (GRCm39) |
T385S |
probably damaging |
Het |
Sfn |
T |
C |
4: 133,328,938 (GRCm39) |
Y48C |
probably damaging |
Het |
Slc38a8 |
A |
G |
8: 120,220,959 (GRCm39) |
I200T |
probably benign |
Het |
Smarcal1 |
T |
C |
1: 72,665,776 (GRCm39) |
V758A |
probably damaging |
Het |
Stmn4 |
A |
G |
14: 66,595,463 (GRCm39) |
M190V |
possibly damaging |
Het |
Syt3 |
T |
G |
7: 44,040,337 (GRCm39) |
L190R |
possibly damaging |
Het |
Tbl1xr1 |
T |
A |
3: 22,246,246 (GRCm39) |
D255E |
probably benign |
Het |
Ttbk2 |
C |
T |
2: 120,608,046 (GRCm39) |
R191H |
probably damaging |
Het |
Vmn1r238 |
G |
T |
18: 3,122,521 (GRCm39) |
L298M |
possibly damaging |
Het |
Vmn2r45 |
A |
C |
7: 8,486,333 (GRCm39) |
Y318* |
probably null |
Het |
Vsig8 |
T |
C |
1: 172,387,196 (GRCm39) |
I24T |
probably damaging |
Het |
Wdr3 |
G |
A |
3: 100,064,643 (GRCm39) |
T166I |
possibly damaging |
Het |
Zfp354c |
A |
G |
11: 50,706,022 (GRCm39) |
I351T |
probably benign |
Het |
Zfp52 |
A |
G |
17: 21,775,329 (GRCm39) |
T8A |
probably benign |
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 |
|
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 |
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'- AGAATTCCAGGCCTGACTGC -3'
(R):5'- TTTGGTCTCTGAATGGAGCCC -3'
Sequencing Primer
(F):5'- GCTTCTCCAGCGTCCTGAAG -3'
(R):5'- TCTGAATGGAGCCCAGGGG -3'
|
Posted On |
2016-09-01 |