Incidental Mutation 'R5846:Lrch4'
| ID |
453608 |
| 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 |
044064-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.173)
|
| Stock # |
R5846 (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 137631919 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Tryptophan
at position 48
(C48W)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000134767
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000031734]
[ENSMUST00000111002]
[ENSMUST00000136028]
[ENSMUST00000175968]
[ENSMUST00000176011]
[ENSMUST00000176667]
[ENSMUST00000177545]
[ENSMUST00000177477]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000031734
AA Change: C102W
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000031734
Gene: ENSMUSG00000093445
AA Change: C102W
| 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: ENSMUST00000111002
|
| SMART Domains |
Protein: ENSMUSP00000106630
Gene: ENSMUSG00000089984
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RCC1
|
247 |
293 |
4.2e-11 |
PFAM |
|
low complexity region
|
303 |
316 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000136028
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000175968
AA Change: C48W
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000134767
Gene: ENSMUSG00000093445
AA Change: C48W
| 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: C102W
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000135832
Gene: ENSMUSG00000093445
AA Change: C102W
| 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: ENSMUST00000176871
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000176988
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000177545
AA Change: C102W
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000135286
Gene: ENSMUSG00000029720
AA Change: C102W
| 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: ENSMUST00000177477
|
| SMART Domains |
Protein: ENSMUSP00000135724
Gene: ENSMUSG00000093445
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
22 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.4434 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.8%
- 20x: 93.4%
|
| Validation Efficiency |
97% (67/69) |
| 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: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4932414N04Rik |
T |
C |
2: 68,562,377 (GRCm39) |
S335P |
unknown |
Het |
| Ace3 |
A |
T |
11: 105,889,188 (GRCm39) |
I473F |
probably benign |
Het |
| Adcy2 |
T |
A |
13: 68,886,707 (GRCm39) |
N281Y |
probably damaging |
Het |
| Adgra1 |
T |
A |
7: 139,455,196 (GRCm39) |
W275R |
probably damaging |
Het |
| Apmap |
T |
C |
2: 150,450,341 (GRCm39) |
D20G |
probably damaging |
Het |
| Arap2 |
T |
C |
5: 62,807,116 (GRCm39) |
T1184A |
probably damaging |
Het |
| Atp13a2 |
T |
C |
4: 140,722,907 (GRCm39) |
V303A |
possibly damaging |
Het |
| BC004004 |
A |
T |
17: 29,501,282 (GRCm39) |
|
probably benign |
Het |
| C1s1 |
G |
A |
6: 124,517,912 (GRCm39) |
P23S |
possibly damaging |
Het |
| C1s2 |
T |
A |
6: 124,608,123 (GRCm39) |
N197Y |
probably damaging |
Het |
| Camsap3 |
A |
G |
8: 3,653,980 (GRCm39) |
H539R |
probably damaging |
Het |
| Catsperb |
A |
T |
12: 101,569,025 (GRCm39) |
N899I |
probably damaging |
Het |
| Cct4 |
T |
C |
11: 22,951,354 (GRCm39) |
|
probably benign |
Het |
| Chrm2 |
A |
T |
6: 36,500,385 (GRCm39) |
T81S |
probably damaging |
Het |
| Dnaaf3 |
A |
T |
7: 4,526,686 (GRCm39) |
S464T |
possibly damaging |
Het |
| Dnah10 |
T |
A |
5: 124,900,437 (GRCm39) |
I3898N |
possibly damaging |
Het |
| Dnah3 |
TTCCTC |
TTC |
7: 119,550,244 (GRCm39) |
|
probably benign |
Het |
| Dnajc13 |
T |
C |
9: 104,067,584 (GRCm39) |
K1187E |
probably damaging |
Het |
| Dock4 |
A |
T |
12: 40,867,735 (GRCm39) |
D1437V |
probably damaging |
Het |
| Dst |
C |
T |
1: 34,234,942 (GRCm39) |
Q3674* |
probably null |
Het |
| Eef1a2 |
T |
C |
2: 180,794,776 (GRCm39) |
Y141C |
probably damaging |
Het |
| Fads3 |
G |
T |
19: 10,030,397 (GRCm39) |
Q178H |
probably null |
Het |
| Fbxw22 |
T |
A |
9: 109,215,829 (GRCm39) |
M140L |
probably benign |
Het |
| Fndc7 |
A |
G |
3: 108,788,707 (GRCm39) |
I178T |
probably damaging |
Het |
| Foxd1 |
T |
C |
13: 98,491,549 (GRCm39) |
M141T |
probably damaging |
Het |
| H4c2 |
T |
C |
13: 23,941,215 (GRCm39) |
V71A |
possibly damaging |
Het |
| Havcr2 |
T |
C |
11: 46,360,343 (GRCm39) |
I141T |
probably benign |
Het |
| Hectd1 |
A |
C |
12: 51,820,618 (GRCm39) |
N1190K |
probably damaging |
Het |
| Hook3 |
T |
A |
8: 26,534,355 (GRCm39) |
|
probably benign |
Het |
| Hpgd |
T |
A |
8: 56,760,702 (GRCm39) |
I133N |
possibly damaging |
Het |
| Itih2 |
T |
C |
2: 10,102,714 (GRCm39) |
R807G |
probably benign |
Het |
| Klhl35 |
G |
A |
7: 99,122,094 (GRCm39) |
G65D |
probably damaging |
Het |
| Mafa |
A |
G |
15: 75,619,627 (GRCm39) |
S49P |
probably benign |
Het |
| Magi1 |
A |
G |
6: 93,662,584 (GRCm39) |
V1170A |
probably damaging |
Het |
| Mprip |
A |
T |
11: 59,649,380 (GRCm39) |
K1028M |
probably damaging |
Het |
| Mtpn |
C |
T |
6: 35,489,225 (GRCm39) |
D100N |
probably benign |
Het |
| Numb |
G |
T |
12: 83,923,521 (GRCm39) |
|
probably benign |
Het |
| Obscn |
A |
G |
11: 58,929,435 (GRCm39) |
L6063P |
probably damaging |
Het |
| Or2y6 |
A |
G |
11: 52,103,881 (GRCm39) |
*312Q |
probably null |
Het |
| Or6c6c |
A |
T |
10: 129,540,756 (GRCm39) |
N3I |
probably damaging |
Het |
| P3h3 |
A |
T |
6: 124,834,157 (GRCm39) |
|
probably null |
Het |
| Pi4k2a |
A |
G |
19: 42,103,477 (GRCm39) |
D329G |
probably benign |
Het |
| Ptch1 |
T |
C |
13: 63,713,268 (GRCm39) |
|
probably benign |
Het |
| Samd9l |
A |
G |
6: 3,376,754 (GRCm39) |
V169A |
probably benign |
Het |
| Sdk1 |
T |
C |
5: 142,100,148 (GRCm39) |
Y1393H |
probably damaging |
Het |
| Slc18a3 |
T |
A |
14: 32,185,880 (GRCm39) |
M168L |
probably benign |
Het |
| Smurf1 |
T |
C |
5: 144,816,190 (GRCm39) |
T722A |
probably damaging |
Het |
| Ssr2 |
C |
T |
3: 88,488,379 (GRCm39) |
P85L |
probably damaging |
Het |
| Syne2 |
G |
T |
12: 76,074,898 (GRCm39) |
A4614S |
probably benign |
Het |
| Tgfbr3 |
C |
A |
5: 107,288,521 (GRCm39) |
G380V |
possibly damaging |
Het |
| Tk1 |
G |
T |
11: 117,706,748 (GRCm39) |
|
probably benign |
Het |
| Tmem245 |
A |
T |
4: 56,903,241 (GRCm39) |
S610T |
probably benign |
Het |
| Tmtc2 |
A |
G |
10: 105,107,302 (GRCm39) |
|
probably benign |
Het |
| Trim30b |
A |
G |
7: 104,006,578 (GRCm39) |
Y93H |
possibly damaging |
Het |
| Tsks |
A |
G |
7: 44,593,412 (GRCm39) |
D126G |
probably damaging |
Het |
| Ttn |
T |
A |
2: 76,733,812 (GRCm39) |
|
probably benign |
Het |
| Usp15 |
A |
G |
10: 123,017,647 (GRCm39) |
W50R |
probably damaging |
Het |
| Vmn2r55 |
A |
T |
7: 12,404,492 (GRCm39) |
F304I |
probably benign |
Het |
| Xirp2 |
T |
A |
2: 67,339,587 (GRCm39) |
D609E |
probably damaging |
Het |
| Zan |
C |
T |
5: 137,392,638 (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 |
|
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 |
|
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 |
|
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'- AGCTGCTTCAGGGGACACTC -3'
(R):5'- TGATAAGCACTCGAAGGGGC -3'
Sequencing Primer
(F):5'- ACTCAGTCCCCATTGTGTGAGG -3'
(R):5'- AACGACGACAGCTGGTTC -3'
|
| Posted On |
2017-02-10 |
Incidental Mutation