Incidental Mutation 'R3910:Lgr5'
| ID | 309347 |
|---|
| Institutional Source |
Beutler Lab
|
|---|
| Gene Symbol |
Lgr5
|
|---|
| Ensembl Gene |
ENSMUSG00000020140 |
|---|
| Gene Name | leucine rich repeat containing G protein coupled receptor 5 |
|---|
| Synonyms | Gpr49 |
|---|
| MMRRC Submission |
040815-MU
|
|---|
| Accession Numbers |
Ncbi RefSeq: NM_010195.2; MGI: 1341817
|
|---|
| Is this an essential gene? |
Essential (E-score: 1.000)
|
|---|
| Stock # | R3910 (G1)
|
|---|
| Quality Score | 163 |
|---|
| Status |
Validated
|
|---|
| Chromosome | 10 |
|---|
| Chromosomal Location | 115450311-115587780 bp(-) (GRCm38) |
|---|
| Type of Mutation | missense |
|---|
| DNA Base Change (assembly) |
A to G
at 115587463 bp
|
|---|
| Zygosity | Heterozygous |
|---|
| Amino Acid Change |
Serine to Proline
at position 11
(S11P)
|
|---|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133707
(fasta)
|
|---|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000020350]
[ENSMUST00000172806]
[ENSMUST00000173740]
|
|---|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000020350
AA Change: S11P
PolyPhen 2
Score 0.734 (Sensitivity: 0.85; Specificity: 0.92)
|
|---|
| SMART Domains |
Protein: ENSMUSP00000020350
Gene: ENSMUSG00000020140
AA Change: S11P
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
21 |
N/A |
INTRINSIC |
|
LRRNT
|
33 |
70 |
1.43e-5 |
SMART |
|
LRR
|
64 |
88 |
1.41e2 |
SMART |
|
LRR_TYP
|
89 |
112 |
3.44e-4 |
SMART |
|
LRR_TYP
|
113 |
136 |
9.88e-5 |
SMART |
|
LRR_TYP
|
137 |
160 |
9.73e-4 |
SMART |
|
LRR_TYP
|
161 |
184 |
5.21e-4 |
SMART |
|
LRR
|
185 |
208 |
6.22e0 |
SMART |
|
LRR_TYP
|
209 |
232 |
3.89e-3 |
SMART |
|
LRR
|
233 |
255 |
9.75e0 |
SMART |
|
LRR_TYP
|
256 |
279 |
1.38e-3 |
SMART |
|
Blast:LRR
|
281 |
303 |
2e-6 |
BLAST |
|
Blast:LRR
|
304 |
328 |
1e-5 |
BLAST |
|
LRR_TYP
|
351 |
374 |
1.56e-2 |
SMART |
|
LRR
|
375 |
396 |
1.09e2 |
SMART |
|
LRR_TYP
|
397 |
420 |
7.26e-3 |
SMART |
|
LRR
|
421 |
444 |
2.86e-1 |
SMART |
|
low complexity region
|
518 |
533 |
N/A |
INTRINSIC |
|
Pfam:7tm_1
|
574 |
820 |
9.5e-7 |
PFAM |
|
|---|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000105272
|
|---|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129309
|
|---|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149008
|
|---|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000172806
AA Change: S11P
PolyPhen 2
Score 0.930 (Sensitivity: 0.81; Specificity: 0.94)
|
|---|
| SMART Domains |
Protein: ENSMUSP00000133860
Gene: ENSMUSG00000020140
AA Change: S11P
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
21 |
N/A |
INTRINSIC |
|
LRRNT
|
33 |
70 |
1.43e-5 |
SMART |
|
LRR
|
64 |
88 |
1.41e2 |
SMART |
|
LRR_TYP
|
89 |
112 |
3.44e-4 |
SMART |
|
LRR_TYP
|
113 |
136 |
9.88e-5 |
SMART |
|
LRR_TYP
|
137 |
160 |
9.73e-4 |
SMART |
|
LRR_TYP
|
161 |
184 |
5.21e-4 |
SMART |
|
LRR
|
185 |
208 |
6.22e0 |
SMART |
|
LRR_TYP
|
209 |
232 |
3.89e-3 |
SMART |
|
LRR
|
233 |
255 |
9.75e0 |
SMART |
|
LRR
|
256 |
279 |
6.57e-1 |
SMART |
|
Blast:LRR
|
280 |
304 |
1e-5 |
BLAST |
|
LRR_TYP
|
327 |
350 |
1.56e-2 |
SMART |
|
LRR
|
351 |
372 |
1.09e2 |
SMART |
|
LRR_TYP
|
373 |
396 |
7.26e-3 |
SMART |
|
LRR
|
397 |
420 |
2.86e-1 |
SMART |
|
low complexity region
|
494 |
509 |
N/A |
INTRINSIC |
|
Pfam:7tm_1
|
550 |
796 |
8.2e-16 |
PFAM |
|
|---|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000173740
AA Change: S11P
PolyPhen 2
Score 0.930 (Sensitivity: 0.81; Specificity: 0.94)
|
|---|
| SMART Domains |
Protein: ENSMUSP00000133707
Gene: ENSMUSG00000020140
AA Change: S11P
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
21 |
N/A |
INTRINSIC |
|
LRRNT
|
33 |
70 |
1.43e-5 |
SMART |
|
LRR
|
64 |
88 |
1.41e2 |
SMART |
|
LRR_TYP
|
89 |
112 |
3.44e-4 |
SMART |
|
LRR_TYP
|
113 |
136 |
9.88e-5 |
SMART |
|
LRR_TYP
|
137 |
160 |
9.08e-4 |
SMART |
|
LRR
|
161 |
183 |
9.75e0 |
SMART |
|
LRR_TYP
|
184 |
207 |
1.38e-3 |
SMART |
|
Blast:LRR
|
209 |
231 |
1e-6 |
BLAST |
|
Blast:LRR
|
232 |
256 |
1e-5 |
BLAST |
|
LRR_TYP
|
279 |
302 |
1.56e-2 |
SMART |
|
LRR
|
303 |
324 |
1.09e2 |
SMART |
|
LRR_TYP
|
325 |
348 |
7.26e-3 |
SMART |
|
LRR
|
349 |
372 |
2.86e-1 |
SMART |
|
low complexity region
|
446 |
461 |
N/A |
INTRINSIC |
|
Pfam:7tm_1
|
502 |
748 |
7.4e-16 |
PFAM |
|
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| Meta Mutation Damage Score |
0.0991
|
|---|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.5%
|
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| Validation Efficiency |
97% (36/37) |
|---|
| MGI Phenotype |
Strain: 3512420
Lethality: D1-D2
FUNCTION: The protein encoded by this gene is a leucine-rich repeat-containing receptor (LGR) and member of the G protein-coupled, 7-transmembrane receptor (GPCR) superfamily. The encoded protein is a receptor for R-spondins and is involved in the canonical Wnt signaling pathway. This protein plays a role in the formation and maintenance of adult intestinal stem cells during postembryonic development. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mice homozygous for a knock-out allele display 100% neonatal lethality associated with ankyloglossia, gastrointestinal distension, cyanosis and respiratory failure. [provided by MGI curators]
|
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| Allele List at MGI |
All alleles(7) : Targeted(7)
|
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| Other mutations in this stock |
Total: 30 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700001C19Rik |
AC |
A |
17: 47,433,423 |
|
probably benign |
Het |
| 4931409K22Rik |
A |
T |
5: 24,545,442 |
|
probably benign |
Het |
| 9030624J02Rik |
A |
G |
7: 118,746,390 |
T49A |
possibly damaging |
Het |
| Bod1l |
T |
C |
5: 41,817,098 |
E2291G |
probably damaging |
Het |
| Cchcr1 |
T |
C |
17: 35,525,336 |
V341A |
probably damaging |
Het |
| Dsg1c |
T |
C |
18: 20,266,196 |
V119A |
possibly damaging |
Het |
| Fap |
A |
G |
2: 62,556,104 |
S58P |
probably damaging |
Het |
| Flnc |
A |
T |
6: 29,459,427 |
T2509S |
probably damaging |
Het |
| Fnip2 |
A |
T |
3: 79,479,505 |
D971E |
possibly damaging |
Het |
| Gab2 |
A |
G |
7: 97,299,073 |
Y290C |
probably damaging |
Het |
| Gm7104 |
C |
T |
12: 88,284,594 |
|
noncoding transcript |
Het |
| Ints10 |
T |
A |
8: 68,813,620 |
S478T |
probably damaging |
Het |
| Kirrel |
C |
T |
3: 87,089,151 |
M380I |
probably null |
Het |
| Krt90 |
G |
A |
15: 101,562,783 |
R15W |
probably damaging |
Het |
| Mycn |
T |
A |
12: 12,937,280 |
N372I |
probably damaging |
Het |
| Olfr459 |
A |
G |
6: 41,772,149 |
V50A |
probably benign |
Het |
| Olfr700 |
A |
T |
7: 106,805,865 |
V199D |
probably damaging |
Het |
| Paxbp1 |
T |
A |
16: 91,042,681 |
E117V |
probably damaging |
Het |
| Phc2 |
T |
C |
4: 128,743,558 |
|
probably null |
Het |
| Prr5 |
T |
A |
15: 84,703,144 |
V365E |
probably benign |
Het |
| Rev3l |
A |
G |
10: 39,820,556 |
I521M |
probably damaging |
Het |
| Robo3 |
A |
T |
9: 37,419,295 |
Y1002N |
probably damaging |
Het |
| Svep1 |
A |
T |
4: 58,145,156 |
|
probably null |
Het |
| Thsd7a |
A |
G |
6: 12,331,549 |
V1342A |
probably damaging |
Het |
| Tmtc3 |
A |
C |
10: 100,449,026 |
N582K |
probably damaging |
Het |
| Tnfrsf11b |
G |
A |
15: 54,256,182 |
|
probably benign |
Het |
| Trim30a |
A |
G |
7: 104,411,141 |
V476A |
probably damaging |
Het |
| Ugt1a8 |
A |
G |
1: 88,088,048 |
E61G |
possibly damaging |
Het |
| Vmn1r75 |
A |
T |
7: 11,880,830 |
N163I |
possibly damaging |
Het |
| Zfp119a |
G |
A |
17: 55,866,520 |
L108F |
probably benign |
Het |
|
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| Other mutations in Lgr5 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00341:Lgr5
|
APN |
10 |
115454464 |
missense |
possibly damaging |
0.69 |
|
IGL01291:Lgr5
|
APN |
10 |
115478534 |
missense |
probably damaging |
1.00 |
|
IGL01432:Lgr5
|
APN |
10 |
115453092 |
missense |
probably damaging |
1.00 |
|
IGL01778:Lgr5
|
APN |
10 |
115462702 |
missense |
probably damaging |
0.97 |
|
IGL01936:Lgr5
|
APN |
10 |
115452414 |
missense |
probably damaging |
1.00 |
|
IGL02079:Lgr5
|
APN |
10 |
115452194 |
missense |
probably damaging |
1.00 |
|
IGL02134:Lgr5
|
APN |
10 |
115452858 |
missense |
possibly damaging |
0.89 |
|
IGL03083:Lgr5
|
APN |
10 |
115453032 |
missense |
probably benign |
0.26 |
|
IGL03350:Lgr5
|
APN |
10 |
115471988 |
missense |
probably damaging |
0.99 |
|
anger
|
UTSW |
10 |
115466346 |
missense |
probably benign |
0.03 |
|
ANU05:Lgr5
|
UTSW |
10 |
115478534 |
missense |
probably damaging |
1.00 |
|
R0378:Lgr5
|
UTSW |
10 |
115454499 |
missense |
probably damaging |
1.00 |
|
R0788:Lgr5
|
UTSW |
10 |
115452997 |
missense |
probably damaging |
0.99 |
|
R1119:Lgr5
|
UTSW |
10 |
115460811 |
critical splice donor site |
probably null |
|
|
R1321:Lgr5
|
UTSW |
10 |
115478457 |
missense |
probably damaging |
1.00 |
|
R1880:Lgr5
|
UTSW |
10 |
115452279 |
missense |
probably damaging |
1.00 |
|
R1985:Lgr5
|
UTSW |
10 |
115495245 |
splice site |
probably benign |
|
|
R2434:Lgr5
|
UTSW |
10 |
115587406 |
missense |
probably benign |
|
|
R3055:Lgr5
|
UTSW |
10 |
115466123 |
splice site |
probably benign |
|
|
R4686:Lgr5
|
UTSW |
10 |
115458743 |
intron |
probably benign |
|
|
R4862:Lgr5
|
UTSW |
10 |
115462764 |
missense |
probably damaging |
1.00 |
|
R4866:Lgr5
|
UTSW |
10 |
115452685 |
missense |
probably benign |
0.00 |
|
R5089:Lgr5
|
UTSW |
10 |
115478423 |
missense |
probably damaging |
1.00 |
|
R5118:Lgr5
|
UTSW |
10 |
115452339 |
missense |
possibly damaging |
0.88 |
|
R5375:Lgr5
|
UTSW |
10 |
115478564 |
missense |
probably benign |
0.00 |
|
R5537:Lgr5
|
UTSW |
10 |
115456689 |
missense |
probably benign |
0.00 |
|
R5583:Lgr5
|
UTSW |
10 |
115478504 |
missense |
probably benign |
0.32 |
|
R6312:Lgr5
|
UTSW |
10 |
115452924 |
missense |
probably damaging |
1.00 |
|
R6362:Lgr5
|
UTSW |
10 |
115478525 |
missense |
probably damaging |
1.00 |
|
R6605:Lgr5
|
UTSW |
10 |
115457867 |
missense |
possibly damaging |
0.69 |
|
R6689:Lgr5
|
UTSW |
10 |
115466608 |
missense |
probably damaging |
0.99 |
|
R6705:Lgr5
|
UTSW |
10 |
115587288 |
missense |
probably damaging |
0.96 |
|
R6925:Lgr5
|
UTSW |
10 |
115466346 |
missense |
probably benign |
0.03 |
|
R7063:Lgr5
|
UTSW |
10 |
115456734 |
missense |
probably damaging |
1.00 |
|
R7261:Lgr5
|
UTSW |
10 |
115587465 |
missense |
possibly damaging |
0.96 |
|
R7274:Lgr5
|
UTSW |
10 |
115452505 |
missense |
probably damaging |
0.99 |
|
R7458:Lgr5
|
UTSW |
10 |
115457755 |
critical splice donor site |
probably null |
|
|
R7569:Lgr5
|
UTSW |
10 |
115462756 |
missense |
probably damaging |
1.00 |
|
R7770:Lgr5
|
UTSW |
10 |
115471994 |
missense |
probably damaging |
0.98 |
|
R7936:Lgr5
|
UTSW |
10 |
115453047 |
missense |
probably damaging |
0.99 |
|
R7964:Lgr5
|
UTSW |
10 |
115452174 |
missense |
probably benign |
0.00 |
|
R8085:Lgr5
|
UTSW |
10 |
115475197 |
missense |
probably benign |
|
|
R8537:Lgr5
|
UTSW |
10 |
115452402 |
missense |
probably damaging |
1.00 |
|
Z1176:Lgr5
|
UTSW |
10 |
115460876 |
missense |
probably damaging |
0.98 |
|
Z1177:Lgr5
|
UTSW |
10 |
115456669 |
missense |
probably benign |
0.00 |
|
|---|
| Predicted Primers |
PCR Primer
(F):5'- GTCACTTACAGGTAGGAGGTG -3'
(R):5'- TTTCACATCTCAGTCGCGGG -3'
Sequencing Primer
(F):5'- TCACTTACAGGTAGGAGGTGAAGAC -3'
(R):5'- TGGGACCACGATTCTCTGC -3'
|
|---|
| Posted On | 2015-04-17 |
|---|
