Incidental Mutation 'R4686:Lgr5'
| ID |
353685 |
| 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 |
041937-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4686 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
115286219-115423685 bp(-) (GRCm39) |
| Type of Mutation |
intron |
| DNA Base Change (assembly) |
A to G
at 115294648 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133707
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000020350]
[ENSMUST00000172806]
[ENSMUST00000173740]
|
| AlphaFold |
Q9Z1P4 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000020350
|
| SMART Domains |
Protein: ENSMUSP00000020350
Gene: ENSMUSG00000020140
| 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: ENSMUST00000144732
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000172806
|
| SMART Domains |
Protein: ENSMUSP00000133860
Gene: ENSMUSG00000020140
| 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 |
noncoding transcript
Transcript: ENSMUST00000173619
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173740
|
| SMART Domains |
Protein: ENSMUSP00000133707
Gene: ENSMUSG00000020140
| 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 |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 95.0%
|
| Validation Efficiency |
97% (68/70) |
| MGI Phenotype |
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]
|
| Allele List at MGI |
All alleles(7) : Targeted(7)
|
| Other mutations in this stock |
Total: 64 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamtsl2 |
A |
G |
2: 26,983,837 (GRCm39) |
N411S |
probably damaging |
Het |
| Adnp |
A |
C |
2: 168,024,309 (GRCm39) |
C995W |
possibly damaging |
Het |
| Akap6 |
CA |
C |
12: 52,934,406 (GRCm39) |
|
probably null |
Het |
| Ano2 |
T |
G |
6: 125,767,254 (GRCm39) |
I228M |
probably benign |
Het |
| Arhgap21 |
T |
C |
2: 20,868,033 (GRCm39) |
D830G |
probably damaging |
Het |
| Atp13a2 |
G |
A |
4: 140,730,587 (GRCm39) |
|
probably null |
Het |
| Ccdc175 |
C |
T |
12: 72,159,052 (GRCm39) |
S629N |
probably damaging |
Het |
| Cdhr4 |
T |
C |
9: 107,872,883 (GRCm39) |
W311R |
probably benign |
Het |
| Chaf1b |
A |
G |
16: 93,681,472 (GRCm39) |
H30R |
probably benign |
Het |
| Clnk |
G |
A |
5: 38,899,180 (GRCm39) |
|
probably benign |
Het |
| Copb1 |
A |
G |
7: 113,820,971 (GRCm39) |
S773P |
possibly damaging |
Het |
| Cse1l |
A |
G |
2: 166,774,080 (GRCm39) |
D198G |
probably damaging |
Het |
| Ears2 |
A |
G |
7: 121,647,427 (GRCm39) |
S286P |
probably damaging |
Het |
| Efcab7 |
A |
G |
4: 99,735,318 (GRCm39) |
E114G |
probably benign |
Het |
| Fanca |
G |
C |
8: 123,995,673 (GRCm39) |
|
probably benign |
Het |
| Flt3 |
A |
G |
5: 147,313,858 (GRCm39) |
L64P |
probably damaging |
Het |
| Gabrb1 |
A |
G |
5: 71,857,365 (GRCm39) |
T3A |
possibly damaging |
Het |
| Gm10384 |
T |
C |
15: 36,871,897 (GRCm39) |
|
noncoding transcript |
Het |
| Gm5117 |
G |
A |
8: 32,229,284 (GRCm39) |
|
noncoding transcript |
Het |
| Gpr141 |
T |
A |
13: 19,935,951 (GRCm39) |
I275F |
probably benign |
Het |
| Greb1l |
A |
T |
18: 10,522,112 (GRCm39) |
E736V |
probably damaging |
Het |
| Hc |
T |
C |
2: 34,929,260 (GRCm39) |
E279G |
possibly damaging |
Het |
| Hivep1 |
C |
T |
13: 42,309,326 (GRCm39) |
T522M |
probably benign |
Het |
| Hspa12a |
T |
A |
19: 58,788,181 (GRCm39) |
E547V |
possibly damaging |
Het |
| Il10ra |
A |
G |
9: 45,180,357 (GRCm39) |
L5S |
probably damaging |
Het |
| Iqcf6 |
G |
T |
9: 106,504,543 (GRCm39) |
W69L |
probably damaging |
Het |
| Iqgap2 |
T |
C |
13: 95,858,117 (GRCm39) |
N379S |
probably damaging |
Het |
| Itpr2 |
A |
G |
6: 146,131,273 (GRCm39) |
I1977T |
probably damaging |
Het |
| Kcnq1 |
A |
T |
7: 142,661,466 (GRCm39) |
Y124F |
probably benign |
Het |
| Lamp5 |
C |
T |
2: 135,900,923 (GRCm39) |
T41M |
probably damaging |
Het |
| Mlec |
A |
G |
5: 115,288,355 (GRCm39) |
I167T |
possibly damaging |
Het |
| Myf6 |
A |
G |
10: 107,329,689 (GRCm39) |
V198A |
probably benign |
Het |
| Nceh1 |
C |
T |
3: 27,295,818 (GRCm39) |
R360C |
probably damaging |
Het |
| Nos2 |
C |
A |
11: 78,819,456 (GRCm39) |
T56N |
possibly damaging |
Het |
| Npw |
T |
G |
17: 24,876,386 (GRCm39) |
H175P |
probably benign |
Het |
| Nrxn3 |
A |
T |
12: 89,477,421 (GRCm39) |
I899F |
probably damaging |
Het |
| Ociad1 |
A |
G |
5: 73,464,078 (GRCm39) |
T179A |
possibly damaging |
Het |
| Or1e19 |
A |
G |
11: 73,316,264 (GRCm39) |
S182P |
probably benign |
Het |
| Or52b4 |
A |
G |
7: 102,184,356 (GRCm39) |
Y134C |
probably damaging |
Het |
| Or8b48 |
T |
A |
9: 38,493,327 (GRCm39) |
F251L |
probably damaging |
Het |
| Pacsin2 |
T |
C |
15: 83,265,976 (GRCm39) |
N74D |
probably benign |
Het |
| Pcdh7 |
A |
G |
5: 58,286,511 (GRCm39) |
I1196V |
probably benign |
Het |
| Pdxk |
A |
T |
10: 78,282,837 (GRCm39) |
|
probably null |
Het |
| Phb2 |
G |
A |
6: 124,690,105 (GRCm39) |
|
probably null |
Het |
| Pus7l |
T |
A |
15: 94,438,092 (GRCm39) |
N251I |
probably damaging |
Het |
| Rgs7bp |
T |
A |
13: 105,100,597 (GRCm39) |
N226I |
probably damaging |
Het |
| Runx2 |
T |
A |
17: 44,950,572 (GRCm39) |
D327V |
probably damaging |
Het |
| Srp68 |
A |
T |
11: 116,156,227 (GRCm39) |
C172S |
probably damaging |
Het |
| Stk25 |
A |
G |
1: 93,551,142 (GRCm39) |
|
probably null |
Het |
| Tbrg4 |
C |
T |
11: 6,568,468 (GRCm39) |
R437Q |
probably benign |
Het |
| Tedc2 |
C |
T |
17: 24,436,862 (GRCm39) |
|
probably null |
Het |
| Teddm1a |
T |
A |
1: 153,768,196 (GRCm39) |
I220N |
probably damaging |
Het |
| Thoc1 |
G |
T |
18: 9,970,312 (GRCm39) |
E221* |
probably null |
Het |
| Tmem132d |
G |
T |
5: 127,869,674 (GRCm39) |
D553E |
possibly damaging |
Het |
| Topors |
A |
T |
4: 40,261,694 (GRCm39) |
V530D |
probably benign |
Het |
| Tpx2 |
T |
C |
2: 152,731,103 (GRCm39) |
V515A |
possibly damaging |
Het |
| Trim24 |
A |
G |
6: 37,885,240 (GRCm39) |
H191R |
probably damaging |
Het |
| Ttn |
G |
A |
2: 76,567,914 (GRCm39) |
R27660W |
probably damaging |
Het |
| Vmn1r203 |
T |
C |
13: 22,708,528 (GRCm39) |
L103P |
probably damaging |
Het |
| Vmn1r233 |
C |
T |
17: 21,214,368 (GRCm39) |
S194N |
probably benign |
Het |
| Vmn2r108 |
T |
C |
17: 20,691,636 (GRCm39) |
K296E |
probably damaging |
Het |
| Vmn2r88 |
G |
A |
14: 51,650,796 (GRCm39) |
E170K |
probably benign |
Het |
| Zfp740 |
C |
T |
15: 102,117,184 (GRCm39) |
|
probably benign |
Het |
| Zmym5 |
A |
G |
14: 57,049,618 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Lgr5 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00341:Lgr5
|
APN |
10 |
115,290,369 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
IGL01291:Lgr5
|
APN |
10 |
115,314,439 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01432:Lgr5
|
APN |
10 |
115,288,997 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01778:Lgr5
|
APN |
10 |
115,298,607 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL01936:Lgr5
|
APN |
10 |
115,288,319 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02079:Lgr5
|
APN |
10 |
115,288,099 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02134:Lgr5
|
APN |
10 |
115,288,763 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
IGL03083:Lgr5
|
APN |
10 |
115,288,937 (GRCm39) |
missense |
probably benign |
0.26 |
|
IGL03350:Lgr5
|
APN |
10 |
115,307,893 (GRCm39) |
missense |
probably damaging |
0.99 |
|
anger
|
UTSW |
10 |
115,302,251 (GRCm39) |
missense |
probably benign |
0.03 |
|
ANU05:Lgr5
|
UTSW |
10 |
115,314,439 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0378:Lgr5
|
UTSW |
10 |
115,290,404 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0788:Lgr5
|
UTSW |
10 |
115,288,902 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1119:Lgr5
|
UTSW |
10 |
115,296,716 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1321:Lgr5
|
UTSW |
10 |
115,314,362 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1880:Lgr5
|
UTSW |
10 |
115,288,184 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1985:Lgr5
|
UTSW |
10 |
115,331,150 (GRCm39) |
splice site |
probably benign |
|
|
R2434:Lgr5
|
UTSW |
10 |
115,423,311 (GRCm39) |
missense |
probably benign |
|
|
R3055:Lgr5
|
UTSW |
10 |
115,302,028 (GRCm39) |
splice site |
probably benign |
|
|
R3910:Lgr5
|
UTSW |
10 |
115,423,368 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R4862:Lgr5
|
UTSW |
10 |
115,298,669 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4866:Lgr5
|
UTSW |
10 |
115,288,590 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5089:Lgr5
|
UTSW |
10 |
115,314,328 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5118:Lgr5
|
UTSW |
10 |
115,288,244 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R5375:Lgr5
|
UTSW |
10 |
115,314,469 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5537:Lgr5
|
UTSW |
10 |
115,292,594 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5583:Lgr5
|
UTSW |
10 |
115,314,409 (GRCm39) |
missense |
probably benign |
0.32 |
|
R6312:Lgr5
|
UTSW |
10 |
115,288,829 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6362:Lgr5
|
UTSW |
10 |
115,314,430 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6605:Lgr5
|
UTSW |
10 |
115,293,772 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R6689:Lgr5
|
UTSW |
10 |
115,302,513 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6705:Lgr5
|
UTSW |
10 |
115,423,193 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6925:Lgr5
|
UTSW |
10 |
115,302,251 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7063:Lgr5
|
UTSW |
10 |
115,292,639 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7261:Lgr5
|
UTSW |
10 |
115,423,370 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
R7274:Lgr5
|
UTSW |
10 |
115,288,410 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7458:Lgr5
|
UTSW |
10 |
115,293,660 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7569:Lgr5
|
UTSW |
10 |
115,298,661 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7770:Lgr5
|
UTSW |
10 |
115,307,899 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7936:Lgr5
|
UTSW |
10 |
115,288,952 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7964:Lgr5
|
UTSW |
10 |
115,288,079 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8085:Lgr5
|
UTSW |
10 |
115,311,102 (GRCm39) |
missense |
probably benign |
|
|
R8537:Lgr5
|
UTSW |
10 |
115,288,307 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8703:Lgr5
|
UTSW |
10 |
115,288,610 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8704:Lgr5
|
UTSW |
10 |
115,288,610 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8706:Lgr5
|
UTSW |
10 |
115,288,610 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8707:Lgr5
|
UTSW |
10 |
115,288,610 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9019:Lgr5
|
UTSW |
10 |
115,314,454 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9043:Lgr5
|
UTSW |
10 |
115,314,343 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9215:Lgr5
|
UTSW |
10 |
115,311,085 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9217:Lgr5
|
UTSW |
10 |
115,423,349 (GRCm39) |
missense |
probably benign |
0.33 |
|
R9427:Lgr5
|
UTSW |
10 |
115,288,913 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9631:Lgr5
|
UTSW |
10 |
115,302,513 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9738:Lgr5
|
UTSW |
10 |
115,288,527 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Lgr5
|
UTSW |
10 |
115,296,781 (GRCm39) |
missense |
probably damaging |
0.98 |
|
Z1177:Lgr5
|
UTSW |
10 |
115,292,574 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGAGCATCTTCCTTGGCCAG -3'
(R):5'- ACAGGGCTGATTTGAAGTTCTG -3'
Sequencing Primer
(F):5'- CAGCACACTGGCTATACATTGGG -3'
(R):5'- GGTTGGCTAGATACTGGATA -3'
|
| Posted On |
2015-10-21 |
Incidental Mutation