Incidental Mutation 'R5583:Lgr5'
| ID |
438575 |
| 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 |
043137-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5583 (G1)
|
| Quality Score |
219 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
115286219-115423685 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 115314409 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 176
(D176G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133860
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000020350]
[ENSMUST00000172806]
[ENSMUST00000173740]
|
| AlphaFold |
Q9Z1P4 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000020350
AA Change: D176G
PolyPhen 2
Score 0.098 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000020350
Gene: ENSMUSG00000020140
AA Change: D176G
| 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: ENSMUST00000149008
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000172806
AA Change: D176G
PolyPhen 2
Score 0.321 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000133860
Gene: ENSMUSG00000020140
AA Change: D176G
| 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 |
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: 99.9%
- 3x: 99.6%
- 10x: 98.4%
- 20x: 95.4%
|
| Validation Efficiency |
97% (60/62) |
| 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: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A1bg |
A |
T |
15: 60,793,083 (GRCm39) |
L8Q |
probably damaging |
Het |
| Abca4 |
T |
C |
3: 121,942,550 (GRCm39) |
V1681A |
probably damaging |
Het |
| Abce1 |
G |
T |
8: 80,416,922 (GRCm39) |
A363E |
probably benign |
Het |
| Adgrl2 |
T |
C |
3: 148,564,800 (GRCm39) |
Y256C |
probably damaging |
Het |
| Afm |
T |
C |
5: 90,695,740 (GRCm39) |
C416R |
probably damaging |
Het |
| Ahnak |
T |
A |
19: 8,984,281 (GRCm39) |
V1855D |
probably damaging |
Het |
| Alb |
A |
T |
5: 90,616,452 (GRCm39) |
H319L |
probably benign |
Het |
| Ankrd35 |
G |
T |
3: 96,592,219 (GRCm39) |
R835L |
probably damaging |
Het |
| Atg2b |
T |
C |
12: 105,615,414 (GRCm39) |
D1014G |
possibly damaging |
Het |
| Cdk6 |
T |
A |
5: 3,394,436 (GRCm39) |
Y24N |
probably damaging |
Het |
| Chd7 |
T |
A |
4: 8,752,473 (GRCm39) |
N323K |
probably damaging |
Het |
| Cops9 |
A |
T |
1: 92,567,489 (GRCm39) |
|
probably benign |
Het |
| Crybg1 |
T |
C |
10: 43,879,506 (GRCm39) |
T561A |
probably benign |
Het |
| Dcdc5 |
T |
C |
2: 106,195,778 (GRCm39) |
|
noncoding transcript |
Het |
| Dnah7b |
G |
T |
1: 46,281,359 (GRCm39) |
A2807S |
probably benign |
Het |
| Fam149b |
A |
G |
14: 20,413,368 (GRCm39) |
T196A |
possibly damaging |
Het |
| Fam217a |
C |
A |
13: 35,094,280 (GRCm39) |
C402F |
probably damaging |
Het |
| Fat2 |
A |
T |
11: 55,144,715 (GRCm39) |
V4053E |
probably benign |
Het |
| Fcgbp |
T |
C |
7: 27,791,004 (GRCm39) |
V755A |
probably damaging |
Het |
| Fxr1 |
C |
A |
3: 34,123,125 (GRCm39) |
S641R |
probably benign |
Het |
| Gata5 |
A |
T |
2: 179,976,047 (GRCm39) |
M39K |
probably benign |
Het |
| Gon4l |
T |
A |
3: 88,807,278 (GRCm39) |
D1658E |
probably damaging |
Het |
| Gpr180 |
C |
T |
14: 118,400,110 (GRCm39) |
T426M |
probably damaging |
Het |
| Gtf2h3 |
C |
T |
5: 124,722,360 (GRCm39) |
T121I |
probably benign |
Het |
| Helq |
T |
C |
5: 100,910,459 (GRCm39) |
E1039G |
probably damaging |
Het |
| Hibch |
T |
A |
1: 52,940,406 (GRCm39) |
Y192N |
probably damaging |
Het |
| Hp1bp3 |
A |
G |
4: 137,949,426 (GRCm39) |
I41M |
probably damaging |
Het |
| Itpripl2 |
G |
T |
7: 118,089,101 (GRCm39) |
P486Q |
probably benign |
Het |
| Kcnj6 |
T |
C |
16: 94,634,060 (GRCm39) |
D17G |
probably benign |
Het |
| Kprp |
T |
A |
3: 92,731,643 (GRCm39) |
Y469F |
unknown |
Het |
| Kremen2 |
T |
C |
17: 23,961,229 (GRCm39) |
T373A |
probably benign |
Het |
| Lgi4 |
A |
G |
7: 30,760,562 (GRCm39) |
Y39C |
possibly damaging |
Het |
| Lrp1 |
T |
C |
10: 127,424,332 (GRCm39) |
S785G |
probably benign |
Het |
| Ltbp1 |
A |
T |
17: 75,598,325 (GRCm39) |
Q920L |
probably benign |
Het |
| Map2 |
A |
G |
1: 66,455,196 (GRCm39) |
E1362G |
probably damaging |
Het |
| Nkx2-6 |
T |
C |
14: 69,409,272 (GRCm39) |
S8P |
probably damaging |
Het |
| Or2h1b |
T |
C |
17: 37,462,485 (GRCm39) |
Q126R |
probably benign |
Het |
| Pde4dip |
C |
T |
3: 97,654,892 (GRCm39) |
R888Q |
possibly damaging |
Het |
| Per1 |
A |
G |
11: 68,994,271 (GRCm39) |
H494R |
probably damaging |
Het |
| Pira2 |
A |
G |
7: 3,845,545 (GRCm39) |
F280L |
probably benign |
Het |
| Plekhm3 |
C |
T |
1: 64,977,145 (GRCm39) |
W108* |
probably null |
Het |
| Ptcd3 |
A |
G |
6: 71,879,920 (GRCm39) |
S113P |
probably damaging |
Het |
| Scarf1 |
T |
C |
11: 75,404,842 (GRCm39) |
L42P |
possibly damaging |
Het |
| Scart2 |
G |
A |
7: 139,876,739 (GRCm39) |
C710Y |
probably damaging |
Het |
| Skint1 |
A |
C |
4: 111,876,253 (GRCm39) |
Q58P |
probably damaging |
Het |
| Spata7 |
A |
T |
12: 98,635,590 (GRCm39) |
N438I |
probably damaging |
Het |
| Spdya |
C |
A |
17: 71,876,126 (GRCm39) |
D164E |
probably damaging |
Het |
| Speer3 |
G |
A |
5: 13,844,782 (GRCm39) |
|
probably null |
Het |
| Ssc4d |
A |
T |
5: 135,999,050 (GRCm39) |
L51H |
probably damaging |
Het |
| Steap1 |
A |
G |
5: 5,790,579 (GRCm39) |
I123T |
possibly damaging |
Het |
| Styx |
T |
A |
14: 45,608,483 (GRCm39) |
F147I |
possibly damaging |
Het |
| Suv39h2 |
T |
A |
2: 3,475,890 (GRCm39) |
|
probably benign |
Het |
| Tfb2m |
A |
G |
1: 179,373,446 (GRCm39) |
V84A |
probably benign |
Het |
| Tlcd1 |
T |
G |
11: 78,069,762 (GRCm39) |
V25G |
probably benign |
Het |
| Tmem79 |
T |
C |
3: 88,239,870 (GRCm39) |
Y280C |
probably damaging |
Het |
| Trim5 |
T |
A |
7: 103,926,042 (GRCm39) |
N173I |
probably damaging |
Het |
| Ttc17 |
A |
T |
2: 94,208,027 (GRCm39) |
D194E |
probably damaging |
Het |
| Zfp2 |
T |
C |
11: 50,790,984 (GRCm39) |
E353G |
possibly damaging |
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 |
|
R4686:Lgr5
|
UTSW |
10 |
115,294,648 (GRCm39) |
intron |
probably benign |
|
|
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 |
|
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'- TTTGAGGTCCATCACTTGAAGGC -3'
(R):5'- ACAGTCTGATTTGCTCTGCC -3'
Sequencing Primer
(F):5'- GGTCCATCACTTGAAGGCTAAGATC -3'
(R):5'- GCTCTGCCTAATGAGCACATG -3'
|
| Posted On |
2016-10-26 |
Incidental Mutation