Incidental Mutation 'R7063:Lgr5'
| ID |
548405 |
| 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 |
045159-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R7063 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
115286219-115423685 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 115292639 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 417
(Y417C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133707
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000020350]
[ENSMUST00000172806]
[ENSMUST00000173740]
|
| AlphaFold |
Q9Z1P4 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000020350
AA Change: Y489C
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000020350
Gene: ENSMUSG00000020140
AA Change: Y489C
| 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 |
probably damaging
Transcript: ENSMUST00000172806
AA Change: Y465C
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000133860
Gene: ENSMUSG00000020140
AA Change: Y465C
| 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 damaging
Transcript: ENSMUST00000173740
AA Change: Y417C
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000133707
Gene: ENSMUSG00000020140
AA Change: Y417C
| 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 |
0.1752 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.0%
|
| Validation Efficiency |
100% (43/43) |
| 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: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Arhgap35 |
A |
G |
7: 16,299,038 (GRCm39) |
V9A |
probably benign |
Het |
| Btbd6 |
A |
G |
12: 112,941,132 (GRCm39) |
Y148C |
probably damaging |
Het |
| Casr |
T |
C |
16: 36,314,936 (GRCm39) |
I968V |
probably benign |
Het |
| Celf1 |
T |
C |
2: 90,843,189 (GRCm39) |
|
probably null |
Het |
| Chst2 |
G |
T |
9: 95,287,621 (GRCm39) |
R242S |
probably benign |
Het |
| Clca3a1 |
T |
A |
3: 144,460,967 (GRCm39) |
D228V |
probably damaging |
Het |
| Cwf19l2 |
A |
G |
9: 3,430,532 (GRCm39) |
Y288C |
probably benign |
Het |
| Cyp2r1 |
A |
G |
7: 114,152,184 (GRCm39) |
S49P |
probably damaging |
Het |
| Dnah5 |
A |
G |
15: 28,233,394 (GRCm39) |
E251G |
probably benign |
Het |
| Eepd1 |
A |
G |
9: 25,394,332 (GRCm39) |
R199G |
possibly damaging |
Het |
| Fat1 |
C |
T |
8: 45,493,812 (GRCm39) |
T3986I |
probably benign |
Het |
| Gbp4 |
G |
A |
5: 105,266,314 (GRCm39) |
R576C |
probably damaging |
Het |
| Glp1r |
A |
G |
17: 31,144,532 (GRCm39) |
Y235C |
probably damaging |
Het |
| Gm6408 |
T |
C |
5: 146,420,594 (GRCm39) |
I158T |
probably benign |
Het |
| Gpr89 |
C |
G |
3: 96,783,014 (GRCm39) |
R312P |
probably damaging |
Het |
| Idh2 |
A |
G |
7: 79,745,432 (GRCm39) |
V403A |
probably damaging |
Het |
| Lclat1 |
A |
G |
17: 73,546,986 (GRCm39) |
E301G |
possibly damaging |
Het |
| Lgmn |
A |
G |
12: 102,368,937 (GRCm39) |
Y181H |
probably damaging |
Het |
| Man1a |
G |
T |
10: 53,906,840 (GRCm39) |
N311K |
probably damaging |
Het |
| Nat10 |
G |
A |
2: 103,578,422 (GRCm39) |
L228F |
probably benign |
Het |
| Or10d3 |
T |
G |
9: 39,461,411 (GRCm39) |
Y252S |
possibly damaging |
Het |
| Or10v5 |
A |
G |
19: 11,805,548 (GRCm39) |
F281L |
probably damaging |
Het |
| Or5b12b |
A |
G |
19: 12,861,449 (GRCm39) |
D68G |
probably damaging |
Het |
| Or5p55 |
C |
A |
7: 107,567,411 (GRCm39) |
A269E |
probably benign |
Het |
| Pcmtd2 |
T |
A |
2: 181,496,776 (GRCm39) |
Y130* |
probably null |
Het |
| Potefam3f |
G |
A |
8: 20,479,013 (GRCm39) |
C7Y |
|
Het |
| Qrfprl |
A |
G |
6: 65,418,387 (GRCm39) |
|
probably benign |
Het |
| Rapgef5 |
A |
G |
12: 117,652,864 (GRCm39) |
D62G |
possibly damaging |
Het |
| Serpina3m |
A |
T |
12: 104,357,726 (GRCm39) |
I217L |
probably benign |
Het |
| Supt16 |
T |
C |
14: 52,409,505 (GRCm39) |
R802G |
possibly damaging |
Het |
| Sypl2 |
A |
T |
3: 108,124,971 (GRCm39) |
M130K |
probably benign |
Het |
| Tmtc2 |
A |
T |
10: 105,184,386 (GRCm39) |
L503Q |
probably damaging |
Het |
| Ubald2 |
A |
G |
11: 116,325,443 (GRCm39) |
Q60R |
probably benign |
Het |
| Vav1 |
C |
T |
17: 57,618,860 (GRCm39) |
Q673* |
probably null |
Het |
| Vgll2 |
T |
C |
10: 51,904,072 (GRCm39) |
S312P |
probably benign |
Het |
| Vmn1r191 |
C |
T |
13: 22,362,864 (GRCm39) |
A297T |
probably benign |
Het |
| Vmn1r7 |
T |
A |
6: 57,001,418 (GRCm39) |
I281F |
possibly damaging |
Het |
| Vmn2r108 |
T |
C |
17: 20,701,410 (GRCm39) |
Y30C |
probably damaging |
Het |
| Vmn2r16 |
A |
G |
5: 109,511,650 (GRCm39) |
N619S |
probably damaging |
Het |
| Vstm5 |
A |
G |
9: 15,150,549 (GRCm39) |
|
probably benign |
Het |
| Zfp7 |
A |
G |
15: 76,775,919 (GRCm39) |
I654V |
possibly damaging |
Het |
| Zmat2 |
A |
G |
18: 36,929,627 (GRCm39) |
N129S |
probably null |
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 |
|
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 |
|
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'- TCCATTTGCTGGGTGATTACAC -3'
(R):5'- AGGAACACCATTGTGCAAATAGC -3'
Sequencing Primer
(F):5'- GCTTTCAGGGTCCATGTA -3'
(R):5'- GGTAACTGGTTTAGGTTAAACTTCC -3'
|
| Posted On |
2019-05-13 |
Incidental Mutation