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
Essential gene? Essential (E-score: 1.000) question?
Stock # R3910 (G1)
Quality Score 163
Status Validated
Chromosome 10
Chromosomal Location 115286219-115423685 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 115423368 bp (GRCm39)
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]
AlphaFold Q9Z1P4
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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 0.0991 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency 97% (36/37)
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: 30 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Bod1l T C 5: 41,974,441 (GRCm39) E2291G probably damaging Het
Cchcr1 T C 17: 35,836,233 (GRCm39) V341A probably damaging Het
Cimip3 AC A 17: 47,744,348 (GRCm39) probably benign Het
Dsg1c T C 18: 20,399,253 (GRCm39) V119A possibly damaging Het
Fap A G 2: 62,386,448 (GRCm39) S58P probably damaging Het
Flnc A T 6: 29,459,426 (GRCm39) T2509S probably damaging Het
Fnip2 A T 3: 79,386,812 (GRCm39) D971E possibly damaging Het
Gab2 A G 7: 96,948,280 (GRCm39) Y290C probably damaging Het
Gm7104 C T 12: 88,251,364 (GRCm39) noncoding transcript Het
Ints10 T A 8: 69,266,272 (GRCm39) S478T probably damaging Het
Iqca1l A T 5: 24,750,440 (GRCm39) probably benign Het
Kirrel1 C T 3: 86,996,458 (GRCm39) M380I probably null Het
Krt90 G A 15: 101,471,218 (GRCm39) R15W probably damaging Het
Mycn T A 12: 12,987,281 (GRCm39) N372I probably damaging Het
Or2ag18 A T 7: 106,405,072 (GRCm39) V199D probably damaging Het
Or9a2 A G 6: 41,749,083 (GRCm39) V50A probably benign Het
Paxbp1 T A 16: 90,839,569 (GRCm39) E117V probably damaging Het
Phc2 T C 4: 128,637,351 (GRCm39) probably null Het
Prr5 T A 15: 84,587,345 (GRCm39) V365E probably benign Het
Rev3l A G 10: 39,696,552 (GRCm39) I521M probably damaging Het
Robo3 A T 9: 37,330,591 (GRCm39) Y1002N probably damaging Het
Svep1 A T 4: 58,145,156 (GRCm39) probably null Het
Thsd7a A G 6: 12,331,548 (GRCm39) V1342A probably damaging Het
Tmtc3 A C 10: 100,284,888 (GRCm39) N582K probably damaging Het
Tnfrsf11b G A 15: 54,119,578 (GRCm39) probably benign Het
Trim30a A G 7: 104,060,348 (GRCm39) V476A probably damaging Het
Ugt1a8 A G 1: 88,015,770 (GRCm39) E61G possibly damaging Het
Vmn1r75 A T 7: 11,614,757 (GRCm39) N163I possibly damaging Het
Vps35l A G 7: 118,345,613 (GRCm39) T49A possibly damaging Het
Zfp119a G A 17: 56,173,520 (GRCm39) L108F probably benign Het
Other mutations in Lgr5
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- GTCACTTACAGGTAGGAGGTG -3'
(R):5'- TTTCACATCTCAGTCGCGGG -3'

Sequencing Primer
(F):5'- TCACTTACAGGTAGGAGGTGAAGAC -3'
(R):5'- TGGGACCACGATTCTCTGC -3'
Posted On 2015-04-17