Incidental Mutation 'IGL03083:Lgr5'
ID 417945
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Lgr5
Ensembl Gene ENSMUSG00000020140
Gene Name leucine rich repeat containing G protein coupled receptor 5
Synonyms Gpr49
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL03083
Quality Score
Status
Chromosome 10
Chromosomal Location 115286219-115423685 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 115288937 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 497 (V497A)
Ref Sequence ENSEMBL: ENSMUSP00000133707 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020350] [ENSMUST00000172806] [ENSMUST00000173740]
AlphaFold Q9Z1P4
Predicted Effect probably benign
Transcript: ENSMUST00000020350
AA Change: V569A

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000020350
Gene: ENSMUSG00000020140
AA Change: V569A

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: ENSMUST00000144732
Predicted Effect probably benign
Transcript: ENSMUST00000172806
AA Change: V545A

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000133860
Gene: ENSMUSG00000020140
AA Change: V545A

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 noncoding transcript
Transcript: ENSMUST00000173619
Predicted Effect probably benign
Transcript: ENSMUST00000173740
AA Change: V497A

PolyPhen 2 Score 0.262 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000133707
Gene: ENSMUSG00000020140
AA Change: V497A

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
Coding Region Coverage
Validation Efficiency
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: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca4 T A 3: 121,932,261 (GRCm39) probably null Het
Acadsb A C 7: 131,042,922 (GRCm39) probably benign Het
Ankk1 A G 9: 49,333,166 (GRCm39) L106P probably benign Het
Ankrd24 G A 10: 81,474,483 (GRCm39) A72T probably benign Het
Ankrd35 A T 3: 96,592,117 (GRCm39) Q801L probably damaging Het
Avil A G 10: 126,852,193 (GRCm39) I659M probably benign Het
Ccnc A G 4: 21,742,683 (GRCm39) D170G possibly damaging Het
Cfap57 T C 4: 118,441,936 (GRCm39) K711E probably damaging Het
Dctn1 T C 6: 83,174,466 (GRCm39) probably benign Het
Dpp6 T C 5: 27,914,548 (GRCm39) probably null Het
Efhb A T 17: 53,706,087 (GRCm39) W817R probably damaging Het
Emilin3 G A 2: 160,750,649 (GRCm39) Q320* probably null Het
Fer1l4 A G 2: 155,881,286 (GRCm39) probably benign Het
Fgf8 T C 19: 45,725,667 (GRCm39) N137S probably damaging Het
Fndc3b T C 3: 27,521,576 (GRCm39) D533G probably benign Het
Fshb A G 2: 106,887,812 (GRCm39) V69A probably benign Het
Galnt7 A T 8: 57,979,223 (GRCm39) H633Q probably damaging Het
Gm5458 A G 14: 19,652,451 (GRCm39) probably null Het
Hjv T A 3: 96,435,922 (GRCm39) D393E probably benign Het
Hpca A C 4: 129,012,319 (GRCm39) F72L probably damaging Het
Inpp5d A T 1: 87,638,863 (GRCm39) D552V probably damaging Het
Lepr C T 4: 101,671,876 (GRCm39) Q967* probably null Het
Matr3 A G 18: 35,705,471 (GRCm39) K132R probably damaging Het
Mib1 T G 18: 10,752,029 (GRCm39) probably null Het
Mios T A 6: 8,215,156 (GRCm39) N117K probably damaging Het
Nab1 T C 1: 52,529,429 (GRCm39) D156G probably benign Het
Nfxl1 C T 5: 72,698,005 (GRCm39) probably benign Het
Nutm2 G A 13: 50,621,480 (GRCm39) G15E probably damaging Het
Oca2 A G 7: 55,945,232 (GRCm39) H280R probably benign Het
Or10al2 C A 17: 37,983,551 (GRCm39) C212* probably null Het
Or4d1 T C 11: 87,804,914 (GRCm39) I273V probably benign Het
P2ry1 A G 3: 60,911,736 (GRCm39) T292A probably benign Het
Pcna C T 2: 132,093,673 (GRCm39) E109K probably benign Het
Pidd1 A G 7: 141,020,369 (GRCm39) probably null Het
Pitpnm2 T C 5: 124,271,445 (GRCm39) E376G possibly damaging Het
Pkd1l2 G A 8: 117,792,484 (GRCm39) T436I probably benign Het
Polr2a T C 11: 69,635,872 (GRCm39) probably null Het
Sbno2 A T 10: 79,893,368 (GRCm39) M1311K probably damaging Het
Senp7 A G 16: 55,992,228 (GRCm39) N701S probably benign Het
Sirpa T A 2: 129,471,848 (GRCm39) I211N probably damaging Het
Slc9a4 A G 1: 40,668,562 (GRCm39) E735G probably benign Het
Sorbs1 C T 19: 40,302,820 (GRCm39) M790I probably damaging Het
Sult1e1 T A 5: 87,737,983 (GRCm39) M33L probably benign Het
Tapbpl G A 6: 125,205,191 (GRCm39) probably null Het
Top1 A G 2: 160,545,498 (GRCm39) T289A probably damaging Het
Trim58 T A 11: 58,542,216 (GRCm39) M392K probably benign Het
Uaca A G 9: 60,770,945 (GRCm39) I371V probably benign Het
Vmn1r54 T C 6: 90,246,854 (GRCm39) I256T possibly damaging Het
Wdr19 T C 5: 65,388,319 (GRCm39) I668T 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
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
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
Posted On 2016-08-02