Incidental Mutation 'R4513:Lgr4'
ID 334499
Institutional Source Beutler Lab
Gene Symbol Lgr4
Ensembl Gene ENSMUSG00000050199
Gene Name leucine-rich repeat-containing G protein-coupled receptor 4
Synonyms Gpr48, A330106J01Rik, A930009A08Rik
MMRRC Submission 041759-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4513 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 109747992-109844602 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 109842361 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Threonine at position 782 (M782T)
Ref Sequence ENSEMBL: ENSMUSP00000047325 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046548] [ENSMUST00000111037]
AlphaFold A2ARI4
Predicted Effect possibly damaging
Transcript: ENSMUST00000046548
AA Change: M782T

PolyPhen 2 Score 0.929 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000047325
Gene: ENSMUSG00000050199
AA Change: M782T

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
LRRNT 28 61 6.68e-6 SMART
LRR 55 79 1.49e1 SMART
LRR 80 103 1.99e0 SMART
LRR_TYP 104 127 2.75e-3 SMART
LRR_TYP 128 151 2.79e-4 SMART
LRR 152 175 2.54e1 SMART
LRR 176 199 4.65e-1 SMART
LRR_TYP 200 223 1.04e-3 SMART
LRR 224 246 6.4e0 SMART
LRR_TYP 247 270 5.99e-4 SMART
LRR 272 294 9.77e1 SMART
LRR 318 341 3e1 SMART
LRR 343 363 4.71e1 SMART
LRR 364 387 1.49e1 SMART
LRR_TYP 388 411 1.15e-5 SMART
LRR 412 435 3.98e1 SMART
low complexity region 500 516 N/A INTRINSIC
Pfam:7tm_1 555 801 2.7e-10 PFAM
low complexity region 824 837 N/A INTRINSIC
low complexity region 910 924 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000111037
AA Change: M758T

PolyPhen 2 Score 0.657 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000106666
Gene: ENSMUSG00000050199
AA Change: M758T

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
LRRNT 28 61 6.68e-6 SMART
LRR 55 79 9.77e1 SMART
LRR_TYP 80 103 2.75e-3 SMART
LRR_TYP 104 127 2.79e-4 SMART
LRR 128 151 2.54e1 SMART
LRR 152 175 4.65e-1 SMART
LRR_TYP 176 199 1.04e-3 SMART
LRR 200 222 6.4e0 SMART
LRR_TYP 223 246 5.99e-4 SMART
LRR 248 270 9.77e1 SMART
LRR 294 317 3e1 SMART
LRR 319 339 4.71e1 SMART
LRR 340 363 1.49e1 SMART
LRR_TYP 364 387 1.15e-5 SMART
LRR 388 411 3.98e1 SMART
low complexity region 476 492 N/A INTRINSIC
Pfam:7tm_1 531 777 9.3e-17 PFAM
low complexity region 800 813 N/A INTRINSIC
low complexity region 886 900 N/A INTRINSIC
Meta Mutation Damage Score 0.0700 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.6%
  • 10x: 96.9%
  • 20x: 94.0%
Validation Efficiency 100% (56/56)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a G-protein coupled receptor that binds R-spondins and activates the Wnt signaling pathway. This Wnt signaling pathway activation is necessary for proper development of many organs of the body. [provided by RefSeq, Oct 2016]
PHENOTYPE: Homozygotes for a knock-out allele show embryonic and perinatal death, open eyelids, and abnormal renal development. One gene trap mutation leads to reduced body weight, sterility, and impaired male reproductive tract development. Another gene trap mutation causes ocular anterior segment anomalies. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgre1 A G 17: 57,717,947 (GRCm39) I320V probably benign Het
Akap6 T C 12: 52,842,787 (GRCm39) V45A probably benign Het
Ankrd28 A T 14: 31,465,242 (GRCm39) S312T probably damaging Het
Cenpn A G 8: 117,660,135 (GRCm39) Y68C probably damaging Het
Cfap96 G T 8: 46,421,175 (GRCm39) T116K probably damaging Het
Cntn3 A T 6: 102,145,943 (GRCm39) I966N probably benign Het
D630003M21Rik T C 2: 158,046,722 (GRCm39) T752A probably benign Het
Dmxl2 A C 9: 54,327,168 (GRCm39) S952R probably null Het
Dop1a G A 9: 86,402,612 (GRCm39) E1271K probably benign Het
Fgfr3 A G 5: 33,880,460 (GRCm39) probably benign Het
Gm10110 A G 14: 90,135,151 (GRCm39) noncoding transcript Het
Got1l1 C T 8: 27,688,513 (GRCm39) M279I probably benign Het
Guf1 T C 5: 69,719,005 (GRCm39) V230A probably benign Het
Hsd17b14 C T 7: 45,212,339 (GRCm39) L124F probably benign Het
Id3 G T 4: 135,871,669 (GRCm39) probably benign Het
Itga8 T C 2: 12,187,547 (GRCm39) S711G probably benign Het
Lsm12 T C 11: 102,057,909 (GRCm39) probably null Het
Map1b T A 13: 99,580,741 (GRCm39) D117V probably damaging Het
Map3k11 A G 19: 5,752,238 (GRCm39) T807A probably damaging Het
Mapk14 T C 17: 28,943,798 (GRCm39) F129S probably damaging Het
Mapkbp1 T A 2: 119,854,174 (GRCm39) I1257N possibly damaging Het
Mcm3 A G 1: 20,880,456 (GRCm39) Y459H probably damaging Het
Mkln1 T C 6: 31,410,093 (GRCm39) probably benign Het
Msh5 A T 17: 35,249,664 (GRCm39) I627N possibly damaging Het
Nfkbiz T C 16: 55,637,204 (GRCm39) H488R probably benign Het
Nrg1 G T 8: 32,967,105 (GRCm39) probably benign Het
Or1j19 A G 2: 36,676,782 (GRCm39) M82V probably benign Het
Or51q1 T C 7: 103,628,648 (GRCm39) V89A probably benign Het
Or51t4 T C 7: 102,597,945 (GRCm39) L81P probably damaging Het
Or5b120 A T 19: 13,479,986 (GRCm39) Y93F probably benign Het
Plec C T 15: 76,070,418 (GRCm39) V931M probably damaging Het
Plekhg4 T A 8: 106,107,034 (GRCm39) C910S probably damaging Het
Ppp1r18 A G 17: 36,179,196 (GRCm39) E357G probably damaging Het
Pramel23 T C 4: 143,424,718 (GRCm39) M242V probably benign Het
Rbm11 T C 16: 75,393,475 (GRCm39) F57S probably damaging Het
Sbp G A 17: 24,164,286 (GRCm39) G183D probably benign Het
Skint5 A G 4: 113,599,382 (GRCm39) V719A unknown Het
Slc16a7 T G 10: 125,069,308 (GRCm39) probably null Het
Slc29a1 A C 17: 45,899,992 (GRCm39) Y232* probably null Het
Slc7a8 C G 14: 54,973,247 (GRCm39) G240A possibly damaging Het
Spanxn4 A T 12: 62,734,886 (GRCm39) noncoding transcript Het
Spata31d1d T C 13: 59,876,368 (GRCm39) Q389R probably benign Het
Srgap1 A G 10: 121,706,231 (GRCm39) probably null Het
St6gal2 A T 17: 55,790,018 (GRCm39) N351Y probably benign Het
Tle2 A G 10: 81,423,394 (GRCm39) D491G probably damaging Het
Tmem33 T C 5: 67,443,468 (GRCm39) V215A probably benign Het
Trav6-3 A G 14: 53,667,548 (GRCm39) T7A probably benign Het
Ube2q2 C A 9: 55,057,084 (GRCm39) P56T probably benign Het
Unc79 T C 12: 102,988,019 (GRCm39) V208A probably damaging Het
Xkr7 T C 2: 152,896,553 (GRCm39) I469T probably benign Het
Other mutations in Lgr4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02043:Lgr4 APN 2 109,841,635 (GRCm39) missense probably damaging 1.00
IGL02247:Lgr4 APN 2 109,838,420 (GRCm39) splice site probably benign
IGL02247:Lgr4 APN 2 109,832,846 (GRCm39) missense probably benign
IGL02302:Lgr4 APN 2 109,832,841 (GRCm39) missense probably damaging 0.99
IGL02309:Lgr4 APN 2 109,842,880 (GRCm39) utr 3 prime probably benign
IGL02511:Lgr4 APN 2 109,841,617 (GRCm39) missense probably benign 0.06
IGL02604:Lgr4 APN 2 109,841,658 (GRCm39) missense probably damaging 1.00
IGL02648:Lgr4 APN 2 109,842,718 (GRCm39) missense probably damaging 1.00
IGL02795:Lgr4 APN 2 109,838,555 (GRCm39) splice site probably benign
IGL02899:Lgr4 APN 2 109,748,598 (GRCm39) missense probably damaging 0.99
R0003:Lgr4 UTSW 2 109,828,010 (GRCm39) critical splice donor site probably null
R0200:Lgr4 UTSW 2 109,801,035 (GRCm39) critical splice acceptor site probably null
R0314:Lgr4 UTSW 2 109,821,438 (GRCm39) splice site probably benign
R0482:Lgr4 UTSW 2 109,838,437 (GRCm39) missense probably damaging 1.00
R0491:Lgr4 UTSW 2 109,837,626 (GRCm39) splice site probably benign
R0517:Lgr4 UTSW 2 109,841,665 (GRCm39) missense probably damaging 1.00
R0546:Lgr4 UTSW 2 109,829,766 (GRCm39) missense probably damaging 0.98
R0658:Lgr4 UTSW 2 109,842,132 (GRCm39) missense possibly damaging 0.83
R1367:Lgr4 UTSW 2 109,821,480 (GRCm39) missense probably damaging 0.98
R1864:Lgr4 UTSW 2 109,841,742 (GRCm39) missense possibly damaging 0.93
R1977:Lgr4 UTSW 2 109,842,273 (GRCm39) missense probably damaging 1.00
R2239:Lgr4 UTSW 2 109,842,738 (GRCm39) missense probably damaging 1.00
R2380:Lgr4 UTSW 2 109,842,738 (GRCm39) missense probably damaging 1.00
R2383:Lgr4 UTSW 2 109,830,960 (GRCm39) missense probably damaging 1.00
R2997:Lgr4 UTSW 2 109,833,862 (GRCm39) missense probably benign 0.30
R3707:Lgr4 UTSW 2 109,801,099 (GRCm39) missense probably damaging 0.99
R3803:Lgr4 UTSW 2 109,838,542 (GRCm39) missense probably benign 0.10
R3804:Lgr4 UTSW 2 109,838,542 (GRCm39) missense probably benign 0.10
R3843:Lgr4 UTSW 2 109,827,118 (GRCm39) splice site probably benign
R4030:Lgr4 UTSW 2 109,820,096 (GRCm39) missense probably benign 0.06
R4777:Lgr4 UTSW 2 109,827,027 (GRCm39) missense probably damaging 0.98
R4912:Lgr4 UTSW 2 109,836,847 (GRCm39) critical splice acceptor site probably null
R4994:Lgr4 UTSW 2 109,842,283 (GRCm39) missense probably damaging 0.99
R5106:Lgr4 UTSW 2 109,827,940 (GRCm39) missense probably damaging 0.97
R5131:Lgr4 UTSW 2 109,842,678 (GRCm39) missense probably benign
R5152:Lgr4 UTSW 2 109,830,948 (GRCm39) missense probably damaging 1.00
R5753:Lgr4 UTSW 2 109,832,857 (GRCm39) nonsense probably null
R5860:Lgr4 UTSW 2 109,821,496 (GRCm39) missense probably damaging 0.96
R5914:Lgr4 UTSW 2 109,748,617 (GRCm39) missense possibly damaging 0.78
R6145:Lgr4 UTSW 2 109,837,588 (GRCm39) nonsense probably null
R6263:Lgr4 UTSW 2 109,842,243 (GRCm39) missense possibly damaging 0.95
R6400:Lgr4 UTSW 2 109,821,478 (GRCm39) missense probably damaging 0.98
R6924:Lgr4 UTSW 2 109,842,784 (GRCm39) missense probably damaging 1.00
R7171:Lgr4 UTSW 2 109,831,314 (GRCm39) missense probably benign 0.11
R7326:Lgr4 UTSW 2 109,826,974 (GRCm39) nonsense probably null
R7593:Lgr4 UTSW 2 109,829,801 (GRCm39) missense probably damaging 1.00
R7659:Lgr4 UTSW 2 109,827,111 (GRCm39) missense probably damaging 1.00
R7707:Lgr4 UTSW 2 109,827,936 (GRCm39) critical splice acceptor site probably null
R7936:Lgr4 UTSW 2 109,836,863 (GRCm39) missense probably damaging 1.00
R7940:Lgr4 UTSW 2 109,836,858 (GRCm39) missense probably damaging 1.00
R8062:Lgr4 UTSW 2 109,831,282 (GRCm39) missense probably damaging 1.00
R8153:Lgr4 UTSW 2 109,830,645 (GRCm39) missense probably damaging 0.99
R9225:Lgr4 UTSW 2 109,842,485 (GRCm39) missense probably benign
R9434:Lgr4 UTSW 2 109,836,907 (GRCm39) missense probably benign
R9557:Lgr4 UTSW 2 109,827,084 (GRCm39) missense probably damaging 1.00
X0053:Lgr4 UTSW 2 109,841,782 (GRCm39) missense possibly damaging 0.52
Predicted Primers PCR Primer
(F):5'- ATTCACTGTGACCCTAGTGC -3'
(R):5'- TCGTAGTAGAAATCCTGTTCCCC -3'

Sequencing Primer
(F):5'- CACTGTGACCCTAGTGCTATTAAAC -3'
(R):5'- GTAGTAGAAATCCTGTTCCCCACAAC -3'
Posted On 2015-08-18