Mutagenetix > Incidental Mutation

Incidental Mutation 'R6925:Lgr5'

541103

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

045043-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6925 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

115286219-115423685 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 115302251 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Glycine at position 308 (S308G)

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: S332G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000020350
Gene: ENSMUSG00000020140
AA Change: S332G

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 benign
Transcript: ENSMUST00000172806
AA Change: S308G

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000133860
Gene: ENSMUSG00000020140
AA Change: S308G

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
AA Change: S260G

PolyPhen 2 Score 0.022 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000133707
Gene: ENSMUSG00000020140
AA Change: S260G

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

0.0787

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 98.0%

Validation Efficiency

100% (91/91)

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acat1	A	T	9: 53,503,329 (GRCm39)	V170E	probably benign	Het
Atp2b2	T	A	6: 113,737,681 (GRCm39)	I902F	probably damaging	Het
Cacna1d	A	G	14: 29,773,594 (GRCm39)	V1697A	probably benign	Het
Ccdc14	T	A	16: 34,511,119 (GRCm39)	F31Y	probably benign	Het
Ccdc17	T	A	4: 116,455,407 (GRCm39)	V250E	probably damaging	Het
Cct7	A	G	6: 85,436,164 (GRCm39)	N25S	probably damaging	Het
Cdcp3	A	G	7: 130,824,436 (GRCm39)	Q177R	possibly damaging	Het
Cep19	G	C	16: 31,922,760 (GRCm39)	G9R	probably damaging	Het
Ces5a	A	T	8: 94,249,685 (GRCm39)		probably null	Het
Chd1l	T	G	3: 97,490,142 (GRCm39)	E471A	probably damaging	Het
Chd6	A	G	2: 160,855,047 (GRCm39)	I787T	probably damaging	Het
Cntnap5c	A	C	17: 58,702,261 (GRCm39)	T1194P	probably benign	Het
Col6a3	T	A	1: 90,743,724 (GRCm39)	M208L	probably benign	Het
Coro7	A	T	16: 4,446,538 (GRCm39)		probably null	Het
Csrnp2	T	C	15: 100,379,839 (GRCm39)	K484R	probably benign	Het
Cyp2c39	T	A	19: 39,501,639 (GRCm39)	V64E	probably damaging	Het
Ddr2	T	C	1: 169,825,701 (GRCm39)	K300E	probably benign	Het
Ddx56	T	C	11: 6,213,980 (GRCm39)	E393G	probably damaging	Het
Diaph1	A	C	18: 37,986,732 (GRCm39)	Y1084*	probably null	Het
Disp1	A	T	1: 182,868,042 (GRCm39)	F1459L	probably benign	Het
Dnajc8	G	A	4: 132,271,424 (GRCm39)	A80T	probably damaging	Het
Elfn1	T	A	5: 139,957,440 (GRCm39)	M148K	probably benign	Het
Emcn	T	A	3: 137,124,763 (GRCm39)	I154N	probably damaging	Het
Enah	T	A	1: 181,733,464 (GRCm39)		probably null	Het
Enah	C	G	1: 181,733,463 (GRCm39)		probably null	Het
Ep300	C	A	15: 81,534,182 (GRCm39)	Q2080K	probably benign	Het
Epha2	T	A	4: 141,036,068 (GRCm39)	M168K	probably benign	Het
Ercc6	T	A	14: 32,284,565 (GRCm39)	I776N	probably damaging	Het
Fan1	T	A	7: 64,022,234 (GRCm39)	N340Y	probably damaging	Het
Fat4	G	T	3: 39,050,353 (GRCm39)		probably null	Het
G3bp1	A	G	11: 55,388,786 (GRCm39)	R333G	possibly damaging	Het
Gm3604	A	G	13: 62,517,204 (GRCm39)	F385L	probably benign	Het
Gm5800	T	C	14: 51,951,157 (GRCm39)	I147M	possibly damaging	Het
Hipk1	A	G	3: 103,685,561 (GRCm39)	F18S	unknown	Het
Ighv3-8	A	T	12: 114,285,950 (GRCm39)	C131S	probably benign	Het
Il23r	T	G	6: 67,400,477 (GRCm39)	T618P	probably damaging	Het
Il31ra	G	A	13: 112,664,063 (GRCm39)	T538I	possibly damaging	Het
Kcns2	A	G	15: 34,840,059 (GRCm39)	D474G	unknown	Het
Klc4	T	C	17: 46,947,155 (GRCm39)	T407A	possibly damaging	Het
Klra5	C	T	6: 129,888,420 (GRCm39)	S2N	probably benign	Het
Krt10	T	C	11: 99,279,677 (GRCm39)	Y161C	probably damaging	Het
Kxd1	A	T	8: 70,975,928 (GRCm39)	M1K	probably null	Het
Lgals1	A	C	15: 78,812,240 (GRCm39)	D27A	possibly damaging	Het
Lrp1	G	A	10: 127,392,857 (GRCm39)	S2736L	probably benign	Het
Lrpap1	G	T	5: 35,259,880 (GRCm39)	H73N	probably benign	Het
Mcpt1	C	A	14: 56,256,522 (GRCm39)	T86K	probably damaging	Het
Megf6	A	T	4: 154,339,044 (GRCm39)	D527V	probably damaging	Het
Mical3	A	T	6: 120,936,351 (GRCm39)	S1392T	probably benign	Het
Mmp2	A	T	8: 93,566,010 (GRCm39)	D437V	probably damaging	Het
Mob4	T	A	1: 55,191,881 (GRCm39)	Y166*	probably null	Het
Mrap2	G	A	9: 87,064,527 (GRCm39)	M89I	possibly damaging	Het
Mug1	G	A	6: 121,858,746 (GRCm39)	A1155T	probably damaging	Het
Myh2	G	T	11: 67,084,044 (GRCm39)	A1556S	probably benign	Het
Nfatc3	A	G	8: 106,845,954 (GRCm39)	D1028G	probably benign	Het
Ngef	T	G	1: 87,430,985 (GRCm39)		probably null	Het
Nlrp1a	A	T	11: 70,983,339 (GRCm39)	L1209Q	probably null	Het
Npr2	C	T	4: 43,647,553 (GRCm39)	R819C	probably damaging	Het
Nsd2	A	T	5: 34,036,454 (GRCm39)	D646V	probably damaging	Het
Nsun7	A	G	5: 66,434,415 (GRCm39)	H252R	probably damaging	Het
Or2a25	T	A	6: 42,888,791 (GRCm39)	C111*	probably null	Het
Or2k2	A	T	4: 58,785,647 (GRCm39)	I25N	possibly damaging	Het
Or51a10	C	T	7: 103,698,947 (GRCm39)	V205I	probably benign	Het
Or8g32	A	T	9: 39,305,156 (GRCm39)	Q20L	probably benign	Het
Or8g32	G	T	9: 39,305,157 (GRCm39)	Q20H	probably benign	Het
Pcdhga2	A	T	18: 37,803,638 (GRCm39)	D494V	probably damaging	Het
Pcsk2	A	G	2: 143,655,667 (GRCm39)	E617G	probably damaging	Het
Pdc	T	C	1: 150,208,931 (GRCm39)	I138T	probably damaging	Het
Phc2	T	A	4: 128,641,927 (GRCm39)	S750T	probably damaging	Het
Pkd2l1	T	A	19: 44,179,947 (GRCm39)	N88Y	possibly damaging	Het
Plcl1	C	T	1: 55,445,757 (GRCm39)	R71*	probably null	Het
Prag1	C	A	8: 36,571,048 (GRCm39)	L544M	probably damaging	Het
Prkg2	A	G	5: 99,114,369 (GRCm39)		probably null	Het
Psd2	G	A	18: 36,112,764 (GRCm39)	S153N	probably damaging	Het
Rab11fip1	A	T	8: 27,643,000 (GRCm39)	S600T	probably damaging	Het
Rbms1	T	G	2: 60,592,648 (GRCm39)	T222P	probably benign	Het
Slfn8	A	T	11: 82,904,243 (GRCm39)	Y382*	probably null	Het
Socs4	T	A	14: 47,527,195 (GRCm39)	C43*	probably null	Het
Sorl1	T	A	9: 41,944,922 (GRCm39)	T868S	probably damaging	Het
St6gal1	A	G	16: 23,174,963 (GRCm39)	Y267C	probably damaging	Het
Syne1	A	G	10: 5,076,682 (GRCm39)	V6879A	probably benign	Het
Syne2	C	A	12: 75,900,906 (GRCm39)	H22N	possibly damaging	Het
Tmeff2	T	A	1: 50,967,180 (GRCm39)	L25Q	probably damaging	Het
Tmprss11g	G	T	5: 86,635,285 (GRCm39)	D396E	probably benign	Het
Tmprss11g	T	A	5: 86,635,295 (GRCm39)	H393L	probably benign	Het
Vmn2r23	A	G	6: 123,681,512 (GRCm39)	E140G	probably damaging	Het
Wapl	T	C	14: 34,399,320 (GRCm39)	S130P	probably benign	Het
Zeb2	T	A	2: 44,884,541 (GRCm39)	K982M	probably damaging	Het
Zfhx3	C	G	8: 109,683,453 (GRCm39)	H3631D	unknown	Het
Zfp719	T	C	7: 43,240,130 (GRCm39)	S573P	probably damaging	Het
Zfp979	A	T	4: 147,697,999 (GRCm39)	C237S	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
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
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'- GCACAGCACTTGGAGATTAGG -3'
(R):5'- GCTCAACCTGTAGTATTGCTGAG -3'

Sequencing Primer
(F):5'- GTAACTGATCACAGACGGCCTG -3'
(R):5'- CCTGTAGTATTGCTGAGAAGACC -3'

Posted On

2018-11-28