Mutagenetix > Incidental Mutations

Incidental Mutation 'IGL02079:Lgr5'

186060

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

Ncbi RefSeq: NM_010195.2; MGI: 1341817

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL02079

Quality Score

Status

Chromosome

Chromosomal Location

115450311-115587780 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 115452194 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 776 (S776R)

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: S848R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000020350
Gene: ENSMUSG00000020140
AA Change: S848R

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: S824R

PolyPhen 2 Score 0.240 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000133860
Gene: ENSMUSG00000020140
AA Change: S824R

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

noncoding transcript
Transcript: ENSMUST00000173619

Predicted Effect

probably damaging
Transcript: ENSMUST00000173740
AA Change: S776R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000133707
Gene: ENSMUSG00000020140
AA Change: S776R

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

Coding Region Coverage

Validation Efficiency

MGI Phenotype

Strain: 3512420
Lethality: D1-D2
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: 37 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5330417C22Rik	T	A	3: 108,481,359	N236I	possibly damaging	Het
Abl1	T	C	2: 31,689,948		probably benign	Het
Ago4	A	T	4: 126,517,084	M204K	probably damaging	Het
Alms1	T	C	6: 85,628,634	V2422A	probably damaging	Het
Ap5z1	T	C	5: 142,477,113		probably null	Het
Arsa	T	C	15: 89,473,351	T470A	probably benign	Het
Bri3bp	T	C	5: 125,454,689	V233A	probably damaging	Het
Cdc45	C	T	16: 18,798,729	M200I	probably benign	Het
Csgalnact1	C	A	8: 68,401,492	G219V	probably damaging	Het
Ephb6	T	A	6: 41,616,014	D395E	possibly damaging	Het
Flt1	T	A	5: 147,568,831		probably benign	Het
Fry	A	T	5: 150,399,624	N1080I	probably damaging	Het
Gdpgp1	T	A	7: 80,239,020	D266E	probably benign	Het
Gspt1	A	G	16: 11,240,829	S123P	probably benign	Het
Kctd17	T	C	15: 78,430,156		probably benign	Het
Lamb2	T	A	9: 108,482,113	C313S	probably damaging	Het
Lcor	T	A	19: 41,555,687	S106R	probably benign	Het
Mettl16	T	G	11: 74,817,624	C510G	probably damaging	Het
Mlip	T	C	9: 77,239,529	T101A	possibly damaging	Het
Myh6	A	T	14: 54,950,541	L1152Q	probably damaging	Het
Mylk	G	A	16: 34,860,631	R87H	possibly damaging	Het
Npepl1	C	T	2: 174,119,390		probably benign	Het
Nrxn1	A	T	17: 90,643,083	M548K	probably damaging	Het
Olfr1205	T	A	2: 88,831,647	C177S	probably damaging	Het
Olfr514	T	A	7: 108,825,936	E21V	probably damaging	Het
Pate3	T	A	9: 35,646,153	Q69L	probably damaging	Het
Piwil1	T	C	5: 128,742,003	V192A	possibly damaging	Het
Plcxd2	A	T	16: 45,972,343	I211N	probably benign	Het
Plekhg3	T	A	12: 76,560,429	Y88N	probably benign	Het
Rabgap1l	C	T	1: 160,738,970	C58Y	probably benign	Het
Rnf123	G	A	9: 108,068,302	R390*	probably null	Het
Rusc2	A	G	4: 43,425,668	S1258G	probably benign	Het
Scn1a	T	C	2: 66,323,360	R710G	probably benign	Het
Wwc1	A	G	11: 35,876,058	S457P	probably damaging	Het
Xdh	C	T	17: 73,891,277	G1205D	probably damaging	Het
Zfp518a	G	A	19: 40,914,617	G997R	probably damaging	Het
Zfp592	T	C	7: 81,039,230	S1080P	probably benign	Het

Other mutations in Lgr5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00341:Lgr5	APN	10	115454464	missense	possibly damaging	0.69
IGL01291:Lgr5	APN	10	115478534	missense	probably damaging	1.00
IGL01432:Lgr5	APN	10	115453092	missense	probably damaging	1.00
IGL01778:Lgr5	APN	10	115462702	missense	probably damaging	0.97
IGL01936:Lgr5	APN	10	115452414	missense	probably damaging	1.00
IGL02134:Lgr5	APN	10	115452858	missense	possibly damaging	0.89
IGL03083:Lgr5	APN	10	115453032	missense	probably benign	0.26
IGL03350:Lgr5	APN	10	115471988	missense	probably damaging	0.99
anger	UTSW	10	115466346	missense	probably benign	0.03
ANU05:Lgr5	UTSW	10	115478534	missense	probably damaging	1.00
R0378:Lgr5	UTSW	10	115454499	missense	probably damaging	1.00
R0788:Lgr5	UTSW	10	115452997	missense	probably damaging	0.99
R1119:Lgr5	UTSW	10	115460811	critical splice donor site	probably null
R1321:Lgr5	UTSW	10	115478457	missense	probably damaging	1.00
R1880:Lgr5	UTSW	10	115452279	missense	probably damaging	1.00
R1985:Lgr5	UTSW	10	115495245	splice site	probably benign
R2434:Lgr5	UTSW	10	115587406	missense	probably benign
R3055:Lgr5	UTSW	10	115466123	splice site	probably benign
R3910:Lgr5	UTSW	10	115587463	missense	possibly damaging	0.93
R4686:Lgr5	UTSW	10	115458743	intron	probably benign
R4862:Lgr5	UTSW	10	115462764	missense	probably damaging	1.00
R4866:Lgr5	UTSW	10	115452685	missense	probably benign	0.00
R5089:Lgr5	UTSW	10	115478423	missense	probably damaging	1.00
R5118:Lgr5	UTSW	10	115452339	missense	possibly damaging	0.88
R5375:Lgr5	UTSW	10	115478564	missense	probably benign	0.00
R5537:Lgr5	UTSW	10	115456689	missense	probably benign	0.00
R5583:Lgr5	UTSW	10	115478504	missense	probably benign	0.32
R6312:Lgr5	UTSW	10	115452924	missense	probably damaging	1.00
R6362:Lgr5	UTSW	10	115478525	missense	probably damaging	1.00
R6605:Lgr5	UTSW	10	115457867	missense	possibly damaging	0.69
R6689:Lgr5	UTSW	10	115466608	missense	probably damaging	0.99
R6705:Lgr5	UTSW	10	115587288	missense	probably damaging	0.96
R6925:Lgr5	UTSW	10	115466346	missense	probably benign	0.03
R7063:Lgr5	UTSW	10	115456734	missense	probably damaging	1.00
R7261:Lgr5	UTSW	10	115587465	missense	possibly damaging	0.96
R7274:Lgr5	UTSW	10	115452505	missense	probably damaging	0.99
R7458:Lgr5	UTSW	10	115457755	critical splice donor site	probably null
R7569:Lgr5	UTSW	10	115462756	missense	probably damaging	1.00
R7770:Lgr5	UTSW	10	115471994	missense	probably damaging	0.98
R7936:Lgr5	UTSW	10	115453047	missense	probably damaging	0.99
R7964:Lgr5	UTSW	10	115452174	missense	probably benign	0.00
R8085:Lgr5	UTSW	10	115475197	missense	probably benign
R8537:Lgr5	UTSW	10	115452402	missense	probably damaging	1.00
R8703:Lgr5	UTSW	10	115452705	missense	probably benign	0.01
R8704:Lgr5	UTSW	10	115452705	missense	probably benign	0.01
R8706:Lgr5	UTSW	10	115452705	missense	probably benign	0.01
R8707:Lgr5	UTSW	10	115452705	missense	probably benign	0.01
R9019:Lgr5	UTSW	10	115478549	missense	probably damaging	1.00
R9043:Lgr5	UTSW	10	115478438	missense	probably damaging	1.00
R9215:Lgr5	UTSW	10	115475180	missense	probably damaging	0.99
R9217:Lgr5	UTSW	10	115587444	missense	probably benign	0.33
R9427:Lgr5	UTSW	10	115453008	missense	probably damaging	1.00
Z1176:Lgr5	UTSW	10	115460876	missense	probably damaging	0.98
Z1177:Lgr5	UTSW	10	115456669	missense	probably benign	0.00

Posted On

2014-05-07