Mutagenetix > Incidental Mutation

Incidental Mutation 'R7261:Lgr5'

564636

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

045387-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7261 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

115286219-115423685 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 115423370 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 10 (L10Q)

Ref Sequence

ENSEMBL: ENSMUSP00000020350 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020350] [ENSMUST00000172806] [ENSMUST00000173740]

AlphaFold

Q9Z1P4

Predicted Effect

possibly damaging
Transcript: ENSMUST00000020350
AA Change: L10Q

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000020350
Gene: ENSMUSG00000020140
AA Change: L10Q

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 null
Transcript: ENSMUST00000172806
AA Change: L10Q

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000133860
Gene: ENSMUSG00000020140
AA Change: L10Q

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 null
Transcript: ENSMUST00000173740
AA Change: L10Q

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000133707
Gene: ENSMUSG00000020140
AA Change: L10Q

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

0.2467

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.5%

Validation Efficiency

99% (84/85)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaca	T	C	11: 84,259,526 (GRCm39)	F1954L	probably damaging	Het
Acmsd	T	G	1: 127,687,561 (GRCm39)	I281R	probably damaging	Het
Adamts2	A	T	11: 50,677,424 (GRCm39)	M742L	possibly damaging	Het
Adgrf4	G	A	17: 42,978,326 (GRCm39)	T339I	probably benign	Het
Aff1	T	C	5: 103,976,245 (GRCm39)	S448P	probably damaging	Het
Agbl2	A	T	2: 90,619,288 (GRCm39)	S38C	possibly damaging	Het
Akap7	C	T	10: 25,147,416 (GRCm39)	D105N	possibly damaging	Het
Arhgap21	A	G	2: 20,885,177 (GRCm39)	F677L	probably benign	Het
Atf6b	G	T	17: 34,869,792 (GRCm39)	V271F	probably damaging	Het
B3gnt5	A	G	16: 19,588,123 (GRCm39)	Y114C	probably damaging	Het
Casp7	T	A	19: 56,424,765 (GRCm39)	D161E	probably benign	Het
Catsper4	TTCTC	TTC	4: 133,954,423 (GRCm39)		probably null	Het
Ccdc162	T	C	10: 41,437,136 (GRCm39)	T1758A	probably benign	Het
Cfap74	C	A	4: 155,549,831 (GRCm39)	P155T	unknown	Het
Champ1	A	G	8: 13,928,517 (GRCm39)	D225G	possibly damaging	Het
Chrng	A	T	1: 87,134,962 (GRCm39)		probably null	Het
Cnksr1	T	C	4: 133,963,084 (GRCm39)		probably null	Het
Col15a1	G	A	4: 47,269,088 (GRCm39)	G582D	probably benign	Het
Cwc25	A	G	11: 97,648,585 (GRCm39)	V81A	possibly damaging	Het
Ddhd1	A	G	14: 45,894,688 (GRCm39)	Y261H	probably damaging	Het
Defa29	A	G	8: 21,816,818 (GRCm39)		probably null	Het
Diaph3	A	C	14: 87,202,893 (GRCm39)	C666G	probably benign	Het
Dlx2	A	G	2: 71,375,019 (GRCm39)	Y282H	probably damaging	Het
Dsc3	A	T	18: 20,113,814 (GRCm39)	Y369*	probably null	Het
Dtwd1	A	G	2: 126,000,424 (GRCm39)	N120S	probably benign	Het
Dysf	G	A	6: 84,169,992 (GRCm39)	S1761N	probably damaging	Het
Enthd1	A	T	15: 80,444,416 (GRCm39)	N46K	probably damaging	Het
Epha7	T	A	4: 28,813,418 (GRCm39)	I12N	probably benign	Het
Fam171a2	T	A	11: 102,328,900 (GRCm39)	N620Y	probably damaging	Het
Garin4	T	C	1: 190,896,308 (GRCm39)	S112G	unknown	Het
Gfpt2	A	T	11: 49,714,078 (GRCm39)	E278D	possibly damaging	Het
Gm3285	A	G	10: 77,698,244 (GRCm39)	Q131R	unknown	Het
Gpcpd1	A	C	2: 132,410,619 (GRCm39)	C23G	probably damaging	Het
Gtpbp4	A	T	13: 9,037,954 (GRCm39)	H228Q	probably benign	Het
Hdac7	A	G	15: 97,704,415 (GRCm39)	V500A	probably benign	Het
Hykk	T	G	9: 54,828,010 (GRCm39)	M83R	possibly damaging	Het
Idi1	A	G	13: 8,936,931 (GRCm39)	I101V	probably benign	Het
Irs2	A	T	8: 11,057,018 (GRCm39)	H471Q	possibly damaging	Het
Itsn1	T	C	16: 91,702,194 (GRCm39)	V12A	probably benign	Het
Jak2	A	G	19: 29,288,385 (GRCm39)	I1079V	possibly damaging	Het
Kcnt2	G	A	1: 140,282,255 (GRCm39)	R80H	possibly damaging	Het
Lamb2	T	C	9: 108,358,496 (GRCm39)	Y178H	probably damaging	Het
Lnx1	G	T	5: 74,838,175 (GRCm39)	S29*	probably null	Het
Lpcat3	T	A	6: 124,675,050 (GRCm39)	F57I	probably benign	Het
Manf	T	C	9: 106,769,088 (GRCm39)	T4A	probably benign	Het
Map2k3	G	A	11: 60,836,393 (GRCm39)		probably null	Het
Myh14	G	A	7: 44,273,761 (GRCm39)	Q1329*	probably null	Het
Myocd	T	C	11: 65,078,422 (GRCm39)	S458G	probably damaging	Het
Ncor2	T	C	5: 125,187,143 (GRCm39)		probably null	Het
Ndufs8	A	T	19: 3,961,606 (GRCm39)	N23K	probably benign	Het
Nkx6-1	T	C	5: 101,812,006 (GRCm39)	K32R	unknown	Het
Nlrp3	T	G	11: 59,439,272 (GRCm39)	V283G	possibly damaging	Het
Nme3	A	G	17: 25,116,037 (GRCm39)		probably null	Het
Or1o3	A	G	17: 37,574,076 (GRCm39)	F160L	probably benign	Het
Or8g23	C	T	9: 38,971,504 (GRCm39)	V153M	possibly damaging	Het
Parvg	T	C	15: 84,215,297 (GRCm39)		probably null	Het
Peg10	T	A	6: 4,756,591 (GRCm39)	M389K	unknown	Het
Phf23	G	T	11: 69,890,091 (GRCm39)	C340F	possibly damaging	Het
Piwil2	A	G	14: 70,611,860 (GRCm39)	Y929H	probably damaging	Het
Prss39	A	G	1: 34,539,369 (GRCm39)	D203G	probably damaging	Het
Prss54	G	T	8: 96,286,367 (GRCm39)	D235E	probably benign	Het
Prtg	T	A	9: 72,815,117 (GRCm39)	M1015K	possibly damaging	Het
Rbbp8	T	C	18: 11,838,799 (GRCm39)	I160T	probably damaging	Het
Rxylt1	A	T	10: 121,924,822 (GRCm39)	D293E	probably benign	Het
Scn10a	C	A	9: 119,438,790 (GRCm39)	C1692F	probably damaging	Het
Scn11a	C	T	9: 119,648,899 (GRCm39)	D55N	probably damaging	Het
Secisbp2	G	T	13: 51,836,498 (GRCm39)	V768F	probably damaging	Het
Skic3	A	G	13: 76,261,698 (GRCm39)	T138A	probably benign	Het
Spag16	T	C	1: 70,338,780 (GRCm39)	I426T	possibly damaging	Het
Sspo	G	A	6: 48,427,011 (GRCm39)	V250M	possibly damaging	Het
Strbp	A	T	2: 37,531,149 (GRCm39)		probably null	Het
Sv2c	C	T	13: 96,224,809 (GRCm39)	V167M	probably damaging	Het
Tdpoz1	G	A	3: 93,577,794 (GRCm39)	S330L	not run	Het
Tigd2	T	A	6: 59,188,052 (GRCm39)	D306E	probably benign	Het
Trrap	C	T	5: 144,782,287 (GRCm39)	P3278S	possibly damaging	Het
Vdac1	A	T	11: 52,265,761 (GRCm39)	K28N	probably damaging	Het
Vmn1r84	A	T	7: 12,096,069 (GRCm39)	M208K	probably damaging	Het
Vmn2r77	A	T	7: 86,460,518 (GRCm39)	K615*	probably null	Het
Vps11	A	G	9: 44,265,800 (GRCm39)	L493P	probably damaging	Het
Zbtb21	T	C	16: 97,754,179 (GRCm39)	I35V	possibly damaging	Het
Zbtb26	A	T	2: 37,326,667 (GRCm39)	M123K	possibly damaging	Het
Zfp236	A	T	18: 82,627,470 (GRCm39)	D1576E	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
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
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'- GGTCACTTACAGGTAGGAGGTG -3'
(R):5'- GCTTTCACATCTCAGTCGCG -3'

Sequencing Primer
(F):5'- TCACTTACAGGTAGGAGGTGAAGAC -3'
(R):5'- TGGGACCACGATTCTCTGC -3'

Posted On

2019-06-26