Mutagenetix > Incidental Mutation

Incidental Mutation 'R0003:Lgr4'

172384

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

038299-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0003 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

109747992-109844602 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (1 bp from exon)

DNA Base Change (assembly)

G to A at 109828010 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000106666 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000046548] [ENSMUST00000111037]

AlphaFold

A2ARI4

Predicted Effect

probably null
Transcript: ENSMUST00000046548

SMART Domains

Protein: ENSMUSP00000047325
Gene: ENSMUSG00000050199

Domain	Start	End	E-Value	Type
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

probably null
Transcript: ENSMUST00000111037

SMART Domains

Protein: ENSMUSP00000106666
Gene: ENSMUSG00000050199

Domain	Start	End	E-Value	Type
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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142869

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152584

Meta Mutation Damage Score

0.9479

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.7%
20x: 90.7%

Validation Efficiency

94% (82/87)

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: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam19	T	A	11: 46,019,616 (GRCm39)	C439S	probably damaging	Het
Adnp2	T	C	18: 80,174,205 (GRCm39)	Y68C	probably damaging	Het
Ahctf1	A	T	1: 179,591,038 (GRCm39)	D1247E	probably benign	Het
Alms1	T	A	6: 85,606,192 (GRCm39)	M2614K	possibly damaging	Het
Alx3	A	G	3: 107,512,292 (GRCm39)	H310R	probably damaging	Het
Ambra1	C	T	2: 91,741,773 (GRCm39)	T1016M	probably damaging	Het
Ankrd35	A	G	3: 96,591,331 (GRCm39)	E539G	probably damaging	Het
Aptx	A	G	4: 40,695,145 (GRCm39)		probably benign	Het
Arsi	C	T	18: 61,050,058 (GRCm39)	R314C	probably benign	Het
Atp1a3	T	C	7: 24,688,989 (GRCm39)		probably benign	Het
Avl9	G	T	6: 56,713,468 (GRCm39)	R242L	probably benign	Het
Bicra	G	T	7: 15,705,812 (GRCm39)	T1543K	probably benign	Het
Bltp2	T	A	11: 78,177,404 (GRCm39)	V1903E	possibly damaging	Het
Bzw2	A	C	12: 36,180,014 (GRCm39)	I71S	probably damaging	Het
Camk2a	C	T	18: 61,093,079 (GRCm39)	A302V	probably damaging	Het
Ccdc12	A	G	9: 110,485,665 (GRCm39)	E12G	possibly damaging	Het
Cd300lb	A	T	11: 114,819,164 (GRCm39)	F19Y	probably benign	Het
Clcn3	A	T	8: 61,380,330 (GRCm39)	C535*	probably null	Het
Cntnap5c	A	G	17: 58,506,012 (GRCm39)	T679A	probably benign	Het
Cpsf7	G	A	19: 10,516,993 (GRCm39)	S365N	possibly damaging	Het
Cspg4b	T	A	13: 113,505,310 (GRCm39)	S2146R	probably benign	Het
Cyp20a1	T	C	1: 60,426,285 (GRCm39)		probably benign	Het
Decr2	A	T	17: 26,302,027 (GRCm39)	N234K	probably benign	Het
Def8	G	A	8: 124,183,234 (GRCm39)	A278T	probably damaging	Het
Dnah12	T	C	14: 26,494,601 (GRCm39)	F1300L	probably damaging	Het
Dock1	T	C	7: 134,331,793 (GRCm39)		probably benign	Het
Dpy19l4	A	T	4: 11,267,619 (GRCm39)	N440K	probably damaging	Het
Eprs1	T	C	1: 185,146,588 (GRCm39)	V1206A	probably damaging	Het
Exoc6b	A	G	6: 84,831,681 (GRCm39)		probably null	Het
Fam184b	A	G	5: 45,712,536 (GRCm39)		probably benign	Het
Fcho1	A	T	8: 72,161,597 (GRCm39)	S858T	probably damaging	Het
Fgfr1	A	G	8: 26,058,214 (GRCm39)	D430G	possibly damaging	Het
Fmnl3	T	C	15: 99,219,013 (GRCm39)	T807A	probably damaging	Het
Gabra5	T	C	7: 57,063,476 (GRCm39)	Y316C	probably damaging	Het
Gh	A	G	11: 106,192,346 (GRCm39)	L16P	probably damaging	Het
Glipr2	A	T	4: 43,970,532 (GRCm39)	I87F	probably damaging	Het
Glrb	T	A	3: 80,763,221 (GRCm39)	I259F	probably damaging	Het
Gpr63	T	C	4: 25,007,651 (GRCm39)	L125P	probably damaging	Het
Grb2	A	G	11: 115,546,251 (GRCm39)	Y37H	probably damaging	Het
Haus2	G	A	2: 120,449,449 (GRCm39)		probably benign	Het
Hmgcr	T	C	13: 96,788,653 (GRCm39)	N749S	probably damaging	Het
Igf1r	T	C	7: 67,814,990 (GRCm39)	V297A	probably damaging	Het
Il12rb2	G	T	6: 67,293,270 (GRCm39)	P69H	probably damaging	Het
Ints3	C	A	3: 90,315,818 (GRCm39)	M315I	probably benign	Het
Izumo2	C	T	7: 44,364,833 (GRCm39)	T116I	probably benign	Het
Kctd19	A	C	8: 106,121,993 (GRCm39)	Y185D	probably damaging	Het
Lama4	A	G	10: 38,936,218 (GRCm39)	N631S	possibly damaging	Het
Lama5	T	G	2: 179,819,872 (GRCm39)		probably null	Het
Lamc1	A	C	1: 153,138,185 (GRCm39)	L223R	probably damaging	Het
Loxhd1	T	C	18: 77,427,196 (GRCm39)	L398P	probably damaging	Het
Mapk9	T	A	11: 49,757,866 (GRCm39)	D103E	possibly damaging	Het
Marchf6	T	C	15: 31,469,678 (GRCm39)		probably benign	Het
Mlxipl	G	A	5: 135,162,043 (GRCm39)		probably benign	Het
Mrgbp	C	A	2: 180,225,231 (GRCm39)	D62E	probably benign	Het
Mtap	A	T	4: 89,070,235 (GRCm39)		probably benign	Het
Myt1	G	A	2: 181,443,664 (GRCm39)	G497S	probably damaging	Het
Naa25	T	G	5: 121,545,247 (GRCm39)		probably benign	Het
Nfat5	C	T	8: 108,065,707 (GRCm39)	R156W	probably damaging	Het
Nkpd1	T	C	7: 19,253,852 (GRCm39)	C73R	probably benign	Het
Nup210l	T	C	3: 90,027,218 (GRCm39)	I200T	probably damaging	Het
Nvl	C	A	1: 180,941,698 (GRCm39)	D581Y	probably damaging	Het
Or51a6	T	C	7: 102,604,185 (GRCm39)	M208V	probably benign	Het
Or51f2	T	C	7: 102,527,068 (GRCm39)	V247A	probably benign	Het
Or5t17	T	A	2: 86,832,710 (GRCm39)	Y132*	probably null	Het
Or8b1c	A	G	9: 38,384,612 (GRCm39)	T190A	probably benign	Het
Or9q1	T	C	19: 13,805,050 (GRCm39)	T237A	probably damaging	Het
Pcdh7	G	T	5: 58,070,590 (GRCm39)	E1089D	probably benign	Het
Pik3cd	A	G	4: 149,740,836 (GRCm39)		probably null	Het
Plekhh2	A	T	17: 84,864,820 (GRCm39)	K69N	probably damaging	Het
Ptgdr2	G	A	19: 10,917,792 (GRCm39)	C103Y	probably damaging	Het
Rrad	A	C	8: 105,355,299 (GRCm39)	H236Q	probably benign	Het
Rslcan18	C	T	13: 67,246,533 (GRCm39)	A236T	probably benign	Het
Ryr2	C	A	13: 11,839,265 (GRCm39)	D503Y	probably damaging	Het
Siglec1	T	C	2: 130,916,980 (GRCm39)	T1092A	probably benign	Het
Siglecf	A	G	7: 43,005,350 (GRCm39)	T437A	probably benign	Het
Spta1	A	T	1: 174,032,839 (GRCm39)	Q965H	probably damaging	Het
Stk10	A	T	11: 32,539,460 (GRCm39)	E280V	probably benign	Het
Tfg	T	C	16: 56,511,351 (GRCm39)	Y326C	possibly damaging	Het
Tpp2	T	A	1: 43,999,299 (GRCm39)	S358T	possibly damaging	Het
Trim25	G	T	11: 88,906,598 (GRCm39)	V437L	probably benign	Het
Ttn	T	C	2: 76,574,027 (GRCm39)	D25622G	probably damaging	Het
Ube3b	T	A	5: 114,536,912 (GRCm39)	S303R	probably benign	Het
Ush2a	T	A	1: 188,310,688 (GRCm39)	V2088D	probably damaging	Het
Vmn2r103	A	G	17: 20,032,241 (GRCm39)	T672A	probably damaging	Het
Wdr11	G	T	7: 129,200,785 (GRCm39)	G79C	probably damaging	Het
Wdr89	T	A	12: 75,679,367 (GRCm39)	T296S	probably benign	Het
Zdhhc24	T	A	19: 4,930,402 (GRCm39)	L179M	possibly damaging	Het
Zfp981	T	C	4: 146,622,217 (GRCm39)	C381R	probably damaging	Het
Zim1	A	G	7: 6,679,947 (GRCm39)	I572T	probably benign	Het

Other mutations in Lgr4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
R4513:Lgr4	UTSW	2	109,842,361 (GRCm39)	missense	possibly damaging	0.93
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'- AGCTGCCTTCTCACCTCAGAGAAC -3'
(R):5'- GGCTCCTGAAATCAGGGAGAAAACC -3'

Sequencing Primer
(F):5'- CGAGTCTGTGTAATAGCCAGC -3'
(R):5'- ATGTCAGAGTTCCCAAACTGTC -3'

Posted On

2014-04-23