Mutagenetix > Incidental Mutation

Incidental Mutation 'R4653:Lrrk1'

351475

Institutional Source

Beutler Lab

Gene Symbol

Lrrk1

Ensembl Gene

ENSMUSG00000015133

Gene Name

leucine-rich repeat kinase 1

Synonyms

MMRRC Submission

041913-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4653 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

66226912-66388350 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 66273053 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 1366 (I1366V)

Ref Sequence

ENSEMBL: ENSMUSP00000015277 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000015277] [ENSMUST00000145954]

AlphaFold

Q3UHC2

Predicted Effect

probably benign
Transcript: ENSMUST00000015277
AA Change: I1366V

PolyPhen 2 Score 0.119 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000015277
Gene: ENSMUSG00000015133
AA Change: I1366V

Domain	Start	End	E-Value	Type
ANK	86	116	9.33e2	SMART
ANK	119	148	1.14e2	SMART
ANK	152	182	8.36e1	SMART
ANK	193	223	2.6e1	SMART
LRR	278	300	2.84e2	SMART
LRR	301	325	7.79e0	SMART
LRR	328	351	3.27e1	SMART
LRR_TYP	379	401	2.53e-2	SMART
LRR	403	427	5.89e1	SMART
LRR	472	493	5.27e1	SMART
LRR	548	569	2.92e2	SMART
LRR	570	594	5.88e0	SMART
Pfam:Arf	625	786	2e-8	PFAM
Pfam:Roc	640	761	3.1e-24	PFAM
Pfam:Ras	640	782	2.2e-7	PFAM
Pfam:COR	844	1046	4.7e-26	PFAM
low complexity region	1109	1119	N/A	INTRINSIC
low complexity region	1209	1222	N/A	INTRINSIC
Pfam:Pkinase	1243	1521	7.8e-40	PFAM
Pfam:Pkinase_Tyr	1244	1520	9.4e-39	PFAM
low complexity region	1642	1654	N/A	INTRINSIC
low complexity region	1839	1846	N/A	INTRINSIC
low complexity region	1852	1871	N/A	INTRINSIC
low complexity region	1957	1970	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131239

Predicted Effect

probably benign
Transcript: ENSMUST00000145954
AA Change: I281V

PolyPhen 2 Score 0.077 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000114938
Gene: ENSMUSG00000015133
AA Change: I281V

Domain	Start	End	E-Value	Type
low complexity region	24	34	N/A	INTRINSIC
low complexity region	124	137	N/A	INTRINSIC
Pfam:Pkinase	158	435	6.6e-46	PFAM
Pfam:Pkinase_Tyr	159	435	5.8e-40	PFAM

Meta Mutation Damage Score

0.1612

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.3%

Validation Efficiency

97% (66/68)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a multi-domain protein that is a leucine-rich repeat kinase and a GDP/GTP binding protein. The encoded protein is thought to play a role in the regulation of bone mass. Mice lacking a similar gene showed severe osteopetrosis, increased bone mineralization and decreased bone resorption. [provided by RefSeq, Jan 2017]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit preweaning lethality. Mice homozygous for another knock-out allele exhibit severe osteopetrosis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610008E11Rik	T	C	10: 79,067,430 (GRCm38)	T351A	probably benign	Het
3930402G23Rik	A	T	8: 10,926,075 (GRCm38)		noncoding transcript	Het
4933409G03Rik	G	A	2: 68,606,215 (GRCm38)	E168K	unknown	Het
Abca4	G	T	3: 122,138,581 (GRCm38)	E295*	probably null	Het
Abi3	T	C	11: 95,832,811 (GRCm38)	I215V	probably benign	Het
Adhfe1	G	T	1: 9,550,578 (GRCm38)		probably benign	Het
Akr1a1	A	G	4: 116,637,959 (GRCm38)		probably benign	Het
Ank	T	A	15: 27,590,361 (GRCm38)	W344R	probably null	Het
Cast	A	G	13: 74,746,014 (GRCm38)	S171P	probably benign	Het
Ccdc39	A	G	3: 33,819,806 (GRCm38)		probably null	Het
Cd180	T	A	13: 102,704,908 (GRCm38)	L154H	probably damaging	Het
Cnp	A	T	11: 100,576,516 (GRCm38)	D95V	probably benign	Het
Cul1	T	C	6: 47,484,963 (GRCm38)	I20T	probably damaging	Het
Dnah6	T	C	6: 73,073,457 (GRCm38)	K3042R	possibly damaging	Het
Dpy19l1	A	C	9: 24,482,054 (GRCm38)	S140A	possibly damaging	Het
Dpys	C	A	15: 39,793,246 (GRCm38)	R475L	probably damaging	Het
Dync1i2	A	G	2: 71,247,855 (GRCm38)	N276S	probably damaging	Het
Ext2	T	C	2: 93,696,159 (GRCm38)	S711G	probably benign	Het
Fancm	A	G	12: 65,083,054 (GRCm38)	Y223C	probably damaging	Het
Folh1	C	A	7: 86,744,425 (GRCm38)	G360*	probably null	Het
Garin5b	T	C	7: 4,758,055 (GRCm38)	R553G	possibly damaging	Het
Gcat	T	C	15: 79,035,287 (GRCm38)	S151P	probably damaging	Het
Gcm2	A	T	13: 41,102,841 (GRCm38)	D477E	probably benign	Het
Git1	A	G	11: 77,505,043 (GRCm38)	N468S	possibly damaging	Het
Gtf3c1	T	C	7: 125,674,100 (GRCm38)	I622V	probably benign	Het
Hsd17b13	G	A	5: 103,965,836 (GRCm38)	L251F	probably damaging	Het
Lamc1	T	G	1: 153,228,777 (GRCm38)	S59R	probably damaging	Het
Llgl1	A	G	11: 60,708,651 (GRCm38)	D486G	possibly damaging	Het
Ly9	G	T	1: 171,594,029 (GRCm38)	H441Q	probably benign	Het
Mtcl2	A	G	2: 157,040,591 (GRCm38)	F514L	probably damaging	Het
Myo15b	G	A	11: 115,879,987 (GRCm38)		probably null	Het
Nomo1	G	T	7: 46,061,813 (GRCm38)	A639S	probably benign	Het
P3h2	T	C	16: 26,105,277 (GRCm38)	D136G	probably damaging	Het
Pde4dip	A	T	3: 97,767,338 (GRCm38)	D87E	probably damaging	Het
Pdpk1	A	T	17: 24,106,897 (GRCm38)	D108E	probably benign	Het
Pex26	C	T	6: 121,190,125 (GRCm38)	S231L	probably damaging	Het
Prpf38b	G	A	3: 108,904,092 (GRCm38)		probably benign	Het
Prpf4b	A	T	13: 34,899,971 (GRCm38)	M908L	probably benign	Het
Prps2	T	C	X: 167,352,292 (GRCm38)	D183G	probably damaging	Het
R3hdm1	T	C	1: 128,184,444 (GRCm38)	S422P	probably damaging	Het
Rhox2a	G	C	X: 37,245,309 (GRCm38)	R43P	probably benign	Het
Rps6-ps2	A	G	8: 88,806,691 (GRCm38)		noncoding transcript	Het
Ryr3	T	A	2: 112,652,763 (GRCm38)	N4213I	probably damaging	Het
Slc7a14	A	G	3: 31,257,682 (GRCm38)	V63A	probably damaging	Het
Sppl2a	C	T	2: 126,920,313 (GRCm38)		probably null	Het
Sspo	T	A	6: 48,478,646 (GRCm38)	W3077R	probably damaging	Het
Stag1	T	A	9: 100,796,716 (GRCm38)	M230K	probably damaging	Het
Sv2a	T	C	3: 96,190,762 (GRCm38)		probably null	Het
Themis2	A	G	4: 132,782,976 (GRCm38)	S638P	probably benign	Het
Trabd	A	G	15: 89,085,839 (GRCm38)	Y346C	probably damaging	Het
Trim38	A	T	13: 23,782,969 (GRCm38)	D133V	probably damaging	Het
Trmt1l	G	A	1: 151,439,569 (GRCm38)	V16I	probably benign	Het
Ube2b	A	G	11: 51,995,372 (GRCm38)		probably null	Het
Usp13	A	T	3: 32,837,924 (GRCm38)	Q84L	probably damaging	Het
Vmn1r172	G	T	7: 23,660,572 (GRCm38)	G294V	probably damaging	Het
Vmn2r59	A	T	7: 42,043,804 (GRCm38)	H457Q	probably benign	Het
Vmn2r63	A	G	7: 42,903,690 (GRCm38)	I714T	possibly damaging	Het
Vps8	T	C	16: 21,500,210 (GRCm38)	Y602H	probably damaging	Het
Zbp1	G	A	2: 173,207,815 (GRCm38)	P385S	possibly damaging	Het

Other mutations in Lrrk1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01365:Lrrk1	APN	7	66,287,701 (GRCm38)	missense	probably damaging	1.00
IGL01511:Lrrk1	APN	7	66,265,450 (GRCm38)	missense	possibly damaging	0.48
IGL02337:Lrrk1	APN	7	66,279,416 (GRCm38)	missense	possibly damaging	0.92
IGL02636:Lrrk1	APN	7	66,308,659 (GRCm38)	critical splice donor site	probably null
IGL02679:Lrrk1	APN	7	66,274,872 (GRCm38)	missense	probably damaging	1.00
IGL02711:Lrrk1	APN	7	66,330,767 (GRCm38)	missense	probably damaging	1.00
IGL02742:Lrrk1	APN	7	66,308,691 (GRCm38)	missense	probably benign	0.12
IGL02878:Lrrk1	APN	7	66,262,563 (GRCm38)	missense	probably benign
IGL03135:Lrrk1	APN	7	66,262,890 (GRCm38)	missense	probably benign	0.00
IGL03191:Lrrk1	APN	7	66,259,959 (GRCm38)	missense	probably damaging	0.99
IGL03198:Lrrk1	APN	7	66,306,894 (GRCm38)	missense	probably damaging	1.00
combustion	UTSW	7	66,262,665 (GRCm38)	missense	possibly damaging	0.94
fluorine	UTSW	7	66,302,710 (GRCm38)	missense	possibly damaging	0.89
halide	UTSW	7	66,265,474 (GRCm38)	missense	possibly damaging	0.82
Heiland	UTSW	7	66,262,733 (GRCm38)	missense	probably damaging	0.96
liebster	UTSW	7	66,294,981 (GRCm38)	missense	probably damaging	1.00
magi	UTSW	7	66,281,648 (GRCm38)	missense	probably damaging	1.00
oxidation	UTSW	7	66,279,372 (GRCm38)	missense	probably benign	0.00
phlogiston	UTSW	7	66,278,520 (GRCm38)	splice site	probably benign
Savior	UTSW	7	66,262,487 (GRCm38)	missense	probably damaging	1.00
wenig	UTSW	7	66,273,001 (GRCm38)	missense	probably damaging	1.00
R0105:Lrrk1	UTSW	7	66,292,341 (GRCm38)	missense	probably damaging	1.00
R0105:Lrrk1	UTSW	7	66,292,341 (GRCm38)	missense	probably damaging	1.00
R0276:Lrrk1	UTSW	7	66,296,263 (GRCm38)	splice site	probably benign
R0505:Lrrk1	UTSW	7	66,290,908 (GRCm38)	splice site	probably null
R0609:Lrrk1	UTSW	7	66,266,615 (GRCm38)	splice site	probably null
R0650:Lrrk1	UTSW	7	66,292,336 (GRCm38)	missense	probably damaging	1.00
R0676:Lrrk1	UTSW	7	66,294,981 (GRCm38)	missense	probably damaging	1.00
R1157:Lrrk1	UTSW	7	66,262,283 (GRCm38)	missense	probably benign	0.00
R1435:Lrrk1	UTSW	7	66,273,028 (GRCm38)	missense	probably damaging	1.00
R1468:Lrrk1	UTSW	7	66,259,974 (GRCm38)	missense	probably damaging	1.00
R1468:Lrrk1	UTSW	7	66,259,974 (GRCm38)	missense	probably damaging	1.00
R1498:Lrrk1	UTSW	7	66,302,671 (GRCm38)	nonsense	probably null
R1620:Lrrk1	UTSW	7	66,381,538 (GRCm38)	missense	probably benign	0.00
R1884:Lrrk1	UTSW	7	66,262,437 (GRCm38)	missense	probably benign
R1891:Lrrk1	UTSW	7	66,279,300 (GRCm38)	missense	probably damaging	1.00
R1989:Lrrk1	UTSW	7	66,281,684 (GRCm38)	missense	probably damaging	1.00
R2107:Lrrk1	UTSW	7	66,279,282 (GRCm38)	missense	probably damaging	1.00
R2140:Lrrk1	UTSW	7	66,330,750 (GRCm38)	missense	probably damaging	1.00
R2144:Lrrk1	UTSW	7	66,296,163 (GRCm38)	missense	probably damaging	0.98
R2147:Lrrk1	UTSW	7	66,285,411 (GRCm38)	splice site	probably null
R3176:Lrrk1	UTSW	7	66,305,521 (GRCm38)	missense	possibly damaging	0.69
R3276:Lrrk1	UTSW	7	66,305,521 (GRCm38)	missense	possibly damaging	0.69
R3886:Lrrk1	UTSW	7	66,292,364 (GRCm38)	missense	probably damaging	1.00
R3893:Lrrk1	UTSW	7	66,278,520 (GRCm38)	splice site	probably benign
R3906:Lrrk1	UTSW	7	66,294,903 (GRCm38)	missense	possibly damaging	0.84
R4259:Lrrk1	UTSW	7	66,330,764 (GRCm38)	missense	probably damaging	1.00
R4649:Lrrk1	UTSW	7	66,273,053 (GRCm38)	missense	probably benign	0.12
R4672:Lrrk1	UTSW	7	66,279,372 (GRCm38)	missense	probably benign	0.00
R4693:Lrrk1	UTSW	7	66,262,487 (GRCm38)	missense	probably damaging	1.00
R4729:Lrrk1	UTSW	7	66,262,293 (GRCm38)	missense	probably benign
R4737:Lrrk1	UTSW	7	66,306,873 (GRCm38)	missense	probably benign	0.09
R4795:Lrrk1	UTSW	7	66,262,665 (GRCm38)	missense	possibly damaging	0.94
R4911:Lrrk1	UTSW	7	66,295,454 (GRCm38)	missense	probably damaging	0.97
R5002:Lrrk1	UTSW	7	66,332,363 (GRCm38)	missense	probably damaging	1.00
R5254:Lrrk1	UTSW	7	66,307,107 (GRCm38)	missense	probably benign	0.00
R5407:Lrrk1	UTSW	7	66,270,797 (GRCm38)	missense	probably benign	0.20
R5482:Lrrk1	UTSW	7	66,330,670 (GRCm38)	missense	probably benign
R5600:Lrrk1	UTSW	7	66,307,215 (GRCm38)	missense	probably benign	0.31
R5615:Lrrk1	UTSW	7	66,287,615 (GRCm38)	missense	probably damaging	1.00
R6041:Lrrk1	UTSW	7	66,262,133 (GRCm38)	missense	probably benign
R6211:Lrrk1	UTSW	7	66,302,710 (GRCm38)	missense	possibly damaging	0.89
R6271:Lrrk1	UTSW	7	66,307,103 (GRCm38)	critical splice donor site	probably null
R6276:Lrrk1	UTSW	7	66,306,839 (GRCm38)	splice site	probably null
R6447:Lrrk1	UTSW	7	66,302,728 (GRCm38)	missense	probably benign	0.19
R6478:Lrrk1	UTSW	7	66,262,733 (GRCm38)	missense	probably damaging	0.96
R6615:Lrrk1	UTSW	7	66,281,648 (GRCm38)	missense	probably damaging	1.00
R6745:Lrrk1	UTSW	7	66,273,001 (GRCm38)	missense	probably damaging	1.00
R6836:Lrrk1	UTSW	7	66,342,779 (GRCm38)	missense	probably benign	0.05
R6995:Lrrk1	UTSW	7	66,292,342 (GRCm38)	missense	probably damaging	1.00
R7107:Lrrk1	UTSW	7	66,287,443 (GRCm38)	missense	possibly damaging	0.94
R7137:Lrrk1	UTSW	7	66,285,279 (GRCm38)	missense	probably benign	0.06
R7203:Lrrk1	UTSW	7	66,270,825 (GRCm38)	missense	probably damaging	1.00
R7224:Lrrk1	UTSW	7	66,332,386 (GRCm38)	missense	probably damaging	0.99
R7239:Lrrk1	UTSW	7	66,262,155 (GRCm38)	missense	probably benign
R7440:Lrrk1	UTSW	7	66,290,854 (GRCm38)	missense	probably damaging	1.00
R7515:Lrrk1	UTSW	7	66,262,562 (GRCm38)	missense	probably benign
R7593:Lrrk1	UTSW	7	66,308,691 (GRCm38)	missense	probably benign	0.12
R7728:Lrrk1	UTSW	7	66,262,715 (GRCm38)	missense	probably benign	0.00
R7984:Lrrk1	UTSW	7	66,300,729 (GRCm38)	splice site	probably null
R7993:Lrrk1	UTSW	7	66,262,454 (GRCm38)	missense	probably benign	0.00
R8009:Lrrk1	UTSW	7	66,265,474 (GRCm38)	missense	possibly damaging	0.82
R8037:Lrrk1	UTSW	7	66,285,341 (GRCm38)	missense	probably benign
R8101:Lrrk1	UTSW	7	66,342,782 (GRCm38)	missense	probably benign
R8116:Lrrk1	UTSW	7	66,262,623 (GRCm38)	missense	possibly damaging	0.95
R8126:Lrrk1	UTSW	7	66,292,315 (GRCm38)	missense	probably damaging	1.00
R8278:Lrrk1	UTSW	7	66,278,684 (GRCm38)	missense	probably benign	0.37
R8559:Lrrk1	UTSW	7	66,282,327 (GRCm38)	missense	possibly damaging	0.48
R8669:Lrrk1	UTSW	7	66,262,596 (GRCm38)	missense	probably benign	0.20
R8690:Lrrk1	UTSW	7	66,302,729 (GRCm38)	missense	probably benign	0.02
R8955:Lrrk1	UTSW	7	66,269,825 (GRCm38)	missense	probably benign	0.09
R9135:Lrrk1	UTSW	7	66,278,609 (GRCm38)	missense	probably damaging	1.00
R9380:Lrrk1	UTSW	7	66,278,583 (GRCm38)	missense	probably damaging	1.00
R9625:Lrrk1	UTSW	7	66,259,918 (GRCm38)	makesense	probably null
R9721:Lrrk1	UTSW	7	66,274,875 (GRCm38)	missense	probably damaging	1.00
RF018:Lrrk1	UTSW	7	66,381,502 (GRCm38)	missense	possibly damaging	0.83

Predicted Primers

PCR Primer
(F):5'- AGGCAGATACCTTCTCGTCATACAC -3'
(R):5'- TCTCCTCCCAATAGTGCTATACAAG -3'

Sequencing Primer
(F):5'- ATACACGATGCGAGGCCTGATC -3'
(R):5'- GCTATACAAGCCAACCCTGAAAC -3'

Posted On

2015-10-08