Mutagenetix > Incidental Mutation

Incidental Mutation 'R1972:Lgmn'

221125

Institutional Source

Beutler Lab

Gene Symbol

Lgmn

Ensembl Gene

ENSMUSG00000021190

Gene Name

legumain

Synonyms

Prsc1, preprolegumain, AEP

MMRRC Submission

039985-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1972 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

102394084-102439813 bp(-) (GRCm38)

Type of Mutation

unclassified

DNA Base Change (assembly)

A to G at 102395821 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000122646 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021607] [ENSMUST00000056950] [ENSMUST00000110020] [ENSMUST00000133820]

AlphaFold

O89017

Predicted Effect

probably benign
Transcript: ENSMUST00000021607

SMART Domains

Protein: ENSMUSP00000021607
Gene: ENSMUSG00000021190

Domain	Start	End	E-Value	Type
low complexity region	5	22	N/A	INTRINSIC
Pfam:Peptidase_C13	31	288	8e-120	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000056950

SMART Domains

Protein: ENSMUSP00000060771
Gene: ENSMUSG00000044456

Domain	Start	End	E-Value	Type
low complexity region	20	32	N/A	INTRINSIC
SH2	61	149	1.89e-2	SMART
low complexity region	254	311	N/A	INTRINSIC
low complexity region	316	325	N/A	INTRINSIC
low complexity region	358	380	N/A	INTRINSIC
low complexity region	448	469	N/A	INTRINSIC
low complexity region	514	523	N/A	INTRINSIC
low complexity region	579	594	N/A	INTRINSIC
low complexity region	714	728	N/A	INTRINSIC
VPS9	736	852	5.75e-38	SMART
RA	873	960	3.5e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000110020

SMART Domains

Protein: ENSMUSP00000105647
Gene: ENSMUSG00000021190

Domain	Start	End	E-Value	Type
low complexity region	5	22	N/A	INTRINSIC
Pfam:Peptidase_C13	31	288	8e-120	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000133820

SMART Domains

Protein: ENSMUSP00000122646
Gene: ENSMUSG00000044456

Domain	Start	End	E-Value	Type
Blast:SH2	1	69	3e-39	BLAST
SCOP:d1a81a2	3	77	2e-4	SMART
low complexity region	174	231	N/A	INTRINSIC
low complexity region	236	245	N/A	INTRINSIC
low complexity region	278	300	N/A	INTRINSIC
low complexity region	368	389	N/A	INTRINSIC
low complexity region	434	443	N/A	INTRINSIC
low complexity region	499	514	N/A	INTRINSIC
low complexity region	634	648	N/A	INTRINSIC
VPS9	656	772	5.75e-38	SMART
RA	793	880	3.5e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146499

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.8%
20x: 94.2%

Validation Efficiency

100% (77/77)

MGI Phenotype

FUNCTION: This gene encodes a member of the cysteine peptidase family C13 that plays an important role in the endosome/lysosomal degradation system. The encoded inactive preproprotein undergoes autocatalytic removal of the C-terminal inhibitory propeptide to generate the active endopeptidase that cleaves protein substrates on the C-terminal side of asparagine residues. Mice lacking the encoded protein exhibit defects in the lysosomal processing of proteins resulting in their accumulation in the lysosomes, and develop symptoms resembling hemophagocytic lymphohistiocytosis. [provided by RefSeq, Aug 2016]
PHENOTYPE: Homozygotes for a null allele exhibit slow postnatal weight gain, develop features of hemophagocytic syndrome, and accumulate giant lysosomes in renal tubule cells. Homozygotes for another null allele display impaired TLR9 signaling in dendritic cells, progressive kidney pathology, and proteinuria. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adat1	A	G	8: 111,990,418		probably benign	Het
Bbs2	A	G	8: 94,081,177		probably benign	Het
Bcl9	A	C	3: 97,207,202	D1035E	probably damaging	Het
Bmpr2	A	G	1: 59,813,603	E31G	possibly damaging	Het
Borcs5	A	G	6: 134,710,174	D164G	probably damaging	Het
Cap2	A	G	13: 46,637,899	R181G	probably damaging	Het
Ccdc113	A	T	8: 95,538,246	H128L	probably benign	Het
Cdh7	G	A	1: 110,061,132	V255I	probably benign	Het
Chat	C	T	14: 32,424,191	V342I	probably benign	Het
Chrm4	C	T	2: 91,927,493	A82V	probably benign	Het
Cyp2d22	A	T	15: 82,375,827	M52K	probably benign	Het
Dennd2c	T	C	3: 103,131,698	V54A	probably benign	Het
Dgka	C	T	10: 128,720,466	G717D	probably damaging	Het
Dnah1	C	T	14: 31,265,391	W3550*	probably null	Het
Eif2ak1	A	G	5: 143,884,714	T283A	probably benign	Het
Fam189a1	A	T	7: 64,775,768	I192N	possibly damaging	Het
Fcgbp	A	T	7: 28,094,192	Y1173F	probably benign	Het
Flt1	G	A	5: 147,655,093		probably benign	Het
Gpr149	T	C	3: 62,530,795	K647R	probably benign	Het
Gsdma2	T	C	11: 98,650,918	V157A	probably benign	Het
Heatr4	T	A	12: 83,955,020	I884F	probably damaging	Het
Il17ra	A	G	6: 120,482,216	E776G	probably benign	Het
Inpp5d	T	C	1: 87,676,314	S235P	probably benign	Het
Iqgap3	T	A	3: 88,083,928		probably null	Het
Isoc2a	T	A	7: 4,892,087	D171E	probably damaging	Het
Itga10	C	T	3: 96,651,738		probably benign	Het
Kcnk12	T	C	17: 87,797,132	D108G	possibly damaging	Het
Klra9	A	T	6: 130,182,382		probably null	Het
Morf4l1	A	T	9: 90,095,214		probably benign	Het
Mthfr	T	C	4: 148,051,927	I380T	probably damaging	Het
Mybpc1	T	C	10: 88,551,542	I436V	probably benign	Het
Naip5	A	G	13: 100,212,770	V1350A	probably damaging	Het
Neil2	A	T	14: 63,186,077	C36S	possibly damaging	Het
Nlrx1	A	G	9: 44,253,456	V897A	probably benign	Het
Nod2	A	T	8: 88,652,873	M8L	probably damaging	Het
Nop2	A	G	6: 125,134,639	T112A	probably benign	Het
Nrap	T	A	19: 56,357,353	T608S	probably damaging	Het
Nuak2	A	T	1: 132,330,602	H257L	probably damaging	Het
Olfr1218	A	T	2: 89,054,547	M293K	probably benign	Het
Olfr1475	T	C	19: 13,479,694	N168S	probably benign	Het
Olfr209	A	T	16: 59,362,113	V35D	probably damaging	Het
Olfr417	T	C	1: 174,369,570	F218L	probably benign	Het
Olfr671	T	C	7: 104,975,899	I33V	possibly damaging	Het
Olfr693	T	C	7: 106,678,219	D89G	probably benign	Het
Olfr889	T	A	9: 38,116,567	M257K	possibly damaging	Het
Pde1a	T	C	2: 79,865,721	E358G	probably damaging	Het
Pdlim1	A	T	19: 40,223,137	S237R	probably damaging	Het
Pithd1	T	C	4: 135,987,029	D36G	probably damaging	Het
Ppp2r3a	A	G	9: 101,211,777	F449S	probably benign	Het
Prr11	G	A	11: 87,098,754	R264C	possibly damaging	Het
Rbm43	A	T	2: 51,925,536	H224Q	probably benign	Het
Rfx5	C	T	3: 94,957,292	L250F	probably damaging	Het
Rgs22	T	A	15: 36,103,836	I160L	probably benign	Het
Rorb	T	A	19: 18,952,203	Q393H	probably damaging	Het
Rpl13a	T	A	7: 45,125,995	K368*	probably null	Het
Scaf8	T	G	17: 3,169,371	S276R	unknown	Het
Scube2	A	T	7: 109,809,214	N675K	probably benign	Het
Sec22c	A	T	9: 121,688,254	M126K	possibly damaging	Het
Serpinb11	T	C	1: 107,369,480	F29L	probably damaging	Het
Sis	A	G	3: 72,921,004	F1217S	probably damaging	Het
Slc18a2	A	G	19: 59,274,653	D294G	possibly damaging	Het
Slc9c1	A	G	16: 45,593,472	T988A	possibly damaging	Het
Smndc1	A	C	19: 53,383,555		probably null	Het
Sned1	G	A	1: 93,265,073	G361S	probably damaging	Het
Spatc1	A	T	15: 76,284,875		probably null	Het
Stab2	A	T	10: 86,960,316	C356S	probably damaging	Het
Stk4	C	T	2: 164,100,528	T360M	probably benign	Het
Tbc1d30	A	T	10: 121,306,230		probably null	Het
Tenm3	T	C	8: 48,228,591	E2668G	probably damaging	Het
Tigar	A	G	6: 127,087,926	V253A	possibly damaging	Het
Tmc2	T	A	2: 130,214,664		probably benign	Het
Ttc26	C	A	6: 38,410,803	N396K	probably benign	Het
Ugt1a10	A	T	1: 88,056,047	Y189F	probably damaging	Het
Vmn2r82	A	G	10: 79,378,846	D221G	probably damaging	Het
Xkr5	C	T	8: 18,941,981	V131M	probably damaging	Het

Other mutations in Lgmn

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00823:Lgmn	APN	12	102398176	splice site	probably benign
IGL02069:Lgmn	APN	12	102404299	missense	possibly damaging	0.92
IGL02150:Lgmn	APN	12	102395727	missense	possibly damaging	0.80
IGL02228:Lgmn	APN	12	102395714	missense	probably benign	0.04
IGL02637:Lgmn	APN	12	102400226	missense	probably damaging	0.98
Getz	UTSW	12	102399989	missense	probably damaging	0.99
R0233:Lgmn	UTSW	12	102399989	missense	probably damaging	0.99
R0233:Lgmn	UTSW	12	102399989	missense	probably damaging	0.99
R0988:Lgmn	UTSW	12	102398277	missense	probably damaging	0.99
R1451:Lgmn	UTSW	12	102405892	splice site	probably benign
R1568:Lgmn	UTSW	12	102394609	missense	possibly damaging	0.95
R1944:Lgmn	UTSW	12	102401924	missense	probably damaging	1.00
R2133:Lgmn	UTSW	12	102394908	missense	probably damaging	1.00
R2298:Lgmn	UTSW	12	102395678	missense	probably damaging	0.99
R3846:Lgmn	UTSW	12	102404329	missense	possibly damaging	0.87
R4610:Lgmn	UTSW	12	102400124	splice site	probably benign
R4788:Lgmn	UTSW	12	102402677	missense	probably benign	0.11
R5050:Lgmn	UTSW	12	102403421	splice site	probably null
R5708:Lgmn	UTSW	12	102404328	missense	possibly damaging	0.87
R5969:Lgmn	UTSW	12	102405827	missense	probably damaging	1.00
R6090:Lgmn	UTSW	12	102400154	missense	probably damaging	1.00
R6420:Lgmn	UTSW	12	102423719	nonsense	probably null
R6496:Lgmn	UTSW	12	102398239	missense	probably benign	0.01
R6592:Lgmn	UTSW	12	102404270	missense	probably damaging	1.00
R6659:Lgmn	UTSW	12	102402692	missense	probably benign	0.03
R7063:Lgmn	UTSW	12	102402678	missense	probably damaging	1.00
R7336:Lgmn	UTSW	12	102423739	start gained	probably benign

Predicted Primers

PCR Primer
(F):5'- ACATCTCAGATGCAGGAGACC -3'
(R):5'- CTTTCCAGTGTCACAGAAACC -3'

Sequencing Primer
(F):5'- AGACCTGAGGACCCTAGCTG -3'
(R):5'- CAAACACATACCTAGCATCTCTCTTG -3'

Posted On

2014-08-25