Mutagenetix > Incidental Mutation

Incidental Mutation 'R1972:Lgmn'

221125

Institutional Source

Beutler Lab

Gene Symbol

Lgmn

Ensembl Gene

ENSMUSG00000021190

Gene Name

legumain

Synonyms

preprolegumain, Prsc1, 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

102360341-102405987 bp(-) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

A to G at 102362080 bp (GRCm39)

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: 112,717,050 (GRCm39)		probably benign	Het
Bbs2	A	G	8: 94,807,805 (GRCm39)		probably benign	Het
Bcl9	A	C	3: 97,114,518 (GRCm39)	D1035E	probably damaging	Het
Bmpr2	A	G	1: 59,852,762 (GRCm39)	E31G	possibly damaging	Het
Borcs5	A	G	6: 134,687,137 (GRCm39)	D164G	probably damaging	Het
Cap2	A	G	13: 46,791,375 (GRCm39)	R181G	probably damaging	Het
Ccdc113	A	T	8: 96,264,874 (GRCm39)	H128L	probably benign	Het
Cdh20	G	A	1: 109,988,862 (GRCm39)	V255I	probably benign	Het
Chat	C	T	14: 32,146,148 (GRCm39)	V342I	probably benign	Het
Chrm4	C	T	2: 91,757,838 (GRCm39)	A82V	probably benign	Het
Cyp2d22	A	T	15: 82,260,028 (GRCm39)	M52K	probably benign	Het
Dennd2c	T	C	3: 103,039,014 (GRCm39)	V54A	probably benign	Het
Dgka	C	T	10: 128,556,335 (GRCm39)	G717D	probably damaging	Het
Dnah1	C	T	14: 30,987,348 (GRCm39)	W3550*	probably null	Het
Eif2ak1	A	G	5: 143,821,532 (GRCm39)	T283A	probably benign	Het
Entrep2	A	T	7: 64,425,516 (GRCm39)	I192N	possibly damaging	Het
Fcgbp	A	T	7: 27,793,617 (GRCm39)	Y1173F	probably benign	Het
Flt1	G	A	5: 147,591,903 (GRCm39)		probably benign	Het
Gpr149	T	C	3: 62,438,216 (GRCm39)	K647R	probably benign	Het
Gsdma2	T	C	11: 98,541,744 (GRCm39)	V157A	probably benign	Het
Heatr4	T	A	12: 84,001,794 (GRCm39)	I884F	probably damaging	Het
Ift56	C	A	6: 38,387,738 (GRCm39)	N396K	probably benign	Het
Il17ra	A	G	6: 120,459,177 (GRCm39)	E776G	probably benign	Het
Inpp5d	T	C	1: 87,604,036 (GRCm39)	S235P	probably benign	Het
Iqgap3	T	A	3: 87,991,235 (GRCm39)		probably null	Het
Isoc2a	T	A	7: 4,895,086 (GRCm39)	D171E	probably damaging	Het
Itga10	C	T	3: 96,559,054 (GRCm39)		probably benign	Het
Kcnk12	T	C	17: 88,104,560 (GRCm39)	D108G	possibly damaging	Het
Klra9	A	T	6: 130,159,345 (GRCm39)		probably null	Het
Morf4l1	A	T	9: 89,977,267 (GRCm39)		probably benign	Het
Mthfr	T	C	4: 148,136,384 (GRCm39)	I380T	probably damaging	Het
Mybpc1	T	C	10: 88,387,404 (GRCm39)	I436V	probably benign	Het
Naip5	A	G	13: 100,349,278 (GRCm39)	V1350A	probably damaging	Het
Neil2	A	T	14: 63,423,526 (GRCm39)	C36S	possibly damaging	Het
Nlrx1	A	G	9: 44,164,753 (GRCm39)	V897A	probably benign	Het
Nod2	A	T	8: 89,379,501 (GRCm39)	M8L	probably damaging	Het
Nop2	A	G	6: 125,111,602 (GRCm39)	T112A	probably benign	Het
Nrap	T	A	19: 56,345,785 (GRCm39)	T608S	probably damaging	Het
Nuak2	A	T	1: 132,258,340 (GRCm39)	H257L	probably damaging	Het
Or10x1	T	C	1: 174,197,136 (GRCm39)	F218L	probably benign	Het
Or2ag12	T	C	7: 106,277,426 (GRCm39)	D89G	probably benign	Het
Or4c113	A	T	2: 88,884,891 (GRCm39)	M293K	probably benign	Het
Or52e8	T	C	7: 104,625,106 (GRCm39)	I33V	possibly damaging	Het
Or5ac25	A	T	16: 59,182,476 (GRCm39)	V35D	probably damaging	Het
Or5b119	T	C	19: 13,457,058 (GRCm39)	N168S	probably benign	Het
Or8b40	T	A	9: 38,027,863 (GRCm39)	M257K	possibly damaging	Het
Pde1a	T	C	2: 79,696,065 (GRCm39)	E358G	probably damaging	Het
Pdlim1	A	T	19: 40,211,581 (GRCm39)	S237R	probably damaging	Het
Pithd1	T	C	4: 135,714,340 (GRCm39)	D36G	probably damaging	Het
Ppp2r3d	A	G	9: 101,088,976 (GRCm39)	F449S	probably benign	Het
Prr11	G	A	11: 86,989,580 (GRCm39)	R264C	possibly damaging	Het
Rbm43	A	T	2: 51,815,548 (GRCm39)	H224Q	probably benign	Het
Rfx5	C	T	3: 94,864,603 (GRCm39)	L250F	probably damaging	Het
Rgs22	T	A	15: 36,103,982 (GRCm39)	I160L	probably benign	Het
Rorb	T	A	19: 18,929,567 (GRCm39)	Q393H	probably damaging	Het
Rpl13a	T	A	7: 44,775,419 (GRCm39)	K368*	probably null	Het
Scaf8	T	G	17: 3,219,646 (GRCm39)	S276R	unknown	Het
Scube2	A	T	7: 109,408,421 (GRCm39)	N675K	probably benign	Het
Sec22c	A	T	9: 121,517,320 (GRCm39)	M126K	possibly damaging	Het
Serpinb11	T	C	1: 107,297,210 (GRCm39)	F29L	probably damaging	Het
Sis	A	G	3: 72,828,337 (GRCm39)	F1217S	probably damaging	Het
Slc18a2	A	G	19: 59,263,085 (GRCm39)	D294G	possibly damaging	Het
Slc9c1	A	G	16: 45,413,835 (GRCm39)	T988A	possibly damaging	Het
Smndc1	A	C	19: 53,371,986 (GRCm39)		probably null	Het
Sned1	G	A	1: 93,192,795 (GRCm39)	G361S	probably damaging	Het
Spatc1	A	T	15: 76,169,075 (GRCm39)		probably null	Het
Stab2	A	T	10: 86,796,180 (GRCm39)	C356S	probably damaging	Het
Stk4	C	T	2: 163,942,448 (GRCm39)	T360M	probably benign	Het
Tbc1d30	A	T	10: 121,142,135 (GRCm39)		probably null	Het
Tenm3	T	C	8: 48,681,626 (GRCm39)	E2668G	probably damaging	Het
Tigar	A	G	6: 127,064,889 (GRCm39)	V253A	possibly damaging	Het
Tmc2	T	A	2: 130,056,584 (GRCm39)		probably benign	Het
Ugt1a10	A	T	1: 87,983,769 (GRCm39)	Y189F	probably damaging	Het
Vmn2r82	A	G	10: 79,214,680 (GRCm39)	D221G	probably damaging	Het
Xkr5	C	T	8: 18,991,997 (GRCm39)	V131M	probably damaging	Het

Other mutations in Lgmn

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00823:Lgmn	APN	12	102,364,435 (GRCm39)	splice site	probably benign
IGL02069:Lgmn	APN	12	102,370,558 (GRCm39)	missense	possibly damaging	0.92
IGL02150:Lgmn	APN	12	102,361,986 (GRCm39)	missense	possibly damaging	0.80
IGL02228:Lgmn	APN	12	102,361,973 (GRCm39)	missense	probably benign	0.04
IGL02637:Lgmn	APN	12	102,366,485 (GRCm39)	missense	probably damaging	0.98
Getz	UTSW	12	102,366,248 (GRCm39)	missense	probably damaging	0.99
R0233:Lgmn	UTSW	12	102,366,248 (GRCm39)	missense	probably damaging	0.99
R0233:Lgmn	UTSW	12	102,366,248 (GRCm39)	missense	probably damaging	0.99
R0988:Lgmn	UTSW	12	102,364,536 (GRCm39)	missense	probably damaging	0.99
R1451:Lgmn	UTSW	12	102,372,151 (GRCm39)	splice site	probably benign
R1568:Lgmn	UTSW	12	102,360,868 (GRCm39)	missense	possibly damaging	0.95
R1944:Lgmn	UTSW	12	102,368,183 (GRCm39)	missense	probably damaging	1.00
R2133:Lgmn	UTSW	12	102,361,167 (GRCm39)	missense	probably damaging	1.00
R2298:Lgmn	UTSW	12	102,361,937 (GRCm39)	missense	probably damaging	0.99
R3846:Lgmn	UTSW	12	102,370,588 (GRCm39)	missense	possibly damaging	0.87
R4610:Lgmn	UTSW	12	102,366,383 (GRCm39)	splice site	probably benign
R4788:Lgmn	UTSW	12	102,368,936 (GRCm39)	missense	probably benign	0.11
R5050:Lgmn	UTSW	12	102,369,680 (GRCm39)	splice site	probably null
R5708:Lgmn	UTSW	12	102,370,587 (GRCm39)	missense	possibly damaging	0.87
R5969:Lgmn	UTSW	12	102,372,086 (GRCm39)	missense	probably damaging	1.00
R6090:Lgmn	UTSW	12	102,366,413 (GRCm39)	missense	probably damaging	1.00
R6420:Lgmn	UTSW	12	102,389,978 (GRCm39)	nonsense	probably null
R6496:Lgmn	UTSW	12	102,364,498 (GRCm39)	missense	probably benign	0.01
R6592:Lgmn	UTSW	12	102,370,529 (GRCm39)	missense	probably damaging	1.00
R6659:Lgmn	UTSW	12	102,368,951 (GRCm39)	missense	probably benign	0.03
R7063:Lgmn	UTSW	12	102,368,937 (GRCm39)	missense	probably damaging	1.00
R7336:Lgmn	UTSW	12	102,389,998 (GRCm39)	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