Incidental Mutation 'R2298:Lgmn'
| ID |
245239 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lgmn
|
| Ensembl Gene |
ENSMUSG00000021190 |
| Gene Name |
legumain |
| Synonyms |
Prsc1, preprolegumain, AEP |
| MMRRC Submission |
040297-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2298 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
12 |
| Chromosomal Location |
102394084-102439813 bp(-) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 102395678 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Serine
at position 388
(F388S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000105647
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021607]
[ENSMUST00000056950]
[ENSMUST00000110020]
[ENSMUST00000133820]
|
| AlphaFold |
O89017 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000021607
AA Change: F388S
PolyPhen 2
Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000021607
Gene: ENSMUSG00000021190
AA Change: F388S
| 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 damaging
Transcript: ENSMUST00000110020
AA Change: F388S
PolyPhen 2
Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000105647
Gene: ENSMUSG00000021190
AA Change: F388S
| 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: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.0%
|
| Validation Efficiency |
|
| 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: 28 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700030K09Rik |
A |
G |
8: 72,455,403 |
D459G |
probably benign |
Het |
| 4921501E09Rik |
T |
C |
17: 33,066,778 |
E350G |
probably damaging |
Het |
| Abhd12 |
C |
A |
2: 150,901,494 |
|
probably benign |
Het |
| Atcay |
A |
T |
10: 81,210,563 |
I309N |
probably damaging |
Het |
| Capn8 |
T |
C |
1: 182,613,420 |
V473A |
probably benign |
Het |
| Cramp1l |
T |
C |
17: 24,997,480 |
I220V |
probably damaging |
Het |
| Creb3l1 |
G |
A |
2: 91,991,976 |
P222S |
probably damaging |
Het |
| Crocc |
G |
A |
4: 141,025,459 |
A1374V |
probably benign |
Het |
| Crybg1 |
A |
G |
10: 43,999,222 |
L630S |
probably damaging |
Het |
| Crygs |
C |
T |
16: 22,805,551 |
G102D |
possibly damaging |
Het |
| Erbb4 |
C |
T |
1: 68,042,531 |
D1115N |
probably damaging |
Het |
| Fasn |
T |
A |
11: 120,813,816 |
L1314F |
possibly damaging |
Het |
| Galm |
T |
A |
17: 80,181,697 |
C84* |
probably null |
Het |
| H3f3a |
C |
T |
1: 180,803,138 |
R117H |
probably benign |
Het |
| Klf13 |
T |
C |
7: 63,891,756 |
K208E |
probably damaging |
Het |
| Kremen1 |
AGGCGG |
AGGCGGCGG |
11: 5,201,788 |
|
probably benign |
Het |
| Mrc2 |
G |
A |
11: 105,348,431 |
|
probably null |
Het |
| Msh2 |
T |
A |
17: 87,708,502 |
Y521N |
probably damaging |
Het |
| Myo5b |
G |
T |
18: 74,625,605 |
R219L |
probably damaging |
Het |
| Myzap |
A |
T |
9: 71,548,757 |
M327K |
probably damaging |
Het |
| Ngfr |
AAGCAGCAGCAGCAGCAGCAGCAG |
AAGCAGCAGCAGCAGCAGCAG |
11: 95,587,490 |
|
probably benign |
Het |
| Rps6ka5 |
A |
G |
12: 100,551,454 |
F796S |
probably damaging |
Het |
| Srl |
T |
C |
16: 4,482,898 |
I332V |
probably damaging |
Het |
| Stab2 |
T |
A |
10: 86,954,474 |
|
probably null |
Het |
| Tenm2 |
T |
C |
11: 36,046,777 |
T1690A |
possibly damaging |
Het |
| Traf4 |
T |
A |
11: 78,160,851 |
D241V |
probably benign |
Het |
| Trpv6 |
A |
G |
6: 41,636,076 |
I52T |
possibly damaging |
Het |
| Zfp768 |
T |
A |
7: 127,344,189 |
M256L |
probably benign |
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 |
|
R1972:Lgmn
|
UTSW |
12 |
102395821 |
unclassified |
probably benign |
|
|
R2133:Lgmn
|
UTSW |
12 |
102394908 |
missense |
probably damaging |
1.00 |
|
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'- GGCAACAGTAATGGGAGTTGTC -3'
(R):5'- GCTGCTTACTATAGAGCCCG -3'
Sequencing Primer
(F):5'- TCACCTATGACTCTGGTAGACAAG -3'
(R):5'- TCTGTCAGAGAGGACCAT -3'
|
| Posted On |
2014-10-30 |
Incidental Mutation