Incidental Mutation 'R3976:Lrp3'
| ID |
312639 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lrp3
|
| Ensembl Gene |
ENSMUSG00000001802 |
| Gene Name |
low density lipoprotein receptor-related protein 3 |
| Synonyms |
|
| MMRRC Submission |
040842-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.111)
|
| Stock # |
R3976 (G1)
|
| Quality Score |
163 |
|
Status
|
Validated
|
| Chromosome |
7 |
| Chromosomal Location |
34900303-34914791 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 34903530 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 251
(D251G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000113406
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001854]
[ENSMUST00000118444]
[ENSMUST00000122409]
[ENSMUST00000131048]
|
| AlphaFold |
E9Q1T6 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000001854
|
| SMART Domains |
Protein: ENSMUSP00000001854
Gene: ENSMUSG00000030495
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
14 |
37 |
N/A |
INTRINSIC |
|
Pfam:AA_permease_2
|
46 |
474 |
4.8e-65 |
PFAM |
|
Pfam:AA_permease
|
51 |
467 |
9.3e-37 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000118444
AA Change: D251G
PolyPhen 2
Score 0.059 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000113406
Gene: ENSMUSG00000001802
AA Change: D251G
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
35 |
N/A |
INTRINSIC |
|
CUB
|
43 |
159 |
9.97e-20 |
SMART |
|
LDLa
|
165 |
202 |
7.21e-11 |
SMART |
|
LDLa
|
211 |
251 |
1.37e-11 |
SMART |
|
CUB
|
254 |
365 |
1.98e-3 |
SMART |
|
LDLa
|
367 |
414 |
1.85e-1 |
SMART |
|
LDLa
|
415 |
453 |
4.44e-3 |
SMART |
|
LDLa
|
454 |
490 |
8.74e-10 |
SMART |
|
transmembrane domain
|
497 |
519 |
N/A |
INTRINSIC |
|
low complexity region
|
584 |
606 |
N/A |
INTRINSIC |
|
low complexity region
|
641 |
652 |
N/A |
INTRINSIC |
|
low complexity region
|
674 |
684 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000122409
AA Change: D272G
PolyPhen 2
Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)
|
| SMART Domains |
Protein: ENSMUSP00000114026
Gene: ENSMUSG00000001802
AA Change: D272G
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
35 |
N/A |
INTRINSIC |
|
CUB
|
64 |
180 |
9.97e-20 |
SMART |
|
LDLa
|
186 |
223 |
7.21e-11 |
SMART |
|
LDLa
|
232 |
272 |
1.37e-11 |
SMART |
|
CUB
|
275 |
386 |
1.98e-3 |
SMART |
|
LDLa
|
388 |
435 |
1.85e-1 |
SMART |
|
LDLa
|
436 |
474 |
4.44e-3 |
SMART |
|
LDLa
|
475 |
511 |
8.74e-10 |
SMART |
|
transmembrane domain
|
518 |
540 |
N/A |
INTRINSIC |
|
low complexity region
|
605 |
627 |
N/A |
INTRINSIC |
|
low complexity region
|
662 |
673 |
N/A |
INTRINSIC |
|
low complexity region
|
695 |
705 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000131048
|
| SMART Domains |
Protein: ENSMUSP00000118331
Gene: ENSMUSG00000030495
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
14 |
37 |
N/A |
INTRINSIC |
|
Pfam:AA_permease_2
|
46 |
346 |
8.6e-48 |
PFAM |
|
Pfam:AA_permease
|
51 |
346 |
1e-28 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000146959
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153163
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155404
|
| Meta Mutation Damage Score |
0.0815 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.8%
- 20x: 93.3%
|
| Validation Efficiency |
98% (49/50) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca9 |
T |
C |
11: 110,039,615 (GRCm39) |
D466G |
probably benign |
Het |
| Asb4 |
A |
T |
6: 5,390,771 (GRCm39) |
M55L |
probably benign |
Het |
| Atxn7l1 |
T |
C |
12: 33,375,954 (GRCm39) |
S10P |
probably damaging |
Het |
| Bola3 |
T |
C |
6: 83,328,249 (GRCm39) |
L45P |
probably benign |
Het |
| Cacna2d4 |
A |
G |
6: 119,255,134 (GRCm39) |
|
probably null |
Het |
| Cfap54 |
A |
G |
10: 92,675,333 (GRCm39) |
S2863P |
possibly damaging |
Het |
| Cyb5r3 |
A |
G |
15: 83,044,330 (GRCm39) |
V180A |
possibly damaging |
Het |
| Dglucy |
A |
T |
12: 100,807,648 (GRCm39) |
T186S |
probably benign |
Het |
| Eml5 |
A |
T |
12: 98,768,724 (GRCm39) |
|
probably benign |
Het |
| Fam90a1a |
G |
A |
8: 22,451,432 (GRCm39) |
D98N |
probably damaging |
Het |
| Fbxo16 |
T |
A |
14: 65,524,606 (GRCm39) |
L42Q |
probably damaging |
Het |
| Fbxw16 |
A |
G |
9: 109,268,697 (GRCm39) |
V231A |
probably benign |
Het |
| Fermt3 |
G |
A |
19: 6,979,792 (GRCm39) |
A447V |
possibly damaging |
Het |
| Fignl2 |
A |
G |
15: 100,950,467 (GRCm39) |
L605P |
unknown |
Het |
| Gcsam |
T |
G |
16: 45,440,192 (GRCm39) |
N78K |
probably damaging |
Het |
| Gdf2 |
T |
A |
14: 33,666,791 (GRCm39) |
V171D |
probably damaging |
Het |
| Gm28042 |
C |
T |
2: 119,867,237 (GRCm39) |
H218Y |
probably benign |
Het |
| Herpud2 |
A |
G |
9: 25,021,734 (GRCm39) |
V304A |
probably damaging |
Het |
| Kcnma1 |
C |
T |
14: 24,053,815 (GRCm39) |
|
probably null |
Het |
| Mapkbp1 |
T |
C |
2: 119,852,339 (GRCm39) |
V957A |
possibly damaging |
Het |
| Mepe |
C |
T |
5: 104,484,944 (GRCm39) |
P28L |
probably benign |
Het |
| Muc2 |
T |
A |
7: 141,300,541 (GRCm39) |
|
probably benign |
Het |
| Nt5dc2 |
T |
C |
14: 30,860,832 (GRCm39) |
S439P |
probably damaging |
Het |
| Opn4 |
C |
T |
14: 34,319,066 (GRCm39) |
R173H |
probably benign |
Het |
| Or2k2 |
A |
G |
4: 58,785,164 (GRCm39) |
L186P |
probably damaging |
Het |
| Or4f14 |
C |
T |
2: 111,742,951 (GRCm39) |
G108D |
possibly damaging |
Het |
| Phf8-ps |
A |
T |
17: 33,285,405 (GRCm39) |
S466T |
probably benign |
Het |
| Ppp1r12a |
T |
C |
10: 108,089,341 (GRCm39) |
V660A |
probably benign |
Het |
| Prdm6 |
T |
C |
18: 53,673,278 (GRCm39) |
I186T |
possibly damaging |
Het |
| Rab18 |
T |
A |
18: 6,778,529 (GRCm39) |
D53E |
probably benign |
Het |
| Rel |
A |
G |
11: 23,692,939 (GRCm39) |
S365P |
probably benign |
Het |
| Rhbg |
C |
A |
3: 88,151,843 (GRCm39) |
G383V |
probably damaging |
Het |
| Rnps1-ps |
A |
T |
6: 7,983,149 (GRCm39) |
|
noncoding transcript |
Het |
| Rp1l1 |
T |
A |
14: 64,267,758 (GRCm39) |
Y1115N |
probably damaging |
Het |
| Runx2 |
T |
C |
17: 44,920,966 (GRCm39) |
T339A |
possibly damaging |
Het |
| Ryr3 |
T |
C |
2: 112,506,182 (GRCm39) |
E3455G |
possibly damaging |
Het |
| Serpina1d |
A |
T |
12: 103,734,107 (GRCm39) |
S66T |
probably benign |
Het |
| Setd3 |
T |
C |
12: 108,131,417 (GRCm39) |
K3R |
possibly damaging |
Het |
| Spg7 |
A |
G |
8: 123,806,187 (GRCm39) |
D299G |
probably damaging |
Het |
| Sptbn5 |
C |
T |
2: 119,878,742 (GRCm39) |
|
noncoding transcript |
Het |
| Srcap |
A |
G |
7: 127,148,411 (GRCm39) |
T1859A |
probably benign |
Het |
| Suox |
A |
G |
10: 128,506,906 (GRCm39) |
V374A |
probably damaging |
Het |
| Tesk1 |
C |
T |
4: 43,445,786 (GRCm39) |
P280S |
possibly damaging |
Het |
| Tsc22d1 |
T |
C |
14: 76,656,049 (GRCm39) |
S761P |
probably damaging |
Het |
| Tubal3 |
C |
T |
13: 3,982,946 (GRCm39) |
S242L |
probably benign |
Het |
| Ugt2b1 |
C |
A |
5: 87,065,534 (GRCm39) |
V502L |
probably benign |
Het |
|
| Other mutations in Lrp3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00656:Lrp3
|
APN |
7 |
34,905,453 (GRCm39) |
splice site |
probably benign |
|
|
IGL01714:Lrp3
|
APN |
7 |
34,905,496 (GRCm39) |
splice site |
probably null |
|
|
IGL03033:Lrp3
|
APN |
7 |
34,902,052 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
IGL03166:Lrp3
|
APN |
7 |
34,901,905 (GRCm39) |
missense |
probably benign |
0.00 |
|
Blackball
|
UTSW |
7 |
34,905,477 (GRCm39) |
missense |
probably damaging |
1.00 |
|
lowball
|
UTSW |
7 |
34,903,593 (GRCm39) |
missense |
probably benign |
0.00 |
|
PIT4434001:Lrp3
|
UTSW |
7 |
34,903,420 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0416:Lrp3
|
UTSW |
7 |
34,901,778 (GRCm39) |
missense |
probably benign |
|
|
R0733:Lrp3
|
UTSW |
7 |
34,901,545 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R0907:Lrp3
|
UTSW |
7 |
34,902,718 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1437:Lrp3
|
UTSW |
7 |
34,912,595 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1591:Lrp3
|
UTSW |
7 |
34,901,790 (GRCm39) |
missense |
probably benign |
0.03 |
|
R1625:Lrp3
|
UTSW |
7 |
34,903,350 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1703:Lrp3
|
UTSW |
7 |
34,912,586 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R4196:Lrp3
|
UTSW |
7 |
34,902,835 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4679:Lrp3
|
UTSW |
7 |
34,903,365 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5686:Lrp3
|
UTSW |
7 |
34,902,910 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R5836:Lrp3
|
UTSW |
7 |
34,902,747 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6160:Lrp3
|
UTSW |
7 |
34,903,548 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
R6342:Lrp3
|
UTSW |
7 |
34,901,731 (GRCm39) |
missense |
probably benign |
0.01 |
|
R6364:Lrp3
|
UTSW |
7 |
34,903,134 (GRCm39) |
missense |
probably benign |
0.03 |
|
R6415:Lrp3
|
UTSW |
7 |
34,903,593 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6502:Lrp3
|
UTSW |
7 |
34,903,413 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R6747:Lrp3
|
UTSW |
7 |
34,910,862 (GRCm39) |
missense |
probably benign |
|
|
R7205:Lrp3
|
UTSW |
7 |
34,902,051 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7232:Lrp3
|
UTSW |
7 |
34,905,477 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7522:Lrp3
|
UTSW |
7 |
34,903,755 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7870:Lrp3
|
UTSW |
7 |
34,910,922 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7963:Lrp3
|
UTSW |
7 |
34,902,404 (GRCm39) |
nonsense |
probably null |
|
|
R9094:Lrp3
|
UTSW |
7 |
34,903,182 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9242:Lrp3
|
UTSW |
7 |
34,901,934 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9474:Lrp3
|
UTSW |
7 |
34,903,489 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1177:Lrp3
|
UTSW |
7 |
34,902,437 (GRCm39) |
nonsense |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GGTAGGAAAGCGTTTGCAGC -3'
(R):5'- TCGGATGAGGGTAACTGCTCAG -3'
Sequencing Primer
(F):5'- GGCCTTCATACACCTGGACATAGTC -3'
(R):5'- AGGGTAACTGCTCAGCACCTG -3'
|
| Posted On |
2015-04-30 |
Incidental Mutation