Incidental Mutation 'R4593:Nub1'
| ID |
344206 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nub1
|
| Ensembl Gene |
ENSMUSG00000028954 |
| Gene Name |
negative regulator of ubiquitin-like proteins 1 |
| Synonyms |
NY-REN-18, 6330412F12Rik, BS4, 4931404D21Rik |
| MMRRC Submission |
041809-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.861)
|
| Stock # |
R4593 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
24890813-24915376 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 24914119 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 624
(Y624C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000143657
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000068693]
[ENSMUST00000068825]
[ENSMUST00000197407]
|
| AlphaFold |
P54729 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000068693
|
| SMART Domains |
Protein: ENSMUSP00000064785
Gene: ENSMUSG00000055235
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
4 |
43 |
1.62e-8 |
SMART |
|
WD40
|
46 |
83 |
3.17e-2 |
SMART |
|
WD40
|
86 |
123 |
1.9e-5 |
SMART |
|
WD40
|
126 |
179 |
3e-3 |
SMART |
|
WD40
|
182 |
221 |
2.78e-7 |
SMART |
|
WD40
|
224 |
261 |
9.9e-4 |
SMART |
|
WD40
|
264 |
301 |
1.29e-2 |
SMART |
|
WD40
|
304 |
341 |
6.28e-6 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000068825
AA Change: Y600C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000070265
Gene: ENSMUSG00000028954
AA Change: Y600C
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
37 |
70 |
N/A |
INTRINSIC |
|
PDB:1WJU|A
|
71 |
162 |
2e-45 |
PDB |
|
low complexity region
|
167 |
186 |
N/A |
INTRINSIC |
|
UBA
|
375 |
412 |
7.29e-8 |
SMART |
|
UBA
|
431 |
468 |
1.61e-9 |
SMART |
|
UBA
|
490 |
527 |
1.95e-8 |
SMART |
|
low complexity region
|
539 |
565 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000127320
|
| SMART Domains |
Protein: ENSMUSP00000119649
Gene: ENSMUSG00000055235
| Domain | Start | End | E-Value | Type |
|---|
|
WD40
|
29 |
63 |
1.27e2 |
SMART |
|
WD40
|
66 |
103 |
6.28e-6 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000142607
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000181925
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000196443
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000197407
AA Change: Y624C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000143657
Gene: ENSMUSG00000028954
AA Change: Y624C
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
61 |
94 |
N/A |
INTRINSIC |
|
PDB:1WJU|A
|
95 |
186 |
2e-45 |
PDB |
|
low complexity region
|
191 |
210 |
N/A |
INTRINSIC |
|
UBA
|
399 |
436 |
3.5e-10 |
SMART |
|
UBA
|
455 |
492 |
8.1e-12 |
SMART |
|
UBA
|
514 |
551 |
9.5e-11 |
SMART |
|
low complexity region
|
563 |
589 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000200337
|
| Meta Mutation Damage Score |
0.3430 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.1%
|
| Validation Efficiency |
96% (45/47) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that functions as a negative regulator of NEDD8, a ubiquitin-like protein that conjugates with cullin family members in order to regulate vital biological events. The protein encoded by this gene regulates the NEDD8 conjugation system post-transcriptionally by recruiting NEDD8 and its conjugates to the proteasome for degradation. This protein interacts with the product of the AIPL1 gene, which is associated with Leber congenital amaurosis, an inherited retinopathy, and mutations in that gene can abolish interaction with this protein, which may contribute to the pathogenesis. This protein is also known to accumulate in Lewy bodies in Parkinson's disease and dementia with Lewy bodies, and in glial cytoplasmic inclusions in multiple system atrophy, with this abnormal accumulation being specific to alpha-synucleinopathy lesions. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2700049A03Rik |
G |
T |
12: 71,211,320 (GRCm39) |
E685* |
probably null |
Het |
| 2700049A03Rik |
A |
T |
12: 71,211,321 (GRCm39) |
E685V |
possibly damaging |
Het |
| Aopep |
T |
C |
13: 63,215,906 (GRCm39) |
S393P |
probably benign |
Het |
| Atm |
G |
T |
9: 53,364,894 (GRCm39) |
A8E |
possibly damaging |
Het |
| Atxn3 |
A |
T |
12: 101,889,436 (GRCm39) |
M333K |
probably benign |
Het |
| Cd86 |
A |
G |
16: 36,426,918 (GRCm39) |
*310R |
probably null |
Het |
| Cyp2s1 |
ACAGCAGCAGCAGCAGCAGCAGCAG |
ACAGCAGCAGCAGCAGCAGCAG |
7: 25,515,867 (GRCm39) |
|
probably benign |
Het |
| Dgat1 |
C |
A |
15: 76,388,889 (GRCm39) |
R111S |
probably damaging |
Het |
| Dner |
T |
C |
1: 84,673,449 (GRCm39) |
M1V |
probably null |
Het |
| Dnhd1 |
G |
A |
7: 105,364,653 (GRCm39) |
D4240N |
probably benign |
Het |
| Emp3 |
A |
G |
7: 45,568,777 (GRCm39) |
L27P |
probably damaging |
Het |
| Glra3 |
G |
T |
8: 56,393,916 (GRCm39) |
G9V |
probably damaging |
Het |
| Gpr149 |
A |
T |
3: 62,510,151 (GRCm39) |
|
probably benign |
Het |
| Ighv1-9 |
T |
C |
12: 114,547,224 (GRCm39) |
T105A |
probably benign |
Het |
| Kcnd3 |
C |
T |
3: 105,566,082 (GRCm39) |
A421V |
probably damaging |
Het |
| Ldhd |
T |
C |
8: 112,355,996 (GRCm39) |
D129G |
probably damaging |
Het |
| Lnpep |
A |
G |
17: 17,799,289 (GRCm39) |
V122A |
probably benign |
Het |
| Lrrc37a |
A |
G |
11: 103,389,795 (GRCm39) |
Y1877H |
possibly damaging |
Het |
| Med13l |
T |
C |
5: 118,880,625 (GRCm39) |
L1239P |
probably damaging |
Het |
| Mib1 |
T |
C |
18: 10,768,191 (GRCm39) |
L480S |
possibly damaging |
Het |
| Mkrn3 |
C |
T |
7: 62,068,552 (GRCm39) |
W413* |
probably null |
Het |
| Myo7b |
A |
G |
18: 32,146,428 (GRCm39) |
V119A |
possibly damaging |
Het |
| Nexn |
T |
A |
3: 151,958,553 (GRCm39) |
R113S |
probably damaging |
Het |
| Npas3 |
A |
T |
12: 54,115,280 (GRCm39) |
Q703L |
probably benign |
Het |
| Npr2 |
A |
G |
4: 43,647,323 (GRCm39) |
|
probably benign |
Het |
| Obscn |
A |
C |
11: 59,024,075 (GRCm39) |
S532A |
probably damaging |
Het |
| Or1e33 |
T |
A |
11: 73,738,140 (GRCm39) |
K270N |
probably benign |
Het |
| Or9g20 |
A |
G |
2: 85,630,008 (GRCm39) |
L202P |
probably damaging |
Het |
| Panx2 |
T |
C |
15: 88,952,118 (GRCm39) |
I195T |
probably damaging |
Het |
| Parp11 |
T |
C |
6: 127,451,262 (GRCm39) |
I104T |
probably benign |
Het |
| Pkd1l1 |
G |
T |
11: 8,851,253 (GRCm39) |
D726E |
probably damaging |
Het |
| Pom121l2 |
C |
T |
13: 22,168,623 (GRCm39) |
R965W |
probably damaging |
Het |
| Prrc2c |
T |
C |
1: 162,525,101 (GRCm39) |
K502E |
probably damaging |
Het |
| Rasa1 |
T |
C |
13: 85,386,340 (GRCm39) |
|
probably null |
Het |
| Sva |
T |
C |
6: 42,019,592 (GRCm39) |
S151P |
possibly damaging |
Het |
| Svep1 |
T |
C |
4: 58,091,944 (GRCm39) |
N1564D |
possibly damaging |
Het |
| Unk |
T |
C |
11: 115,939,882 (GRCm39) |
I129T |
probably benign |
Het |
| Urb1 |
T |
C |
16: 90,584,332 (GRCm39) |
D550G |
probably damaging |
Het |
| Vmn1r194 |
T |
A |
13: 22,428,461 (GRCm39) |
M26K |
possibly damaging |
Het |
| Vmn1r59 |
A |
T |
7: 5,457,686 (GRCm39) |
F25I |
possibly damaging |
Het |
| Vmn1r88 |
A |
G |
7: 12,911,769 (GRCm39) |
K42E |
probably damaging |
Het |
| Zbtb24 |
A |
G |
10: 41,327,953 (GRCm39) |
R280G |
possibly damaging |
Het |
|
| Other mutations in Nub1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02367:Nub1
|
APN |
5 |
24,894,392 (GRCm39) |
start codon destroyed |
probably null |
0.99 |
|
IGL02626:Nub1
|
APN |
5 |
24,908,462 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
IGL02629:Nub1
|
APN |
5 |
24,908,462 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
IGL02633:Nub1
|
APN |
5 |
24,897,931 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02798:Nub1
|
APN |
5 |
24,897,812 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03384:Nub1
|
APN |
5 |
24,902,424 (GRCm39) |
splice site |
probably null |
|
|
IGL03384:Nub1
|
APN |
5 |
24,902,425 (GRCm39) |
splice site |
probably benign |
|
|
R2484:Nub1
|
UTSW |
5 |
24,913,700 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R2679:Nub1
|
UTSW |
5 |
24,897,923 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R3825:Nub1
|
UTSW |
5 |
24,912,851 (GRCm39) |
missense |
probably benign |
0.21 |
|
R4180:Nub1
|
UTSW |
5 |
24,897,875 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4921:Nub1
|
UTSW |
5 |
24,906,467 (GRCm39) |
missense |
probably benign |
0.38 |
|
R5175:Nub1
|
UTSW |
5 |
24,907,446 (GRCm39) |
missense |
probably benign |
0.28 |
|
R5282:Nub1
|
UTSW |
5 |
24,900,533 (GRCm39) |
missense |
probably benign |
0.04 |
|
R5346:Nub1
|
UTSW |
5 |
24,902,414 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R5533:Nub1
|
UTSW |
5 |
24,907,379 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R5567:Nub1
|
UTSW |
5 |
24,913,814 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R5802:Nub1
|
UTSW |
5 |
24,907,439 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R6966:Nub1
|
UTSW |
5 |
24,894,470 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6967:Nub1
|
UTSW |
5 |
24,913,709 (GRCm39) |
missense |
probably benign |
|
|
R7540:Nub1
|
UTSW |
5 |
24,906,527 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7787:Nub1
|
UTSW |
5 |
24,913,801 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8478:Nub1
|
UTSW |
5 |
24,906,422 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9746:Nub1
|
UTSW |
5 |
24,908,483 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9760:Nub1
|
UTSW |
5 |
24,897,965 (GRCm39) |
missense |
possibly damaging |
0.76 |
|
Z1177:Nub1
|
UTSW |
5 |
24,907,456 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GCTACCAAAGGCACTGTCAAG -3'
(R):5'- AGACTGTCCTCTGACTGACAAAG -3'
Sequencing Primer
(F):5'- TACCAAAGGCACTGTCAAGGGTAC -3'
(R):5'- GACAAAGTCTCTTCAATACACTGGG -3'
|
| Posted On |
2015-09-25 |
Incidental Mutation