Incidental Mutation 'R2850:Nedd4'
| ID |
252102 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nedd4
|
| Ensembl Gene |
ENSMUSG00000032216 |
| Gene Name |
neural precursor cell expressed, developmentally down-regulated 4 |
| Synonyms |
E430025J12Rik, Nedd4a, Nedd4, Nedd4-1 |
| MMRRC Submission |
040443-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2850 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
9 |
| Chromosomal Location |
72569628-72657134 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 72632356 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Phenylalanine
at position 397
(L397F)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000034740
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000034740]
[ENSMUST00000184333]
[ENSMUST00000184450]
|
| AlphaFold |
P46935 |
| PDB Structure |
Crystal structure of the Nedd4 C2/Grb10 SH2 complex [X-RAY DIFFRACTION]
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000034740
AA Change: L397F
PolyPhen 2
Score 0.767 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000034740
Gene: ENSMUSG00000032216
AA Change: L397F
| Domain | Start | End | E-Value | Type |
|---|
|
C2
|
79 |
181 |
5.38e-21 |
SMART |
|
WW
|
250 |
282 |
2.32e-13 |
SMART |
|
low complexity region
|
283 |
293 |
N/A |
INTRINSIC |
|
WW
|
406 |
438 |
1.31e-12 |
SMART |
|
WW
|
461 |
493 |
1.26e-14 |
SMART |
|
HECTc
|
550 |
886 |
2.37e-194 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000184333
|
| SMART Domains |
Protein: ENSMUSP00000139190
Gene: ENSMUSG00000032216
| Domain | Start | End | E-Value | Type |
|---|
|
C2
|
4 |
71 |
3.38e-4 |
SMART |
|
WW
|
140 |
172 |
2.32e-13 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000184450
|
| SMART Domains |
Protein: ENSMUSP00000138983
Gene: ENSMUSG00000032216
| Domain | Start | End | E-Value | Type |
|---|
|
C2
|
79 |
181 |
5.38e-21 |
SMART |
|
WW
|
250 |
282 |
2.32e-13 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194508
|
| Meta Mutation Damage Score |
0.0934 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.7%
|
| Validation Efficiency |
100% (57/57) |
| MGI Phenotype |
PHENOTYPE: Homozygous mutation of this gene results in neonatal lethality and heterozygous mice have decreased body weights. Mice homozygous for a knockout allele exhibit impaired neurite development. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Actn2 |
T |
A |
13: 12,290,065 (GRCm39) |
T734S |
probably damaging |
Het |
| Ago1 |
T |
C |
4: 126,336,868 (GRCm39) |
|
probably benign |
Het |
| Ahi1 |
C |
T |
10: 20,876,492 (GRCm39) |
T801I |
probably benign |
Het |
| Alms1 |
T |
C |
6: 85,598,281 (GRCm39) |
S1505P |
probably benign |
Het |
| Alms1 |
C |
A |
6: 85,644,945 (GRCm39) |
|
probably benign |
Het |
| Anxa6 |
T |
A |
11: 54,901,852 (GRCm39) |
Y95F |
possibly damaging |
Het |
| Cacna1b |
C |
T |
2: 24,651,800 (GRCm39) |
M126I |
probably damaging |
Het |
| Clk1 |
A |
G |
1: 58,451,438 (GRCm39) |
L457S |
probably damaging |
Het |
| Cngb3 |
T |
C |
4: 19,415,690 (GRCm39) |
I400T |
possibly damaging |
Het |
| Cntnap5c |
T |
A |
17: 58,717,343 (GRCm39) |
|
probably benign |
Het |
| Corin |
A |
G |
5: 72,462,298 (GRCm39) |
V837A |
probably damaging |
Het |
| Ctr9 |
C |
T |
7: 110,652,653 (GRCm39) |
R984C |
unknown |
Het |
| Cubn |
G |
A |
2: 13,327,764 (GRCm39) |
T2687I |
probably damaging |
Het |
| Cypt3 |
T |
A |
X: 152,342,274 (GRCm39) |
N168K |
probably damaging |
Het |
| E330020D12Rik |
A |
G |
1: 153,282,336 (GRCm39) |
|
noncoding transcript |
Het |
| Fbxl4 |
T |
C |
4: 22,403,624 (GRCm39) |
M399T |
probably benign |
Het |
| Fbxo22 |
T |
C |
9: 55,130,699 (GRCm39) |
F323L |
probably damaging |
Het |
| Fnip1 |
A |
T |
11: 54,393,503 (GRCm39) |
E646D |
probably benign |
Het |
| Gid4 |
G |
A |
11: 60,329,400 (GRCm39) |
|
probably null |
Het |
| Gnb5 |
A |
T |
9: 75,234,511 (GRCm39) |
D70V |
probably damaging |
Het |
| Gpank1 |
A |
G |
17: 35,343,557 (GRCm39) |
S346G |
probably benign |
Het |
| Gtf3c6 |
T |
C |
10: 40,130,254 (GRCm39) |
|
probably benign |
Het |
| Hdx |
T |
C |
X: 110,502,720 (GRCm39) |
I562V |
probably benign |
Het |
| Ifrd2 |
T |
C |
9: 107,468,908 (GRCm39) |
|
probably benign |
Het |
| Itch |
A |
C |
2: 155,044,141 (GRCm39) |
Q482P |
probably benign |
Het |
| Kif11 |
C |
A |
19: 37,397,941 (GRCm39) |
D630E |
probably benign |
Het |
| Lpl |
G |
T |
8: 69,352,164 (GRCm39) |
E372* |
probably null |
Het |
| Mrps26 |
T |
C |
2: 130,406,967 (GRCm39) |
V198A |
probably benign |
Het |
| Mucl1 |
T |
C |
15: 103,782,348 (GRCm39) |
N201S |
possibly damaging |
Het |
| Nfat5 |
A |
G |
8: 108,020,492 (GRCm39) |
D12G |
probably damaging |
Het |
| Or5b102 |
T |
C |
19: 13,040,934 (GRCm39) |
L53P |
probably damaging |
Het |
| Pik3r3 |
A |
G |
4: 116,127,981 (GRCm39) |
|
probably benign |
Het |
| Pkd1l3 |
T |
A |
8: 110,350,622 (GRCm39) |
V489E |
possibly damaging |
Het |
| Pkhd1 |
T |
C |
1: 20,579,300 (GRCm39) |
E1802G |
possibly damaging |
Het |
| Plb1 |
T |
A |
5: 32,450,568 (GRCm39) |
S370T |
probably benign |
Het |
| Ppat |
G |
A |
5: 77,067,222 (GRCm39) |
T337I |
probably benign |
Het |
| Prkd3 |
A |
G |
17: 79,262,025 (GRCm39) |
V763A |
possibly damaging |
Het |
| Prr9 |
A |
T |
3: 92,030,476 (GRCm39) |
S55T |
probably benign |
Het |
| Rbpms |
G |
T |
8: 34,324,405 (GRCm39) |
N108K |
possibly damaging |
Het |
| Rc3h2 |
A |
T |
2: 37,267,427 (GRCm39) |
D972E |
probably benign |
Het |
| Rrbp1 |
C |
T |
2: 143,791,269 (GRCm39) |
R1378Q |
probably benign |
Het |
| Slc26a7 |
T |
A |
4: 14,593,806 (GRCm39) |
|
probably benign |
Het |
| Stard6 |
T |
A |
18: 70,616,522 (GRCm39) |
H60Q |
probably benign |
Het |
| Sult6b2 |
T |
C |
6: 142,743,613 (GRCm39) |
T138A |
probably benign |
Het |
| Th |
G |
A |
7: 142,447,812 (GRCm39) |
Q329* |
probably null |
Het |
| Tmco3 |
A |
G |
8: 13,345,024 (GRCm39) |
H268R |
probably benign |
Het |
| Tnn |
T |
C |
1: 159,966,857 (GRCm39) |
D429G |
probably benign |
Het |
| Tnrc6a |
G |
A |
7: 122,779,023 (GRCm39) |
G1245R |
probably damaging |
Het |
| Trem3 |
C |
A |
17: 48,556,669 (GRCm39) |
L47M |
probably benign |
Het |
| Trpm6 |
T |
A |
19: 18,769,454 (GRCm39) |
C307S |
possibly damaging |
Het |
| Ube2j1 |
T |
A |
4: 33,049,696 (GRCm39) |
N231K |
probably benign |
Het |
| Urb1 |
A |
G |
16: 90,571,144 (GRCm39) |
Y1222H |
probably benign |
Het |
| Wdr81 |
A |
T |
11: 75,341,998 (GRCm39) |
S1090T |
probably damaging |
Het |
| Ythdf3 |
T |
C |
3: 16,257,982 (GRCm39) |
|
probably benign |
Het |
| Zfp280d |
A |
G |
9: 72,219,371 (GRCm39) |
T183A |
probably benign |
Het |
| Zfp354c |
G |
A |
11: 50,706,158 (GRCm39) |
Q306* |
probably null |
Het |
| Zp2 |
T |
C |
7: 119,737,529 (GRCm39) |
H252R |
probably benign |
Het |
|
| Other mutations in Nedd4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00332:Nedd4
|
APN |
9 |
72,642,371 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00573:Nedd4
|
APN |
9 |
72,593,338 (GRCm39) |
splice site |
probably null |
|
|
IGL01973:Nedd4
|
APN |
9 |
72,644,216 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
IGL02177:Nedd4
|
APN |
9 |
72,654,439 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03082:Nedd4
|
APN |
9 |
72,584,676 (GRCm39) |
critical splice donor site |
probably null |
|
|
Evaporation
|
UTSW |
9 |
72,593,377 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Reduction
|
UTSW |
9 |
72,638,553 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
Snookie
|
UTSW |
9 |
72,632,346 (GRCm39) |
missense |
probably benign |
0.04 |
|
Sublimation
|
UTSW |
9 |
72,584,661 (GRCm39) |
nonsense |
probably null |
|
|
R0194:Nedd4
|
UTSW |
9 |
72,577,335 (GRCm39) |
missense |
possibly damaging |
0.72 |
|
R0714:Nedd4
|
UTSW |
9 |
72,638,728 (GRCm39) |
splice site |
probably benign |
|
|
R1331:Nedd4
|
UTSW |
9 |
72,584,668 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1633:Nedd4
|
UTSW |
9 |
72,578,539 (GRCm39) |
missense |
possibly damaging |
0.50 |
|
R1764:Nedd4
|
UTSW |
9 |
72,638,189 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2192:Nedd4
|
UTSW |
9 |
72,650,000 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2196:Nedd4
|
UTSW |
9 |
72,632,356 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R2220:Nedd4
|
UTSW |
9 |
72,643,989 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2994:Nedd4
|
UTSW |
9 |
72,638,185 (GRCm39) |
missense |
probably benign |
0.04 |
|
R3040:Nedd4
|
UTSW |
9 |
72,577,243 (GRCm39) |
missense |
probably benign |
|
|
R3697:Nedd4
|
UTSW |
9 |
72,647,469 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3884:Nedd4
|
UTSW |
9 |
72,632,359 (GRCm39) |
missense |
probably benign |
0.16 |
|
R4475:Nedd4
|
UTSW |
9 |
72,578,521 (GRCm39) |
nonsense |
probably null |
|
|
R4476:Nedd4
|
UTSW |
9 |
72,578,521 (GRCm39) |
nonsense |
probably null |
|
|
R4883:Nedd4
|
UTSW |
9 |
72,647,515 (GRCm39) |
splice site |
probably null |
|
|
R5066:Nedd4
|
UTSW |
9 |
72,617,801 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5947:Nedd4
|
UTSW |
9 |
72,638,132 (GRCm39) |
intron |
probably benign |
|
|
R5974:Nedd4
|
UTSW |
9 |
72,650,920 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6247:Nedd4
|
UTSW |
9 |
72,633,720 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6651:Nedd4
|
UTSW |
9 |
72,638,553 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R6661:Nedd4
|
UTSW |
9 |
72,593,377 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7170:Nedd4
|
UTSW |
9 |
72,577,381 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7237:Nedd4
|
UTSW |
9 |
72,632,346 (GRCm39) |
missense |
probably benign |
0.04 |
|
R7653:Nedd4
|
UTSW |
9 |
72,650,910 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7772:Nedd4
|
UTSW |
9 |
72,584,608 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R7905:Nedd4
|
UTSW |
9 |
72,584,661 (GRCm39) |
nonsense |
probably null |
|
|
R8194:Nedd4
|
UTSW |
9 |
72,593,389 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8229:Nedd4
|
UTSW |
9 |
72,638,670 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8422:Nedd4
|
UTSW |
9 |
72,649,964 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8487:Nedd4
|
UTSW |
9 |
72,577,321 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8733:Nedd4
|
UTSW |
9 |
72,633,766 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
R8956:Nedd4
|
UTSW |
9 |
72,633,708 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9261:Nedd4
|
UTSW |
9 |
72,584,656 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R9447:Nedd4
|
UTSW |
9 |
72,577,381 (GRCm39) |
missense |
probably benign |
|
|
Z1088:Nedd4
|
UTSW |
9 |
72,577,360 (GRCm39) |
missense |
probably benign |
0.22 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGTCGTGTCTACAACTACATTGG -3'
(R):5'- AGACAGTTCTCTTGAGGCTTG -3'
Sequencing Primer
(F):5'- AGAGAAGGCATCCCCCGTTTTAG -3'
(R):5'- AGACAGTTCTCTTGAGGCTTGACTTC -3'
|
| Posted On |
2014-12-04 |
Incidental Mutation