Incidental Mutation 'R1508:Usp4'
| ID |
168071 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Usp4
|
| Ensembl Gene |
ENSMUSG00000032612 |
| Gene Name |
ubiquitin specific peptidase 4 (proto-oncogene) |
| Synonyms |
Unp, F730026I20Rik |
| MMRRC Submission |
040869-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.139)
|
| Stock # |
R1508 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
9 |
| Chromosomal Location |
108225052-108269744 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 108249873 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 467
(V467A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000035237
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000035237]
[ENSMUST00000194224]
[ENSMUST00000194959]
|
| AlphaFold |
P35123 |
| PDB Structure |
Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4) [X-RAY DIFFRACTION]
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000035237
AA Change: V467A
PolyPhen 2
Score 0.139 (Sensitivity: 0.92; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000035237
Gene: ENSMUSG00000032612
AA Change: V467A
| Domain | Start | End | E-Value | Type |
|---|
|
DUSP
|
27 |
125 |
1.39e-46 |
SMART |
|
Pfam:Ubiquitin_3
|
139 |
226 |
6.7e-34 |
PFAM |
|
low complexity region
|
263 |
286 |
N/A |
INTRINSIC |
|
Pfam:UCH
|
301 |
919 |
2.2e-84 |
PFAM |
|
Pfam:UCH_1
|
302 |
507 |
2.8e-8 |
PFAM |
|
Pfam:UCH_1
|
605 |
901 |
1.4e-15 |
PFAM |
|
low complexity region
|
927 |
938 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000193288
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194065
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194224
AA Change: V467A
PolyPhen 2
Score 0.073 (Sensitivity: 0.93; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000141321
Gene: ENSMUSG00000032612
AA Change: V467A
| Domain | Start | End | E-Value | Type |
|---|
|
DUSP
|
27 |
125 |
5.5e-49 |
SMART |
|
Pfam:Ubiquitin_3
|
139 |
226 |
1.3e-30 |
PFAM |
|
low complexity region
|
263 |
286 |
N/A |
INTRINSIC |
|
Pfam:UCH
|
301 |
633 |
1.4e-50 |
PFAM |
|
Pfam:UCH_1
|
302 |
520 |
2.3e-8 |
PFAM |
|
low complexity region
|
657 |
673 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194959
AA Change: V420A
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000141368
Gene: ENSMUSG00000032612
AA Change: V420A
| Domain | Start | End | E-Value | Type |
|---|
|
DUSP
|
27 |
125 |
5.5e-49 |
SMART |
|
Pfam:Ubiquitin_3
|
139 |
226 |
1.7e-30 |
PFAM |
|
Pfam:UCH
|
254 |
872 |
7e-89 |
PFAM |
|
Pfam:UCH_1
|
255 |
469 |
3.5e-8 |
PFAM |
|
Pfam:UCH_1
|
566 |
854 |
2.5e-14 |
PFAM |
|
low complexity region
|
880 |
891 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.4%
- 10x: 96.7%
- 20x: 93.8%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a protease that deubiquitinates target proteins such as ADORA2A and TRIM21. The encoded protein shuttles between the nucleus and cytoplasm and is involved in maintaining operational fidelity in the endoplasmic reticulum. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit increased irradiation-induced apoptosis, slow cellular growth, resistance to oncogenic transformation, and early cellular replicative senescence. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Agbl4 |
T |
C |
4: 111,513,595 (GRCm39) |
I447T |
probably benign |
Het |
| Albfm1 |
A |
G |
5: 90,729,780 (GRCm39) |
E401G |
probably benign |
Het |
| Alpk2 |
C |
A |
18: 65,482,376 (GRCm39) |
G544V |
probably damaging |
Het |
| Apob |
T |
C |
12: 8,061,481 (GRCm39) |
I3321T |
possibly damaging |
Het |
| Ccdc47 |
C |
T |
11: 106,093,242 (GRCm39) |
D70N |
probably damaging |
Het |
| Ceacam13 |
T |
A |
7: 17,744,996 (GRCm39) |
V22D |
possibly damaging |
Het |
| Cep76 |
A |
G |
18: 67,756,358 (GRCm39) |
M491T |
probably damaging |
Het |
| Clec4a3 |
A |
T |
6: 122,944,467 (GRCm39) |
N171I |
probably benign |
Het |
| Col20a1 |
A |
G |
2: 180,634,370 (GRCm39) |
I112V |
probably damaging |
Het |
| Col4a4 |
A |
T |
1: 82,433,557 (GRCm39) |
L1462H |
unknown |
Het |
| Cubn |
A |
G |
2: 13,431,916 (GRCm39) |
F1226L |
probably benign |
Het |
| Cyp4a31 |
T |
A |
4: 115,422,250 (GRCm39) |
I77K |
possibly damaging |
Het |
| Dcaf1 |
A |
T |
9: 106,731,376 (GRCm39) |
T618S |
probably damaging |
Het |
| Echdc3 |
A |
T |
2: 6,211,231 (GRCm39) |
S129T |
probably benign |
Het |
| Efcab3 |
T |
C |
11: 104,601,503 (GRCm39) |
V272A |
probably benign |
Het |
| Fabp3 |
C |
T |
4: 130,206,180 (GRCm39) |
T57I |
probably benign |
Het |
| Fat1 |
T |
C |
8: 45,479,899 (GRCm39) |
F2982L |
probably benign |
Het |
| Gm9476 |
A |
T |
10: 100,142,700 (GRCm39) |
|
noncoding transcript |
Het |
| Golga1 |
A |
G |
2: 38,913,261 (GRCm39) |
M542T |
probably benign |
Het |
| H2-D1 |
T |
A |
17: 35,482,844 (GRCm39) |
C125S |
probably damaging |
Het |
| Jazf1 |
G |
A |
6: 52,789,166 (GRCm39) |
H103Y |
probably damaging |
Het |
| Klhl12 |
T |
C |
1: 134,416,712 (GRCm39) |
V478A |
possibly damaging |
Het |
| Lpcat2b |
A |
T |
5: 107,581,330 (GRCm39) |
T220S |
probably damaging |
Het |
| Myocd |
C |
T |
11: 65,075,342 (GRCm39) |
C594Y |
probably damaging |
Het |
| Nf1 |
A |
G |
11: 79,331,735 (GRCm39) |
E700G |
probably damaging |
Het |
| Or52z15 |
T |
C |
7: 103,332,678 (GRCm39) |
V251A |
possibly damaging |
Het |
| Or6k2 |
T |
A |
1: 173,986,930 (GRCm39) |
M197K |
possibly damaging |
Het |
| Papln |
A |
G |
12: 83,829,690 (GRCm39) |
Q937R |
probably damaging |
Het |
| Pex14 |
T |
C |
4: 149,052,029 (GRCm39) |
R147G |
probably damaging |
Het |
| Plppr3 |
A |
T |
10: 79,703,374 (GRCm39) |
Y37N |
probably damaging |
Het |
| Polr1b |
A |
G |
2: 128,955,654 (GRCm39) |
T522A |
probably benign |
Het |
| Ppp3cb |
T |
C |
14: 20,574,492 (GRCm39) |
N201S |
probably damaging |
Het |
| Prf1 |
A |
G |
10: 61,139,329 (GRCm39) |
D429G |
probably damaging |
Het |
| Ptprn2 |
T |
C |
12: 117,148,342 (GRCm39) |
S701P |
probably damaging |
Het |
| Rp1l1 |
C |
T |
14: 64,268,341 (GRCm39) |
T1309I |
possibly damaging |
Het |
| Sipa1l1 |
T |
A |
12: 82,487,667 (GRCm39) |
M1647K |
probably damaging |
Het |
| Skint11 |
T |
C |
4: 114,088,963 (GRCm39) |
|
probably null |
Het |
| Slc8a2 |
T |
C |
7: 15,874,522 (GRCm39) |
Y257H |
probably benign |
Het |
| Slfn1 |
T |
A |
11: 83,012,181 (GRCm39) |
I99N |
probably damaging |
Het |
| Slit2 |
A |
G |
5: 48,349,591 (GRCm39) |
T282A |
probably damaging |
Het |
| Slit3 |
A |
T |
11: 35,461,448 (GRCm39) |
D228V |
probably damaging |
Het |
| Specc1l |
A |
G |
10: 75,143,072 (GRCm39) |
N1031S |
probably benign |
Het |
| Supt6 |
A |
G |
11: 78,107,029 (GRCm39) |
|
probably null |
Het |
| Tdrd1 |
G |
A |
19: 56,839,790 (GRCm39) |
E617K |
probably damaging |
Het |
| Tex15 |
C |
G |
8: 34,066,880 (GRCm39) |
F2103L |
probably damaging |
Het |
| Trim21 |
T |
A |
7: 102,208,783 (GRCm39) |
Q312L |
possibly damaging |
Het |
| Trim56 |
C |
T |
5: 137,142,791 (GRCm39) |
A242T |
probably benign |
Het |
| Vmn2r65 |
T |
A |
7: 84,589,886 (GRCm39) |
I677L |
probably benign |
Het |
| Vstm4 |
T |
C |
14: 32,585,511 (GRCm39) |
V26A |
probably damaging |
Het |
| Zbtb14 |
C |
G |
17: 69,694,759 (GRCm39) |
I152M |
probably benign |
Het |
| Zfat |
T |
A |
15: 68,050,600 (GRCm39) |
K807I |
probably damaging |
Het |
|
| Other mutations in Usp4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01530:Usp4
|
APN |
9 |
108,240,099 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL01663:Usp4
|
APN |
9 |
108,243,079 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
IGL02105:Usp4
|
APN |
9 |
108,262,131 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02486:Usp4
|
APN |
9 |
108,228,228 (GRCm39) |
missense |
probably damaging |
1.00 |
|
kleinesrot
|
UTSW |
9 |
108,233,661 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R0148:Usp4
|
UTSW |
9 |
108,268,870 (GRCm39) |
splice site |
probably null |
|
|
R0285:Usp4
|
UTSW |
9 |
108,255,763 (GRCm39) |
missense |
probably benign |
0.33 |
|
R0591:Usp4
|
UTSW |
9 |
108,225,228 (GRCm39) |
splice site |
probably benign |
|
|
R0594:Usp4
|
UTSW |
9 |
108,248,080 (GRCm39) |
splice site |
probably null |
|
|
R0616:Usp4
|
UTSW |
9 |
108,244,003 (GRCm39) |
missense |
probably benign |
|
|
R1329:Usp4
|
UTSW |
9 |
108,249,765 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1752:Usp4
|
UTSW |
9 |
108,251,441 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1824:Usp4
|
UTSW |
9 |
108,225,207 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1846:Usp4
|
UTSW |
9 |
108,249,935 (GRCm39) |
missense |
probably benign |
|
|
R2196:Usp4
|
UTSW |
9 |
108,250,885 (GRCm39) |
missense |
probably benign |
0.07 |
|
R2925:Usp4
|
UTSW |
9 |
108,245,055 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4126:Usp4
|
UTSW |
9 |
108,237,316 (GRCm39) |
missense |
probably benign |
0.10 |
|
R4345:Usp4
|
UTSW |
9 |
108,245,222 (GRCm39) |
intron |
probably benign |
|
|
R4965:Usp4
|
UTSW |
9 |
108,239,819 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4981:Usp4
|
UTSW |
9 |
108,258,617 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5110:Usp4
|
UTSW |
9 |
108,239,877 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5580:Usp4
|
UTSW |
9 |
108,243,058 (GRCm39) |
missense |
probably benign |
0.09 |
|
R5586:Usp4
|
UTSW |
9 |
108,233,661 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R5927:Usp4
|
UTSW |
9 |
108,268,959 (GRCm39) |
missense |
probably benign |
0.09 |
|
R6025:Usp4
|
UTSW |
9 |
108,237,322 (GRCm39) |
missense |
possibly damaging |
0.70 |
|
R6112:Usp4
|
UTSW |
9 |
108,233,703 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6197:Usp4
|
UTSW |
9 |
108,248,154 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6742:Usp4
|
UTSW |
9 |
108,251,438 (GRCm39) |
missense |
possibly damaging |
0.74 |
|
R7320:Usp4
|
UTSW |
9 |
108,265,505 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7458:Usp4
|
UTSW |
9 |
108,245,055 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7531:Usp4
|
UTSW |
9 |
108,249,879 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7563:Usp4
|
UTSW |
9 |
108,256,543 (GRCm39) |
missense |
probably benign |
|
|
R8022:Usp4
|
UTSW |
9 |
108,255,670 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8510:Usp4
|
UTSW |
9 |
108,265,581 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8996:Usp4
|
UTSW |
9 |
108,268,909 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9151:Usp4
|
UTSW |
9 |
108,244,011 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9775:Usp4
|
UTSW |
9 |
108,239,780 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0026:Usp4
|
UTSW |
9 |
108,225,069 (GRCm39) |
unclassified |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- CTACGGTACACTAAAAGCTCTCGGC -3'
(R):5'- CAATGGTGTTTCCCATGCAGCAG -3'
Sequencing Primer
(F):5'- AAAAGCTCTCGGCTGTTCAC -3'
(R):5'- CAGATAGAACGTAGTCCCATCTGG -3'
|
| Posted On |
2014-04-13 |
Incidental Mutation