Incidental Mutation 'R6781:Yod1'
| ID |
531398 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Yod1
|
| Ensembl Gene |
ENSMUSG00000046404 |
| Gene Name |
YOD1 deubiquitinase |
| Synonyms |
9930028C20Rik |
| MMRRC Submission |
044895-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R6781 (G1)
|
| Quality Score |
161.009 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
130645064-130652093 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 130645275 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glycine to Serine
at position 19
(G19S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000055318
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000049813]
[ENSMUST00000050406]
[ENSMUST00000066863]
[ENSMUST00000169659]
[ENSMUST00000171479]
[ENSMUST00000185233]
[ENSMUST00000186777]
[ENSMUST00000189534]
[ENSMUST00000186867]
[ENSMUST00000188520]
[ENSMUST00000191301]
[ENSMUST00000187089]
[ENSMUST00000189167]
[ENSMUST00000191347]
|
| AlphaFold |
Q8CB27 |
| PDB Structure |
Solution NMR Structure of Ubiquitin thioesterase OTU1 (EC 3.1.2.-) from Mus musculus, Northeast Structural Genomics Consortium Target MmT2A [SOLUTION NMR]
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000049813
AA Change: G19S
PolyPhen 2
Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000055318
Gene: ENSMUSG00000046404
AA Change: G19S
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:2KZR|A
|
42 |
127 |
3e-54 |
PDB |
|
Blast:UBQ
|
43 |
118 |
2e-20 |
BLAST |
|
Pfam:OTU
|
150 |
268 |
3.4e-8 |
PFAM |
|
ZnF_C2H2
|
313 |
337 |
2.12e1 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000050406
|
| SMART Domains |
Protein: ENSMUSP00000133073
Gene: ENSMUSG00000026409
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:6PF2K
|
28 |
251 |
8.1e-107 |
PFAM |
|
Pfam:KTI12
|
40 |
206 |
9.6e-8 |
PFAM |
|
Pfam:AAA_33
|
42 |
198 |
3.1e-9 |
PFAM |
|
PGAM
|
253 |
400 |
3.82e-16 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000066863
|
| SMART Domains |
Protein: ENSMUSP00000066426
Gene: ENSMUSG00000026409
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:6PF2K
|
28 |
251 |
1.2e-106 |
PFAM |
|
Pfam:KTI12
|
41 |
207 |
3.5e-8 |
PFAM |
|
Pfam:AAA_33
|
42 |
199 |
1.2e-10 |
PFAM |
|
PGAM
|
253 |
400 |
3.82e-16 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000169659
|
| SMART Domains |
Protein: ENSMUSP00000127587
Gene: ENSMUSG00000026409
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:6PF2K
|
28 |
251 |
1.3e-106 |
PFAM |
|
Pfam:KTI12
|
41 |
207 |
4.3e-8 |
PFAM |
|
Pfam:AAA_33
|
42 |
199 |
1.2e-10 |
PFAM |
|
PGAM
|
253 |
400 |
3.82e-16 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000171479
|
| SMART Domains |
Protein: ENSMUSP00000129747
Gene: ENSMUSG00000026409
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:6PF2K
|
28 |
251 |
1.2e-106 |
PFAM |
|
Pfam:KTI12
|
41 |
208 |
3.7e-8 |
PFAM |
|
Pfam:AAA_33
|
42 |
199 |
1.1e-10 |
PFAM |
|
PGAM
|
253 |
400 |
3.82e-16 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000185233
|
| SMART Domains |
Protein: ENSMUSP00000140551
Gene: ENSMUSG00000026409
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:6PF2K
|
28 |
251 |
1.2e-106 |
PFAM |
|
Pfam:KTI12
|
41 |
207 |
3.5e-8 |
PFAM |
|
Pfam:AAA_33
|
42 |
199 |
1.2e-10 |
PFAM |
|
PGAM
|
253 |
400 |
3.82e-16 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000186777
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000189534
|
| SMART Domains |
Protein: ENSMUSP00000140355
Gene: ENSMUSG00000026409
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:6PF2K
|
28 |
251 |
1.2e-106 |
PFAM |
|
Pfam:KTI12
|
41 |
208 |
3.7e-8 |
PFAM |
|
Pfam:AAA_33
|
42 |
199 |
1.1e-10 |
PFAM |
|
PGAM
|
253 |
400 |
3.82e-16 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000186867
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000188520
|
| SMART Domains |
Protein: ENSMUSP00000140786
Gene: ENSMUSG00000101904
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:6PF2K
|
28 |
251 |
6.3e-107 |
PFAM |
|
Pfam:KTI12
|
41 |
209 |
2.3e-8 |
PFAM |
|
Pfam:AAA_33
|
42 |
199 |
6.4e-11 |
PFAM |
|
PGAM
|
253 |
342 |
1.31e-5 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000191301
|
| SMART Domains |
Protein: ENSMUSP00000140995
Gene: ENSMUSG00000026409
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:6PF2K
|
28 |
181 |
9.5e-70 |
PFAM |
|
Pfam:KTI12
|
41 |
183 |
3.2e-8 |
PFAM |
|
Pfam:AAA_33
|
42 |
184 |
1.1e-10 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000187089
|
| SMART Domains |
Protein: ENSMUSP00000140612
Gene: ENSMUSG00000026409
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:6PF2K
|
28 |
251 |
1e-103 |
PFAM |
|
Pfam:KTI12
|
41 |
207 |
2.3e-5 |
PFAM |
|
Pfam:AAA_33
|
42 |
199 |
1.4e-8 |
PFAM |
|
PGAM
|
253 |
400 |
2.9e-20 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000189167
|
| SMART Domains |
Protein: ENSMUSP00000140984
Gene: ENSMUSG00000026409
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:6PF2K
|
28 |
251 |
6.3e-107 |
PFAM |
|
Pfam:KTI12
|
41 |
209 |
2.3e-8 |
PFAM |
|
Pfam:AAA_33
|
42 |
199 |
6.4e-11 |
PFAM |
|
PGAM
|
253 |
342 |
1.31e-5 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000191347
|
| SMART Domains |
Protein: ENSMUSP00000140698
Gene: ENSMUSG00000026409
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:6PF2K
|
28 |
251 |
1.2e-103 |
PFAM |
|
Pfam:KTI12
|
41 |
207 |
2.4e-5 |
PFAM |
|
Pfam:AAA_33
|
42 |
199 |
1.6e-8 |
PFAM |
|
PGAM
|
253 |
400 |
2.9e-20 |
SMART |
|
| Meta Mutation Damage Score |
0.0977 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.1%
- 20x: 94.4%
|
| Validation Efficiency |
98% (45/46) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Protein ubiquitination controls many intracellular processes, including cell cycle progression, transcriptional activation, and signal transduction. This dynamic process, involving ubiquitin conjugating enzymes and deubiquitinating enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are cysteine proteases that specifically cleave ubiquitin from ubiquitin-conjugated protein substrates. The protein encoded by this gene belongs to a DUB subfamily characterized by an ovarian tumor (OTU) domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca3 |
T |
A |
17: 24,593,380 (GRCm39) |
I259N |
possibly damaging |
Het |
| Acot12 |
G |
T |
13: 91,932,531 (GRCm39) |
|
probably null |
Het |
| AI182371 |
G |
T |
2: 34,974,717 (GRCm39) |
|
probably benign |
Het |
| Amigo3 |
T |
C |
9: 107,931,162 (GRCm39) |
L195P |
probably damaging |
Het |
| Aox4 |
A |
T |
1: 58,284,268 (GRCm39) |
D556V |
probably benign |
Het |
| Arhgef40 |
A |
C |
14: 52,235,354 (GRCm39) |
|
probably benign |
Het |
| Asb15 |
T |
C |
6: 24,558,674 (GRCm39) |
V63A |
probably benign |
Het |
| Bicd1 |
T |
C |
6: 149,414,664 (GRCm39) |
I459T |
possibly damaging |
Het |
| Bub1 |
C |
A |
2: 127,649,777 (GRCm39) |
G694W |
probably damaging |
Het |
| C4b |
A |
T |
17: 34,961,928 (GRCm39) |
I106N |
probably damaging |
Het |
| Clca4b |
T |
C |
3: 144,628,562 (GRCm39) |
I382V |
probably benign |
Het |
| Cntnap5a |
A |
C |
1: 116,220,127 (GRCm39) |
S646R |
probably benign |
Het |
| Cntnap5c |
C |
T |
17: 58,445,648 (GRCm39) |
Q563* |
probably null |
Het |
| Cpn1 |
A |
G |
19: 43,969,343 (GRCm39) |
F107L |
possibly damaging |
Het |
| Csrnp3 |
T |
A |
2: 65,852,615 (GRCm39) |
C336S |
probably benign |
Het |
| Defa3 |
T |
A |
8: 21,778,277 (GRCm39) |
M87K |
probably benign |
Het |
| Dennd2b |
T |
C |
7: 109,124,511 (GRCm39) |
D1110G |
possibly damaging |
Het |
| Dmbt1 |
T |
C |
7: 130,648,291 (GRCm39) |
F274L |
probably benign |
Het |
| Dnah8 |
TTA |
TTATA |
17: 30,984,698 (GRCm39) |
|
probably null |
Het |
| Dnase2b |
T |
C |
3: 146,288,126 (GRCm39) |
H323R |
probably benign |
Het |
| Fam83e |
A |
T |
7: 45,371,571 (GRCm39) |
|
probably benign |
Het |
| Fbn1 |
T |
C |
2: 125,158,958 (GRCm39) |
N2269S |
probably damaging |
Het |
| Foxa1 |
A |
T |
12: 57,590,043 (GRCm39) |
M59K |
possibly damaging |
Het |
| Fpr3 |
T |
C |
17: 18,190,978 (GRCm39) |
V83A |
probably benign |
Het |
| Frmd6 |
A |
G |
12: 70,946,417 (GRCm39) |
D615G |
possibly damaging |
Het |
| Gfra3 |
T |
C |
18: 34,844,375 (GRCm39) |
K55R |
possibly damaging |
Het |
| Gm5414 |
A |
T |
15: 101,534,096 (GRCm39) |
S296T |
possibly damaging |
Het |
| Gtf3c1 |
T |
A |
7: 125,258,369 (GRCm39) |
K1234* |
probably null |
Het |
| Hltf |
T |
A |
3: 20,152,330 (GRCm39) |
Y609N |
probably benign |
Het |
| Idh2 |
TCCCAGG |
T |
7: 79,748,079 (GRCm39) |
|
probably benign |
Het |
| Ift74 |
A |
G |
4: 94,515,539 (GRCm39) |
D152G |
probably damaging |
Het |
| Kcnk6 |
T |
C |
7: 28,924,480 (GRCm39) |
Y308C |
probably damaging |
Het |
| Klhl29 |
A |
G |
12: 5,141,347 (GRCm39) |
S546P |
probably damaging |
Het |
| Map7d1 |
AGGGCAGCC |
AGGGCAGCCGGGCAGCC |
4: 126,134,544 (GRCm39) |
|
probably null |
Het |
| Meis2 |
T |
A |
2: 115,879,636 (GRCm39) |
H228L |
probably benign |
Het |
| Mfsd10 |
A |
T |
5: 34,791,853 (GRCm39) |
M344K |
possibly damaging |
Het |
| Mrps33 |
T |
C |
6: 39,782,757 (GRCm39) |
|
probably benign |
Het |
| Or2a52 |
A |
G |
6: 43,144,322 (GRCm39) |
E110G |
probably damaging |
Het |
| Or4p23 |
A |
T |
2: 88,577,174 (GRCm39) |
N19K |
probably benign |
Het |
| Pik3cb |
T |
C |
9: 98,923,045 (GRCm39) |
T996A |
possibly damaging |
Het |
| Plekha7 |
A |
G |
7: 115,757,090 (GRCm39) |
|
probably null |
Het |
| Ppp1cb |
A |
G |
5: 32,638,106 (GRCm39) |
Y86C |
probably damaging |
Het |
| Sass6 |
T |
G |
3: 116,388,773 (GRCm39) |
|
probably benign |
Het |
| Slc6a15 |
A |
T |
10: 103,230,928 (GRCm39) |
I218F |
probably damaging |
Het |
| Tcf23 |
C |
T |
5: 31,126,304 (GRCm39) |
P61L |
probably benign |
Het |
| Zc3h6 |
T |
C |
2: 128,857,341 (GRCm39) |
F620S |
probably damaging |
Het |
|
| Other mutations in Yod1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00585:Yod1
|
APN |
1 |
130,646,870 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02321:Yod1
|
APN |
1 |
130,646,688 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03018:Yod1
|
APN |
1 |
130,646,695 (GRCm39) |
missense |
probably benign |
0.08 |
|
R1310:Yod1
|
UTSW |
1 |
130,646,567 (GRCm39) |
missense |
probably benign |
|
|
R5825:Yod1
|
UTSW |
1 |
130,646,743 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6115:Yod1
|
UTSW |
1 |
130,646,800 (GRCm39) |
missense |
possibly damaging |
0.48 |
|
R6367:Yod1
|
UTSW |
1 |
130,645,275 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6437:Yod1
|
UTSW |
1 |
130,646,885 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6489:Yod1
|
UTSW |
1 |
130,645,275 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6491:Yod1
|
UTSW |
1 |
130,645,275 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6729:Yod1
|
UTSW |
1 |
130,645,275 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6731:Yod1
|
UTSW |
1 |
130,645,275 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6732:Yod1
|
UTSW |
1 |
130,645,275 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6742:Yod1
|
UTSW |
1 |
130,645,275 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6743:Yod1
|
UTSW |
1 |
130,645,275 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6766:Yod1
|
UTSW |
1 |
130,647,008 (GRCm39) |
nonsense |
probably null |
|
|
R7831:Yod1
|
UTSW |
1 |
130,646,986 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8058:Yod1
|
UTSW |
1 |
130,646,806 (GRCm39) |
nonsense |
probably null |
|
|
R8369:Yod1
|
UTSW |
1 |
130,645,360 (GRCm39) |
missense |
probably benign |
0.31 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTCTGCTCTGCTAGACTCGG -3'
(R):5'- AGGTCCCCAAGAGTGATGTC -3'
Sequencing Primer
(F):5'- TCTGCTAGACTCGGGAACTC -3'
(R):5'- AAGAGTGATGTCCCGGTCG -3'
|
| Posted On |
2018-08-29 |
Incidental Mutation