Incidental Mutation 'R3783:Psmd4'
| ID |
272112 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Psmd4
|
| Ensembl Gene |
ENSMUSG00000005625 |
| Gene Name |
proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 |
| Synonyms |
angiocidin, Mcb1, Af1, multiubiquitin-chain-binding protein |
| MMRRC Submission |
040875-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R3783 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
94939999-94949880 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 94942562 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 6
(D6G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000114545
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000071664]
[ENSMUST00000107237]
[ENSMUST00000117355]
[ENSMUST00000140348]
|
| AlphaFold |
O35226 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000071664
AA Change: D119G
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000071589
Gene: ENSMUSG00000005625
AA Change: D119G
| Domain | Start | End | E-Value | Type |
|---|
|
VWA
|
2 |
188 |
7.38e-12 |
SMART |
|
low complexity region
|
189 |
201 |
N/A |
INTRINSIC |
|
UIM
|
211 |
230 |
2.04e0 |
SMART |
|
UIM
|
285 |
304 |
1.49e-2 |
SMART |
|
low complexity region
|
307 |
320 |
N/A |
INTRINSIC |
|
low complexity region
|
367 |
379 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000107237
AA Change: D119G
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000102857
Gene: ENSMUSG00000005625
AA Change: D119G
| Domain | Start | End | E-Value | Type |
|---|
|
VWA
|
2 |
188 |
7.38e-12 |
SMART |
|
low complexity region
|
189 |
201 |
N/A |
INTRINSIC |
|
UIM
|
211 |
230 |
2.04e0 |
SMART |
|
UIM
|
282 |
301 |
1.49e-2 |
SMART |
|
low complexity region
|
304 |
317 |
N/A |
INTRINSIC |
|
low complexity region
|
364 |
376 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000117355
AA Change: D119G
PolyPhen 2
Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)
|
| SMART Domains |
Protein: ENSMUSP00000113554
Gene: ENSMUSG00000005625
AA Change: D119G
| Domain | Start | End | E-Value | Type |
|---|
|
VWA
|
2 |
188 |
7.38e-12 |
SMART |
|
low complexity region
|
189 |
201 |
N/A |
INTRINSIC |
|
UIM
|
211 |
230 |
2.04e0 |
SMART |
|
UIM
|
285 |
304 |
1.49e-2 |
SMART |
|
low complexity region
|
307 |
320 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000136868
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140280
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000140348
AA Change: D6G
PolyPhen 2
Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000114545
Gene: ENSMUSG00000005625
AA Change: D6G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:UIM
|
34 |
42 |
2.4e-3 |
PFAM |
|
UIM
|
100 |
119 |
1.49e-2 |
SMART |
|
low complexity region
|
122 |
135 |
N/A |
INTRINSIC |
|
low complexity region
|
182 |
194 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143688
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147960
|
| Meta Mutation Damage Score |
0.0826 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.6%
|
| Validation Efficiency |
98% (45/46) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes one of the non-ATPase subunits of the 19S regulator lid. Pseudogenes have been identified on chromosomes 10 and 21. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele exhibit embryonic lethality and abnormal embryogenesis. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700012B07Rik |
G |
T |
11: 109,684,980 (GRCm39) |
C172* |
probably null |
Het |
| Akap6 |
A |
G |
12: 52,927,552 (GRCm39) |
H154R |
probably damaging |
Het |
| Aoc1 |
T |
C |
6: 48,882,589 (GRCm39) |
L177P |
probably damaging |
Het |
| Ascc3 |
A |
G |
10: 50,604,350 (GRCm39) |
T1357A |
probably damaging |
Het |
| Atp13a3 |
A |
T |
16: 30,173,067 (GRCm39) |
V270D |
probably damaging |
Het |
| Carmil3 |
T |
C |
14: 55,734,433 (GRCm39) |
F418S |
probably damaging |
Het |
| Ccdc93 |
A |
G |
1: 121,365,598 (GRCm39) |
N77S |
probably damaging |
Het |
| Cpt1b |
T |
C |
15: 89,309,392 (GRCm39) |
K47R |
probably damaging |
Het |
| Cyp4f14 |
A |
G |
17: 33,135,736 (GRCm39) |
Y42H |
probably benign |
Het |
| Dmxl1 |
G |
A |
18: 49,998,189 (GRCm39) |
S763N |
probably damaging |
Het |
| Fancd2 |
T |
G |
6: 113,542,165 (GRCm39) |
S770A |
probably damaging |
Het |
| Firrm |
A |
T |
1: 163,815,252 (GRCm39) |
C90S |
probably benign |
Het |
| Flnb |
T |
G |
14: 7,889,236 (GRCm38) |
W529G |
probably benign |
Het |
| Fryl |
T |
C |
5: 73,258,819 (GRCm39) |
Y655C |
probably benign |
Het |
| Gml |
C |
T |
15: 74,685,521 (GRCm39) |
V155M |
probably damaging |
Het |
| Gpr174 |
A |
G |
X: 106,336,670 (GRCm39) |
T161A |
probably benign |
Het |
| Heatr1 |
G |
T |
13: 12,449,341 (GRCm39) |
L1946F |
probably damaging |
Het |
| Inpp5k |
T |
C |
11: 75,538,512 (GRCm39) |
L461P |
probably damaging |
Het |
| Isy1 |
T |
C |
6: 87,798,527 (GRCm39) |
E209G |
possibly damaging |
Het |
| Kdm5b |
A |
G |
1: 134,558,280 (GRCm39) |
H1429R |
probably benign |
Het |
| Magi2 |
C |
T |
5: 20,670,907 (GRCm39) |
T580M |
probably damaging |
Het |
| Map3k1 |
C |
T |
13: 111,892,754 (GRCm39) |
V834I |
probably benign |
Het |
| Mdn1 |
A |
T |
4: 32,720,818 (GRCm39) |
E2310D |
probably benign |
Het |
| Myo15a |
A |
T |
11: 60,368,398 (GRCm39) |
Y386F |
probably damaging |
Het |
| Neurod1 |
T |
A |
2: 79,284,939 (GRCm39) |
N148I |
probably damaging |
Het |
| Niban1 |
C |
T |
1: 151,565,399 (GRCm39) |
S243L |
possibly damaging |
Het |
| Nsa2 |
G |
T |
13: 97,272,042 (GRCm39) |
Q60K |
possibly damaging |
Het |
| Pcdha1 |
T |
A |
18: 37,063,855 (GRCm39) |
L173Q |
probably damaging |
Het |
| Pdpk1 |
T |
C |
17: 24,329,824 (GRCm39) |
T71A |
possibly damaging |
Het |
| Plxna2 |
T |
A |
1: 194,489,829 (GRCm39) |
V1692E |
probably damaging |
Het |
| Pmepa1 |
G |
A |
2: 173,069,926 (GRCm39) |
R210W |
probably damaging |
Het |
| Psg27 |
T |
A |
7: 18,294,279 (GRCm39) |
Q376L |
probably damaging |
Het |
| Ptch1 |
T |
G |
13: 63,672,773 (GRCm39) |
E944A |
probably benign |
Het |
| Rala |
T |
A |
13: 18,057,031 (GRCm39) |
E185V |
probably benign |
Het |
| Sall4 |
A |
G |
2: 168,598,043 (GRCm39) |
S266P |
probably damaging |
Het |
| Scn10a |
T |
C |
9: 119,520,628 (GRCm39) |
T91A |
probably damaging |
Het |
| Synrg |
T |
C |
11: 83,892,746 (GRCm39) |
F613S |
probably damaging |
Het |
| Tekt1 |
A |
G |
11: 72,235,720 (GRCm39) |
I376T |
probably damaging |
Het |
| Tet2 |
T |
C |
3: 133,185,124 (GRCm39) |
K1182R |
possibly damaging |
Het |
| Thbs4 |
T |
C |
13: 92,909,672 (GRCm39) |
N375S |
probably benign |
Het |
| Thoc5 |
A |
G |
11: 4,870,372 (GRCm39) |
|
probably benign |
Het |
| Tmprss9 |
G |
T |
10: 80,723,301 (GRCm39) |
V254F |
probably damaging |
Het |
| Tro |
G |
A |
X: 149,438,048 (GRCm39) |
T203I |
possibly damaging |
Het |
| Ttbk2 |
A |
T |
2: 120,604,296 (GRCm39) |
|
probably benign |
Het |
| Usf2 |
A |
G |
7: 30,655,256 (GRCm39) |
V133A |
probably benign |
Het |
| Wap |
G |
A |
11: 6,588,550 (GRCm39) |
Q25* |
probably null |
Het |
| Xdh |
C |
T |
17: 74,200,590 (GRCm39) |
|
probably benign |
Het |
| Xrn1 |
G |
T |
9: 95,851,338 (GRCm39) |
M153I |
probably benign |
Het |
|
| Other mutations in Psmd4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02396:Psmd4
|
APN |
3 |
94,943,221 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0173:Psmd4
|
UTSW |
3 |
94,940,234 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1962:Psmd4
|
UTSW |
3 |
94,944,012 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R2907:Psmd4
|
UTSW |
3 |
94,941,273 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R3781:Psmd4
|
UTSW |
3 |
94,944,039 (GRCm39) |
missense |
probably benign |
0.09 |
|
R4902:Psmd4
|
UTSW |
3 |
94,943,170 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5090:Psmd4
|
UTSW |
3 |
94,942,559 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
R8031:Psmd4
|
UTSW |
3 |
94,943,203 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9221:Psmd4
|
UTSW |
3 |
94,942,604 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9312:Psmd4
|
UTSW |
3 |
94,940,729 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9428:Psmd4
|
UTSW |
3 |
94,940,767 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9464:Psmd4
|
UTSW |
3 |
94,940,735 (GRCm39) |
missense |
probably benign |
0.02 |
|
X0024:Psmd4
|
UTSW |
3 |
94,944,028 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTGCCTCACAGACGCATACAG -3'
(R):5'- GTCCACTTGAGGCACAACAG -3'
Sequencing Primer
(F):5'- GAAATTCAGCATCCTACCAAAGGTC -3'
(R):5'- CATGTACCGAGTGAGCATTATG -3'
|
| Posted On |
2015-03-25 |
Incidental Mutation