Incidental Mutation 'R2869:Psmd13'
| ID |
253445 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Psmd13
|
| Ensembl Gene |
ENSMUSG00000025487 |
| Gene Name |
proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 |
| Synonyms |
26S proteasome subunit p40.5, S11 |
| MMRRC Submission |
040457-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.965)
|
| Stock # |
R2869 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
7 |
| Chromosomal Location |
140462307-140478555 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 140466968 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Serine
at position 116
(T116S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000130580
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026559]
[ENSMUST00000026560]
[ENSMUST00000163610]
[ENSMUST00000164681]
[ENSMUST00000211179]
[ENSMUST00000210296]
[ENSMUST00000166889]
|
| AlphaFold |
Q9WVJ2 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000026559
|
| SMART Domains |
Protein: ENSMUSP00000026559
Gene: ENSMUSG00000025486
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SIR2
|
3 |
184 |
5.3e-57 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000026560
AA Change: T116S
PolyPhen 2
Score 0.094 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000026560
Gene: ENSMUSG00000025487
AA Change: T116S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
9 |
14 |
N/A |
INTRINSIC |
|
PINT
|
263 |
356 |
2.26e-21 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000121585
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000125668
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129683
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000130462
|
| SMART Domains |
Protein: ENSMUSP00000126160
Gene: ENSMUSG00000025487
| Domain | Start | End | E-Value | Type |
|---|
|
PINT
|
100 |
189 |
6.59e-14 |
SMART |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140411
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000163610
AA Change: T116S
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000130580
Gene: ENSMUSG00000025487
AA Change: T116S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
9 |
14 |
N/A |
INTRINSIC |
|
PDB:4CR4|O
|
16 |
347 |
7e-44 |
PDB |
|
Blast:PINT
|
245 |
329 |
9e-26 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146875
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151644
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000164681
AA Change: T116S
PolyPhen 2
Score 0.393 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000132405
Gene: ENSMUSG00000025487
AA Change: T116S
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
9 |
14 |
N/A |
INTRINSIC |
|
PDB:4CR4|O
|
16 |
184 |
1e-12 |
PDB |
|
low complexity region
|
217 |
232 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000211179
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000210398
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000210296
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000166889
|
| SMART Domains |
Protein: ENSMUSP00000126532
Gene: ENSMUSG00000025487
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
9 |
14 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 99.6%
- 3x: 98.4%
- 10x: 93.9%
- 20x: 77.8%
|
| Validation Efficiency |
|
| 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 a non-ATPase subunit of the 19S regulator. Two transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Als2 |
A |
G |
1: 59,250,296 (GRCm39) |
S483P |
probably damaging |
Het |
| Ccl27a |
C |
T |
4: 41,769,640 (GRCm39) |
R73Q |
probably benign |
Het |
| Cd6 |
A |
G |
19: 10,771,990 (GRCm39) |
I307T |
possibly damaging |
Het |
| Ch25h |
T |
A |
19: 34,452,210 (GRCm39) |
H106L |
probably benign |
Het |
| Dennd2b |
A |
T |
7: 109,156,637 (GRCm39) |
Y38N |
probably benign |
Het |
| Dhx57 |
A |
T |
17: 80,558,805 (GRCm39) |
D1051E |
probably benign |
Het |
| Eef2 |
GCCC |
GCCCC |
10: 81,014,601 (GRCm39) |
|
probably null |
Het |
| Eif4enif1 |
C |
T |
11: 3,192,586 (GRCm39) |
P805S |
probably damaging |
Het |
| Fan1 |
A |
G |
7: 64,012,938 (GRCm39) |
I668T |
probably benign |
Het |
| Frmpd4 |
A |
T |
X: 166,260,243 (GRCm39) |
D1166E |
probably benign |
Het |
| Gbp11 |
C |
T |
5: 105,478,866 (GRCm39) |
D191N |
probably benign |
Het |
| Ggt6 |
A |
T |
11: 72,328,187 (GRCm39) |
N229I |
probably benign |
Het |
| Gria2 |
G |
A |
3: 80,609,799 (GRCm39) |
T670I |
probably damaging |
Het |
| Gsdme |
A |
T |
6: 50,185,157 (GRCm39) |
C432* |
probably null |
Het |
| Hjurp |
GT |
GTT |
1: 88,194,246 (GRCm39) |
|
probably null |
Het |
| Hmcn1 |
A |
T |
1: 150,614,467 (GRCm39) |
V1313D |
possibly damaging |
Het |
| Kcnb1 |
A |
G |
2: 166,947,855 (GRCm39) |
L331P |
probably damaging |
Het |
| Klf8 |
A |
T |
X: 152,165,678 (GRCm39) |
E82D |
probably damaging |
Het |
| Krt13 |
A |
G |
11: 100,008,475 (GRCm39) |
S421P |
unknown |
Het |
| Lactbl1 |
G |
A |
4: 136,354,097 (GRCm39) |
C37Y |
probably damaging |
Het |
| Lzts2 |
C |
A |
19: 45,012,534 (GRCm39) |
S321* |
probably null |
Het |
| Meikin |
T |
C |
11: 54,264,333 (GRCm39) |
V103A |
possibly damaging |
Het |
| Mki67 |
G |
A |
7: 135,309,878 (GRCm39) |
P191L |
probably benign |
Het |
| Mlxip |
A |
G |
5: 123,590,730 (GRCm39) |
M878V |
probably benign |
Het |
| Mpp7 |
G |
A |
18: 7,461,678 (GRCm39) |
P65L |
possibly damaging |
Het |
| Mroh2a |
GCCC |
GC |
1: 88,159,979 (GRCm39) |
|
probably null |
Het |
| Myo9b |
G |
A |
8: 71,786,981 (GRCm39) |
R721Q |
probably benign |
Het |
| Nbn |
T |
A |
4: 15,963,810 (GRCm39) |
D70E |
probably damaging |
Het |
| Nomo1 |
C |
A |
7: 45,696,361 (GRCm39) |
T293N |
probably damaging |
Het |
| Notum |
A |
G |
11: 120,551,022 (GRCm39) |
V48A |
probably benign |
Het |
| Nwd2 |
A |
T |
5: 63,957,671 (GRCm39) |
I334L |
probably benign |
Het |
| Or10z1 |
T |
C |
1: 174,078,092 (GRCm39) |
S134G |
probably benign |
Het |
| Or4k2 |
T |
C |
14: 50,423,811 (GRCm39) |
T288A |
probably benign |
Het |
| Or6c211 |
A |
T |
10: 129,505,628 (GRCm39) |
C253* |
probably null |
Het |
| Ostc |
T |
C |
3: 130,497,157 (GRCm39) |
N80S |
probably damaging |
Het |
| Otud4 |
T |
A |
8: 80,387,702 (GRCm39) |
N300K |
possibly damaging |
Het |
| Palmd |
T |
C |
3: 116,717,400 (GRCm39) |
R366G |
possibly damaging |
Het |
| Parp1 |
A |
G |
1: 180,401,230 (GRCm39) |
D45G |
probably damaging |
Het |
| Pes1 |
C |
A |
11: 3,926,834 (GRCm39) |
T372K |
probably benign |
Het |
| Plcl1 |
A |
T |
1: 55,736,309 (GRCm39) |
D550V |
probably benign |
Het |
| Ppp1r7 |
T |
A |
1: 93,285,585 (GRCm39) |
|
probably null |
Het |
| Prdx4 |
A |
G |
X: 154,123,460 (GRCm39) |
V15A |
probably benign |
Het |
| Psmb8 |
T |
C |
17: 34,419,144 (GRCm39) |
I146T |
probably damaging |
Het |
| Pzp |
A |
T |
6: 128,462,519 (GRCm39) |
|
probably null |
Het |
| Serinc2 |
A |
G |
4: 130,159,005 (GRCm39) |
S29P |
probably damaging |
Het |
| Slc39a8 |
T |
A |
3: 135,592,554 (GRCm39) |
|
probably null |
Het |
| Sppl2c |
C |
T |
11: 104,078,141 (GRCm39) |
P314S |
probably benign |
Het |
| St7 |
C |
T |
6: 17,819,276 (GRCm39) |
P60L |
probably damaging |
Het |
| Stx3 |
A |
T |
19: 11,766,938 (GRCm39) |
V91D |
probably damaging |
Het |
| Tafa2 |
A |
T |
10: 123,540,270 (GRCm39) |
H42L |
possibly damaging |
Het |
| Tnni3k |
C |
T |
3: 154,644,387 (GRCm39) |
|
probably null |
Het |
| Tprg1 |
T |
C |
16: 25,231,590 (GRCm39) |
W189R |
probably damaging |
Het |
| Trim32 |
A |
G |
4: 65,532,694 (GRCm39) |
D417G |
probably damaging |
Het |
| Vmn2r68 |
A |
C |
7: 84,882,834 (GRCm39) |
M306R |
probably benign |
Het |
| Vwa7 |
G |
A |
17: 35,240,218 (GRCm39) |
M395I |
probably damaging |
Het |
| Ybx3 |
G |
A |
6: 131,347,376 (GRCm39) |
A253V |
probably damaging |
Het |
| Zfp53 |
A |
T |
17: 21,728,340 (GRCm39) |
E124D |
probably benign |
Het |
|
| Other mutations in Psmd13 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00233:Psmd13
|
APN |
7 |
140,477,534 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL02265:Psmd13
|
APN |
7 |
140,462,431 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0326:Psmd13
|
UTSW |
7 |
140,477,624 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1163:Psmd13
|
UTSW |
7 |
140,477,367 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R1667:Psmd13
|
UTSW |
7 |
140,470,522 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1721:Psmd13
|
UTSW |
7 |
140,463,430 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1867:Psmd13
|
UTSW |
7 |
140,463,430 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1993:Psmd13
|
UTSW |
7 |
140,478,107 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2070:Psmd13
|
UTSW |
7 |
140,477,561 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2844:Psmd13
|
UTSW |
7 |
140,477,653 (GRCm39) |
intron |
probably benign |
|
|
R2845:Psmd13
|
UTSW |
7 |
140,477,653 (GRCm39) |
intron |
probably benign |
|
|
R2846:Psmd13
|
UTSW |
7 |
140,477,653 (GRCm39) |
intron |
probably benign |
|
|
R2869:Psmd13
|
UTSW |
7 |
140,466,968 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2871:Psmd13
|
UTSW |
7 |
140,466,968 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2871:Psmd13
|
UTSW |
7 |
140,466,968 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4358:Psmd13
|
UTSW |
7 |
140,469,418 (GRCm39) |
intron |
probably benign |
|
|
R4973:Psmd13
|
UTSW |
7 |
140,466,766 (GRCm39) |
nonsense |
probably null |
|
|
R5197:Psmd13
|
UTSW |
7 |
140,474,374 (GRCm39) |
splice site |
probably null |
|
|
R6700:Psmd13
|
UTSW |
7 |
140,470,522 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8239:Psmd13
|
UTSW |
7 |
140,466,450 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8798:Psmd13
|
UTSW |
7 |
140,477,663 (GRCm39) |
nonsense |
probably null |
|
|
R9516:Psmd13
|
UTSW |
7 |
140,478,455 (GRCm39) |
missense |
|
|
|
Z1176:Psmd13
|
UTSW |
7 |
140,462,339 (GRCm39) |
unclassified |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TTTTCTGGAAAAGACTCGTGAGAAG -3'
(R):5'- AGTAACAGCGGGGACATCTC -3'
Sequencing Primer
(F):5'- GCATTTTCTAGTATTTACGTGATTCG -3'
(R):5'- CATCTCGGTTAGAATACGAGAGTGC -3'
|
| Posted On |
2014-12-04 |
Incidental Mutation