Incidental Mutation 'R6671:Vps53'
| ID |
527147 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps53
|
| Ensembl Gene |
ENSMUSG00000017288 |
| Gene Name |
VPS53 GARP complex subunit |
| Synonyms |
2310040I21Rik, 3100002B05Rik, 2010002A08Rik |
| MMRRC Submission |
044791-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6671 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 76025332 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 171
(Y171H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000130499
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056601]
[ENSMUST00000094015]
[ENSMUST00000108419]
[ENSMUST00000163878]
[ENSMUST00000166752]
[ENSMUST00000169734]
[ENSMUST00000167114]
[ENSMUST00000170730]
|
| AlphaFold |
Q8CCB4 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000056601
AA Change: Y171H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: Y171H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
19 |
N/A |
INTRINSIC |
|
Pfam:DUF2450
|
25 |
225 |
5.9e-11 |
PFAM |
|
Pfam:Vps53_N
|
39 |
453 |
1.9e-176 |
PFAM |
|
low complexity region
|
520 |
533 |
N/A |
INTRINSIC |
|
low complexity region
|
820 |
832 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000094015
AA Change: Y142H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: Y142H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
19 |
N/A |
INTRINSIC |
|
Pfam:Vps53_N
|
39 |
96 |
6.2e-21 |
PFAM |
|
Pfam:Vps53_N
|
93 |
424 |
1.4e-133 |
PFAM |
|
low complexity region
|
491 |
504 |
N/A |
INTRINSIC |
|
low complexity region
|
791 |
803 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000108419
AA Change: Y171H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: Y171H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
19 |
N/A |
INTRINSIC |
|
Pfam:DUF2450
|
25 |
224 |
4e-11 |
PFAM |
|
Pfam:Vps53_N
|
39 |
233 |
5.2e-87 |
PFAM |
|
Pfam:Vps53_N
|
226 |
276 |
1.6e-14 |
PFAM |
|
low complexity region
|
343 |
356 |
N/A |
INTRINSIC |
|
low complexity region
|
643 |
655 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141773
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143459
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000163878
AA Change: V37A
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000166084
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000166436
AA Change: Y99H
|
| SMART Domains |
Protein: ENSMUSP00000131387
Gene: ENSMUSG00000017288
AA Change: Y99H
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF2450
|
1 |
155 |
1.6e-8 |
PFAM |
|
Pfam:Vps53_N
|
1 |
204 |
6.1e-91 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000166752
AA Change: Y171H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
AA Change: Y171H
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
19 |
N/A |
INTRINSIC |
|
Pfam:DUF2450
|
25 |
225 |
8.2e-12 |
PFAM |
|
Pfam:Vps53_N
|
39 |
230 |
6e-87 |
PFAM |
|
Pfam:Vps53_N
|
226 |
405 |
1.4e-60 |
PFAM |
|
low complexity region
|
472 |
485 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000169734
AA Change: Y171H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288
AA Change: Y171H
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF2450
|
5 |
225 |
5.1e-12 |
PFAM |
|
Pfam:Vps53_N
|
39 |
329 |
1e-137 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000167114
|
| SMART Domains |
Protein: ENSMUSP00000131663
Gene: ENSMUSG00000017288
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
19 |
N/A |
INTRINSIC |
|
Pfam:Vps53_N
|
39 |
101 |
1.2e-21 |
PFAM |
|
Pfam:Vps53_N
|
104 |
176 |
3.1e-15 |
PFAM |
|
low complexity region
|
243 |
256 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000169532
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170143
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000170730
|
| SMART Domains |
Protein: ENSMUSP00000127364
Gene: ENSMUSG00000017288
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
19 |
N/A |
INTRINSIC |
|
Pfam:Vps53_N
|
54 |
123 |
3e-34 |
PFAM |
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.2%
- 20x: 95.0%
|
| Validation Efficiency |
97% (32/33) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with sequence similarity to the yeast Vps53p protein. Vps53p is involved in retrograde vesicle trafficking in late Golgi. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality prior to E12.5 with trophoblast cell hyperplasia. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 30 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5430401F13Rik |
T |
C |
6: 131,528,313 (GRCm39) |
|
probably null |
Het |
| Abce1 |
A |
G |
8: 80,415,806 (GRCm39) |
V404A |
probably benign |
Het |
| Cpd |
T |
A |
11: 76,686,359 (GRCm39) |
I990F |
probably damaging |
Het |
| Ddhd1 |
CA |
C |
14: 45,894,689 (GRCm39) |
|
probably null |
Het |
| Dnajb6 |
A |
G |
5: 29,953,418 (GRCm39) |
E17G |
probably damaging |
Het |
| Fastk |
T |
C |
5: 24,646,607 (GRCm39) |
D308G |
probably damaging |
Het |
| Fkbp14 |
A |
G |
6: 54,556,662 (GRCm39) |
Y69H |
probably damaging |
Het |
| Gldn |
T |
C |
9: 54,245,691 (GRCm39) |
L414P |
probably damaging |
Het |
| Glmn |
T |
A |
5: 107,697,280 (GRCm39) |
M487L |
probably benign |
Het |
| Gm3404 |
C |
A |
5: 146,464,487 (GRCm39) |
R163S |
probably benign |
Het |
| Gm5591 |
T |
G |
7: 38,219,523 (GRCm39) |
D450A |
possibly damaging |
Het |
| Gucy1b1 |
T |
C |
3: 81,941,715 (GRCm39) |
T575A |
probably benign |
Het |
| Hydin |
T |
A |
8: 111,327,950 (GRCm39) |
V4819D |
probably damaging |
Het |
| Ikbip |
A |
G |
10: 90,932,469 (GRCm39) |
|
probably null |
Het |
| Mertk |
G |
T |
2: 128,593,943 (GRCm39) |
|
probably null |
Het |
| Mfsd1 |
T |
C |
3: 67,492,995 (GRCm39) |
V93A |
possibly damaging |
Het |
| Myh11 |
A |
T |
16: 14,044,480 (GRCm39) |
M641K |
possibly damaging |
Het |
| Myo3a |
A |
T |
2: 22,299,333 (GRCm39) |
N269Y |
probably damaging |
Het |
| Nisch |
A |
T |
14: 30,926,420 (GRCm39) |
|
probably benign |
Het |
| Otof |
A |
G |
5: 30,576,877 (GRCm39) |
V125A |
probably benign |
Het |
| Pla2g4a |
A |
G |
1: 149,763,382 (GRCm39) |
I93T |
probably benign |
Het |
| Prrc2c |
A |
G |
1: 162,525,154 (GRCm39) |
I484T |
probably damaging |
Het |
| Qrich1 |
T |
A |
9: 108,410,985 (GRCm39) |
I170N |
probably benign |
Het |
| Rb1 |
A |
T |
14: 73,434,706 (GRCm39) |
M904K |
probably damaging |
Het |
| Rgs11 |
A |
T |
17: 26,427,272 (GRCm39) |
K399M |
probably damaging |
Het |
| Tmprss13 |
C |
T |
9: 45,254,529 (GRCm39) |
T432M |
probably damaging |
Het |
| Tpp1 |
C |
T |
7: 105,398,814 (GRCm39) |
R205H |
probably benign |
Het |
| Zbtb8b |
C |
T |
4: 129,321,577 (GRCm39) |
R395Q |
probably damaging |
Het |
| Zfp81 |
A |
T |
17: 33,554,413 (GRCm39) |
C134S |
probably benign |
Het |
| Zranb1 |
A |
G |
7: 132,573,042 (GRCm39) |
D403G |
probably damaging |
Het |
|
| Other mutations in Vps53 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00475:Vps53
|
APN |
11 |
75,967,861 (GRCm39) |
splice site |
probably null |
|
|
IGL01596:Vps53
|
APN |
11 |
75,953,863 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01655:Vps53
|
APN |
11 |
75,953,860 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL02275:Vps53
|
APN |
11 |
75,937,949 (GRCm39) |
missense |
probably benign |
0.03 |
|
IGL02321:Vps53
|
APN |
11 |
75,939,364 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
IGL02581:Vps53
|
APN |
11 |
75,992,883 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02821:Vps53
|
APN |
11 |
76,027,143 (GRCm39) |
splice site |
probably benign |
|
|
IGL02958:Vps53
|
APN |
11 |
76,008,537 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03001:Vps53
|
APN |
11 |
76,029,150 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4519001:Vps53
|
UTSW |
11 |
76,007,999 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0257:Vps53
|
UTSW |
11 |
76,068,211 (GRCm39) |
intron |
probably benign |
|
|
R0391:Vps53
|
UTSW |
11 |
76,012,405 (GRCm39) |
missense |
probably benign |
0.31 |
|
R0421:Vps53
|
UTSW |
11 |
75,973,496 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0882:Vps53
|
UTSW |
11 |
75,973,485 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2509:Vps53
|
UTSW |
11 |
75,957,661 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R3622:Vps53
|
UTSW |
11 |
76,008,609 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5137:Vps53
|
UTSW |
11 |
76,057,074 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5338:Vps53
|
UTSW |
11 |
75,972,034 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5756:Vps53
|
UTSW |
11 |
75,983,156 (GRCm39) |
splice site |
probably benign |
|
|
R5786:Vps53
|
UTSW |
11 |
75,953,833 (GRCm39) |
missense |
probably benign |
0.08 |
|
R5961:Vps53
|
UTSW |
11 |
75,939,316 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6059:Vps53
|
UTSW |
11 |
75,957,693 (GRCm39) |
missense |
possibly damaging |
0.57 |
|
R6273:Vps53
|
UTSW |
11 |
75,992,844 (GRCm39) |
missense |
probably benign |
0.16 |
|
R6490:Vps53
|
UTSW |
11 |
75,967,881 (GRCm39) |
missense |
probably benign |
0.03 |
|
R6657:Vps53
|
UTSW |
11 |
76,025,253 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6772:Vps53
|
UTSW |
11 |
76,070,324 (GRCm39) |
start codon destroyed |
probably null |
|
|
R7378:Vps53
|
UTSW |
11 |
75,967,900 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R7735:Vps53
|
UTSW |
11 |
75,937,962 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8066:Vps53
|
UTSW |
11 |
76,027,133 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1177:Vps53
|
UTSW |
11 |
76,027,024 (GRCm39) |
critical splice donor site |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TAGCATCTGCAGCTGCTTC -3'
(R):5'- GATGTCACCTTGAGAGTTGGAGC -3'
Sequencing Primer
(F):5'- CTGCAGCTGCTTCCTAGAATAAGG -3'
(R):5'- CACCTTGAGAGTTGGAGCTAAATCC -3'
|
| Posted On |
2018-07-23 |
Incidental Mutation