Incidental Mutation 'IGL01596:Vps53'
| ID |
91932 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Vps53
|
| Ensembl Gene |
ENSMUSG00000017288 |
| Gene Name |
VPS53 GARP complex subunit |
| Synonyms |
2310040I21Rik, 3100002B05Rik, 2010002A08Rik |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
IGL01596
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
11 |
| Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 75953863 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Serine
at position 501
(F501S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000104057
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056601]
[ENSMUST00000094015]
[ENSMUST00000108419]
[ENSMUST00000166752]
[ENSMUST00000167114]
[ENSMUST00000169734]
|
| AlphaFold |
Q8CCB4 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000056601
AA Change: F678S
PolyPhen 2
Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: F678S
| 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: F649S
PolyPhen 2
Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: F649S
| 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: F501S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: F501S
| 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: ENSMUST00000143163
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000166752
|
| SMART Domains |
Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
| 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 |
possibly damaging
Transcript: ENSMUST00000167114
AA Change: F401S
PolyPhen 2
Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000131663
Gene: ENSMUSG00000017288
AA Change: F401S
| 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 |
probably benign
Transcript: ENSMUST00000169734
|
| SMART Domains |
Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF2450
|
5 |
225 |
5.1e-12 |
PFAM |
|
Pfam:Vps53_N
|
39 |
329 |
1e-137 |
PFAM |
|
| Coding Region Coverage |
|
| Validation Efficiency |
|
| 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: 27 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adh7 |
T |
C |
3: 137,932,003 (GRCm39) |
S206P |
probably damaging |
Het |
| Arhgef10 |
G |
T |
8: 15,049,468 (GRCm39) |
E869* |
probably null |
Het |
| C87436 |
T |
A |
6: 86,423,201 (GRCm39) |
D258E |
probably damaging |
Het |
| Casp8ap2 |
A |
G |
4: 32,646,365 (GRCm39) |
K1813E |
probably damaging |
Het |
| Cd209b |
T |
A |
8: 3,968,744 (GRCm39) |
D304V |
probably damaging |
Het |
| Chmp2b |
T |
C |
16: 65,359,363 (GRCm39) |
D11G |
probably benign |
Het |
| Comp |
A |
G |
8: 70,831,285 (GRCm39) |
N384S |
probably damaging |
Het |
| Dbnl |
A |
G |
11: 5,748,279 (GRCm39) |
Y336C |
probably damaging |
Het |
| Faf2 |
G |
T |
13: 54,769,716 (GRCm39) |
Q21H |
probably null |
Het |
| Fam117b |
A |
T |
1: 59,992,130 (GRCm39) |
K260* |
probably null |
Het |
| Gramd1b |
A |
G |
9: 40,214,809 (GRCm39) |
L379P |
probably damaging |
Het |
| Iars1 |
A |
G |
13: 49,856,652 (GRCm39) |
N302D |
probably benign |
Het |
| Kcnh6 |
C |
T |
11: 105,917,572 (GRCm39) |
T702I |
probably benign |
Het |
| Kdelr2 |
A |
G |
5: 143,398,330 (GRCm39) |
Y59C |
probably damaging |
Het |
| Mgam |
T |
C |
6: 40,635,204 (GRCm39) |
Y300H |
probably damaging |
Het |
| Or3a1d |
T |
C |
11: 74,238,245 (GRCm39) |
E55G |
possibly damaging |
Het |
| Or4e1 |
C |
T |
14: 52,700,822 (GRCm39) |
V215M |
probably damaging |
Het |
| Or4k40 |
A |
G |
2: 111,251,237 (GRCm39) |
S20P |
probably benign |
Het |
| Pcdh17 |
T |
C |
14: 84,685,632 (GRCm39) |
W700R |
probably damaging |
Het |
| Pigq |
T |
G |
17: 26,146,660 (GRCm39) |
H615P |
possibly damaging |
Het |
| Pkhd1l1 |
T |
A |
15: 44,392,806 (GRCm39) |
S1714T |
possibly damaging |
Het |
| Polr1b |
G |
T |
2: 128,952,046 (GRCm39) |
R358I |
probably benign |
Het |
| Tmprss11a |
C |
A |
5: 86,570,378 (GRCm39) |
V194F |
probably damaging |
Het |
| Trhr |
T |
C |
15: 44,092,708 (GRCm39) |
I315T |
probably damaging |
Het |
| Ttc38 |
G |
A |
15: 85,720,274 (GRCm39) |
V79M |
possibly damaging |
Het |
| Ubr4 |
T |
A |
4: 139,189,845 (GRCm39) |
|
probably benign |
Het |
| Vmn2r45 |
T |
C |
7: 8,486,272 (GRCm39) |
T339A |
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 |
|
|
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 |
|
R6671:Vps53
|
UTSW |
11 |
76,025,332 (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 |
|
|
| Posted On |
2013-12-09 |
Incidental Mutation