Incidental Mutation 'IGL02275:Vps53'
ID |
287309 |
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 # |
IGL02275
|
Quality Score |
|
Status
|
|
Chromosome |
11 |
Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 75937949 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Tyrosine to Cysteine
at position 728
(Y728C)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000091554
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056601]
[ENSMUST00000094015]
[ENSMUST00000108419]
|
AlphaFold |
Q8CCB4 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000056601
AA Change: Y757C
PolyPhen 2
Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
|
SMART Domains |
Protein: ENSMUSP00000061317 Gene: ENSMUSG00000017288 AA Change: Y757C
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 benign
Transcript: ENSMUST00000094015
AA Change: Y728C
PolyPhen 2
Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
|
SMART Domains |
Protein: ENSMUSP00000091554 Gene: ENSMUSG00000017288 AA Change: Y728C
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 |
unknown
Transcript: ENSMUST00000108419
AA Change: Y580C
|
SMART Domains |
Protein: ENSMUSP00000104057 Gene: ENSMUSG00000017288 AA Change: Y580C
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 |
|
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: 24 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700037C18Rik |
T |
A |
16: 3,724,146 (GRCm39) |
D130V |
probably damaging |
Het |
4930596D02Rik |
T |
C |
14: 35,533,880 (GRCm39) |
T9A |
probably benign |
Het |
Anapc1 |
C |
A |
2: 128,501,772 (GRCm39) |
A757S |
probably benign |
Het |
Bpifa6 |
A |
T |
2: 153,834,192 (GRCm39) |
D328V |
probably benign |
Het |
Cdh19 |
T |
A |
1: 110,853,616 (GRCm39) |
K275I |
probably benign |
Het |
Col18a1 |
A |
G |
10: 76,895,217 (GRCm39) |
I1148T |
possibly damaging |
Het |
Commd1 |
A |
T |
11: 22,850,017 (GRCm39) |
V222D |
probably damaging |
Het |
Crim1 |
T |
A |
17: 78,677,427 (GRCm39) |
M876K |
possibly damaging |
Het |
Dennd1b |
C |
A |
1: 139,008,992 (GRCm39) |
H232N |
probably damaging |
Het |
Dhx57 |
T |
C |
17: 80,582,268 (GRCm39) |
T393A |
probably benign |
Het |
Dnai7 |
T |
C |
6: 145,123,090 (GRCm39) |
Y592C |
probably damaging |
Het |
Gabrb2 |
G |
T |
11: 42,482,721 (GRCm39) |
R193L |
probably benign |
Het |
Gm5828 |
T |
A |
1: 16,839,342 (GRCm39) |
|
noncoding transcript |
Het |
Gm6483 |
C |
T |
8: 19,741,629 (GRCm39) |
P55S |
probably damaging |
Het |
Hsp90ab1 |
T |
C |
17: 45,879,364 (GRCm39) |
Y619C |
possibly damaging |
Het |
Kctd19 |
A |
G |
8: 106,123,006 (GRCm39) |
I136T |
probably damaging |
Het |
Or2n1 |
G |
T |
17: 38,486,577 (GRCm39) |
V201L |
probably benign |
Het |
Or2w6 |
A |
C |
13: 21,843,170 (GRCm39) |
F108V |
probably benign |
Het |
Sel1l |
T |
C |
12: 91,781,789 (GRCm39) |
Y532C |
probably damaging |
Het |
Sirpb1a |
A |
G |
3: 15,475,469 (GRCm39) |
|
probably null |
Het |
Ush2a |
C |
T |
1: 187,995,466 (GRCm39) |
T79M |
possibly damaging |
Het |
Usp24 |
T |
C |
4: 106,244,690 (GRCm39) |
V1215A |
probably damaging |
Het |
Vdac3-ps1 |
T |
C |
13: 18,205,379 (GRCm39) |
|
noncoding transcript |
Het |
Vmn2r75 |
T |
C |
7: 85,814,348 (GRCm39) |
T382A |
probably benign |
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 |
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 |
2015-04-16 |