Incidental Mutation 'IGL02321:Vps53'
ID |
288226 |
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 # |
IGL02321
|
Quality Score |
|
Status
|
|
Chromosome |
11 |
Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 75939364 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Asparagine
at position 680
(D680N)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000091554
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056601]
[ENSMUST00000094015]
[ENSMUST00000108419]
|
AlphaFold |
Q8CCB4 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000056601
AA Change: D709N
PolyPhen 2
Score 0.602 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000061317 Gene: ENSMUSG00000017288 AA Change: D709N
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 |
possibly damaging
Transcript: ENSMUST00000094015
AA Change: D680N
PolyPhen 2
Score 0.602 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000091554 Gene: ENSMUSG00000017288 AA Change: D680N
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: D532N
|
SMART Domains |
Protein: ENSMUSP00000104057 Gene: ENSMUSG00000017288 AA Change: D532N
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: 43 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acsf3 |
C |
T |
8: 123,506,853 (GRCm39) |
R49C |
possibly damaging |
Het |
Alg2 |
T |
C |
4: 47,474,249 (GRCm39) |
Y13C |
probably benign |
Het |
Apoa4 |
A |
G |
9: 46,154,218 (GRCm39) |
D273G |
probably damaging |
Het |
Axl |
C |
T |
7: 25,458,194 (GRCm39) |
V854I |
probably damaging |
Het |
Bicral |
A |
G |
17: 47,122,873 (GRCm39) |
S673P |
probably benign |
Het |
Camkk2 |
A |
G |
5: 122,902,190 (GRCm39) |
S40P |
probably damaging |
Het |
Ccdc39 |
A |
G |
3: 33,871,107 (GRCm39) |
|
probably benign |
Het |
Ccdc87 |
A |
G |
19: 4,891,059 (GRCm39) |
E517G |
probably damaging |
Het |
Cd22 |
A |
G |
7: 30,569,308 (GRCm39) |
S603P |
probably damaging |
Het |
Cdk5rap3 |
A |
T |
11: 96,804,291 (GRCm39) |
C21S |
probably damaging |
Het |
Chml |
G |
A |
1: 175,519,900 (GRCm39) |
P68L |
possibly damaging |
Het |
Cplane1 |
A |
G |
15: 8,246,056 (GRCm39) |
E1476G |
probably benign |
Het |
Cstdc6 |
A |
G |
16: 36,143,388 (GRCm39) |
|
probably benign |
Het |
Ephb3 |
T |
C |
16: 21,033,139 (GRCm39) |
V41A |
probably damaging |
Het |
Gm4781 |
T |
A |
10: 100,232,752 (GRCm39) |
|
noncoding transcript |
Het |
Hip1r |
A |
T |
5: 124,137,953 (GRCm39) |
I760F |
probably damaging |
Het |
Hyal5 |
T |
C |
6: 24,891,614 (GRCm39) |
L476P |
probably benign |
Het |
Isyna1 |
A |
G |
8: 71,048,920 (GRCm39) |
N333S |
probably damaging |
Het |
Kcnmb1 |
A |
T |
11: 33,920,091 (GRCm39) |
|
probably benign |
Het |
Mark4 |
T |
C |
7: 19,160,314 (GRCm39) |
T649A |
probably benign |
Het |
Mgat1 |
T |
C |
11: 49,152,536 (GRCm39) |
F340L |
probably benign |
Het |
Mical1 |
G |
A |
10: 41,362,660 (GRCm39) |
E932K |
possibly damaging |
Het |
Mmaa |
T |
G |
8: 80,000,759 (GRCm39) |
Y233S |
probably damaging |
Het |
Ntsr1 |
G |
T |
2: 180,180,627 (GRCm39) |
|
probably null |
Het |
Or2o1 |
T |
G |
11: 49,051,602 (GRCm39) |
Y254D |
probably damaging |
Het |
Orm2 |
T |
C |
4: 63,281,229 (GRCm39) |
Y56H |
probably damaging |
Het |
Pex26 |
C |
T |
6: 121,170,468 (GRCm39) |
|
probably benign |
Het |
Pik3r4 |
C |
T |
9: 105,521,677 (GRCm39) |
A81V |
probably benign |
Het |
Pramel32 |
A |
G |
4: 88,548,340 (GRCm39) |
S22P |
probably benign |
Het |
Prr14l |
G |
T |
5: 32,985,151 (GRCm39) |
T1448K |
probably benign |
Het |
Ralgapa2 |
A |
T |
2: 146,254,736 (GRCm39) |
Y799* |
probably null |
Het |
Ryr1 |
A |
C |
7: 28,778,121 (GRCm39) |
L2132R |
probably damaging |
Het |
Sec23b |
T |
C |
2: 144,421,325 (GRCm39) |
|
probably null |
Het |
Sirt5 |
C |
T |
13: 43,533,164 (GRCm39) |
T164I |
probably damaging |
Het |
Slc9c1 |
T |
C |
16: 45,376,977 (GRCm39) |
V429A |
probably benign |
Het |
Spen |
T |
C |
4: 141,244,441 (GRCm39) |
D198G |
unknown |
Het |
Syne2 |
A |
G |
12: 75,965,773 (GRCm39) |
N832D |
possibly damaging |
Het |
Traf7 |
C |
A |
17: 24,732,020 (GRCm39) |
C193F |
possibly damaging |
Het |
Vmn1r191 |
T |
A |
13: 22,363,068 (GRCm39) |
R229* |
probably null |
Het |
Wbp1l |
G |
T |
19: 46,642,749 (GRCm39) |
G234V |
probably benign |
Het |
Wdfy3 |
A |
T |
5: 102,070,475 (GRCm39) |
S1098T |
probably damaging |
Het |
Yod1 |
T |
A |
1: 130,646,688 (GRCm39) |
D188E |
probably damaging |
Het |
Zbtb25 |
T |
C |
12: 76,396,907 (GRCm39) |
D105G |
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 |
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 |