Incidental Mutation 'IGL03001:Vps53'
| ID |
407332 |
| 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 # |
IGL03001
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
11 |
| Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 76029150 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 119
(E119G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000130499
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056601]
[ENSMUST00000094015]
[ENSMUST00000108419]
[ENSMUST00000163878]
[ENSMUST00000170730]
[ENSMUST00000169734]
[ENSMUST00000166752]
[ENSMUST00000167114]
|
| AlphaFold |
Q8CCB4 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000056601
AA Change: E119G
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: E119G
| 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
|
| SMART Domains |
Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
| 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: E119G
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: E119G
| 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 |
probably benign
Transcript: ENSMUST00000163878
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000166084
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000170730
AA Change: E80G
PolyPhen 2
Score 0.907 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000127364
Gene: ENSMUSG00000017288
AA Change: E80G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
19 |
N/A |
INTRINSIC |
|
Pfam:Vps53_N
|
54 |
123 |
3e-34 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000169734
AA Change: E119G
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288
AA Change: E119G
| 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 damaging
Transcript: ENSMUST00000166752
AA Change: E119G
PolyPhen 2
Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
AA Change: E119G
| 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 |
unknown
Transcript: ENSMUST00000166436
AA Change: E47G
|
| SMART Domains |
Protein: ENSMUSP00000131387
Gene: ENSMUSG00000017288
AA Change: E47G
| 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 |
noncoding transcript
Transcript: ENSMUST00000169532
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170143
|
| 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 |
|
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acan |
A |
C |
7: 78,761,042 (GRCm39) |
D1918A |
probably damaging |
Het |
| Ahcy |
C |
A |
2: 154,906,748 (GRCm39) |
D182Y |
probably damaging |
Het |
| Aldob |
T |
G |
4: 49,542,844 (GRCm39) |
D110A |
probably damaging |
Het |
| Alkbh8 |
A |
T |
9: 3,344,602 (GRCm39) |
M53L |
probably benign |
Het |
| Aqr |
T |
C |
2: 113,977,400 (GRCm39) |
D363G |
probably benign |
Het |
| Asxl3 |
A |
G |
18: 22,650,455 (GRCm39) |
R815G |
probably damaging |
Het |
| Atf4 |
T |
A |
15: 80,140,858 (GRCm39) |
W83R |
probably damaging |
Het |
| Baz1a |
A |
T |
12: 54,969,896 (GRCm39) |
M587K |
possibly damaging |
Het |
| Btbd8 |
T |
C |
5: 107,645,708 (GRCm39) |
I9T |
probably damaging |
Het |
| Cactin |
T |
A |
10: 81,161,568 (GRCm39) |
I700N |
probably damaging |
Het |
| Catsperg2 |
T |
C |
7: 29,424,504 (GRCm39) |
S95G |
probably benign |
Het |
| Cd1d1 |
C |
T |
3: 86,905,468 (GRCm39) |
S175N |
probably benign |
Het |
| Chd4 |
C |
A |
6: 125,078,529 (GRCm39) |
A217E |
possibly damaging |
Het |
| Cnbd2 |
T |
C |
2: 156,175,554 (GRCm39) |
|
probably null |
Het |
| Cntnap5c |
G |
A |
17: 58,362,634 (GRCm39) |
C329Y |
probably damaging |
Het |
| Col12a1 |
C |
T |
9: 79,540,955 (GRCm39) |
G2391R |
probably damaging |
Het |
| Col5a3 |
T |
A |
9: 20,719,040 (GRCm39) |
D238V |
unknown |
Het |
| Cuedc1 |
T |
C |
11: 88,073,315 (GRCm39) |
V160A |
probably benign |
Het |
| Depdc5 |
T |
C |
5: 33,102,434 (GRCm39) |
V342A |
possibly damaging |
Het |
| Dnah6 |
T |
C |
6: 73,126,123 (GRCm39) |
D1338G |
probably benign |
Het |
| Dpyd |
T |
C |
3: 118,710,891 (GRCm39) |
V433A |
probably benign |
Het |
| Epb41l5 |
T |
C |
1: 119,545,374 (GRCm39) |
H179R |
probably damaging |
Het |
| Fbf1 |
T |
C |
11: 116,056,712 (GRCm39) |
|
probably benign |
Het |
| Flnb |
T |
C |
14: 7,934,680 (GRCm38) |
S2251P |
probably damaging |
Het |
| Fsip2 |
A |
T |
2: 82,820,968 (GRCm39) |
|
probably benign |
Het |
| Grin2b |
C |
T |
6: 135,716,113 (GRCm39) |
V735M |
probably damaging |
Het |
| Itpr3 |
T |
G |
17: 27,308,586 (GRCm39) |
|
probably benign |
Het |
| Lingo4 |
C |
T |
3: 94,309,703 (GRCm39) |
R214C |
probably damaging |
Het |
| Lrp1b |
C |
T |
2: 40,817,901 (GRCm39) |
R2329H |
probably damaging |
Het |
| Lrrc47 |
T |
C |
4: 154,100,450 (GRCm39) |
L342P |
probably damaging |
Het |
| Mmp15 |
T |
C |
8: 96,094,845 (GRCm39) |
S240P |
probably damaging |
Het |
| Ndufaf4 |
T |
A |
4: 24,901,747 (GRCm39) |
N95K |
probably benign |
Het |
| Nms |
C |
T |
1: 38,980,993 (GRCm39) |
P60S |
probably benign |
Het |
| Npas3 |
A |
T |
12: 53,547,975 (GRCm39) |
Y77F |
probably damaging |
Het |
| Or2ak7 |
T |
G |
11: 58,574,702 (GRCm39) |
M1R |
probably null |
Het |
| Or51f5 |
G |
T |
7: 102,424,460 (GRCm39) |
C243F |
probably damaging |
Het |
| Or5d43 |
T |
A |
2: 88,105,189 (GRCm39) |
D68V |
probably damaging |
Het |
| Or8d2b |
A |
G |
9: 38,789,374 (GRCm39) |
M301V |
probably benign |
Het |
| Or9m2 |
T |
A |
2: 87,820,493 (GRCm39) |
Y13N |
probably benign |
Het |
| Or9s27 |
T |
A |
1: 92,516,273 (GRCm39) |
S74T |
probably damaging |
Het |
| Picalm |
T |
C |
7: 89,831,454 (GRCm39) |
V429A |
probably benign |
Het |
| Pkhd1l1 |
T |
A |
15: 44,421,400 (GRCm39) |
I3056N |
probably damaging |
Het |
| Pomt1 |
G |
T |
2: 32,134,338 (GRCm39) |
M286I |
probably benign |
Het |
| Popdc2 |
A |
T |
16: 38,189,881 (GRCm39) |
Y176F |
probably benign |
Het |
| Psg21 |
A |
T |
7: 18,386,410 (GRCm39) |
M192K |
probably benign |
Het |
| Psma1 |
C |
A |
7: 113,865,674 (GRCm39) |
A219S |
probably benign |
Het |
| Rad21l |
T |
G |
2: 151,510,389 (GRCm39) |
H22P |
probably damaging |
Het |
| Rnf213 |
A |
G |
11: 119,370,767 (GRCm39) |
T4791A |
probably damaging |
Het |
| Sdk2 |
A |
G |
11: 113,712,452 (GRCm39) |
V1609A |
probably benign |
Het |
| Sema3e |
T |
A |
5: 14,291,057 (GRCm39) |
S606T |
probably benign |
Het |
| Slc16a4 |
A |
T |
3: 107,218,858 (GRCm39) |
R486S |
possibly damaging |
Het |
| Slc17a3 |
T |
C |
13: 24,040,767 (GRCm39) |
L331P |
probably damaging |
Het |
| Slc38a11 |
A |
T |
2: 65,184,159 (GRCm39) |
V164D |
probably damaging |
Het |
| Slc38a6 |
A |
G |
12: 73,383,827 (GRCm39) |
I173V |
probably benign |
Het |
| Synpo2 |
T |
C |
3: 122,873,604 (GRCm39) |
T1121A |
probably benign |
Het |
| Tfcp2 |
T |
C |
15: 100,426,302 (GRCm39) |
D83G |
possibly damaging |
Het |
| Thnsl1 |
A |
G |
2: 21,216,455 (GRCm39) |
T70A |
probably damaging |
Het |
| Tnfrsf21 |
A |
G |
17: 43,398,786 (GRCm39) |
I631V |
probably damaging |
Het |
| Tor2a |
C |
A |
2: 32,647,329 (GRCm39) |
H6Q |
possibly damaging |
Het |
| Ttn |
T |
C |
2: 76,565,267 (GRCm39) |
N19993S |
probably benign |
Het |
| Zkscan6 |
T |
C |
11: 65,705,495 (GRCm39) |
W69R |
probably damaging |
Het |
| Zng1 |
T |
C |
19: 24,900,002 (GRCm39) |
K301E |
probably benign |
Het |
| Zswim8 |
T |
C |
14: 20,764,459 (GRCm39) |
S610P |
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 |
|
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 |
2016-08-02 |
Incidental Mutation