Incidental Mutation 'IGL01655:Vps53'
| ID |
102955 |
| 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 # |
IGL01655
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
11 |
| Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 75953860 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 402
(I402N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000131663
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056601]
[ENSMUST00000094015]
[ENSMUST00000108419]
[ENSMUST00000166752]
[ENSMUST00000167114]
[ENSMUST00000169734]
|
| AlphaFold |
Q8CCB4 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000056601
AA Change: I679N
PolyPhen 2
Score 0.927 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: I679N
| 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: I650N
PolyPhen 2
Score 0.877 (Sensitivity: 0.83; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: I650N
| 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: I502N
|
| SMART Domains |
Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: I502N
| 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 |
probably damaging
Transcript: ENSMUST00000167114
AA Change: I402N
PolyPhen 2
Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000131663
Gene: ENSMUSG00000017288
AA Change: I402N
| 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: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acp6 |
G |
A |
3: 97,073,288 (GRCm39) |
|
probably null |
Het |
| Aida |
T |
A |
1: 183,094,618 (GRCm39) |
Y104* |
probably null |
Het |
| Cd300lg |
T |
C |
11: 101,937,901 (GRCm39) |
S244P |
probably benign |
Het |
| Ces4a |
T |
A |
8: 105,873,806 (GRCm39) |
L425Q |
probably damaging |
Het |
| Chrnb3 |
T |
C |
8: 27,884,202 (GRCm39) |
V298A |
probably damaging |
Het |
| Cnot6 |
A |
C |
11: 49,568,131 (GRCm39) |
F486C |
probably damaging |
Het |
| Ctnna3 |
A |
G |
10: 64,708,949 (GRCm39) |
T663A |
probably benign |
Het |
| Cyp2j12 |
T |
A |
4: 96,003,814 (GRCm39) |
K267N |
possibly damaging |
Het |
| Dclre1a |
A |
T |
19: 56,535,489 (GRCm39) |
Y32N |
probably damaging |
Het |
| Ddx21 |
A |
G |
10: 62,423,270 (GRCm39) |
I644T |
probably damaging |
Het |
| Epha6 |
A |
C |
16: 59,659,666 (GRCm39) |
N817K |
probably benign |
Het |
| Ercc6l2 |
T |
A |
13: 63,967,566 (GRCm39) |
Y55* |
probably null |
Het |
| Esyt1 |
A |
G |
10: 128,358,181 (GRCm39) |
I183T |
possibly damaging |
Het |
| Exoc8 |
T |
C |
8: 125,622,967 (GRCm39) |
T467A |
probably benign |
Het |
| Fance |
T |
C |
17: 28,541,753 (GRCm39) |
|
probably benign |
Het |
| Fbxo46 |
C |
T |
7: 18,870,235 (GRCm39) |
R285W |
probably damaging |
Het |
| Ffar2 |
A |
T |
7: 30,519,012 (GRCm39) |
V176E |
probably damaging |
Het |
| Fnbp1l |
T |
C |
3: 122,362,398 (GRCm39) |
|
probably null |
Het |
| Gm10288 |
T |
C |
3: 146,544,565 (GRCm39) |
|
noncoding transcript |
Het |
| Gm12588 |
T |
A |
11: 121,798,777 (GRCm39) |
|
|
Het |
| Gm9755 |
G |
A |
8: 67,967,885 (GRCm39) |
|
noncoding transcript |
Het |
| Gpr33 |
A |
T |
12: 52,070,343 (GRCm39) |
M232K |
probably damaging |
Het |
| Haus5 |
A |
T |
7: 30,362,719 (GRCm39) |
|
probably benign |
Het |
| Ilvbl |
A |
G |
10: 78,413,167 (GRCm39) |
|
probably benign |
Het |
| Kifap3 |
G |
A |
1: 163,623,618 (GRCm39) |
|
probably benign |
Het |
| Klhl26 |
T |
C |
8: 70,904,533 (GRCm39) |
Y378C |
probably damaging |
Het |
| Lama4 |
G |
A |
10: 38,936,209 (GRCm39) |
S628N |
probably benign |
Het |
| Lamc3 |
G |
A |
2: 31,788,290 (GRCm39) |
R150H |
probably damaging |
Het |
| Mrgprx2 |
A |
T |
7: 48,132,439 (GRCm39) |
C126* |
probably null |
Het |
| Myo3a |
A |
T |
2: 22,428,137 (GRCm39) |
D798V |
probably damaging |
Het |
| Ndufs1 |
A |
T |
1: 63,190,716 (GRCm39) |
L44Q |
probably damaging |
Het |
| Nfrkb |
G |
T |
9: 31,314,755 (GRCm39) |
R525L |
probably benign |
Het |
| Or10ag58 |
T |
A |
2: 87,265,229 (GRCm39) |
C133S |
probably damaging |
Het |
| Or1e34 |
T |
C |
11: 73,778,753 (GRCm39) |
I148M |
probably benign |
Het |
| Or2p2 |
T |
C |
13: 21,257,075 (GRCm39) |
Y132C |
probably damaging |
Het |
| Or2r11 |
T |
C |
6: 42,437,474 (GRCm39) |
T160A |
probably benign |
Het |
| Or4k41 |
T |
C |
2: 111,280,234 (GRCm39) |
F250L |
probably benign |
Het |
| Or4q3 |
A |
G |
14: 50,583,641 (GRCm39) |
M86T |
probably benign |
Het |
| Or5w1 |
A |
G |
2: 87,486,773 (GRCm39) |
F164S |
probably damaging |
Het |
| Or8g17 |
T |
A |
9: 38,930,214 (GRCm39) |
I208F |
probably benign |
Het |
| Or9r7 |
G |
T |
10: 129,962,860 (GRCm39) |
T22K |
probably benign |
Het |
| Pias4 |
T |
C |
10: 80,991,492 (GRCm39) |
K352E |
probably benign |
Het |
| Pkhd1 |
G |
A |
1: 20,604,857 (GRCm39) |
Q1153* |
probably null |
Het |
| Pon1 |
C |
A |
6: 5,175,760 (GRCm39) |
W254C |
probably damaging |
Het |
| Prr14 |
A |
G |
7: 127,074,939 (GRCm39) |
T447A |
probably benign |
Het |
| Serpinb9g |
T |
A |
13: 33,679,088 (GRCm39) |
C319* |
probably null |
Het |
| Slc9c1 |
A |
T |
16: 45,403,335 (GRCm39) |
M801L |
probably benign |
Het |
| Tenm4 |
C |
T |
7: 96,202,931 (GRCm39) |
T182M |
probably damaging |
Het |
| Ubr4 |
T |
A |
4: 139,135,107 (GRCm39) |
L813Q |
probably damaging |
Het |
| Uimc1 |
T |
C |
13: 55,176,517 (GRCm39) |
E667G |
probably benign |
Het |
| Unc79 |
A |
G |
12: 103,134,546 (GRCm39) |
T2173A |
probably benign |
Het |
| Unkl |
T |
C |
17: 25,429,822 (GRCm39) |
S142P |
probably benign |
Het |
| Vezt |
A |
G |
10: 93,832,859 (GRCm39) |
V204A |
probably benign |
Het |
| Zfyve9 |
T |
C |
4: 108,499,289 (GRCm39) |
D1343G |
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 |
|
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 |
2014-01-21 |
Incidental Mutation