Incidental Mutation 'R6657:Vps53'
| ID |
526674 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps53
|
| Ensembl Gene |
ENSMUSG00000017288 |
| Gene Name |
VPS53 GARP complex subunit |
| Synonyms |
2310040I21Rik, 3100002B05Rik, 2010002A08Rik |
| MMRRC Submission |
044778-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6657 (G1)
|
| Quality Score |
187.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 76025253 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 197
(I197N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000130499
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056601]
[ENSMUST00000094015]
[ENSMUST00000108419]
[ENSMUST00000163878]
[ENSMUST00000166752]
[ENSMUST00000169734]
[ENSMUST00000167114]
[ENSMUST00000170730]
|
| AlphaFold |
Q8CCB4 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000056601
AA Change: I197N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: I197N
| 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: I168N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: I168N
| 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: I197N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: I197N
| 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 |
unknown
Transcript: ENSMUST00000166436
AA Change: I125N
|
| SMART Domains |
Protein: ENSMUSP00000131387
Gene: ENSMUSG00000017288
AA Change: I125N
| 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 |
probably damaging
Transcript: ENSMUST00000166752
AA Change: I197N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
AA Change: I197N
| 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: ENSMUST00000169734
AA Change: I197N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288
AA Change: I197N
| 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 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000169532
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170143
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000170730
|
| SMART Domains |
Protein: ENSMUSP00000127364
Gene: ENSMUSG00000017288
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
19 |
N/A |
INTRINSIC |
|
Pfam:Vps53_N
|
54 |
123 |
3e-34 |
PFAM |
|
| Meta Mutation Damage Score |
0.9159 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.9%
- 20x: 94.0%
|
| Validation Efficiency |
98% (48/49) |
| 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: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4933405L10Rik |
T |
G |
8: 106,435,450 (GRCm39) |
L36R |
probably damaging |
Het |
| Akr1b1 |
C |
T |
6: 34,286,939 (GRCm39) |
V206M |
possibly damaging |
Het |
| Akr1b7 |
A |
C |
6: 34,393,135 (GRCm39) |
D106A |
probably damaging |
Het |
| Bhlhe40 |
TG |
TGG |
6: 108,641,818 (GRCm39) |
254 |
probably null |
Het |
| Chst5 |
C |
T |
8: 112,616,906 (GRCm39) |
R238Q |
probably benign |
Het |
| Cpxm2 |
T |
C |
7: 131,650,806 (GRCm39) |
Y618C |
probably damaging |
Het |
| Csnk1d |
T |
C |
11: 120,855,820 (GRCm39) |
E405G |
possibly damaging |
Het |
| Ctsh |
A |
T |
9: 89,942,555 (GRCm39) |
M37L |
probably benign |
Het |
| Eml5 |
T |
G |
12: 98,757,664 (GRCm39) |
I1843L |
probably damaging |
Het |
| Ep400 |
C |
A |
5: 110,841,411 (GRCm39) |
|
probably benign |
Het |
| Fbln2 |
A |
G |
6: 91,236,732 (GRCm39) |
N749S |
possibly damaging |
Het |
| Gpc5 |
A |
G |
14: 115,607,610 (GRCm39) |
H404R |
probably benign |
Het |
| Hyal6 |
A |
G |
6: 24,734,757 (GRCm39) |
D230G |
possibly damaging |
Het |
| Itga5 |
T |
C |
15: 103,259,222 (GRCm39) |
D735G |
probably damaging |
Het |
| Kansl2 |
T |
A |
15: 98,422,551 (GRCm39) |
Q339L |
possibly damaging |
Het |
| Lrp4 |
T |
A |
2: 91,322,398 (GRCm39) |
M1078K |
probably benign |
Het |
| Mmp24 |
A |
T |
2: 155,640,099 (GRCm39) |
Y143F |
probably damaging |
Het |
| Mroh7 |
A |
T |
4: 106,559,697 (GRCm39) |
C743* |
probably null |
Het |
| Myh14 |
T |
C |
7: 44,287,270 (GRCm39) |
N618D |
probably damaging |
Het |
| Myo19 |
A |
T |
11: 84,788,022 (GRCm39) |
M324L |
probably benign |
Het |
| Nectin2 |
T |
C |
7: 19,472,065 (GRCm39) |
N108S |
probably benign |
Het |
| Nrg2 |
A |
G |
18: 36,329,642 (GRCm39) |
I191T |
probably damaging |
Het |
| Odf4 |
T |
C |
11: 68,817,638 (GRCm39) |
N18D |
probably benign |
Het |
| Or5aq6 |
T |
A |
2: 86,923,403 (GRCm39) |
I113F |
probably benign |
Het |
| Pcsk2 |
T |
G |
2: 143,532,286 (GRCm39) |
L145V |
probably damaging |
Het |
| Pdzrn3 |
C |
A |
6: 101,127,983 (GRCm39) |
Q894H |
probably benign |
Het |
| Pfpl |
G |
A |
19: 12,407,290 (GRCm39) |
V514I |
probably benign |
Het |
| Plbd1 |
A |
T |
6: 136,594,250 (GRCm39) |
M333K |
probably damaging |
Het |
| Plec |
A |
T |
15: 76,062,356 (GRCm39) |
M2554K |
possibly damaging |
Het |
| Psmb5 |
A |
G |
14: 54,851,840 (GRCm39) |
Y115H |
possibly damaging |
Het |
| Rictor |
A |
G |
15: 6,788,977 (GRCm39) |
N198D |
possibly damaging |
Het |
| Rsrc2 |
A |
G |
5: 123,877,630 (GRCm39) |
|
probably benign |
Het |
| Sec16a |
C |
T |
2: 26,315,876 (GRCm39) |
W262* |
probably null |
Het |
| Sfmbt1 |
A |
G |
14: 30,488,053 (GRCm39) |
D8G |
possibly damaging |
Het |
| Sptbn5 |
T |
G |
2: 119,906,881 (GRCm39) |
|
probably benign |
Het |
| Sqor |
A |
G |
2: 122,649,514 (GRCm39) |
D139G |
possibly damaging |
Het |
| Sugt1 |
A |
T |
14: 79,844,701 (GRCm39) |
T139S |
probably benign |
Het |
| Tcp11 |
G |
A |
17: 28,290,646 (GRCm39) |
P159S |
probably damaging |
Het |
| Tmem262 |
A |
G |
19: 6,130,542 (GRCm39) |
T89A |
possibly damaging |
Het |
| Tnfaip6 |
C |
A |
2: 51,933,795 (GRCm39) |
T50N |
probably damaging |
Het |
| Ttll9 |
T |
C |
2: 152,826,182 (GRCm39) |
Y131H |
probably damaging |
Het |
| Vmn1r173 |
T |
A |
7: 23,402,320 (GRCm39) |
M185K |
probably damaging |
Het |
| Vmn2r111 |
T |
C |
17: 22,778,032 (GRCm39) |
N549S |
possibly damaging |
Het |
| Vmn2r52 |
G |
A |
7: 9,893,090 (GRCm39) |
T683I |
probably damaging |
Het |
| Washc4 |
T |
A |
10: 83,394,482 (GRCm39) |
F269L |
possibly damaging |
Het |
| Wdfy4 |
C |
T |
14: 32,769,208 (GRCm39) |
V2086M |
possibly damaging |
Het |
| Zfp592 |
A |
T |
7: 80,675,234 (GRCm39) |
T733S |
possibly damaging |
Het |
| Zfp599 |
A |
G |
9: 22,161,538 (GRCm39) |
F209S |
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 |
|
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 |
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TGCAGACAATGGAGAGTTGTGC -3'
(R):5'- GATATCTGGGTCTCGCAAGTC -3'
Sequencing Primer
(F):5'- CACATGAGTGTACTAGTTGACTTG -3'
(R):5'- GTCTCGCAAGTCGTCCCAC -3'
|
| Posted On |
2018-07-23 |
Incidental Mutation