Incidental Mutation 'PIT4519001:Vps53'
| ID |
555126 |
| Institutional Source |
Beutler Lab
|
| 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 # |
PIT4519001 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 76007999 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Leucine
at position 287
(R287L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000061317
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056601]
[ENSMUST00000094015]
[ENSMUST00000108419]
[ENSMUST00000163878]
[ENSMUST00000166752]
[ENSMUST00000167114]
[ENSMUST00000169734]
|
| AlphaFold |
Q8CCB4 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000056601
AA Change: R287L
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: R287L
| 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: R258L
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: R258L
| 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 benign
Transcript: ENSMUST00000108419
|
| SMART Domains |
Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
| 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 |
probably benign
Transcript: ENSMUST00000163878
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000166436
|
| SMART Domains |
Protein: ENSMUSP00000131387
Gene: ENSMUSG00000017288
| 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: R239L
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
AA Change: R239L
| 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 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 |
probably damaging
Transcript: ENSMUST00000169734
AA Change: R287L
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288
AA Change: R287L
| 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 |
- 1x: 93.5%
- 3x: 90.9%
- 10x: 84.7%
- 20x: 70.8%
|
| 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: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2700049A03Rik |
T |
A |
12: 71,217,440 (GRCm39) |
M803K |
probably benign |
Het |
| 4930590J08Rik |
C |
A |
6: 91,894,038 (GRCm39) |
N218K |
probably damaging |
Het |
| Abcc2 |
G |
A |
19: 43,807,836 (GRCm39) |
V826M |
possibly damaging |
Het |
| Abcg2 |
T |
C |
6: 58,651,792 (GRCm39) |
S395P |
probably damaging |
Het |
| Adam1b |
C |
T |
5: 121,640,010 (GRCm39) |
G345D |
probably damaging |
Het |
| Alx4 |
T |
A |
2: 93,505,773 (GRCm39) |
C292S |
probably benign |
Het |
| Amd2 |
C |
A |
10: 35,586,627 (GRCm39) |
C310F |
possibly damaging |
Het |
| BC051665 |
A |
T |
13: 60,931,989 (GRCm39) |
S137T |
possibly damaging |
Het |
| Bmp1 |
A |
G |
14: 70,727,469 (GRCm39) |
F705L |
possibly damaging |
Het |
| Coil |
C |
T |
11: 88,863,552 (GRCm39) |
|
probably benign |
Het |
| Col6a6 |
G |
A |
9: 105,609,462 (GRCm39) |
P1609S |
probably benign |
Het |
| Cpt1b |
A |
T |
15: 89,303,066 (GRCm39) |
F633I |
probably damaging |
Het |
| Dcun1d2 |
A |
T |
8: 13,311,406 (GRCm39) |
D194E |
probably benign |
Het |
| Defb4 |
A |
G |
8: 19,248,752 (GRCm39) |
R2G |
possibly damaging |
Het |
| Dll4 |
T |
C |
2: 119,162,897 (GRCm39) |
V506A |
probably benign |
Het |
| Dop1b |
A |
G |
16: 93,558,942 (GRCm39) |
S563G |
probably benign |
Het |
| Dpp7 |
C |
A |
2: 25,242,460 (GRCm39) |
G498W |
probably damaging |
Het |
| Fam210a |
A |
T |
18: 68,409,020 (GRCm39) |
S97T |
possibly damaging |
Het |
| Fastkd1 |
T |
A |
2: 69,520,501 (GRCm39) |
D767V |
probably damaging |
Het |
| Fgg |
A |
T |
3: 82,920,246 (GRCm39) |
N342Y |
probably damaging |
Het |
| Gimap6 |
T |
G |
6: 48,684,995 (GRCm39) |
R30S |
probably benign |
Het |
| Gm10840 |
T |
C |
11: 106,051,959 (GRCm39) |
V95A |
unknown |
Het |
| Herc3 |
T |
A |
6: 58,853,796 (GRCm39) |
I614N |
probably damaging |
Het |
| Kdr |
A |
T |
5: 76,097,556 (GRCm39) |
S1233R |
possibly damaging |
Het |
| Lrp1 |
C |
G |
10: 127,443,843 (GRCm39) |
Q141H |
possibly damaging |
Het |
| Magi2 |
A |
T |
5: 20,866,344 (GRCm39) |
K1078N |
probably damaging |
Het |
| Meioc |
A |
T |
11: 102,570,783 (GRCm39) |
E838V |
probably damaging |
Het |
| Mmp20 |
A |
G |
9: 7,628,302 (GRCm39) |
K17E |
probably benign |
Het |
| Mtor |
C |
T |
4: 148,608,957 (GRCm39) |
R1538W |
probably damaging |
Het |
| Notch2 |
C |
T |
3: 98,005,424 (GRCm39) |
T296I |
probably damaging |
Het |
| Nup98 |
T |
C |
7: 101,784,171 (GRCm39) |
S1054G |
probably benign |
Het |
| Or10ac1 |
T |
C |
6: 42,515,534 (GRCm39) |
T141A |
probably damaging |
Het |
| Or2a12 |
T |
C |
6: 42,904,578 (GRCm39) |
C138R |
probably damaging |
Het |
| Or5b109 |
A |
C |
19: 13,212,216 (GRCm39) |
I201L |
probably benign |
Het |
| Or6f1 |
T |
C |
7: 85,970,941 (GRCm39) |
Y73C |
probably damaging |
Het |
| Pipox |
C |
A |
11: 77,774,001 (GRCm39) |
W205L |
probably damaging |
Het |
| Plin4 |
T |
G |
17: 56,410,828 (GRCm39) |
T1068P |
probably benign |
Het |
| Pou6f2 |
A |
G |
13: 18,414,149 (GRCm39) |
S209P |
unknown |
Het |
| Ptpdc1 |
T |
C |
13: 48,736,632 (GRCm39) |
T713A |
probably benign |
Het |
| Rgsl1 |
T |
C |
1: 153,701,716 (GRCm39) |
Y246C |
possibly damaging |
Het |
| Rnf19b |
C |
T |
4: 128,969,446 (GRCm39) |
A354V |
probably damaging |
Het |
| Rsph4a |
A |
G |
10: 33,785,126 (GRCm39) |
T346A |
probably benign |
Het |
| Rsrc2 |
T |
C |
5: 123,883,135 (GRCm39) |
T16A |
unknown |
Het |
| Scrn3 |
T |
C |
2: 73,148,768 (GRCm39) |
V113A |
possibly damaging |
Het |
| Scrn3 |
T |
A |
2: 73,161,347 (GRCm39) |
I311K |
possibly damaging |
Het |
| Sfmbt1 |
T |
C |
14: 30,506,148 (GRCm39) |
|
probably null |
Het |
| Sin3a |
A |
G |
9: 57,002,740 (GRCm39) |
I211V |
possibly damaging |
Het |
| Strn3 |
T |
C |
12: 51,680,491 (GRCm39) |
T370A |
probably benign |
Het |
| Sulf1 |
T |
G |
1: 12,918,395 (GRCm39) |
N786K |
probably damaging |
Het |
| Taf1b |
T |
A |
12: 24,597,118 (GRCm39) |
Y352* |
probably null |
Het |
| Tas2r120 |
T |
A |
6: 132,634,297 (GRCm39) |
N126K |
probably benign |
Het |
| Tjap1 |
C |
A |
17: 46,572,432 (GRCm39) |
R68L |
probably benign |
Het |
| Tnfsf12 |
C |
T |
11: 69,586,230 (GRCm39) |
R66Q |
probably benign |
Het |
| Traj45 |
A |
G |
14: 54,410,303 (GRCm39) |
D6G |
|
Het |
| Trappc9 |
T |
C |
15: 72,824,943 (GRCm39) |
T541A |
probably benign |
Het |
| Ttc29 |
A |
C |
8: 79,052,106 (GRCm39) |
E329A |
probably benign |
Het |
| Vmn1r117 |
T |
G |
7: 20,617,160 (GRCm39) |
D296A |
possibly damaging |
Het |
| Vmn1r203 |
A |
G |
13: 22,708,765 (GRCm39) |
N182S |
probably benign |
Het |
| Vwce |
G |
A |
19: 10,641,946 (GRCm39) |
E891K |
possibly damaging |
Het |
| Zfp608 |
T |
C |
18: 55,079,783 (GRCm39) |
N334S |
possibly damaging |
Het |
| Zfp648 |
A |
G |
1: 154,080,687 (GRCm39) |
H282R |
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 |
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TGCAGGACACATGGATACTAAG -3'
(R):5'- AGATCCCCAGGCTGATTTGC -3'
Sequencing Primer
(F):5'- CACATGGATACTAAGTCAGGCCTG -3'
(R):5'- CCCAGAAGAGTTTACCTGTGC -3'
|
| Posted On |
2019-06-07 |
Incidental Mutation