Incidental Mutation 'R6772:Vps53'
ID |
532216 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps53
|
Ensembl Gene |
ENSMUSG00000017288 |
Gene Name |
VPS53 GARP complex subunit |
Synonyms |
2310040I21Rik, 3100002B05Rik, 2010002A08Rik |
MMRRC Submission |
044888-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R6772 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
11 |
Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
Type of Mutation |
start codon destroyed |
DNA Base Change (assembly) |
A to T
at 76070324 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Methionine to Lysine
at position 1
(M1K)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000127364
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056601]
[ENSMUST00000094015]
[ENSMUST00000108419]
[ENSMUST00000129256]
[ENSMUST00000129853]
[ENSMUST00000163878]
[ENSMUST00000166752]
[ENSMUST00000167114]
[ENSMUST00000169734]
[ENSMUST00000170730]
|
AlphaFold |
Q8CCB4 |
Predicted Effect |
probably null
Transcript: ENSMUST00000056601
AA Change: M1K
|
SMART Domains |
Protein: ENSMUSP00000061317 Gene: ENSMUSG00000017288 AA Change: M1K
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 null
Transcript: ENSMUST00000094015
AA Change: M1K
|
SMART Domains |
Protein: ENSMUSP00000091554 Gene: ENSMUSG00000017288 AA Change: M1K
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 null
Transcript: ENSMUST00000108419
AA Change: M1K
|
SMART Domains |
Protein: ENSMUSP00000104057 Gene: ENSMUSG00000017288 AA Change: M1K
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 null
Transcript: ENSMUST00000129256
AA Change: M1K
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000129853
|
SMART Domains |
Protein: ENSMUSP00000114936 Gene: ENSMUSG00000069808
Domain | Start | End | E-Value | Type |
TLC
|
1 |
166 |
6.2e-8 |
SMART |
|
Predicted Effect |
probably null
Transcript: ENSMUST00000163878
AA Change: M1K
|
Predicted Effect |
probably null
Transcript: ENSMUST00000166752
AA Change: M1K
|
SMART Domains |
Protein: ENSMUSP00000129159 Gene: ENSMUSG00000017288 AA Change: M1K
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 null
Transcript: ENSMUST00000167114
AA Change: M1K
|
SMART Domains |
Protein: ENSMUSP00000131663 Gene: ENSMUSG00000017288 AA Change: M1K
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 null
Transcript: ENSMUST00000169734
AA Change: M1K
|
SMART Domains |
Protein: ENSMUSP00000130499 Gene: ENSMUSG00000017288 AA Change: M1K
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 null
Transcript: ENSMUST00000170730
AA Change: M1K
|
SMART Domains |
Protein: ENSMUSP00000127364 Gene: ENSMUSG00000017288 AA Change: M1K
Domain | Start | End | E-Value | Type |
low complexity region
|
3 |
19 |
N/A |
INTRINSIC |
Pfam:Vps53_N
|
54 |
123 |
3e-34 |
PFAM |
|
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.8%
- 20x: 96.7%
|
Validation Efficiency |
97% (36/37) |
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: 36 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca16 |
A |
T |
7: 120,126,276 (GRCm39) |
D1144V |
probably damaging |
Het |
Ankrd13a |
A |
G |
5: 114,939,804 (GRCm39) |
H477R |
probably benign |
Het |
Anxa3 |
A |
T |
5: 96,958,972 (GRCm39) |
I27F |
probably damaging |
Het |
Aplf |
T |
C |
6: 87,640,781 (GRCm39) |
E76G |
possibly damaging |
Het |
Bbs1 |
A |
G |
19: 4,956,618 (GRCm39) |
|
probably benign |
Het |
Camk2a |
T |
C |
18: 61,102,092 (GRCm39) |
S332P |
probably benign |
Het |
Casz1 |
T |
A |
4: 149,027,663 (GRCm39) |
F1013L |
probably damaging |
Het |
Cd109 |
A |
T |
9: 78,588,092 (GRCm39) |
I707F |
possibly damaging |
Het |
Cd4 |
G |
A |
6: 124,849,421 (GRCm39) |
T202I |
probably benign |
Het |
Celsr1 |
A |
G |
15: 85,914,983 (GRCm39) |
S997P |
probably benign |
Het |
Cfap77 |
T |
C |
2: 28,944,951 (GRCm39) |
T24A |
probably damaging |
Het |
Dscaml1 |
G |
A |
9: 45,621,609 (GRCm39) |
R1019H |
probably damaging |
Het |
Epb41l4b |
C |
A |
4: 57,063,140 (GRCm39) |
V517F |
probably benign |
Het |
Exosc10 |
G |
A |
4: 148,665,591 (GRCm39) |
D818N |
probably damaging |
Het |
Furin |
C |
T |
7: 80,043,240 (GRCm39) |
G324S |
probably damaging |
Het |
Idh2 |
TCCCAGG |
T |
7: 79,748,079 (GRCm39) |
|
probably benign |
Het |
Ifi206 |
T |
C |
1: 173,308,773 (GRCm39) |
M408V |
unknown |
Het |
Kdm4a |
T |
C |
4: 117,999,752 (GRCm39) |
|
probably null |
Het |
Neo1 |
T |
A |
9: 58,810,259 (GRCm39) |
Q1064L |
probably damaging |
Het |
Nphp4 |
G |
A |
4: 152,628,863 (GRCm39) |
V750I |
probably benign |
Het |
Pcdhac1 |
T |
C |
18: 37,223,289 (GRCm39) |
V34A |
probably benign |
Het |
Pdk4 |
T |
C |
6: 5,487,141 (GRCm39) |
I302V |
probably benign |
Het |
Prl6a1 |
A |
G |
13: 27,503,031 (GRCm39) |
D209G |
probably damaging |
Het |
Pspn |
T |
C |
17: 57,306,515 (GRCm39) |
Q138R |
probably benign |
Het |
Ptgs2 |
A |
G |
1: 149,977,829 (GRCm39) |
Y134C |
probably damaging |
Het |
Rlbp1 |
G |
A |
7: 79,033,798 (GRCm39) |
|
probably benign |
Het |
Rpia |
T |
C |
6: 70,762,532 (GRCm39) |
I108V |
probably benign |
Het |
Tcaf1 |
A |
T |
6: 42,652,210 (GRCm39) |
H757Q |
probably damaging |
Het |
Ttc8 |
A |
C |
12: 98,909,848 (GRCm39) |
S143R |
probably damaging |
Het |
Uba6 |
A |
G |
5: 86,294,932 (GRCm39) |
|
probably benign |
Het |
Ubr4 |
A |
T |
4: 139,194,541 (GRCm39) |
K4280* |
probably null |
Het |
Vmn2r15 |
C |
A |
5: 109,434,238 (GRCm39) |
S822I |
probably damaging |
Het |
Zfp362 |
A |
G |
4: 128,684,053 (GRCm39) |
M18T |
possibly damaging |
Het |
Zfp429 |
A |
G |
13: 67,538,317 (GRCm39) |
C376R |
probably damaging |
Het |
Zfyve9 |
T |
C |
4: 108,496,466 (GRCm39) |
N1395S |
probably damaging |
Het |
Zmynd8 |
T |
A |
2: 165,649,521 (GRCm39) |
Q857H |
probably benign |
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 |
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 |
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'- TTCCGCTCAGCATAAGAACC -3'
(R):5'- TTTCCAGGGACTTGACAGCC -3'
Sequencing Primer
(F):5'- GCATAAGAACCGCCACCTTTC -3'
(R):5'- ACTTGACAGCCATGCCTG -3'
|
Posted On |
2018-08-29 |