Incidental Mutation 'R5961:Vps53'
| ID |
471846 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps53
|
| Ensembl Gene |
ENSMUSG00000017288 |
| Gene Name |
VPS53 GARP complex subunit |
| Synonyms |
2310040I21Rik, 3100002B05Rik, 2010002A08Rik |
| MMRRC Submission |
043247-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5961 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 75939316 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 696
(Y696H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000091554
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056601]
[ENSMUST00000094015]
[ENSMUST00000108419]
|
| AlphaFold |
Q8CCB4 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000056601
AA Change: Y725H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: Y725H
| 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: Y696H
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: Y696H
| 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: Y548H
|
| SMART Domains |
Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: Y548H
| 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 |
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.0%
- 20x: 93.7%
|
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ackr4 |
A |
G |
9: 103,976,338 (GRCm39) |
L203P |
probably damaging |
Het |
| Aen |
C |
G |
7: 78,556,907 (GRCm39) |
H252D |
probably damaging |
Het |
| Alkbh6 |
T |
A |
7: 30,013,617 (GRCm39) |
|
probably null |
Het |
| Birc6 |
T |
C |
17: 74,953,596 (GRCm39) |
V3286A |
probably damaging |
Het |
| Cacna1h |
A |
G |
17: 25,596,246 (GRCm39) |
M1925T |
probably benign |
Het |
| Caprin2 |
A |
C |
6: 148,765,038 (GRCm39) |
S554R |
probably damaging |
Het |
| Celsr3 |
T |
C |
9: 108,708,993 (GRCm39) |
S1280P |
probably damaging |
Het |
| Cfap57 |
T |
C |
4: 118,428,942 (GRCm39) |
E1008G |
probably benign |
Het |
| Csmd1 |
A |
G |
8: 16,120,366 (GRCm39) |
I1813T |
probably damaging |
Het |
| Dnah10 |
A |
G |
5: 124,888,546 (GRCm39) |
E3050G |
probably benign |
Het |
| Dnah2 |
A |
G |
11: 69,321,974 (GRCm39) |
F3782S |
probably damaging |
Het |
| Dnah2 |
C |
T |
11: 69,349,746 (GRCm39) |
R2399Q |
probably benign |
Het |
| Dnajc17 |
T |
C |
2: 119,016,527 (GRCm39) |
T64A |
possibly damaging |
Het |
| Dvl3 |
T |
G |
16: 20,349,729 (GRCm39) |
S567R |
possibly damaging |
Het |
| Epb41l1 |
T |
A |
2: 156,363,706 (GRCm39) |
S738R |
probably benign |
Het |
| Exph5 |
T |
C |
9: 53,288,555 (GRCm39) |
W1879R |
probably damaging |
Het |
| Fam83a |
T |
A |
15: 57,872,992 (GRCm39) |
F274I |
possibly damaging |
Het |
| Ggt1 |
A |
G |
10: 75,421,736 (GRCm39) |
|
probably null |
Het |
| Ido2 |
C |
T |
8: 25,023,786 (GRCm39) |
V351M |
probably damaging |
Het |
| Kcnt2 |
A |
G |
1: 140,435,440 (GRCm39) |
E469G |
possibly damaging |
Het |
| Kdm2b |
A |
G |
5: 123,070,724 (GRCm39) |
S403P |
probably benign |
Het |
| Klhl2 |
C |
T |
8: 65,202,818 (GRCm39) |
R460H |
probably damaging |
Het |
| Mfsd6l |
A |
G |
11: 68,447,368 (GRCm39) |
Y73C |
possibly damaging |
Het |
| Mlec |
A |
T |
5: 115,288,159 (GRCm39) |
C205* |
probably null |
Het |
| Mlx |
T |
C |
11: 100,980,053 (GRCm39) |
Y129H |
probably damaging |
Het |
| Mmadhc |
T |
C |
2: 50,181,421 (GRCm39) |
H83R |
probably damaging |
Het |
| Mmp16 |
T |
C |
4: 17,853,842 (GRCm39) |
F41S |
probably benign |
Het |
| Mroh6 |
G |
A |
15: 75,759,617 (GRCm39) |
Q187* |
probably null |
Het |
| Myh14 |
T |
A |
7: 44,272,518 (GRCm39) |
E1437V |
probably damaging |
Het |
| Nrxn1 |
A |
C |
17: 90,762,371 (GRCm39) |
L37R |
probably damaging |
Het |
| Or6c209 |
T |
C |
10: 129,483,723 (GRCm39) |
M242T |
possibly damaging |
Het |
| Pkhd1l1 |
A |
C |
15: 44,322,859 (GRCm39) |
R48S |
probably damaging |
Het |
| Prokr2 |
A |
G |
2: 132,215,595 (GRCm39) |
Y128H |
possibly damaging |
Het |
| Prtg |
T |
C |
9: 72,764,228 (GRCm39) |
V567A |
probably benign |
Het |
| Rbis |
T |
C |
3: 14,676,124 (GRCm39) |
T26A |
possibly damaging |
Het |
| Srrm2 |
G |
A |
17: 24,039,083 (GRCm39) |
|
probably benign |
Het |
| Stat4 |
A |
T |
1: 52,104,543 (GRCm39) |
I115L |
possibly damaging |
Het |
| Tnxb |
G |
A |
17: 34,937,609 (GRCm39) |
V3833M |
probably damaging |
Het |
| Ugt2b36 |
C |
T |
5: 87,228,724 (GRCm39) |
|
probably null |
Het |
| Usp45 |
A |
C |
4: 21,810,797 (GRCm39) |
D331A |
probably damaging |
Het |
| Usp47 |
T |
C |
7: 111,652,523 (GRCm39) |
S47P |
probably damaging |
Het |
| Zfp384 |
T |
C |
6: 125,000,997 (GRCm39) |
I23T |
probably damaging |
Het |
| Zfp804a |
A |
G |
2: 82,088,346 (GRCm39) |
Y725C |
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 |
|
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'- CTGACTCTCAGCTGTTGGAC -3'
(R):5'- AGTGAGTGTGTCCATGCTCAG -3'
Sequencing Primer
(F):5'- GAAAGAATTTCTGATCCCTAGGTAAC -3'
(R):5'- ATGCTCAGCGTGGACATG -3'
|
| Posted On |
2017-03-31 |
Incidental Mutation