Incidental Mutation 'R0882:Vps53'
| ID |
80663 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps53
|
| Ensembl Gene |
ENSMUSG00000017288 |
| Gene Name |
VPS53 GARP complex subunit |
| Synonyms |
2310040I21Rik, 3100002B05Rik, 2010002A08Rik |
| MMRRC Submission |
039049-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R0882 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 75973485 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Leucine
at position 170
(F170L)
|
| 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: F447L
PolyPhen 2
Score 0.942 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: F447L
| 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: F418L
PolyPhen 2
Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: F418L
| 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
AA Change: F270L
PolyPhen 2
Score 0.096 (Sensitivity: 0.93; Specificity: 0.85)
|
| SMART Domains |
Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: F270L
| 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 |
possibly damaging
Transcript: ENSMUST00000166752
AA Change: F399L
PolyPhen 2
Score 0.853 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
AA Change: F399L
| 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: F170L
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000131663
Gene: ENSMUSG00000017288
AA Change: F170L
| 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 |
|
| Meta Mutation Damage Score |
0.6990 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 99.0%
- 10x: 97.8%
- 20x: 96.0%
|
| Validation Efficiency |
100% (49/49) |
| 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 |
|---|
| Aasdh |
G |
A |
5: 77,024,130 (GRCm39) |
T174M |
probably damaging |
Het |
| Adh1 |
A |
T |
3: 137,992,558 (GRCm39) |
I225F |
possibly damaging |
Het |
| Agap2 |
A |
G |
10: 126,923,319 (GRCm39) |
K691E |
unknown |
Het |
| Alcam |
T |
C |
16: 52,073,573 (GRCm39) |
D564G |
possibly damaging |
Het |
| Apbb2 |
T |
A |
5: 66,557,598 (GRCm39) |
T289S |
probably damaging |
Het |
| Cacna1c |
C |
T |
6: 118,589,586 (GRCm39) |
R1446H |
probably damaging |
Het |
| Cep68 |
T |
C |
11: 20,189,393 (GRCm39) |
I540V |
probably benign |
Het |
| Ctla4 |
T |
C |
1: 60,948,397 (GRCm39) |
V23A |
probably benign |
Het |
| Dnah7b |
T |
A |
1: 46,379,292 (GRCm39) |
D3675E |
probably benign |
Het |
| Fam209 |
G |
T |
2: 172,314,555 (GRCm39) |
V15F |
probably benign |
Het |
| Fat3 |
A |
G |
9: 15,942,664 (GRCm39) |
V1236A |
possibly damaging |
Het |
| Gabbr2 |
A |
G |
4: 46,718,904 (GRCm39) |
I38T |
probably damaging |
Het |
| Gdpd4 |
T |
C |
7: 97,615,505 (GRCm39) |
I110T |
probably damaging |
Het |
| Gm4841 |
C |
T |
18: 60,402,852 (GRCm39) |
A414T |
possibly damaging |
Het |
| Gtf3c4 |
A |
T |
2: 28,724,782 (GRCm39) |
Y176N |
probably damaging |
Het |
| H2bc18 |
G |
A |
3: 96,177,060 (GRCm39) |
|
probably null |
Het |
| Igsf9b |
T |
C |
9: 27,230,612 (GRCm39) |
Y264H |
probably damaging |
Het |
| Itih4 |
A |
T |
14: 30,614,231 (GRCm39) |
N394Y |
probably damaging |
Het |
| Kmt2c |
T |
C |
5: 25,500,605 (GRCm39) |
T3815A |
possibly damaging |
Het |
| Lrwd1 |
T |
C |
5: 136,152,254 (GRCm39) |
|
probably null |
Het |
| Mc3r |
A |
G |
2: 172,091,711 (GRCm39) |
K311R |
probably benign |
Het |
| Myb |
T |
C |
10: 21,032,259 (GRCm39) |
T41A |
possibly damaging |
Het |
| Nfix |
T |
C |
8: 85,454,554 (GRCm39) |
D201G |
probably damaging |
Het |
| Nos1 |
T |
C |
5: 118,085,512 (GRCm39) |
V1280A |
probably damaging |
Het |
| Or51a5 |
A |
C |
7: 102,771,782 (GRCm39) |
S66A |
probably benign |
Het |
| Or8a1b |
T |
C |
9: 37,623,168 (GRCm39) |
M136V |
probably benign |
Het |
| Pcdh15 |
A |
G |
10: 74,178,488 (GRCm39) |
T582A |
probably damaging |
Het |
| Pcdhb12 |
C |
A |
18: 37,570,375 (GRCm39) |
A507E |
probably damaging |
Het |
| Pdia3 |
G |
A |
2: 121,262,858 (GRCm39) |
G275S |
probably damaging |
Het |
| Pkp2 |
C |
A |
16: 16,087,575 (GRCm39) |
A753E |
probably damaging |
Het |
| Plekha3 |
G |
A |
2: 76,513,142 (GRCm39) |
V76I |
possibly damaging |
Het |
| Pnpla6 |
T |
C |
8: 3,567,081 (GRCm39) |
L33P |
probably damaging |
Het |
| Pot1b |
C |
T |
17: 55,973,400 (GRCm39) |
|
probably benign |
Het |
| Prr5l |
T |
C |
2: 101,588,886 (GRCm39) |
E88G |
possibly damaging |
Het |
| Prss57 |
G |
A |
10: 79,621,699 (GRCm39) |
H97Y |
probably damaging |
Het |
| Rttn |
C |
T |
18: 88,991,813 (GRCm39) |
Q131* |
probably null |
Het |
| Scaf11 |
G |
T |
15: 96,316,176 (GRCm39) |
S1129R |
possibly damaging |
Het |
| Slc25a20 |
T |
A |
9: 108,559,189 (GRCm39) |
M185K |
possibly damaging |
Het |
| Sorbs3 |
T |
A |
14: 70,445,021 (GRCm39) |
E19V |
probably damaging |
Het |
| Srgap2 |
A |
T |
1: 131,217,253 (GRCm39) |
C1020S |
probably benign |
Het |
| Thoc2l |
T |
C |
5: 104,666,875 (GRCm39) |
S466P |
probably benign |
Het |
| Tmem109 |
T |
C |
19: 10,849,205 (GRCm39) |
R217G |
possibly damaging |
Het |
| Trio |
A |
T |
15: 27,732,980 (GRCm39) |
I2967N |
probably damaging |
Het |
| Vars2 |
T |
C |
17: 35,968,191 (GRCm39) |
E899G |
probably benign |
Het |
| Vmn2r109 |
A |
G |
17: 20,774,842 (GRCm39) |
|
probably benign |
Het |
| Zc2hc1a |
G |
A |
3: 7,591,422 (GRCm39) |
S149N |
possibly damaging |
Het |
| Zfp820 |
A |
G |
17: 22,042,817 (GRCm39) |
|
probably benign |
Het |
| Zhx3 |
A |
C |
2: 160,622,629 (GRCm39) |
F513V |
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 |
|
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'- ATATCAGGAGCCTCAATTCCCCGC -3'
(R):5'- AGATGCCTGGAGCAAAGCAATCTAC -3'
Sequencing Primer
(F):5'- CAGGACTCACTTAGGCAGGTTG -3'
(R):5'- atctgcctgcctctgcc -3'
|
| Posted On |
2013-11-07 |
Incidental Mutation