Incidental Mutation 'R3622:Vps53'
ID |
268685 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps53
|
Ensembl Gene |
ENSMUSG00000017288 |
Gene Name |
VPS53 GARP complex subunit |
Synonyms |
2310040I21Rik, 3100002B05Rik, 2010002A08Rik |
MMRRC Submission |
040677-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R3622 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
11 |
Chromosomal Location |
75937052-76070464 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to C
at 76008609 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Glycine
at position 237
(V237G)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000130499
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000056601]
[ENSMUST00000094015]
[ENSMUST00000108419]
[ENSMUST00000163878]
[ENSMUST00000169734]
[ENSMUST00000167114]
[ENSMUST00000166752]
|
AlphaFold |
Q8CCB4 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000056601
AA Change: V237G
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
SMART Domains |
Protein: ENSMUSP00000061317 Gene: ENSMUSG00000017288 AA Change: V237G
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 benign
Transcript: ENSMUST00000094015
AA Change: V208G
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
SMART Domains |
Protein: ENSMUSP00000091554 Gene: ENSMUSG00000017288 AA Change: V208G
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 |
noncoding transcript
Transcript: ENSMUST00000141773
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000163878
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000166084
|
Predicted Effect |
unknown
Transcript: ENSMUST00000166436
AA Change: V167G
|
SMART Domains |
Protein: ENSMUSP00000131387 Gene: ENSMUSG00000017288 AA Change: V167G
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 benign
Transcript: ENSMUST00000169734
AA Change: V237G
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
SMART Domains |
Protein: ENSMUSP00000130499 Gene: ENSMUSG00000017288 AA Change: V237G
Domain | Start | End | E-Value | Type |
Pfam:DUF2450
|
5 |
225 |
5.1e-12 |
PFAM |
Pfam:Vps53_N
|
39 |
329 |
1e-137 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000170143
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000169532
|
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 benign
Transcript: ENSMUST00000166752
|
SMART Domains |
Protein: ENSMUSP00000129159 Gene: ENSMUSG00000017288
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 |
|
Meta Mutation Damage Score |
0.1808 |
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.2%
- 20x: 95.1%
|
Validation Efficiency |
100% (42/42) |
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: 42 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca15 |
T |
A |
7: 119,950,036 (GRCm39) |
Y503* |
probably null |
Het |
Akap9 |
C |
A |
5: 4,026,235 (GRCm39) |
Q1297K |
possibly damaging |
Het |
Dffb |
T |
C |
4: 154,049,976 (GRCm39) |
T296A |
probably damaging |
Het |
Dpf1 |
G |
A |
7: 29,015,631 (GRCm39) |
|
probably null |
Het |
Elp1 |
A |
T |
4: 56,759,925 (GRCm39) |
|
probably null |
Het |
Grid2ip |
T |
C |
5: 143,371,774 (GRCm39) |
S666P |
probably damaging |
Het |
Gucy2e |
T |
A |
11: 69,115,877 (GRCm39) |
E835V |
probably damaging |
Het |
Hdac5 |
G |
A |
11: 102,086,644 (GRCm39) |
P120S |
probably benign |
Het |
Htr1d |
T |
C |
4: 136,170,815 (GRCm39) |
I348T |
probably damaging |
Het |
Hyal4 |
A |
T |
6: 24,765,737 (GRCm39) |
S364C |
probably damaging |
Het |
Igkv1-133 |
A |
T |
6: 67,701,944 (GRCm39) |
Q16L |
probably benign |
Het |
Itga10 |
C |
T |
3: 96,559,054 (GRCm39) |
|
probably benign |
Het |
Met |
A |
T |
6: 17,549,085 (GRCm39) |
D979V |
probably damaging |
Het |
Mga |
A |
G |
2: 119,772,245 (GRCm39) |
T1702A |
probably damaging |
Het |
Midn |
A |
G |
10: 79,986,144 (GRCm39) |
D78G |
probably benign |
Het |
Muc5b |
T |
C |
7: 141,405,595 (GRCm39) |
|
probably benign |
Het |
Oma1 |
T |
C |
4: 103,223,288 (GRCm39) |
I491T |
probably benign |
Het |
Or1e30 |
A |
G |
11: 73,678,567 (GRCm39) |
T268A |
probably benign |
Het |
Or5ak24 |
C |
T |
2: 85,260,837 (GRCm39) |
C112Y |
probably benign |
Het |
Or5b107 |
T |
A |
19: 13,143,020 (GRCm39) |
M214K |
probably benign |
Het |
Or8b48 |
A |
G |
9: 38,492,792 (GRCm39) |
Y73C |
probably damaging |
Het |
Pbld2 |
T |
C |
10: 62,897,470 (GRCm39) |
L57P |
probably damaging |
Het |
Phka2 |
T |
A |
X: 159,327,291 (GRCm39) |
Y334* |
probably null |
Het |
Plin4 |
G |
T |
17: 56,411,112 (GRCm39) |
T973K |
possibly damaging |
Het |
R3hdm4 |
C |
T |
10: 79,748,515 (GRCm39) |
R143H |
possibly damaging |
Het |
Rps18 |
G |
C |
17: 34,171,247 (GRCm39) |
|
probably null |
Het |
Samd9l |
A |
T |
6: 3,374,032 (GRCm39) |
C1076* |
probably null |
Het |
Scml4 |
T |
C |
10: 42,806,607 (GRCm39) |
|
probably benign |
Het |
Slc16a10 |
A |
G |
10: 40,017,890 (GRCm39) |
V48A |
probably benign |
Het |
Slc6a5 |
T |
C |
7: 49,567,371 (GRCm39) |
V275A |
probably benign |
Het |
Smad9 |
C |
T |
3: 54,696,705 (GRCm39) |
R257W |
probably damaging |
Het |
Snrpb |
C |
A |
2: 130,017,299 (GRCm39) |
R73L |
probably null |
Het |
Srsf9 |
C |
T |
5: 115,468,571 (GRCm39) |
A69V |
probably damaging |
Het |
Stfa2 |
A |
G |
16: 36,224,433 (GRCm39) |
Y90H |
probably damaging |
Het |
Tgm6 |
T |
A |
2: 129,993,681 (GRCm39) |
V640E |
possibly damaging |
Het |
Tnrc6c |
C |
T |
11: 117,640,451 (GRCm39) |
R1414C |
probably damaging |
Het |
Tyk2 |
A |
T |
9: 21,038,606 (GRCm39) |
C8S |
probably damaging |
Het |
Upp2 |
G |
A |
2: 58,680,128 (GRCm39) |
R300Q |
possibly damaging |
Het |
Utp20 |
A |
G |
10: 88,593,855 (GRCm39) |
|
probably benign |
Het |
Veph1 |
C |
T |
3: 66,122,858 (GRCm39) |
V224I |
probably benign |
Het |
Vmn1r30 |
A |
T |
6: 58,412,437 (GRCm39) |
F132I |
probably benign |
Het |
Vmn2r116 |
A |
G |
17: 23,605,025 (GRCm39) |
S113G |
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 |
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'- CAGGAGGAAGGCAACATTAGTTTC -3'
(R):5'- GGTTGGCTACTGCAAGACTAG -3'
Sequencing Primer
(F):5'- GGAAGGCAACATTAGTTTCTTTTTC -3'
(R):5'- GGCTACTGCAAGACTAGCTTAATG -3'
|
Posted On |
2015-02-19 |