Incidental Mutation 'IGL01722:Vps52'
| ID |
105154 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Vps52
|
| Ensembl Gene |
ENSMUSG00000024319 |
| Gene Name |
VPS52 GARP complex subunit |
| Synonyms |
tclw5, ARE1, D430041K17Rik, tcl-w5, Sacm2l |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
IGL01722
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
17 |
| Chromosomal Location |
34174786-34186009 bp(+) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
T to A
at 34180589 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Stop codon
at position 308
(Y308*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133926
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025178]
[ENSMUST00000173196]
|
| AlphaFold |
Q8C754 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000025178
AA Change: Y376*
|
| SMART Domains |
Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: Y376*
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
1 |
11 |
N/A |
INTRINSIC |
|
low complexity region
|
24 |
45 |
N/A |
INTRINSIC |
|
Pfam:Sec3_C
|
79 |
244 |
4.6e-13 |
PFAM |
|
Pfam:Vps52
|
94 |
601 |
5.1e-233 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000122652
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172558
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000173196
AA Change: Y308*
|
| SMART Domains |
Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: Y308*
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
18 |
39 |
N/A |
INTRINSIC |
|
Pfam:Vps52
|
88 |
120 |
2.7e-6 |
PFAM |
|
Pfam:Vps52
|
116 |
527 |
3e-181 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173318
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173445
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174588
|
| Coding Region Coverage |
|
| 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 that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
PHENOTYPE: Mice homozygous for a null mutation display early embryonic lethality. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 29 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acvr1c |
T |
A |
2: 58,173,561 (GRCm39) |
|
probably benign |
Het |
| Alb |
G |
A |
5: 90,618,698 (GRCm39) |
|
probably null |
Het |
| Ankrd9 |
A |
G |
12: 110,943,797 (GRCm39) |
V46A |
probably damaging |
Het |
| Apol11a |
A |
T |
15: 77,401,307 (GRCm39) |
M265L |
probably benign |
Het |
| Ccdc158 |
T |
C |
5: 92,810,598 (GRCm39) |
N97D |
possibly damaging |
Het |
| Cobl |
T |
G |
11: 12,203,987 (GRCm39) |
H823P |
probably benign |
Het |
| Dnaja2 |
A |
T |
8: 86,279,908 (GRCm39) |
H90Q |
probably benign |
Het |
| Dpagt1 |
T |
C |
9: 44,238,899 (GRCm39) |
F73S |
possibly damaging |
Het |
| Dph3 |
C |
T |
14: 31,807,417 (GRCm39) |
E20K |
possibly damaging |
Het |
| Fbxl13 |
G |
T |
5: 21,695,412 (GRCm39) |
T660K |
possibly damaging |
Het |
| Gask1a |
G |
A |
9: 121,794,149 (GRCm39) |
S101N |
possibly damaging |
Het |
| Glt6d1 |
T |
C |
2: 25,684,431 (GRCm39) |
T192A |
probably benign |
Het |
| Mroh7 |
C |
T |
4: 106,560,358 (GRCm39) |
V649I |
probably benign |
Het |
| Mta3 |
T |
C |
17: 84,063,072 (GRCm39) |
Y4H |
possibly damaging |
Het |
| Myh14 |
A |
G |
7: 44,292,956 (GRCm39) |
L369P |
probably damaging |
Het |
| Or2y1 |
G |
T |
11: 49,385,793 (GRCm39) |
L144F |
probably damaging |
Het |
| Or4c52 |
T |
C |
2: 89,845,351 (GRCm39) |
C26R |
probably benign |
Het |
| Paxx |
T |
C |
2: 25,350,277 (GRCm39) |
D110G |
probably damaging |
Het |
| Pcyox1 |
T |
G |
6: 86,365,735 (GRCm39) |
D493A |
probably damaging |
Het |
| Plk2 |
A |
G |
13: 110,535,976 (GRCm39) |
E560G |
probably benign |
Het |
| Rnf6 |
A |
G |
5: 146,147,036 (GRCm39) |
F661L |
probably benign |
Het |
| Sema4a |
T |
C |
3: 88,345,491 (GRCm39) |
K531E |
probably benign |
Het |
| Svs5 |
T |
C |
2: 164,079,446 (GRCm39) |
K154E |
possibly damaging |
Het |
| Tbx4 |
A |
T |
11: 85,802,769 (GRCm39) |
Q242L |
probably damaging |
Het |
| Tgm3 |
A |
T |
2: 129,886,488 (GRCm39) |
I570F |
probably damaging |
Het |
| Thrap3 |
A |
T |
4: 126,059,322 (GRCm39) |
M908K |
possibly damaging |
Het |
| Trmo |
A |
G |
4: 46,386,092 (GRCm39) |
|
probably null |
Het |
| Usp8 |
T |
A |
2: 126,600,072 (GRCm39) |
L997Q |
probably damaging |
Het |
| Vmn1r202 |
T |
C |
13: 22,685,890 (GRCm39) |
R176G |
probably benign |
Het |
|
| Other mutations in Vps52 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00946:Vps52
|
APN |
17 |
34,175,932 (GRCm39) |
missense |
possibly damaging |
0.96 |
|
IGL01098:Vps52
|
APN |
17 |
34,181,704 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
IGL01705:Vps52
|
APN |
17 |
34,185,042 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02992:Vps52
|
APN |
17 |
34,177,324 (GRCm39) |
missense |
probably damaging |
0.97 |
|
IGL03279:Vps52
|
APN |
17 |
34,176,848 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R0363:Vps52
|
UTSW |
17 |
34,181,091 (GRCm39) |
missense |
probably benign |
0.26 |
|
R0762:Vps52
|
UTSW |
17 |
34,178,985 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1065:Vps52
|
UTSW |
17 |
34,180,213 (GRCm39) |
missense |
probably benign |
0.02 |
|
R1506:Vps52
|
UTSW |
17 |
34,176,868 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3760:Vps52
|
UTSW |
17 |
34,179,162 (GRCm39) |
missense |
possibly damaging |
0.64 |
|
R4714:Vps52
|
UTSW |
17 |
34,180,153 (GRCm39) |
missense |
probably benign |
0.25 |
|
R5381:Vps52
|
UTSW |
17 |
34,177,275 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R5590:Vps52
|
UTSW |
17 |
34,180,195 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5928:Vps52
|
UTSW |
17 |
34,180,100 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R6003:Vps52
|
UTSW |
17 |
34,175,068 (GRCm39) |
start codon destroyed |
probably null |
0.01 |
|
R6302:Vps52
|
UTSW |
17 |
34,182,189 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6574:Vps52
|
UTSW |
17 |
34,181,452 (GRCm39) |
missense |
probably null |
0.34 |
|
R6695:Vps52
|
UTSW |
17 |
34,182,173 (GRCm39) |
nonsense |
probably null |
|
|
R6888:Vps52
|
UTSW |
17 |
34,182,180 (GRCm39) |
missense |
probably benign |
0.06 |
|
R7022:Vps52
|
UTSW |
17 |
34,178,293 (GRCm39) |
missense |
probably benign |
0.04 |
|
R7136:Vps52
|
UTSW |
17 |
34,184,262 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7380:Vps52
|
UTSW |
17 |
34,177,283 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R7727:Vps52
|
UTSW |
17 |
34,181,108 (GRCm39) |
missense |
probably benign |
0.21 |
|
R7888:Vps52
|
UTSW |
17 |
34,184,725 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8385:Vps52
|
UTSW |
17 |
34,181,791 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8956:Vps52
|
UTSW |
17 |
34,177,049 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9457:Vps52
|
UTSW |
17 |
34,181,156 (GRCm39) |
missense |
probably damaging |
0.97 |
|
| Posted On |
2014-01-21 |
Incidental Mutation