Incidental Mutation 'IGL01705:Vps52'
ID |
104554 |
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 # |
IGL01705
|
Quality Score |
|
Status
|
|
Chromosome |
17 |
Chromosomal Location |
34174786-34186009 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 34185042 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Leucine to Proline
at position 712
(L712P)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000025178
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025178]
[ENSMUST00000173196]
|
AlphaFold |
Q8C754 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000025178
AA Change: L712P
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000025178 Gene: ENSMUSG00000024319 AA Change: L712P
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: ENSMUST00000172558
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000173196
|
SMART Domains |
Protein: ENSMUSP00000133926 Gene: ENSMUSG00000024319
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: 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: 31 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adamts19 |
A |
G |
18: 59,166,038 (GRCm39) |
T1077A |
possibly damaging |
Het |
Akap13 |
T |
C |
7: 75,396,515 (GRCm39) |
V2504A |
possibly damaging |
Het |
Anks3 |
A |
T |
16: 4,765,587 (GRCm39) |
W172R |
probably benign |
Het |
Asap2 |
T |
A |
12: 21,299,369 (GRCm39) |
N633K |
possibly damaging |
Het |
Astn1 |
A |
T |
1: 158,331,883 (GRCm39) |
S326C |
probably damaging |
Het |
Cachd1 |
A |
G |
4: 100,840,736 (GRCm39) |
K900E |
possibly damaging |
Het |
Cd5 |
A |
T |
19: 10,703,659 (GRCm39) |
|
probably null |
Het |
D130043K22Rik |
T |
A |
13: 25,041,924 (GRCm39) |
N284K |
probably benign |
Het |
Dtna |
C |
T |
18: 23,678,788 (GRCm39) |
A38V |
probably damaging |
Het |
Eny2 |
C |
A |
15: 44,295,831 (GRCm39) |
|
probably null |
Het |
Grm5 |
A |
G |
7: 87,779,254 (GRCm39) |
Q930R |
possibly damaging |
Het |
Igkv4-73 |
A |
T |
6: 69,174,709 (GRCm39) |
|
noncoding transcript |
Het |
Lama2 |
A |
T |
10: 27,065,270 (GRCm39) |
|
probably benign |
Het |
Lipg |
A |
G |
18: 75,081,042 (GRCm39) |
|
probably null |
Het |
Neto2 |
T |
C |
8: 86,367,632 (GRCm39) |
K371E |
probably damaging |
Het |
Or8g52 |
T |
C |
9: 39,630,877 (GRCm39) |
M118T |
possibly damaging |
Het |
Paxbp1 |
A |
G |
16: 90,813,876 (GRCm39) |
F834L |
probably benign |
Het |
Paxip1 |
A |
T |
5: 27,953,857 (GRCm39) |
S946R |
probably damaging |
Het |
Pclo |
A |
G |
5: 14,727,879 (GRCm39) |
|
probably benign |
Het |
Plcg2 |
T |
C |
8: 118,308,401 (GRCm39) |
L331P |
probably damaging |
Het |
Reep1 |
A |
G |
6: 71,750,272 (GRCm39) |
T95A |
probably damaging |
Het |
Rfx2 |
A |
G |
17: 57,092,303 (GRCm39) |
Y332H |
possibly damaging |
Het |
Smchd1 |
A |
T |
17: 71,688,393 (GRCm39) |
D1288E |
probably damaging |
Het |
Spag17 |
A |
G |
3: 99,930,046 (GRCm39) |
M582V |
probably benign |
Het |
Susd1 |
A |
G |
4: 59,332,931 (GRCm39) |
|
probably benign |
Het |
Syt9 |
T |
G |
7: 107,035,559 (GRCm39) |
L192R |
probably damaging |
Het |
Tlr6 |
T |
C |
5: 65,111,473 (GRCm39) |
K478R |
probably benign |
Het |
Tmem115 |
G |
T |
9: 107,412,403 (GRCm39) |
L242F |
probably benign |
Het |
Tmt1b |
T |
A |
10: 128,794,731 (GRCm39) |
I198F |
probably benign |
Het |
Tnfaip1 |
T |
C |
11: 78,416,294 (GRCm39) |
D263G |
probably benign |
Het |
Ubqln3 |
T |
A |
7: 103,791,884 (GRCm39) |
I69F |
probably damaging |
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 |
IGL01722:Vps52
|
APN |
17 |
34,180,589 (GRCm39) |
nonsense |
probably null |
|
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 |