Incidental Mutation 'IGL01098:Vps52'
ID |
53059 |
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 # |
IGL01098
|
Quality Score |
|
Status
|
|
Chromosome |
17 |
Chromosomal Location |
34174786-34186009 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 34181704 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Isoleucine
at position 510
(T510I)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000025178
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025178]
[ENSMUST00000173196]
|
AlphaFold |
Q8C754 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000025178
AA Change: T510I
PolyPhen 2
Score 0.905 (Sensitivity: 0.82; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000025178 Gene: ENSMUSG00000024319 AA Change: T510I
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 |
possibly damaging
Transcript: ENSMUST00000173196
AA Change: T442I
PolyPhen 2
Score 0.507 (Sensitivity: 0.88; Specificity: 0.90)
|
SMART Domains |
Protein: ENSMUSP00000133926 Gene: ENSMUSG00000024319 AA Change: T442I
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: 37 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4921509C19Rik |
T |
C |
2: 151,315,453 (GRCm39) |
D75G |
possibly damaging |
Het |
Brip1 |
G |
T |
11: 85,999,688 (GRCm39) |
R765S |
possibly damaging |
Het |
Btbd16 |
T |
C |
7: 130,424,975 (GRCm39) |
I452T |
probably damaging |
Het |
Cdc42ep4 |
T |
G |
11: 113,620,328 (GRCm39) |
D21A |
probably damaging |
Het |
Cdx2 |
T |
A |
5: 147,243,792 (GRCm39) |
M1L |
possibly damaging |
Het |
Cfap206 |
C |
T |
4: 34,721,562 (GRCm39) |
S162N |
probably damaging |
Het |
Csmd2 |
C |
T |
4: 127,952,845 (GRCm39) |
T98M |
probably damaging |
Het |
Cyp26a1 |
A |
T |
19: 37,688,450 (GRCm39) |
Q324L |
probably benign |
Het |
Etaa1 |
A |
G |
11: 17,896,059 (GRCm39) |
V686A |
probably damaging |
Het |
Gpr6 |
G |
A |
10: 40,946,739 (GRCm39) |
T281I |
probably damaging |
Het |
Herc1 |
T |
A |
9: 66,369,204 (GRCm39) |
|
probably null |
Het |
Lama2 |
A |
T |
10: 26,907,108 (GRCm39) |
I2351N |
possibly damaging |
Het |
Lman1 |
A |
G |
18: 66,124,711 (GRCm39) |
F343L |
probably damaging |
Het |
Lmo1 |
A |
G |
7: 108,742,657 (GRCm39) |
|
probably benign |
Het |
Lrrc17 |
T |
A |
5: 21,780,269 (GRCm39) |
F414L |
probably benign |
Het |
Man2b2 |
A |
T |
5: 36,972,900 (GRCm39) |
L538Q |
probably damaging |
Het |
Map3k9 |
A |
G |
12: 81,770,928 (GRCm39) |
S910P |
probably damaging |
Het |
Mapk1ip1 |
G |
A |
7: 138,438,191 (GRCm39) |
P80S |
probably damaging |
Het |
Mindy4 |
G |
T |
6: 55,261,727 (GRCm39) |
|
probably benign |
Het |
Msh4 |
A |
T |
3: 153,583,619 (GRCm39) |
|
probably benign |
Het |
Mta2 |
A |
G |
19: 8,924,081 (GRCm39) |
D187G |
probably damaging |
Het |
Olfml2a |
A |
G |
2: 38,837,226 (GRCm39) |
|
probably null |
Het |
Pink1 |
A |
T |
4: 138,047,408 (GRCm39) |
|
probably null |
Het |
Plekha6 |
T |
C |
1: 133,209,903 (GRCm39) |
F575L |
possibly damaging |
Het |
Rpe |
C |
A |
1: 66,745,674 (GRCm39) |
D71E |
probably benign |
Het |
Slc5a7 |
C |
T |
17: 54,599,988 (GRCm39) |
A142T |
probably benign |
Het |
Sptbn1 |
C |
T |
11: 30,109,385 (GRCm39) |
R70K |
probably damaging |
Het |
Taf1c |
G |
T |
8: 120,329,580 (GRCm39) |
Q159K |
probably damaging |
Het |
Tgfb1i1 |
T |
C |
7: 127,851,693 (GRCm39) |
F311S |
probably damaging |
Het |
Tmc8 |
T |
C |
11: 117,683,389 (GRCm39) |
V648A |
possibly damaging |
Het |
Tmed8 |
G |
T |
12: 87,223,445 (GRCm39) |
A98E |
probably benign |
Het |
Tmem200a |
A |
G |
10: 25,870,041 (GRCm39) |
I76T |
probably damaging |
Het |
Vmn2r104 |
T |
C |
17: 20,268,358 (GRCm39) |
E37G |
probably benign |
Het |
Vmn2r18 |
A |
T |
5: 151,496,296 (GRCm39) |
V474E |
probably damaging |
Het |
Wwox |
G |
T |
8: 115,172,118 (GRCm39) |
G71* |
probably null |
Het |
Zer1 |
C |
T |
2: 29,998,232 (GRCm39) |
|
probably null |
Het |
Zfp296 |
A |
T |
7: 19,311,845 (GRCm39) |
K117N |
possibly 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 |
IGL01705:Vps52
|
APN |
17 |
34,185,042 (GRCm39) |
missense |
probably damaging |
1.00 |
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 |
2013-06-21 |