Incidental Mutation 'IGL02992:Vps52'
| ID |
406972 |
| 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 # |
IGL02992
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
17 |
| Chromosomal Location |
34174786-34186009 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 34177324 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 122
(V122A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133926
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000008812]
[ENSMUST00000025178]
[ENSMUST00000173196]
[ENSMUST00000174609]
|
| AlphaFold |
Q8C754 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000008812
|
| SMART Domains |
Protein: ENSMUSP00000008812
Gene: ENSMUSG00000008668
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Ribosomal_S13
|
14 |
142 |
2.2e-59 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000025178
AA Change: V122A
PolyPhen 2
Score 0.250 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: V122A
| 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: ENSMUST00000172550
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172558
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172799
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000173196
AA Change: V122A
PolyPhen 2
Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: V122A
| 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: ENSMUST00000174662
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174745
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174588
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174175
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174620
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173445
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000174609
|
| SMART Domains |
Protein: ENSMUSP00000138296
Gene: ENSMUSG00000008668
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Ribosomal_S13
|
14 |
107 |
2.1e-21 |
PFAM |
|
| 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: 47 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca4 |
A |
G |
3: 121,921,935 (GRCm39) |
K1164E |
probably damaging |
Het |
| Arhgap42 |
G |
A |
9: 8,998,249 (GRCm39) |
|
probably benign |
Het |
| Arhgef12 |
T |
C |
9: 42,910,373 (GRCm39) |
D612G |
probably damaging |
Het |
| Cpne3 |
T |
C |
4: 19,532,486 (GRCm39) |
D309G |
probably benign |
Het |
| Daw1 |
T |
C |
1: 83,174,934 (GRCm39) |
|
probably benign |
Het |
| Daxx |
T |
A |
17: 34,130,722 (GRCm39) |
C246S |
probably damaging |
Het |
| Dpp7 |
T |
C |
2: 25,244,589 (GRCm39) |
D264G |
possibly damaging |
Het |
| Dync2h1 |
T |
A |
9: 7,137,074 (GRCm39) |
H1472L |
probably benign |
Het |
| Fastkd2 |
T |
C |
1: 63,777,083 (GRCm39) |
|
probably benign |
Het |
| Fcrl2 |
T |
G |
3: 87,166,773 (GRCm39) |
R73S |
probably damaging |
Het |
| Gatb |
A |
G |
3: 85,526,223 (GRCm39) |
D367G |
probably damaging |
Het |
| Gm20547 |
T |
A |
17: 35,076,095 (GRCm39) |
E654V |
probably damaging |
Het |
| Gm839 |
T |
A |
6: 89,189,509 (GRCm39) |
|
noncoding transcript |
Het |
| Gtf2ird2 |
A |
T |
5: 134,246,456 (GRCm39) |
M905L |
possibly damaging |
Het |
| Hoxb2 |
A |
T |
11: 96,243,910 (GRCm39) |
I174F |
probably damaging |
Het |
| Hrh3 |
A |
G |
2: 179,742,608 (GRCm39) |
V308A |
probably benign |
Het |
| Ints9 |
A |
G |
14: 65,217,613 (GRCm39) |
K47E |
probably benign |
Het |
| Irak3 |
A |
T |
10: 120,018,566 (GRCm39) |
Y61N |
probably damaging |
Het |
| Itpr1 |
A |
G |
6: 108,358,276 (GRCm39) |
E614G |
probably damaging |
Het |
| Lgals3 |
A |
T |
14: 47,622,982 (GRCm39) |
I214L |
probably benign |
Het |
| Msh4 |
G |
T |
3: 153,577,962 (GRCm39) |
T444K |
possibly damaging |
Het |
| Myh7b |
C |
A |
2: 155,463,330 (GRCm39) |
Q521K |
probably damaging |
Het |
| Naip5 |
T |
A |
13: 100,359,536 (GRCm39) |
I567F |
probably damaging |
Het |
| Nf1 |
A |
G |
11: 79,325,759 (GRCm39) |
|
probably benign |
Het |
| Nlrc3 |
C |
T |
16: 3,771,887 (GRCm39) |
|
probably benign |
Het |
| Nlrc5 |
A |
C |
8: 95,233,201 (GRCm39) |
E1353A |
possibly damaging |
Het |
| Nr1h3 |
T |
A |
2: 91,020,911 (GRCm39) |
I260F |
probably damaging |
Het |
| Pcnx1 |
G |
A |
12: 82,010,894 (GRCm39) |
R1211Q |
probably damaging |
Het |
| Pde10a |
A |
G |
17: 9,168,293 (GRCm39) |
K605E |
probably damaging |
Het |
| Pdzd2 |
T |
C |
15: 12,382,708 (GRCm39) |
E1215G |
possibly damaging |
Het |
| Pex12 |
A |
G |
11: 83,188,753 (GRCm39) |
S81P |
probably damaging |
Het |
| Pik3c2b |
C |
A |
1: 132,994,718 (GRCm39) |
Y227* |
probably null |
Het |
| Ppef2 |
C |
T |
5: 92,383,759 (GRCm39) |
W450* |
probably null |
Het |
| Prkg2 |
T |
G |
5: 99,172,365 (GRCm39) |
S117R |
probably benign |
Het |
| Prl3d2 |
A |
T |
13: 27,311,266 (GRCm39) |
E179D |
probably benign |
Het |
| Relch |
T |
A |
1: 105,647,189 (GRCm39) |
L684M |
possibly damaging |
Het |
| Rxfp2 |
T |
C |
5: 149,975,021 (GRCm39) |
V210A |
probably benign |
Het |
| Scn10a |
T |
C |
9: 119,438,626 (GRCm39) |
T1748A |
possibly damaging |
Het |
| Septin10 |
T |
C |
10: 59,028,000 (GRCm39) |
N107S |
possibly damaging |
Het |
| Smu1 |
T |
A |
4: 40,739,550 (GRCm39) |
N420I |
probably damaging |
Het |
| Sos1 |
A |
G |
17: 80,726,445 (GRCm39) |
F835L |
probably benign |
Het |
| Spg11 |
T |
C |
2: 121,888,879 (GRCm39) |
D2164G |
probably damaging |
Het |
| Svbp |
A |
G |
4: 119,053,127 (GRCm39) |
E8G |
probably damaging |
Het |
| Tgm3 |
T |
A |
2: 129,883,899 (GRCm39) |
M519K |
probably damaging |
Het |
| Tspan12 |
A |
G |
6: 21,799,876 (GRCm39) |
|
probably null |
Het |
| Wipf1 |
T |
C |
2: 73,264,427 (GRCm39) |
Y458C |
probably damaging |
Het |
| Zfp369 |
T |
A |
13: 65,442,265 (GRCm39) |
D286E |
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 |
|
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 |
|
IGL01722:Vps52
|
APN |
17 |
34,180,589 (GRCm39) |
nonsense |
probably null |
|
|
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 |
2016-08-02 |
Incidental Mutation