Incidental Mutation 'R1065:Vps52'
| ID |
85980 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps52
|
| Ensembl Gene |
ENSMUSG00000024319 |
| Gene Name |
VPS52 GARP complex subunit |
| Synonyms |
tclw5, ARE1, D430041K17Rik, tcl-w5, Sacm2l |
| MMRRC Submission |
039151-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1065 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
34174786-34186009 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 34180213 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamine to Lysine
at position 306
(Q306K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000133926
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025178]
[ENSMUST00000173196]
|
| AlphaFold |
Q8C754 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000025178
AA Change: Q374K
PolyPhen 2
Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
|
| SMART Domains |
Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: Q374K
| 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 benign
Transcript: ENSMUST00000173196
AA Change: Q306K
PolyPhen 2
Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: Q306K
| 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
|
| Meta Mutation Damage Score |
0.0616 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.9%
- 10x: 97.6%
- 20x: 95.5%
|
| Validation Efficiency |
97% (36/37) |
| 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: 35 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Cd300ld2 |
T |
C |
11: 114,904,586 (GRCm39) |
T94A |
probably damaging |
Het |
| Cdc42bpg |
G |
A |
19: 6,372,856 (GRCm39) |
S1515N |
probably damaging |
Het |
| Ckb |
T |
C |
12: 111,637,681 (GRCm39) |
E150G |
probably benign |
Het |
| Clec2m |
A |
G |
6: 129,300,013 (GRCm39) |
I155T |
possibly damaging |
Het |
| Cobl |
T |
A |
11: 12,204,327 (GRCm39) |
M785L |
possibly damaging |
Het |
| Col6a5 |
T |
C |
9: 105,758,982 (GRCm39) |
N2075D |
probably damaging |
Het |
| Commd7 |
G |
C |
2: 153,461,447 (GRCm39) |
|
probably benign |
Het |
| Corin |
G |
A |
5: 72,458,993 (GRCm39) |
R927* |
probably null |
Het |
| Dync2i1 |
C |
T |
12: 116,219,696 (GRCm39) |
R82H |
probably damaging |
Het |
| Ift122 |
A |
T |
6: 115,852,286 (GRCm39) |
|
probably null |
Het |
| Il1b |
G |
A |
2: 129,209,927 (GRCm39) |
T83I |
probably benign |
Het |
| Ints4 |
T |
C |
7: 97,157,099 (GRCm39) |
|
probably null |
Het |
| Msh6 |
T |
G |
17: 88,295,891 (GRCm39) |
|
probably benign |
Het |
| Mtmr3 |
T |
C |
11: 4,442,859 (GRCm39) |
K392E |
probably damaging |
Het |
| Or5t9 |
A |
G |
2: 86,659,888 (GRCm39) |
H264R |
probably damaging |
Het |
| Pde3a |
T |
C |
6: 141,422,458 (GRCm39) |
|
probably benign |
Het |
| Pde6h |
A |
C |
6: 136,936,368 (GRCm39) |
K37T |
probably damaging |
Het |
| Plat |
C |
A |
8: 23,266,879 (GRCm39) |
D290E |
probably damaging |
Het |
| Polk |
A |
C |
13: 96,644,760 (GRCm39) |
L122R |
probably damaging |
Het |
| Ppp1r3g |
T |
A |
13: 36,153,418 (GRCm39) |
D279E |
probably benign |
Het |
| Ptpru |
T |
C |
4: 131,535,651 (GRCm39) |
E370G |
possibly damaging |
Het |
| Ralgapa2 |
T |
C |
2: 146,292,478 (GRCm39) |
Y187C |
probably benign |
Het |
| Rps6ka2 |
C |
T |
17: 7,549,157 (GRCm39) |
|
probably benign |
Het |
| Slit3 |
T |
C |
11: 35,012,462 (GRCm39) |
S41P |
possibly damaging |
Het |
| Smarca5 |
A |
T |
8: 81,431,343 (GRCm39) |
L958Q |
probably damaging |
Het |
| Snx9 |
T |
C |
17: 5,952,636 (GRCm39) |
|
probably benign |
Het |
| Stkld1 |
A |
T |
2: 26,830,050 (GRCm39) |
N72I |
probably damaging |
Het |
| Strc |
C |
A |
2: 121,197,132 (GRCm39) |
D1532Y |
probably damaging |
Het |
| Sucla2 |
C |
T |
14: 73,798,074 (GRCm39) |
|
probably benign |
Het |
| Svil |
T |
G |
18: 5,063,777 (GRCm39) |
|
probably benign |
Het |
| Traf3ip1 |
T |
A |
1: 91,428,506 (GRCm39) |
D122E |
unknown |
Het |
| Vmn2r7 |
A |
T |
3: 64,614,559 (GRCm39) |
D509E |
possibly damaging |
Het |
| Zfp407 |
C |
T |
18: 84,577,898 (GRCm39) |
A1072T |
probably benign |
Het |
| Zfp418 |
C |
A |
7: 7,184,561 (GRCm39) |
Q175K |
probably benign |
Het |
| Zxdc |
T |
C |
6: 90,355,885 (GRCm39) |
S465P |
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 |
|
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 |
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTCTCTAAGAAGCACTCGCCGC -3'
(R):5'- CACCCTGAACAGGCACTGAAGATG -3'
Sequencing Primer
(F):5'- CCTTGACAGCCATTAAGGGTG -3'
(R):5'- GATGGGGCACAGGTCAC -3'
|
| Posted On |
2013-11-18 |
Incidental Mutation