Incidental Mutation 'R7888:Vps52'
| ID |
609180 |
| 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 |
045940-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R7888 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
34174786-34186009 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 34184725 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Serine
at position 666
(N666S)
|
| 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: N666S
PolyPhen 2
Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: N666S
| 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 |
possibly damaging
Transcript: ENSMUST00000173196
AA Change: N598S
PolyPhen 2
Score 0.667 (Sensitivity: 0.86; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: N598S
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
100% (45/45) |
| 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: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acox2 |
G |
T |
14: 8,246,415 (GRCm38) |
Q459K |
probably benign |
Het |
| Ano3 |
T |
A |
2: 110,496,773 (GRCm39) |
Y792F |
probably damaging |
Het |
| Aoc3 |
C |
T |
11: 101,223,323 (GRCm39) |
H520Y |
probably damaging |
Het |
| Atp4b |
A |
G |
8: 13,439,811 (GRCm39) |
F137S |
probably damaging |
Het |
| Blvrb |
A |
G |
7: 27,165,159 (GRCm39) |
T160A |
probably damaging |
Het |
| Brd2 |
G |
A |
17: 34,335,995 (GRCm39) |
R73W |
probably damaging |
Het |
| Btaf1 |
A |
G |
19: 36,943,036 (GRCm39) |
T306A |
probably benign |
Het |
| Ccdc154 |
G |
A |
17: 25,383,578 (GRCm39) |
V212M |
possibly damaging |
Het |
| Ccdc40 |
A |
G |
11: 119,119,967 (GRCm39) |
E3G |
unknown |
Het |
| Cenpb |
T |
A |
2: 131,021,762 (GRCm39) |
E12V |
probably damaging |
Het |
| Cnot8 |
T |
C |
11: 58,002,137 (GRCm39) |
S57P |
probably benign |
Het |
| Cryba4 |
T |
C |
5: 112,398,918 (GRCm39) |
E42G |
probably benign |
Het |
| Fam72a |
T |
A |
1: 131,456,578 (GRCm39) |
I47N |
probably damaging |
Het |
| Gm27027 |
A |
C |
2: 93,787,880 (GRCm39) |
|
probably null |
Het |
| Itgb2 |
T |
C |
10: 77,400,478 (GRCm39) |
V697A |
probably benign |
Het |
| Jakmip1 |
A |
G |
5: 37,262,208 (GRCm39) |
N336D |
probably damaging |
Het |
| Kansl1 |
T |
C |
11: 104,233,248 (GRCm39) |
T760A |
probably benign |
Het |
| Lrrc37a |
T |
A |
11: 103,392,307 (GRCm39) |
E1039D |
probably benign |
Het |
| Meaf6 |
T |
G |
4: 125,003,213 (GRCm39) |
|
probably null |
Het |
| Mpz |
T |
C |
1: 170,987,204 (GRCm39) |
|
probably null |
Het |
| Mtss1 |
A |
T |
15: 58,844,373 (GRCm39) |
M82K |
probably damaging |
Het |
| Myo6 |
T |
C |
9: 80,203,947 (GRCm39) |
S1063P |
probably damaging |
Het |
| Niban2 |
T |
A |
2: 32,812,137 (GRCm39) |
Y406* |
probably null |
Het |
| Nsun6 |
T |
A |
2: 15,001,355 (GRCm39) |
E400D |
probably benign |
Het |
| Or10al5 |
A |
T |
17: 38,062,888 (GRCm39) |
N48Y |
probably damaging |
Het |
| Or1e26 |
T |
C |
11: 73,480,354 (GRCm39) |
D70G |
probably damaging |
Het |
| Or1l4b |
A |
T |
2: 37,036,334 (GRCm39) |
M37L |
probably benign |
Het |
| Or2t26 |
T |
C |
11: 49,039,266 (GRCm39) |
Y61H |
probably damaging |
Het |
| Or52ae7 |
T |
A |
7: 103,120,006 (GRCm39) |
Y253* |
probably null |
Het |
| Or5au1 |
A |
G |
14: 52,273,347 (GRCm39) |
S74P |
probably damaging |
Het |
| Or8j3b |
C |
A |
2: 86,205,270 (GRCm39) |
C162F |
probably benign |
Het |
| Pfdn5 |
T |
A |
15: 102,237,024 (GRCm39) |
V92E |
probably damaging |
Het |
| Pik3c2g |
T |
C |
6: 139,842,470 (GRCm39) |
V801A |
|
Het |
| Psme2b |
T |
A |
11: 48,836,402 (GRCm39) |
T182S |
possibly damaging |
Het |
| Ptcd3 |
G |
A |
6: 71,860,431 (GRCm39) |
A592V |
probably damaging |
Het |
| Rabgap1 |
T |
A |
2: 37,427,319 (GRCm39) |
Y633* |
probably null |
Het |
| Rnf39 |
A |
T |
17: 37,258,133 (GRCm39) |
T222S |
probably damaging |
Het |
| Scnn1g |
A |
G |
7: 121,342,878 (GRCm39) |
N277S |
probably damaging |
Het |
| Slc16a13 |
T |
G |
11: 70,109,806 (GRCm39) |
I232L |
possibly damaging |
Het |
| Slco2b1 |
T |
G |
7: 99,338,050 (GRCm39) |
R111S |
unknown |
Het |
| Sltm |
C |
G |
9: 70,493,955 (GRCm39) |
P802R |
possibly damaging |
Het |
| Tmc3 |
T |
C |
7: 83,249,217 (GRCm39) |
W269R |
probably damaging |
Het |
| Vmn2r4 |
T |
C |
3: 64,313,943 (GRCm39) |
E346G |
probably damaging |
Het |
| Wdfy4 |
C |
T |
14: 32,812,920 (GRCm39) |
D1618N |
|
Het |
| Zfp773 |
C |
A |
7: 7,135,978 (GRCm39) |
C206F |
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 |
|
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 |
|
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'- GCTTGATGGTGAGCACAGATG -3'
(R):5'- CAGACTCATGGTGACCTGAG -3'
Sequencing Primer
(F):5'- AGGCCTTGCTGGGTCAC -3'
(R):5'- ACTCATGGTGACCTGAGCTGTC -3'
|
| Posted On |
2019-12-20 |
Incidental Mutation