Incidental Mutation 'R6003:Vps52'
ID |
478480 |
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 |
043252-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R6003 (G1)
|
Quality Score |
95.0077 |
Status
|
Not validated
|
Chromosome |
17 |
Chromosomal Location |
34174786-34186009 bp(+) (GRCm39) |
Type of Mutation |
start codon destroyed |
DNA Base Change (assembly) |
T to A
at 34175068 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Methionine to Lysine
at position 1
(M1K)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000133926
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000008812]
[ENSMUST00000025178]
[ENSMUST00000087543]
[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 null
Transcript: ENSMUST00000025178
AA Change: M1K
|
SMART Domains |
Protein: ENSMUSP00000025178 Gene: ENSMUSG00000024319 AA Change: M1K
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 |
probably benign
Transcript: ENSMUST00000087543
|
SMART Domains |
Protein: ENSMUSP00000084823 Gene: ENSMUSG00000067370
Domain | Start | End | E-Value | Type |
transmembrane domain
|
5 |
24 |
N/A |
INTRINSIC |
Pfam:Galactosyl_T
|
85 |
302 |
1.3e-66 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000122652
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172550
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172799
|
Predicted Effect |
probably null
Transcript: ENSMUST00000173196
AA Change: M1K
PolyPhen 2
Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
|
SMART Domains |
Protein: ENSMUSP00000133926 Gene: ENSMUSG00000024319 AA Change: M1K
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: ENSMUST00000173445
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173318
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174758
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174175
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174662
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174745
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173323
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174620
|
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 |
- 1x: 99.9%
- 3x: 99.4%
- 10x: 97.2%
- 20x: 90.9%
|
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: 44 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
A4galt |
T |
C |
15: 83,112,312 (GRCm39) |
E157G |
probably benign |
Het |
Abcb11 |
T |
C |
2: 69,073,811 (GRCm39) |
K1238R |
probably benign |
Het |
Ankar |
T |
A |
1: 72,738,046 (GRCm39) |
E45D |
probably damaging |
Het |
Antxrl |
G |
T |
14: 33,797,592 (GRCm39) |
K522N |
possibly damaging |
Het |
Ap1m1 |
A |
G |
8: 73,003,011 (GRCm39) |
Y93C |
probably damaging |
Het |
As3mt |
C |
T |
19: 46,696,567 (GRCm39) |
T35M |
possibly damaging |
Het |
Aspg |
T |
C |
12: 112,079,476 (GRCm39) |
S85P |
probably damaging |
Het |
Cachd1 |
T |
C |
4: 100,809,216 (GRCm39) |
S234P |
possibly damaging |
Het |
Ccdc3 |
T |
C |
2: 5,146,218 (GRCm39) |
|
probably null |
Het |
Cnpy1 |
T |
C |
5: 28,450,759 (GRCm39) |
T16A |
probably benign |
Het |
Cope |
T |
C |
8: 70,757,285 (GRCm39) |
L43P |
probably benign |
Het |
E2f8 |
T |
C |
7: 48,520,525 (GRCm39) |
M599V |
probably benign |
Het |
Eif3a |
A |
T |
19: 60,755,319 (GRCm39) |
D954E |
unknown |
Het |
Gfpt1 |
T |
A |
6: 87,065,230 (GRCm39) |
|
probably null |
Het |
Ggps1 |
T |
G |
13: 14,228,587 (GRCm39) |
S145R |
probably benign |
Het |
Gon4l |
A |
G |
3: 88,803,400 (GRCm39) |
D1337G |
probably damaging |
Het |
Gtf2a1l |
G |
T |
17: 89,001,531 (GRCm39) |
G82V |
probably damaging |
Het |
Gucy1b1 |
C |
A |
3: 81,965,584 (GRCm39) |
L87F |
probably damaging |
Het |
Hoxc9 |
T |
C |
15: 102,890,311 (GRCm39) |
V76A |
probably benign |
Het |
Ints2 |
T |
C |
11: 86,129,294 (GRCm39) |
E460G |
probably damaging |
Het |
Kdm4b |
C |
T |
17: 56,703,916 (GRCm39) |
R756W |
probably damaging |
Het |
Lax1 |
T |
A |
1: 133,611,834 (GRCm39) |
I34F |
probably benign |
Het |
Marveld3 |
A |
T |
8: 110,680,960 (GRCm39) |
C312S |
probably damaging |
Het |
Ncoa2 |
T |
C |
1: 13,237,254 (GRCm39) |
D824G |
possibly damaging |
Het |
Nrxn2 |
C |
A |
19: 6,548,358 (GRCm39) |
A17D |
possibly damaging |
Het |
Nup133 |
A |
T |
8: 124,665,031 (GRCm39) |
I220N |
probably damaging |
Het |
Nup205 |
T |
C |
6: 35,189,751 (GRCm39) |
V984A |
probably benign |
Het |
Nup54 |
A |
T |
5: 92,570,853 (GRCm39) |
D318E |
probably damaging |
Het |
Obp2a |
A |
T |
2: 25,591,151 (GRCm39) |
K94N |
probably damaging |
Het |
Or2ak5 |
A |
T |
11: 58,611,196 (GRCm39) |
I226N |
probably benign |
Het |
Or5b3 |
T |
C |
19: 13,388,403 (GRCm39) |
S157P |
probably benign |
Het |
Pappa2 |
T |
C |
1: 158,763,820 (GRCm39) |
I564V |
probably benign |
Het |
Parpbp |
A |
G |
10: 87,969,020 (GRCm39) |
V142A |
possibly damaging |
Het |
Rdh16f2 |
A |
T |
10: 127,712,201 (GRCm39) |
R219S |
probably benign |
Het |
Rfx6 |
C |
T |
10: 51,584,683 (GRCm39) |
R228C |
probably damaging |
Het |
Rpap2 |
A |
G |
5: 107,749,767 (GRCm39) |
|
probably null |
Het |
Rskr |
T |
G |
11: 78,183,846 (GRCm39) |
|
probably null |
Het |
Slc15a2 |
T |
C |
16: 36,574,910 (GRCm39) |
I531V |
probably benign |
Het |
Srebf1 |
T |
C |
11: 60,097,930 (GRCm39) |
E58G |
possibly damaging |
Het |
Tmem214 |
C |
A |
5: 31,028,068 (GRCm39) |
T96K |
possibly damaging |
Het |
Usp19 |
T |
C |
9: 108,373,579 (GRCm39) |
Y691H |
probably damaging |
Het |
Vmn1r86 |
C |
T |
7: 12,836,125 (GRCm39) |
W200* |
probably null |
Het |
Vmn2r8 |
A |
T |
5: 108,945,248 (GRCm39) |
S786R |
probably damaging |
Het |
Zzef1 |
T |
A |
11: 72,714,891 (GRCm39) |
|
probably null |
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 |
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'- GGTTCCGGAACAGAGTTGTG -3'
(R):5'- GCTCCGAACCTCTTGTCTAAATG -3'
Sequencing Primer
(F):5'- CTGTTTGCACTTGACCGAAATG -3'
(R):5'- TGTCTAAATGGAGCCTACGC -3'
|
Posted On |
2017-06-26 |