Incidental Mutation 'IGL00946:Vps52'
| ID | 29300 |
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| Institutional Source |
Australian Phenomics Network
(link to record)
|
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| Gene Symbol |
Vps52
|
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| Ensembl Gene |
ENSMUSG00000024319 |
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| Gene Name | VPS52 GARP complex subunit |
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| Synonyms | tclw5, ARE1, Sacm2l, D430041K17Rik, tcl-w5 |
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| Accession Numbers | |
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| Is this an essential gene? |
Essential (E-score: 1.000)
|
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| Stock # | IGL00946
|
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| Quality Score | |
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| Status |
|
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| Chromosome | 17 |
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| Chromosomal Location | 33955812-33966984 bp(+) (GRCm38) |
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| Type of Mutation | missense |
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| DNA Base Change (assembly) |
T to C
at 33956958 bp
|
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| Zygosity | Heterozygous |
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| Amino Acid Change |
Leucine to Proline
at position 40
(L40P)
|
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| Ref Sequence |
ENSEMBL: ENSMUSP00000025178
(fasta)
|
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| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000008812]
[ENSMUST00000025178]
[ENSMUST00000173196]
[ENSMUST00000174609]
|
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| Predicted Effect |
probably benign
Transcript: ENSMUST00000008812
|
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| SMART Domains |
Protein: ENSMUSP00000008812
Gene: ENSMUSG00000008668
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Ribosomal_S13
|
14 |
142 |
2.2e-59 |
PFAM |
|
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| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000025178
AA Change: L40P
PolyPhen 2
Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
|
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| SMART Domains |
Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: L40P
| 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 |
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000122652
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172550
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172558
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000172799
|
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| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000173196
AA Change: L40P
PolyPhen 2
Score 0.720 (Sensitivity: 0.86; Specificity: 0.92)
|
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| SMART Domains |
Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: L40P
| 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 |
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173318
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173323
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173445
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174175
|
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| Predicted Effect |
probably benign
Transcript: ENSMUST00000174609
|
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| SMART Domains |
Protein: ENSMUSP00000138296
Gene: ENSMUSG00000008668
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Ribosomal_S13
|
14 |
107 |
2.1e-21 |
PFAM |
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174620
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174662
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174745
|
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| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174758
|
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| Coding Region Coverage |
|
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| Validation Efficiency |
|
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| 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]
|
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| Allele List at MGI | |
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| Other mutations in this stock |
Total: 33 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ahdc1 |
T |
C |
4: 133,063,062 |
I538T |
probably benign |
Het |
| Bmp10 |
A |
T |
6: 87,434,362 |
Q379L |
probably damaging |
Het |
| Cacna2d4 |
G |
A |
6: 119,271,915 |
A446T |
possibly damaging |
Het |
| Chrdl1 |
G |
A |
X: 143,294,168 |
|
probably benign |
Het |
| Crtc2 |
A |
G |
3: 90,260,805 |
H370R |
probably damaging |
Het |
| Cubn |
T |
C |
2: 13,456,623 |
T698A |
probably damaging |
Het |
| Deup1 |
T |
C |
9: 15,561,238 |
T593A |
possibly damaging |
Het |
| Dus1l |
T |
C |
11: 120,793,875 |
T157A |
probably damaging |
Het |
| Efcab6 |
T |
C |
15: 84,018,696 |
N151S |
probably benign |
Het |
| Eif2b5 |
T |
A |
16: 20,505,252 |
H448Q |
probably benign |
Het |
| Epha8 |
T |
C |
4: 136,945,810 |
D221G |
probably damaging |
Het |
| Eprs |
G |
A |
1: 185,407,701 |
G996S |
probably benign |
Het |
| Fn1 |
G |
A |
1: 71,645,540 |
|
probably benign |
Het |
| Gfpt1 |
A |
G |
6: 87,050,942 |
Y10C |
probably damaging |
Het |
| Ghitm |
C |
T |
14: 37,125,246 |
M290I |
probably benign |
Het |
| Gpd2 |
T |
C |
2: 57,268,084 |
|
probably null |
Het |
| Htr2a |
T |
A |
14: 74,706,142 |
Y387* |
probably null |
Het |
| Lrrc7 |
T |
A |
3: 158,161,356 |
Q916L |
probably benign |
Het |
| Mfsd9 |
A |
C |
1: 40,773,780 |
D458E |
probably benign |
Het |
| Nmb |
T |
C |
7: 80,902,460 |
I123M |
probably benign |
Het |
| Nrap |
A |
T |
19: 56,340,626 |
|
probably null |
Het |
| Olfr1299 |
T |
A |
2: 111,665,144 |
M306K |
probably benign |
Het |
| Olfr1406 |
A |
T |
1: 173,183,623 |
D270E |
probably benign |
Het |
| Olfr984 |
A |
G |
9: 40,101,154 |
I112T |
probably benign |
Het |
| Pola1 |
T |
C |
X: 93,480,539 |
I1165M |
probably benign |
Het |
| Sdk1 |
G |
T |
5: 142,084,613 |
|
probably null |
Het |
| Selenon |
T |
A |
4: 134,539,726 |
|
probably benign |
Het |
| Stk39 |
T |
A |
2: 68,314,564 |
T389S |
possibly damaging |
Het |
| Tmx3 |
A |
G |
18: 90,540,054 |
E410G |
possibly damaging |
Het |
| Utp20 |
A |
T |
10: 88,748,315 |
V2660E |
possibly damaging |
Het |
| Wdr25 |
C |
T |
12: 109,025,027 |
S380F |
possibly damaging |
Het |
| Xpo7 |
T |
C |
14: 70,671,658 |
T808A |
probably benign |
Het |
| Zc3h14 |
T |
C |
12: 98,759,883 |
|
probably benign |
Het |
|
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| Other mutations in Vps52 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01098:Vps52
|
APN |
17 |
33962730 |
missense |
possibly damaging |
0.90 |
|
IGL01705:Vps52
|
APN |
17 |
33966068 |
missense |
probably damaging |
1.00 |
|
IGL01722:Vps52
|
APN |
17 |
33961615 |
nonsense |
probably null |
|
|
IGL02992:Vps52
|
APN |
17 |
33958350 |
missense |
probably damaging |
0.97 |
|
IGL03279:Vps52
|
APN |
17 |
33957874 |
missense |
probably damaging |
0.96 |
|
R0363:Vps52
|
UTSW |
17 |
33962117 |
missense |
probably benign |
0.26 |
|
R0762:Vps52
|
UTSW |
17 |
33960011 |
missense |
probably damaging |
1.00 |
|
R1065:Vps52
|
UTSW |
17 |
33961239 |
missense |
probably benign |
0.02 |
|
R1506:Vps52
|
UTSW |
17 |
33957894 |
missense |
probably damaging |
1.00 |
|
R3760:Vps52
|
UTSW |
17 |
33960188 |
missense |
possibly damaging |
0.64 |
|
R4714:Vps52
|
UTSW |
17 |
33961179 |
missense |
probably benign |
0.25 |
|
R5381:Vps52
|
UTSW |
17 |
33958301 |
missense |
possibly damaging |
0.77 |
|
R5590:Vps52
|
UTSW |
17 |
33961221 |
missense |
probably benign |
0.01 |
|
R5928:Vps52
|
UTSW |
17 |
33961126 |
missense |
possibly damaging |
0.85 |
|
R6003:Vps52
|
UTSW |
17 |
33956094 |
start codon destroyed |
probably null |
0.01 |
|
R6302:Vps52
|
UTSW |
17 |
33963215 |
missense |
probably damaging |
1.00 |
|
R6574:Vps52
|
UTSW |
17 |
33962478 |
missense |
probably null |
0.34 |
|
R6695:Vps52
|
UTSW |
17 |
33963199 |
nonsense |
probably null |
|
|
R6888:Vps52
|
UTSW |
17 |
33963206 |
missense |
probably benign |
0.06 |
|
R7022:Vps52
|
UTSW |
17 |
33959319 |
missense |
probably benign |
0.04 |
|
R7136:Vps52
|
UTSW |
17 |
33965288 |
missense |
probably benign |
0.00 |
|
R7380:Vps52
|
UTSW |
17 |
33958309 |
missense |
possibly damaging |
0.82 |
|
R7727:Vps52
|
UTSW |
17 |
33962134 |
missense |
probably benign |
0.21 |
|
R7888:Vps52
|
UTSW |
17 |
33965751 |
missense |
probably damaging |
0.98 |
|
R7971:Vps52
|
UTSW |
17 |
33965751 |
missense |
probably damaging |
0.98 |
|
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| Posted On | 2013-04-17 |
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