Incidental Mutation 'R1506:Vps52'
| ID |
167959 |
| 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 |
039554-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1506 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
34174786-34186009 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 34176868 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Proline
at position 74
(L74P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000025178
(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 damaging
Transcript: ENSMUST00000025178
AA Change: L74P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: L74P
| 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 benign
Transcript: ENSMUST00000173196
AA Change: L74P
PolyPhen 2
Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
|
| SMART Domains |
Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: L74P
| 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: ENSMUST00000174620
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174175
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173445
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174588
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174745
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000174662
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173318
|
| 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 |
|
| Meta Mutation Damage Score |
0.8314 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.4%
- 10x: 96.5%
- 20x: 93.7%
|
| Validation Efficiency |
98% (61/62) |
| 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: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc3 |
G |
T |
11: 94,248,144 (GRCm39) |
T1152K |
possibly damaging |
Het |
| Acp3 |
T |
A |
9: 104,201,373 (GRCm39) |
T82S |
probably damaging |
Het |
| Adam23 |
C |
T |
1: 63,586,973 (GRCm39) |
P445S |
probably benign |
Het |
| Ap3b1 |
T |
A |
13: 94,582,651 (GRCm39) |
|
probably benign |
Het |
| Artn |
A |
G |
4: 117,784,058 (GRCm39) |
V136A |
probably damaging |
Het |
| Ash1l |
A |
G |
3: 88,965,806 (GRCm39) |
T2403A |
probably damaging |
Het |
| Bbof1 |
G |
T |
12: 84,470,273 (GRCm39) |
V120L |
probably damaging |
Het |
| Boc |
A |
G |
16: 44,323,928 (GRCm39) |
Y158H |
probably damaging |
Het |
| Casp8 |
A |
G |
1: 58,863,355 (GRCm39) |
E105G |
probably damaging |
Het |
| Cers4 |
T |
C |
8: 4,570,557 (GRCm39) |
F206L |
probably benign |
Het |
| Chrna9 |
A |
G |
5: 66,126,479 (GRCm39) |
T78A |
probably benign |
Het |
| Creb3 |
A |
T |
4: 43,566,193 (GRCm39) |
T263S |
possibly damaging |
Het |
| Cyp2c40 |
A |
G |
19: 39,766,443 (GRCm39) |
V384A |
probably damaging |
Het |
| Dip2b |
G |
A |
15: 100,080,994 (GRCm39) |
V879M |
probably damaging |
Het |
| Dnah17 |
C |
A |
11: 118,016,213 (GRCm39) |
V14F |
possibly damaging |
Het |
| Epb41l4b |
T |
A |
4: 57,088,824 (GRCm39) |
K144N |
probably damaging |
Het |
| Ercc6 |
A |
T |
14: 32,291,821 (GRCm39) |
I1062F |
probably benign |
Het |
| Fabp3 |
C |
T |
4: 130,206,180 (GRCm39) |
T57I |
probably benign |
Het |
| Fat2 |
C |
A |
11: 55,175,090 (GRCm39) |
E1874D |
probably benign |
Het |
| Fbxw21 |
T |
A |
9: 108,977,257 (GRCm39) |
I151F |
probably damaging |
Het |
| Fhip2a |
A |
G |
19: 57,357,007 (GRCm39) |
I33V |
probably benign |
Het |
| Foxn1 |
A |
G |
11: 78,256,761 (GRCm39) |
|
probably benign |
Het |
| Gpr63 |
G |
A |
4: 25,008,227 (GRCm39) |
R317H |
probably damaging |
Het |
| Grip1 |
C |
A |
10: 119,814,356 (GRCm39) |
H296N |
probably damaging |
Het |
| Gtdc1 |
A |
T |
2: 44,465,506 (GRCm39) |
M288K |
possibly damaging |
Het |
| Guf1 |
T |
A |
5: 69,724,509 (GRCm39) |
D488E |
possibly damaging |
Het |
| Gvin3 |
C |
T |
7: 106,200,788 (GRCm39) |
D819N |
probably benign |
Het |
| Heatr5b |
C |
A |
17: 79,060,576 (GRCm39) |
R2033L |
probably damaging |
Het |
| Hsd17b2 |
T |
A |
8: 118,429,004 (GRCm39) |
|
probably null |
Het |
| Ino80 |
A |
T |
2: 119,255,746 (GRCm39) |
L913* |
probably null |
Het |
| Inppl1 |
A |
C |
7: 101,473,174 (GRCm39) |
S1159A |
probably benign |
Het |
| Kcnk7 |
G |
A |
19: 5,756,140 (GRCm39) |
C122Y |
probably damaging |
Het |
| Mtor |
A |
G |
4: 148,620,962 (GRCm39) |
|
probably benign |
Het |
| Muc4 |
A |
T |
16: 32,574,033 (GRCm39) |
S704C |
possibly damaging |
Het |
| Nckap5 |
A |
T |
1: 125,953,650 (GRCm39) |
C967* |
probably null |
Het |
| Nek10 |
T |
C |
14: 14,999,078 (GRCm38) |
|
probably benign |
Het |
| Oas1h |
A |
T |
5: 121,009,951 (GRCm39) |
D342V |
possibly damaging |
Het |
| Or10j2 |
A |
G |
1: 173,098,336 (GRCm39) |
N198S |
probably benign |
Het |
| Or2ak7 |
T |
A |
11: 58,575,014 (GRCm39) |
L105Q |
probably benign |
Het |
| Or2n1 |
A |
T |
17: 38,486,091 (GRCm39) |
M39L |
probably benign |
Het |
| Or4m1 |
A |
G |
14: 50,557,941 (GRCm39) |
V117A |
probably benign |
Het |
| Or8b1b |
T |
C |
9: 38,375,439 (GRCm39) |
M34T |
probably benign |
Het |
| Prex1 |
A |
T |
2: 166,429,001 (GRCm39) |
V694E |
probably damaging |
Het |
| Rad50 |
G |
A |
11: 53,570,312 (GRCm39) |
A810V |
probably damaging |
Het |
| Rcor1 |
T |
C |
12: 111,076,271 (GRCm39) |
S410P |
probably damaging |
Het |
| Rps14 |
A |
T |
18: 60,909,551 (GRCm39) |
N26I |
probably benign |
Het |
| Slc38a1 |
T |
C |
15: 96,483,431 (GRCm39) |
D299G |
probably benign |
Het |
| Slc5a1 |
T |
A |
5: 33,312,052 (GRCm39) |
N481K |
possibly damaging |
Het |
| Slco3a1 |
A |
T |
7: 74,009,683 (GRCm39) |
|
probably null |
Het |
| Spart |
T |
C |
3: 55,024,992 (GRCm39) |
S196P |
probably damaging |
Het |
| Speg |
A |
G |
1: 75,394,307 (GRCm39) |
T1701A |
probably benign |
Het |
| Sugt1 |
A |
G |
14: 79,862,365 (GRCm39) |
N271S |
probably benign |
Het |
| Tbx15 |
A |
T |
3: 99,259,228 (GRCm39) |
L366F |
possibly damaging |
Het |
| Tnc |
G |
A |
4: 63,925,921 (GRCm39) |
T953I |
possibly damaging |
Het |
| Uqcc1 |
A |
G |
2: 155,753,738 (GRCm39) |
S46P |
probably damaging |
Het |
| Vmn2r18 |
T |
C |
5: 151,499,099 (GRCm39) |
|
probably null |
Het |
| Vmn2r7 |
T |
A |
3: 64,614,500 (GRCm39) |
Y438F |
probably benign |
Het |
| Vmn2r72 |
T |
A |
7: 85,398,419 (GRCm39) |
K520N |
probably benign |
Het |
| Xpo5 |
G |
T |
17: 46,538,814 (GRCm39) |
M673I |
probably benign |
Het |
| Zscan18 |
A |
G |
7: 12,508,129 (GRCm39) |
V457A |
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 |
|
R1065:Vps52
|
UTSW |
17 |
34,180,213 (GRCm39) |
missense |
probably benign |
0.02 |
|
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'- CGCAGACAGCTAAGACTGAGTGAC -3'
(R):5'- CTCCAGCTCCACCTGCTTTGAATAG -3'
Sequencing Primer
(F):5'- aggcaggcacagcacac -3'
(R):5'- TTGAATAGTGTCGAAGATCCACACC -3'
|
| Posted On |
2014-04-13 |
Incidental Mutation