Incidental Mutation 'R0385:Vps54'
| ID |
31241 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
038591-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.933)
|
| Stock # |
R0385 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 21256381 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Glutamic Acid
at position 467
(K467E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000116739
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
| AlphaFold |
Q5SPW0 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000006221
AA Change: K629E
PolyPhen 2
Score 0.421 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: K629E
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
16 |
N/A |
INTRINSIC |
|
Pfam:DUF2450
|
198 |
364 |
2.1e-12 |
PFAM |
|
Pfam:Vps54
|
736 |
868 |
3.3e-56 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000109578
AA Change: K617E
PolyPhen 2
Score 0.738 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: K617E
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
3 |
16 |
N/A |
INTRINSIC |
|
Pfam:DUF2450
|
186 |
352 |
2.3e-12 |
PFAM |
|
Pfam:Vps54
|
723 |
857 |
1.6e-63 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000132017
AA Change: K467E
PolyPhen 2
Score 0.938 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: K467E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF2450
|
72 |
238 |
1.4e-12 |
PFAM |
|
Pfam:Vps54
|
573 |
707 |
7.8e-64 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143932
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.2%
- 10x: 96.0%
- 20x: 92.0%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes for a protein that in yeast forms part of a trimeric vacuolar-protein-sorting complex that is required for retrograde transport of proteins from prevacuoles to the late Golgi compartment. As in yeast, mammalian Vps54 proteins contain a coiled-coil region and dileucine motifs. Alternative splicing results in multiple transcript variants encoding different isoforms [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutants show progressive ataxia, tremors, and limb paralysis with degeneration of motor nerve cells of brainstem and spinal cord and atrophy of skeletal muscle beginning about 3-weeks of age. Mutants are sterile and most die by 3-months of age. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 65 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acaca |
A |
G |
11: 84,122,574 (GRCm39) |
N331S |
probably benign |
Het |
| Adk |
A |
G |
14: 21,368,142 (GRCm39) |
N189S |
probably benign |
Het |
| Apc |
T |
A |
18: 34,448,997 (GRCm39) |
N1930K |
probably damaging |
Het |
| Arhgap28 |
T |
C |
17: 68,171,601 (GRCm39) |
D391G |
probably damaging |
Het |
| Atn1 |
G |
T |
6: 124,720,334 (GRCm39) |
|
probably benign |
Het |
| C2cd5 |
T |
C |
6: 142,987,216 (GRCm39) |
E471G |
probably damaging |
Het |
| Camta1 |
C |
A |
4: 151,159,597 (GRCm39) |
R1614L |
probably damaging |
Het |
| Cap2 |
T |
C |
13: 46,714,023 (GRCm39) |
L34P |
probably damaging |
Het |
| Cdc42ep2 |
T |
A |
19: 5,968,553 (GRCm39) |
M51L |
probably benign |
Het |
| Cntn5 |
C |
T |
9: 9,972,875 (GRCm39) |
A254T |
probably damaging |
Het |
| Dicer1 |
A |
T |
12: 104,670,433 (GRCm39) |
L1044H |
probably damaging |
Het |
| Dkk3 |
A |
C |
7: 111,757,430 (GRCm39) |
M58R |
probably damaging |
Het |
| Dpy19l3 |
G |
A |
7: 35,452,130 (GRCm39) |
R5W |
probably damaging |
Het |
| Dsg1c |
C |
T |
18: 20,416,711 (GRCm39) |
P871S |
probably damaging |
Het |
| Dusp1 |
A |
T |
17: 26,726,670 (GRCm39) |
S131T |
probably benign |
Het |
| Enpp2 |
C |
T |
15: 54,745,555 (GRCm39) |
G314R |
probably damaging |
Het |
| Entr1 |
T |
C |
2: 26,277,671 (GRCm39) |
E41G |
possibly damaging |
Het |
| Fam222b |
C |
A |
11: 78,045,756 (GRCm39) |
P439Q |
probably benign |
Het |
| Fastkd2 |
A |
T |
1: 63,776,970 (GRCm39) |
I369F |
probably benign |
Het |
| Fdps |
G |
A |
3: 89,002,201 (GRCm39) |
S205F |
probably damaging |
Het |
| Fmo1 |
A |
T |
1: 162,663,773 (GRCm39) |
V252E |
possibly damaging |
Het |
| Frmd5 |
A |
G |
2: 121,386,055 (GRCm39) |
Y230H |
probably damaging |
Het |
| Gal |
C |
T |
19: 3,461,171 (GRCm39) |
V88I |
probably benign |
Het |
| Gnptab |
T |
C |
10: 88,272,387 (GRCm39) |
I1009T |
probably damaging |
Het |
| Idh2 |
C |
T |
7: 79,748,005 (GRCm39) |
A232T |
probably damaging |
Het |
| Klhdc7a |
A |
T |
4: 139,694,016 (GRCm39) |
D310E |
probably benign |
Het |
| Klk4 |
T |
C |
7: 43,533,432 (GRCm39) |
M97T |
probably benign |
Het |
| Krt82 |
C |
T |
15: 101,454,028 (GRCm39) |
V227M |
probably damaging |
Het |
| Lpp |
T |
C |
16: 24,580,587 (GRCm39) |
V226A |
probably damaging |
Het |
| Mbd1 |
AGCTGACTCGGTAC |
A |
18: 74,406,312 (GRCm39) |
|
probably null |
Het |
| Mcm10 |
T |
C |
2: 5,008,965 (GRCm39) |
K335E |
possibly damaging |
Het |
| Mpv17l |
A |
T |
16: 13,758,863 (GRCm39) |
I96L |
probably benign |
Het |
| Muc6 |
G |
A |
7: 141,218,313 (GRCm39) |
S2120F |
possibly damaging |
Het |
| Myb |
T |
C |
10: 21,030,611 (GRCm39) |
D62G |
possibly damaging |
Het |
| Nasp |
A |
T |
4: 116,467,892 (GRCm39) |
N364K |
probably benign |
Het |
| Npsr1 |
A |
G |
9: 24,224,573 (GRCm39) |
N317D |
probably damaging |
Het |
| Nup210 |
A |
G |
6: 91,005,777 (GRCm39) |
V619A |
possibly damaging |
Het |
| Oser1 |
C |
T |
2: 163,253,316 (GRCm39) |
|
probably null |
Het |
| Pcdhb4 |
T |
C |
18: 37,442,268 (GRCm39) |
F526S |
probably damaging |
Het |
| Plekhh3 |
T |
C |
11: 101,055,967 (GRCm39) |
N444S |
probably damaging |
Het |
| Pnpla5 |
G |
T |
15: 84,004,920 (GRCm39) |
L144M |
probably damaging |
Het |
| Pou2f2 |
G |
A |
7: 24,815,501 (GRCm39) |
Q89* |
probably null |
Het |
| Ptprb |
A |
G |
10: 116,186,083 (GRCm39) |
I1713V |
probably benign |
Het |
| Ptprd |
A |
G |
4: 76,046,902 (GRCm39) |
Y442H |
probably damaging |
Het |
| Rad21 |
A |
T |
15: 51,837,259 (GRCm39) |
I152N |
possibly damaging |
Het |
| Ralgapa1 |
A |
G |
12: 55,723,823 (GRCm39) |
S1568P |
probably damaging |
Het |
| Rhag |
T |
A |
17: 41,145,618 (GRCm39) |
V357E |
probably damaging |
Het |
| Rnf121 |
A |
T |
7: 101,678,324 (GRCm39) |
D174E |
possibly damaging |
Het |
| Sf3b4 |
T |
C |
3: 96,080,298 (GRCm39) |
Y16H |
probably damaging |
Het |
| Slc1a3 |
C |
T |
15: 8,668,619 (GRCm39) |
V449I |
probably damaging |
Het |
| Slc20a2 |
A |
G |
8: 23,058,409 (GRCm39) |
I648M |
probably benign |
Het |
| Slc25a25 |
T |
A |
2: 32,307,834 (GRCm39) |
I254F |
probably damaging |
Het |
| Slit3 |
A |
G |
11: 35,591,109 (GRCm39) |
H1307R |
probably damaging |
Het |
| Sorl1 |
C |
A |
9: 41,943,205 (GRCm39) |
M890I |
probably damaging |
Het |
| Supt16 |
A |
C |
14: 52,414,175 (GRCm39) |
M468R |
probably benign |
Het |
| Taf4b |
T |
C |
18: 14,916,817 (GRCm39) |
S56P |
probably benign |
Het |
| Tapt1 |
T |
C |
5: 44,375,443 (GRCm39) |
|
probably null |
Het |
| Tmco3 |
T |
G |
8: 13,346,027 (GRCm39) |
C288W |
probably damaging |
Het |
| Tpcn2 |
A |
G |
7: 144,830,911 (GRCm39) |
Y145H |
probably damaging |
Het |
| Ttn |
C |
T |
2: 76,712,061 (GRCm39) |
|
probably benign |
Het |
| Usb1 |
G |
T |
8: 96,071,946 (GRCm39) |
W215C |
probably damaging |
Het |
| Usp2 |
C |
G |
9: 44,004,047 (GRCm39) |
T305R |
probably damaging |
Het |
| Vmn1r13 |
G |
A |
6: 57,187,690 (GRCm39) |
S283N |
probably benign |
Het |
| Wnk2 |
G |
T |
13: 49,221,604 (GRCm39) |
S1121Y |
probably damaging |
Het |
| Zbed6 |
A |
T |
1: 133,584,522 (GRCm39) |
D938E |
probably damaging |
Het |
|
| Other mutations in Vps54 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00272:Vps54
|
APN |
11 |
21,227,909 (GRCm39) |
missense |
possibly damaging |
0.74 |
|
IGL01070:Vps54
|
APN |
11 |
21,262,268 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01398:Vps54
|
APN |
11 |
21,245,403 (GRCm39) |
splice site |
probably benign |
|
|
IGL01450:Vps54
|
APN |
11 |
21,241,135 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01611:Vps54
|
APN |
11 |
21,261,082 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01801:Vps54
|
APN |
11 |
21,225,131 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL01872:Vps54
|
APN |
11 |
21,256,940 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02071:Vps54
|
APN |
11 |
21,225,071 (GRCm39) |
missense |
probably null |
0.00 |
|
IGL02186:Vps54
|
APN |
11 |
21,256,947 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03358:Vps54
|
APN |
11 |
21,218,799 (GRCm39) |
missense |
probably damaging |
1.00 |
|
muddle
|
UTSW |
11 |
21,227,670 (GRCm39) |
splice site |
probably null |
|
|
R0031:Vps54
|
UTSW |
11 |
21,262,899 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0147:Vps54
|
UTSW |
11 |
21,250,259 (GRCm39) |
missense |
probably benign |
0.02 |
|
R0158:Vps54
|
UTSW |
11 |
21,256,962 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0420:Vps54
|
UTSW |
11 |
21,261,071 (GRCm39) |
splice site |
probably benign |
|
|
R0582:Vps54
|
UTSW |
11 |
21,250,137 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0602:Vps54
|
UTSW |
11 |
21,256,434 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R1051:Vps54
|
UTSW |
11 |
21,228,001 (GRCm39) |
frame shift |
probably null |
|
|
R1280:Vps54
|
UTSW |
11 |
21,227,868 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R1720:Vps54
|
UTSW |
11 |
21,256,519 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1875:Vps54
|
UTSW |
11 |
21,250,251 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1883:Vps54
|
UTSW |
11 |
21,262,967 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R1971:Vps54
|
UTSW |
11 |
21,242,051 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2063:Vps54
|
UTSW |
11 |
21,227,955 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2171:Vps54
|
UTSW |
11 |
21,248,810 (GRCm39) |
missense |
probably benign |
0.16 |
|
R2518:Vps54
|
UTSW |
11 |
21,256,394 (GRCm39) |
missense |
probably benign |
0.01 |
|
R3801:Vps54
|
UTSW |
11 |
21,218,832 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4049:Vps54
|
UTSW |
11 |
21,250,183 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4108:Vps54
|
UTSW |
11 |
21,262,877 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4560:Vps54
|
UTSW |
11 |
21,262,260 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R4668:Vps54
|
UTSW |
11 |
21,249,989 (GRCm39) |
missense |
probably benign |
0.04 |
|
R4772:Vps54
|
UTSW |
11 |
21,262,952 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5061:Vps54
|
UTSW |
11 |
21,269,881 (GRCm39) |
utr 3 prime |
probably benign |
|
|
R5611:Vps54
|
UTSW |
11 |
21,261,130 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R5638:Vps54
|
UTSW |
11 |
21,258,799 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5670:Vps54
|
UTSW |
11 |
21,214,864 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7095:Vps54
|
UTSW |
11 |
21,221,720 (GRCm39) |
missense |
probably benign |
0.12 |
|
R7175:Vps54
|
UTSW |
11 |
21,265,028 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7179:Vps54
|
UTSW |
11 |
21,248,791 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7269:Vps54
|
UTSW |
11 |
21,227,670 (GRCm39) |
splice site |
probably null |
|
|
R7286:Vps54
|
UTSW |
11 |
21,225,005 (GRCm39) |
missense |
probably benign |
0.30 |
|
R7344:Vps54
|
UTSW |
11 |
21,224,999 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7552:Vps54
|
UTSW |
11 |
21,248,831 (GRCm39) |
missense |
probably benign |
0.08 |
|
R7897:Vps54
|
UTSW |
11 |
21,213,307 (GRCm39) |
missense |
probably benign |
0.02 |
|
R8011:Vps54
|
UTSW |
11 |
21,225,095 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8193:Vps54
|
UTSW |
11 |
21,242,045 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8282:Vps54
|
UTSW |
11 |
21,250,464 (GRCm39) |
intron |
probably benign |
|
|
R8534:Vps54
|
UTSW |
11 |
21,227,706 (GRCm39) |
missense |
probably benign |
0.05 |
|
R8559:Vps54
|
UTSW |
11 |
21,214,815 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9034:Vps54
|
UTSW |
11 |
21,213,273 (GRCm39) |
missense |
probably benign |
0.29 |
|
R9096:Vps54
|
UTSW |
11 |
21,227,913 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R9253:Vps54
|
UTSW |
11 |
21,258,771 (GRCm39) |
missense |
probably benign |
|
|
R9359:Vps54
|
UTSW |
11 |
21,242,108 (GRCm39) |
missense |
probably benign |
|
|
R9367:Vps54
|
UTSW |
11 |
21,250,234 (GRCm39) |
missense |
probably benign |
0.00 |
|
Z1177:Vps54
|
UTSW |
11 |
21,213,206 (GRCm39) |
start gained |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GACCGGCTTTAGACATCTTCAGCTC -3'
(R):5'- GGCCTGTGATCAACTACGTTTACCC -3'
Sequencing Primer
(F):5'- GCTTTAGACATCTTCAGCTCTGTATG -3'
(R):5'- GTGATCAACTACGTTTACCCTTTAAC -3'
|
| Posted On |
2013-04-24 |
Incidental Mutation