Incidental Mutation 'R1280:Vps54'
ID | 151007 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps54
|
Ensembl Gene |
ENSMUSG00000020128 |
Gene Name | VPS54 GARP complex subunit |
Synonyms | 5330404P15Rik, wr, mSLP8, Vps54l |
MMRRC Submission |
039346-MU
|
Accession Numbers | |
Is this an essential gene? |
Probably essential (E-score: 0.939)
|
Stock # | R1280 (G1)
|
Quality Score | 225 |
Status |
Not validated
|
Chromosome | 11 |
Chromosomal Location | 21239281-21321136 bp(+) (GRCm38) |
Type of Mutation | missense |
DNA Base Change (assembly) |
T to A
at 21277868 bp
|
Zygosity | Heterozygous |
Amino Acid Change |
Isoleucine to Asparagine
at position 273
(I273N)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000006221
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
PDB Structure |
C-terminal domain of Vps54 subunit of the GARP complex [X-RAY DIFFRACTION]
Vps54 C-terminal domain [X-RAY DIFFRACTION]
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000006221
AA Change: I273N
PolyPhen 2
Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000006221 Gene: ENSMUSG00000020128 AA Change: I273N
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: I261N
PolyPhen 2
Score 0.719 (Sensitivity: 0.86; Specificity: 0.92)
|
SMART Domains |
Protein: ENSMUSP00000105206 Gene: ENSMUSG00000020128 AA Change: I261N
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 |
noncoding transcript
Transcript: ENSMUST00000118219
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000132017
AA Change: I147N
PolyPhen 2
Score 0.470 (Sensitivity: 0.89; Specificity: 0.90)
|
SMART Domains |
Protein: ENSMUSP00000116739 Gene: ENSMUSG00000020128 AA Change: I147N
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: ENSMUST00000132146
|
Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.2%
- 10x: 96.1%
- 20x: 92.1%
|
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: 20 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Alkbh2 |
C |
T |
5: 114,124,226 |
E148K |
probably damaging |
Het |
Atp5g3 |
G |
T |
2: 73,909,370 |
T42K |
possibly damaging |
Het |
Brd2 |
T |
C |
17: 34,114,150 |
M60V |
possibly damaging |
Het |
Cabp1 |
T |
C |
5: 115,175,471 |
N226S |
probably benign |
Het |
Cers6 |
G |
A |
2: 69,068,689 |
V224I |
probably benign |
Het |
Entpd2 |
C |
T |
2: 25,399,484 |
S326F |
probably damaging |
Het |
Fez1 |
GACAAACA |
GACA |
9: 36,870,549 |
|
probably null |
Het |
Gjb3 |
G |
A |
4: 127,326,431 |
R103W |
probably damaging |
Het |
Klhdc7a |
G |
A |
4: 139,965,453 |
R728C |
probably benign |
Het |
Myo18b |
A |
G |
5: 112,723,805 |
|
probably null |
Het |
Mzf1 |
A |
T |
7: 13,053,083 |
L20Q |
probably damaging |
Het |
Neil1 |
T |
C |
9: 57,146,901 |
Y45C |
probably damaging |
Het |
Olfr1368 |
C |
T |
13: 21,142,167 |
V297I |
probably benign |
Het |
Rbm12 |
T |
C |
2: 156,096,829 |
K508E |
probably damaging |
Het |
Socs4 |
A |
T |
14: 47,290,913 |
Q435L |
probably benign |
Het |
Tdrd9 |
T |
C |
12: 112,039,408 |
V905A |
probably damaging |
Het |
Tekt4 |
T |
A |
17: 25,471,887 |
W56R |
probably damaging |
Het |
Ttn |
A |
T |
2: 76,778,164 |
I16059N |
possibly damaging |
Het |
Ubqln3 |
A |
G |
7: 104,142,076 |
V269A |
possibly damaging |
Het |
Zfp831 |
A |
G |
2: 174,704,059 |
K1319R |
probably benign |
Het |
|
Other mutations in Vps54 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00272:Vps54
|
APN |
11 |
21277909 |
missense |
possibly damaging |
0.74 |
IGL01070:Vps54
|
APN |
11 |
21312268 |
missense |
probably damaging |
1.00 |
IGL01398:Vps54
|
APN |
11 |
21295403 |
splice site |
probably benign |
|
IGL01450:Vps54
|
APN |
11 |
21291135 |
missense |
probably benign |
0.00 |
IGL01611:Vps54
|
APN |
11 |
21311082 |
missense |
probably damaging |
1.00 |
IGL01801:Vps54
|
APN |
11 |
21275131 |
critical splice donor site |
probably null |
|
IGL01872:Vps54
|
APN |
11 |
21306940 |
missense |
probably damaging |
0.99 |
IGL02071:Vps54
|
APN |
11 |
21275071 |
missense |
probably null |
0.00 |
IGL02186:Vps54
|
APN |
11 |
21306947 |
missense |
probably damaging |
1.00 |
IGL03358:Vps54
|
APN |
11 |
21268799 |
missense |
probably damaging |
1.00 |
muddle
|
UTSW |
11 |
21277670 |
splice site |
probably null |
|
R0031:Vps54
|
UTSW |
11 |
21312899 |
missense |
probably damaging |
1.00 |
R0147:Vps54
|
UTSW |
11 |
21300259 |
missense |
probably benign |
0.02 |
R0158:Vps54
|
UTSW |
11 |
21306962 |
missense |
probably damaging |
1.00 |
R0385:Vps54
|
UTSW |
11 |
21306381 |
missense |
possibly damaging |
0.94 |
R0420:Vps54
|
UTSW |
11 |
21311071 |
splice site |
probably benign |
|
R0582:Vps54
|
UTSW |
11 |
21300137 |
missense |
probably damaging |
1.00 |
R0602:Vps54
|
UTSW |
11 |
21306434 |
missense |
possibly damaging |
0.92 |
R1051:Vps54
|
UTSW |
11 |
21278001 |
frame shift |
probably null |
|
R1720:Vps54
|
UTSW |
11 |
21306519 |
missense |
probably damaging |
1.00 |
R1875:Vps54
|
UTSW |
11 |
21300251 |
missense |
probably benign |
0.00 |
R1883:Vps54
|
UTSW |
11 |
21312967 |
missense |
possibly damaging |
0.91 |
R1971:Vps54
|
UTSW |
11 |
21292051 |
missense |
probably damaging |
1.00 |
R2063:Vps54
|
UTSW |
11 |
21277955 |
missense |
probably damaging |
1.00 |
R2171:Vps54
|
UTSW |
11 |
21298810 |
missense |
probably benign |
0.16 |
R2518:Vps54
|
UTSW |
11 |
21306394 |
missense |
probably benign |
0.01 |
R3801:Vps54
|
UTSW |
11 |
21268832 |
missense |
probably benign |
0.00 |
R4049:Vps54
|
UTSW |
11 |
21300183 |
missense |
probably benign |
0.00 |
R4108:Vps54
|
UTSW |
11 |
21312877 |
missense |
probably benign |
0.02 |
R4560:Vps54
|
UTSW |
11 |
21312260 |
missense |
possibly damaging |
0.91 |
R4668:Vps54
|
UTSW |
11 |
21299989 |
missense |
probably benign |
0.04 |
R4772:Vps54
|
UTSW |
11 |
21312952 |
missense |
probably damaging |
1.00 |
R5061:Vps54
|
UTSW |
11 |
21319881 |
utr 3 prime |
probably benign |
|
R5611:Vps54
|
UTSW |
11 |
21311130 |
missense |
possibly damaging |
0.65 |
R5638:Vps54
|
UTSW |
11 |
21308799 |
missense |
probably damaging |
1.00 |
R5670:Vps54
|
UTSW |
11 |
21264864 |
missense |
probably damaging |
1.00 |
R7095:Vps54
|
UTSW |
11 |
21271720 |
missense |
probably benign |
0.12 |
R7175:Vps54
|
UTSW |
11 |
21315028 |
critical splice donor site |
probably null |
|
R7179:Vps54
|
UTSW |
11 |
21298791 |
missense |
probably damaging |
1.00 |
R7269:Vps54
|
UTSW |
11 |
21277670 |
splice site |
probably null |
|
R7286:Vps54
|
UTSW |
11 |
21275005 |
missense |
probably benign |
0.30 |
R7344:Vps54
|
UTSW |
11 |
21274999 |
missense |
probably damaging |
1.00 |
R7552:Vps54
|
UTSW |
11 |
21298831 |
missense |
probably benign |
0.08 |
R7897:Vps54
|
UTSW |
11 |
21263307 |
missense |
probably benign |
0.02 |
R8011:Vps54
|
UTSW |
11 |
21275095 |
missense |
probably damaging |
0.99 |
R8193:Vps54
|
UTSW |
11 |
21292045 |
missense |
probably benign |
0.00 |
R8282:Vps54
|
UTSW |
11 |
21300464 |
intron |
probably benign |
|
R8534:Vps54
|
UTSW |
11 |
21277706 |
missense |
probably benign |
0.05 |
R8559:Vps54
|
UTSW |
11 |
21264815 |
missense |
probably damaging |
1.00 |
Z1177:Vps54
|
UTSW |
11 |
21263206 |
start gained |
probably benign |
|
|
Predicted Primers |
PCR Primer
(F):5'- GAGGCTGTTACCTTTGGGGAAGAAG -3'
(R):5'- AGACATACCGGAAGCTGTGAATGC -3'
Sequencing Primer
(F):5'- GTAAGTGAACATGTCTCCTTTGCAC -3'
(R):5'- TGTGAATGCCCTGAAGCTC -3'
|
Posted On | 2014-01-29 |