Incidental Mutation 'R4560:Vps54'
| ID |
343051 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.933)
|
| Stock # |
R4560 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to G
at 21262260 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Tryptophan
at position 785
(C785W)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000006221
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
| AlphaFold |
Q5SPW0 |
| 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: C785W
PolyPhen 2
Score 0.912 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: C785W
| 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: C773W
PolyPhen 2
Score 0.892 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: C773W
| 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: C623W
PolyPhen 2
Score 0.464 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: C623W
| 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: ENSMUST00000153159
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153411
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.2%
|
| 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: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adcy4 |
A |
C |
14: 56,016,407 (GRCm39) |
|
probably null |
Het |
| Atp8b1 |
A |
T |
18: 64,689,950 (GRCm39) |
L594* |
probably null |
Het |
| Atp8b1 |
C |
T |
18: 64,701,318 (GRCm39) |
V347I |
probably benign |
Het |
| Axin1 |
A |
G |
17: 26,392,745 (GRCm39) |
D342G |
probably damaging |
Het |
| Bace2 |
G |
A |
16: 97,223,180 (GRCm39) |
R368Q |
probably damaging |
Het |
| Capn10 |
T |
C |
1: 92,867,084 (GRCm39) |
Y105H |
probably damaging |
Het |
| Ccdc89 |
T |
G |
7: 90,076,336 (GRCm39) |
L182R |
probably damaging |
Het |
| Cdk5rap2 |
A |
G |
4: 70,233,568 (GRCm39) |
F537S |
probably benign |
Het |
| Cidec |
A |
T |
6: 113,405,399 (GRCm39) |
M118K |
probably damaging |
Het |
| Cog8 |
A |
T |
8: 107,778,843 (GRCm39) |
|
probably null |
Het |
| Ctif |
A |
T |
18: 75,652,952 (GRCm39) |
L435Q |
probably damaging |
Het |
| Dhx9 |
A |
G |
1: 153,342,903 (GRCm39) |
V533A |
probably damaging |
Het |
| Drc1 |
T |
A |
5: 30,520,441 (GRCm39) |
M594K |
probably benign |
Het |
| Dthd1 |
C |
T |
5: 62,984,435 (GRCm39) |
T380I |
probably damaging |
Het |
| Fat2 |
A |
G |
11: 55,156,777 (GRCm39) |
S3475P |
possibly damaging |
Het |
| G6pd2 |
G |
A |
5: 61,967,686 (GRCm39) |
R487H |
possibly damaging |
Het |
| Hcrtr2 |
A |
G |
9: 76,161,970 (GRCm39) |
V140A |
probably damaging |
Het |
| Ikbke |
C |
T |
1: 131,199,857 (GRCm39) |
C243Y |
probably damaging |
Het |
| Il21 |
C |
A |
3: 37,279,633 (GRCm39) |
E128* |
probably null |
Het |
| Kdm7a |
C |
T |
6: 39,129,757 (GRCm39) |
R473Q |
probably damaging |
Het |
| Me3 |
G |
T |
7: 89,498,938 (GRCm39) |
R506L |
probably benign |
Het |
| Mtf2 |
T |
A |
5: 108,234,855 (GRCm39) |
|
probably null |
Het |
| Nbas |
A |
G |
12: 13,633,528 (GRCm39) |
N2311S |
probably benign |
Het |
| Nomo1 |
G |
T |
7: 45,690,904 (GRCm39) |
V97L |
probably damaging |
Het |
| Pcdhb11 |
G |
A |
18: 37,556,787 (GRCm39) |
V706I |
possibly damaging |
Het |
| Pkhd1 |
G |
A |
1: 20,282,082 (GRCm39) |
R2920C |
probably damaging |
Het |
| Prox2 |
T |
C |
12: 85,141,817 (GRCm39) |
T129A |
probably benign |
Het |
| Rgs18 |
T |
G |
1: 144,631,720 (GRCm39) |
I131L |
probably benign |
Het |
| Rnf19b |
G |
T |
4: 128,965,616 (GRCm39) |
C57F |
probably damaging |
Het |
| Rpl11 |
T |
C |
4: 135,778,522 (GRCm39) |
Y122C |
probably damaging |
Het |
| Sarnp |
A |
G |
10: 128,682,412 (GRCm39) |
K5R |
probably damaging |
Het |
| Scg2 |
A |
T |
1: 79,412,898 (GRCm39) |
H568Q |
probably damaging |
Het |
| Septin10 |
T |
C |
10: 59,019,417 (GRCm39) |
Y150C |
probably damaging |
Het |
| Slco1b2 |
A |
G |
6: 141,616,893 (GRCm39) |
T409A |
probably benign |
Het |
| Smco2 |
T |
A |
6: 146,772,674 (GRCm39) |
V292D |
possibly damaging |
Het |
| Smok3c |
A |
G |
5: 138,062,746 (GRCm39) |
M78V |
probably benign |
Het |
| Spag16 |
C |
A |
1: 69,883,455 (GRCm39) |
F61L |
probably benign |
Het |
| Spata22 |
G |
A |
11: 73,236,585 (GRCm39) |
R297H |
probably damaging |
Het |
| Spata31d1e |
A |
G |
13: 59,889,571 (GRCm39) |
S750P |
probably damaging |
Het |
| Syt3 |
C |
A |
7: 44,045,368 (GRCm39) |
P536Q |
probably benign |
Het |
| Tmem117 |
A |
T |
15: 94,992,677 (GRCm39) |
M446L |
probably benign |
Het |
| Trim9 |
A |
C |
12: 70,393,892 (GRCm39) |
Y17* |
probably null |
Het |
| Tsga10 |
A |
G |
1: 37,846,163 (GRCm39) |
M321T |
probably benign |
Het |
| Ttc13 |
A |
G |
8: 125,402,016 (GRCm39) |
L657P |
probably damaging |
Het |
| Ubxn1 |
C |
T |
19: 8,851,588 (GRCm39) |
T207I |
probably benign |
Het |
| Vmn2r117 |
A |
T |
17: 23,678,851 (GRCm39) |
V791D |
probably damaging |
Het |
| Zfp616 |
A |
G |
11: 73,973,860 (GRCm39) |
D43G |
probably benign |
Het |
| Zfp952 |
A |
G |
17: 33,222,928 (GRCm39) |
H469R |
probably benign |
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 |
|
R0385:Vps54
|
UTSW |
11 |
21,256,381 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
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 |
|
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'- AAGTCAGTATGGAGCATACCTG -3'
(R):5'- CAGCACCTGCCACTTTACAG -3'
Sequencing Primer
(F):5'- AATCTCAGCACTTTGGAGGC -3'
(R):5'- ACTTTACAGGCTCTTCTCTGAG -3'
|
| Posted On |
2015-09-24 |
Incidental Mutation