Incidental Mutation 'R0582:Vps54'
ID |
56478 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps54
|
Ensembl Gene |
ENSMUSG00000020128 |
Gene Name |
VPS54 GARP complex subunit |
Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
MMRRC Submission |
038772-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.931)
|
Stock # |
R0582 (G1)
|
Quality Score |
134 |
Status
|
Validated
|
Chromosome |
11 |
Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to T
at 21250137 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Tyrosine
at position 508
(D508Y)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000105206
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
AlphaFold |
Q5SPW0 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000006221
AA Change: D520Y
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000006221 Gene: ENSMUSG00000020128 AA Change: D520Y
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 |
probably damaging
Transcript: ENSMUST00000109578
AA Change: D508Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000105206 Gene: ENSMUSG00000020128 AA Change: D508Y
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: ENSMUST00000120479
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000132017
AA Change: D358Y
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000116739 Gene: ENSMUSG00000020128 AA Change: D358Y
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
|
Meta Mutation Damage Score |
0.4790 |
Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.9%
- 10x: 97.4%
- 20x: 94.6%
|
Validation Efficiency |
100% (45/45) |
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: 40 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abcb5 |
A |
T |
12: 118,904,147 (GRCm39) |
M186K |
probably benign |
Het |
Afm |
T |
C |
5: 90,672,639 (GRCm39) |
|
probably benign |
Het |
Arfgef3 |
G |
A |
10: 18,487,038 (GRCm39) |
A1332V |
probably damaging |
Het |
Atp11a |
T |
C |
8: 12,881,214 (GRCm39) |
S451P |
probably benign |
Het |
Birc6 |
T |
A |
17: 74,950,332 (GRCm39) |
V3189E |
probably damaging |
Het |
Ccdc150 |
C |
T |
1: 54,368,670 (GRCm39) |
A626V |
probably benign |
Het |
Ccdc50 |
G |
A |
16: 27,263,409 (GRCm39) |
|
probably benign |
Het |
Cntln |
T |
C |
4: 84,802,978 (GRCm39) |
S93P |
probably damaging |
Het |
Ctnna2 |
C |
A |
6: 77,735,400 (GRCm39) |
V106L |
probably benign |
Het |
Ctnnal1 |
G |
C |
4: 56,813,228 (GRCm39) |
Q668E |
probably damaging |
Het |
Cyp1a2 |
G |
A |
9: 57,587,529 (GRCm39) |
|
probably benign |
Het |
Dnah8 |
A |
G |
17: 30,937,935 (GRCm39) |
D1604G |
probably benign |
Het |
Dscaml1 |
A |
T |
9: 45,579,562 (GRCm39) |
I370F |
possibly damaging |
Het |
Duxf4 |
A |
T |
10: 58,071,508 (GRCm39) |
S235R |
probably benign |
Het |
Ears2 |
T |
C |
7: 121,654,881 (GRCm39) |
E129G |
probably benign |
Het |
Igsf10 |
T |
C |
3: 59,227,188 (GRCm39) |
I2162V |
probably benign |
Het |
Ints9 |
C |
T |
14: 65,217,598 (GRCm39) |
P42S |
probably damaging |
Het |
Ipp |
T |
C |
4: 116,372,664 (GRCm39) |
L231S |
probably damaging |
Het |
Lyn |
T |
A |
4: 3,743,296 (GRCm39) |
L72Q |
probably damaging |
Het |
Nfe2l2 |
T |
A |
2: 75,507,112 (GRCm39) |
E329D |
probably damaging |
Het |
Or2h2c |
G |
C |
17: 37,422,347 (GRCm39) |
L176V |
probably benign |
Het |
Or52a24 |
G |
A |
7: 103,381,880 (GRCm39) |
C249Y |
possibly damaging |
Het |
Pdyn |
A |
C |
2: 129,531,658 (GRCm39) |
L44R |
probably damaging |
Het |
Pkd1l1 |
A |
G |
11: 8,881,699 (GRCm39) |
|
probably benign |
Het |
Prpf40a |
A |
T |
2: 53,035,704 (GRCm39) |
F695L |
probably damaging |
Het |
Rnf217 |
A |
G |
10: 31,484,763 (GRCm39) |
Y140H |
possibly damaging |
Het |
Sema6c |
C |
T |
3: 95,076,508 (GRCm39) |
R265C |
probably damaging |
Het |
Slc7a8 |
C |
A |
14: 54,995,901 (GRCm39) |
C167F |
probably damaging |
Het |
Snap47 |
A |
T |
11: 59,319,259 (GRCm39) |
L293* |
probably null |
Het |
Snx3 |
A |
T |
10: 42,409,276 (GRCm39) |
|
probably benign |
Het |
Sycp2l |
T |
A |
13: 41,291,431 (GRCm39) |
|
probably benign |
Het |
Taar3 |
A |
G |
10: 23,825,715 (GRCm39) |
Y87C |
probably damaging |
Het |
Tm4sf4 |
T |
C |
3: 57,341,278 (GRCm39) |
|
probably benign |
Het |
Tssc4 |
T |
C |
7: 142,624,246 (GRCm39) |
S185P |
probably damaging |
Het |
Ttc28 |
G |
T |
5: 111,331,162 (GRCm39) |
A430S |
probably damaging |
Het |
Ulbp3 |
G |
A |
10: 3,075,082 (GRCm39) |
|
noncoding transcript |
Het |
Vmn2r27 |
T |
C |
6: 124,201,249 (GRCm39) |
D236G |
probably benign |
Het |
Wdr53 |
G |
A |
16: 32,070,726 (GRCm39) |
V24M |
probably damaging |
Het |
Xirp2 |
T |
G |
2: 67,339,210 (GRCm39) |
L484V |
probably benign |
Het |
Zfyve26 |
T |
C |
12: 79,292,996 (GRCm39) |
D2051G |
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 |
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 |
|
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'- AAGCTGTAGTGAGCTTCCCTCTCC -3'
(R):5'- AGCTCCTCACCACTCTAAGATCCTG -3'
Sequencing Primer
(F):5'- CCTGTGTGACTGATTTTCACAAG -3'
(R):5'- ATAATCTCTATACCTCCTGGAGGAGC -3'
|
Posted On |
2013-07-11 |