Incidental Mutation 'R0602:Vps54'
ID |
55500 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps54
|
Ensembl Gene |
ENSMUSG00000020128 |
Gene Name |
VPS54 GARP complex subunit |
Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
MMRRC Submission |
038791-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.931)
|
Stock # |
R0602 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
11 |
Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 21256434 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Isoleucine to Methionine
at position 634
(I634M)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000105206
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
AlphaFold |
Q5SPW0 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000006221
AA Change: I646M
PolyPhen 2
Score 0.880 (Sensitivity: 0.82; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000006221 Gene: ENSMUSG00000020128 AA Change: I646M
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: I634M
PolyPhen 2
Score 0.921 (Sensitivity: 0.81; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000105206 Gene: ENSMUSG00000020128 AA Change: I634M
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: I484M
PolyPhen 2
Score 0.871 (Sensitivity: 0.83; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000116739 Gene: ENSMUSG00000020128 AA Change: I484M
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 |
0.1795 |
Coding Region Coverage |
- 1x: 99.6%
- 3x: 99.1%
- 10x: 97.5%
- 20x: 94.7%
|
Validation Efficiency |
95% (58/61) |
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: 55 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
9430038I01Rik |
T |
C |
7: 136,978,090 (GRCm39) |
|
probably benign |
Het |
Arih1 |
A |
G |
9: 59,302,154 (GRCm39) |
|
probably benign |
Het |
Bcl9 |
T |
C |
3: 97,113,102 (GRCm39) |
I1118V |
probably benign |
Het |
Cap1 |
T |
C |
4: 122,766,202 (GRCm39) |
E12G |
probably damaging |
Het |
Ccdc168 |
T |
A |
1: 44,099,127 (GRCm39) |
K657I |
possibly damaging |
Het |
Ccr2 |
A |
G |
9: 123,906,658 (GRCm39) |
I313V |
probably benign |
Het |
Cd1d2 |
T |
C |
3: 86,895,110 (GRCm39) |
S161P |
probably benign |
Het |
Cd226 |
C |
T |
18: 89,287,135 (GRCm39) |
T311I |
probably benign |
Het |
Col25a1 |
A |
G |
3: 130,369,063 (GRCm39) |
|
probably null |
Het |
Cspg4 |
T |
C |
9: 56,795,301 (GRCm39) |
F1012S |
probably damaging |
Het |
Dnah7b |
A |
G |
1: 46,364,002 (GRCm39) |
M3541V |
probably damaging |
Het |
Erbb2 |
G |
A |
11: 98,325,097 (GRCm39) |
V852M |
probably damaging |
Het |
Fer1l6 |
A |
C |
15: 58,449,794 (GRCm39) |
T667P |
probably damaging |
Het |
Gal3st2c |
A |
G |
1: 93,936,901 (GRCm39) |
Y282C |
probably damaging |
Het |
Glp1r |
T |
C |
17: 31,128,201 (GRCm39) |
L60P |
probably benign |
Het |
Gtf2h2 |
A |
G |
13: 100,605,533 (GRCm39) |
V358A |
probably benign |
Het |
H2ac18 |
T |
C |
3: 96,152,866 (GRCm39) |
|
probably benign |
Het |
Hephl1 |
T |
A |
9: 15,000,347 (GRCm39) |
I302F |
probably damaging |
Het |
Lgi2 |
T |
C |
5: 52,711,765 (GRCm39) |
D185G |
probably damaging |
Het |
Lrtm1 |
T |
C |
14: 28,744,179 (GRCm39) |
|
probably benign |
Het |
Megf10 |
T |
G |
18: 57,395,172 (GRCm39) |
D511E |
probably damaging |
Het |
Myo5c |
A |
G |
9: 75,173,478 (GRCm39) |
|
probably null |
Het |
Nrbf2 |
G |
A |
10: 67,103,605 (GRCm39) |
T166M |
probably damaging |
Het |
Nrm |
C |
A |
17: 36,175,156 (GRCm39) |
Y61* |
probably null |
Het |
Ola1 |
A |
G |
2: 72,924,056 (GRCm39) |
Y368H |
probably damaging |
Het |
Or52s1 |
A |
C |
7: 102,861,787 (GRCm39) |
H229P |
possibly damaging |
Het |
Or9i1b |
A |
G |
19: 13,897,145 (GRCm39) |
T254A |
probably benign |
Het |
Or9q2 |
T |
C |
19: 13,772,026 (GRCm39) |
|
probably null |
Het |
Panx1 |
A |
G |
9: 14,921,500 (GRCm39) |
L125P |
probably damaging |
Het |
Pappa2 |
A |
G |
1: 158,590,625 (GRCm39) |
|
probably benign |
Het |
Parp6 |
A |
G |
9: 59,556,648 (GRCm39) |
|
probably benign |
Het |
Pomgnt2 |
A |
G |
9: 121,811,339 (GRCm39) |
Y481H |
probably benign |
Het |
Ppp4c |
A |
G |
7: 126,388,254 (GRCm39) |
|
probably benign |
Het |
Prl8a8 |
T |
A |
13: 27,692,533 (GRCm39) |
|
probably benign |
Het |
Prpf40b |
C |
A |
15: 99,202,352 (GRCm39) |
A70E |
unknown |
Het |
Ptgfr |
G |
A |
3: 151,540,839 (GRCm39) |
T223M |
probably damaging |
Het |
Ptprc |
C |
T |
1: 138,017,223 (GRCm39) |
|
probably benign |
Het |
Rgs22 |
T |
C |
15: 36,140,018 (GRCm39) |
|
probably benign |
Het |
Rpgrip1 |
A |
G |
14: 52,371,313 (GRCm39) |
E344G |
possibly damaging |
Het |
Sgca |
A |
T |
11: 94,854,061 (GRCm39) |
I383N |
possibly damaging |
Het |
Sgms2 |
T |
A |
3: 131,118,756 (GRCm39) |
|
probably null |
Het |
Slc9b1 |
C |
A |
3: 135,103,516 (GRCm39) |
Q549K |
probably benign |
Het |
Smc4 |
G |
C |
3: 68,916,871 (GRCm39) |
A187P |
probably damaging |
Het |
Smco1 |
A |
G |
16: 32,092,062 (GRCm39) |
S47G |
probably damaging |
Het |
Sobp |
T |
A |
10: 42,898,385 (GRCm39) |
E400V |
probably damaging |
Het |
Sp140l1 |
C |
G |
1: 85,077,226 (GRCm39) |
K113N |
probably benign |
Het |
Stil |
T |
A |
4: 114,881,620 (GRCm39) |
|
probably benign |
Het |
Sult3a2 |
A |
T |
10: 33,658,044 (GRCm39) |
M23K |
probably benign |
Het |
Syne2 |
AGAGTGAG |
AGAGTGAGTGAG |
12: 76,144,734 (GRCm39) |
|
probably null |
Het |
Tcam1 |
G |
A |
11: 106,174,904 (GRCm39) |
E120K |
probably benign |
Het |
Tcof1 |
C |
A |
18: 60,966,605 (GRCm39) |
G329W |
probably damaging |
Het |
Ttc13 |
A |
T |
8: 125,401,105 (GRCm39) |
S624T |
probably damaging |
Het |
Vmn1r171 |
G |
T |
7: 23,332,602 (GRCm39) |
V276L |
probably benign |
Het |
Vps13b |
T |
C |
15: 35,422,514 (GRCm39) |
L158P |
probably damaging |
Het |
Vwa8 |
T |
G |
14: 79,258,060 (GRCm39) |
S736R |
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 |
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'- TGGCCTGTGATCAACTACGTTTACC -3'
Sequencing Primer
(F):5'- GCTTTAGACATCTTCAGCTCTGTATG -3'
(R):5'- GTGATCAACTACGTTTACCCTTTAAC -3'
|
Posted On |
2013-07-11 |