Incidental Mutation 'R8011:Vps54'
| ID |
616917 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
046051-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.933)
|
| Stock # |
R8011 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 21225095 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Leucine
at position 197
(R197L)
|
| 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 |
probably damaging
Transcript: ENSMUST00000006221
AA Change: R197L
PolyPhen 2
Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: R197L
| 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: R185L
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: R185L
| 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 |
probably damaging
Transcript: ENSMUST00000132017
AA Change: R71L
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: R71L
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF2450
|
72 |
238 |
1.4e-12 |
PFAM |
|
Pfam:Vps54
|
573 |
707 |
7.8e-64 |
PFAM |
|
| Meta Mutation Damage Score |
0.1162 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.4%
|
| Validation Efficiency |
100% (46/46) |
| 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: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2010315B03Rik |
C |
T |
9: 124,056,529 (GRCm39) |
E132K |
|
Het |
| Acss2 |
T |
C |
2: 155,397,877 (GRCm39) |
I313T |
possibly damaging |
Het |
| Akap13 |
G |
A |
7: 75,380,213 (GRCm39) |
R462H |
probably damaging |
Het |
| Ankrd27 |
T |
C |
7: 35,316,306 (GRCm39) |
V524A |
probably benign |
Het |
| Cacna1e |
T |
C |
1: 154,341,568 (GRCm39) |
I1209V |
probably benign |
Het |
| Cntn3 |
A |
T |
6: 102,414,860 (GRCm39) |
I29N |
possibly damaging |
Het |
| Col5a1 |
G |
A |
2: 27,870,533 (GRCm39) |
|
probably benign |
Het |
| Cttnbp2 |
G |
C |
6: 18,426,092 (GRCm39) |
A762G |
possibly damaging |
Het |
| Edc3 |
C |
A |
9: 57,620,659 (GRCm39) |
|
probably benign |
Het |
| Egflam |
A |
T |
15: 7,276,525 (GRCm39) |
M547K |
possibly damaging |
Het |
| Fgr |
T |
C |
4: 132,725,790 (GRCm39) |
Y400H |
probably damaging |
Het |
| Gaa |
C |
T |
11: 119,163,762 (GRCm39) |
P205S |
probably benign |
Het |
| Gpr6 |
T |
A |
10: 40,946,911 (GRCm39) |
T224S |
probably benign |
Het |
| Hes3 |
T |
C |
4: 152,371,938 (GRCm39) |
|
probably benign |
Het |
| Hydin |
T |
C |
8: 111,310,541 (GRCm39) |
F4079S |
probably damaging |
Het |
| Igf2bp2 |
A |
T |
16: 21,894,849 (GRCm39) |
I366N |
probably damaging |
Het |
| Kmt2c |
A |
G |
5: 25,556,232 (GRCm39) |
V1171A |
probably damaging |
Het |
| Kndc1 |
T |
A |
7: 139,490,536 (GRCm39) |
F346Y |
possibly damaging |
Het |
| Lpin2 |
G |
A |
17: 71,537,370 (GRCm39) |
G306R |
probably benign |
Het |
| Mok |
T |
C |
12: 110,781,351 (GRCm39) |
|
probably benign |
Het |
| Nolc1 |
T |
C |
19: 46,070,023 (GRCm39) |
V265A |
unknown |
Het |
| Ogfr |
GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG |
GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG |
2: 180,237,059 (GRCm39) |
|
probably benign |
Het |
| Or2ah1 |
T |
G |
2: 85,653,957 (GRCm39) |
L214R |
possibly damaging |
Het |
| Or4c103 |
G |
A |
2: 88,513,537 (GRCm39) |
Q180* |
probably null |
Het |
| Or5j1 |
A |
C |
2: 86,879,190 (GRCm39) |
L130R |
probably damaging |
Het |
| Or6b2b |
A |
G |
1: 92,418,997 (GRCm39) |
V160A |
possibly damaging |
Het |
| Parp14 |
G |
A |
16: 35,677,004 (GRCm39) |
T988I |
probably benign |
Het |
| Pdk1 |
A |
T |
2: 71,705,796 (GRCm39) |
Q81H |
probably benign |
Het |
| Plekha6 |
A |
G |
1: 133,191,544 (GRCm39) |
T38A |
probably benign |
Het |
| Pou2f1 |
A |
G |
1: 165,722,472 (GRCm39) |
|
probably null |
Het |
| Rgs6 |
A |
G |
12: 83,163,066 (GRCm39) |
D424G |
probably null |
Het |
| Rnf13 |
T |
G |
3: 57,714,491 (GRCm39) |
Y183* |
probably null |
Het |
| Ryr2 |
A |
T |
13: 11,603,026 (GRCm39) |
|
probably null |
Het |
| Serpinb7 |
T |
A |
1: 107,362,487 (GRCm39) |
S64T |
possibly damaging |
Het |
| Six2 |
T |
C |
17: 85,995,100 (GRCm39) |
E94G |
probably damaging |
Het |
| Slc44a5 |
A |
G |
3: 153,953,447 (GRCm39) |
I276M |
possibly damaging |
Het |
| Smco2 |
A |
G |
6: 146,769,633 (GRCm39) |
Y239C |
probably damaging |
Het |
| Ssx2ip |
T |
C |
3: 146,128,666 (GRCm39) |
S148P |
probably damaging |
Het |
| Tiam2 |
T |
C |
17: 3,498,671 (GRCm39) |
Y816H |
possibly damaging |
Het |
| Tnk2 |
C |
T |
16: 32,487,183 (GRCm39) |
R127C |
probably benign |
Het |
| Tpd52l1 |
T |
C |
10: 31,208,913 (GRCm39) |
N185S |
probably benign |
Het |
| Try5 |
T |
C |
6: 41,290,421 (GRCm39) |
D21G |
probably benign |
Het |
| Vmn2r20 |
A |
G |
6: 123,373,369 (GRCm39) |
V491A |
possibly damaging |
Het |
| Xkr5 |
G |
T |
8: 18,998,736 (GRCm39) |
Y27* |
probably null |
Het |
| Zfp1004 |
A |
G |
2: 150,034,266 (GRCm39) |
S196G |
possibly damaging |
Het |
| Zfp626 |
T |
A |
7: 27,518,140 (GRCm39) |
C374S |
possibly 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 |
|
|
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 |
|
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'- TTGCCTTTTACATTCAAGATCCAAG -3'
(R):5'- TCAGGGTTAACTATGAGTGGCAAC -3'
Sequencing Primer
(F):5'- ATCCAAGTTAATTTTGTTTCATGGTC -3'
(R):5'- ACTTGACCTGCTATGGATGAAGCC -3'
|
| Posted On |
2020-01-23 |
Incidental Mutation