Incidental Mutation 'R8193:Vps54'
ID |
635303 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps54
|
Ensembl Gene |
ENSMUSG00000020128 |
Gene Name |
VPS54 GARP complex subunit |
Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
MMRRC Submission |
067616-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.931)
|
Stock # |
R8193 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
11 |
Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 21242045 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Phenylalanine to Leucine
at position 387
(F387L)
|
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 benign
Transcript: ENSMUST00000006221
AA Change: F387L
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
SMART Domains |
Protein: ENSMUSP00000006221 Gene: ENSMUSG00000020128 AA Change: F387L
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 benign
Transcript: ENSMUST00000109578
AA Change: F375L
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
SMART Domains |
Protein: ENSMUSP00000105206 Gene: ENSMUSG00000020128 AA Change: F375L
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 benign
Transcript: ENSMUST00000132017
|
SMART Domains |
Protein: ENSMUSP00000116739 Gene: ENSMUSG00000020128
Domain | Start | End | E-Value | Type |
Pfam:DUF2450
|
72 |
238 |
1.4e-12 |
PFAM |
Pfam:Vps54
|
573 |
707 |
7.8e-64 |
PFAM |
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.5%
- 20x: 98.4%
|
Validation Efficiency |
98% (62/63) |
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: 63 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700006A11Rik |
A |
T |
3: 124,213,517 (GRCm39) |
V48E |
possibly damaging |
Het |
4930522H14Rik |
A |
G |
4: 109,381,529 (GRCm39) |
L83S |
probably benign |
Het |
Abhd18 |
C |
A |
3: 40,884,660 (GRCm39) |
T233K |
probably benign |
Het |
Adam26a |
A |
T |
8: 44,022,273 (GRCm39) |
C406S |
probably damaging |
Het |
Anp32e |
G |
A |
3: 95,836,710 (GRCm39) |
|
probably benign |
Het |
Cd33 |
C |
T |
7: 43,181,696 (GRCm39) |
A155T |
possibly damaging |
Het |
Cdc25c |
A |
T |
18: 34,882,675 (GRCm39) |
|
probably null |
Het |
Cep350 |
A |
G |
1: 155,737,825 (GRCm39) |
S2673P |
probably benign |
Het |
Chodl |
T |
C |
16: 78,738,412 (GRCm39) |
S127P |
probably damaging |
Het |
Clstn2 |
A |
G |
9: 97,465,683 (GRCm39) |
S103P |
probably damaging |
Het |
Crocc2 |
T |
A |
1: 93,117,888 (GRCm39) |
|
probably null |
Het |
Cyp24a1 |
A |
G |
2: 170,327,622 (GRCm39) |
L507P |
probably damaging |
Het |
Dcbld2 |
T |
A |
16: 58,284,373 (GRCm39) |
|
probably null |
Het |
Dnah14 |
T |
C |
1: 181,515,770 (GRCm39) |
Y1991H |
probably damaging |
Het |
Dnajb8 |
C |
T |
6: 88,199,940 (GRCm39) |
R159C |
possibly damaging |
Het |
Edrf1 |
C |
T |
7: 133,263,606 (GRCm39) |
T971I |
possibly damaging |
Het |
Ermap |
A |
G |
4: 119,041,140 (GRCm39) |
I290T |
possibly damaging |
Het |
Eva1a |
A |
T |
6: 82,068,921 (GRCm39) |
S83C |
probably benign |
Het |
Fcgbp |
A |
T |
7: 27,804,276 (GRCm39) |
N1795Y |
probably damaging |
Het |
Foxg1 |
A |
G |
12: 49,432,377 (GRCm39) |
H370R |
possibly damaging |
Het |
Gabra1 |
A |
G |
11: 42,037,968 (GRCm39) |
Y217H |
probably damaging |
Het |
Gm3086 |
A |
G |
12: 70,016,264 (GRCm39) |
N62S |
noncoding transcript |
Het |
Hmcn1 |
A |
T |
1: 150,453,228 (GRCm39) |
Y5362* |
probably null |
Het |
Igkv5-37 |
C |
A |
6: 69,940,796 (GRCm39) |
|
probably benign |
Het |
Ints3 |
A |
G |
3: 90,307,929 (GRCm39) |
V647A |
possibly damaging |
Het |
Itga1 |
A |
G |
13: 115,104,991 (GRCm39) |
|
probably null |
Het |
Limk2 |
T |
C |
11: 3,297,691 (GRCm39) |
K481E |
possibly damaging |
Het |
Lonp2 |
G |
T |
8: 87,358,091 (GRCm39) |
G104V |
probably damaging |
Het |
Lpar5 |
T |
C |
6: 125,058,302 (GRCm39) |
S8P |
probably benign |
Het |
Map2k7 |
T |
C |
8: 4,294,059 (GRCm39) |
F202L |
probably benign |
Het |
Mark1 |
T |
G |
1: 184,660,249 (GRCm39) |
M136L |
probably damaging |
Het |
Myo15b |
T |
C |
11: 115,775,973 (GRCm39) |
S590P |
probably damaging |
Het |
Nbas |
T |
C |
12: 13,483,010 (GRCm39) |
V1429A |
probably damaging |
Het |
Nbeal1 |
T |
A |
1: 60,292,640 (GRCm39) |
Y1097* |
probably null |
Het |
Ncf4 |
T |
C |
15: 78,146,466 (GRCm39) |
S299P |
probably damaging |
Het |
Nfkbiz |
T |
C |
16: 55,642,214 (GRCm39) |
D68G |
probably damaging |
Het |
Nomo1 |
T |
C |
7: 45,692,037 (GRCm39) |
S154P |
possibly damaging |
Het |
Nrp1 |
G |
T |
8: 129,187,187 (GRCm39) |
W411L |
probably damaging |
Het |
Or10d1b |
T |
C |
9: 39,613,498 (GRCm39) |
D189G |
possibly damaging |
Het |
Or4c105 |
T |
A |
2: 88,647,803 (GRCm39) |
M96K |
probably damaging |
Het |
Or5t18 |
T |
G |
2: 86,637,209 (GRCm39) |
I45L |
noncoding transcript |
Het |
Or8g2b |
T |
C |
9: 39,750,757 (GRCm39) |
I9T |
probably benign |
Het |
Or9g4b |
T |
C |
2: 85,616,305 (GRCm39) |
V150A |
probably benign |
Het |
Pcsk5 |
A |
G |
19: 17,563,415 (GRCm39) |
V574A |
possibly damaging |
Het |
Prex1 |
C |
A |
2: 166,435,780 (GRCm39) |
R589L |
possibly damaging |
Het |
Prl7d1 |
A |
G |
13: 27,893,230 (GRCm39) |
V227A |
|
Het |
Prpf40b |
T |
A |
15: 99,201,949 (GRCm39) |
F16I |
unknown |
Het |
Rasa2 |
G |
A |
9: 96,484,791 (GRCm39) |
P141L |
probably damaging |
Het |
Rtl1 |
A |
G |
12: 109,558,650 (GRCm39) |
V1063A |
probably benign |
Het |
Sema4d |
A |
T |
13: 51,859,192 (GRCm39) |
C512* |
probably null |
Het |
Slc19a2 |
A |
G |
1: 164,084,794 (GRCm39) |
N228S |
probably benign |
Het |
Tcf4 |
A |
T |
18: 69,633,994 (GRCm39) |
|
probably benign |
Het |
Tnks2 |
T |
C |
19: 36,832,353 (GRCm39) |
V264A |
possibly damaging |
Het |
Ugt2b35 |
T |
A |
5: 87,149,302 (GRCm39) |
S184R |
probably damaging |
Het |
Usp53 |
T |
C |
3: 122,741,012 (GRCm39) |
E746G |
probably benign |
Het |
Utp18 |
T |
C |
11: 93,766,903 (GRCm39) |
D268G |
probably damaging |
Het |
Vmn1r172 |
T |
A |
7: 23,359,752 (GRCm39) |
Y212* |
probably null |
Het |
Vmn2r100 |
T |
A |
17: 19,725,102 (GRCm39) |
C10* |
probably null |
Het |
Vmn2r113 |
G |
T |
17: 23,164,501 (GRCm39) |
V135F |
probably benign |
Het |
Xab2 |
A |
C |
8: 3,663,389 (GRCm39) |
D450E |
probably benign |
Het |
Zfp408 |
G |
T |
2: 91,475,361 (GRCm39) |
R598S |
probably benign |
Het |
Zfp788 |
T |
A |
7: 41,298,038 (GRCm39) |
C225S |
probably benign |
Het |
Zfp944 |
T |
A |
17: 22,558,861 (GRCm39) |
K129* |
probably null |
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 |
R8011:Vps54
|
UTSW |
11 |
21,225,095 (GRCm39) |
missense |
probably damaging |
0.99 |
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'- TGGGAGGGGTCACATCATAC -3'
(R):5'- AAAGTAGTGGTCCTGGCTGC -3'
Sequencing Primer
(F):5'- GGGTCACATCATACTTCTGGAAGC -3'
(R):5'- TGACCAAGTATTACTATTATGCTGC -3'
|
Posted On |
2020-07-13 |