Incidental Mutation 'R4772:Vps54'
ID |
367622 |
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: 0.931)
|
Stock # |
R4772 (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 T
at 21262952 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Histidine to Tyrosine
at position 680
(H680Y)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000116739
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
AlphaFold |
Q5SPW0 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000006221
AA Change: H842Y
PolyPhen 2
Score 0.622 (Sensitivity: 0.87; Specificity: 0.91)
|
SMART Domains |
Protein: ENSMUSP00000006221 Gene: ENSMUSG00000020128 AA Change: H842Y
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: H830Y
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000105206 Gene: ENSMUSG00000020128 AA Change: H830Y
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: H680Y
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000116739 Gene: ENSMUSG00000020128 AA Change: H680Y
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: 99.1%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.1%
|
Validation Efficiency |
95% (74/78) |
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: 74 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca13 |
T |
A |
11: 9,265,339 (GRCm39) |
|
probably null |
Het |
Adamts19 |
A |
G |
18: 58,970,848 (GRCm39) |
Q144R |
possibly damaging |
Het |
Adgrb3 |
C |
A |
1: 25,570,956 (GRCm39) |
C507F |
probably damaging |
Het |
Atg9b |
T |
C |
5: 24,590,237 (GRCm39) |
*923W |
probably null |
Het |
Atp13a4 |
T |
C |
16: 29,239,653 (GRCm39) |
|
probably benign |
Het |
Baz2b |
G |
T |
2: 59,788,795 (GRCm39) |
R697S |
probably damaging |
Het |
Bicdl1 |
A |
G |
5: 115,799,537 (GRCm39) |
I184T |
probably benign |
Het |
Bpifb4 |
C |
T |
2: 153,784,903 (GRCm39) |
L204F |
possibly damaging |
Het |
Cep120 |
C |
T |
18: 53,851,561 (GRCm39) |
R577Q |
probably damaging |
Het |
Cplx4 |
T |
C |
18: 66,103,048 (GRCm39) |
E24G |
possibly damaging |
Het |
Dcxr |
T |
C |
11: 120,616,923 (GRCm39) |
T147A |
probably benign |
Het |
Dnajc10 |
C |
A |
2: 80,170,870 (GRCm39) |
H454N |
probably damaging |
Het |
Dsp |
G |
T |
13: 38,351,504 (GRCm39) |
G108* |
probably null |
Het |
Entpd6 |
T |
A |
2: 150,609,014 (GRCm39) |
I366K |
probably damaging |
Het |
Fam111a |
A |
G |
19: 12,565,057 (GRCm39) |
K269E |
probably benign |
Het |
Grid2ip |
T |
G |
5: 143,361,455 (GRCm39) |
V222G |
possibly damaging |
Het |
Hmcn2 |
T |
G |
2: 31,335,326 (GRCm39) |
V4421G |
probably benign |
Het |
Ifi207 |
T |
C |
1: 173,555,253 (GRCm39) |
T817A |
probably damaging |
Het |
Irak2 |
A |
T |
6: 113,670,683 (GRCm39) |
E533V |
probably damaging |
Het |
Katnip |
A |
G |
7: 125,464,523 (GRCm39) |
S1297G |
probably damaging |
Het |
Kbtbd6 |
T |
C |
14: 79,689,596 (GRCm39) |
F97S |
probably damaging |
Het |
Kctd14 |
A |
T |
7: 97,106,883 (GRCm39) |
E99V |
probably damaging |
Het |
Klhl10 |
A |
T |
11: 100,338,557 (GRCm39) |
Y432F |
probably benign |
Het |
Lrrc49 |
T |
C |
9: 60,592,335 (GRCm39) |
N53S |
possibly damaging |
Het |
Mief2 |
T |
A |
11: 60,621,288 (GRCm39) |
|
probably benign |
Het |
Mog |
A |
T |
17: 37,334,049 (GRCm39) |
S15T |
unknown |
Het |
Mpi |
T |
C |
9: 57,452,181 (GRCm39) |
D365G |
probably damaging |
Het |
Mpp7 |
A |
G |
18: 7,379,983 (GRCm39) |
|
probably null |
Het |
Nes |
A |
G |
3: 87,883,486 (GRCm39) |
T582A |
probably benign |
Het |
Nlrp14 |
A |
G |
7: 106,780,393 (GRCm39) |
D5G |
probably benign |
Het |
Nr1i3 |
C |
T |
1: 171,044,719 (GRCm39) |
T218I |
probably damaging |
Het |
Nup43 |
C |
T |
10: 7,554,433 (GRCm39) |
R339* |
probably null |
Het |
Nup58 |
T |
A |
14: 60,457,471 (GRCm39) |
R577S |
probably benign |
Het |
Olfr908 |
C |
T |
9: 38,427,897 (GRCm39) |
|
probably benign |
Het |
Or4l15 |
AAATTTGAA |
AAA |
14: 50,198,452 (GRCm39) |
|
probably benign |
Het |
Or52n4b |
T |
A |
7: 108,144,092 (GRCm39) |
M120K |
probably damaging |
Het |
Or5d35 |
T |
A |
2: 87,855,207 (GRCm39) |
I47K |
probably damaging |
Het |
Or6c38 |
A |
T |
10: 128,929,537 (GRCm39) |
V102D |
possibly damaging |
Het |
Or9g20 |
G |
A |
2: 85,630,338 (GRCm39) |
S92F |
probably damaging |
Het |
Orc1 |
T |
C |
4: 108,436,765 (GRCm39) |
|
probably benign |
Het |
Pax6 |
C |
A |
2: 105,526,847 (GRCm39) |
P251Q |
probably benign |
Het |
Phactr3 |
C |
T |
2: 177,925,729 (GRCm39) |
R330W |
probably damaging |
Het |
Phldb1 |
G |
A |
9: 44,622,324 (GRCm39) |
R81W |
probably damaging |
Het |
Pip5k1c |
C |
T |
10: 81,151,774 (GRCm39) |
P656L |
probably benign |
Het |
Pkn3 |
T |
G |
2: 29,974,692 (GRCm39) |
|
probably null |
Het |
Plcb2 |
T |
A |
2: 118,543,615 (GRCm39) |
H752L |
probably benign |
Het |
Plch1 |
G |
A |
3: 63,660,746 (GRCm39) |
T291M |
probably damaging |
Het |
Plekhg1 |
A |
T |
10: 3,823,127 (GRCm39) |
M32L |
probably benign |
Het |
Plekhg1 |
A |
T |
10: 3,823,130 (GRCm39) |
T33S |
probably damaging |
Het |
Plk4 |
A |
G |
3: 40,759,625 (GRCm39) |
T174A |
probably damaging |
Het |
Ppip5k2 |
C |
A |
1: 97,648,792 (GRCm39) |
|
probably benign |
Het |
Prl2a1 |
G |
A |
13: 27,988,961 (GRCm39) |
V29M |
probably benign |
Het |
R3hcc1l |
T |
C |
19: 42,571,996 (GRCm39) |
|
probably benign |
Het |
Rasa3 |
C |
T |
8: 13,648,289 (GRCm39) |
G125D |
probably damaging |
Het |
Sema3f |
A |
T |
9: 107,566,919 (GRCm39) |
Y136* |
probably null |
Het |
Slc13a5 |
T |
A |
11: 72,141,672 (GRCm39) |
|
probably null |
Het |
Slc16a1 |
T |
C |
3: 104,560,880 (GRCm39) |
V395A |
possibly damaging |
Het |
Sparcl1 |
C |
T |
5: 104,236,356 (GRCm39) |
A466T |
probably benign |
Het |
Srrm1 |
G |
A |
4: 135,069,690 (GRCm39) |
|
probably benign |
Het |
Styxl1 |
G |
A |
5: 135,797,755 (GRCm39) |
R50* |
probably null |
Het |
Tex264 |
T |
A |
9: 106,550,901 (GRCm39) |
I99F |
possibly damaging |
Het |
Tgtp2 |
T |
C |
11: 48,949,811 (GRCm39) |
T254A |
probably damaging |
Het |
Tmem245 |
A |
C |
4: 56,937,989 (GRCm39) |
|
probably null |
Het |
Tnik |
A |
T |
3: 28,661,359 (GRCm39) |
T587S |
probably benign |
Het |
Tpr |
T |
G |
1: 150,288,864 (GRCm39) |
S648A |
possibly damaging |
Het |
Ttn |
T |
C |
2: 76,596,313 (GRCm39) |
E18454G |
probably damaging |
Het |
Utp20 |
A |
C |
10: 88,645,797 (GRCm39) |
H527Q |
probably benign |
Het |
Vmn1r1 |
A |
T |
1: 181,985,111 (GRCm39) |
S185T |
probably benign |
Het |
Vwa5b2 |
A |
G |
16: 20,419,553 (GRCm39) |
|
probably null |
Het |
Wscd1 |
T |
C |
11: 71,662,802 (GRCm39) |
|
probably null |
Het |
Zbtb41 |
C |
T |
1: 139,375,152 (GRCm39) |
P871S |
probably damaging |
Het |
Zcchc4 |
T |
C |
5: 52,953,549 (GRCm39) |
L186P |
possibly damaging |
Het |
Zdhhc13 |
A |
G |
7: 48,449,621 (GRCm39) |
Y73C |
probably benign |
Het |
Zfp12 |
A |
G |
5: 143,225,755 (GRCm39) |
E21G |
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 |
|
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 |
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 |
|
Posted On |
2015-12-29 |