Incidental Mutation 'R4049:Vps54'
ID |
314050 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps54
|
Ensembl Gene |
ENSMUSG00000020128 |
Gene Name |
VPS54 GARP complex subunit |
Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
MMRRC Submission |
041616-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.931)
|
Stock # |
R4049 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
11 |
Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to A
at 21250183 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Asparagine
at position 373
(T373N)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000116739
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
AlphaFold |
Q5SPW0 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000006221
AA Change: T535N
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
SMART Domains |
Protein: ENSMUSP00000006221 Gene: ENSMUSG00000020128 AA Change: T535N
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: T523N
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
SMART Domains |
Protein: ENSMUSP00000105206 Gene: ENSMUSG00000020128 AA Change: T523N
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 benign
Transcript: ENSMUST00000132017
AA Change: T373N
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
SMART Domains |
Protein: ENSMUSP00000116739 Gene: ENSMUSG00000020128 AA Change: T373N
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 |
0.0597 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 94.6%
|
Validation Efficiency |
100% (65/65) |
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: 65 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abcb5 |
T |
A |
12: 118,832,404 (GRCm39) |
E1190V |
probably damaging |
Het |
Arhgef10 |
A |
G |
8: 15,029,998 (GRCm39) |
T928A |
probably benign |
Het |
Arhgef10l |
T |
A |
4: 140,242,762 (GRCm39) |
I836F |
probably benign |
Het |
Blm |
T |
A |
7: 80,152,610 (GRCm39) |
T446S |
probably benign |
Het |
Ccdc63 |
T |
A |
5: 122,260,813 (GRCm39) |
Q237L |
probably damaging |
Het |
Ccn5 |
A |
G |
2: 163,670,904 (GRCm39) |
D137G |
probably damaging |
Het |
Cep57l1 |
G |
T |
10: 41,605,356 (GRCm39) |
R130S |
probably damaging |
Het |
Clstn2 |
T |
G |
9: 97,339,613 (GRCm39) |
E786A |
possibly damaging |
Het |
Col16a1 |
C |
T |
4: 129,962,545 (GRCm39) |
P540L |
probably damaging |
Het |
Csf2 |
A |
G |
11: 54,140,159 (GRCm39) |
F61L |
probably damaging |
Het |
Ctr9 |
C |
T |
7: 110,654,750 (GRCm39) |
R1094C |
unknown |
Het |
Cyp3a41a |
A |
G |
5: 145,650,350 (GRCm39) |
C98R |
probably damaging |
Het |
Dthd1 |
T |
A |
5: 62,984,508 (GRCm39) |
C404* |
probably null |
Het |
Egfem1 |
A |
C |
3: 29,740,880 (GRCm39) |
H518P |
probably benign |
Het |
Elf3 |
T |
C |
1: 135,182,015 (GRCm39) |
S369G |
probably benign |
Het |
Eml6 |
C |
T |
11: 29,788,577 (GRCm39) |
V503M |
probably damaging |
Het |
Enthd1 |
T |
C |
15: 80,444,240 (GRCm39) |
D105G |
probably damaging |
Het |
Eral1 |
A |
G |
11: 77,966,428 (GRCm39) |
L250P |
probably damaging |
Het |
Gdf15 |
A |
T |
8: 71,082,605 (GRCm39) |
M167K |
probably benign |
Het |
Ggps1 |
T |
C |
13: 14,228,284 (GRCm39) |
K300E |
probably benign |
Het |
Gm8074 |
G |
A |
9: 78,229,618 (GRCm39) |
|
noncoding transcript |
Het |
Herc3 |
A |
G |
6: 58,853,822 (GRCm39) |
I623V |
probably damaging |
Het |
Mad1l1 |
A |
G |
5: 140,118,571 (GRCm39) |
S457P |
probably damaging |
Het |
Map1lc3a |
G |
T |
2: 155,119,462 (GRCm39) |
V91F |
possibly damaging |
Het |
Map4k3 |
A |
G |
17: 80,913,394 (GRCm39) |
V617A |
probably benign |
Het |
Mov10l1 |
T |
A |
15: 88,879,235 (GRCm39) |
|
probably benign |
Het |
Mroh2a |
A |
G |
1: 88,186,386 (GRCm39) |
S64G |
probably benign |
Het |
Ncor1 |
G |
T |
11: 62,220,494 (GRCm39) |
|
probably null |
Het |
Nfe2 |
C |
T |
15: 103,159,364 (GRCm39) |
E36K |
possibly damaging |
Het |
Oprm1 |
G |
A |
10: 6,779,087 (GRCm39) |
V95I |
probably benign |
Het |
Or4a78 |
T |
C |
2: 89,498,006 (GRCm39) |
I75V |
probably benign |
Het |
Or4c107 |
A |
G |
2: 88,789,617 (GRCm39) |
K269R |
probably benign |
Het |
Or52d3 |
T |
C |
7: 104,229,575 (GRCm39) |
F241L |
probably benign |
Het |
Or5d46 |
T |
C |
2: 88,174,144 (GRCm39) |
|
probably null |
Het |
Pcdha9 |
T |
A |
18: 37,130,995 (GRCm39) |
H21Q |
probably benign |
Het |
Pcolce2 |
A |
T |
9: 95,520,808 (GRCm39) |
I62F |
probably damaging |
Het |
Pfpl |
T |
A |
19: 12,407,053 (GRCm39) |
C435S |
probably damaging |
Het |
Pkhd1l1 |
G |
A |
15: 44,361,953 (GRCm39) |
C542Y |
probably damaging |
Het |
Plekha5 |
T |
C |
6: 140,529,597 (GRCm39) |
S75P |
probably damaging |
Het |
Pphln1 |
C |
A |
15: 93,362,987 (GRCm39) |
A202E |
probably damaging |
Het |
Ppp1r1a |
A |
G |
15: 103,440,881 (GRCm39) |
L92P |
probably damaging |
Het |
Prokr2 |
T |
C |
2: 132,223,414 (GRCm39) |
T43A |
probably benign |
Het |
Rai14 |
T |
C |
15: 10,592,298 (GRCm39) |
N199S |
probably benign |
Het |
Rasgrp2 |
T |
C |
19: 6,454,757 (GRCm39) |
L199P |
probably damaging |
Het |
Rnf213 |
A |
C |
11: 119,373,274 (GRCm39) |
M4939L |
possibly damaging |
Het |
Slc23a2 |
C |
T |
2: 131,902,603 (GRCm39) |
R533Q |
probably benign |
Het |
Slc7a7 |
T |
C |
14: 54,610,548 (GRCm39) |
|
probably null |
Het |
Snrpd2 |
T |
A |
7: 18,885,232 (GRCm39) |
V31E |
probably damaging |
Het |
Spire1 |
G |
T |
18: 67,662,101 (GRCm39) |
|
probably null |
Het |
Srsf4 |
T |
C |
4: 131,627,854 (GRCm39) |
|
probably benign |
Het |
Tcf20 |
A |
G |
15: 82,737,630 (GRCm39) |
S1274P |
probably damaging |
Het |
Tcof1 |
C |
A |
18: 60,965,975 (GRCm39) |
A376S |
possibly damaging |
Het |
Thsd1 |
T |
A |
8: 22,733,180 (GRCm39) |
Y76N |
possibly damaging |
Het |
Timm44 |
A |
G |
8: 4,310,561 (GRCm39) |
V397A |
probably benign |
Het |
Tmc6 |
G |
A |
11: 117,669,087 (GRCm39) |
T89I |
possibly damaging |
Het |
Trbv31 |
C |
A |
6: 41,534,639 (GRCm39) |
C107F |
probably damaging |
Het |
Trim37 |
T |
A |
11: 87,031,429 (GRCm39) |
|
probably null |
Het |
Ttll5 |
T |
C |
12: 86,059,573 (GRCm39) |
V1226A |
probably benign |
Het |
Ube3b |
T |
C |
5: 114,550,931 (GRCm39) |
V865A |
probably benign |
Het |
Vmn2r86 |
A |
T |
10: 130,282,966 (GRCm39) |
M550K |
probably damaging |
Het |
Wdr64 |
T |
G |
1: 175,633,422 (GRCm39) |
I891S |
probably benign |
Het |
Zfhx4 |
C |
T |
3: 5,463,919 (GRCm39) |
S1384L |
probably damaging |
Het |
Zfp703 |
A |
G |
8: 27,469,113 (GRCm39) |
E259G |
possibly damaging |
Het |
Zfp933 |
T |
C |
4: 147,910,969 (GRCm39) |
H209R |
probably damaging |
Het |
Zfp980 |
A |
G |
4: 145,429,170 (GRCm39) |
H633R |
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 |
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'- TCCACAGTGTTGTTCTGTCAG -3'
(R):5'- TTCCATAGTGCTGAAGGGAGG -3'
Sequencing Primer
(F):5'- CTGTCAGTTCTTGAGAAAAGCC -3'
(R):5'- AGTCCTACTGCAGCAGAGCTATTG -3'
|
Posted On |
2015-04-30 |