Incidental Mutation 'R3801:Vps54'
ID |
272992 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps54
|
Ensembl Gene |
ENSMUSG00000020128 |
Gene Name |
VPS54 GARP complex subunit |
Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
MMRRC Submission |
040760-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.931)
|
Stock # |
R3801 (G1)
|
Quality Score |
219 |
Status
|
Not validated
|
Chromosome |
11 |
Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 21218832 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Aspartic acid to Glutamic Acid
at position 130
(D130E)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000105206
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
AlphaFold |
Q5SPW0 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000006221
AA Change: D142E
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
SMART Domains |
Protein: ENSMUSP00000006221 Gene: ENSMUSG00000020128 AA Change: D142E
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: D130E
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
SMART Domains |
Protein: ENSMUSP00000105206 Gene: ENSMUSG00000020128 AA Change: D130E
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
AA Change: D16E
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
SMART Domains |
Protein: ENSMUSP00000116739 Gene: ENSMUSG00000020128 AA Change: D16E
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: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.0%
|
Validation Efficiency |
|
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: 66 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700011L22Rik |
C |
T |
8: 79,974,922 (GRCm39) |
E54K |
probably benign |
Het |
Als2 |
A |
C |
1: 59,206,358 (GRCm39) |
M1634R |
probably damaging |
Het |
Ankfy1 |
T |
C |
11: 72,640,246 (GRCm39) |
S531P |
probably benign |
Het |
Atp6v1e1 |
A |
G |
6: 120,778,020 (GRCm39) |
Y172H |
probably benign |
Het |
Brd1 |
C |
T |
15: 88,601,243 (GRCm39) |
V464M |
probably damaging |
Het |
Btaf1 |
A |
T |
19: 36,963,948 (GRCm39) |
T840S |
probably benign |
Het |
Btaf1 |
A |
T |
19: 36,966,373 (GRCm39) |
H1047L |
probably benign |
Het |
Cacnb2 |
A |
G |
2: 14,829,074 (GRCm39) |
D3G |
possibly damaging |
Het |
Capn13 |
G |
A |
17: 73,646,396 (GRCm39) |
P339L |
probably benign |
Het |
Cgrrf1 |
G |
T |
14: 47,069,820 (GRCm39) |
G30C |
probably damaging |
Het |
Crnkl1 |
T |
C |
2: 145,761,715 (GRCm39) |
D614G |
probably benign |
Het |
Cyp2c23 |
C |
T |
19: 43,995,478 (GRCm39) |
V430I |
probably benign |
Het |
Dazl |
G |
A |
17: 50,588,309 (GRCm39) |
R289W |
probably benign |
Het |
Dsg1b |
C |
T |
18: 20,523,260 (GRCm39) |
P96S |
probably damaging |
Het |
Dusp14 |
A |
G |
11: 83,939,535 (GRCm39) |
S169P |
possibly damaging |
Het |
Egfem1 |
A |
G |
3: 29,206,075 (GRCm39) |
D91G |
probably benign |
Het |
Eif1 |
A |
G |
11: 100,211,650 (GRCm39) |
K95E |
probably damaging |
Het |
Fap |
C |
T |
2: 62,376,994 (GRCm39) |
V191I |
probably benign |
Het |
Flnc |
T |
C |
6: 29,447,403 (GRCm39) |
Y1069H |
probably damaging |
Het |
Fndc7 |
T |
C |
3: 108,776,464 (GRCm39) |
T526A |
possibly damaging |
Het |
Fras1 |
A |
T |
5: 96,881,791 (GRCm39) |
T2508S |
probably benign |
Het |
Gast |
T |
C |
11: 100,227,636 (GRCm39) |
S73P |
probably damaging |
Het |
Grap2 |
A |
G |
15: 80,507,947 (GRCm39) |
T4A |
possibly damaging |
Het |
Grm8 |
T |
G |
6: 28,125,635 (GRCm39) |
N164H |
possibly damaging |
Het |
Hyal5 |
A |
T |
6: 24,876,523 (GRCm39) |
H132L |
probably benign |
Het |
Iqcm |
C |
A |
8: 76,396,021 (GRCm39) |
T188K |
possibly damaging |
Het |
Kank4 |
A |
G |
4: 98,668,370 (GRCm39) |
S26P |
probably damaging |
Het |
Lipo3 |
C |
T |
19: 33,762,257 (GRCm39) |
C80Y |
probably damaging |
Het |
Lrrk2 |
A |
G |
15: 91,621,314 (GRCm39) |
R963G |
probably benign |
Het |
Lrtm2 |
G |
A |
6: 119,294,444 (GRCm39) |
T229I |
probably damaging |
Het |
Mb21d2 |
A |
T |
16: 28,646,755 (GRCm39) |
D406E |
possibly damaging |
Het |
Meikin |
T |
A |
11: 54,290,697 (GRCm39) |
|
probably null |
Het |
Mybl1 |
A |
T |
1: 9,743,439 (GRCm39) |
F538I |
probably damaging |
Het |
Nectin2 |
T |
C |
7: 19,451,561 (GRCm39) |
D491G |
probably benign |
Het |
Nf1 |
A |
G |
11: 79,450,347 (GRCm39) |
D511G |
probably null |
Het |
Nid2 |
T |
C |
14: 19,860,065 (GRCm39) |
C1328R |
probably damaging |
Het |
Nlrp1a |
T |
A |
11: 71,013,529 (GRCm39) |
M574L |
probably benign |
Het |
Nrap |
C |
T |
19: 56,310,211 (GRCm39) |
D1595N |
probably damaging |
Het |
Nrg3 |
G |
A |
14: 38,098,391 (GRCm39) |
P496S |
probably damaging |
Het |
Or4k41 |
A |
T |
2: 111,279,910 (GRCm39) |
I142F |
probably benign |
Het |
Pak3 |
G |
A |
X: 142,492,727 (GRCm39) |
V87I |
probably damaging |
Het |
Phf8 |
T |
C |
X: 150,355,572 (GRCm39) |
S512P |
possibly damaging |
Het |
Phkb |
G |
T |
8: 86,648,858 (GRCm39) |
E225* |
probably null |
Het |
Plaa |
T |
C |
4: 94,458,125 (GRCm39) |
D615G |
probably damaging |
Het |
Prdm12 |
A |
G |
2: 31,541,959 (GRCm39) |
K223E |
probably damaging |
Het |
Prkd1 |
C |
A |
12: 50,430,205 (GRCm39) |
R634L |
possibly damaging |
Het |
Rassf3 |
T |
A |
10: 121,250,271 (GRCm39) |
I181F |
possibly damaging |
Het |
Samd8 |
G |
A |
14: 21,825,133 (GRCm39) |
V30M |
probably damaging |
Het |
Sema4f |
A |
T |
6: 82,895,608 (GRCm39) |
H308Q |
possibly damaging |
Het |
Skint4 |
G |
T |
4: 111,975,378 (GRCm39) |
V113L |
probably damaging |
Het |
Slc16a10 |
G |
C |
10: 39,932,620 (GRCm39) |
H314D |
possibly damaging |
Het |
Slpi |
A |
G |
2: 164,198,158 (GRCm39) |
L12P |
probably damaging |
Het |
Smco1 |
A |
G |
16: 32,092,716 (GRCm39) |
Y129C |
probably benign |
Het |
Spag17 |
A |
G |
3: 99,961,169 (GRCm39) |
K985R |
possibly damaging |
Het |
Stc1 |
T |
C |
14: 69,275,924 (GRCm39) |
I239T |
probably benign |
Het |
Suclg2 |
A |
T |
6: 95,474,649 (GRCm39) |
I372N |
probably damaging |
Het |
Tmed4 |
C |
A |
11: 6,224,233 (GRCm39) |
V80F |
probably damaging |
Het |
Tnpo2 |
T |
A |
8: 85,781,800 (GRCm39) |
|
probably null |
Het |
Top1 |
A |
G |
2: 160,544,688 (GRCm39) |
H268R |
probably damaging |
Het |
Triobp |
A |
T |
15: 78,857,900 (GRCm39) |
Q1167L |
probably benign |
Het |
Txndc16 |
G |
A |
14: 45,388,809 (GRCm39) |
P536L |
possibly damaging |
Het |
Usp13 |
C |
T |
3: 32,935,657 (GRCm39) |
A360V |
possibly damaging |
Het |
Vhl |
G |
A |
6: 113,606,423 (GRCm39) |
V147I |
probably benign |
Het |
Vldlr |
A |
T |
19: 27,195,021 (GRCm39) |
T3S |
probably damaging |
Het |
Zfp808 |
T |
A |
13: 62,319,897 (GRCm39) |
H375Q |
probably damaging |
Het |
Zfp87 |
A |
T |
13: 67,669,334 (GRCm39) |
N37K |
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 |
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'- CCTCCATAATGGTATTTGGTTCTG -3'
(R):5'- CAGCCTAGCATACTAAGTTTCAATCC -3'
Sequencing Primer
(F):5'- GAACATTTTGATGCTTTGAGT -3'
(R):5'- GTTAAGCTATGCTTATTGTCTA -3'
|
Posted On |
2015-03-25 |