Incidental Mutation 'IGL01398:Vps54'
ID |
79546 |
Institutional Source |
Australian Phenomics Network
(link to record)
|
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: 0.933)
|
Stock # |
IGL01398
|
Quality Score |
|
Status
|
|
Chromosome |
11 |
Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
Type of Mutation |
splice site |
DNA Base Change (assembly) |
A to G
at 21245403 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000116739
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
AlphaFold |
Q5SPW0 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000006221
|
SMART Domains |
Protein: ENSMUSP00000006221 Gene: ENSMUSG00000020128
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
|
SMART Domains |
Protein: ENSMUSP00000105206 Gene: ENSMUSG00000020128
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
|
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 |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000132146
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143932
|
Coding Region Coverage |
|
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: 28 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acap1 |
T |
C |
11: 69,772,548 (GRCm39) |
D521G |
probably damaging |
Het |
Apol11b |
G |
A |
15: 77,522,219 (GRCm39) |
T26M |
probably damaging |
Het |
Best2 |
T |
A |
8: 85,735,956 (GRCm39) |
Y326F |
probably damaging |
Het |
Clca3a1 |
T |
C |
3: 144,722,512 (GRCm39) |
T287A |
possibly damaging |
Het |
Cyp26a1 |
C |
T |
19: 37,686,395 (GRCm39) |
T13I |
probably damaging |
Het |
Dhcr7 |
T |
C |
7: 143,395,056 (GRCm39) |
S188P |
probably damaging |
Het |
Eml3 |
T |
G |
19: 8,911,598 (GRCm39) |
|
probably benign |
Het |
Faf1 |
A |
T |
4: 109,593,793 (GRCm39) |
I124F |
probably damaging |
Het |
Fkbp9 |
T |
A |
6: 56,837,790 (GRCm39) |
|
probably benign |
Het |
Foxq1 |
G |
A |
13: 31,743,434 (GRCm39) |
D179N |
probably damaging |
Het |
Frem1 |
C |
T |
4: 82,868,599 (GRCm39) |
V1443M |
possibly damaging |
Het |
Gpnmb |
T |
A |
6: 49,027,365 (GRCm39) |
M363K |
probably benign |
Het |
Grm3 |
T |
C |
5: 9,535,762 (GRCm39) |
|
probably benign |
Het |
Ints3 |
A |
G |
3: 90,300,130 (GRCm39) |
L929P |
probably damaging |
Het |
Myh11 |
T |
A |
16: 14,019,964 (GRCm39) |
I1823F |
probably damaging |
Het |
Nudt9 |
T |
C |
5: 104,212,979 (GRCm39) |
*351Q |
probably null |
Het |
Or2ak6 |
A |
T |
11: 58,592,593 (GRCm39) |
H22L |
probably benign |
Het |
Or4c107 |
C |
T |
2: 88,789,193 (GRCm39) |
P128S |
probably damaging |
Het |
Or8k38 |
A |
T |
2: 86,488,032 (GRCm39) |
F257I |
probably damaging |
Het |
Pgr15l |
C |
T |
X: 96,121,785 (GRCm39) |
T392I |
probably benign |
Het |
Sdk1 |
C |
A |
5: 141,923,332 (GRCm39) |
L318I |
probably benign |
Het |
Sult1c2 |
C |
A |
17: 54,269,180 (GRCm39) |
V279L |
possibly damaging |
Het |
Tek |
T |
C |
4: 94,738,014 (GRCm39) |
I688T |
probably damaging |
Het |
Telo2 |
A |
T |
17: 25,324,748 (GRCm39) |
D477E |
probably benign |
Het |
Ubr3 |
T |
A |
2: 69,789,997 (GRCm39) |
Y884N |
probably damaging |
Het |
Upf3a |
C |
A |
8: 13,836,221 (GRCm39) |
H92Q |
probably damaging |
Het |
Vmn2r51 |
C |
T |
7: 9,836,341 (GRCm39) |
E147K |
probably benign |
Het |
Zdhhc14 |
T |
C |
17: 5,762,738 (GRCm39) |
I214T |
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 |
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 |
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 |
|
|
Posted On |
2013-11-05 |