Incidental Mutation 'IGL02071:Vps54'
| ID |
185824 |
| 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: 0.931)
|
| Stock # |
IGL02071
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
11 |
| Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 21225071 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Serine
at position 177
(N177S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000105206
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
| AlphaFold |
Q5SPW0 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000006221
AA Change: N189S
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: N189S
| 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 null
Transcript: ENSMUST00000109578
AA Change: N177S
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: N177S
| 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: ENSMUST00000118219
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000132017
AA Change: N63S
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: N63S
| 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
|
| 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: 39 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abat |
C |
T |
16: 8,400,676 (GRCm39) |
R92C |
probably damaging |
Het |
| Adam29 |
C |
A |
8: 56,324,589 (GRCm39) |
V622L |
possibly damaging |
Het |
| Bzw2 |
T |
C |
12: 36,157,502 (GRCm39) |
H321R |
probably benign |
Het |
| C2cd2 |
C |
T |
16: 97,671,432 (GRCm39) |
R489Q |
probably damaging |
Het |
| Cdh23 |
G |
A |
10: 60,359,339 (GRCm39) |
T253I |
possibly damaging |
Het |
| Col4a3 |
T |
G |
1: 82,638,608 (GRCm39) |
|
probably null |
Het |
| D630039A03Rik |
T |
C |
4: 57,910,309 (GRCm39) |
T168A |
possibly damaging |
Het |
| Dnajc19 |
A |
G |
3: 34,132,914 (GRCm39) |
L97P |
possibly damaging |
Het |
| Dpep2 |
A |
T |
8: 106,711,776 (GRCm39) |
H550Q |
probably benign |
Het |
| Dvl2 |
C |
A |
11: 69,895,626 (GRCm39) |
|
probably null |
Het |
| Fam234b |
A |
G |
6: 135,204,149 (GRCm39) |
|
probably null |
Het |
| Fxyd5 |
A |
G |
7: 30,739,613 (GRCm39) |
V32A |
possibly damaging |
Het |
| Itprid1 |
C |
A |
6: 55,944,710 (GRCm39) |
S477* |
probably null |
Het |
| Mak16 |
A |
T |
8: 31,650,557 (GRCm39) |
S251T |
probably benign |
Het |
| Med10 |
T |
C |
13: 69,963,747 (GRCm39) |
V116A |
probably benign |
Het |
| Mycbp2 |
G |
A |
14: 103,392,343 (GRCm39) |
R50* |
probably null |
Het |
| Nckap5 |
G |
A |
1: 125,909,305 (GRCm39) |
P272L |
probably damaging |
Het |
| Nf1 |
T |
A |
11: 79,334,947 (GRCm39) |
V933E |
possibly damaging |
Het |
| Nrxn2 |
T |
A |
19: 6,531,783 (GRCm39) |
V749E |
probably damaging |
Het |
| Or51e2 |
A |
C |
7: 102,391,355 (GRCm39) |
V285G |
probably damaging |
Het |
| Or5al1 |
C |
A |
2: 85,990,219 (GRCm39) |
R165L |
probably benign |
Het |
| Osbpl9 |
T |
C |
4: 108,929,176 (GRCm39) |
Y417C |
probably damaging |
Het |
| Otop1 |
G |
A |
5: 38,445,327 (GRCm39) |
A162T |
probably damaging |
Het |
| Patl1 |
C |
A |
19: 11,917,054 (GRCm39) |
P634T |
probably damaging |
Het |
| Ppl |
A |
T |
16: 4,930,936 (GRCm39) |
S28T |
probably benign |
Het |
| Prkar2b |
C |
T |
12: 32,013,016 (GRCm39) |
G367R |
probably damaging |
Het |
| Rbl2 |
G |
A |
8: 91,828,826 (GRCm39) |
V576I |
probably damaging |
Het |
| Rgl3 |
C |
T |
9: 21,899,559 (GRCm39) |
A53T |
probably benign |
Het |
| Rp1 |
T |
A |
1: 4,415,533 (GRCm39) |
I1860F |
possibly damaging |
Het |
| Sbno2 |
A |
T |
10: 79,896,475 (GRCm39) |
D877E |
probably damaging |
Het |
| Sectm1b |
C |
T |
11: 120,946,761 (GRCm39) |
V45I |
probably damaging |
Het |
| Sfmbt2 |
G |
A |
2: 10,582,763 (GRCm39) |
V741I |
probably benign |
Het |
| Sugt1 |
T |
A |
14: 79,847,723 (GRCm39) |
L191* |
probably null |
Het |
| Tcf21 |
A |
T |
10: 22,693,709 (GRCm39) |
V156E |
possibly damaging |
Het |
| Tep1 |
T |
A |
14: 51,071,506 (GRCm39) |
R2046S |
possibly damaging |
Het |
| Tmem181a |
T |
C |
17: 6,347,531 (GRCm39) |
F241S |
probably damaging |
Het |
| Traf6 |
G |
A |
2: 101,527,138 (GRCm39) |
C296Y |
probably benign |
Het |
| Trim40 |
A |
G |
17: 37,200,070 (GRCm39) |
S3P |
probably benign |
Het |
| Ttll2 |
A |
T |
17: 7,619,130 (GRCm39) |
Y266N |
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 |
|
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 |
2014-05-07 |
Incidental Mutation