Incidental Mutation 'R5061:Vps54'
ID |
386629 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps54
|
Ensembl Gene |
ENSMUSG00000020128 |
Gene Name |
VPS54 GARP complex subunit |
Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
MMRRC Submission |
042651-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.931)
|
Stock # |
R5061 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
11 |
Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
Type of Mutation |
utr 3 prime |
DNA Base Change (assembly) |
G to A
at 21269881 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000116739
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000060895]
[ENSMUST00000102875]
[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: ENSMUST00000060895
|
SMART Domains |
Protein: ENSMUSP00000056324 Gene: ENSMUSG00000001891
Domain | Start | End | E-Value | Type |
low complexity region
|
14 |
29 |
N/A |
INTRINSIC |
Pfam:UDPGP
|
43 |
462 |
2.1e-197 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000102875
|
SMART Domains |
Protein: ENSMUSP00000099939 Gene: ENSMUSG00000001891
Domain | Start | End | E-Value | Type |
low complexity region
|
25 |
40 |
N/A |
INTRINSIC |
Pfam:UDPGP
|
55 |
473 |
3.5e-201 |
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 |
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: ENSMUST00000133343
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143890
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153159
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153411
|
Meta Mutation Damage Score |
0.0898 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 93.7%
|
Validation Efficiency |
100% (71/71) |
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: 69 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700009N14Rik |
A |
G |
4: 39,450,953 (GRCm39) |
H53R |
probably benign |
Het |
Abcg1 |
A |
G |
17: 31,311,366 (GRCm39) |
K124E |
probably damaging |
Het |
Acot4 |
G |
T |
12: 84,085,475 (GRCm39) |
R64L |
probably benign |
Het |
Adam22 |
G |
C |
5: 8,230,238 (GRCm39) |
|
probably benign |
Het |
Add2 |
G |
A |
6: 86,064,029 (GRCm39) |
|
probably null |
Het |
Adgrb3 |
G |
A |
1: 25,107,209 (GRCm39) |
|
probably benign |
Het |
Akap8l |
T |
G |
17: 32,551,868 (GRCm39) |
K441T |
probably damaging |
Het |
Aspn |
T |
A |
13: 49,720,080 (GRCm39) |
S365R |
probably damaging |
Het |
Atxn1 |
T |
G |
13: 45,710,569 (GRCm39) |
K788Q |
probably damaging |
Het |
Atxn2l |
G |
T |
7: 126,099,375 (GRCm39) |
H135N |
probably damaging |
Het |
Borcs8 |
T |
G |
8: 70,593,008 (GRCm39) |
|
probably null |
Het |
Col5a1 |
G |
A |
2: 27,842,390 (GRCm39) |
D422N |
unknown |
Het |
Cstad |
A |
T |
2: 30,498,275 (GRCm39) |
T37S |
unknown |
Het |
Dgkq |
A |
T |
5: 108,801,989 (GRCm39) |
D455E |
probably benign |
Het |
Dop1a |
T |
C |
9: 86,385,161 (GRCm39) |
|
probably benign |
Het |
Ebf3 |
T |
C |
7: 136,915,288 (GRCm39) |
I84V |
possibly damaging |
Het |
Ehmt2 |
C |
T |
17: 35,118,067 (GRCm39) |
R40* |
probably null |
Het |
Eif3e |
A |
T |
15: 43,115,657 (GRCm39) |
W370R |
probably damaging |
Het |
Eya3 |
T |
A |
4: 132,431,689 (GRCm39) |
D323E |
probably damaging |
Het |
F5 |
T |
C |
1: 164,021,749 (GRCm39) |
L1408P |
probably benign |
Het |
Fam110d |
T |
C |
4: 133,979,041 (GRCm39) |
T146A |
probably benign |
Het |
Gfod1 |
C |
T |
13: 43,353,992 (GRCm39) |
G328S |
probably benign |
Het |
Gja1 |
T |
A |
10: 56,263,752 (GRCm39) |
L37Q |
probably damaging |
Het |
Gm10650 |
T |
A |
3: 127,833,666 (GRCm39) |
|
noncoding transcript |
Het |
Gm14226 |
T |
A |
2: 154,867,106 (GRCm39) |
H354Q |
probably benign |
Het |
Gm15056 |
T |
C |
8: 21,390,758 (GRCm39) |
T60A |
probably benign |
Het |
Hsd11b1 |
A |
T |
1: 192,924,553 (GRCm39) |
N6K |
probably benign |
Het |
Ighv1-36 |
T |
C |
12: 114,843,742 (GRCm39) |
I39M |
probably benign |
Het |
Igkv4-80 |
A |
C |
6: 68,993,649 (GRCm39) |
S81A |
probably benign |
Het |
Kdm7a |
G |
A |
6: 39,128,386 (GRCm39) |
P482S |
possibly damaging |
Het |
Lama5 |
C |
A |
2: 179,840,579 (GRCm39) |
E607* |
probably null |
Het |
Lao1 |
T |
A |
4: 118,824,673 (GRCm39) |
S252T |
probably benign |
Het |
Lrp12 |
A |
G |
15: 39,741,650 (GRCm39) |
F355S |
probably damaging |
Het |
Mlycd |
T |
C |
8: 120,137,043 (GRCm39) |
F421S |
probably damaging |
Het |
Nectin3 |
T |
C |
16: 46,268,812 (GRCm39) |
E530G |
probably benign |
Het |
Nifk |
T |
C |
1: 118,260,669 (GRCm39) |
*270R |
probably null |
Het |
Ocln |
T |
C |
13: 100,676,106 (GRCm39) |
Y129C |
probably damaging |
Het |
Or10ag60 |
C |
T |
2: 87,438,176 (GRCm39) |
T148I |
probably benign |
Het |
Or4f54 |
T |
A |
2: 111,122,832 (GRCm39) |
L73H |
probably damaging |
Het |
Or52l1 |
T |
A |
7: 104,829,864 (GRCm39) |
I219F |
possibly damaging |
Het |
Or5b117 |
A |
T |
19: 13,431,349 (GRCm39) |
C177* |
probably null |
Het |
Otx1 |
C |
A |
11: 21,947,037 (GRCm39) |
A91S |
probably damaging |
Het |
Pcdhb22 |
G |
T |
18: 37,652,179 (GRCm39) |
G216C |
probably damaging |
Het |
Ppcs |
T |
C |
4: 119,276,412 (GRCm39) |
K58E |
probably damaging |
Het |
Prss38 |
T |
C |
11: 59,265,196 (GRCm39) |
T123A |
probably damaging |
Het |
Rap1gap |
T |
A |
4: 137,447,744 (GRCm39) |
|
probably null |
Het |
Rbm18 |
A |
G |
2: 36,017,217 (GRCm39) |
F54L |
possibly damaging |
Het |
Rwdd3 |
G |
A |
3: 120,953,432 (GRCm39) |
|
probably benign |
Het |
Ryr2 |
T |
C |
13: 11,650,422 (GRCm39) |
K138E |
possibly damaging |
Het |
Sec24a |
T |
C |
11: 51,604,359 (GRCm39) |
|
probably null |
Het |
Serpinb10 |
A |
G |
1: 107,468,701 (GRCm39) |
T115A |
probably benign |
Het |
Slco1a8 |
T |
A |
6: 141,954,414 (GRCm39) |
M20L |
probably benign |
Het |
Slx4ip |
T |
G |
2: 136,885,930 (GRCm39) |
F83L |
probably damaging |
Het |
St3gal1 |
A |
T |
15: 66,980,078 (GRCm39) |
S274T |
probably benign |
Het |
Stab1 |
A |
C |
14: 30,885,056 (GRCm39) |
C121W |
probably damaging |
Het |
Stab2 |
A |
G |
10: 86,743,249 (GRCm39) |
L1149P |
probably damaging |
Het |
Svil |
T |
G |
18: 5,048,954 (GRCm39) |
I77R |
probably benign |
Het |
Tbk1 |
T |
G |
10: 121,412,241 (GRCm39) |
E47A |
possibly damaging |
Het |
Tert |
C |
T |
13: 73,782,397 (GRCm39) |
T557I |
probably damaging |
Het |
Tfap2c |
A |
G |
2: 172,393,947 (GRCm39) |
D252G |
probably damaging |
Het |
Tll1 |
C |
A |
8: 64,506,983 (GRCm39) |
C586F |
probably damaging |
Het |
Tln2 |
T |
G |
9: 67,261,750 (GRCm39) |
N663T |
probably benign |
Het |
Tmem245 |
T |
A |
4: 56,946,945 (GRCm39) |
Y156F |
possibly damaging |
Het |
Uhrf1 |
G |
T |
17: 56,627,542 (GRCm39) |
|
probably null |
Het |
Unc79 |
T |
A |
12: 103,134,700 (GRCm39) |
M2417K |
possibly damaging |
Het |
Ush2a |
T |
C |
1: 188,689,471 (GRCm39) |
V5011A |
probably benign |
Het |
Virma |
T |
C |
4: 11,494,840 (GRCm39) |
V47A |
possibly damaging |
Het |
Vmn2r53 |
A |
C |
7: 12,315,741 (GRCm39) |
S693A |
probably benign |
Het |
Znfx1 |
T |
C |
2: 166,907,318 (GRCm39) |
|
probably benign |
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 |
R4772:Vps54
|
UTSW |
11 |
21,262,952 (GRCm39) |
missense |
probably damaging |
1.00 |
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'- TCATCCCTAGCAATTCTGGATC -3'
(R):5'- TACTCAGGGATGCACAGAATG -3'
Sequencing Primer
(F):5'- CGTTGTTCCTTTACTATCAGAAGAG -3'
(R):5'- GATGCACAGAATGGCTTTCTC -3'
|
Posted On |
2016-06-06 |