Incidental Mutation 'R7179:Vps54'
| ID |
558852 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
045269-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.931)
|
| Stock # |
R7179 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to G
at 21248791 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tryptophan to Glycine
at position 447
(W447G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000006221
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
| AlphaFold |
Q5SPW0 |
| PDB Structure |
C-terminal domain of Vps54 subunit of the GARP complex [X-RAY DIFFRACTION]
Vps54 C-terminal domain [X-RAY DIFFRACTION]
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000006221
AA Change: W447G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: W447G
| 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 damaging
Transcript: ENSMUST00000109578
AA Change: W435G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: W435G
| 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 damaging
Transcript: ENSMUST00000132017
AA Change: W285G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: W285G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF2450
|
72 |
238 |
1.4e-12 |
PFAM |
|
Pfam:Vps54
|
573 |
707 |
7.8e-64 |
PFAM |
|
| Meta Mutation Damage Score |
0.8470 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.5%
- 20x: 98.1%
|
| Validation Efficiency |
100% (76/76) |
| 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: 75 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acot13 |
A |
T |
13: 25,002,154 (GRCm39) |
I96K |
probably benign |
Het |
| Adam6a |
A |
G |
12: 113,509,291 (GRCm39) |
T555A |
probably benign |
Het |
| Alms1 |
C |
T |
6: 85,598,351 (GRCm39) |
P1059L |
probably benign |
Het |
| Apol7c |
T |
C |
15: 77,409,843 (GRCm39) |
T368A |
probably benign |
Het |
| Arfgef3 |
A |
T |
10: 18,475,015 (GRCm39) |
L1557Q |
probably damaging |
Het |
| Baz2a |
C |
T |
10: 127,960,326 (GRCm39) |
R1514W |
probably damaging |
Het |
| Bmp3 |
T |
A |
5: 99,020,622 (GRCm39) |
D348E |
probably damaging |
Het |
| Bves |
A |
G |
10: 45,230,913 (GRCm39) |
S295G |
probably damaging |
Het |
| Carmil1 |
A |
G |
13: 24,204,052 (GRCm39) |
C1328R |
probably benign |
Het |
| Ccnk |
T |
A |
12: 108,153,517 (GRCm39) |
Y93N |
probably damaging |
Het |
| Ccr1 |
A |
T |
9: 123,764,089 (GRCm39) |
V147D |
probably damaging |
Het |
| Cd24a |
G |
A |
10: 43,458,636 (GRCm39) |
G36S |
probably benign |
Het |
| Cep104 |
A |
G |
4: 154,077,324 (GRCm39) |
Y569C |
probably damaging |
Het |
| Chd2 |
A |
T |
7: 73,125,168 (GRCm39) |
I884N |
probably damaging |
Het |
| Cnst |
A |
T |
1: 179,406,947 (GRCm39) |
|
probably benign |
Het |
| Col22a1 |
A |
G |
15: 71,805,262 (GRCm39) |
L146P |
unknown |
Het |
| Col25a1 |
G |
T |
3: 130,323,768 (GRCm39) |
R321L |
probably damaging |
Het |
| Ctnnd2 |
T |
C |
15: 30,683,510 (GRCm39) |
Y504H |
possibly damaging |
Het |
| D3Ertd751e |
C |
A |
3: 41,703,143 (GRCm39) |
Q73K |
probably damaging |
Het |
| Dsc2 |
C |
T |
18: 20,168,332 (GRCm39) |
|
probably null |
Het |
| Eya1 |
A |
T |
1: 14,373,076 (GRCm39) |
S14R |
probably damaging |
Het |
| Fam131c |
A |
T |
4: 141,110,328 (GRCm39) |
|
probably null |
Het |
| Flvcr2 |
T |
C |
12: 85,793,965 (GRCm39) |
F114L |
possibly damaging |
Het |
| Fyn |
A |
G |
10: 39,408,120 (GRCm39) |
D321G |
possibly damaging |
Het |
| Galnt5 |
A |
C |
2: 57,888,621 (GRCm39) |
M74L |
probably benign |
Het |
| Garin4 |
G |
A |
1: 190,896,218 (GRCm39) |
R142C |
probably damaging |
Het |
| Gas2l2 |
G |
A |
11: 83,313,288 (GRCm39) |
P675S |
probably benign |
Het |
| Gm9508 |
G |
T |
10: 77,532,470 (GRCm39) |
Q200K |
unknown |
Het |
| Greb1l |
G |
A |
18: 10,544,576 (GRCm39) |
S1390N |
probably benign |
Het |
| Hdac5 |
G |
T |
11: 102,095,385 (GRCm39) |
T430K |
possibly damaging |
Het |
| Hjurp |
TCTGGGAGGGCTTGCTCCGGGGGCAGTGTGTCCTGTTCTTGTGCAGCCCCTGCT |
TCT |
1: 88,194,000 (GRCm39) |
|
probably benign |
Het |
| Khnyn |
C |
T |
14: 56,131,811 (GRCm39) |
P578S |
probably damaging |
Het |
| Lepr |
A |
T |
4: 101,602,856 (GRCm39) |
T215S |
probably benign |
Het |
| Lrfn5 |
G |
A |
12: 61,890,768 (GRCm39) |
V686I |
probably benign |
Het |
| Mapkap1 |
T |
A |
2: 34,408,712 (GRCm39) |
H233Q |
possibly damaging |
Het |
| Mcm3 |
A |
G |
1: 20,885,081 (GRCm39) |
I201T |
probably damaging |
Het |
| Metrnl |
G |
A |
11: 121,606,734 (GRCm39) |
R263Q |
probably damaging |
Het |
| Mettl22 |
A |
G |
16: 8,295,924 (GRCm39) |
E71G |
probably benign |
Het |
| Muc16 |
T |
C |
9: 18,553,304 (GRCm39) |
T4330A |
probably benign |
Het |
| Mug1 |
A |
G |
6: 121,834,379 (GRCm39) |
T387A |
probably benign |
Het |
| Myh4 |
A |
G |
11: 67,135,550 (GRCm39) |
D379G |
probably benign |
Het |
| Nbas |
A |
G |
12: 13,455,398 (GRCm39) |
D1204G |
possibly damaging |
Het |
| Ncor2 |
T |
C |
5: 125,132,847 (GRCm39) |
K478E |
unknown |
Het |
| Or14a256 |
A |
T |
7: 86,265,574 (GRCm39) |
L93Q |
possibly damaging |
Het |
| Or51d1 |
A |
G |
7: 102,347,477 (GRCm39) |
T11A |
probably benign |
Het |
| Or5k1 |
T |
A |
16: 58,617,250 (GRCm39) |
I320F |
probably benign |
Het |
| Osbpl7 |
G |
A |
11: 96,941,662 (GRCm39) |
V62I |
probably benign |
Het |
| Pak1ip1 |
A |
G |
13: 41,163,018 (GRCm39) |
N246S |
probably damaging |
Het |
| Prim1 |
A |
G |
10: 127,851,845 (GRCm39) |
Y39C |
probably damaging |
Het |
| Prl3b1 |
G |
T |
13: 27,427,827 (GRCm39) |
V46L |
probably benign |
Het |
| Prss54 |
A |
T |
8: 96,292,199 (GRCm39) |
S127T |
probably benign |
Het |
| Rasal3 |
G |
A |
17: 32,611,391 (GRCm39) |
T912M |
probably damaging |
Het |
| Rrp12 |
T |
A |
19: 41,872,217 (GRCm39) |
T420S |
probably benign |
Het |
| Rspo1 |
A |
G |
4: 124,898,831 (GRCm39) |
N51D |
probably damaging |
Het |
| Rufy4 |
A |
G |
1: 74,172,035 (GRCm39) |
R253G |
probably benign |
Het |
| Scaf1 |
G |
A |
7: 44,657,167 (GRCm39) |
R571C |
unknown |
Het |
| Scn2a |
A |
T |
2: 65,532,323 (GRCm39) |
H645L |
probably damaging |
Het |
| Sec24b |
A |
G |
3: 129,782,595 (GRCm39) |
S1132P |
probably damaging |
Het |
| Slc1a2 |
A |
G |
2: 102,586,290 (GRCm39) |
K298R |
probably damaging |
Het |
| Slc25a54 |
T |
A |
3: 109,014,573 (GRCm39) |
N230K |
probably benign |
Het |
| Slc27a4 |
T |
G |
2: 29,705,664 (GRCm39) |
Y617* |
probably null |
Het |
| Slc2a10 |
T |
C |
2: 165,357,269 (GRCm39) |
S310P |
probably damaging |
Het |
| Snx33 |
C |
T |
9: 56,833,151 (GRCm39) |
R306H |
probably damaging |
Het |
| Spag9 |
A |
T |
11: 93,980,258 (GRCm39) |
|
probably null |
Het |
| Spg11 |
A |
T |
2: 121,932,270 (GRCm39) |
|
probably null |
Het |
| Sycp2l |
A |
G |
13: 41,283,258 (GRCm39) |
T165A |
probably damaging |
Het |
| Syt14 |
A |
G |
1: 192,615,571 (GRCm39) |
C189R |
probably damaging |
Het |
| Taar9 |
A |
T |
10: 23,984,882 (GRCm39) |
L184Q |
probably damaging |
Het |
| Tkt |
C |
T |
14: 30,281,815 (GRCm39) |
P111L |
probably damaging |
Het |
| Trpc1 |
A |
T |
9: 95,603,197 (GRCm39) |
L445Q |
possibly damaging |
Het |
| Usp53 |
A |
G |
3: 122,743,359 (GRCm39) |
S526P |
probably benign |
Het |
| Xirp2 |
A |
T |
2: 67,340,177 (GRCm39) |
H806L |
probably benign |
Het |
| Zfp451 |
A |
T |
1: 33,841,651 (GRCm39) |
H410Q |
unknown |
Het |
| Zfp688 |
A |
G |
7: 127,018,484 (GRCm39) |
C214R |
probably damaging |
Het |
| Zic4 |
A |
G |
9: 91,261,174 (GRCm39) |
D143G |
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 |
|
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 |
|
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 |
|
|
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'- TGACCTCTTTAGCTCAGGAACC -3'
(R):5'- ACACATCAAAGGCAGACTGG -3'
Sequencing Primer
(F):5'- CTCAGGAACCTATGATTCTAGTGAGG -3'
(R):5'- CAAGGCCCAAAGATATCATTATGTAC -3'
|
| Posted On |
2019-06-26 |
Incidental Mutation