Incidental Mutation 'R7344:Vps54'
| ID |
570100 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
045434-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.931)
|
| Stock # |
R7344 (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 C
at 21224999 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Threonine
at position 165
(I165T)
|
| 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: I165T
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: I165T
| 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: I153T
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: I153T
| 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: I39T
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: I39T
| 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: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.2%
|
| Validation Efficiency |
100% (58/58) |
| 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: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930438A08Rik |
A |
C |
11: 58,182,273 (GRCm39) |
Y216S |
|
Het |
| Anpep |
G |
T |
7: 79,488,398 (GRCm39) |
S477R |
possibly damaging |
Het |
| Atp7b |
T |
C |
8: 22,487,515 (GRCm39) |
D1293G |
probably damaging |
Het |
| Caprin2 |
A |
G |
6: 148,774,565 (GRCm39) |
V249A |
probably benign |
Het |
| Cep41 |
C |
T |
6: 30,693,655 (GRCm39) |
R5K |
probably benign |
Het |
| Cyp2c23 |
A |
T |
19: 44,010,176 (GRCm39) |
|
probably null |
Het |
| Dazap2 |
T |
A |
15: 100,514,824 (GRCm39) |
V15E |
possibly damaging |
Het |
| Ecpas |
A |
T |
4: 58,824,770 (GRCm39) |
D1070E |
probably benign |
Het |
| Epha8 |
T |
A |
4: 136,661,849 (GRCm39) |
H582L |
probably benign |
Het |
| Fam193a |
A |
G |
5: 34,643,074 (GRCm39) |
T1513A |
possibly damaging |
Het |
| Fancd2 |
T |
C |
6: 113,545,670 (GRCm39) |
V901A |
probably benign |
Het |
| Fbl |
T |
A |
7: 27,878,360 (GRCm39) |
V284E |
probably damaging |
Het |
| Fbln2 |
A |
G |
6: 91,246,955 (GRCm39) |
E1065G |
probably damaging |
Het |
| Fbxw16 |
A |
G |
9: 109,278,103 (GRCm39) |
V25A |
probably benign |
Het |
| Fcgbpl1 |
C |
T |
7: 27,852,185 (GRCm39) |
T1236I |
possibly damaging |
Het |
| Fcgbpl1 |
T |
C |
7: 27,839,704 (GRCm39) |
S506P |
possibly damaging |
Het |
| Gm11562 |
T |
G |
11: 99,511,195 (GRCm39) |
T2P |
unknown |
Het |
| Gm17728 |
G |
T |
17: 9,640,955 (GRCm39) |
G22W |
probably damaging |
Het |
| Gm30083 |
A |
G |
14: 33,721,537 (GRCm39) |
Y190H |
probably benign |
Het |
| Gm6793 |
T |
A |
8: 112,741,561 (GRCm39) |
D27V |
probably damaging |
Het |
| Gm7324 |
A |
G |
14: 43,952,134 (GRCm39) |
D259G |
probably benign |
Het |
| Gtf2a1l |
G |
A |
17: 89,001,531 (GRCm39) |
G129D |
probably damaging |
Het |
| Ildr2 |
T |
A |
1: 166,122,166 (GRCm39) |
V203E |
probably damaging |
Het |
| Ipo4 |
C |
T |
14: 55,872,988 (GRCm39) |
R23Q |
probably benign |
Het |
| Irx5 |
A |
G |
8: 93,086,183 (GRCm39) |
T89A |
probably benign |
Het |
| Itga7 |
A |
G |
10: 128,776,798 (GRCm39) |
N221S |
possibly damaging |
Het |
| Lpcat2 |
T |
C |
8: 93,602,195 (GRCm39) |
W259R |
probably damaging |
Het |
| Lrrc8e |
C |
T |
8: 4,284,815 (GRCm39) |
R347C |
probably damaging |
Het |
| Lyst |
T |
A |
13: 13,881,140 (GRCm39) |
D2790E |
probably benign |
Het |
| Magi2 |
G |
A |
5: 20,755,238 (GRCm39) |
R604Q |
probably benign |
Het |
| Mertk |
C |
A |
2: 128,613,417 (GRCm39) |
H478N |
probably benign |
Het |
| Mical3 |
T |
A |
6: 121,013,505 (GRCm39) |
K293* |
probably null |
Het |
| Nod2 |
T |
C |
8: 89,387,210 (GRCm39) |
L168P |
probably damaging |
Het |
| Npnt |
T |
C |
3: 132,614,100 (GRCm39) |
|
probably null |
Het |
| Or1x6 |
T |
G |
11: 50,939,122 (GRCm39) |
F63V |
probably damaging |
Het |
| Or5af1 |
A |
T |
11: 58,722,308 (GRCm39) |
E109D |
probably damaging |
Het |
| Or8b37 |
T |
C |
9: 37,959,253 (GRCm39) |
M245T |
probably benign |
Het |
| Or9g4 |
A |
T |
2: 85,505,275 (GRCm39) |
Y73* |
probably null |
Het |
| Plcd4 |
A |
T |
1: 74,593,811 (GRCm39) |
D312V |
probably damaging |
Het |
| Prss58 |
A |
G |
6: 40,872,399 (GRCm39) |
I208T |
probably damaging |
Het |
| Pus7l |
A |
G |
15: 94,438,498 (GRCm39) |
S116P |
probably benign |
Het |
| Rcc1l |
A |
T |
5: 134,205,276 (GRCm39) |
I93N |
probably benign |
Het |
| Rftn2 |
A |
C |
1: 55,265,311 (GRCm39) |
Y36* |
probably null |
Het |
| Rp1l1 |
G |
A |
14: 64,267,069 (GRCm39) |
R885Q |
probably benign |
Het |
| Rpgrip1 |
A |
T |
14: 52,378,116 (GRCm39) |
D488V |
probably damaging |
Het |
| Sacs |
A |
G |
14: 61,444,893 (GRCm39) |
Y2313C |
possibly damaging |
Het |
| Scrib |
T |
C |
15: 75,921,107 (GRCm39) |
Y1332C |
probably damaging |
Het |
| Serpinb10 |
T |
C |
1: 107,468,672 (GRCm39) |
V105A |
probably damaging |
Het |
| Slc35d1 |
A |
T |
4: 103,070,243 (GRCm39) |
|
probably null |
Het |
| Slfn3 |
T |
C |
11: 83,103,648 (GRCm39) |
V173A |
probably benign |
Het |
| Smpd3 |
C |
T |
8: 106,991,825 (GRCm39) |
V243M |
probably damaging |
Het |
| Stard9 |
A |
T |
2: 120,535,167 (GRCm39) |
D3808V |
possibly damaging |
Het |
| Supt16 |
A |
T |
14: 52,411,028 (GRCm39) |
V692D |
probably damaging |
Het |
| Tapt1 |
A |
T |
5: 44,345,999 (GRCm39) |
V317E |
probably damaging |
Het |
| Vmn2r101 |
T |
C |
17: 19,832,059 (GRCm39) |
I685T |
probably benign |
Het |
| Vmn2r92 |
A |
G |
17: 18,387,513 (GRCm39) |
I173V |
probably benign |
Het |
| Zswim4 |
G |
A |
8: 84,950,327 (GRCm39) |
R628* |
probably null |
Het |
| Zzz3 |
T |
C |
3: 152,157,736 (GRCm39) |
S770P |
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 |
|
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 |
|
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'- TCTGCACTAGTAAAGGCAAAAGC -3'
(R):5'- CACTTAATCAGAATACCGTTTCCTG -3'
Sequencing Primer
(F):5'- CACAGATGTGTACCTGGTACCTATG -3'
(R):5'- CCGTTTCCTGTATGAAAGAAATCAG -3'
|
| Posted On |
2019-09-13 |
Incidental Mutation