Incidental Mutation 'R7095:Vps54'
| ID |
550438 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
045243-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.933)
|
| Stock # |
R7095 (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 21221720 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glutamic Acid
at position 158
(D158E)
|
| 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 benign
Transcript: ENSMUST00000006221
AA Change: D158E
PolyPhen 2
Score 0.115 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: D158E
| 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
AA Change: D146E
PolyPhen 2
Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: D146E
| 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
AA Change: D32E
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: D32E
| 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: 99.7%
- 20x: 99.2%
|
| Validation Efficiency |
99% (71/72) |
| 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: 70 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcf1 |
A |
G |
17: 36,268,403 (GRCm39) |
V809A |
possibly damaging |
Het |
| Adam32 |
T |
A |
8: 25,404,086 (GRCm39) |
D242V |
probably damaging |
Het |
| Adamts9 |
T |
A |
6: 92,864,672 (GRCm39) |
H763L |
probably benign |
Het |
| Aff1 |
A |
G |
5: 103,990,951 (GRCm39) |
D967G |
probably damaging |
Het |
| Anpep |
A |
T |
7: 79,491,950 (GRCm39) |
L17Q |
possibly damaging |
Het |
| Appbp2 |
G |
T |
11: 85,125,553 (GRCm39) |
S28* |
probably null |
Het |
| Bach1 |
G |
A |
16: 87,516,179 (GRCm39) |
R240Q |
probably benign |
Het |
| Bod1l |
A |
G |
5: 41,952,411 (GRCm39) |
|
probably null |
Het |
| Capn5 |
G |
A |
7: 97,775,038 (GRCm39) |
T534I |
probably benign |
Het |
| Cbx2 |
T |
C |
11: 118,918,885 (GRCm39) |
I150T |
probably damaging |
Het |
| Cdh11 |
A |
G |
8: 103,384,899 (GRCm39) |
V392A |
probably damaging |
Het |
| Cenpf |
A |
T |
1: 189,391,373 (GRCm39) |
C803S |
probably benign |
Het |
| Cep135 |
A |
G |
5: 76,741,905 (GRCm39) |
T114A |
probably benign |
Het |
| Chd2 |
A |
T |
7: 73,121,629 (GRCm39) |
D994E |
probably damaging |
Het |
| Chtf18 |
C |
A |
17: 25,941,652 (GRCm39) |
W584C |
probably damaging |
Het |
| Dclk2 |
C |
T |
3: 86,700,566 (GRCm39) |
R638H |
probably damaging |
Het |
| Dgkh |
C |
A |
14: 78,865,224 (GRCm39) |
M172I |
probably benign |
Het |
| Dpy19l2 |
T |
G |
9: 24,607,110 (GRCm39) |
H117P |
probably benign |
Het |
| Dzip3 |
A |
T |
16: 48,748,153 (GRCm39) |
N908K |
probably benign |
Het |
| Erc2 |
A |
T |
14: 27,620,550 (GRCm39) |
N393Y |
probably damaging |
Het |
| Fam118b |
T |
C |
9: 35,132,786 (GRCm39) |
E291G |
possibly damaging |
Het |
| Fam193a |
C |
T |
5: 34,615,378 (GRCm39) |
L816F |
probably damaging |
Het |
| Fat2 |
A |
G |
11: 55,202,157 (GRCm39) |
Y306H |
probably damaging |
Het |
| Fndc10 |
C |
T |
4: 155,779,574 (GRCm39) |
T206I |
probably damaging |
Het |
| Fzd1 |
GGGACTCCTCCACCTCCCTGGA |
GGGA |
5: 4,805,824 (GRCm39) |
|
probably benign |
Het |
| Gsk3a |
A |
T |
7: 24,933,279 (GRCm39) |
Y177N |
probably damaging |
Het |
| Haus5 |
T |
C |
7: 30,358,997 (GRCm39) |
T222A |
probably benign |
Het |
| Igfbp7 |
G |
T |
5: 77,549,337 (GRCm39) |
Q189K |
probably benign |
Het |
| Inppl1 |
A |
T |
7: 101,476,663 (GRCm39) |
Y771* |
probably null |
Het |
| Iqck |
A |
T |
7: 118,514,814 (GRCm39) |
Y234F |
probably damaging |
Het |
| Irs1 |
G |
T |
1: 82,267,819 (GRCm39) |
C132* |
probably null |
Het |
| Jmjd1c |
T |
G |
10: 67,055,411 (GRCm39) |
V277G |
probably benign |
Het |
| Klhl22 |
G |
A |
16: 17,610,614 (GRCm39) |
V622M |
probably damaging |
Het |
| Kri1 |
C |
T |
9: 21,190,728 (GRCm39) |
E378K |
|
Het |
| Lilra6 |
C |
T |
7: 3,916,196 (GRCm39) |
G221D |
probably damaging |
Het |
| Mecom |
T |
C |
3: 30,035,103 (GRCm39) |
E191G |
probably damaging |
Het |
| Mgrn1 |
T |
A |
16: 4,745,528 (GRCm39) |
|
probably null |
Het |
| Mical1 |
C |
T |
10: 41,355,206 (GRCm39) |
|
probably null |
Het |
| Mlxipl |
T |
C |
5: 135,162,884 (GRCm39) |
Y711H |
possibly damaging |
Het |
| Mpl |
T |
A |
4: 118,301,260 (GRCm39) |
H535L |
|
Het |
| Mtarc1 |
A |
G |
1: 184,527,437 (GRCm39) |
L297P |
probably damaging |
Het |
| Mtfr2 |
C |
A |
10: 20,228,666 (GRCm39) |
H71N |
probably benign |
Het |
| Mtrf1 |
GCCTTC |
GC |
14: 79,660,931 (GRCm39) |
|
probably null |
Het |
| Myh15 |
A |
G |
16: 48,992,272 (GRCm39) |
Q1582R |
possibly damaging |
Het |
| Neb |
C |
T |
2: 52,067,635 (GRCm39) |
E6062K |
possibly damaging |
Het |
| Nlrp4c |
G |
A |
7: 6,063,792 (GRCm39) |
A67T |
probably damaging |
Het |
| Noc3l |
T |
A |
19: 38,800,789 (GRCm39) |
H231L |
probably benign |
Het |
| Odf1 |
T |
C |
15: 38,219,803 (GRCm39) |
Y44H |
possibly damaging |
Het |
| Or52e2 |
G |
A |
7: 102,804,537 (GRCm39) |
T139I |
probably damaging |
Het |
| Or52s1b |
C |
T |
7: 102,822,253 (GRCm39) |
R197H |
probably benign |
Het |
| Or5j3 |
C |
T |
2: 86,129,021 (GRCm39) |
P287L |
probably benign |
Het |
| Otol1 |
G |
T |
3: 69,926,027 (GRCm39) |
E67D |
probably benign |
Het |
| Otud7b |
A |
G |
3: 96,062,554 (GRCm39) |
S598G |
probably benign |
Het |
| Ppwd1 |
T |
A |
13: 104,342,134 (GRCm39) |
T607S |
probably benign |
Het |
| Prag1 |
A |
G |
8: 36,569,714 (GRCm39) |
N99S |
probably benign |
Het |
| Ralgds |
C |
A |
2: 28,439,320 (GRCm39) |
Q737K |
possibly damaging |
Het |
| Scyl2 |
T |
C |
10: 89,505,549 (GRCm39) |
H98R |
probably damaging |
Het |
| Secisbp2 |
A |
C |
13: 51,831,290 (GRCm39) |
Q575H |
probably benign |
Het |
| Slc9a5 |
A |
T |
8: 106,084,268 (GRCm39) |
H497L |
probably benign |
Het |
| Sufu |
T |
A |
19: 46,464,027 (GRCm39) |
V414E |
probably damaging |
Het |
| Tbc1d22b |
A |
T |
17: 29,818,843 (GRCm39) |
E399V |
probably damaging |
Het |
| Tcp10c |
G |
A |
17: 13,576,196 (GRCm39) |
V59I |
probably benign |
Het |
| Tdpoz3 |
T |
C |
3: 93,734,368 (GRCm39) |
S348P |
probably benign |
Het |
| Tmem219 |
A |
T |
7: 126,490,928 (GRCm39) |
F176L |
probably damaging |
Het |
| Trav6-2 |
A |
G |
14: 52,905,291 (GRCm39) |
D104G |
probably damaging |
Het |
| Uba7 |
A |
G |
9: 107,860,538 (GRCm39) |
K927R |
probably benign |
Het |
| Xpnpep1 |
C |
T |
19: 53,000,196 (GRCm39) |
|
probably null |
Het |
| Xpo7 |
G |
A |
14: 70,942,146 (GRCm39) |
R73W |
probably damaging |
Het |
| Zfp532 |
A |
T |
18: 65,815,969 (GRCm39) |
M781L |
probably benign |
Het |
| Zfp930 |
T |
A |
8: 69,681,193 (GRCm39) |
I295K |
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 |
|
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 |
|
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'- CATTGCGGCCTATTAGAGTGG -3'
(R):5'- TAAGGGAGCAGAGCCTCAAC -3'
Sequencing Primer
(F):5'- CGGCCTATTAGAGTGGAGACAG -3'
(R):5'- GCCTCAACAAAGCAAATTTCATTTC -3'
|
| Posted On |
2019-05-15 |
Incidental Mutation