Incidental Mutation 'R9367:Vps54'
| ID |
709067 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.931)
|
| Stock # |
R9367 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 21250234 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 552
(V552A)
|
| 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: V552A
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: V552A
| 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: V540A
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: V540A
| 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: V390A
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: V390A
| 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 |
|
| 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: 76 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2200002D01Rik |
CCTTCTCCTTCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC |
CCTTCTCCTTCTTCTCCTTCTTCTCCATCTTCTCCTTCTTC |
7: 28,947,048 (GRCm39) |
|
probably benign |
Het |
| 4930568D16Rik |
A |
T |
2: 35,244,939 (GRCm39) |
Y138N |
probably benign |
Het |
| Abca4 |
T |
C |
3: 121,838,197 (GRCm39) |
M1T |
probably null |
Het |
| Acer3 |
A |
G |
7: 97,908,621 (GRCm39) |
V104A |
probably damaging |
Het |
| Agpat4 |
A |
G |
17: 12,435,597 (GRCm39) |
E287G |
probably benign |
Het |
| Akip1 |
C |
T |
7: 109,308,156 (GRCm39) |
A146V |
unknown |
Het |
| Ank2 |
T |
C |
3: 126,738,678 (GRCm39) |
N2402S |
unknown |
Het |
| Arhgdig |
A |
T |
17: 26,418,451 (GRCm39) |
Y177* |
probably null |
Het |
| Arhgef38 |
T |
A |
3: 132,847,998 (GRCm39) |
T355S |
unknown |
Het |
| Atp8a2 |
C |
A |
14: 60,249,827 (GRCm39) |
|
probably null |
Het |
| Atp8b4 |
A |
G |
2: 126,216,430 (GRCm39) |
I672T |
probably damaging |
Het |
| Baat |
T |
A |
4: 49,503,008 (GRCm39) |
D38V |
probably damaging |
Het |
| Bcl9 |
T |
C |
3: 97,117,861 (GRCm39) |
S278G |
probably benign |
Het |
| Ccdc150 |
C |
T |
1: 54,324,760 (GRCm39) |
L350F |
probably damaging |
Het |
| Ceacam20 |
T |
G |
7: 19,705,533 (GRCm39) |
S175A |
probably damaging |
Het |
| Chd6 |
A |
T |
2: 160,871,784 (GRCm39) |
I217K |
possibly damaging |
Het |
| Cnppd1 |
T |
C |
1: 75,117,617 (GRCm39) |
I35V |
probably benign |
Het |
| Col15a1 |
T |
C |
4: 47,245,603 (GRCm39) |
I118T |
probably damaging |
Het |
| Csmd3 |
A |
T |
15: 47,567,564 (GRCm39) |
Y1289N |
|
Het |
| Dio2 |
T |
C |
12: 90,696,587 (GRCm39) |
T134A |
probably benign |
Het |
| Dnaaf9 |
A |
T |
2: 130,581,380 (GRCm39) |
N678K |
probably benign |
Het |
| Dnah17 |
A |
G |
11: 117,987,464 (GRCm39) |
V1282A |
possibly damaging |
Het |
| Dnah17 |
A |
G |
11: 118,012,212 (GRCm39) |
S517P |
possibly damaging |
Het |
| Dync2h1 |
C |
T |
9: 7,125,730 (GRCm39) |
|
probably null |
Het |
| Echdc2 |
C |
A |
4: 108,036,111 (GRCm39) |
P274Q |
probably damaging |
Het |
| Fam117a |
T |
A |
11: 95,271,570 (GRCm39) |
C381S |
probably damaging |
Het |
| Fbxl12 |
A |
G |
9: 20,550,130 (GRCm39) |
F122S |
probably damaging |
Het |
| Gen1 |
G |
A |
12: 11,291,309 (GRCm39) |
Q892* |
probably null |
Het |
| Gimap4 |
A |
G |
6: 48,667,746 (GRCm39) |
Y167C |
probably damaging |
Het |
| Gle1 |
T |
A |
2: 29,839,014 (GRCm39) |
F476L |
probably damaging |
Het |
| Gpr135 |
A |
T |
12: 72,117,473 (GRCm39) |
V98E |
possibly damaging |
Het |
| Greb1l |
A |
T |
18: 10,522,130 (GRCm39) |
H742L |
probably benign |
Het |
| Habp2 |
G |
T |
19: 56,304,781 (GRCm39) |
C392F |
probably damaging |
Het |
| Hapln3 |
G |
T |
7: 78,771,455 (GRCm39) |
R145S |
probably damaging |
Het |
| Ikbkb |
A |
G |
8: 23,171,711 (GRCm39) |
C179R |
probably damaging |
Het |
| Kat6a |
A |
T |
8: 23,400,156 (GRCm39) |
I306L |
possibly damaging |
Het |
| Lmo3 |
A |
T |
6: 138,342,958 (GRCm39) |
Y140* |
probably null |
Het |
| Lrrc32 |
T |
A |
7: 98,148,937 (GRCm39) |
N572K |
probably damaging |
Het |
| Lrrn1 |
T |
A |
6: 107,545,093 (GRCm39) |
M297K |
probably damaging |
Het |
| Magi2 |
G |
A |
5: 20,766,308 (GRCm39) |
V676I |
probably damaging |
Het |
| Mdga1 |
T |
C |
17: 30,051,282 (GRCm39) |
*957W |
probably null |
Het |
| Mip |
G |
T |
10: 128,063,029 (GRCm39) |
G158V |
probably damaging |
Het |
| Mmp14 |
T |
C |
14: 54,677,960 (GRCm39) |
I527T |
probably benign |
Het |
| Mmp27 |
G |
A |
9: 7,573,550 (GRCm39) |
G188D |
probably damaging |
Het |
| Mylk4 |
A |
T |
13: 32,960,236 (GRCm39) |
C17S |
possibly damaging |
Het |
| Naa50 |
T |
G |
16: 43,977,554 (GRCm39) |
I94R |
probably damaging |
Het |
| Nyap1 |
A |
T |
5: 137,734,248 (GRCm39) |
Y262N |
probably damaging |
Het |
| Obsl1 |
A |
G |
1: 75,466,177 (GRCm39) |
V1517A |
probably benign |
Het |
| P4htm |
T |
A |
9: 108,459,147 (GRCm39) |
M262L |
probably benign |
Het |
| Pappa2 |
T |
C |
1: 158,784,542 (GRCm39) |
E156G |
probably benign |
Het |
| Pcdhb15 |
A |
T |
18: 37,607,971 (GRCm39) |
Y401F |
possibly damaging |
Het |
| Pde2a |
G |
A |
7: 101,160,361 (GRCm39) |
R845H |
probably damaging |
Het |
| Peg10 |
CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG |
CCACATCAGGATCCACATCAGGATGCACATCAG |
6: 4,756,398 (GRCm39) |
|
probably benign |
Het |
| Penk |
C |
T |
4: 4,134,097 (GRCm39) |
M183I |
probably benign |
Het |
| Pole |
T |
C |
5: 110,444,955 (GRCm39) |
V437A |
probably damaging |
Het |
| Ppp1r7 |
T |
C |
1: 93,279,262 (GRCm39) |
I114T |
probably damaging |
Het |
| Prr27 |
C |
A |
5: 87,990,994 (GRCm39) |
P202Q |
probably benign |
Het |
| Pwp2 |
G |
A |
10: 78,014,827 (GRCm39) |
Q386* |
probably null |
Het |
| Rad17 |
A |
T |
13: 100,769,720 (GRCm39) |
S280T |
possibly damaging |
Het |
| Rhebl1 |
C |
T |
15: 98,776,414 (GRCm39) |
E128K |
possibly damaging |
Het |
| Sema3e |
G |
T |
5: 14,291,084 (GRCm39) |
V615L |
probably benign |
Het |
| Slc22a2 |
A |
T |
17: 12,824,837 (GRCm39) |
Y233F |
probably benign |
Het |
| Ssu2 |
A |
G |
6: 112,357,975 (GRCm39) |
S123P |
probably damaging |
Het |
| Stk10 |
A |
G |
11: 32,538,878 (GRCm39) |
E239G |
|
Het |
| Surf6 |
G |
T |
2: 26,782,380 (GRCm39) |
Q316K |
probably damaging |
Het |
| Tcerg1 |
G |
A |
18: 42,685,573 (GRCm39) |
D637N |
possibly damaging |
Het |
| Tm7sf3 |
C |
T |
6: 146,525,179 (GRCm39) |
D89N |
possibly damaging |
Het |
| Tnxb |
C |
A |
17: 34,931,993 (GRCm39) |
F2175L |
probably damaging |
Het |
| Trp53i11 |
G |
C |
2: 93,029,273 (GRCm39) |
V91L |
probably benign |
Het |
| Tspan9 |
A |
G |
6: 127,944,102 (GRCm39) |
V66A |
probably damaging |
Het |
| Usp16 |
C |
T |
16: 87,261,669 (GRCm39) |
T95M |
probably benign |
Het |
| Usp9y |
A |
T |
Y: 1,324,982 (GRCm39) |
F1691Y |
probably damaging |
Het |
| Uty |
A |
T |
Y: 1,099,584 (GRCm39) |
L1204I |
possibly damaging |
Het |
| Vmn1r192 |
A |
T |
13: 22,371,800 (GRCm39) |
V140D |
possibly damaging |
Het |
| Vps8 |
T |
C |
16: 21,340,668 (GRCm39) |
V804A |
possibly damaging |
Het |
| Zfp869 |
A |
C |
8: 70,161,057 (GRCm39) |
L33R |
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 |
|
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 |
|
|
Z1177:Vps54
|
UTSW |
11 |
21,213,206 (GRCm39) |
start gained |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TCCACAGTGTTGTTCTGTCAG -3'
(R):5'- TCCATAGTGCTGAAGGGAGG -3'
Sequencing Primer
(F):5'- CTGTCAGTTCTTGAGAAAAGCC -3'
(R):5'- TGGCTCAGGAAATAATTCAAGCTCC -3'
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| Posted On |
2022-04-18 |
Incidental Mutation