Incidental Mutation 'R8282:Vps54'
| ID |
656530 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
067705-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.933)
|
| Stock # |
R8282 (G1)
|
| Quality Score |
187.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
| Type of Mutation |
intron |
| DNA Base Change (assembly) |
T to A
at 21250464 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000116739
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[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: 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.9%
|
| Validation Efficiency |
98% (57/58) |
| 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 |
|---|
| Adcy10 |
T |
A |
1: 165,337,906 (GRCm39) |
D173E |
probably benign |
Het |
| Ahctf1 |
T |
C |
1: 179,605,371 (GRCm39) |
D721G |
possibly damaging |
Het |
| Allc |
T |
C |
12: 28,607,356 (GRCm39) |
T299A |
probably damaging |
Het |
| Ankrd55 |
T |
A |
13: 112,459,575 (GRCm39) |
|
probably benign |
Het |
| Axl |
C |
T |
7: 25,463,379 (GRCm39) |
D633N |
probably benign |
Het |
| Brf2 |
G |
T |
8: 27,614,621 (GRCm39) |
R30S |
|
Het |
| Bsn |
A |
G |
9: 107,984,890 (GRCm39) |
S283P |
possibly damaging |
Het |
| Ccng2 |
C |
G |
5: 93,421,202 (GRCm39) |
S237R |
probably benign |
Het |
| Ces1d |
A |
T |
8: 93,912,740 (GRCm39) |
S233T |
possibly damaging |
Het |
| Chst15 |
T |
A |
7: 131,871,879 (GRCm39) |
H134L |
probably benign |
Het |
| Col14a1 |
A |
G |
15: 55,284,276 (GRCm39) |
T846A |
unknown |
Het |
| Cwh43 |
A |
T |
5: 73,591,572 (GRCm39) |
D555V |
probably damaging |
Het |
| Cyld |
C |
A |
8: 89,432,043 (GRCm39) |
P14T |
probably benign |
Het |
| Dctn1 |
G |
A |
6: 83,176,738 (GRCm39) |
R1264H |
possibly damaging |
Het |
| Dkk3 |
T |
A |
7: 111,717,489 (GRCm39) |
S327C |
probably damaging |
Het |
| Dnmbp |
T |
G |
19: 43,879,005 (GRCm39) |
H22P |
unknown |
Het |
| Duxf4 |
T |
G |
10: 58,072,148 (GRCm39) |
Q22P |
possibly damaging |
Het |
| Fabp4 |
T |
A |
3: 10,270,342 (GRCm39) |
T103S |
probably benign |
Het |
| Fam43a |
T |
C |
16: 30,420,106 (GRCm39) |
L230P |
probably damaging |
Het |
| Fam83h |
ACTCCCCTTGCGCTCAGGGTAAGCTGGGGTAGGGCTCCCCTTGCGCTCAGGGTAAGCTGGGGTAGGGCTCCCCTTGCGCTCAGGGTAAGCTGGGGTAGGGCTCCCCTTGCGCTCAGGGTAAGCTGGGGT |
ACTCCCCTTGCGCTCAGGGTAAGCTGGGGTAGGGCTCCCCTTGCGCTCAGGGTAAGCTGGGGTAGGGCTCCCCTTGCGCTCAGGGTAAGCTGGGGT |
15: 75,874,624 (GRCm39) |
|
probably benign |
Het |
| Fank1 |
T |
A |
7: 133,478,493 (GRCm39) |
Y186N |
probably damaging |
Het |
| Fbxo8 |
G |
A |
8: 57,044,555 (GRCm39) |
R286K |
possibly damaging |
Het |
| Fmnl2 |
G |
A |
2: 52,997,678 (GRCm39) |
|
probably null |
Het |
| Gli2 |
T |
A |
1: 118,765,701 (GRCm39) |
S817C |
probably damaging |
Het |
| Gm10110 |
C |
T |
14: 90,135,677 (GRCm39) |
V76M |
noncoding transcript |
Het |
| Gstt2 |
C |
G |
10: 75,668,291 (GRCm39) |
A155P |
probably benign |
Het |
| Ints9 |
T |
A |
14: 65,244,757 (GRCm39) |
M213K |
probably benign |
Het |
| Jak1 |
G |
A |
4: 101,036,738 (GRCm39) |
R301* |
probably null |
Het |
| Kdsr |
T |
C |
1: 106,652,727 (GRCm39) |
T302A |
probably benign |
Het |
| Khsrp |
T |
C |
17: 57,331,123 (GRCm39) |
E460G |
probably damaging |
Het |
| Larp1b |
G |
A |
3: 40,991,245 (GRCm39) |
R193H |
probably damaging |
Het |
| Nedd4l |
A |
G |
18: 65,324,560 (GRCm39) |
K487R |
probably damaging |
Het |
| Niban2 |
A |
G |
2: 32,809,029 (GRCm39) |
E205G |
probably benign |
Het |
| Nwd1 |
T |
A |
8: 73,431,580 (GRCm39) |
S1193T |
probably damaging |
Het |
| Or10ag57 |
A |
T |
2: 87,218,852 (GRCm39) |
T268S |
probably benign |
Het |
| Or5k3 |
T |
A |
16: 58,969,529 (GRCm39) |
C105* |
probably null |
Het |
| Or8b54 |
G |
A |
9: 38,686,577 (GRCm39) |
V9M |
noncoding transcript |
Het |
| Padi1 |
T |
C |
4: 140,542,014 (GRCm39) |
H636R |
probably damaging |
Het |
| Pdilt |
A |
G |
7: 119,097,293 (GRCm39) |
I266T |
probably damaging |
Het |
| Rell2 |
A |
T |
18: 38,090,665 (GRCm39) |
Q114L |
probably benign |
Het |
| Rfc1 |
A |
G |
5: 65,426,289 (GRCm39) |
|
probably null |
Het |
| Rpia |
T |
C |
6: 70,748,002 (GRCm39) |
N265D |
possibly damaging |
Het |
| Rsf1 |
CGGCGGCGG |
CGGCGGCGGGGCGGCGG |
7: 97,229,127 (GRCm39) |
|
probably null |
Het |
| Samd12 |
T |
C |
15: 53,723,645 (GRCm39) |
D16G |
probably damaging |
Het |
| Slc25a54 |
T |
C |
3: 109,006,005 (GRCm39) |
|
probably null |
Het |
| Slc6a3 |
T |
A |
13: 73,705,200 (GRCm39) |
D230E |
probably benign |
Het |
| Sorbs1 |
G |
C |
19: 40,365,244 (GRCm39) |
R180G |
probably benign |
Het |
| Synpo2l |
A |
G |
14: 20,711,204 (GRCm39) |
V472A |
probably benign |
Het |
| Taf6l |
A |
G |
19: 8,750,714 (GRCm39) |
I120T |
possibly damaging |
Het |
| Tent5c |
A |
G |
3: 100,380,327 (GRCm39) |
V143A |
probably damaging |
Het |
| Trappc11 |
T |
C |
8: 47,969,624 (GRCm39) |
D328G |
probably damaging |
Het |
| Trp53bp1 |
A |
G |
2: 121,029,523 (GRCm39) |
S1836P |
probably damaging |
Het |
| Ugt2b37 |
G |
A |
5: 87,402,440 (GRCm39) |
L64F |
probably benign |
Het |
| Vmn2r56 |
A |
T |
7: 12,449,601 (GRCm39) |
Y212* |
probably null |
Het |
| Zfp268 |
A |
T |
4: 145,349,547 (GRCm39) |
D328V |
possibly damaging |
Het |
| Zfp648 |
T |
A |
1: 154,080,535 (GRCm39) |
H231Q |
probably benign |
Het |
| Zscan4d |
T |
A |
7: 10,896,369 (GRCm39) |
T334S |
possibly damaging |
Het |
| Zswim9 |
T |
C |
7: 12,995,536 (GRCm39) |
M207V |
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 |
|
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 |
|
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'- ACACGTCTCCACATAGCGAG -3'
(R):5'- TGAGAAACCAATGCATAAGGCC -3'
Sequencing Primer
(F):5'- CAGCAGTGATTCGGTATCAGAACC -3'
(R):5'- TGCATAAGGCCAACACATCTTTAC -3'
|
| Posted On |
2020-12-14 |
Incidental Mutation