Incidental Mutation 'R4108:Vps54'
ID |
321483 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps54
|
Ensembl Gene |
ENSMUSG00000020128 |
Gene Name |
VPS54 GARP complex subunit |
Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
MMRRC Submission |
040987-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.931)
|
Stock # |
R4108 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
11 |
Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 21262877 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Isoleucine to Valine
at position 655
(I655V)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000116739
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000132017]
|
AlphaFold |
Q5SPW0 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000006221
AA Change: I817V
PolyPhen 2
Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
|
SMART Domains |
Protein: ENSMUSP00000006221 Gene: ENSMUSG00000020128 AA Change: I817V
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: I805V
PolyPhen 2
Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)
|
SMART Domains |
Protein: ENSMUSP00000105206 Gene: ENSMUSG00000020128 AA Change: I805V
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: I655V
PolyPhen 2
Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
|
SMART Domains |
Protein: ENSMUSP00000116739 Gene: ENSMUSG00000020128 AA Change: I655V
Domain | Start | End | E-Value | Type |
Pfam:DUF2450
|
72 |
238 |
1.4e-12 |
PFAM |
Pfam:Vps54
|
573 |
707 |
7.8e-64 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153159
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153411
|
Meta Mutation Damage Score |
0.0598 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.7%
|
Validation Efficiency |
97% (65/67) |
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: 60 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700113H08Rik |
A |
G |
10: 87,061,796 (GRCm39) |
Y82C |
probably damaging |
Het |
4930579F01Rik |
T |
C |
3: 137,889,431 (GRCm39) |
N62S |
probably benign |
Het |
Acad10 |
G |
T |
5: 121,769,527 (GRCm39) |
S643Y |
probably damaging |
Het |
Acox3 |
T |
C |
5: 35,758,896 (GRCm39) |
F369S |
probably damaging |
Het |
Arhgap31 |
A |
G |
16: 38,422,788 (GRCm39) |
S1093P |
probably damaging |
Het |
Atp4b |
A |
G |
8: 13,446,640 (GRCm39) |
|
probably null |
Het |
Bmper |
G |
A |
9: 23,136,059 (GRCm39) |
V47I |
probably benign |
Het |
Caskin1 |
C |
A |
17: 24,721,121 (GRCm39) |
T487K |
probably benign |
Het |
Ccr7 |
C |
T |
11: 99,036,204 (GRCm39) |
M239I |
probably damaging |
Het |
Cdh23 |
C |
A |
10: 60,246,601 (GRCm39) |
V944L |
possibly damaging |
Het |
Cenpf |
A |
G |
1: 189,416,065 (GRCm39) |
S87P |
probably damaging |
Het |
Chd9 |
A |
T |
8: 91,737,304 (GRCm39) |
D1461V |
probably benign |
Het |
Col1a2 |
G |
A |
6: 4,518,822 (GRCm39) |
|
probably benign |
Het |
Cyb5r2 |
A |
T |
7: 107,353,136 (GRCm39) |
M102K |
probably damaging |
Het |
Cyp2j7 |
T |
C |
4: 96,087,687 (GRCm39) |
T408A |
possibly damaging |
Het |
Dnajb2 |
G |
T |
1: 75,213,543 (GRCm39) |
E6* |
probably null |
Het |
Dtx4 |
G |
A |
19: 12,478,487 (GRCm39) |
A32V |
probably damaging |
Het |
Eml5 |
T |
C |
12: 98,807,807 (GRCm39) |
|
probably null |
Het |
Eml6 |
A |
C |
11: 29,755,136 (GRCm39) |
S880A |
probably damaging |
Het |
Fsd2 |
C |
T |
7: 81,194,715 (GRCm39) |
V483I |
probably benign |
Het |
Inf2 |
T |
C |
12: 112,574,015 (GRCm39) |
L773P |
unknown |
Het |
Kif26b |
A |
G |
1: 178,744,530 (GRCm39) |
Q1095R |
possibly damaging |
Het |
Leprotl1 |
A |
G |
8: 34,607,913 (GRCm39) |
|
probably null |
Het |
Lrp1b |
A |
G |
2: 40,555,099 (GRCm39) |
V340A |
unknown |
Het |
Myh1 |
T |
C |
11: 67,102,403 (GRCm39) |
V898A |
probably benign |
Het |
Ncstn |
G |
T |
1: 171,900,111 (GRCm39) |
N254K |
probably damaging |
Het |
Nfatc1 |
T |
A |
18: 80,741,583 (GRCm39) |
H139L |
possibly damaging |
Het |
Nfe2l1 |
C |
T |
11: 96,710,220 (GRCm39) |
|
probably null |
Het |
Nfya |
G |
T |
17: 48,699,912 (GRCm39) |
Y37* |
probably null |
Het |
Obscn |
T |
C |
11: 59,022,472 (GRCm39) |
R758G |
possibly damaging |
Het |
Or2b6 |
A |
G |
13: 21,822,952 (GRCm39) |
V247A |
probably damaging |
Het |
Or7g26 |
T |
A |
9: 19,230,608 (GRCm39) |
Y265* |
probably null |
Het |
Otogl |
C |
T |
10: 107,607,105 (GRCm39) |
V2093I |
probably benign |
Het |
Phc2 |
A |
G |
4: 128,601,776 (GRCm39) |
Y77C |
probably damaging |
Het |
Pik3c2g |
C |
A |
6: 139,676,096 (GRCm39) |
A80E |
probably benign |
Het |
Plxnd1 |
G |
T |
6: 115,936,276 (GRCm39) |
H1675N |
probably damaging |
Het |
Pou4f3 |
A |
G |
18: 42,528,987 (GRCm39) |
K310R |
probably damaging |
Het |
Ppp1r12c |
T |
C |
7: 4,489,565 (GRCm39) |
D199G |
probably damaging |
Het |
Prss22 |
A |
G |
17: 24,212,847 (GRCm39) |
Y297H |
probably benign |
Het |
Psmb7 |
T |
A |
2: 38,532,211 (GRCm39) |
H78L |
probably damaging |
Het |
Rad51ap2 |
T |
C |
12: 11,508,396 (GRCm39) |
C773R |
probably damaging |
Het |
Rpl12 |
A |
T |
2: 32,851,836 (GRCm39) |
N8Y |
probably damaging |
Het |
Ryr3 |
C |
G |
2: 112,506,218 (GRCm39) |
R3443P |
probably damaging |
Het |
Sbf1 |
T |
C |
15: 89,172,788 (GRCm39) |
|
probably benign |
Het |
Scn3a |
A |
G |
2: 65,325,379 (GRCm39) |
I1046T |
probably benign |
Het |
Setd1a |
G |
A |
7: 127,398,374 (GRCm39) |
|
probably benign |
Het |
Slc15a2 |
G |
T |
16: 36,602,755 (GRCm39) |
|
probably benign |
Het |
Slc34a2 |
G |
A |
5: 53,221,351 (GRCm39) |
V266I |
possibly damaging |
Het |
Smtn |
G |
A |
11: 3,476,449 (GRCm39) |
T144I |
probably benign |
Het |
Spta1 |
A |
G |
1: 174,002,122 (GRCm39) |
N84S |
probably benign |
Het |
Sult6b1 |
G |
T |
17: 79,214,291 (GRCm39) |
T6N |
probably damaging |
Het |
Supt16 |
T |
C |
14: 52,400,188 (GRCm39) |
E985G |
probably damaging |
Het |
Tbcd |
T |
A |
11: 121,384,637 (GRCm39) |
H39Q |
probably benign |
Het |
Tpo |
G |
A |
12: 30,142,585 (GRCm39) |
P713L |
probably damaging |
Het |
Tsg101 |
T |
A |
7: 46,542,242 (GRCm39) |
D99V |
probably damaging |
Het |
Ttn |
G |
C |
2: 76,581,215 (GRCm39) |
A23226G |
probably damaging |
Het |
Ttn |
C |
T |
2: 76,608,809 (GRCm39) |
V15990I |
probably benign |
Het |
Ubald1 |
C |
A |
16: 4,693,731 (GRCm39) |
M61I |
probably benign |
Het |
Ush1c |
C |
T |
7: 45,847,869 (GRCm39) |
D465N |
probably damaging |
Het |
Vmn2r129 |
G |
T |
4: 156,686,692 (GRCm39) |
|
noncoding transcript |
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 |
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 |
|
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'- CCAGTGAGAAAGCAGTGTGC -3'
(R):5'- TATCCATTATCGCTACAAGCTTAGCTG -3'
Sequencing Primer
(F):5'- AGTGTGCTCGTTACCTAATTATTTTC -3'
(R):5'- CGCTACAAGCTTAGCTGAAATTTC -3'
|
Posted On |
2015-06-12 |