Incidental Mutation 'R1875:Vps54'
| ID |
211163 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
039897-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.933)
|
| Stock # |
R1875 (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 21250251 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 396
(T396A)
|
| 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: T558A
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: T558A
| 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: T546A
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: T546A
| 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 |
noncoding transcript
Transcript: ENSMUST00000120479
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000132017
AA Change: T396A
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: T396A
| 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: ENSMUST00000143932
|
| Meta Mutation Damage Score |
0.0593 |
| Coding Region Coverage |
- 1x: 97.4%
- 3x: 96.8%
- 10x: 95.1%
- 20x: 92.1%
|
| Validation Efficiency |
98% (85/87) |
| 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: 80 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca14 |
A |
T |
7: 119,847,190 (GRCm39) |
M685L |
possibly damaging |
Het |
| Abi3bp |
A |
G |
16: 56,394,862 (GRCm39) |
Y190C |
probably damaging |
Het |
| Adam26a |
C |
A |
8: 44,022,888 (GRCm39) |
V201L |
probably benign |
Het |
| Adamts20 |
G |
T |
15: 94,229,277 (GRCm39) |
D947E |
probably benign |
Het |
| Ankrd26 |
A |
G |
6: 118,517,410 (GRCm39) |
|
probably null |
Het |
| Apol11a |
C |
A |
15: 77,397,766 (GRCm39) |
T39N |
possibly damaging |
Het |
| Arhgef38 |
T |
A |
3: 132,839,501 (GRCm39) |
|
probably null |
Het |
| Armh4 |
T |
C |
14: 49,919,815 (GRCm39) |
D772G |
probably damaging |
Het |
| Atp11b |
T |
C |
3: 35,893,296 (GRCm39) |
L883P |
probably damaging |
Het |
| Btnl10 |
T |
A |
11: 58,814,586 (GRCm39) |
I422N |
probably damaging |
Het |
| C2cd3 |
A |
G |
7: 100,056,232 (GRCm39) |
K547E |
possibly damaging |
Het |
| Cdh2 |
T |
A |
18: 16,757,934 (GRCm39) |
L549F |
probably benign |
Het |
| Celsr3 |
T |
C |
9: 108,713,037 (GRCm39) |
V1825A |
probably benign |
Het |
| Cfap221 |
T |
C |
1: 119,881,389 (GRCm39) |
I358V |
probably benign |
Het |
| Cimap2 |
G |
A |
4: 106,470,453 (GRCm39) |
|
probably benign |
Het |
| Csmd1 |
T |
C |
8: 15,979,101 (GRCm39) |
K2828E |
probably damaging |
Het |
| Ddah2 |
T |
C |
17: 35,279,821 (GRCm39) |
F137S |
probably damaging |
Het |
| Ddx21 |
A |
G |
10: 62,429,847 (GRCm39) |
I299T |
probably damaging |
Het |
| Dnah7a |
A |
T |
1: 53,495,691 (GRCm39) |
|
probably benign |
Het |
| Elmod1 |
A |
G |
9: 53,843,151 (GRCm39) |
I9T |
probably benign |
Het |
| Epha2 |
A |
G |
4: 141,036,290 (GRCm39) |
E242G |
probably benign |
Het |
| Erbb3 |
T |
C |
10: 128,410,335 (GRCm39) |
H641R |
possibly damaging |
Het |
| Fbxl18 |
G |
A |
5: 142,871,978 (GRCm39) |
A419V |
probably damaging |
Het |
| Fli1 |
T |
C |
9: 32,335,209 (GRCm39) |
M408V |
probably benign |
Het |
| Fmo4 |
T |
C |
1: 162,631,187 (GRCm39) |
N260S |
possibly damaging |
Het |
| Fry |
A |
G |
5: 150,249,597 (GRCm39) |
E136G |
probably damaging |
Het |
| Gm10477 |
T |
A |
X: 55,570,127 (GRCm39) |
F9Y |
probably damaging |
Het |
| Gm8258 |
A |
G |
5: 104,924,320 (GRCm39) |
|
noncoding transcript |
Het |
| Gpr68 |
T |
A |
12: 100,845,049 (GRCm39) |
D165V |
probably damaging |
Het |
| Htt |
T |
A |
5: 34,951,456 (GRCm39) |
M139K |
probably benign |
Het |
| Jup |
A |
G |
11: 100,263,120 (GRCm39) |
|
probably null |
Het |
| Kifc5b |
G |
A |
17: 27,136,264 (GRCm39) |
|
probably null |
Het |
| Krba1 |
T |
A |
6: 48,390,983 (GRCm39) |
|
probably null |
Het |
| Lamp1 |
G |
A |
8: 13,217,257 (GRCm39) |
G89R |
probably damaging |
Het |
| Lrrc17 |
C |
T |
5: 21,765,650 (GRCm39) |
S44F |
possibly damaging |
Het |
| Mdga1 |
T |
C |
17: 30,071,581 (GRCm39) |
T347A |
probably damaging |
Het |
| Mical3 |
A |
T |
6: 121,019,025 (GRCm39) |
W66R |
probably damaging |
Het |
| Mpl |
A |
G |
4: 118,314,026 (GRCm39) |
Y73H |
probably benign |
Het |
| Mterf1b |
T |
A |
5: 4,247,364 (GRCm39) |
I335N |
possibly damaging |
Het |
| Mylk3 |
A |
G |
8: 86,079,494 (GRCm39) |
I388T |
probably damaging |
Het |
| Myo15a |
C |
T |
11: 60,398,354 (GRCm39) |
R2775W |
probably damaging |
Het |
| Myoz2 |
A |
T |
3: 122,819,765 (GRCm39) |
S65T |
probably damaging |
Het |
| Ndrg1 |
T |
C |
15: 66,802,940 (GRCm39) |
T137A |
possibly damaging |
Het |
| Neil3 |
G |
T |
8: 54,052,454 (GRCm39) |
N381K |
probably damaging |
Het |
| Obsl1 |
T |
C |
1: 75,474,877 (GRCm39) |
Y841C |
probably damaging |
Het |
| Or2b4 |
A |
G |
17: 38,115,996 (GRCm39) |
|
probably benign |
Het |
| Or6b6 |
G |
A |
7: 106,571,389 (GRCm39) |
S54F |
possibly damaging |
Het |
| Otogl |
T |
C |
10: 107,735,451 (GRCm39) |
D111G |
probably damaging |
Het |
| Parp10 |
T |
C |
15: 76,127,051 (GRCm39) |
E103G |
probably damaging |
Het |
| Pars2 |
T |
C |
4: 106,510,913 (GRCm39) |
F232L |
possibly damaging |
Het |
| Pcdh18 |
A |
T |
3: 49,709,154 (GRCm39) |
F720L |
probably damaging |
Het |
| Phf3 |
T |
C |
1: 30,869,704 (GRCm39) |
E448G |
possibly damaging |
Het |
| Pigc |
A |
G |
1: 161,798,516 (GRCm39) |
Y166C |
probably damaging |
Het |
| Pik3c2a |
A |
T |
7: 116,017,206 (GRCm39) |
S184T |
probably benign |
Het |
| Pkd1l1 |
A |
G |
11: 8,794,670 (GRCm39) |
|
probably benign |
Het |
| Plch2 |
G |
A |
4: 155,082,965 (GRCm39) |
S485F |
probably damaging |
Het |
| Plxnd1 |
G |
T |
6: 115,955,045 (GRCm39) |
|
probably null |
Het |
| Pnliprp2 |
G |
T |
19: 58,751,821 (GRCm39) |
V189L |
probably benign |
Het |
| Prl8a2 |
T |
C |
13: 27,535,037 (GRCm39) |
V103A |
probably benign |
Het |
| Psg23 |
G |
A |
7: 18,344,375 (GRCm39) |
T360I |
probably benign |
Het |
| Rad51c |
A |
T |
11: 87,279,469 (GRCm39) |
I323N |
probably damaging |
Het |
| Rsbn1l |
C |
T |
5: 21,156,696 (GRCm39) |
E30K |
probably benign |
Het |
| Serpina3c |
C |
A |
12: 104,118,145 (GRCm39) |
L64F |
probably damaging |
Het |
| Shroom1 |
A |
G |
11: 53,356,502 (GRCm39) |
D392G |
probably damaging |
Het |
| Slc26a5 |
T |
A |
5: 22,020,725 (GRCm39) |
I540L |
probably benign |
Het |
| Slc37a4 |
A |
G |
9: 44,312,808 (GRCm39) |
T321A |
probably damaging |
Het |
| Slc41a2 |
A |
G |
10: 83,091,949 (GRCm39) |
L438S |
probably damaging |
Het |
| Spef2 |
C |
T |
15: 9,584,194 (GRCm39) |
E1624K |
probably damaging |
Het |
| Spef2 |
C |
T |
15: 9,597,487 (GRCm39) |
G1390R |
possibly damaging |
Het |
| Spmap2l |
A |
T |
5: 77,202,431 (GRCm39) |
K284M |
probably benign |
Het |
| Synj2 |
G |
T |
17: 6,078,825 (GRCm39) |
A740S |
possibly damaging |
Het |
| Tigd4 |
A |
C |
3: 84,502,394 (GRCm39) |
D437A |
probably benign |
Het |
| Timm21 |
G |
C |
18: 84,967,387 (GRCm39) |
L130V |
probably damaging |
Het |
| Tmem106a |
CAGCTCAACACGACGGTA |
CAGCTCAACACGACGGTAAGCTCAACACGACGGTA |
11: 101,477,204 (GRCm39) |
|
probably benign |
Het |
| Tmem131l |
A |
T |
3: 83,812,383 (GRCm39) |
C1313* |
probably null |
Het |
| Tmem86b |
A |
T |
7: 4,632,698 (GRCm39) |
I47N |
possibly damaging |
Het |
| Tspan13 |
T |
C |
12: 36,070,550 (GRCm39) |
|
probably null |
Het |
| Zfp106 |
A |
T |
2: 120,344,096 (GRCm39) |
|
probably null |
Het |
| Zfp668 |
T |
C |
7: 127,465,654 (GRCm39) |
|
probably null |
Het |
| Zfp809 |
A |
T |
9: 22,150,027 (GRCm39) |
R175* |
probably null |
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 |
|
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 |
|
|
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'- ACAGCTCCTTGGACACAGAC -3'
(R):5'- CTAAGATCCTGTAATCTCTCCACTG -3'
Sequencing Primer
(F):5'- AGACGTGGCTTACCTGACAC -3'
(R):5'- GTAATCTCTCCACTGTCTCCACGG -3'
|
| Posted On |
2014-06-30 |
Incidental Mutation