Incidental Mutation 'R2518:Vps54'
| ID |
254091 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
040422-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.931)
|
| Stock # |
R2518 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
11 |
| Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 21256394 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Methionine
at position 633
(T633M)
|
| 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: T633M
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: T633M
| 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: T621M
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: T621M
| 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: T471M
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: T471M
| 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
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.7%
|
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam18 |
A |
G |
8: 25,127,157 (GRCm39) |
C480R |
probably damaging |
Het |
| Aftph |
G |
T |
11: 20,675,797 (GRCm39) |
T604K |
probably damaging |
Het |
| Bivm |
T |
C |
1: 44,168,775 (GRCm39) |
V279A |
probably damaging |
Het |
| C2cd2 |
G |
A |
16: 97,723,286 (GRCm39) |
T77I |
probably benign |
Het |
| Ccdc146 |
T |
C |
5: 21,510,526 (GRCm39) |
H527R |
probably benign |
Het |
| Cd226 |
A |
G |
18: 89,225,451 (GRCm39) |
N116S |
probably benign |
Het |
| Cit |
A |
G |
5: 116,125,105 (GRCm39) |
K1612E |
probably damaging |
Het |
| Cmtr1 |
T |
A |
17: 29,900,954 (GRCm39) |
Y663* |
probably null |
Het |
| Col3a1 |
T |
A |
1: 45,376,672 (GRCm39) |
|
probably benign |
Het |
| Copa |
A |
G |
1: 171,947,468 (GRCm39) |
N1095D |
probably benign |
Het |
| Cpne1 |
G |
T |
2: 155,915,891 (GRCm39) |
A433E |
probably damaging |
Het |
| Cyfip1 |
C |
T |
7: 55,578,032 (GRCm39) |
L1181F |
probably damaging |
Het |
| Dnajc6 |
T |
A |
4: 101,470,127 (GRCm39) |
I220N |
probably damaging |
Het |
| Duxbl1 |
G |
C |
14: 25,988,172 (GRCm39) |
|
probably benign |
Het |
| Fam135b |
C |
T |
15: 71,335,760 (GRCm39) |
R478H |
probably benign |
Het |
| Fam91a1 |
T |
A |
15: 58,322,449 (GRCm39) |
S734T |
possibly damaging |
Het |
| Fut10 |
T |
G |
8: 31,726,495 (GRCm39) |
S417A |
probably benign |
Het |
| Gm9945 |
C |
T |
11: 53,371,163 (GRCm39) |
|
probably benign |
Het |
| Golga4 |
A |
G |
9: 118,385,680 (GRCm39) |
E934G |
probably damaging |
Het |
| Gpat2 |
G |
A |
2: 127,270,211 (GRCm39) |
V75M |
probably damaging |
Het |
| Hdac5 |
A |
G |
11: 102,087,962 (GRCm39) |
V949A |
probably damaging |
Het |
| Hdgfl1 |
G |
T |
13: 26,953,732 (GRCm39) |
L114I |
probably benign |
Het |
| Ifi27l2b |
T |
A |
12: 103,422,083 (GRCm39) |
M94L |
unknown |
Het |
| Irs2 |
C |
A |
8: 11,055,352 (GRCm39) |
A1027S |
probably benign |
Het |
| Itga2 |
A |
T |
13: 115,017,578 (GRCm39) |
C111S |
probably damaging |
Het |
| Khdrbs1 |
T |
C |
4: 129,614,540 (GRCm39) |
T338A |
probably benign |
Het |
| Klk1 |
T |
C |
7: 43,870,161 (GRCm39) |
|
probably null |
Het |
| Kmt2b |
T |
C |
7: 30,275,493 (GRCm39) |
N1822S |
probably benign |
Het |
| Lrig3 |
T |
C |
10: 125,830,310 (GRCm39) |
I136T |
probably benign |
Het |
| Lyar |
T |
A |
5: 38,385,276 (GRCm39) |
D105E |
probably benign |
Het |
| Mat1a |
T |
A |
14: 40,844,469 (GRCm39) |
D366E |
probably benign |
Het |
| Mrc2 |
G |
A |
11: 105,239,257 (GRCm39) |
|
probably null |
Het |
| Naip1 |
A |
T |
13: 100,559,727 (GRCm39) |
D1092E |
probably benign |
Het |
| Neb |
T |
A |
2: 52,139,523 (GRCm39) |
K95* |
probably null |
Het |
| Nectin4 |
A |
G |
1: 171,207,776 (GRCm39) |
D56G |
probably benign |
Het |
| Nup58 |
A |
T |
14: 60,470,109 (GRCm39) |
F334Y |
probably damaging |
Het |
| Or14a256 |
A |
T |
7: 86,265,395 (GRCm39) |
F153I |
probably benign |
Het |
| Or9i1 |
A |
G |
19: 13,839,673 (GRCm39) |
N172S |
probably damaging |
Het |
| Pde8a |
C |
A |
7: 80,967,170 (GRCm39) |
T437K |
probably benign |
Het |
| Ppp1r3a |
A |
T |
6: 14,719,377 (GRCm39) |
N512K |
possibly damaging |
Het |
| Pramel12 |
A |
G |
4: 143,144,473 (GRCm39) |
Q273R |
possibly damaging |
Het |
| Rad51ap2 |
A |
G |
12: 11,507,068 (GRCm39) |
D330G |
probably damaging |
Het |
| Ren1 |
G |
A |
1: 133,287,862 (GRCm39) |
A399T |
probably damaging |
Het |
| Rnft2 |
G |
T |
5: 118,332,670 (GRCm39) |
|
probably benign |
Het |
| Septin14 |
A |
T |
5: 129,776,099 (GRCm39) |
S27T |
probably benign |
Het |
| Shld1 |
T |
A |
2: 132,592,447 (GRCm39) |
S165T |
probably damaging |
Het |
| Shox2 |
T |
C |
3: 66,885,692 (GRCm39) |
K128E |
possibly damaging |
Het |
| Skint1 |
T |
C |
4: 111,882,678 (GRCm39) |
W241R |
probably benign |
Het |
| Slc24a4 |
T |
A |
12: 102,188,310 (GRCm39) |
H134Q |
probably benign |
Het |
| Slc25a36 |
A |
T |
9: 96,961,124 (GRCm39) |
L165Q |
possibly damaging |
Het |
| Slc35f1 |
A |
G |
10: 52,949,630 (GRCm39) |
I240V |
probably benign |
Het |
| Slc66a1 |
A |
G |
4: 139,029,810 (GRCm39) |
F74L |
probably damaging |
Het |
| Tab2 |
G |
A |
10: 7,783,245 (GRCm39) |
P679L |
probably damaging |
Het |
| Tarbp2 |
A |
G |
15: 102,426,992 (GRCm39) |
E3G |
possibly damaging |
Het |
| Tas2r130 |
A |
T |
6: 131,607,036 (GRCm39) |
I253K |
probably damaging |
Het |
| Timm44 |
A |
C |
8: 4,316,588 (GRCm39) |
C319G |
probably null |
Het |
| Tjap1 |
A |
T |
17: 46,571,021 (GRCm39) |
N165K |
probably damaging |
Het |
| Tmem63b |
A |
G |
17: 45,977,080 (GRCm39) |
I429T |
probably benign |
Het |
| Trabd2b |
A |
T |
4: 114,457,100 (GRCm39) |
D339V |
probably damaging |
Het |
| Tst |
T |
C |
15: 78,290,033 (GRCm39) |
M1V |
probably null |
Het |
| Ube4a |
A |
T |
9: 44,859,435 (GRCm39) |
N335K |
probably benign |
Het |
| Zfhx4 |
C |
T |
3: 5,468,418 (GRCm39) |
P2859S |
probably benign |
Het |
| Zfp953 |
A |
G |
13: 67,496,003 (GRCm39) |
Y13H |
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 |
|
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'- CGGCTTTAGACATCTTCAGCTC -3'
(R):5'- ACGTTTACCCTTTAACCACAGC -3'
Sequencing Primer
(F):5'- GCTTTAGACATCTTCAGCTCTGTATG -3'
(R):5'- ACCCTTTAACCACAGCTGTTC -3'
|
| Posted On |
2014-12-04 |
Incidental Mutation