Incidental Mutation 'R9034:Vps54'
| ID |
687236 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
068863-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.933)
|
| Stock # |
R9034 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 21213273 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Leucine
at position 19
(F19L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000006221
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000109578]
|
| 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: F19L
PolyPhen 2
Score 0.289 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: F19L
| 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: F19L
PolyPhen 2
Score 0.412 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: F19L
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.4%
- 20x: 97.9%
|
| Validation Efficiency |
95% (57/60) |
| 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: 62 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca9 |
T |
C |
11: 110,039,615 (GRCm39) |
D466G |
probably benign |
Het |
| Acvr2a |
T |
C |
2: 48,763,381 (GRCm39) |
Y142H |
probably damaging |
Het |
| Agfg1 |
C |
T |
1: 82,853,913 (GRCm39) |
Q188* |
probably null |
Het |
| Akap11 |
C |
A |
14: 78,748,299 (GRCm39) |
V1363F |
|
Het |
| Aldh3a1 |
A |
G |
11: 61,104,475 (GRCm39) |
T121A |
probably benign |
Het |
| Arid1b |
T |
A |
17: 5,387,180 (GRCm39) |
D1491E |
probably benign |
Het |
| Baz2a |
A |
G |
10: 127,952,268 (GRCm39) |
T617A |
probably damaging |
Het |
| Cacna1c |
T |
C |
6: 118,728,359 (GRCm39) |
M362V |
|
Het |
| Cant1 |
T |
A |
11: 118,302,128 (GRCm39) |
H63L |
probably benign |
Het |
| Cdkn2aip |
C |
A |
8: 48,164,243 (GRCm39) |
C490F |
probably damaging |
Het |
| Cenpn |
T |
A |
8: 117,661,478 (GRCm39) |
D192E |
probably benign |
Het |
| Clint1 |
C |
A |
11: 45,799,782 (GRCm39) |
L514M |
probably benign |
Het |
| Clint1 |
T |
A |
11: 45,799,783 (GRCm39) |
L514Q |
possibly damaging |
Het |
| Cmklr1 |
G |
C |
5: 113,752,043 (GRCm39) |
H319Q |
probably benign |
Het |
| Cspg5 |
T |
C |
9: 110,080,089 (GRCm39) |
F419S |
probably damaging |
Het |
| Ehmt2 |
C |
A |
17: 35,122,417 (GRCm39) |
A328E |
probably benign |
Het |
| Ercc6l2 |
T |
C |
13: 63,992,447 (GRCm39) |
S299P |
probably damaging |
Het |
| F13b |
T |
C |
1: 139,435,961 (GRCm39) |
C256R |
probably damaging |
Het |
| F830016B08Rik |
A |
G |
18: 60,433,141 (GRCm39) |
T75A |
probably damaging |
Het |
| Fam227a |
T |
C |
15: 79,532,952 (GRCm39) |
M69V |
probably benign |
Het |
| Gm40460 |
GCAGCAGCTGGACTGGCAGCAGCAGGGCTTACAGCAGCTGGACTGGCAGCAGCAGGGCTTACAGCAGCTGGACTGGCAGCAGCAGGGCTTACAGCAGCTGGACTGGCAGCAG |
GCAGCAGCTGGACTGGCAGCAGCAGGGCTTACAGCAGCTGGACTGGCAGCAGCAGGGCTTACAGCAGCTGGACTGGCAGCAG |
7: 141,794,171 (GRCm39) |
|
probably benign |
Het |
| Grin2c |
C |
T |
11: 115,142,065 (GRCm39) |
E785K |
probably damaging |
Het |
| H2-M2 |
A |
T |
17: 37,792,176 (GRCm39) |
S325T |
probably benign |
Het |
| Hmgcr |
A |
G |
13: 96,795,885 (GRCm39) |
S261P |
probably damaging |
Het |
| Impg1 |
T |
A |
9: 80,347,351 (GRCm39) |
|
probably benign |
Het |
| Irag2 |
T |
C |
6: 145,083,273 (GRCm39) |
V4A |
probably benign |
Het |
| Krit1 |
A |
G |
5: 3,862,996 (GRCm39) |
|
probably benign |
Het |
| Krtap26-1 |
A |
T |
16: 88,444,161 (GRCm39) |
N153K |
probably benign |
Het |
| Mfsd14b |
G |
T |
13: 65,223,500 (GRCm39) |
A178E |
probably damaging |
Het |
| Muc4 |
CAC |
CACTAC |
16: 32,575,367 (GRCm39) |
|
probably benign |
Het |
| Myh6 |
A |
T |
14: 55,185,596 (GRCm39) |
I1531N |
possibly damaging |
Het |
| Myo7a |
G |
T |
7: 97,728,465 (GRCm39) |
A836D |
probably benign |
Het |
| Ncam1 |
A |
T |
9: 49,481,198 (GRCm39) |
S19T |
probably benign |
Het |
| Nes |
T |
A |
3: 87,885,735 (GRCm39) |
D1331E |
probably damaging |
Het |
| Nsd2 |
G |
A |
5: 34,037,478 (GRCm39) |
R700Q |
possibly damaging |
Het |
| Nxt1 |
A |
T |
2: 148,517,331 (GRCm39) |
Y24F |
possibly damaging |
Het |
| Or14c39 |
G |
A |
7: 86,343,969 (GRCm39) |
V102I |
probably benign |
Het |
| Or52n4 |
T |
A |
7: 104,293,835 (GRCm39) |
H248L |
probably damaging |
Het |
| Or5g24-ps1 |
A |
T |
2: 85,464,144 (GRCm39) |
T124S |
probably benign |
Het |
| Or6f2 |
G |
A |
7: 139,756,884 (GRCm39) |
V284I |
probably benign |
Het |
| Or8b40 |
G |
A |
9: 38,027,550 (GRCm39) |
V158M |
possibly damaging |
Het |
| Or8g50 |
G |
A |
9: 39,648,886 (GRCm39) |
M258I |
probably benign |
Het |
| Or9g20 |
G |
T |
2: 85,630,302 (GRCm39) |
A104E |
possibly damaging |
Het |
| Pex5l |
T |
A |
3: 33,006,683 (GRCm39) |
Q562L |
probably damaging |
Het |
| Plxna2 |
A |
G |
1: 194,476,197 (GRCm39) |
Y1139C |
probably damaging |
Het |
| Prelp |
T |
C |
1: 133,842,329 (GRCm39) |
N272S |
probably damaging |
Het |
| Rtkn2 |
A |
G |
10: 67,841,416 (GRCm39) |
K188R |
probably damaging |
Het |
| Sbno2 |
G |
A |
10: 79,898,591 (GRCm39) |
R624W |
probably damaging |
Het |
| Scn8a |
T |
A |
15: 100,927,642 (GRCm39) |
C1374S |
probably damaging |
Het |
| Serpina1e |
T |
A |
12: 103,917,361 (GRCm39) |
T103S |
probably benign |
Het |
| Sh3tc2 |
A |
G |
18: 62,107,571 (GRCm39) |
E194G |
probably benign |
Het |
| Slc36a3 |
A |
T |
11: 55,016,515 (GRCm39) |
I360N |
probably damaging |
Het |
| Sphk1 |
T |
C |
11: 116,426,449 (GRCm39) |
V135A |
probably damaging |
Het |
| Tnfsf10 |
G |
A |
3: 27,389,379 (GRCm39) |
D147N |
probably benign |
Het |
| Tnip2 |
C |
T |
5: 34,671,177 (GRCm39) |
C22Y |
probably damaging |
Het |
| Trmt9b |
C |
T |
8: 36,978,954 (GRCm39) |
R186* |
probably null |
Het |
| Trp73 |
T |
C |
4: 154,152,088 (GRCm39) |
T187A |
probably benign |
Het |
| Tspan33 |
C |
T |
6: 29,717,611 (GRCm39) |
Q276* |
probably null |
Het |
| Ttn |
C |
T |
2: 76,542,871 (GRCm39) |
G33372R |
probably damaging |
Het |
| Vmn2r31 |
T |
A |
7: 7,397,680 (GRCm39) |
T193S |
probably benign |
Het |
| Vwa8 |
A |
G |
14: 79,296,179 (GRCm39) |
T856A |
probably damaging |
Het |
| Zscan4b |
A |
T |
7: 10,634,840 (GRCm39) |
Y468N |
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 |
|
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 |
|
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'- GAGGAAGTACTACCTTGTTTTGCT -3'
(R):5'- TTCCCCAATTGACTACACGTTT -3'
Sequencing Primer
(F):5'- GATAGAAGGTTTCTCCGTATAGCCC -3'
(R):5'- ACCTCTAGAAGAGCTGTCAGTGTTC -3'
|
| Posted On |
2021-11-19 |
Incidental Mutation