Incidental Mutation 'R8534:Vps54'
| ID |
659166 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
068503-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.931)
|
| Stock # |
R8534 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 21227706 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Serine
at position 93
(N93S)
|
| 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: N219S
PolyPhen 2
Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: N219S
| 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: N207S
PolyPhen 2
Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: N207S
| 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: N93S
PolyPhen 2
Score 0.046 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: N93S
| 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: 100.0%
- 10x: 99.8%
- 20x: 99.2%
|
| Validation Efficiency |
100% (57/57) |
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4921504E06Rik |
A |
C |
2: 19,545,153 (GRCm39) |
L100R |
probably damaging |
Het |
| 6820408C15Rik |
A |
G |
2: 152,283,182 (GRCm39) |
D282G |
probably damaging |
Het |
| Abcb11 |
G |
T |
2: 69,154,190 (GRCm39) |
N125K |
possibly damaging |
Het |
| Acbd7 |
A |
T |
2: 3,341,750 (GRCm39) |
D71V |
probably damaging |
Het |
| Adgrb1 |
A |
T |
15: 74,415,357 (GRCm39) |
T646S |
probably damaging |
Het |
| Adgrv1 |
A |
G |
13: 81,534,887 (GRCm39) |
Y5793H |
probably benign |
Het |
| Agmo |
A |
G |
12: 37,302,538 (GRCm39) |
D125G |
probably damaging |
Het |
| Ahrr |
A |
G |
13: 74,368,799 (GRCm39) |
S125P |
probably damaging |
Het |
| B020011L13Rik |
C |
A |
1: 117,729,034 (GRCm39) |
H180Q |
probably benign |
Het |
| Cbfa2t3 |
T |
C |
8: 123,365,653 (GRCm39) |
D219G |
probably damaging |
Het |
| Ccdc187 |
A |
G |
2: 26,165,577 (GRCm39) |
S860P |
possibly damaging |
Het |
| Ceacam5 |
A |
T |
7: 17,484,671 (GRCm39) |
Q471L |
probably benign |
Het |
| Cyp2c54 |
A |
C |
19: 40,036,030 (GRCm39) |
D293E |
probably damaging |
Het |
| Dnah1 |
G |
T |
14: 31,023,805 (GRCm39) |
N962K |
probably benign |
Het |
| Dst |
C |
T |
1: 34,229,388 (GRCm39) |
T2002I |
probably benign |
Het |
| Elavl1 |
A |
T |
8: 4,339,864 (GRCm39) |
N239K |
probably benign |
Het |
| Elmod3 |
A |
G |
6: 72,543,667 (GRCm39) |
F375L |
probably benign |
Het |
| G6pc2 |
T |
A |
2: 69,050,469 (GRCm39) |
N31K |
probably benign |
Het |
| Ggnbp2 |
C |
T |
11: 84,728,815 (GRCm39) |
|
probably null |
Het |
| Gm6569 |
G |
T |
15: 73,711,673 (GRCm39) |
|
probably benign |
Het |
| Insig1 |
C |
T |
5: 28,280,116 (GRCm39) |
S236L |
probably damaging |
Het |
| Itih4 |
A |
T |
14: 30,622,979 (GRCm39) |
N882I |
probably benign |
Het |
| Kmt5a |
C |
A |
5: 124,598,635 (GRCm39) |
D309E |
probably benign |
Het |
| Kndc1 |
C |
A |
7: 139,503,669 (GRCm39) |
T991N |
probably benign |
Het |
| Lingo1 |
T |
A |
9: 56,528,353 (GRCm39) |
T79S |
probably benign |
Het |
| Myh4 |
A |
T |
11: 67,134,335 (GRCm39) |
E330V |
probably benign |
Het |
| Nlrx1 |
A |
G |
9: 44,174,070 (GRCm39) |
V377A |
probably benign |
Het |
| Npy5r |
C |
A |
8: 67,134,688 (GRCm39) |
G35V |
probably benign |
Het |
| Or5b102 |
T |
A |
19: 13,041,432 (GRCm39) |
I219N |
probably damaging |
Het |
| Or7g33 |
C |
T |
9: 19,448,605 (GRCm39) |
G207D |
possibly damaging |
Het |
| Pabpn1l |
T |
C |
8: 123,349,358 (GRCm39) |
T20A |
probably benign |
Het |
| Pcf11 |
A |
G |
7: 92,302,432 (GRCm39) |
V1226A |
probably benign |
Het |
| Per2 |
G |
A |
1: 91,351,659 (GRCm39) |
T949M |
probably benign |
Het |
| Phc1 |
G |
A |
6: 122,315,539 (GRCm39) |
|
probably benign |
Het |
| Pias2 |
A |
G |
18: 77,185,083 (GRCm39) |
I55V |
possibly damaging |
Het |
| Pik3r2 |
A |
T |
8: 71,227,312 (GRCm39) |
S104T |
probably benign |
Het |
| Pip |
T |
C |
6: 41,828,421 (GRCm39) |
V85A |
probably benign |
Het |
| Pms2 |
T |
C |
5: 143,860,445 (GRCm39) |
V86A |
probably benign |
Het |
| Potefam1 |
G |
A |
2: 111,058,380 (GRCm39) |
P138S |
possibly damaging |
Het |
| Rab44 |
A |
G |
17: 29,363,547 (GRCm39) |
|
probably null |
Het |
| Rrbp1 |
A |
G |
2: 143,830,095 (GRCm39) |
S691P |
probably damaging |
Het |
| Ruvbl2 |
A |
T |
7: 45,079,118 (GRCm39) |
|
probably null |
Het |
| Setbp1 |
T |
C |
18: 78,826,542 (GRCm39) |
D1357G |
possibly damaging |
Het |
| Slc12a6 |
T |
A |
2: 112,174,312 (GRCm39) |
I476N |
probably damaging |
Het |
| Slc1a1 |
C |
T |
19: 28,882,746 (GRCm39) |
P337S |
probably damaging |
Het |
| Slc35b3 |
T |
A |
13: 39,128,566 (GRCm39) |
T174S |
probably benign |
Het |
| Slc4a4 |
A |
T |
5: 89,283,581 (GRCm39) |
I467F |
probably damaging |
Het |
| Slc50a1 |
G |
A |
3: 89,177,710 (GRCm39) |
|
probably null |
Het |
| Spink14 |
G |
A |
18: 44,164,079 (GRCm39) |
|
probably null |
Het |
| Spmap2l |
T |
A |
5: 77,207,325 (GRCm39) |
I361N |
probably damaging |
Het |
| Tmem59 |
T |
C |
4: 107,043,082 (GRCm39) |
|
probably null |
Het |
| Tnr |
G |
A |
1: 159,746,585 (GRCm39) |
E1235K |
probably benign |
Het |
| Trpm6 |
A |
T |
19: 18,869,459 (GRCm39) |
R2015S |
probably benign |
Het |
| Tsnaxip1 |
A |
G |
8: 106,565,370 (GRCm39) |
E132G |
probably damaging |
Het |
| Wdr17 |
T |
G |
8: 55,101,265 (GRCm39) |
I994L |
probably benign |
Het |
| Zfat |
G |
T |
15: 68,037,696 (GRCm39) |
H926Q |
probably damaging |
Het |
| Zfp2 |
C |
T |
11: 50,791,627 (GRCm39) |
E139K |
possibly 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 |
|
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 |
|
|
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'- TGTGTACCAGATTTCAAGATCCC -3'
(R):5'- TGGTGTACAGTGGCCATTAAC -3'
Sequencing Primer
(F):5'- ACCAGATTTCAAGATCCCTTAATTC -3'
(R):5'- GTGTACAGTGGCCATTAACTTCAG -3'
|
| Posted On |
2021-01-18 |
Incidental Mutation