Incidental Mutation 'R7175:Vps54'
| ID |
558558 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps54
|
| Ensembl Gene |
ENSMUSG00000020128 |
| Gene Name |
VPS54 GARP complex subunit |
| Synonyms |
5330404P15Rik, Vps54l, mSLP8, wr |
| MMRRC Submission |
045231-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.931)
|
| Stock # |
R7175 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
11 |
| Chromosomal Location |
21189281-21271136 bp(+) (GRCm39) |
| Type of Mutation |
critical splice donor site (2 bp from exon) |
| DNA Base Change (assembly) |
T to C
at 21265028 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000006221
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006221]
[ENSMUST00000006221]
[ENSMUST00000109578]
[ENSMUST00000109578]
[ENSMUST00000132017]
[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 null
Transcript: ENSMUST00000006221
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
| 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 null
Transcript: ENSMUST00000006221
|
| SMART Domains |
Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
| 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 null
Transcript: ENSMUST00000109578
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
| 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 null
Transcript: ENSMUST00000109578
|
| SMART Domains |
Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
| 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 null
Transcript: ENSMUST00000132017
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF2450
|
72 |
238 |
1.4e-12 |
PFAM |
|
Pfam:Vps54
|
573 |
707 |
7.8e-64 |
PFAM |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000132017
|
| SMART Domains |
Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
| 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: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
100% (63/63) |
| 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 |
|---|
| Abcb5 |
G |
A |
12: 118,831,611 (GRCm39) |
T1247I |
probably benign |
Het |
| Afdn |
T |
C |
17: 14,108,869 (GRCm39) |
L1479P |
probably damaging |
Het |
| Alox12e |
T |
C |
11: 70,210,534 (GRCm39) |
R363G |
probably damaging |
Het |
| Ank2 |
A |
T |
3: 126,740,590 (GRCm39) |
S1765T |
unknown |
Het |
| Anks6 |
T |
C |
4: 47,046,268 (GRCm39) |
|
probably null |
Het |
| Apob |
A |
C |
12: 8,057,034 (GRCm39) |
I1839L |
probably benign |
Het |
| Bdp1 |
C |
A |
13: 100,186,478 (GRCm39) |
R1658I |
probably damaging |
Het |
| Ccs |
T |
A |
19: 4,883,390 (GRCm39) |
D136V |
probably damaging |
Het |
| Cd200 |
T |
C |
16: 45,220,578 (GRCm39) |
|
probably null |
Het |
| Cirbp |
T |
C |
10: 80,006,297 (GRCm39) |
S130P |
probably benign |
Het |
| Cpb1 |
A |
G |
3: 20,317,927 (GRCm39) |
I199T |
probably benign |
Het |
| Csn3 |
C |
T |
5: 88,077,586 (GRCm39) |
R31C |
probably damaging |
Het |
| Dcaf1 |
A |
T |
9: 106,735,775 (GRCm39) |
I908F |
probably benign |
Het |
| Dhcr7 |
C |
T |
7: 143,399,227 (GRCm39) |
T199I |
probably damaging |
Het |
| Dnah9 |
T |
A |
11: 66,024,463 (GRCm39) |
Q277L |
probably benign |
Het |
| Echdc2 |
C |
A |
4: 108,031,366 (GRCm39) |
P237T |
probably damaging |
Het |
| Efcab3 |
T |
C |
11: 104,838,237 (GRCm39) |
V3625A |
unknown |
Het |
| Eif4g3 |
A |
G |
4: 137,853,526 (GRCm39) |
N364S |
probably damaging |
Het |
| Eml6 |
T |
A |
11: 29,734,231 (GRCm39) |
I1170L |
probably benign |
Het |
| Epha3 |
C |
T |
16: 63,403,863 (GRCm39) |
R746Q |
probably damaging |
Het |
| Exosc5 |
G |
A |
7: 25,363,794 (GRCm39) |
C102Y |
probably damaging |
Het |
| Fam91a1 |
A |
T |
15: 58,302,527 (GRCm39) |
Y289F |
probably benign |
Het |
| Fbxo38 |
A |
C |
18: 62,648,544 (GRCm39) |
F665V |
probably benign |
Het |
| Fcrl5 |
T |
C |
3: 87,353,645 (GRCm39) |
V330A |
probably benign |
Het |
| Fer |
T |
A |
17: 64,231,090 (GRCm39) |
D280E |
probably benign |
Het |
| Gpr158 |
A |
G |
2: 21,373,113 (GRCm39) |
H16R |
probably benign |
Het |
| Gzmg |
C |
T |
14: 56,396,979 (GRCm39) |
M1I |
probably null |
Het |
| Hectd4 |
C |
T |
5: 121,411,692 (GRCm39) |
A456V |
possibly damaging |
Het |
| Hk2 |
T |
A |
6: 82,711,830 (GRCm39) |
Q613L |
probably benign |
Het |
| Inhca |
A |
G |
9: 103,128,988 (GRCm39) |
|
probably null |
Het |
| Itsn1 |
T |
C |
16: 91,664,938 (GRCm39) |
F1121L |
unknown |
Het |
| Lztr1 |
G |
T |
16: 17,340,895 (GRCm39) |
C557F |
possibly damaging |
Het |
| Mdn1 |
A |
G |
4: 32,694,634 (GRCm39) |
Y1119C |
probably damaging |
Het |
| Nfkb1 |
A |
T |
3: 135,319,751 (GRCm39) |
L248Q |
probably damaging |
Het |
| Or1a1 |
T |
A |
11: 74,087,004 (GRCm39) |
L225* |
probably null |
Het |
| Or1p1b |
T |
C |
11: 74,130,803 (GRCm39) |
F138L |
probably benign |
Het |
| Or2g7 |
T |
A |
17: 38,378,370 (GRCm39) |
S103T |
probably damaging |
Het |
| Or52e19 |
T |
C |
7: 102,959,054 (GRCm39) |
V42A |
probably benign |
Het |
| Otulinl |
A |
C |
15: 27,658,374 (GRCm39) |
D165E |
probably damaging |
Het |
| Pate1 |
T |
G |
9: 35,596,408 (GRCm39) |
D119A |
probably damaging |
Het |
| Pcdhgc4 |
T |
C |
18: 37,949,424 (GRCm39) |
V280A |
possibly damaging |
Het |
| Pik3ap1 |
T |
C |
19: 41,275,929 (GRCm39) |
D717G |
probably damaging |
Het |
| Prdm13 |
A |
T |
4: 21,679,473 (GRCm39) |
L339Q |
unknown |
Het |
| Rasgrf1 |
T |
A |
9: 89,862,802 (GRCm39) |
N519K |
probably benign |
Het |
| Rergl |
A |
G |
6: 139,473,533 (GRCm39) |
V39A |
probably benign |
Het |
| Runx2 |
G |
A |
17: 45,125,079 (GRCm39) |
P80L |
probably damaging |
Het |
| Sema4b |
T |
A |
7: 79,848,402 (GRCm39) |
M1K |
probably null |
Het |
| Slc20a1 |
T |
G |
2: 129,052,662 (GRCm39) |
L648R |
probably damaging |
Het |
| Spata31h1 |
T |
A |
10: 82,122,583 (GRCm39) |
S3476C |
probably damaging |
Het |
| Speg |
A |
G |
1: 75,399,134 (GRCm39) |
T2194A |
probably benign |
Het |
| Spns1 |
T |
C |
7: 125,972,961 (GRCm39) |
D215G |
probably damaging |
Het |
| Tle4 |
A |
T |
19: 14,429,071 (GRCm39) |
V717E |
probably damaging |
Het |
| Trim50 |
T |
A |
5: 135,382,151 (GRCm39) |
M1K |
probably null |
Het |
| Trpa1 |
A |
G |
1: 14,963,431 (GRCm39) |
V597A |
possibly damaging |
Het |
| Usp13 |
C |
T |
3: 32,971,757 (GRCm39) |
Q746* |
probably null |
Het |
| Vmn1r35 |
A |
T |
6: 66,655,906 (GRCm39) |
W255R |
probably benign |
Het |
| Vps35 |
A |
T |
8: 85,990,189 (GRCm39) |
|
probably null |
Het |
| Zfp318 |
T |
A |
17: 46,697,774 (GRCm39) |
L210Q |
probably damaging |
Het |
| Zfp319 |
C |
A |
8: 96,055,410 (GRCm39) |
K264N |
probably damaging |
Het |
| Zfp62 |
C |
T |
11: 49,107,580 (GRCm39) |
S557L |
probably damaging |
Het |
| Zgrf1 |
T |
C |
3: 127,357,239 (GRCm39) |
S822P |
probably damaging |
Het |
| Zxdc |
A |
G |
6: 90,346,645 (GRCm39) |
D2G |
possibly damaging |
Het |
| Zzef1 |
T |
C |
11: 72,742,727 (GRCm39) |
I769T |
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 |
|
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'- GACACAGCTCAGAGATTGTCC -3'
(R):5'- CCTCCAGCAATGGGTTACTAG -3'
Sequencing Primer
(F):5'- CTCAGAGATTGTCCAGAAGACTAAGC -3'
(R):5'- GGTGGTGTTAAAGTTCTCACCTAAC -3'
|
| Posted On |
2019-06-26 |
Incidental Mutation