Incidental Mutation 'R5989:Vps51'
ID |
481908 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps51
|
Ensembl Gene |
ENSMUSG00000024797 |
Gene Name |
VPS51 GARP complex subunit |
Synonyms |
3110057M17Rik, 1110014N23Rik |
MMRRC Submission |
044169-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R5989 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
19 |
Chromosomal Location |
6117872-6127217 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 6126402 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Proline
at position 117
(S117P)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000123857
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025707]
[ENSMUST00000025711]
[ENSMUST00000143303]
[ENSMUST00000149347]
[ENSMUST00000159832]
[ENSMUST00000160590]
[ENSMUST00000160233]
[ENSMUST00000160977]
|
AlphaFold |
Q3UVL4 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000025707
|
SMART Domains |
Protein: ENSMUSP00000025707 Gene: ENSMUSG00000024792
Domain | Start | End | E-Value | Type |
RING
|
53 |
100 |
1.14e-1 |
SMART |
low complexity region
|
149 |
160 |
N/A |
INTRINSIC |
low complexity region
|
184 |
193 |
N/A |
INTRINSIC |
transmembrane domain
|
265 |
287 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000025711
AA Change: S117P
PolyPhen 2
Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000025711 Gene: ENSMUSG00000024799 AA Change: S117P
Domain | Start | End | E-Value | Type |
low complexity region
|
2 |
25 |
N/A |
INTRINSIC |
Pfam:COG2
|
56 |
191 |
2.6e-10 |
PFAM |
Pfam:DUF2450
|
62 |
250 |
2.3e-14 |
PFAM |
Pfam:Vps51
|
63 |
149 |
1.1e-26 |
PFAM |
Pfam:Dor1
|
75 |
246 |
1.8e-19 |
PFAM |
Pfam:Zw10
|
83 |
291 |
2.2e-8 |
PFAM |
Pfam:Sec5
|
101 |
275 |
6.5e-24 |
PFAM |
low complexity region
|
377 |
391 |
N/A |
INTRINSIC |
low complexity region
|
523 |
532 |
N/A |
INTRINSIC |
low complexity region
|
743 |
758 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000143303
|
SMART Domains |
Protein: ENSMUSP00000121339 Gene: ENSMUSG00000047733
Domain | Start | End | E-Value | Type |
transmembrane domain
|
7 |
29 |
N/A |
INTRINSIC |
transmembrane domain
|
53 |
75 |
N/A |
INTRINSIC |
transmembrane domain
|
82 |
99 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000149347
|
SMART Domains |
Protein: ENSMUSP00000116436 Gene: ENSMUSG00000047733
Domain | Start | End | E-Value | Type |
transmembrane domain
|
7 |
29 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000159211
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000159832
AA Change: S117P
PolyPhen 2
Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000123994 Gene: ENSMUSG00000024797 AA Change: S117P
Domain | Start | End | E-Value | Type |
low complexity region
|
2 |
25 |
N/A |
INTRINSIC |
Pfam:COG2
|
56 |
191 |
2e-10 |
PFAM |
Pfam:DUF2450
|
62 |
250 |
1.9e-14 |
PFAM |
Pfam:Vps51
|
63 |
149 |
8.3e-27 |
PFAM |
Pfam:Dor1
|
75 |
246 |
1.8e-19 |
PFAM |
Pfam:Sec5
|
101 |
275 |
1.6e-19 |
PFAM |
low complexity region
|
276 |
292 |
N/A |
INTRINSIC |
low complexity region
|
377 |
391 |
N/A |
INTRINSIC |
low complexity region
|
523 |
532 |
N/A |
INTRINSIC |
low complexity region
|
743 |
758 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160131
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000160590
AA Change: S117P
PolyPhen 2
Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000123857 Gene: ENSMUSG00000024797 AA Change: S117P
Domain | Start | End | E-Value | Type |
low complexity region
|
2 |
25 |
N/A |
INTRINSIC |
Pfam:Vps51
|
63 |
121 |
2.4e-18 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160519
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000162374
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000160233
|
SMART Domains |
Protein: ENSMUSP00000124842 Gene: ENSMUSG00000024797
Domain | Start | End | E-Value | Type |
low complexity region
|
2 |
25 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000160977
|
SMART Domains |
Protein: ENSMUSP00000125176 Gene: ENSMUSG00000024792
Domain | Start | End | E-Value | Type |
RING
|
53 |
100 |
1.14e-1 |
SMART |
low complexity region
|
149 |
160 |
N/A |
INTRINSIC |
low complexity region
|
184 |
193 |
N/A |
INTRINSIC |
|
Coding Region Coverage |
- 1x: 99.8%
- 3x: 99.4%
- 10x: 97.0%
- 20x: 90.6%
|
Validation Efficiency |
|
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the vacuolar protein sorting-associated protein 51 family. The encoded protein is a component of the Golgi-associated retrograde protein complex which acts as a tethering factor for carriers in retrograde transport from the early and late endosomes to the trans-Golgi network. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 26 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Cartpt |
T |
A |
13: 100,035,492 (GRCm39) |
I109F |
probably damaging |
Het |
Csmd3 |
G |
A |
15: 47,454,160 (GRCm39) |
P3562L |
possibly damaging |
Het |
Cyp2c40 |
T |
C |
19: 39,796,024 (GRCm39) |
D118G |
probably benign |
Het |
Dmrt1 |
T |
A |
19: 25,523,245 (GRCm39) |
S199T |
possibly damaging |
Het |
Drgx |
A |
G |
14: 32,330,145 (GRCm39) |
N116S |
probably benign |
Het |
Ebf1 |
G |
T |
11: 44,886,998 (GRCm39) |
C565F |
probably damaging |
Het |
Ggnbp1 |
A |
G |
17: 27,248,721 (GRCm39) |
R97G |
probably benign |
Het |
Gm10271 |
A |
T |
10: 116,808,497 (GRCm39) |
F6L |
probably damaging |
Het |
Gm42417 |
A |
G |
1: 36,571,273 (GRCm39) |
F183L |
probably damaging |
Het |
Ipcef1 |
A |
T |
10: 6,929,532 (GRCm39) |
Y69* |
probably null |
Het |
Lcp1 |
A |
T |
14: 75,436,827 (GRCm39) |
M58L |
probably benign |
Het |
Mtif2 |
A |
G |
11: 29,480,098 (GRCm39) |
T55A |
probably damaging |
Het |
Nefm |
A |
G |
14: 68,361,778 (GRCm39) |
V162A |
probably benign |
Het |
Nmral1 |
G |
A |
16: 4,536,902 (GRCm39) |
|
probably benign |
Het |
Or5h23 |
A |
T |
16: 58,906,697 (GRCm39) |
W50R |
probably benign |
Het |
Panx2 |
T |
C |
15: 88,944,455 (GRCm39) |
L60P |
probably damaging |
Het |
Prkag3 |
T |
C |
1: 74,780,433 (GRCm39) |
N411D |
probably benign |
Het |
Ramacl |
G |
A |
13: 67,056,050 (GRCm39) |
M14I |
probably damaging |
Het |
Rnd2 |
C |
T |
11: 101,359,825 (GRCm39) |
L57F |
probably damaging |
Het |
Rttn |
G |
A |
18: 88,991,750 (GRCm39) |
D110N |
probably damaging |
Het |
Sfta2 |
G |
T |
17: 35,960,672 (GRCm39) |
|
probably benign |
Het |
Slc17a3 |
A |
G |
13: 24,026,411 (GRCm39) |
|
probably benign |
Het |
Spem1 |
G |
A |
11: 69,711,951 (GRCm39) |
P238S |
possibly damaging |
Het |
Tmem200c |
G |
T |
17: 69,144,431 (GRCm39) |
|
probably benign |
Het |
Trpm2 |
A |
G |
10: 77,795,734 (GRCm39) |
F131S |
probably damaging |
Het |
Zbtb21 |
G |
A |
16: 97,752,699 (GRCm39) |
P556L |
probably damaging |
Het |
|
Other mutations in Vps51 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL03095:Vps51
|
APN |
19 |
6,120,078 (GRCm39) |
missense |
probably damaging |
1.00 |
R0238:Vps51
|
UTSW |
19 |
6,121,467 (GRCm39) |
nonsense |
probably null |
|
R0238:Vps51
|
UTSW |
19 |
6,121,467 (GRCm39) |
nonsense |
probably null |
|
R0239:Vps51
|
UTSW |
19 |
6,121,467 (GRCm39) |
nonsense |
probably null |
|
R0239:Vps51
|
UTSW |
19 |
6,121,467 (GRCm39) |
nonsense |
probably null |
|
R1533:Vps51
|
UTSW |
19 |
6,121,497 (GRCm39) |
missense |
probably benign |
0.04 |
R1909:Vps51
|
UTSW |
19 |
6,119,499 (GRCm39) |
missense |
probably benign |
0.03 |
R2022:Vps51
|
UTSW |
19 |
6,121,612 (GRCm39) |
missense |
probably benign |
0.02 |
R2146:Vps51
|
UTSW |
19 |
6,118,164 (GRCm39) |
missense |
probably benign |
0.25 |
R2148:Vps51
|
UTSW |
19 |
6,118,164 (GRCm39) |
missense |
probably benign |
0.25 |
R2149:Vps51
|
UTSW |
19 |
6,118,164 (GRCm39) |
missense |
probably benign |
0.25 |
R2901:Vps51
|
UTSW |
19 |
6,126,468 (GRCm39) |
missense |
probably damaging |
0.99 |
R3717:Vps51
|
UTSW |
19 |
6,127,198 (GRCm39) |
utr 3 prime |
probably benign |
|
R3769:Vps51
|
UTSW |
19 |
6,126,378 (GRCm39) |
missense |
possibly damaging |
0.54 |
R5192:Vps51
|
UTSW |
19 |
6,120,497 (GRCm39) |
missense |
possibly damaging |
0.88 |
R5210:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5256:Vps51
|
UTSW |
19 |
6,120,518 (GRCm39) |
missense |
probably benign |
0.00 |
R5260:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5261:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5274:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5294:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5295:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5389:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5391:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5392:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5393:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5421:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5422:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5497:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5498:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5499:Vps51
|
UTSW |
19 |
6,121,063 (GRCm39) |
missense |
probably benign |
0.00 |
R5671:Vps51
|
UTSW |
19 |
6,118,224 (GRCm39) |
missense |
probably benign |
0.18 |
R5963:Vps51
|
UTSW |
19 |
6,118,320 (GRCm39) |
missense |
probably damaging |
1.00 |
R6427:Vps51
|
UTSW |
19 |
6,120,947 (GRCm39) |
missense |
possibly damaging |
0.77 |
R7247:Vps51
|
UTSW |
19 |
6,127,419 (GRCm39) |
utr 3 prime |
probably benign |
|
R9344:Vps51
|
UTSW |
19 |
6,126,345 (GRCm39) |
missense |
unknown |
|
|
Predicted Primers |
PCR Primer
(F):5'- GTGCTGCAGAGAAACTCACTG -3'
(R):5'- TCCAACTAACGTAAAGCAGGG -3'
Sequencing Primer
(F):5'- CAGAGAAACTCACTGCATTTCATTC -3'
(R):5'- CAACTAACGTAAAGCAGGGTAGCAG -3'
|
Posted On |
2017-06-26 |