Incidental Mutation 'R5274:Vps51'
| ID |
403857 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps51
|
| Ensembl Gene |
ENSMUSG00000024797 |
| Gene Name |
VPS51 GARP complex subunit |
| Synonyms |
3110057M17Rik, 1110014N23Rik |
| MMRRC Submission |
042837-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5274 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
19 |
| Chromosomal Location |
6117872-6127217 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to G
at 6121063 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Aspartic acid
at position 283
(E283D)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000123994
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025711]
[ENSMUST00000025713]
[ENSMUST00000113543]
[ENSMUST00000159084]
[ENSMUST00000159832]
[ENSMUST00000160590]
[ENSMUST00000160233]
[ENSMUST00000161718]
[ENSMUST00000160028]
[ENSMUST00000161528]
[ENSMUST00000161090]
[ENSMUST00000162810]
[ENSMUST00000162575]
|
| AlphaFold |
Q3UVL4 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000025711
AA Change: E283D
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000025711
Gene: ENSMUSG00000024799
AA Change: E283D
| 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: ENSMUST00000025713
|
| SMART Domains |
Protein: ENSMUSP00000025713
Gene: ENSMUSG00000024799
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:ERG4_ERG24
|
7 |
418 |
1.6e-141 |
PFAM |
|
Pfam:DUF1295
|
250 |
409 |
9.4e-9 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000113543
|
| SMART Domains |
Protein: ENSMUSP00000109171
Gene: ENSMUSG00000024799
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:ERG4_ERG24
|
7 |
373 |
9.9e-112 |
PFAM |
|
Pfam:DUF1295
|
249 |
396 |
2.6e-8 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000159084
|
| SMART Domains |
Protein: ENSMUSP00000124868
Gene: ENSMUSG00000024799
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:ERG4_ERG24
|
7 |
300 |
6.4e-75 |
PFAM |
|
Pfam:ERG4_ERG24
|
292 |
391 |
2.2e-48 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000159211
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000159475
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000159832
AA Change: E283D
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000123994
Gene: ENSMUSG00000024797
AA Change: E283D
| 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: ENSMUST00000160519
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160354
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161222
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161634
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160417
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000159836
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160324
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000159869
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160590
|
| SMART Domains |
Protein: ENSMUSP00000123857
Gene: ENSMUSG00000024797
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
25 |
N/A |
INTRINSIC |
|
Pfam:Vps51
|
63 |
121 |
2.4e-18 |
PFAM |
|
| 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: ENSMUST00000161718
|
| SMART Domains |
Protein: ENSMUSP00000124283
Gene: ENSMUSG00000024799
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:ERG4_ERG24
|
1 |
197 |
5.7e-86 |
PFAM |
|
Pfam:DUF1295
|
46 |
185 |
1e-8 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160028
|
| SMART Domains |
Protein: ENSMUSP00000124847
Gene: ENSMUSG00000024799
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
7 |
29 |
N/A |
INTRINSIC |
|
transmembrane domain
|
39 |
61 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161528
|
| SMART Domains |
Protein: ENSMUSP00000123989
Gene: ENSMUSG00000024799
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:ERG4_ERG24
|
7 |
109 |
5.3e-9 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161090
|
| SMART Domains |
Protein: ENSMUSP00000125543
Gene: ENSMUSG00000024799
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
13 |
35 |
N/A |
INTRINSIC |
|
transmembrane domain
|
57 |
79 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162721
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162549
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000162810
|
| SMART Domains |
Protein: ENSMUSP00000124825
Gene: ENSMUSG00000024799
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:ERG4_ERG24
|
9 |
124 |
6.9e-34 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000162575
|
| SMART Domains |
Protein: ENSMUSP00000125586
Gene: ENSMUSG00000024799
| Domain | Start | End | E-Value | Type |
|---|
|
transmembrane domain
|
13 |
35 |
N/A |
INTRINSIC |
|
Pfam:ERG4_ERG24
|
51 |
229 |
5.5e-59 |
PFAM |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.5%
- 3x: 98.9%
- 10x: 98.0%
- 20x: 96.9%
|
| 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: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4921539E11Rik |
C |
T |
4: 103,092,856 (GRCm39) |
R155H |
probably benign |
Het |
| Ace |
T |
C |
11: 105,858,863 (GRCm39) |
M19T |
probably benign |
Het |
| Agl |
A |
G |
3: 116,566,135 (GRCm39) |
L995P |
probably damaging |
Het |
| AY761185 |
T |
C |
8: 21,433,889 (GRCm39) |
N90S |
unknown |
Het |
| Brca2 |
T |
C |
5: 150,463,154 (GRCm39) |
S973P |
probably benign |
Het |
| Cacna1e |
T |
C |
1: 154,576,250 (GRCm39) |
T66A |
probably damaging |
Het |
| Cbarp |
T |
C |
10: 79,967,649 (GRCm39) |
S531G |
possibly damaging |
Het |
| Cby2 |
A |
G |
14: 75,820,666 (GRCm39) |
V362A |
probably benign |
Het |
| Cd96 |
G |
T |
16: 45,890,066 (GRCm39) |
T319K |
possibly damaging |
Het |
| Ceacam23 |
T |
C |
7: 17,649,642 (GRCm39) |
|
probably null |
Het |
| Chil5 |
A |
C |
3: 105,936,169 (GRCm39) |
F41C |
probably damaging |
Het |
| Col24a1 |
A |
C |
3: 145,190,433 (GRCm39) |
E1239D |
probably benign |
Het |
| Dip2b |
A |
G |
15: 100,109,985 (GRCm39) |
E1490G |
possibly damaging |
Het |
| Dync1li1 |
T |
C |
9: 114,544,273 (GRCm39) |
V315A |
possibly damaging |
Het |
| Dync2h1 |
T |
C |
9: 7,116,540 (GRCm39) |
S99G |
probably benign |
Het |
| Dynlt5 |
A |
T |
4: 102,859,768 (GRCm39) |
T103S |
possibly damaging |
Het |
| E2f8 |
C |
T |
7: 48,516,925 (GRCm39) |
R818H |
probably damaging |
Het |
| Eomes |
T |
C |
9: 118,309,597 (GRCm39) |
V250A |
probably damaging |
Het |
| Esyt3 |
T |
C |
9: 99,200,350 (GRCm39) |
T615A |
probably benign |
Het |
| Fbxo38 |
A |
T |
18: 62,648,140 (GRCm39) |
D799E |
probably damaging |
Het |
| Fdft1 |
A |
G |
14: 63,389,792 (GRCm39) |
F288S |
probably damaging |
Het |
| Gm14325 |
G |
A |
2: 177,474,777 (GRCm39) |
H102Y |
possibly damaging |
Het |
| Gm4871 |
C |
G |
5: 144,967,180 (GRCm39) |
E185Q |
probably damaging |
Het |
| Gm5901 |
C |
A |
7: 105,026,655 (GRCm39) |
P141Q |
probably damaging |
Het |
| Herc1 |
T |
A |
9: 66,306,691 (GRCm39) |
I933N |
probably benign |
Het |
| Ifih1 |
T |
C |
2: 62,442,062 (GRCm39) |
Q385R |
probably benign |
Het |
| Ighmbp2 |
T |
C |
19: 3,315,518 (GRCm39) |
E634G |
probably damaging |
Het |
| Klk6 |
C |
G |
7: 43,478,553 (GRCm39) |
|
probably null |
Het |
| Kmt2d |
A |
G |
15: 98,752,111 (GRCm39) |
|
probably benign |
Het |
| Lig3 |
T |
A |
11: 82,688,118 (GRCm39) |
|
probably null |
Het |
| Lrp1b |
T |
C |
2: 41,234,456 (GRCm39) |
D310G |
probably null |
Het |
| Mroh6 |
A |
G |
15: 75,756,849 (GRCm39) |
V571A |
possibly damaging |
Het |
| Olfm5 |
A |
G |
7: 103,809,190 (GRCm39) |
S132P |
probably damaging |
Het |
| Or52n20 |
T |
C |
7: 104,320,733 (GRCm39) |
S275P |
probably damaging |
Het |
| Or5p64 |
A |
T |
7: 107,854,842 (GRCm39) |
F168I |
probably benign |
Het |
| Pacc1 |
T |
C |
1: 191,080,665 (GRCm39) |
V295A |
probably damaging |
Het |
| Patj |
G |
C |
4: 98,407,218 (GRCm39) |
S4T |
probably damaging |
Het |
| Pcdhga12 |
T |
A |
18: 37,899,475 (GRCm39) |
C102* |
probably null |
Het |
| Pik3ap1 |
T |
C |
19: 41,270,391 (GRCm39) |
D766G |
possibly damaging |
Het |
| Plch2 |
A |
T |
4: 155,083,411 (GRCm39) |
L408Q |
probably damaging |
Het |
| Pnma2 |
G |
T |
14: 67,154,209 (GRCm39) |
R211L |
probably damaging |
Het |
| Prkg2 |
T |
A |
5: 99,117,850 (GRCm39) |
H468L |
probably damaging |
Het |
| Rad1 |
T |
A |
15: 10,488,059 (GRCm39) |
|
probably null |
Het |
| Rims3 |
A |
G |
4: 120,748,571 (GRCm39) |
D264G |
probably damaging |
Het |
| Rnf123 |
AT |
ATT |
9: 107,941,202 (GRCm39) |
|
probably null |
Het |
| Rrm2 |
T |
A |
12: 24,760,406 (GRCm39) |
Y75* |
probably null |
Het |
| Sall3 |
T |
C |
18: 81,013,052 (GRCm39) |
N1128S |
probably benign |
Het |
| Slc26a5 |
T |
C |
5: 22,018,899 (GRCm39) |
T610A |
possibly damaging |
Het |
| Snx29 |
G |
T |
16: 11,556,268 (GRCm39) |
E766D |
probably damaging |
Het |
| Sox17 |
A |
G |
1: 4,562,111 (GRCm39) |
V298A |
possibly damaging |
Het |
| Ss18 |
G |
A |
18: 14,774,106 (GRCm39) |
Q228* |
probably null |
Het |
| Tas2r121 |
A |
G |
6: 132,677,811 (GRCm39) |
S54P |
probably damaging |
Het |
| Ttc21b |
T |
C |
2: 66,066,627 (GRCm39) |
E342G |
possibly damaging |
Het |
| Ubap2l |
A |
G |
3: 89,920,037 (GRCm39) |
Y818H |
probably damaging |
Het |
| Usp15 |
C |
A |
10: 123,004,256 (GRCm39) |
R166I |
probably damaging |
Het |
| Vmn1r34 |
T |
G |
6: 66,614,123 (GRCm39) |
H205P |
probably damaging |
Het |
| Vmn2r22 |
A |
T |
6: 123,627,593 (GRCm39) |
M1K |
probably null |
Het |
| Zdhhc1 |
T |
C |
8: 106,210,402 (GRCm39) |
N5S |
probably benign |
Het |
| Zfp758 |
T |
A |
17: 22,594,836 (GRCm39) |
C441S |
probably benign |
Het |
| Zp2 |
T |
C |
7: 119,737,315 (GRCm39) |
E291G |
possibly 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 |
|
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 |
|
R5989:Vps51
|
UTSW |
19 |
6,126,402 (GRCm39) |
missense |
probably damaging |
0.96 |
|
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'- TGAGTTGTCACTACCACCCTG -3'
(R):5'- GCCTGGTCATTGTTCTCCAAAC -3'
Sequencing Primer
(F):5'- CTCAACCAGTGCAAAGTAGCGG -3'
(R):5'- TCCAAACACATCGAGTGC -3'
|
| Posted On |
2016-07-22 |
Incidental Mutation