Incidental Mutation 'R5260:Vps51'
| ID |
401412 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps51
|
| Ensembl Gene |
ENSMUSG00000024797 |
| Gene Name |
VPS51 GARP complex subunit |
| Synonyms |
3110057M17Rik, 1110014N23Rik |
| MMRRC Submission |
042829-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5260 (G1)
|
| Quality Score |
225 |
|
Status
|
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: 99.2%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 95.0%
|
| Validation Efficiency |
99% (77/78) |
| 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: 71 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abraxas2 |
A |
T |
7: 132,461,003 (GRCm39) |
I14F |
probably damaging |
Het |
| Acin1 |
T |
C |
14: 54,880,279 (GRCm39) |
|
probably benign |
Het |
| Adamts9 |
C |
A |
6: 92,784,118 (GRCm39) |
V1579L |
probably benign |
Het |
| Adra2a |
T |
A |
19: 54,035,039 (GRCm39) |
C132S |
probably damaging |
Het |
| Aif1 |
T |
A |
17: 35,390,917 (GRCm39) |
|
probably null |
Het |
| Atf5 |
A |
T |
7: 44,464,510 (GRCm39) |
Y27* |
probably null |
Het |
| Atm |
A |
G |
9: 53,417,911 (GRCm39) |
S799P |
probably damaging |
Het |
| Bmp2k |
T |
G |
5: 97,235,210 (GRCm39) |
|
probably benign |
Het |
| Chaf1a |
C |
T |
17: 56,372,000 (GRCm39) |
H723Y |
probably damaging |
Het |
| Clint1 |
T |
C |
11: 45,798,769 (GRCm39) |
W493R |
probably damaging |
Het |
| Cyb561a3 |
T |
A |
19: 10,565,230 (GRCm39) |
V198D |
possibly damaging |
Het |
| Cyp2j8 |
T |
C |
4: 96,389,301 (GRCm39) |
E174G |
possibly damaging |
Het |
| Cyp4v3 |
C |
T |
8: 45,760,017 (GRCm39) |
G512S |
probably damaging |
Het |
| Dnah8 |
T |
A |
17: 30,919,393 (GRCm39) |
V1122D |
probably benign |
Het |
| Doc2b |
C |
A |
11: 75,676,989 (GRCm39) |
G128V |
probably damaging |
Het |
| Dysf |
T |
C |
6: 84,127,016 (GRCm39) |
V1378A |
probably damaging |
Het |
| Efcab5 |
A |
T |
11: 77,028,477 (GRCm39) |
S421T |
possibly damaging |
Het |
| Efcab6 |
T |
G |
15: 83,829,324 (GRCm39) |
D672A |
probably benign |
Het |
| Eif2ak3 |
C |
A |
6: 70,870,113 (GRCm39) |
H933Q |
probably damaging |
Het |
| Erc1 |
A |
T |
6: 119,738,120 (GRCm39) |
N574K |
probably damaging |
Het |
| Eri2 |
A |
T |
7: 119,387,069 (GRCm39) |
|
probably benign |
Het |
| Faxc |
A |
G |
4: 21,948,744 (GRCm39) |
Y152C |
probably damaging |
Het |
| Fbxl7 |
T |
A |
15: 26,543,585 (GRCm39) |
Y354F |
probably damaging |
Het |
| Fras1 |
T |
A |
5: 96,883,046 (GRCm39) |
I2526N |
possibly damaging |
Het |
| Gm5424 |
A |
T |
10: 61,907,374 (GRCm39) |
|
noncoding transcript |
Het |
| Gm6728 |
T |
C |
6: 136,463,701 (GRCm39) |
|
noncoding transcript |
Het |
| Golgb1 |
A |
T |
16: 36,733,503 (GRCm39) |
S917C |
probably benign |
Het |
| Gtpbp3 |
T |
C |
8: 71,942,062 (GRCm39) |
|
probably benign |
Het |
| Gusb |
A |
T |
5: 130,028,829 (GRCm39) |
Y220* |
probably null |
Het |
| Gvin3 |
A |
G |
7: 106,198,411 (GRCm39) |
|
noncoding transcript |
Het |
| Hmcn1 |
A |
G |
1: 150,471,612 (GRCm39) |
V4914A |
possibly damaging |
Het |
| Iars2 |
C |
A |
1: 185,055,931 (GRCm39) |
C211F |
probably damaging |
Het |
| Kif5b |
A |
G |
18: 6,211,058 (GRCm39) |
L802P |
probably damaging |
Het |
| Kif5c |
A |
G |
2: 49,625,602 (GRCm39) |
E624G |
probably damaging |
Het |
| Kmt2d |
G |
T |
15: 98,740,741 (GRCm39) |
|
probably benign |
Het |
| Krt82 |
C |
A |
15: 101,456,823 (GRCm39) |
G186C |
possibly damaging |
Het |
| Lca5 |
G |
A |
9: 83,305,276 (GRCm39) |
R177C |
probably damaging |
Het |
| Mab21l4 |
A |
T |
1: 93,087,700 (GRCm39) |
V51E |
probably damaging |
Het |
| Mier1 |
T |
C |
4: 103,019,907 (GRCm39) |
S318P |
probably benign |
Het |
| Obscn |
A |
T |
11: 58,894,195 (GRCm39) |
I1207N |
probably damaging |
Het |
| Oog4 |
C |
T |
4: 143,164,424 (GRCm39) |
G369D |
probably benign |
Het |
| Or4c126 |
A |
G |
2: 89,824,526 (GRCm39) |
D263G |
probably damaging |
Het |
| Or4k52 |
A |
G |
2: 111,611,526 (GRCm39) |
Y287C |
probably damaging |
Het |
| Or52d13 |
A |
G |
7: 103,109,822 (GRCm39) |
F198L |
probably benign |
Het |
| Or5d35 |
A |
C |
2: 87,855,818 (GRCm39) |
I251L |
probably benign |
Het |
| Plec |
T |
C |
15: 76,060,824 (GRCm39) |
T3060A |
probably damaging |
Het |
| Plekhh2 |
C |
T |
17: 84,884,593 (GRCm39) |
T769I |
probably damaging |
Het |
| Prkaa1 |
A |
T |
15: 5,190,149 (GRCm39) |
S65C |
probably damaging |
Het |
| Psma3 |
T |
C |
12: 71,031,416 (GRCm39) |
|
probably benign |
Het |
| Ptpn18 |
T |
A |
1: 34,502,591 (GRCm39) |
|
probably benign |
Het |
| Ptprv |
T |
C |
1: 135,039,998 (GRCm39) |
|
noncoding transcript |
Het |
| Rac1 |
C |
A |
5: 143,493,886 (GRCm39) |
V104L |
probably benign |
Het |
| Serpinb7 |
A |
T |
1: 107,362,479 (GRCm39) |
N61I |
possibly damaging |
Het |
| Sirt7 |
A |
C |
11: 120,511,347 (GRCm39) |
|
probably benign |
Het |
| Srl |
G |
A |
16: 4,300,759 (GRCm39) |
R333* |
probably null |
Het |
| Srprb |
A |
T |
9: 103,079,119 (GRCm39) |
L756Q |
probably damaging |
Het |
| Tchhl1 |
T |
C |
3: 93,378,102 (GRCm39) |
S269P |
probably damaging |
Het |
| Tdo2 |
C |
T |
3: 81,882,630 (GRCm39) |
|
probably null |
Het |
| Teddm1a |
T |
C |
1: 153,767,646 (GRCm39) |
Y37H |
probably benign |
Het |
| Tenm3 |
T |
C |
8: 48,689,890 (GRCm39) |
Y1899C |
probably damaging |
Het |
| Tep1 |
T |
C |
14: 51,076,088 (GRCm39) |
T1681A |
probably benign |
Het |
| Timm44 |
G |
T |
8: 4,325,919 (GRCm39) |
|
probably null |
Het |
| Trp73 |
A |
G |
4: 154,147,059 (GRCm39) |
V322A |
possibly damaging |
Het |
| Tsr1 |
A |
C |
11: 74,796,781 (GRCm39) |
E611A |
probably damaging |
Het |
| Unc80 |
A |
G |
1: 66,685,746 (GRCm39) |
N2290S |
possibly damaging |
Het |
| Ush2a |
T |
C |
1: 188,679,276 (GRCm39) |
V4828A |
possibly damaging |
Het |
| Wnt9b |
C |
A |
11: 103,622,875 (GRCm39) |
S176I |
possibly damaging |
Het |
| Zfp329 |
A |
G |
7: 12,540,453 (GRCm39) |
|
probably benign |
Het |
| Zfp352 |
T |
A |
4: 90,112,697 (GRCm39) |
V279D |
probably damaging |
Het |
| Zfp932 |
C |
T |
5: 110,157,501 (GRCm39) |
Q400* |
probably null |
Het |
| Zxdc |
T |
A |
6: 90,359,075 (GRCm39) |
L569Q |
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 |
|
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 |
|
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'- CAACCAGTGCAAAGTAGCGG -3'
(R):5'- GCCTGGTCATTGTTCTCCAAAC -3'
Sequencing Primer
(F):5'- CCAGCTCCTGCGCAAAG -3'
(R):5'- TCCAAACACATCGAGTGC -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation