Incidental Mutation 'R5389:Vps51'
| ID |
425500 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps51
|
| Ensembl Gene |
ENSMUSG00000024797 |
| Gene Name |
VPS51 GARP complex subunit |
| Synonyms |
3110057M17Rik, 1110014N23Rik |
| MMRRC Submission |
042961-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5389 (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: 99.4%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.7%
|
| Validation Efficiency |
98% (65/66) |
| 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: 64 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4921524L21Rik |
T |
C |
18: 6,638,795 (GRCm39) |
V398A |
probably benign |
Het |
| A430033K04Rik |
T |
A |
5: 138,644,559 (GRCm39) |
V148E |
probably benign |
Het |
| Acyp2 |
C |
T |
11: 30,456,354 (GRCm39) |
E98K |
possibly damaging |
Het |
| Ankrd26 |
T |
A |
6: 118,485,536 (GRCm39) |
Q1446L |
possibly damaging |
Het |
| Anks6 |
A |
T |
4: 47,038,900 (GRCm39) |
|
probably benign |
Het |
| Arrb2 |
T |
C |
11: 70,329,484 (GRCm39) |
S265P |
probably damaging |
Het |
| Baiap2 |
T |
C |
11: 119,887,496 (GRCm39) |
S264P |
probably damaging |
Het |
| Cadps2 |
A |
G |
6: 23,329,103 (GRCm39) |
V938A |
probably damaging |
Het |
| Cavin4 |
G |
T |
4: 48,663,907 (GRCm39) |
V96F |
probably damaging |
Het |
| Cenpe |
T |
C |
3: 134,965,149 (GRCm39) |
|
probably null |
Het |
| Crocc2 |
C |
A |
1: 93,143,363 (GRCm39) |
Q1322K |
probably benign |
Het |
| Cryzl2 |
T |
A |
1: 157,289,546 (GRCm39) |
C61* |
probably null |
Het |
| Dazl |
T |
C |
17: 50,595,718 (GRCm39) |
I56V |
probably benign |
Het |
| Dnah12 |
A |
T |
14: 26,456,904 (GRCm39) |
D890V |
probably damaging |
Het |
| Dnah9 |
C |
A |
11: 65,986,140 (GRCm39) |
E1165* |
probably null |
Het |
| Dnmt3l |
T |
A |
10: 77,892,665 (GRCm39) |
|
probably null |
Het |
| Elp2 |
A |
G |
18: 24,739,960 (GRCm39) |
N62S |
possibly damaging |
Het |
| Entr1 |
T |
C |
2: 26,275,559 (GRCm39) |
D244G |
probably damaging |
Het |
| Fam216b |
T |
A |
14: 78,322,503 (GRCm39) |
H26L |
possibly damaging |
Het |
| Fbxw25 |
T |
A |
9: 109,481,954 (GRCm39) |
Q244L |
possibly damaging |
Het |
| G530012D18Rik |
G |
C |
1: 85,504,923 (GRCm39) |
|
probably benign |
Het |
| Gvin3 |
T |
C |
7: 106,197,442 (GRCm39) |
|
noncoding transcript |
Het |
| Igf2r |
T |
C |
17: 12,944,303 (GRCm39) |
Y400C |
probably damaging |
Het |
| Iqcc |
A |
G |
4: 129,512,413 (GRCm39) |
F20L |
probably benign |
Het |
| Klhl5 |
T |
A |
5: 65,298,625 (GRCm39) |
L135M |
possibly damaging |
Het |
| Klk1b16 |
A |
T |
7: 43,790,412 (GRCm39) |
M196L |
possibly damaging |
Het |
| Ltf |
T |
C |
9: 110,858,719 (GRCm39) |
M489T |
possibly damaging |
Het |
| Mctp2 |
G |
T |
7: 71,863,835 (GRCm39) |
R343S |
possibly damaging |
Het |
| Nbas |
T |
A |
12: 13,584,578 (GRCm39) |
|
probably null |
Het |
| Ncr1 |
A |
T |
7: 4,343,932 (GRCm39) |
M177L |
probably benign |
Het |
| Net1 |
C |
T |
13: 3,936,170 (GRCm39) |
E305K |
probably damaging |
Het |
| Nfx1 |
T |
C |
4: 40,985,000 (GRCm39) |
F375L |
probably damaging |
Het |
| Notch3 |
T |
A |
17: 32,358,163 (GRCm39) |
I1687L |
probably benign |
Het |
| Obsl1 |
A |
T |
1: 75,479,905 (GRCm39) |
|
probably benign |
Het |
| Or2ag16 |
A |
T |
7: 106,352,290 (GRCm39) |
F102I |
probably damaging |
Het |
| Or2t46 |
C |
G |
11: 58,471,825 (GRCm39) |
L52V |
possibly damaging |
Het |
| Or51v14 |
G |
T |
7: 103,260,797 (GRCm39) |
Y254* |
probably null |
Het |
| Or5g23 |
A |
G |
2: 85,438,627 (GRCm39) |
F209S |
probably benign |
Het |
| Or5j3 |
G |
A |
2: 86,128,561 (GRCm39) |
V134M |
possibly damaging |
Het |
| Or5p79 |
A |
C |
7: 108,221,924 (GRCm39) |
I302L |
probably damaging |
Het |
| Orai1 |
A |
T |
5: 123,167,564 (GRCm39) |
M246L |
probably benign |
Het |
| Pcdhga12 |
G |
A |
18: 37,899,785 (GRCm39) |
A206T |
probably damaging |
Het |
| Plxdc2 |
C |
A |
2: 16,654,998 (GRCm39) |
T199K |
probably damaging |
Het |
| Prkd1 |
T |
A |
12: 50,389,920 (GRCm39) |
I819F |
probably damaging |
Het |
| Ptpn9 |
T |
C |
9: 56,964,121 (GRCm39) |
|
probably benign |
Het |
| Rabl6 |
T |
C |
2: 25,478,666 (GRCm39) |
E255G |
probably damaging |
Het |
| Sema3e |
T |
C |
5: 14,286,099 (GRCm39) |
|
probably benign |
Het |
| Serpina3c |
T |
C |
12: 104,115,699 (GRCm39) |
M282V |
possibly damaging |
Het |
| Slco1a7 |
A |
G |
6: 141,686,193 (GRCm39) |
F216L |
probably benign |
Het |
| Slco2b1 |
A |
G |
7: 99,335,132 (GRCm39) |
I216T |
probably damaging |
Het |
| Slco6b1 |
T |
C |
1: 96,916,309 (GRCm39) |
|
noncoding transcript |
Het |
| Slco6d1 |
A |
T |
1: 98,371,369 (GRCm39) |
I285F |
probably benign |
Het |
| Sp110 |
C |
G |
1: 85,516,839 (GRCm39) |
E219D |
probably damaging |
Het |
| Sp9 |
C |
A |
2: 73,104,641 (GRCm39) |
N398K |
probably damaging |
Het |
| Sycp2 |
A |
C |
2: 178,019,495 (GRCm39) |
|
probably null |
Het |
| Tbc1d23 |
T |
C |
16: 57,019,291 (GRCm39) |
D219G |
probably damaging |
Het |
| Tdpoz3 |
A |
G |
3: 93,734,179 (GRCm39) |
R285G |
probably benign |
Het |
| Trim2 |
T |
A |
3: 84,074,960 (GRCm39) |
Q694L |
probably null |
Het |
| Trim23 |
T |
A |
13: 104,328,541 (GRCm39) |
V293D |
probably damaging |
Het |
| Ttn |
A |
G |
2: 76,665,183 (GRCm39) |
|
probably benign |
Het |
| Vmn2r12 |
T |
A |
5: 109,238,261 (GRCm39) |
Y493F |
probably benign |
Het |
| Vps41 |
T |
A |
13: 19,046,708 (GRCm39) |
I753N |
probably damaging |
Het |
| Yme1l1 |
G |
A |
2: 23,083,246 (GRCm39) |
G571R |
probably damaging |
Het |
| Zfp322a |
A |
T |
13: 23,541,149 (GRCm39) |
C198S |
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 |
|
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'- AACCAGTGCAAAGTAGCGGC -3'
(R):5'- AGGTCATCACAGCTCGCTTG -3'
Sequencing Primer
(F):5'- CCAGCTCCTGCGCAAAG -3'
(R):5'- GGCCTGGTCATTGTTCTCCAAAC -3'
|
| Posted On |
2016-08-04 |
Incidental Mutation