Incidental Mutation 'R5422:Vps51'
| ID |
426675 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps51
|
| Ensembl Gene |
ENSMUSG00000024797 |
| Gene Name |
VPS51 GARP complex subunit |
| Synonyms |
3110057M17Rik, 1110014N23Rik |
| MMRRC Submission |
042846-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5422 (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: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 94.9%
|
| 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: 62 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamts18 |
T |
C |
8: 114,425,606 (GRCm39) |
S1219G |
probably benign |
Het |
| Adgrg5 |
T |
A |
8: 95,660,580 (GRCm39) |
I73N |
probably damaging |
Het |
| Agmat |
C |
A |
4: 141,483,144 (GRCm39) |
H193N |
probably damaging |
Het |
| Ambn |
T |
C |
5: 88,612,370 (GRCm39) |
|
probably null |
Het |
| Atp8b5 |
T |
A |
4: 43,366,644 (GRCm39) |
C803S |
probably benign |
Het |
| Btaf1 |
A |
T |
19: 36,928,507 (GRCm39) |
R109S |
probably benign |
Het |
| Btnl6 |
C |
T |
17: 34,733,081 (GRCm39) |
G261R |
possibly damaging |
Het |
| Clk3 |
A |
G |
9: 57,672,721 (GRCm39) |
V27A |
probably benign |
Het |
| Clu |
A |
G |
14: 66,213,051 (GRCm39) |
S146G |
probably damaging |
Het |
| Cyp2w1 |
T |
C |
5: 139,338,528 (GRCm39) |
F43L |
probably benign |
Het |
| Elf3 |
C |
T |
1: 135,182,778 (GRCm39) |
E316K |
probably damaging |
Het |
| Epha5 |
A |
T |
5: 84,479,349 (GRCm39) |
D218E |
probably damaging |
Het |
| Ereg |
T |
C |
5: 91,222,666 (GRCm39) |
|
probably null |
Het |
| Ewsr1 |
A |
G |
11: 5,030,668 (GRCm39) |
|
probably benign |
Het |
| Fat4 |
A |
G |
3: 38,941,394 (GRCm39) |
I96V |
possibly damaging |
Het |
| Fgl2 |
T |
G |
5: 21,580,808 (GRCm39) |
N383K |
probably damaging |
Het |
| Fkbp11 |
A |
T |
15: 98,625,989 (GRCm39) |
|
probably null |
Het |
| Fn3k |
C |
A |
11: 121,340,948 (GRCm39) |
P201Q |
probably damaging |
Het |
| Fsip2 |
A |
G |
2: 82,812,572 (GRCm39) |
I2964V |
probably benign |
Het |
| Gbx1 |
C |
T |
5: 24,709,667 (GRCm39) |
V393I |
possibly damaging |
Het |
| Gch1 |
C |
T |
14: 47,394,906 (GRCm39) |
A187T |
probably damaging |
Het |
| Ghdc |
C |
A |
11: 100,660,020 (GRCm39) |
K242N |
probably benign |
Het |
| Ghrhr |
A |
G |
6: 55,365,188 (GRCm39) |
H394R |
probably benign |
Het |
| Gje1 |
G |
A |
10: 14,592,428 (GRCm39) |
S118L |
probably damaging |
Het |
| Hnrnpa2b1 |
A |
T |
6: 51,442,208 (GRCm39) |
S236R |
probably benign |
Het |
| Kcnj5 |
A |
G |
9: 32,229,001 (GRCm39) |
Y66H |
probably benign |
Het |
| Kif15 |
T |
A |
9: 122,813,954 (GRCm39) |
|
probably null |
Het |
| Magi3 |
C |
T |
3: 103,958,684 (GRCm39) |
C467Y |
probably damaging |
Het |
| Map7 |
G |
T |
10: 20,142,512 (GRCm39) |
V303F |
probably damaging |
Het |
| Mapk11 |
A |
G |
15: 89,030,488 (GRCm39) |
L135P |
probably damaging |
Het |
| Mapkapk5 |
T |
A |
5: 121,669,785 (GRCm39) |
|
probably null |
Het |
| Myh7b |
A |
C |
2: 155,472,954 (GRCm39) |
Q1405P |
probably damaging |
Het |
| Nalcn |
A |
T |
14: 123,752,777 (GRCm39) |
I328N |
probably damaging |
Het |
| Nprl2 |
C |
A |
9: 107,420,796 (GRCm39) |
R144S |
probably benign |
Het |
| Ogfr |
G |
T |
2: 180,237,067 (GRCm39) |
D551Y |
possibly damaging |
Het |
| Ogfr |
A |
T |
2: 180,237,068 (GRCm39) |
D551V |
probably benign |
Het |
| Or6b13 |
A |
T |
7: 139,782,305 (GRCm39) |
V126E |
probably damaging |
Het |
| Or8c10 |
A |
T |
9: 38,279,270 (GRCm39) |
T143S |
probably benign |
Het |
| Parp14 |
T |
C |
16: 35,686,545 (GRCm39) |
K101E |
probably benign |
Het |
| Pcdhb16 |
A |
T |
18: 37,612,920 (GRCm39) |
T627S |
probably damaging |
Het |
| Pdzrn4 |
G |
A |
15: 92,575,502 (GRCm39) |
G303S |
probably benign |
Het |
| Plcl1 |
A |
T |
1: 55,736,543 (GRCm39) |
Y628F |
probably benign |
Het |
| Ptpn9 |
T |
A |
9: 56,940,441 (GRCm39) |
W194R |
probably damaging |
Het |
| Ranbp9 |
A |
T |
13: 43,573,102 (GRCm39) |
M474K |
probably benign |
Het |
| Rasgef1a |
T |
A |
6: 118,065,095 (GRCm39) |
F370Y |
probably damaging |
Het |
| Rassf5 |
C |
A |
1: 131,108,911 (GRCm39) |
R218L |
possibly damaging |
Het |
| Scart1 |
A |
T |
7: 139,804,068 (GRCm39) |
H422L |
probably benign |
Het |
| Serpine2 |
C |
A |
1: 79,794,592 (GRCm39) |
V114L |
probably benign |
Het |
| Serpine2 |
T |
C |
1: 79,799,206 (GRCm39) |
Y16C |
probably benign |
Het |
| Sgms1 |
G |
T |
19: 32,137,232 (GRCm39) |
N111K |
probably damaging |
Het |
| Sh3bp5 |
C |
A |
14: 31,099,452 (GRCm39) |
R265L |
probably benign |
Het |
| Slc45a2 |
C |
T |
15: 11,027,871 (GRCm39) |
T480I |
probably damaging |
Het |
| Tbc1d17 |
A |
T |
7: 44,498,292 (GRCm39) |
M1K |
probably null |
Het |
| Tcf12 |
A |
T |
9: 71,776,320 (GRCm39) |
H403Q |
probably damaging |
Het |
| Thoc2l |
T |
C |
5: 104,667,512 (GRCm39) |
I678T |
probably damaging |
Het |
| Thsd7b |
T |
C |
1: 129,849,071 (GRCm39) |
S928P |
probably benign |
Het |
| Tjp1 |
A |
T |
7: 64,952,715 (GRCm39) |
F1540I |
probably damaging |
Het |
| Tph2 |
T |
A |
10: 114,915,669 (GRCm39) |
D457V |
possibly damaging |
Het |
| Usp9y |
T |
C |
Y: 1,314,676 (GRCm39) |
I2112V |
probably benign |
Het |
| Zfp335 |
T |
C |
2: 164,749,650 (GRCm39) |
K249R |
probably damaging |
Het |
| Zfp54 |
C |
A |
17: 21,654,788 (GRCm39) |
S427R |
probably benign |
Het |
| Zfp607b |
A |
G |
7: 27,401,813 (GRCm39) |
T90A |
probably benign |
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 |
|
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'- CTCAACCAGTGCAAAGTAGC -3'
(R):5'- GCCTGGTCATTGTTCTCCAAAC -3'
Sequencing Primer
(F):5'- CAGTGCAAAGTAGCGGCCG -3'
(R):5'- TCCAAACACATCGAGTGC -3'
|
| Posted On |
2016-09-01 |
Incidental Mutation