Incidental Mutation 'R6427:Vps51'
| ID |
518384 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps51
|
| Ensembl Gene |
ENSMUSG00000024797 |
| Gene Name |
VPS51 GARP complex subunit |
| Synonyms |
3110057M17Rik, 1110014N23Rik |
| MMRRC Submission |
044566-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R6427 (G1)
|
| Quality Score |
192.009 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
6117872-6127217 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 6120947 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 322
(Y322C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000123994
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025711]
[ENSMUST00000025713]
[ENSMUST00000113543]
[ENSMUST00000159084]
[ENSMUST00000159832]
[ENSMUST00000161090]
[ENSMUST00000160590]
[ENSMUST00000160028]
[ENSMUST00000161718]
[ENSMUST00000160233]
[ENSMUST00000161528]
[ENSMUST00000162575]
[ENSMUST00000162810]
|
| AlphaFold |
Q3UVL4 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000025711
AA Change: Y322C
PolyPhen 2
Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000025711
Gene: ENSMUSG00000024799
AA Change: Y322C
| 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 |
possibly damaging
Transcript: ENSMUST00000159832
AA Change: Y322C
PolyPhen 2
Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000123994
Gene: ENSMUSG00000024797
AA Change: Y322C
| 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 |
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 |
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 |
noncoding transcript
Transcript: ENSMUST00000160324
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000159836
|
| 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: ENSMUST00000160233
|
| SMART Domains |
Protein: ENSMUSP00000124842
Gene: ENSMUSG00000024797
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
2 |
25 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160519
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161634
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000159869
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161222
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160354
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000160417
|
| 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 |
noncoding transcript
Transcript: ENSMUST00000162549
|
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000162721
|
| 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 |
|
| Meta Mutation Damage Score |
0.8615 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 97.8%
- 20x: 93.1%
|
| Validation Efficiency |
93% (39/42) |
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abat |
C |
T |
16: 8,420,300 (GRCm39) |
|
probably benign |
Het |
| Ankmy2 |
A |
G |
12: 36,237,710 (GRCm39) |
S270G |
possibly damaging |
Het |
| Anxa2 |
T |
A |
9: 69,383,431 (GRCm39) |
|
probably null |
Het |
| Arid1a |
G |
T |
4: 133,408,835 (GRCm39) |
P1891T |
unknown |
Het |
| Atn1 |
G |
T |
6: 124,723,139 (GRCm39) |
|
probably benign |
Het |
| Atp8b3 |
A |
T |
10: 80,356,157 (GRCm39) |
|
probably null |
Het |
| Cab39l |
A |
C |
14: 59,743,719 (GRCm39) |
K94N |
possibly damaging |
Het |
| Cacna2d2 |
G |
T |
9: 107,392,641 (GRCm39) |
M528I |
possibly damaging |
Het |
| Ccnc |
T |
A |
4: 21,747,578 (GRCm39) |
|
probably null |
Het |
| Cfap251 |
T |
C |
5: 123,464,596 (GRCm39) |
L1268P |
probably damaging |
Het |
| Clasp2 |
C |
T |
9: 113,721,512 (GRCm39) |
T774I |
probably damaging |
Het |
| Cngb1 |
C |
T |
8: 96,024,387 (GRCm39) |
|
probably benign |
Het |
| Cpt1a |
T |
A |
19: 3,412,156 (GRCm39) |
F209L |
probably damaging |
Het |
| Cyp2j7 |
C |
A |
4: 96,115,904 (GRCm39) |
D181Y |
probably damaging |
Het |
| Daam2 |
C |
T |
17: 49,776,404 (GRCm39) |
E828K |
probably damaging |
Het |
| Ddr1 |
C |
A |
17: 35,998,114 (GRCm39) |
R477L |
probably benign |
Het |
| Ech1 |
A |
G |
7: 28,525,310 (GRCm39) |
T22A |
probably benign |
Het |
| Fbln5 |
T |
C |
12: 101,728,081 (GRCm39) |
D294G |
possibly damaging |
Het |
| Fkbp15 |
T |
C |
4: 62,241,439 (GRCm39) |
I569V |
probably benign |
Het |
| Hmcn1 |
G |
T |
1: 150,573,227 (GRCm39) |
R2141S |
possibly damaging |
Het |
| Kat6b |
T |
C |
14: 21,567,480 (GRCm39) |
S180P |
probably benign |
Het |
| Lepr |
G |
A |
4: 101,631,454 (GRCm39) |
E655K |
possibly damaging |
Het |
| Mro |
T |
A |
18: 74,005,104 (GRCm39) |
L69Q |
probably damaging |
Het |
| Nipbl |
A |
T |
15: 8,381,049 (GRCm39) |
L581H |
probably benign |
Het |
| Nkiras2 |
C |
T |
11: 100,515,861 (GRCm39) |
R63W |
probably damaging |
Het |
| Nlrp4e |
T |
A |
7: 23,020,058 (GRCm39) |
S182T |
possibly damaging |
Het |
| Obi1 |
T |
C |
14: 104,717,662 (GRCm39) |
K237R |
possibly damaging |
Het |
| Or52b4i |
A |
T |
7: 102,191,895 (GRCm39) |
I251F |
probably benign |
Het |
| Otud4 |
T |
C |
8: 80,395,126 (GRCm39) |
S553P |
probably benign |
Het |
| Pcdha4 |
T |
C |
18: 37,086,786 (GRCm39) |
I323T |
probably benign |
Het |
| Polr1b |
G |
T |
2: 128,965,181 (GRCm39) |
A756S |
probably damaging |
Het |
| Prex2 |
A |
T |
1: 11,252,255 (GRCm39) |
Y1100F |
probably damaging |
Het |
| Serpinb6a |
A |
T |
13: 34,102,242 (GRCm39) |
S328T |
probably damaging |
Het |
| Srsf11 |
C |
T |
3: 157,728,981 (GRCm39) |
|
probably benign |
Het |
| Stxbp5 |
T |
C |
10: 9,774,998 (GRCm39) |
T52A |
probably damaging |
Het |
| Taf3 |
A |
T |
2: 9,956,164 (GRCm39) |
F515I |
probably damaging |
Het |
| Unc13b |
A |
G |
4: 43,176,966 (GRCm39) |
|
probably benign |
Het |
| Vmn2r106 |
C |
T |
17: 20,488,725 (GRCm39) |
C558Y |
probably damaging |
Het |
| Zfp735 |
G |
A |
11: 73,581,140 (GRCm39) |
C59Y |
possibly damaging |
Het |
| Zfp759 |
A |
G |
13: 67,287,162 (GRCm39) |
|
probably null |
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 |
|
R5989:Vps51
|
UTSW |
19 |
6,126,402 (GRCm39) |
missense |
probably damaging |
0.96 |
|
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'- CTCTGTGGCTGACTCTGAAAG -3'
(R):5'- TGTCACTACAGGGAAGGCTG -3'
Sequencing Primer
(F):5'- TGGCTGACTCTGAAAGCCCAG -3'
(R):5'- CACTACAGGGAAGGCTGCTCAG -3'
|
| Posted On |
2018-05-24 |
Incidental Mutation