Incidental Mutation 'R5392:Vps51'
| ID |
425930 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps51
|
| Ensembl Gene |
ENSMUSG00000024797 |
| Gene Name |
VPS51 GARP complex subunit |
| Synonyms |
3110057M17Rik, 1110014N23Rik |
| MMRRC Submission |
042964-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5392 (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: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.8%
|
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acoxl |
T |
C |
2: 127,852,088 (GRCm39) |
|
probably null |
Het |
| Acyp1 |
T |
C |
12: 85,325,759 (GRCm39) |
|
probably benign |
Het |
| Ces1b |
G |
A |
8: 93,798,590 (GRCm39) |
R199C |
probably damaging |
Het |
| Col6a3 |
C |
A |
1: 90,729,017 (GRCm39) |
R1308L |
probably benign |
Het |
| Cpa5 |
C |
T |
6: 30,630,829 (GRCm39) |
Q364* |
probably null |
Het |
| Cyth4 |
T |
A |
15: 78,491,185 (GRCm39) |
L88Q |
probably damaging |
Het |
| Dock7 |
A |
G |
4: 98,896,243 (GRCm39) |
V59A |
probably damaging |
Het |
| Drd2 |
A |
G |
9: 49,306,928 (GRCm39) |
N5D |
possibly damaging |
Het |
| Epsti1 |
T |
C |
14: 78,224,184 (GRCm39) |
I272T |
probably benign |
Het |
| Fndc3b |
A |
T |
3: 27,519,936 (GRCm39) |
C568* |
probably null |
Het |
| Frmd4a |
C |
T |
2: 4,599,384 (GRCm39) |
A161V |
probably damaging |
Het |
| Gfpt1 |
A |
G |
6: 87,054,139 (GRCm39) |
T465A |
probably damaging |
Het |
| Hecw1 |
C |
A |
13: 14,420,347 (GRCm39) |
Q1025H |
probably damaging |
Het |
| Irak4 |
A |
T |
15: 94,454,565 (GRCm39) |
M237L |
probably benign |
Het |
| Irak4 |
T |
C |
15: 94,454,566 (GRCm39) |
M237T |
probably benign |
Het |
| Kdsr |
T |
A |
1: 106,680,971 (GRCm39) |
I76F |
possibly damaging |
Het |
| Kif15 |
T |
C |
9: 122,825,360 (GRCm39) |
F533S |
probably damaging |
Het |
| Kmt5b |
T |
C |
19: 3,852,127 (GRCm39) |
F103L |
possibly damaging |
Het |
| Krtcap2 |
C |
T |
3: 89,154,186 (GRCm39) |
L36F |
probably benign |
Het |
| Mroh7 |
A |
G |
4: 106,568,448 (GRCm39) |
|
probably null |
Het |
| Mta1 |
T |
C |
12: 113,096,856 (GRCm39) |
V559A |
probably benign |
Het |
| N4bp1 |
A |
G |
8: 87,587,048 (GRCm39) |
|
probably null |
Het |
| Oas1d |
T |
C |
5: 121,055,003 (GRCm39) |
S192P |
possibly damaging |
Het |
| Or1n1b |
T |
A |
2: 36,780,686 (GRCm39) |
Y58F |
probably benign |
Het |
| Or6c76 |
A |
G |
10: 129,612,184 (GRCm39) |
I149V |
probably benign |
Het |
| Or6d15 |
A |
G |
6: 116,559,379 (GRCm39) |
F176S |
probably damaging |
Het |
| Rabgap1 |
T |
A |
2: 37,359,501 (GRCm39) |
N21K |
probably damaging |
Het |
| Rad9b |
A |
T |
5: 122,489,641 (GRCm39) |
C25S |
probably damaging |
Het |
| Spg7 |
T |
C |
8: 123,814,102 (GRCm39) |
S454P |
probably damaging |
Het |
| Spink2 |
T |
A |
5: 77,354,872 (GRCm39) |
H40L |
probably benign |
Het |
| Syne1 |
T |
A |
10: 5,298,661 (GRCm39) |
D1082V |
probably damaging |
Het |
| Syt2 |
A |
G |
1: 134,671,759 (GRCm39) |
D179G |
probably damaging |
Het |
| Tm7sf2 |
T |
C |
19: 6,113,998 (GRCm39) |
D181G |
probably damaging |
Het |
| Vmn1r174 |
A |
G |
7: 23,454,227 (GRCm39) |
I298V |
unknown |
Het |
| Vmn2r23 |
A |
T |
6: 123,681,323 (GRCm39) |
H77L |
probably benign |
Het |
| Vps9d1 |
T |
C |
8: 123,980,752 (GRCm39) |
E25G |
probably damaging |
Het |
| Zfp119a |
T |
C |
17: 56,173,328 (GRCm39) |
R172G |
probably benign |
Het |
| Zfp51 |
A |
T |
17: 21,685,584 (GRCm39) |
Y733F |
possibly damaging |
Het |
| Zfp658 |
A |
C |
7: 43,222,355 (GRCm39) |
E210A |
probably benign |
Het |
| Zp2 |
C |
A |
7: 119,734,987 (GRCm39) |
E433* |
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 |
|
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 |
2016-08-04 |
Incidental Mutation