Incidental Mutation 'R5497:Vps51'
| ID |
432446 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps51
|
| Ensembl Gene |
ENSMUSG00000024797 |
| Gene Name |
VPS51 GARP complex subunit |
| Synonyms |
3110057M17Rik, 1110014N23Rik |
| MMRRC Submission |
043058-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5497 (G1)
|
| Quality Score |
198 |
|
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: 98.3%
- 3x: 97.3%
- 10x: 95.3%
- 20x: 91.2%
|
| 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: 56 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4933427D14Rik |
A |
T |
11: 72,056,360 (GRCm39) |
M800K |
probably benign |
Het |
| Abca9 |
G |
A |
11: 110,021,518 (GRCm39) |
A1064V |
probably damaging |
Het |
| Acsm2 |
A |
T |
7: 119,172,543 (GRCm39) |
T129S |
possibly damaging |
Het |
| Adamts9 |
A |
T |
6: 92,831,346 (GRCm39) |
C755S |
probably damaging |
Het |
| Adarb1 |
T |
C |
10: 77,161,723 (GRCm39) |
D2G |
probably damaging |
Het |
| Apaf1 |
G |
A |
10: 90,835,518 (GRCm39) |
A1098V |
probably damaging |
Het |
| Asap3 |
A |
G |
4: 135,966,533 (GRCm39) |
H537R |
probably benign |
Het |
| Atp2a2 |
C |
T |
5: 122,596,232 (GRCm39) |
C887Y |
probably damaging |
Het |
| Atp6v0a1 |
G |
A |
11: 100,920,011 (GRCm39) |
V215M |
probably damaging |
Het |
| Cacng8 |
A |
G |
7: 3,464,069 (GRCm39) |
E407G |
probably benign |
Het |
| Capn8 |
G |
A |
1: 182,447,745 (GRCm39) |
E535K |
probably benign |
Het |
| Cebpe |
A |
G |
14: 54,948,052 (GRCm39) |
F264L |
probably benign |
Het |
| Ces1c |
A |
C |
8: 93,857,343 (GRCm39) |
N79K |
possibly damaging |
Het |
| Cfap58 |
T |
G |
19: 48,017,548 (GRCm39) |
S803A |
probably benign |
Het |
| Cpa1 |
A |
G |
6: 30,640,729 (GRCm39) |
T124A |
probably benign |
Het |
| Csmd1 |
A |
G |
8: 16,135,195 (GRCm39) |
S1654P |
probably benign |
Het |
| Dmbt1 |
A |
T |
7: 130,665,133 (GRCm39) |
|
probably benign |
Het |
| Eif3e |
T |
C |
15: 43,134,366 (GRCm39) |
Y127C |
probably damaging |
Het |
| Fhip2a |
G |
C |
19: 57,369,583 (GRCm39) |
|
probably null |
Het |
| Galnt5 |
T |
C |
2: 57,915,340 (GRCm39) |
M632T |
probably damaging |
Het |
| Gja8 |
A |
G |
3: 96,827,513 (GRCm39) |
S50P |
probably damaging |
Het |
| Gon7 |
A |
G |
12: 102,720,363 (GRCm39) |
S90P |
probably benign |
Het |
| Gucy2g |
C |
T |
19: 55,187,133 (GRCm39) |
V1096I |
probably benign |
Het |
| Gxylt2 |
A |
G |
6: 100,764,290 (GRCm39) |
N325S |
probably benign |
Het |
| H2-Ob |
A |
G |
17: 34,460,144 (GRCm39) |
D85G |
probably benign |
Het |
| Heatr1 |
T |
A |
13: 12,435,945 (GRCm39) |
I1161N |
possibly damaging |
Het |
| Hjurp |
G |
A |
1: 88,194,042 (GRCm39) |
H289Y |
possibly damaging |
Het |
| Hsd3b7 |
A |
G |
7: 127,401,060 (GRCm39) |
Y99C |
probably damaging |
Het |
| Ifnar1 |
T |
G |
16: 91,302,252 (GRCm39) |
Y21D |
probably benign |
Het |
| Isoc2b |
C |
T |
7: 4,853,782 (GRCm39) |
V131I |
probably benign |
Het |
| Klc3 |
T |
C |
7: 19,128,595 (GRCm39) |
I500V |
probably benign |
Het |
| Lrp5 |
C |
A |
19: 3,652,319 (GRCm39) |
G1184W |
probably damaging |
Het |
| Map2k4 |
A |
G |
11: 65,626,031 (GRCm39) |
I136T |
probably damaging |
Het |
| Map3k7 |
T |
C |
4: 31,991,719 (GRCm39) |
F319S |
possibly damaging |
Het |
| Muc5ac |
A |
G |
7: 141,361,380 (GRCm39) |
T1564A |
probably damaging |
Het |
| Nptx2 |
A |
T |
5: 144,492,999 (GRCm39) |
D362V |
probably damaging |
Het |
| Nutf2-ps1 |
A |
T |
19: 53,577,265 (GRCm39) |
I52N |
probably damaging |
Het |
| Or2aj4 |
C |
T |
16: 19,385,080 (GRCm39) |
M184I |
probably benign |
Het |
| Pkhd1 |
T |
A |
1: 20,447,628 (GRCm39) |
Y2255F |
possibly damaging |
Het |
| Primpol |
A |
T |
8: 47,045,657 (GRCm39) |
Y308* |
probably null |
Het |
| Retreg2 |
G |
A |
1: 75,121,633 (GRCm39) |
V219I |
probably damaging |
Het |
| Rnd2 |
C |
T |
11: 101,359,825 (GRCm39) |
L57F |
probably damaging |
Het |
| Rph3a |
T |
A |
5: 121,080,253 (GRCm39) |
E675V |
probably benign |
Het |
| Ryr2 |
A |
T |
13: 11,720,587 (GRCm39) |
M2687K |
probably null |
Het |
| Shank2 |
A |
G |
7: 143,963,271 (GRCm39) |
D293G |
probably damaging |
Het |
| Snx6 |
A |
G |
12: 54,803,846 (GRCm39) |
V154A |
probably damaging |
Het |
| Srm |
G |
T |
4: 148,678,566 (GRCm39) |
Q264H |
probably benign |
Het |
| Styk1 |
A |
T |
6: 131,281,670 (GRCm39) |
I316N |
probably damaging |
Het |
| Syne2 |
A |
G |
12: 75,927,163 (GRCm39) |
N103S |
probably benign |
Het |
| Tas2r105 |
G |
A |
6: 131,663,805 (GRCm39) |
|
probably null |
Het |
| Tbcel |
T |
A |
9: 42,363,041 (GRCm39) |
M1L |
possibly damaging |
Het |
| Tlr3 |
C |
T |
8: 45,851,851 (GRCm39) |
D349N |
possibly damaging |
Het |
| Tm9sf3 |
T |
C |
19: 41,203,555 (GRCm39) |
S574G |
probably benign |
Het |
| Usp31 |
A |
T |
7: 121,250,824 (GRCm39) |
V783E |
probably damaging |
Het |
| Vmn2r61 |
T |
A |
7: 41,924,906 (GRCm39) |
Y487N |
possibly damaging |
Het |
| Zfp980 |
A |
G |
4: 145,428,017 (GRCm39) |
K249E |
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 |
|
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 |
|
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'- CAACCAGTGCAAAGTAGCG -3'
(R):5'- GCCTGGTCATTGTTCTCCAAAC -3'
Sequencing Primer
(F):5'- CCAGCTCCTGCGCAAAG -3'
(R):5'- TCCAAACACATCGAGTGC -3'
|
| Posted On |
2016-10-05 |
Incidental Mutation