Incidental Mutation 'R5393:Vps51'
| ID |
425992 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps51
|
| Ensembl Gene |
ENSMUSG00000024797 |
| Gene Name |
VPS51 GARP complex subunit |
| Synonyms |
3110057M17Rik, 1110014N23Rik |
| MMRRC Submission |
042965-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R5393 (G1)
|
| Quality Score |
202 |
|
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: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.9%
|
| Validation Efficiency |
99% (72/73) |
| 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 |
|---|
| 1110025L11Rik |
A |
T |
16: 88,860,653 (GRCm39) |
Y60* |
probably null |
Het |
| Abca6 |
T |
A |
11: 110,135,121 (GRCm39) |
E221D |
probably benign |
Het |
| Acyp2 |
C |
T |
11: 30,456,354 (GRCm39) |
E98K |
possibly damaging |
Het |
| Adi1 |
A |
G |
12: 28,725,274 (GRCm39) |
D8G |
probably benign |
Het |
| Adnp |
T |
C |
2: 168,024,869 (GRCm39) |
K809E |
possibly damaging |
Het |
| Aldh18a1 |
T |
C |
19: 40,574,011 (GRCm39) |
H4R |
probably benign |
Het |
| Atp6v0a1 |
T |
C |
11: 100,929,633 (GRCm39) |
S485P |
possibly damaging |
Het |
| C1galt1 |
T |
C |
6: 7,864,143 (GRCm39) |
|
probably null |
Het |
| Cacna2d4 |
A |
T |
6: 119,216,015 (GRCm39) |
N94I |
probably benign |
Het |
| Catsperg1 |
T |
C |
7: 28,884,924 (GRCm39) |
N899S |
probably damaging |
Het |
| Cilk1 |
A |
G |
9: 78,067,997 (GRCm39) |
T463A |
probably benign |
Het |
| Coro2a |
A |
G |
4: 46,542,255 (GRCm39) |
S373P |
probably damaging |
Het |
| Cpsf6 |
G |
C |
10: 117,197,921 (GRCm39) |
|
probably benign |
Het |
| Csmd3 |
A |
T |
15: 47,497,099 (GRCm39) |
N3099K |
probably damaging |
Het |
| Ctla2b |
T |
A |
13: 61,043,946 (GRCm39) |
E74D |
probably damaging |
Het |
| Dnah2 |
T |
A |
11: 69,391,683 (GRCm39) |
T671S |
probably benign |
Het |
| Drd5 |
T |
A |
5: 38,478,248 (GRCm39) |
S414T |
probably benign |
Het |
| Dyrk2 |
C |
T |
10: 118,695,753 (GRCm39) |
D502N |
probably damaging |
Het |
| Ecel1 |
A |
T |
1: 87,080,598 (GRCm39) |
L376Q |
possibly damaging |
Het |
| Efcab8 |
G |
A |
2: 153,622,903 (GRCm39) |
R24Q |
unknown |
Het |
| Eloc |
A |
C |
1: 16,718,192 (GRCm39) |
|
probably benign |
Het |
| Ep300 |
A |
G |
15: 81,515,819 (GRCm39) |
|
probably benign |
Het |
| Fam89b |
T |
C |
19: 5,778,733 (GRCm39) |
D152G |
probably damaging |
Het |
| Gm15455 |
G |
A |
1: 33,875,927 (GRCm39) |
|
noncoding transcript |
Het |
| Greb1l |
A |
G |
18: 10,458,312 (GRCm39) |
T30A |
probably benign |
Het |
| Hdac10 |
T |
C |
15: 89,010,887 (GRCm39) |
Y238C |
probably damaging |
Het |
| Ighv2-5 |
T |
C |
12: 113,649,502 (GRCm39) |
T12A |
possibly damaging |
Het |
| Insrr |
T |
C |
3: 87,718,007 (GRCm39) |
|
probably null |
Het |
| Irf9 |
T |
C |
14: 55,843,914 (GRCm39) |
|
probably benign |
Het |
| Itpr2 |
A |
T |
6: 146,277,653 (GRCm39) |
C280* |
probably null |
Het |
| Kcnk18 |
T |
C |
19: 59,208,271 (GRCm39) |
C36R |
probably damaging |
Het |
| Khdc4 |
T |
A |
3: 88,603,913 (GRCm39) |
H243Q |
probably benign |
Het |
| Klhl14 |
G |
T |
18: 21,785,051 (GRCm39) |
N125K |
probably benign |
Het |
| Lce1i |
T |
C |
3: 92,685,042 (GRCm39) |
S45G |
unknown |
Het |
| Lrmda |
A |
C |
14: 22,077,374 (GRCm39) |
D37A |
probably damaging |
Het |
| Marco |
A |
C |
1: 120,413,583 (GRCm39) |
D280E |
probably damaging |
Het |
| Meak7 |
T |
C |
8: 120,499,157 (GRCm39) |
I112V |
probably benign |
Het |
| Miox |
C |
T |
15: 89,220,450 (GRCm39) |
Q180* |
probably null |
Het |
| Npdc1 |
A |
T |
2: 25,298,682 (GRCm39) |
M265L |
probably damaging |
Het |
| Nudcd3 |
T |
C |
11: 6,063,274 (GRCm39) |
K205R |
probably damaging |
Het |
| Or2ak6 |
T |
A |
11: 58,593,326 (GRCm39) |
H266Q |
probably damaging |
Het |
| Or2t46 |
C |
G |
11: 58,471,825 (GRCm39) |
L52V |
possibly damaging |
Het |
| Pcdhga5 |
C |
T |
18: 37,829,720 (GRCm39) |
R723C |
probably benign |
Het |
| Pdlim5 |
T |
A |
3: 141,964,947 (GRCm39) |
E295D |
probably damaging |
Het |
| Poli |
C |
A |
18: 70,650,499 (GRCm39) |
E314* |
probably null |
Het |
| Ptpro |
A |
G |
6: 137,357,222 (GRCm39) |
N238D |
probably benign |
Het |
| R3hdm1 |
A |
G |
1: 128,159,084 (GRCm39) |
I920V |
probably benign |
Het |
| Ralgapa2 |
C |
T |
2: 146,187,375 (GRCm39) |
V1338M |
probably damaging |
Het |
| Saa3 |
T |
C |
7: 46,362,085 (GRCm39) |
Y53C |
probably damaging |
Het |
| Septin14 |
T |
A |
5: 129,760,650 (GRCm39) |
E398D |
probably benign |
Het |
| Six3 |
T |
C |
17: 85,931,270 (GRCm39) |
S309P |
possibly damaging |
Het |
| Slc7a14 |
A |
G |
3: 31,311,919 (GRCm39) |
S34P |
probably damaging |
Het |
| Smarca2 |
C |
A |
19: 26,617,829 (GRCm39) |
Q287K |
probably benign |
Het |
| Stard9 |
C |
T |
2: 120,533,387 (GRCm39) |
L522F |
possibly damaging |
Het |
| Sycp1 |
T |
C |
3: 102,748,363 (GRCm39) |
|
probably null |
Het |
| Tbc1d8 |
A |
T |
1: 39,465,169 (GRCm39) |
V73E |
probably damaging |
Het |
| Tmem120a |
T |
C |
5: 135,765,104 (GRCm39) |
|
probably null |
Het |
| Tsc2 |
T |
C |
17: 24,819,370 (GRCm39) |
E1251G |
possibly damaging |
Het |
| Wnt5b |
A |
C |
6: 119,417,394 (GRCm39) |
L157R |
probably damaging |
Het |
| Zbtb24 |
T |
A |
10: 41,340,578 (GRCm39) |
V536E |
probably damaging |
Het |
| Zfp593 |
G |
A |
4: 133,972,615 (GRCm39) |
A67V |
probably benign |
Het |
| Zfp995 |
A |
T |
17: 22,099,473 (GRCm39) |
F254I |
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 |
|
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'- CTCAACCAGTGCAAAGTAGC -3'
(R):5'- GCCTGGTCATTGTTCTCCAAAC -3'
Sequencing Primer
(F):5'- CAGTGCAAAGTAGCGGCCG -3'
(R):5'- TCCAAACACATCGAGTGC -3'
|
| Posted On |
2016-08-04 |
Incidental Mutation