Incidental Mutation 'R2055:Vps50'
| ID |
226581 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps50
|
| Ensembl Gene |
ENSMUSG00000001376 |
| Gene Name |
VPS50 EARP/GARPII complex subunit |
| Synonyms |
Ccdc132, 1700034M03Rik, 8430415E05Rik |
| MMRRC Submission |
040060-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.902)
|
| Stock # |
R2055 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
3498393-3603531 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 3522265 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Lysine
at position 144
(N144K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000128323
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001412]
[ENSMUST00000164052]
[ENSMUST00000170873]
|
| AlphaFold |
Q8CI71 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000001412
AA Change: N144K
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000001412
Gene: ENSMUSG00000001376
AA Change: N144K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF2450
|
54 |
345 |
2.5e-112 |
PFAM |
|
low complexity region
|
659 |
676 |
N/A |
INTRINSIC |
|
Pfam:DUF2451
|
723 |
957 |
2.2e-98 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000164052
AA Change: N144K
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000125872
Gene: ENSMUSG00000001376
AA Change: N144K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF2450
|
54 |
345 |
5.2e-111 |
PFAM |
|
low complexity region
|
659 |
676 |
N/A |
INTRINSIC |
|
Pfam:DUF2451
|
723 |
929 |
1.1e-90 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000170873
AA Change: N144K
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000128323
Gene: ENSMUSG00000001376
AA Change: N144K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF2450
|
54 |
345 |
5.3e-111 |
PFAM |
|
low complexity region
|
659 |
676 |
N/A |
INTRINSIC |
|
Pfam:DUF2451
|
723 |
933 |
2.6e-90 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000183935
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000184780
|
| Meta Mutation Damage Score |
0.0651 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
| Validation Efficiency |
100% (74/74) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 74 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700123K08Rik |
T |
C |
5: 138,561,107 (GRCm39) |
E185G |
probably damaging |
Het |
| 3425401B19Rik |
A |
G |
14: 32,384,508 (GRCm39) |
S486P |
probably benign |
Het |
| A630023A22Rik |
T |
C |
14: 33,774,707 (GRCm39) |
|
probably benign |
Het |
| Abca1 |
T |
C |
4: 53,069,881 (GRCm39) |
N1271S |
probably benign |
Het |
| AI597479 |
C |
T |
1: 43,150,280 (GRCm39) |
A130V |
probably benign |
Het |
| Angptl4 |
A |
G |
17: 33,999,498 (GRCm39) |
|
probably null |
Het |
| Arhgef25 |
T |
A |
10: 127,021,004 (GRCm39) |
N294I |
probably damaging |
Het |
| Atp2b1 |
T |
C |
10: 98,850,421 (GRCm39) |
V848A |
probably damaging |
Het |
| Bard1 |
T |
C |
1: 71,114,031 (GRCm39) |
T317A |
probably benign |
Het |
| C1rl |
T |
C |
6: 124,470,781 (GRCm39) |
W30R |
probably benign |
Het |
| Cchcr1 |
A |
G |
17: 35,837,317 (GRCm39) |
E379G |
probably damaging |
Het |
| Cfap36 |
G |
T |
11: 29,197,122 (GRCm39) |
A3E |
probably damaging |
Het |
| Cilp |
G |
A |
9: 65,186,997 (GRCm39) |
G1031S |
probably damaging |
Het |
| Clca4a |
A |
G |
3: 144,676,489 (GRCm39) |
Y64H |
probably damaging |
Het |
| Cops5 |
A |
G |
1: 10,102,562 (GRCm39) |
|
probably null |
Het |
| Cracr2a |
G |
T |
6: 127,585,564 (GRCm39) |
E121* |
probably null |
Het |
| Cstf1 |
A |
G |
2: 172,222,403 (GRCm39) |
E387G |
probably benign |
Het |
| D630044L22Rik |
A |
C |
17: 26,180,951 (GRCm39) |
D733E |
probably damaging |
Het |
| Dlc1 |
A |
T |
8: 37,060,535 (GRCm39) |
C514S |
probably damaging |
Het |
| Dmwd |
G |
T |
7: 18,810,610 (GRCm39) |
R139L |
probably benign |
Het |
| Dnah17 |
A |
T |
11: 117,958,357 (GRCm39) |
S2709T |
probably benign |
Het |
| Dnmt3a |
T |
C |
12: 3,922,859 (GRCm39) |
I154T |
probably benign |
Het |
| Dpp7 |
T |
C |
2: 25,244,490 (GRCm39) |
N297S |
possibly damaging |
Het |
| Ern2 |
A |
T |
7: 121,783,168 (GRCm39) |
V34D |
possibly damaging |
Het |
| Erp27 |
A |
G |
6: 136,885,227 (GRCm39) |
|
probably benign |
Het |
| F2 |
T |
C |
2: 91,458,787 (GRCm39) |
T508A |
probably benign |
Het |
| Fam181b |
A |
G |
7: 92,729,634 (GRCm39) |
T136A |
probably benign |
Het |
| Fam227b |
C |
A |
2: 125,942,874 (GRCm39) |
V308L |
probably benign |
Het |
| Fbxw20 |
A |
T |
9: 109,050,442 (GRCm39) |
H394Q |
probably damaging |
Het |
| G530012D18Rik |
CAGAGAGA |
CAGAGAGAGA |
1: 85,504,945 (GRCm39) |
|
probably null |
Het |
| Glt8d1 |
T |
G |
14: 30,731,693 (GRCm39) |
S111A |
probably benign |
Het |
| Gm11146 |
A |
T |
16: 77,391,969 (GRCm39) |
|
probably benign |
Het |
| Grip1 |
C |
T |
10: 119,885,416 (GRCm39) |
|
probably benign |
Het |
| H2-Q2 |
A |
T |
17: 35,564,247 (GRCm39) |
T334S |
probably benign |
Het |
| Hcrtr1 |
A |
G |
4: 130,024,680 (GRCm39) |
V402A |
probably benign |
Het |
| Hmcn2 |
C |
A |
2: 31,268,294 (GRCm39) |
A1130D |
probably benign |
Het |
| Hsd17b2 |
T |
C |
8: 118,428,913 (GRCm39) |
L60P |
possibly damaging |
Het |
| Htr1f |
A |
T |
16: 64,746,398 (GRCm39) |
I298N |
probably damaging |
Het |
| Ighmbp2 |
G |
T |
19: 3,315,095 (GRCm39) |
A775D |
probably benign |
Het |
| Kcnn3 |
A |
G |
3: 89,428,682 (GRCm39) |
T303A |
probably damaging |
Het |
| Kiz |
C |
A |
2: 146,733,203 (GRCm39) |
Q460K |
probably benign |
Het |
| Krt75 |
C |
T |
15: 101,481,196 (GRCm39) |
V193I |
probably benign |
Het |
| Lsp1 |
G |
A |
7: 142,043,144 (GRCm39) |
|
probably null |
Het |
| Mfsd12 |
A |
G |
10: 81,196,063 (GRCm39) |
H146R |
probably damaging |
Het |
| Mmp23 |
T |
C |
4: 155,736,444 (GRCm39) |
K199R |
possibly damaging |
Het |
| Naip2 |
A |
G |
13: 100,315,880 (GRCm39) |
V300A |
probably benign |
Het |
| Nbeal1 |
C |
T |
1: 60,350,216 (GRCm39) |
L2422F |
probably damaging |
Het |
| Nbeal2 |
G |
T |
9: 110,464,375 (GRCm39) |
D1094E |
possibly damaging |
Het |
| Nckap5 |
T |
C |
1: 125,954,635 (GRCm39) |
E639G |
probably damaging |
Het |
| Nr4a3 |
A |
G |
4: 48,067,771 (GRCm39) |
I456V |
possibly damaging |
Het |
| Or2t43 |
A |
G |
11: 58,457,673 (GRCm39) |
F166S |
probably damaging |
Het |
| Parp9 |
G |
T |
16: 35,773,984 (GRCm39) |
V86L |
probably damaging |
Het |
| Phactr1 |
A |
G |
13: 43,231,416 (GRCm39) |
N386S |
probably damaging |
Het |
| Pold2 |
A |
T |
11: 5,823,516 (GRCm39) |
Y304* |
probably null |
Het |
| Pou5f2 |
A |
G |
13: 78,173,940 (GRCm39) |
Y294C |
probably benign |
Het |
| Rars1 |
A |
G |
11: 35,717,410 (GRCm39) |
|
probably benign |
Het |
| Rbm12b1 |
A |
G |
4: 12,145,606 (GRCm39) |
E526G |
probably benign |
Het |
| Sacs |
T |
C |
14: 61,451,498 (GRCm39) |
Y4515H |
probably damaging |
Het |
| Sdk2 |
C |
A |
11: 113,741,780 (GRCm39) |
R813L |
probably damaging |
Het |
| Six5 |
T |
C |
7: 18,829,154 (GRCm39) |
V198A |
possibly damaging |
Het |
| Slco1a7 |
A |
T |
6: 141,671,181 (GRCm39) |
H430Q |
probably benign |
Het |
| Spata31e2 |
A |
T |
1: 26,724,813 (GRCm39) |
N122K |
possibly damaging |
Het |
| Spn |
A |
G |
7: 126,736,388 (GRCm39) |
S40P |
probably damaging |
Het |
| Ssr1 |
A |
G |
13: 38,171,761 (GRCm39) |
|
probably benign |
Het |
| Tlr6 |
C |
A |
5: 65,111,269 (GRCm39) |
C546F |
probably damaging |
Het |
| Top1 |
T |
A |
2: 160,544,748 (GRCm39) |
|
probably benign |
Het |
| Trhr2 |
A |
G |
8: 123,085,532 (GRCm39) |
S151P |
probably damaging |
Het |
| Tubb2b |
T |
G |
13: 34,311,708 (GRCm39) |
K362Q |
probably benign |
Het |
| Unc13c |
T |
C |
9: 73,643,832 (GRCm39) |
T1211A |
probably damaging |
Het |
| Vmn1r15 |
T |
C |
6: 57,235,729 (GRCm39) |
V199A |
possibly damaging |
Het |
| Vnn1 |
A |
G |
10: 23,776,475 (GRCm39) |
|
probably benign |
Het |
| Vps41 |
T |
A |
13: 19,038,786 (GRCm39) |
N737K |
possibly damaging |
Het |
| Zc3h7a |
A |
T |
16: 10,955,340 (GRCm39) |
N911K |
probably benign |
Het |
| Zkscan7 |
T |
A |
9: 122,718,002 (GRCm39) |
S132R |
probably damaging |
Het |
|
| Other mutations in Vps50 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00338:Vps50
|
APN |
6 |
3,602,670 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL00764:Vps50
|
APN |
6 |
3,532,177 (GRCm39) |
nonsense |
probably null |
|
|
IGL00844:Vps50
|
APN |
6 |
3,532,177 (GRCm39) |
nonsense |
probably null |
|
|
IGL00845:Vps50
|
APN |
6 |
3,532,177 (GRCm39) |
nonsense |
probably null |
|
|
IGL00850:Vps50
|
APN |
6 |
3,532,177 (GRCm39) |
nonsense |
probably null |
|
|
IGL01417:Vps50
|
APN |
6 |
3,522,377 (GRCm39) |
splice site |
probably benign |
|
|
IGL01648:Vps50
|
APN |
6 |
3,498,545 (GRCm39) |
missense |
probably benign |
0.25 |
|
IGL03238:Vps50
|
APN |
6 |
3,594,771 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
IGL03285:Vps50
|
APN |
6 |
3,555,011 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R0309:Vps50
|
UTSW |
6 |
3,536,853 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R0513:Vps50
|
UTSW |
6 |
3,520,210 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0714:Vps50
|
UTSW |
6 |
3,571,105 (GRCm39) |
missense |
probably benign |
0.05 |
|
R1066:Vps50
|
UTSW |
6 |
3,533,565 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1210:Vps50
|
UTSW |
6 |
3,594,884 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1420:Vps50
|
UTSW |
6 |
3,588,007 (GRCm39) |
nonsense |
probably null |
|
|
R1437:Vps50
|
UTSW |
6 |
3,517,852 (GRCm39) |
nonsense |
probably null |
|
|
R1451:Vps50
|
UTSW |
6 |
3,565,628 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R1470:Vps50
|
UTSW |
6 |
3,517,777 (GRCm39) |
splice site |
probably benign |
|
|
R1576:Vps50
|
UTSW |
6 |
3,545,568 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
R1599:Vps50
|
UTSW |
6 |
3,565,537 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1860:Vps50
|
UTSW |
6 |
3,520,279 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2109:Vps50
|
UTSW |
6 |
3,555,379 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R3408:Vps50
|
UTSW |
6 |
3,600,212 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3732:Vps50
|
UTSW |
6 |
3,519,243 (GRCm39) |
synonymous |
silent |
|
|
R3764:Vps50
|
UTSW |
6 |
3,588,063 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3828:Vps50
|
UTSW |
6 |
3,533,500 (GRCm39) |
missense |
probably benign |
|
|
R4092:Vps50
|
UTSW |
6 |
3,551,037 (GRCm39) |
missense |
probably benign |
|
|
R4385:Vps50
|
UTSW |
6 |
3,516,694 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4588:Vps50
|
UTSW |
6 |
3,562,306 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4843:Vps50
|
UTSW |
6 |
3,536,974 (GRCm39) |
critical splice donor site |
probably null |
|
|
R4978:Vps50
|
UTSW |
6 |
3,517,808 (GRCm39) |
missense |
probably benign |
|
|
R5368:Vps50
|
UTSW |
6 |
3,567,739 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R5867:Vps50
|
UTSW |
6 |
3,536,965 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6591:Vps50
|
UTSW |
6 |
3,504,939 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6626:Vps50
|
UTSW |
6 |
3,551,101 (GRCm39) |
nonsense |
probably null |
|
|
R6691:Vps50
|
UTSW |
6 |
3,504,939 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6707:Vps50
|
UTSW |
6 |
3,545,583 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6751:Vps50
|
UTSW |
6 |
3,600,274 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6773:Vps50
|
UTSW |
6 |
3,592,560 (GRCm39) |
missense |
probably benign |
0.25 |
|
R6867:Vps50
|
UTSW |
6 |
3,517,835 (GRCm39) |
missense |
probably benign |
0.16 |
|
R6883:Vps50
|
UTSW |
6 |
3,498,513 (GRCm39) |
unclassified |
probably benign |
|
|
R6963:Vps50
|
UTSW |
6 |
3,592,577 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7147:Vps50
|
UTSW |
6 |
3,567,750 (GRCm39) |
nonsense |
probably null |
|
|
R7150:Vps50
|
UTSW |
6 |
3,578,854 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R7167:Vps50
|
UTSW |
6 |
3,600,256 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7235:Vps50
|
UTSW |
6 |
3,588,078 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7385:Vps50
|
UTSW |
6 |
3,602,708 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7662:Vps50
|
UTSW |
6 |
3,562,304 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7782:Vps50
|
UTSW |
6 |
3,532,202 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8188:Vps50
|
UTSW |
6 |
3,562,297 (GRCm39) |
nonsense |
probably null |
|
|
R8232:Vps50
|
UTSW |
6 |
3,600,139 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8535:Vps50
|
UTSW |
6 |
3,565,612 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R8808:Vps50
|
UTSW |
6 |
3,522,338 (GRCm39) |
nonsense |
probably null |
|
|
R8845:Vps50
|
UTSW |
6 |
3,504,926 (GRCm39) |
missense |
probably benign |
|
|
R8889:Vps50
|
UTSW |
6 |
3,536,967 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8892:Vps50
|
UTSW |
6 |
3,536,967 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8911:Vps50
|
UTSW |
6 |
3,516,710 (GRCm39) |
missense |
probably benign |
|
|
R9089:Vps50
|
UTSW |
6 |
3,536,884 (GRCm39) |
missense |
probably benign |
0.02 |
|
R9116:Vps50
|
UTSW |
6 |
3,588,091 (GRCm39) |
splice site |
probably benign |
|
|
R9381:Vps50
|
UTSW |
6 |
3,592,433 (GRCm39) |
missense |
probably benign |
|
|
R9440:Vps50
|
UTSW |
6 |
3,516,724 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9485:Vps50
|
UTSW |
6 |
3,592,557 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9585:Vps50
|
UTSW |
6 |
3,600,348 (GRCm39) |
missense |
probably benign |
0.03 |
|
R9645:Vps50
|
UTSW |
6 |
3,516,706 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R9761:Vps50
|
UTSW |
6 |
3,519,218 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9796:Vps50
|
UTSW |
6 |
3,562,300 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0025:Vps50
|
UTSW |
6 |
3,571,012 (GRCm39) |
missense |
probably benign |
0.02 |
|
X0062:Vps50
|
UTSW |
6 |
3,594,833 (GRCm39) |
missense |
probably benign |
|
|
Z1176:Vps50
|
UTSW |
6 |
3,578,792 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
Z1177:Vps50
|
UTSW |
6 |
3,562,312 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1177:Vps50
|
UTSW |
6 |
3,555,367 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GGGACAGGGTTATCATCTCAC -3'
(R):5'- AATTGTGTGTATGCAGCAGC -3'
Sequencing Primer
(F):5'- CTCACAATGATATGTTCAAGATGCC -3'
(R):5'- AACCCAGGTCTTCTAGTTGAGCAG -3'
|
| Posted On |
2014-09-17 |
Incidental Mutation