Incidental Mutation 'R7235:Vps50'
| ID |
562757 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps50
|
| Ensembl Gene |
ENSMUSG00000001376 |
| Gene Name |
VPS50 EARP/GARPII complex subunit |
| Synonyms |
Ccdc132, 1700034M03Rik, 8430415E05Rik |
| MMRRC Submission |
045305-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.890)
|
| Stock # |
R7235 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
6 |
| Chromosomal Location |
3498393-3603531 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 3588078 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 684
(I684V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000001412
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001412]
[ENSMUST00000164052]
[ENSMUST00000170873]
|
| AlphaFold |
Q8CI71 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000001412
AA Change: I684V
PolyPhen 2
Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
|
| SMART Domains |
Protein: ENSMUSP00000001412
Gene: ENSMUSG00000001376
AA Change: I684V
| 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: I684V
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000125872
Gene: ENSMUSG00000001376
AA Change: I684V
| 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: I684V
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000128323
Gene: ENSMUSG00000001376
AA Change: I684V
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.9%
|
| Validation Efficiency |
98% (61/62) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ahnak |
T |
A |
19: 8,989,852 (GRCm39) |
M3712K |
unknown |
Het |
| Bri3bp |
A |
G |
5: 125,518,748 (GRCm39) |
E8G |
unknown |
Het |
| Brip1 |
C |
T |
11: 86,029,701 (GRCm39) |
R611Q |
possibly damaging |
Het |
| Carm1 |
T |
G |
9: 21,498,701 (GRCm39) |
|
probably benign |
Het |
| Catsper4 |
A |
T |
4: 133,939,892 (GRCm39) |
|
probably null |
Het |
| Ccng2 |
C |
G |
5: 93,421,202 (GRCm39) |
S237R |
probably benign |
Het |
| Cip2a |
T |
A |
16: 48,821,422 (GRCm39) |
L176H |
probably damaging |
Het |
| Clk4 |
A |
G |
11: 51,167,012 (GRCm39) |
D330G |
probably damaging |
Het |
| Dcdc2c |
A |
G |
12: 28,520,718 (GRCm39) |
S453P |
|
Het |
| Ddx46 |
G |
A |
13: 55,811,053 (GRCm39) |
V550I |
probably benign |
Het |
| Dennd1a |
T |
C |
2: 37,691,073 (GRCm39) |
N676D |
probably benign |
Het |
| Dnah3 |
T |
C |
7: 119,631,893 (GRCm39) |
N1365S |
probably damaging |
Het |
| Dsg1b |
T |
C |
18: 20,532,480 (GRCm39) |
V508A |
probably benign |
Het |
| Dus2 |
T |
C |
8: 106,742,587 (GRCm39) |
V39A |
possibly damaging |
Het |
| Dync1li1 |
T |
C |
9: 114,544,231 (GRCm39) |
V301A |
possibly damaging |
Het |
| Efcc1 |
T |
G |
6: 87,730,780 (GRCm39) |
S513A |
probably benign |
Het |
| Eif3f |
T |
C |
7: 108,537,295 (GRCm39) |
V167A |
possibly damaging |
Het |
| Ephb2 |
A |
G |
4: 136,421,139 (GRCm39) |
Y404H |
probably damaging |
Het |
| Eqtn |
A |
T |
4: 94,811,936 (GRCm39) |
D152E |
probably damaging |
Het |
| Ercc5 |
A |
C |
1: 44,217,363 (GRCm39) |
K902T |
possibly damaging |
Het |
| Erlec1 |
T |
A |
11: 30,900,751 (GRCm39) |
E139V |
possibly damaging |
Het |
| Evl |
G |
A |
12: 108,614,719 (GRCm39) |
G38R |
probably damaging |
Het |
| Fads2b |
T |
G |
2: 85,330,563 (GRCm39) |
H248P |
probably damaging |
Het |
| Foxd2 |
T |
C |
4: 114,765,468 (GRCm39) |
N184S |
unknown |
Het |
| Frem3 |
T |
C |
8: 81,417,354 (GRCm39) |
Y2020H |
probably benign |
Het |
| Ganc |
T |
C |
2: 120,264,198 (GRCm39) |
F384L |
probably damaging |
Het |
| Grin2a |
A |
G |
16: 9,397,129 (GRCm39) |
L986P |
probably damaging |
Het |
| Ift140 |
A |
T |
17: 25,239,619 (GRCm39) |
D92V |
possibly damaging |
Het |
| Inpp5b |
A |
G |
4: 124,645,185 (GRCm39) |
K158E |
probably benign |
Het |
| Iscu |
T |
A |
5: 113,914,943 (GRCm39) |
S152T |
probably benign |
Het |
| Isl2 |
C |
T |
9: 55,451,455 (GRCm39) |
T115I |
probably benign |
Het |
| Kalrn |
T |
A |
16: 33,996,131 (GRCm39) |
T1542S |
probably benign |
Het |
| Kat6a |
A |
G |
8: 23,404,285 (GRCm39) |
D454G |
possibly damaging |
Het |
| Kcnj10 |
T |
C |
1: 172,196,993 (GRCm39) |
I169T |
probably damaging |
Het |
| Klk12 |
T |
C |
7: 43,422,723 (GRCm39) |
S217P |
probably damaging |
Het |
| Lancl1 |
T |
C |
1: 67,077,694 (GRCm39) |
N14S |
probably benign |
Het |
| Map2 |
A |
G |
1: 66,453,807 (GRCm39) |
Y899C |
probably damaging |
Het |
| Msantd5f9 |
G |
T |
4: 73,835,808 (GRCm39) |
L219M |
probably benign |
Het |
| Nr1h5 |
C |
T |
3: 102,856,358 (GRCm39) |
|
probably null |
Het |
| Nup98 |
T |
C |
7: 101,774,491 (GRCm39) |
T1515A |
probably damaging |
Het |
| Obscn |
A |
C |
11: 58,971,666 (GRCm39) |
V2183G |
probably damaging |
Het |
| Or52n2 |
C |
T |
7: 104,541,926 (GRCm39) |
R303Q |
probably benign |
Het |
| Osbpl8 |
A |
G |
10: 111,105,288 (GRCm39) |
T248A |
probably benign |
Het |
| Pias3 |
T |
A |
3: 96,611,679 (GRCm39) |
S533T |
probably benign |
Het |
| Pkd1l3 |
GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA |
GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA |
8: 110,350,827 (GRCm39) |
|
probably benign |
Het |
| Plxna1 |
A |
G |
6: 89,317,573 (GRCm39) |
Y680H |
probably damaging |
Het |
| Pnliprp2 |
A |
G |
19: 58,763,659 (GRCm39) |
N436S |
probably benign |
Het |
| Pold1 |
T |
A |
7: 44,191,244 (GRCm39) |
M196L |
probably benign |
Het |
| Prkdc |
G |
A |
16: 15,532,127 (GRCm39) |
V1464I |
probably benign |
Het |
| Ptk2b |
G |
A |
14: 66,394,536 (GRCm39) |
Q857* |
probably null |
Het |
| Qars1 |
T |
A |
9: 108,387,331 (GRCm39) |
L185Q |
probably damaging |
Het |
| Rabep1 |
A |
G |
11: 70,831,290 (GRCm39) |
N859S |
probably benign |
Het |
| Rnf19b |
A |
G |
4: 128,977,571 (GRCm39) |
H156R |
|
Het |
| Sart3 |
T |
C |
5: 113,891,703 (GRCm39) |
Q423R |
probably damaging |
Het |
| Selplg |
GTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCT |
GTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCTGCCTCCATGGGTGCTGGCTGCGAGGTCTCT |
5: 113,957,756 (GRCm39) |
|
probably benign |
Het |
| Slc6a21 |
C |
T |
7: 44,930,182 (GRCm39) |
H194Y |
probably damaging |
Het |
| Tcf4 |
G |
A |
18: 69,790,866 (GRCm39) |
V420I |
probably damaging |
Het |
| Tjp1 |
T |
C |
7: 64,968,321 (GRCm39) |
D701G |
probably benign |
Het |
| Trim42 |
T |
C |
9: 97,251,761 (GRCm39) |
D46G |
probably damaging |
Het |
| Usp19 |
C |
T |
9: 108,372,123 (GRCm39) |
R429* |
probably null |
Het |
| Uxs1 |
T |
C |
1: 43,804,087 (GRCm39) |
N276S |
probably damaging |
Het |
| Yars2 |
T |
A |
16: 16,122,556 (GRCm39) |
D307E |
probably benign |
Het |
| Zfp934 |
A |
T |
13: 62,665,964 (GRCm39) |
C258S |
|
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 |
|
|
R2055:Vps50
|
UTSW |
6 |
3,522,265 (GRCm39) |
missense |
probably benign |
0.01 |
|
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 |
|
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'- TGTTGCCCTGACCTTCAAGG -3'
(R):5'- CCAATTGGAGATACATCAAGGC -3'
Sequencing Primer
(F):5'- CTGACCTTCAAGGACTCATGAATAG -3'
(R):5'- ACATCAAGGCTATTAACAATAGGTTC -3'
|
| Posted On |
2019-06-26 |
Incidental Mutation