Incidental Mutation 'R5908:Vps9d1'
ID |
460790 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps9d1
|
Ensembl Gene |
ENSMUSG00000001062 |
Gene Name |
VPS9 domain containing 1 |
Synonyms |
2410004N05Rik, 1300018I17Rik |
MMRRC Submission |
044105-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R5908 (G1)
|
Quality Score |
203 |
Status
|
Validated
|
Chromosome |
8 |
Chromosomal Location |
123969095-123980961 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to T
at 123973563 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Glutamine to Lysine
at position 407
(Q407K)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000113634
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000117643]
[ENSMUST00000118279]
[ENSMUST00000122363]
[ENSMUST00000127664]
[ENSMUST00000155869]
|
AlphaFold |
Q8C190 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000117643
AA Change: Q407K
PolyPhen 2
Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
|
SMART Domains |
Protein: ENSMUSP00000113748 Gene: ENSMUSG00000001062 AA Change: Q407K
Domain | Start | End | E-Value | Type |
low complexity region
|
96 |
108 |
N/A |
INTRINSIC |
coiled coil region
|
187 |
220 |
N/A |
INTRINSIC |
low complexity region
|
266 |
279 |
N/A |
INTRINSIC |
low complexity region
|
442 |
453 |
N/A |
INTRINSIC |
Pfam:VPS9
|
528 |
645 |
8.5e-27 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000118279
AA Change: Q407K
PolyPhen 2
Score 0.285 (Sensitivity: 0.91; Specificity: 0.88)
|
SMART Domains |
Protein: ENSMUSP00000113634 Gene: ENSMUSG00000001062 AA Change: Q407K
Domain | Start | End | E-Value | Type |
low complexity region
|
96 |
108 |
N/A |
INTRINSIC |
coiled coil region
|
187 |
220 |
N/A |
INTRINSIC |
low complexity region
|
266 |
279 |
N/A |
INTRINSIC |
low complexity region
|
442 |
453 |
N/A |
INTRINSIC |
Pfam:VPS9
|
528 |
645 |
1.2e-25 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000122363
AA Change: Q407K
PolyPhen 2
Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
|
SMART Domains |
Protein: ENSMUSP00000113575 Gene: ENSMUSG00000001062 AA Change: Q407K
Domain | Start | End | E-Value | Type |
low complexity region
|
96 |
108 |
N/A |
INTRINSIC |
coiled coil region
|
187 |
220 |
N/A |
INTRINSIC |
low complexity region
|
266 |
279 |
N/A |
INTRINSIC |
low complexity region
|
442 |
453 |
N/A |
INTRINSIC |
Pfam:VPS9
|
528 |
644 |
5.6e-27 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124508
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000127664
|
SMART Domains |
Protein: ENSMUSP00000118564 Gene: ENSMUSG00000092329
Domain | Start | End | E-Value | Type |
Pfam:Glycos_transf_2
|
104 |
287 |
7.4e-31 |
PFAM |
Pfam:Glyco_transf_7C
|
261 |
331 |
4.9e-8 |
PFAM |
RICIN
|
406 |
531 |
9.28e-27 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000127978
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129591
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130275
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146136
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149490
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155853
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137569
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000181432
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130965
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000211876
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000155869
|
SMART Domains |
Protein: ENSMUSP00000122184 Gene: ENSMUSG00000001062
Domain | Start | End | E-Value | Type |
low complexity region
|
96 |
108 |
N/A |
INTRINSIC |
coiled coil region
|
187 |
223 |
N/A |
INTRINSIC |
|
Coding Region Coverage |
- 1x: 99.8%
- 3x: 99.4%
- 10x: 97.3%
- 20x: 91.8%
|
Validation Efficiency |
97% (69/71) |
Allele List at MGI |
|
Other mutations in this stock |
Total: 61 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abcc10 |
A |
T |
17: 46,624,730 (GRCm39) |
L198H |
probably damaging |
Het |
Anks1 |
C |
T |
17: 28,214,993 (GRCm39) |
T480I |
probably damaging |
Het |
Arhgef18 |
G |
A |
8: 3,503,165 (GRCm39) |
R857Q |
probably damaging |
Het |
B230208B08Rik |
A |
G |
4: 78,132,297 (GRCm39) |
|
noncoding transcript |
Het |
B9d2 |
T |
A |
7: 25,382,724 (GRCm39) |
W33R |
probably damaging |
Het |
Bcl2a1c |
A |
G |
9: 114,159,572 (GRCm39) |
T117A |
probably benign |
Het |
Btbd8 |
T |
G |
5: 107,655,460 (GRCm39) |
D574E |
probably damaging |
Het |
Cabin1 |
A |
G |
10: 75,557,366 (GRCm39) |
S1091P |
probably damaging |
Het |
Clip3 |
C |
A |
7: 29,996,298 (GRCm39) |
D64E |
probably damaging |
Het |
Col6a5 |
C |
G |
9: 105,740,000 (GRCm39) |
D2540H |
possibly damaging |
Het |
Commd5 |
A |
T |
15: 76,785,136 (GRCm39) |
M178L |
probably benign |
Het |
Crtc3 |
T |
A |
7: 80,245,542 (GRCm39) |
H361L |
possibly damaging |
Het |
Dip2b |
T |
A |
15: 100,049,065 (GRCm39) |
L153Q |
possibly damaging |
Het |
Eif2s1 |
T |
A |
12: 78,926,817 (GRCm39) |
V189D |
probably damaging |
Het |
Etl4 |
C |
T |
2: 20,748,718 (GRCm39) |
A483V |
probably damaging |
Het |
Foxo3 |
T |
C |
10: 42,072,583 (GRCm39) |
I645V |
probably benign |
Het |
Gm4841 |
A |
G |
18: 60,403,506 (GRCm39) |
S196P |
possibly damaging |
Het |
Hip1 |
A |
G |
5: 135,453,717 (GRCm39) |
|
probably null |
Het |
Il36rn |
G |
T |
2: 24,167,502 (GRCm39) |
|
probably benign |
Het |
Ints2 |
A |
G |
11: 86,106,371 (GRCm39) |
|
probably null |
Het |
Khnyn |
A |
G |
14: 56,124,523 (GRCm39) |
D259G |
probably benign |
Het |
Lyst |
T |
A |
13: 13,871,346 (GRCm39) |
Y2694* |
probably null |
Het |
Map4k2 |
T |
C |
19: 6,401,346 (GRCm39) |
|
probably benign |
Het |
Marchf10 |
C |
T |
11: 105,281,065 (GRCm39) |
V407I |
probably benign |
Het |
Mast4 |
C |
A |
13: 102,874,764 (GRCm39) |
V1367F |
probably damaging |
Het |
Mrgprb3 |
A |
T |
7: 48,293,366 (GRCm39) |
S62T |
probably damaging |
Het |
Mthfd1l |
T |
C |
10: 4,039,392 (GRCm39) |
F801S |
probably damaging |
Het |
Nhsl3 |
A |
G |
4: 129,115,941 (GRCm39) |
S908P |
probably damaging |
Het |
Notch2 |
T |
C |
3: 98,031,239 (GRCm39) |
|
probably benign |
Het |
Nr2e1 |
T |
C |
10: 42,448,765 (GRCm39) |
S158G |
probably benign |
Het |
Nup214 |
A |
G |
2: 31,881,353 (GRCm39) |
I404V |
probably benign |
Het |
Or13n4 |
T |
C |
7: 106,423,404 (GRCm39) |
T110A |
probably benign |
Het |
Pik3c2g |
G |
A |
6: 139,714,436 (GRCm39) |
R196H |
|
Het |
Pik3r3 |
A |
T |
4: 116,129,955 (GRCm39) |
D213V |
probably benign |
Het |
Pip5k1b |
A |
T |
19: 24,374,501 (GRCm39) |
S27T |
possibly damaging |
Het |
Pkp1 |
G |
A |
1: 135,846,621 (GRCm39) |
Q44* |
probably null |
Het |
Pnma8b |
C |
T |
7: 16,680,968 (GRCm39) |
R651C |
unknown |
Het |
Pnpt1 |
T |
A |
11: 29,080,887 (GRCm39) |
S44T |
probably benign |
Het |
Polb |
A |
T |
8: 23,132,319 (GRCm39) |
|
probably null |
Het |
Pom121l2 |
A |
G |
13: 22,165,984 (GRCm39) |
N85S |
probably damaging |
Het |
Prim1 |
A |
G |
10: 127,853,893 (GRCm39) |
K104E |
probably damaging |
Het |
Prl8a1 |
T |
A |
13: 27,758,040 (GRCm39) |
Y223F |
probably benign |
Het |
Rbak |
T |
G |
5: 143,159,391 (GRCm39) |
H554P |
probably damaging |
Het |
Serpina3c |
T |
C |
12: 104,117,970 (GRCm39) |
R123G |
probably benign |
Het |
Sh3bp4 |
T |
G |
1: 89,073,605 (GRCm39) |
S818A |
probably damaging |
Het |
Sh3rf3 |
C |
G |
10: 58,885,270 (GRCm39) |
H384Q |
probably benign |
Het |
Slc9a8 |
C |
T |
2: 167,293,090 (GRCm39) |
|
probably benign |
Het |
Sptbn4 |
T |
C |
7: 27,103,678 (GRCm39) |
E1181G |
probably benign |
Het |
Taf2 |
G |
A |
15: 54,935,402 (GRCm39) |
|
probably benign |
Het |
Taf7l2 |
A |
T |
10: 115,949,133 (GRCm39) |
I131N |
probably benign |
Het |
Tbc1d9 |
A |
T |
8: 83,976,174 (GRCm39) |
M578L |
probably benign |
Het |
Tinagl1 |
G |
T |
4: 130,066,763 (GRCm39) |
Y111* |
probably null |
Het |
Tor2a |
T |
C |
2: 32,651,697 (GRCm39) |
L304P |
probably damaging |
Het |
Trp53bp1 |
A |
G |
2: 121,067,304 (GRCm39) |
V474A |
probably benign |
Het |
Trrap |
C |
A |
5: 144,723,518 (GRCm39) |
A325E |
probably damaging |
Het |
Ube4a |
A |
G |
9: 44,859,322 (GRCm39) |
|
probably null |
Het |
Use1 |
G |
C |
8: 71,822,257 (GRCm39) |
K239N |
probably damaging |
Het |
Zfp36l1 |
A |
T |
12: 80,156,449 (GRCm39) |
S311T |
possibly damaging |
Het |
Zfp729b |
T |
C |
13: 67,739,374 (GRCm39) |
K964E |
probably benign |
Het |
Zfp974 |
T |
A |
7: 27,610,382 (GRCm39) |
M448L |
probably benign |
Het |
Zfyve28 |
A |
T |
5: 34,374,214 (GRCm39) |
V600E |
possibly damaging |
Het |
|
Other mutations in Vps9d1 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00549:Vps9d1
|
APN |
8 |
123,971,937 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01112:Vps9d1
|
APN |
8 |
123,972,769 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01729:Vps9d1
|
APN |
8 |
123,973,739 (GRCm39) |
missense |
probably damaging |
1.00 |
R0568:Vps9d1
|
UTSW |
8 |
123,973,487 (GRCm39) |
missense |
probably damaging |
1.00 |
R1191:Vps9d1
|
UTSW |
8 |
123,974,706 (GRCm39) |
missense |
possibly damaging |
0.95 |
R1813:Vps9d1
|
UTSW |
8 |
123,973,778 (GRCm39) |
missense |
probably damaging |
0.99 |
R1896:Vps9d1
|
UTSW |
8 |
123,973,778 (GRCm39) |
missense |
probably damaging |
0.99 |
R2193:Vps9d1
|
UTSW |
8 |
123,979,404 (GRCm39) |
missense |
probably damaging |
1.00 |
R2256:Vps9d1
|
UTSW |
8 |
123,971,860 (GRCm39) |
missense |
probably benign |
0.18 |
R4305:Vps9d1
|
UTSW |
8 |
123,974,976 (GRCm39) |
intron |
probably benign |
|
R4458:Vps9d1
|
UTSW |
8 |
123,974,487 (GRCm39) |
missense |
probably benign |
0.30 |
R4707:Vps9d1
|
UTSW |
8 |
123,975,351 (GRCm39) |
critical splice donor site |
probably benign |
|
R5366:Vps9d1
|
UTSW |
8 |
123,971,853 (GRCm39) |
missense |
possibly damaging |
0.89 |
R5392:Vps9d1
|
UTSW |
8 |
123,980,752 (GRCm39) |
missense |
probably damaging |
0.99 |
R5423:Vps9d1
|
UTSW |
8 |
123,974,704 (GRCm39) |
critical splice donor site |
probably null |
|
R5645:Vps9d1
|
UTSW |
8 |
123,974,487 (GRCm39) |
missense |
probably benign |
0.30 |
R5647:Vps9d1
|
UTSW |
8 |
123,975,598 (GRCm39) |
missense |
probably damaging |
1.00 |
R5695:Vps9d1
|
UTSW |
8 |
123,973,655 (GRCm39) |
missense |
probably benign |
|
R6061:Vps9d1
|
UTSW |
8 |
123,972,410 (GRCm39) |
missense |
probably damaging |
0.99 |
R6250:Vps9d1
|
UTSW |
8 |
123,974,947 (GRCm39) |
critical splice acceptor site |
probably null |
|
R6416:Vps9d1
|
UTSW |
8 |
123,975,378 (GRCm39) |
missense |
probably damaging |
1.00 |
R6747:Vps9d1
|
UTSW |
8 |
123,980,746 (GRCm39) |
missense |
probably damaging |
1.00 |
R7049:Vps9d1
|
UTSW |
8 |
123,973,882 (GRCm39) |
nonsense |
probably null |
|
R7584:Vps9d1
|
UTSW |
8 |
123,977,456 (GRCm39) |
missense |
probably damaging |
1.00 |
R8321:Vps9d1
|
UTSW |
8 |
123,975,544 (GRCm39) |
missense |
possibly damaging |
0.47 |
R9178:Vps9d1
|
UTSW |
8 |
123,975,574 (GRCm39) |
missense |
probably damaging |
0.97 |
R9218:Vps9d1
|
UTSW |
8 |
123,977,674 (GRCm39) |
missense |
probably benign |
0.12 |
R9366:Vps9d1
|
UTSW |
8 |
123,974,486 (GRCm39) |
nonsense |
probably null |
|
R9542:Vps9d1
|
UTSW |
8 |
123,970,522 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- TAGACACAGGTCCTTGCTGTC -3'
(R):5'- AGAGCCTCTACTGCATGCTTTC -3'
Sequencing Primer
(F):5'- TCCTTGCTGTCCCGGGC -3'
(R):5'- CTCCGAGCCCAGTGCAG -3'
|
Posted On |
2017-02-28 |