Incidental Mutation 'R0568:Vps9d1'
| ID |
46266 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps9d1
|
| Ensembl Gene |
ENSMUSG00000001062 |
| Gene Name |
VPS9 domain containing 1 |
| Synonyms |
2410004N05Rik, 1300018I17Rik |
| MMRRC Submission |
038759-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R0568 (G1)
|
| Quality Score |
116 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
123969095-123980961 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 123973487 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 432
(V432A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000113575
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000117643]
[ENSMUST00000118279]
[ENSMUST00000122363]
[ENSMUST00000127664]
[ENSMUST00000155869]
|
| AlphaFold |
Q8C190 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000117643
AA Change: V432A
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000113748
Gene: ENSMUSG00000001062
AA Change: V432A
| 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 damaging
Transcript: ENSMUST00000118279
AA Change: V432A
PolyPhen 2
Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000113634
Gene: ENSMUSG00000001062
AA Change: V432A
| 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 damaging
Transcript: ENSMUST00000122363
AA Change: V432A
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000113575
Gene: ENSMUSG00000001062
AA Change: V432A
| 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: ENSMUST00000130965
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146136
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149490
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000181432
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000211876
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137569
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130275
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155853
|
| 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 |
|
| Meta Mutation Damage Score |
0.4168 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.4%
- 10x: 96.5%
- 20x: 93.4%
|
| Validation Efficiency |
100% (38/38) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 37 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acnat1 |
G |
A |
4: 49,451,003 (GRCm39) |
T36I |
possibly damaging |
Het |
| Adamts20 |
T |
C |
15: 94,189,594 (GRCm39) |
|
probably benign |
Het |
| Adamtsl1 |
T |
C |
4: 86,336,789 (GRCm39) |
L1558S |
probably damaging |
Het |
| Ap3b2 |
A |
G |
7: 81,114,377 (GRCm39) |
|
probably null |
Het |
| Bag2 |
T |
C |
1: 33,786,059 (GRCm39) |
M88V |
probably benign |
Het |
| Brms1l |
A |
G |
12: 55,908,173 (GRCm39) |
|
probably null |
Het |
| C8b |
A |
G |
4: 104,650,577 (GRCm39) |
I462V |
probably benign |
Het |
| Cfap410 |
C |
T |
10: 77,818,872 (GRCm39) |
T181I |
possibly damaging |
Het |
| Cfap410 |
A |
T |
10: 77,820,381 (GRCm39) |
*250C |
probably null |
Het |
| Cnpy4 |
A |
G |
5: 138,190,839 (GRCm39) |
E167G |
probably damaging |
Het |
| Copa |
T |
C |
1: 171,939,704 (GRCm39) |
V624A |
possibly damaging |
Het |
| Gm4553 |
G |
T |
7: 141,719,357 (GRCm39) |
P24T |
unknown |
Het |
| Gna12 |
A |
G |
5: 140,746,638 (GRCm39) |
V269A |
possibly damaging |
Het |
| Gtf2ird2 |
G |
T |
5: 134,240,083 (GRCm39) |
E302* |
probably null |
Het |
| Hmcn2 |
C |
A |
2: 31,305,248 (GRCm39) |
S3140R |
probably benign |
Het |
| Hspa4 |
A |
G |
11: 53,153,703 (GRCm39) |
|
probably benign |
Het |
| Hspbp1 |
A |
T |
7: 4,687,431 (GRCm39) |
L60* |
probably null |
Het |
| Lats1 |
A |
T |
10: 7,588,292 (GRCm39) |
I970F |
possibly damaging |
Het |
| Lipo3 |
T |
C |
19: 33,559,442 (GRCm39) |
|
probably benign |
Het |
| Lrrc3 |
T |
A |
10: 77,737,419 (GRCm39) |
R6W |
probably damaging |
Het |
| Lxn |
C |
T |
3: 67,368,335 (GRCm39) |
A143T |
probably damaging |
Het |
| Mga |
T |
C |
2: 119,765,903 (GRCm39) |
I1390T |
probably damaging |
Het |
| Ncapg2 |
T |
A |
12: 116,386,835 (GRCm39) |
I286N |
probably damaging |
Het |
| Or4c107 |
T |
A |
2: 88,789,387 (GRCm39) |
Y192* |
probably null |
Het |
| Pitpnm2 |
A |
G |
5: 124,278,580 (GRCm39) |
|
probably benign |
Het |
| Plxna2 |
T |
C |
1: 194,433,694 (GRCm39) |
V581A |
probably benign |
Het |
| Polr3d |
A |
T |
14: 70,676,959 (GRCm39) |
H378Q |
possibly damaging |
Het |
| Ptpn13 |
T |
C |
5: 103,637,631 (GRCm39) |
V173A |
probably damaging |
Het |
| Rbpms2 |
ACTGCTGCTGCTGCTGC |
ACTGCTGCTGCTGCTGCTGC |
9: 65,558,948 (GRCm39) |
|
probably benign |
Het |
| Smc4 |
T |
C |
3: 68,929,794 (GRCm39) |
|
probably null |
Het |
| Snrnp40 |
C |
G |
4: 130,271,836 (GRCm39) |
|
probably null |
Het |
| Syngr3 |
C |
T |
17: 24,905,555 (GRCm39) |
A140T |
probably benign |
Het |
| Tent2 |
A |
G |
13: 93,291,500 (GRCm39) |
S381P |
probably benign |
Het |
| Tprn |
T |
C |
2: 25,154,333 (GRCm39) |
V545A |
probably damaging |
Het |
| Trim66 |
T |
C |
7: 109,059,902 (GRCm39) |
H828R |
probably benign |
Het |
| Ugt2b5 |
G |
A |
5: 87,285,224 (GRCm39) |
|
probably benign |
Het |
| Zswim9 |
A |
T |
7: 12,994,952 (GRCm39) |
D401E |
probably 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 |
|
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 |
|
|
R5908:Vps9d1
|
UTSW |
8 |
123,973,563 (GRCm39) |
missense |
probably benign |
0.28 |
|
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'- TCTGAGGCACTAAAGTAGGCTAGGG -3'
(R):5'- TGCGCTGTATCCGATTGTGAGC -3'
Sequencing Primer
(F):5'- TAGGCTAGGGCCTGCTCTC -3'
(R):5'- TGCTGGATGGACCTCCTC -3'
|
| Posted On |
2013-06-11 |
Incidental Mutation