Incidental Mutation 'R5647:Vps9d1'
ID |
441223 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps9d1
|
Ensembl Gene |
ENSMUSG00000001062 |
Gene Name |
VPS9 domain containing 1 |
Synonyms |
2410004N05Rik, 1300018I17Rik |
MMRRC Submission |
043295-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R5647 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
8 |
Chromosomal Location |
123969095-123980961 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 123975598 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Leucine to Glutamine
at position 149
(L149Q)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000122184
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000117643]
[ENSMUST00000118279]
[ENSMUST00000122363]
[ENSMUST00000127664]
[ENSMUST00000155869]
|
AlphaFold |
Q8C190 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000117643
AA Change: L149Q
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000113748 Gene: ENSMUSG00000001062 AA Change: L149Q
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: L149Q
PolyPhen 2
Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000113634 Gene: ENSMUSG00000001062 AA Change: L149Q
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: L149Q
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000113575 Gene: ENSMUSG00000001062 AA Change: L149Q
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: ENSMUST00000137569
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130965
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146136
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000155869
AA Change: L149Q
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000122184 Gene: ENSMUSG00000001062 AA Change: L149Q
Domain | Start | End | E-Value | Type |
low complexity region
|
96 |
108 |
N/A |
INTRINSIC |
coiled coil region
|
187 |
223 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155853
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130275
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129591
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149490
|
Meta Mutation Damage Score |
0.1997 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.0%
- 20x: 94.7%
|
Validation Efficiency |
95% (55/58) |
Allele List at MGI |
|
Other mutations in this stock |
Total: 49 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700010L04Rik |
T |
C |
7: 82,505,606 (GRCm39) |
|
noncoding transcript |
Het |
9330159F19Rik |
A |
T |
10: 29,101,250 (GRCm39) |
D541V |
probably damaging |
Het |
Abcc5 |
T |
C |
16: 20,218,597 (GRCm39) |
I262V |
probably damaging |
Het |
Acvr1c |
T |
A |
2: 58,185,976 (GRCm39) |
D169V |
probably damaging |
Het |
Aldh16a1 |
A |
G |
7: 44,803,889 (GRCm39) |
V6A |
probably benign |
Het |
Brd10 |
A |
G |
19: 29,731,210 (GRCm39) |
S601P |
possibly damaging |
Het |
Cd36 |
A |
C |
5: 18,019,763 (GRCm39) |
S113A |
probably damaging |
Het |
Cdt1 |
G |
T |
8: 123,296,947 (GRCm39) |
R247L |
possibly damaging |
Het |
Ces4a |
G |
A |
8: 105,872,712 (GRCm39) |
V322M |
probably benign |
Het |
Cngb3 |
A |
T |
4: 19,364,266 (GRCm39) |
T157S |
possibly damaging |
Het |
Cpped1 |
T |
C |
16: 11,646,010 (GRCm39) |
|
probably benign |
Het |
Ctr9 |
G |
T |
7: 110,654,751 (GRCm39) |
R1094L |
unknown |
Het |
Cyld |
A |
T |
8: 89,461,554 (GRCm39) |
I664L |
probably benign |
Het |
Dvl2 |
C |
T |
11: 69,900,275 (GRCm39) |
P690S |
possibly damaging |
Het |
Fbxo7 |
A |
C |
10: 85,864,974 (GRCm39) |
E94D |
probably damaging |
Het |
Fstl5 |
A |
C |
3: 76,496,399 (GRCm39) |
K387N |
probably damaging |
Het |
Gm9845 |
A |
C |
3: 39,412,520 (GRCm39) |
|
noncoding transcript |
Het |
Hk1 |
T |
C |
10: 62,111,523 (GRCm39) |
D746G |
probably damaging |
Het |
Lmbr1 |
A |
G |
5: 29,468,391 (GRCm39) |
|
probably null |
Het |
Lrp2 |
C |
T |
2: 69,350,258 (GRCm39) |
A705T |
probably null |
Het |
Lrrc37 |
T |
C |
11: 103,508,300 (GRCm39) |
|
probably benign |
Het |
Mybpc3 |
A |
G |
2: 90,952,067 (GRCm39) |
|
probably null |
Het |
Myo15b |
T |
A |
11: 115,762,337 (GRCm39) |
L1219Q |
probably damaging |
Het |
Naa35 |
G |
A |
13: 59,770,680 (GRCm39) |
|
probably benign |
Het |
Or4g16 |
G |
T |
2: 111,137,392 (GRCm39) |
A281S |
possibly damaging |
Het |
Or5b111 |
A |
T |
19: 13,291,553 (GRCm39) |
I32N |
probably damaging |
Het |
Or5b113 |
T |
C |
19: 13,342,541 (GRCm39) |
V183A |
probably damaging |
Het |
Pcdhb18 |
G |
A |
18: 37,623,537 (GRCm39) |
R289Q |
probably benign |
Het |
Pcnt |
T |
C |
10: 76,221,675 (GRCm39) |
T1984A |
probably benign |
Het |
Plcg1 |
T |
C |
2: 160,593,588 (GRCm39) |
L251P |
probably benign |
Het |
Plin1 |
T |
A |
7: 79,371,320 (GRCm39) |
D468V |
probably benign |
Het |
Pmp2 |
A |
G |
3: 10,248,845 (GRCm39) |
V12A |
probably benign |
Het |
Rnf19a |
T |
A |
15: 36,266,109 (GRCm39) |
|
probably benign |
Het |
Rnf214 |
G |
A |
9: 45,779,344 (GRCm39) |
Q469* |
probably null |
Het |
Rrp1b |
T |
G |
17: 32,274,985 (GRCm39) |
|
probably benign |
Het |
Rtl1 |
C |
T |
12: 109,561,113 (GRCm39) |
R242Q |
unknown |
Het |
Sema3e |
A |
T |
5: 14,275,567 (GRCm39) |
E224V |
probably damaging |
Het |
Sphkap |
A |
G |
1: 83,385,720 (GRCm39) |
S5P |
probably damaging |
Het |
Stab1 |
A |
C |
14: 30,879,397 (GRCm39) |
Y694* |
probably null |
Het |
Stambpl1 |
T |
C |
19: 34,211,686 (GRCm39) |
L249P |
probably benign |
Het |
Thap4 |
A |
T |
1: 93,642,665 (GRCm39) |
H515Q |
probably damaging |
Het |
Ticam1 |
TCACACA |
TCACA |
17: 56,577,629 (GRCm39) |
|
probably null |
Het |
Uaca |
A |
G |
9: 60,779,380 (GRCm39) |
R1256G |
probably benign |
Het |
Usp17lb |
T |
A |
7: 104,489,881 (GRCm39) |
N348Y |
possibly damaging |
Het |
Vmn1r42 |
A |
G |
6: 89,822,314 (GRCm39) |
I85T |
probably benign |
Het |
Zdhhc17 |
A |
T |
10: 110,809,694 (GRCm39) |
I153N |
probably damaging |
Het |
Zfp207 |
G |
A |
11: 80,283,959 (GRCm39) |
S293N |
possibly damaging |
Het |
Zfp346 |
A |
G |
13: 55,270,170 (GRCm39) |
D198G |
probably damaging |
Het |
Zfp953 |
A |
T |
13: 67,491,536 (GRCm39) |
C139S |
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 |
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'- TCCATCATCTGCCGCTGTAG -3'
(R):5'- CTAGATCAGACTTCTGCATCCCG -3'
Sequencing Primer
(F):5'- TGTAGAGACAGGGTCTAAGGG -3'
(R):5'- CGTTCCTCCTCACCGACG -3'
|
Posted On |
2016-11-08 |