Incidental Mutation 'R4458:Vps9d1'
ID |
330017 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps9d1
|
Ensembl Gene |
ENSMUSG00000001062 |
Gene Name |
VPS9 domain containing 1 |
Synonyms |
2410004N05Rik, 1300018I17Rik |
MMRRC Submission |
041718-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R4458 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
8 |
Chromosomal Location |
123969095-123980961 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 123974487 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Proline
at position 267
(S267P)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000113575
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000117643]
[ENSMUST00000118279]
[ENSMUST00000122363]
[ENSMUST00000127664]
[ENSMUST00000155869]
|
AlphaFold |
Q8C190 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000117643
AA Change: S267P
PolyPhen 2
Score 0.304 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000113748 Gene: ENSMUSG00000001062 AA Change: S267P
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: S267P
PolyPhen 2
Score 0.036 (Sensitivity: 0.94; Specificity: 0.82)
|
SMART Domains |
Protein: ENSMUSP00000113634 Gene: ENSMUSG00000001062 AA Change: S267P
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: S267P
PolyPhen 2
Score 0.304 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000113575 Gene: ENSMUSG00000001062 AA Change: S267P
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: ENSMUST00000149490
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146136
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155853
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130965
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137569
|
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: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.1%
|
Validation Efficiency |
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 54 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
A630076J17Rik |
G |
A |
3: 107,139,997 (GRCm39) |
|
probably null |
Het |
Akap13 |
A |
G |
7: 75,389,213 (GRCm39) |
D2377G |
probably damaging |
Het |
Ankrd44 |
A |
T |
1: 54,801,550 (GRCm39) |
I56N |
possibly damaging |
Het |
Apob |
T |
A |
12: 8,065,445 (GRCm39) |
I4105N |
probably damaging |
Het |
Arhgap5 |
T |
A |
12: 52,564,740 (GRCm39) |
N570K |
probably benign |
Het |
Arid1b |
A |
T |
17: 5,293,191 (GRCm39) |
Q703L |
probably damaging |
Het |
Atp4a |
G |
A |
7: 30,419,650 (GRCm39) |
R671Q |
probably benign |
Het |
Cad |
T |
A |
5: 31,218,570 (GRCm39) |
V499D |
probably damaging |
Het |
Cdkn2d |
C |
G |
9: 21,202,185 (GRCm39) |
V21L |
probably benign |
Het |
Celsr2 |
A |
C |
3: 108,302,313 (GRCm39) |
I2605S |
probably damaging |
Het |
Chd6 |
T |
A |
2: 160,871,796 (GRCm39) |
Y213F |
possibly damaging |
Het |
Clec18a |
T |
A |
8: 111,802,102 (GRCm39) |
T296S |
probably damaging |
Het |
Crybg2 |
C |
T |
4: 133,802,205 (GRCm39) |
P1122S |
probably benign |
Het |
Cyld |
G |
T |
8: 89,445,929 (GRCm39) |
S309I |
probably benign |
Het |
Dctn5 |
G |
T |
7: 121,734,303 (GRCm39) |
R49L |
probably damaging |
Het |
Egr2 |
GAA |
GA |
10: 67,375,733 (GRCm39) |
|
probably null |
Het |
Erbin |
C |
A |
13: 103,970,065 (GRCm39) |
V1184F |
probably damaging |
Het |
Ercc2 |
G |
T |
7: 19,127,771 (GRCm39) |
R406L |
probably damaging |
Het |
Eya1 |
C |
T |
1: 14,253,420 (GRCm39) |
V519M |
probably damaging |
Het |
Flad1 |
T |
C |
3: 89,316,241 (GRCm39) |
H107R |
probably benign |
Het |
Fsip2 |
G |
T |
2: 82,821,120 (GRCm39) |
A5618S |
possibly damaging |
Het |
Gabbr1 |
G |
T |
17: 37,378,667 (GRCm39) |
|
probably null |
Het |
Haghl |
A |
T |
17: 26,003,994 (GRCm39) |
V30E |
probably damaging |
Het |
Itga5 |
C |
T |
15: 103,258,630 (GRCm39) |
E822K |
probably damaging |
Het |
Klhl26 |
T |
A |
8: 70,905,342 (GRCm39) |
E108D |
possibly damaging |
Het |
Kpnb1 |
A |
T |
11: 97,059,996 (GRCm39) |
L558Q |
probably damaging |
Het |
Lias |
T |
C |
5: 65,551,383 (GRCm39) |
|
probably null |
Het |
Ltbp1 |
A |
T |
17: 75,583,502 (GRCm39) |
K434M |
possibly damaging |
Het |
Marchf1 |
C |
A |
8: 66,908,823 (GRCm39) |
A177E |
probably damaging |
Het |
Naip2 |
T |
A |
13: 100,291,419 (GRCm39) |
H1173L |
probably benign |
Het |
Nol4 |
T |
C |
18: 22,885,052 (GRCm39) |
I419V |
probably damaging |
Het |
Nol6 |
A |
G |
4: 41,115,888 (GRCm39) |
L1068P |
probably damaging |
Het |
Nrcam |
T |
C |
12: 44,606,513 (GRCm39) |
S420P |
probably damaging |
Het |
Or10c1 |
A |
T |
17: 37,522,204 (GRCm39) |
I180N |
possibly damaging |
Het |
Pitpnm2 |
T |
C |
5: 124,259,439 (GRCm39) |
T1299A |
probably benign |
Het |
Prdm16 |
A |
G |
4: 154,406,765 (GRCm39) |
V1220A |
probably benign |
Het |
Saraf |
T |
C |
8: 34,621,870 (GRCm39) |
S25P |
unknown |
Het |
Serpine3 |
C |
A |
14: 62,911,922 (GRCm39) |
L295I |
probably damaging |
Het |
Sntb2 |
G |
A |
8: 107,718,239 (GRCm39) |
|
probably null |
Het |
Surf6 |
T |
C |
2: 26,782,721 (GRCm39) |
E202G |
probably benign |
Het |
Tent5a |
T |
C |
9: 85,208,527 (GRCm39) |
I99V |
possibly damaging |
Het |
Th |
A |
T |
7: 142,450,690 (GRCm39) |
D135E |
probably benign |
Het |
Traf1 |
A |
G |
2: 34,835,445 (GRCm39) |
Y326H |
probably damaging |
Het |
Tshz2 |
G |
A |
2: 169,727,008 (GRCm39) |
A66T |
probably benign |
Het |
Ttn |
T |
C |
2: 76,777,257 (GRCm39) |
M1382V |
probably benign |
Het |
Ubqlnl |
A |
G |
7: 103,798,396 (GRCm39) |
V367A |
probably benign |
Het |
Uspl1 |
T |
A |
5: 149,150,962 (GRCm39) |
S707T |
possibly damaging |
Het |
Utp18 |
A |
G |
11: 93,761,359 (GRCm39) |
S350P |
possibly damaging |
Het |
Vmn1r177 |
A |
G |
7: 23,565,645 (GRCm39) |
V77A |
possibly damaging |
Het |
Vmn1r229 |
A |
G |
17: 21,034,894 (GRCm39) |
I46M |
probably damaging |
Het |
Vnn3 |
T |
C |
10: 23,741,567 (GRCm39) |
Y291H |
probably benign |
Het |
Wrn |
T |
A |
8: 33,785,026 (GRCm39) |
T692S |
probably damaging |
Het |
Yeats2 |
T |
C |
16: 20,032,071 (GRCm39) |
I19T |
probably damaging |
Het |
Zfp13 |
G |
A |
17: 23,800,150 (GRCm39) |
A36V |
probably benign |
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 |
|
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'- TAGTGTGACCCATGCAATCTG -3'
(R):5'- TCACATGGGCCTATAGGACTC -3'
Sequencing Primer
(F):5'- CCATGCAATCTGGGGAAGC -3'
(R):5'- ACATGGGCCTATAGGACTCAGTTC -3'
|
Posted On |
2015-07-21 |