Incidental Mutation 'R4305:Vps9d1'
ID |
324000 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps9d1
|
Ensembl Gene |
ENSMUSG00000001062 |
Gene Name |
VPS9 domain containing 1 |
Synonyms |
2410004N05Rik, 1300018I17Rik |
MMRRC Submission |
041091-MU
|
Accession Numbers |
|
Essential gene? |
Non essential
(E-score: 0.000)
|
Stock # |
R4305 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
8 |
Chromosomal Location |
123969095-123980961 bp(-) (GRCm39) |
Type of Mutation |
intron |
DNA Base Change (assembly) |
G to T
at 123974976 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
|
Ref Sequence |
ENSEMBL: ENSMUSP00000122184
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000117643]
[ENSMUST00000118279]
[ENSMUST00000122363]
[ENSMUST00000127664]
[ENSMUST00000155869]
|
AlphaFold |
Q8C190 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000117643
|
SMART Domains |
Protein: ENSMUSP00000113748 Gene: ENSMUSG00000001062
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
|
SMART Domains |
Protein: ENSMUSP00000113634 Gene: ENSMUSG00000001062
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
|
SMART Domains |
Protein: ENSMUSP00000113575 Gene: ENSMUSG00000001062
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: ENSMUST00000149490
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137569
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146136
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130275
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130965
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129591
|
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 |
|
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.3%
- 20x: 95.2%
|
Validation Efficiency |
92% (36/39) |
Allele List at MGI |
|
Other mutations in this stock |
Total: 26 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
A830018L16Rik |
C |
A |
1: 12,042,300 (GRCm39) |
S440* |
probably null |
Het |
Abl2 |
T |
A |
1: 156,469,133 (GRCm39) |
M695K |
probably damaging |
Het |
Asap2 |
T |
C |
12: 21,279,482 (GRCm39) |
I426T |
probably damaging |
Het |
Atxn7l1 |
T |
C |
12: 33,391,991 (GRCm39) |
M93T |
probably damaging |
Het |
Ccr5 |
T |
C |
9: 123,925,111 (GRCm39) |
L238P |
possibly damaging |
Het |
Cd27 |
A |
G |
6: 125,211,633 (GRCm39) |
V98A |
probably benign |
Het |
Ceacam23 |
T |
A |
7: 17,639,118 (GRCm39) |
Y372N |
probably benign |
Het |
Cfap47 |
C |
G |
X: 78,541,635 (GRCm39) |
K469N |
probably damaging |
Het |
Chrdl2 |
A |
G |
7: 99,671,229 (GRCm39) |
T116A |
probably damaging |
Het |
Epha6 |
T |
C |
16: 60,346,883 (GRCm39) |
|
probably null |
Het |
Garin1b |
A |
G |
6: 29,326,611 (GRCm39) |
S243G |
probably damaging |
Het |
Gart |
T |
C |
16: 91,430,880 (GRCm39) |
E394G |
possibly damaging |
Het |
Krt1 |
AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC |
AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC |
15: 101,758,813 (GRCm39) |
|
probably benign |
Het |
Lpar6 |
G |
A |
14: 73,476,381 (GRCm39) |
R114Q |
probably damaging |
Het |
Med23 |
G |
T |
10: 24,780,168 (GRCm39) |
E573* |
probably null |
Het |
Mtch2 |
A |
G |
2: 90,689,827 (GRCm39) |
I183V |
probably benign |
Het |
Nlrp3 |
C |
T |
11: 59,438,836 (GRCm39) |
R138* |
probably null |
Het |
Notch1 |
T |
C |
2: 26,367,936 (GRCm39) |
D657G |
probably damaging |
Het |
Or4k37 |
A |
G |
2: 111,159,643 (GRCm39) |
D293G |
probably null |
Het |
Rbm20 |
A |
G |
19: 53,831,691 (GRCm39) |
S642G |
probably damaging |
Het |
Tex11 |
C |
A |
X: 99,977,021 (GRCm39) |
A487S |
possibly damaging |
Het |
Ttn |
T |
C |
2: 76,748,681 (GRCm39) |
S4123G |
probably benign |
Het |
Ugt3a1 |
A |
C |
15: 9,306,360 (GRCm39) |
S170R |
possibly damaging |
Het |
Vmn2r71 |
G |
T |
7: 85,273,360 (GRCm39) |
D725Y |
probably damaging |
Het |
Yeats2 |
A |
G |
16: 20,027,172 (GRCm39) |
T808A |
probably damaging |
Het |
Zdhhc4 |
C |
T |
5: 143,310,099 (GRCm39) |
|
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 |
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'- GAGCAACTTGACTGCAGAACC -3'
(R):5'- AGCACTAATTAGGTGCTCTCTACC -3'
Sequencing Primer
(F):5'- TTGACTGCAGAACCTCCTGAG -3'
(R):5'- CTTCAAGTCTGCCTTCCTGAGTAAAG -3'
|
Posted On |
2015-06-24 |