Incidental Mutation 'R2193:Vps9d1'
| ID |
238271 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps9d1
|
| Ensembl Gene |
ENSMUSG00000001062 |
| Gene Name |
VPS9 domain containing 1 |
| Synonyms |
2410004N05Rik, 1300018I17Rik |
| MMRRC Submission |
040195-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R2193 (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 T
at 123979404 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Asparagine
at position 39
(Y39N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000122184
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000001092]
[ENSMUST00000117643]
[ENSMUST00000118279]
[ENSMUST00000122363]
[ENSMUST00000127664]
[ENSMUST00000155869]
[ENSMUST00000154450]
|
| AlphaFold |
Q8C190 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000001092
|
| SMART Domains |
Protein: ENSMUSP00000001092
Gene: ENSMUSG00000001065
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
18 |
41 |
N/A |
INTRINSIC |
|
low complexity region
|
59 |
72 |
N/A |
INTRINSIC |
|
Pfam:zf-AD
|
79 |
159 |
1.2e-13 |
PFAM |
|
low complexity region
|
402 |
422 |
N/A |
INTRINSIC |
|
ZnF_C2H2
|
434 |
458 |
2.24e-3 |
SMART |
|
ZnF_C2H2
|
465 |
490 |
6.67e-2 |
SMART |
|
ZnF_C2H2
|
496 |
518 |
1.38e-3 |
SMART |
|
ZnF_C2H2
|
524 |
546 |
1.82e-3 |
SMART |
|
ZnF_C2H2
|
554 |
577 |
4.79e-3 |
SMART |
|
low complexity region
|
586 |
602 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000117643
AA Change: Y39N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000113748
Gene: ENSMUSG00000001062
AA Change: Y39N
| 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: Y39N
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000113634
Gene: ENSMUSG00000001062
AA Change: Y39N
| 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: Y39N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000113575
Gene: ENSMUSG00000001062
AA Change: Y39N
| 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 |
probably damaging
Transcript: ENSMUST00000155869
AA Change: Y39N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000122184
Gene: ENSMUSG00000001062
AA Change: Y39N
| 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: ENSMUST00000156896
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000211828
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146136
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130965
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130275
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129591
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149490
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150356
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137569
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000154450
|
| SMART Domains |
Protein: ENSMUSP00000119771
Gene: ENSMUSG00000001065
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
18 |
41 |
N/A |
INTRINSIC |
|
low complexity region
|
59 |
72 |
N/A |
INTRINSIC |
|
Pfam:zf-AD
|
79 |
159 |
1.9e-14 |
PFAM |
|
low complexity region
|
183 |
203 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.8%
- 10x: 97.6%
- 20x: 96.1%
|
| Validation Efficiency |
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 25 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acp4 |
T |
C |
7: 43,902,993 (GRCm39) |
R289G |
probably benign |
Het |
| Bfar |
A |
G |
16: 13,515,335 (GRCm39) |
N183D |
probably benign |
Het |
| Cdca3 |
A |
G |
6: 124,808,409 (GRCm39) |
T69A |
probably damaging |
Het |
| Ces1b |
A |
T |
8: 93,806,505 (GRCm39) |
C14S |
probably benign |
Het |
| Clcn3 |
T |
A |
8: 61,382,221 (GRCm39) |
I456F |
possibly damaging |
Het |
| Dab1 |
C |
T |
4: 104,588,948 (GRCm39) |
A524V |
probably benign |
Het |
| Dcpp2 |
A |
C |
17: 24,119,393 (GRCm39) |
D69A |
probably damaging |
Het |
| Dlgap2 |
T |
A |
8: 14,793,431 (GRCm39) |
I475N |
possibly damaging |
Het |
| Dnah6 |
T |
A |
6: 73,115,623 (GRCm39) |
M1592L |
probably damaging |
Het |
| Dscaml1 |
A |
G |
9: 45,596,532 (GRCm39) |
Q792R |
probably benign |
Het |
| Eif2ak4 |
A |
G |
2: 118,252,747 (GRCm39) |
I440V |
probably benign |
Het |
| Frrs1 |
T |
C |
3: 116,671,994 (GRCm39) |
S31P |
probably damaging |
Het |
| Isoc2b |
T |
C |
7: 4,853,823 (GRCm39) |
H117R |
probably benign |
Het |
| Kalrn |
C |
T |
16: 33,810,180 (GRCm39) |
D2525N |
possibly damaging |
Het |
| Klf5 |
C |
T |
14: 99,536,406 (GRCm39) |
|
probably benign |
Het |
| Ltn1 |
G |
A |
16: 87,224,535 (GRCm39) |
S63F |
probably damaging |
Het |
| Nsf |
C |
T |
11: 103,821,578 (GRCm39) |
E26K |
possibly damaging |
Het |
| Oas1f |
A |
C |
5: 120,989,648 (GRCm39) |
T196P |
probably damaging |
Het |
| Obscn |
T |
C |
11: 59,022,472 (GRCm39) |
R758G |
possibly damaging |
Het |
| Ocln |
T |
C |
13: 100,676,412 (GRCm39) |
D27G |
probably damaging |
Het |
| Or2av9 |
A |
T |
11: 58,380,732 (GRCm39) |
M283K |
probably damaging |
Het |
| Or2y17 |
A |
G |
11: 49,231,770 (GRCm39) |
H137R |
possibly damaging |
Het |
| Rasgrf2 |
A |
C |
13: 92,160,221 (GRCm39) |
|
probably null |
Het |
| Sars2 |
G |
T |
7: 28,448,422 (GRCm39) |
V268L |
probably damaging |
Het |
| Sin3a |
T |
A |
9: 57,024,761 (GRCm39) |
S1040R |
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 |
|
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'- CCCTCATCTGAAAACATTTGGCG -3'
(R):5'- TCCTCAGCACAGTGTTGAAG -3'
Sequencing Primer
(F):5'- AGTCTGAAGGCATACCTG -3'
(R):5'- GACAGTATAGATACCATCTGTGTCC -3'
|
| Posted On |
2014-10-02 |
Incidental Mutation