Incidental Mutation 'R5423:Vps9d1'
| ID |
484586 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps9d1
|
| Ensembl Gene |
ENSMUSG00000001062 |
| Gene Name |
VPS9 domain containing 1 |
| Synonyms |
2410004N05Rik, 1300018I17Rik |
| MMRRC Submission |
042989-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5423 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
8 |
| Chromosomal Location |
123969095-123980961 bp(-) (GRCm39) |
| Type of Mutation |
critical splice donor site (2 bp from exon) |
| DNA Base Change (assembly) |
A to C
at 123974704 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| 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
|
| 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 null
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 null
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: ENSMUST00000129591
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146136
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149490
|
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130275
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155853
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130965
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137569
|
| Meta Mutation Damage Score |
0.9494 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
| Validation Efficiency |
98% (60/61) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acyp2 |
C |
T |
11: 30,456,354 (GRCm39) |
E98K |
possibly damaging |
Het |
| Adam22 |
C |
A |
5: 8,140,182 (GRCm39) |
G202W |
probably damaging |
Het |
| Adamts9 |
A |
G |
6: 92,857,678 (GRCm39) |
I289T |
possibly damaging |
Het |
| Ak4 |
T |
G |
4: 101,317,760 (GRCm39) |
I110S |
probably damaging |
Het |
| Arhgap9 |
T |
G |
10: 127,165,418 (GRCm39) |
I609S |
probably damaging |
Het |
| Arid4a |
C |
A |
12: 71,116,634 (GRCm39) |
S242* |
probably null |
Het |
| Ceacam1 |
T |
G |
7: 25,173,951 (GRCm39) |
I235L |
probably benign |
Het |
| Chil3 |
T |
C |
3: 106,055,978 (GRCm39) |
D365G |
probably damaging |
Het |
| Ckap2 |
A |
C |
8: 22,667,212 (GRCm39) |
S216R |
probably benign |
Het |
| Cyp2e1 |
G |
T |
7: 140,350,031 (GRCm39) |
V239L |
probably benign |
Het |
| Dnah7b |
T |
A |
1: 46,397,431 (GRCm39) |
M3954K |
probably benign |
Het |
| Ercc6l2 |
A |
T |
13: 64,020,072 (GRCm39) |
|
probably benign |
Het |
| Etv5 |
T |
C |
16: 22,202,404 (GRCm39) |
D468G |
probably damaging |
Het |
| Fbxo44 |
T |
A |
4: 148,238,686 (GRCm39) |
I213F |
probably benign |
Het |
| Gm5084 |
A |
G |
13: 60,360,356 (GRCm39) |
|
noncoding transcript |
Het |
| Gpr17 |
G |
A |
18: 32,080,694 (GRCm39) |
T123I |
probably damaging |
Het |
| Grin3a |
A |
G |
4: 49,770,376 (GRCm39) |
|
probably benign |
Het |
| H2-D1 |
T |
G |
17: 35,484,883 (GRCm39) |
L248R |
probably damaging |
Het |
| Hmcn1 |
T |
C |
1: 150,577,723 (GRCm39) |
I2013V |
probably damaging |
Het |
| Hp1bp3 |
A |
T |
4: 137,953,208 (GRCm39) |
D84V |
probably damaging |
Het |
| Ift140 |
T |
C |
17: 25,252,059 (GRCm39) |
F33S |
probably damaging |
Het |
| Inhbc |
C |
G |
10: 127,193,296 (GRCm39) |
C240S |
probably damaging |
Het |
| Iqgap1 |
T |
A |
7: 80,449,610 (GRCm39) |
E62V |
probably damaging |
Het |
| Kcna4 |
G |
A |
2: 107,126,151 (GRCm39) |
W295* |
probably null |
Het |
| Kdm4a |
C |
T |
4: 117,996,105 (GRCm39) |
A975T |
probably damaging |
Het |
| Lrrtm3 |
T |
C |
10: 63,923,931 (GRCm39) |
D412G |
possibly damaging |
Het |
| Midn |
A |
C |
10: 79,991,027 (GRCm39) |
I346L |
probably benign |
Het |
| Ndufa10 |
C |
T |
1: 92,390,042 (GRCm39) |
D259N |
probably benign |
Het |
| Nefh |
C |
A |
11: 4,890,985 (GRCm39) |
A545S |
possibly damaging |
Het |
| Prpf8 |
A |
G |
11: 75,399,784 (GRCm39) |
Y2281C |
probably damaging |
Het |
| Psip1 |
G |
A |
4: 83,378,367 (GRCm39) |
|
probably benign |
Het |
| Ptpro |
G |
T |
6: 137,419,705 (GRCm39) |
A184S |
probably damaging |
Het |
| Rab37 |
T |
A |
11: 115,047,853 (GRCm39) |
I65K |
possibly damaging |
Het |
| Rasgrp4 |
T |
C |
7: 28,844,561 (GRCm39) |
L247P |
probably damaging |
Het |
| Rnf20 |
T |
C |
4: 49,644,620 (GRCm39) |
V295A |
probably damaging |
Het |
| Serpina3g |
A |
G |
12: 104,204,253 (GRCm39) |
|
probably benign |
Het |
| Shox2 |
A |
G |
3: 66,881,087 (GRCm39) |
|
probably benign |
Het |
| Skint6 |
T |
G |
4: 112,707,937 (GRCm39) |
D977A |
possibly damaging |
Het |
| Slc25a23 |
C |
T |
17: 57,360,597 (GRCm39) |
V248M |
probably damaging |
Het |
| Slco1a7 |
T |
A |
6: 141,690,188 (GRCm39) |
K188N |
probably damaging |
Het |
| Smg1 |
A |
T |
7: 117,745,294 (GRCm39) |
D3008E |
possibly damaging |
Het |
| St18 |
A |
G |
1: 6,872,840 (GRCm39) |
S192G |
possibly damaging |
Het |
| Supt20 |
T |
A |
3: 54,616,746 (GRCm39) |
V306E |
probably damaging |
Het |
| T |
T |
C |
17: 8,660,597 (GRCm39) |
Y403H |
probably damaging |
Het |
| Tars3 |
C |
A |
7: 65,333,567 (GRCm39) |
N588K |
probably benign |
Het |
| Tmem132c |
T |
C |
5: 127,640,907 (GRCm39) |
V1026A |
probably benign |
Het |
| Trpv4 |
T |
C |
5: 114,774,506 (GRCm39) |
T193A |
probably benign |
Het |
| Ubqln4 |
A |
G |
3: 88,470,506 (GRCm39) |
N326S |
probably damaging |
Het |
| Uggt2 |
G |
A |
14: 119,256,898 (GRCm39) |
T1112I |
probably damaging |
Het |
| Vasn |
C |
T |
16: 4,466,284 (GRCm39) |
P77L |
probably benign |
Het |
| Washc4 |
C |
A |
10: 83,415,418 (GRCm39) |
Q803K |
possibly damaging |
Het |
| Zcchc2 |
C |
T |
1: 105,958,430 (GRCm39) |
T967I |
probably damaging |
Het |
| Zfp874a |
G |
A |
13: 67,590,473 (GRCm39) |
L404F |
possibly damaging |
Het |
| Zscan30 |
T |
C |
18: 24,104,773 (GRCm39) |
|
noncoding transcript |
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 |
|
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'- TGAATACCTGAGCAAGTGGG -3'
(R):5'- TCCCTGTCTCATAGGCATGC -3'
Sequencing Primer
(F):5'- TGGTCACTAGCGACAGGTCTC -3'
(R):5'- CATGCTGGTATGCCTGGAAG -3'
|
| Posted On |
2017-08-16 |
Incidental Mutation