Incidental Mutation 'R0118:Vps35'
ID |
20929 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps35
|
Ensembl Gene |
ENSMUSG00000031696 |
Gene Name |
VPS35 retromer complex component |
Synonyms |
Mem3 |
MMRRC Submission |
038404-MU
|
Accession Numbers |
|
Essential gene? |
Essential
(E-score: 1.000)
|
Stock # |
R0118 (G1)
|
Quality Score |
222 |
Status
|
Validated
(trace)
|
Chromosome |
8 |
Chromosomal Location |
85987014-86026146 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to A
at 86021582 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Isoleucine
at position 3
(T3I)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000034131
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000034131]
[ENSMUST00000034132]
[ENSMUST00000170141]
[ENSMUST00000210146]
[ENSMUST00000211396]
[ENSMUST00000211597]
|
AlphaFold |
Q9EQH3 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000034131
AA Change: T3I
PolyPhen 2
Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)
|
SMART Domains |
Protein: ENSMUSP00000034131 Gene: ENSMUSG00000031696 AA Change: T3I
Domain | Start | End | E-Value | Type |
Pfam:Vps35
|
15 |
753 |
6.8e-303 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000034132
|
SMART Domains |
Protein: ENSMUSP00000034132 Gene: ENSMUSG00000031697
Domain | Start | End | E-Value | Type |
Pfam:ORC6
|
6 |
108 |
1.5e-16 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000170141
|
SMART Domains |
Protein: ENSMUSP00000126925 Gene: ENSMUSG00000031697
Domain | Start | End | E-Value | Type |
PDB:3M03|C
|
18 |
111 |
2e-51 |
PDB |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000209228
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000209733
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000210146
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000211154
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000211479
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000211396
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000211597
|
Meta Mutation Damage Score |
0.0825 |
Coding Region Coverage |
- 1x: 98.8%
- 3x: 97.2%
- 10x: 89.3%
- 20x: 67.4%
|
Validation Efficiency |
98% (50/51) |
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to a group of vacuolar protein sorting (VPS) genes. The encoded protein is a component of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. The close structural similarity between the yeast and human proteins that make up this complex suggests a similarity in function. Expression studies in yeast and mammalian cells indicate that this protein interacts directly with VPS35, which serves as the core of the retromer complex. [provided by RefSeq, Jul 2008] PHENOTYPE: Mice homozygous for a gene trap allele die prior to E10. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 49 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adamts15 |
T |
C |
9: 30,823,040 (GRCm39) |
R343G |
probably damaging |
Het |
Asxl2 |
T |
G |
12: 3,546,923 (GRCm39) |
V569G |
probably damaging |
Het |
Azin2 |
A |
C |
4: 128,843,430 (GRCm39) |
H85Q |
probably damaging |
Het |
Cacna1a |
C |
T |
8: 85,262,712 (GRCm39) |
R324C |
probably damaging |
Het |
Ccr3 |
C |
A |
9: 123,829,647 (GRCm39) |
Y327* |
probably null |
Het |
Cers2 |
T |
C |
3: 95,227,537 (GRCm39) |
F55S |
probably benign |
Het |
Cic |
C |
T |
7: 24,985,459 (GRCm39) |
S301L |
probably damaging |
Het |
Cntnap2 |
T |
C |
6: 45,037,326 (GRCm39) |
|
probably null |
Het |
Cpn2 |
T |
C |
16: 30,079,186 (GRCm39) |
R172G |
probably benign |
Het |
Ctdnep1 |
T |
C |
11: 69,879,557 (GRCm39) |
|
probably null |
Het |
Dennd3 |
T |
A |
15: 73,436,925 (GRCm39) |
Y1051N |
probably damaging |
Het |
Dmap1 |
T |
G |
4: 117,533,680 (GRCm39) |
Y196S |
probably damaging |
Het |
Entpd7 |
G |
A |
19: 43,692,751 (GRCm39) |
W102* |
probably null |
Het |
Frem2 |
A |
T |
3: 53,442,664 (GRCm39) |
C2624* |
probably null |
Het |
Gdpd3 |
A |
G |
7: 126,370,165 (GRCm39) |
Y238C |
probably damaging |
Het |
Gjb3 |
A |
G |
4: 127,220,451 (GRCm39) |
V27A |
probably damaging |
Het |
Kat6b |
T |
C |
14: 21,720,042 (GRCm39) |
F1465L |
probably damaging |
Het |
Klra17 |
A |
T |
6: 129,808,552 (GRCm39) |
M227K |
probably benign |
Het |
Map6 |
A |
G |
7: 98,966,824 (GRCm39) |
D348G |
possibly damaging |
Het |
Mapkbp1 |
T |
C |
2: 119,855,696 (GRCm39) |
S1472P |
probably benign |
Het |
Megf6 |
C |
A |
4: 154,339,098 (GRCm39) |
P545Q |
probably damaging |
Het |
Mertk |
C |
T |
2: 128,601,086 (GRCm39) |
R357W |
probably damaging |
Het |
Mesd |
T |
A |
7: 83,544,835 (GRCm39) |
I104N |
probably damaging |
Het |
Mrm3 |
T |
A |
11: 76,140,781 (GRCm39) |
V263E |
possibly damaging |
Het |
Ndst4 |
T |
A |
3: 125,405,210 (GRCm39) |
Y488* |
probably null |
Het |
Nfat5 |
C |
T |
8: 108,065,707 (GRCm39) |
R156W |
probably damaging |
Het |
Nfs1 |
T |
C |
2: 155,976,444 (GRCm39) |
H150R |
probably damaging |
Het |
Odad3 |
A |
T |
9: 21,906,353 (GRCm39) |
N224K |
probably benign |
Het |
Or1n1b |
A |
G |
2: 36,780,035 (GRCm39) |
M275T |
probably benign |
Het |
Or8b56 |
T |
C |
9: 38,739,154 (GRCm39) |
S50P |
possibly damaging |
Het |
Or8g19 |
T |
A |
9: 39,055,399 (GRCm39) |
M1K |
probably null |
Het |
Or9q1 |
A |
G |
19: 13,804,929 (GRCm39) |
F277S |
possibly damaging |
Het |
Pcdh8 |
T |
C |
14: 80,004,848 (GRCm39) |
Y1059C |
probably damaging |
Het |
Pik3r5 |
T |
A |
11: 68,381,306 (GRCm39) |
L164Q |
probably damaging |
Het |
Polr3g |
T |
C |
13: 81,824,240 (GRCm39) |
|
probably benign |
Het |
Ppm1e |
T |
A |
11: 87,122,564 (GRCm39) |
K464N |
probably benign |
Het |
Rims1 |
T |
C |
1: 22,416,631 (GRCm39) |
T1037A |
probably damaging |
Het |
Rpgrip1l |
A |
T |
8: 91,996,750 (GRCm39) |
I108N |
probably damaging |
Het |
Sfi1 |
CCTCTC |
CCTCTCTC |
11: 3,127,419 (GRCm39) |
|
probably benign |
Het |
Spem1 |
T |
C |
11: 69,712,371 (GRCm39) |
K98E |
possibly damaging |
Het |
St7l |
T |
C |
3: 104,796,619 (GRCm39) |
V237A |
probably damaging |
Het |
Tbc1d16 |
T |
C |
11: 119,048,642 (GRCm39) |
H337R |
probably damaging |
Het |
Tbc1d32 |
T |
A |
10: 55,893,701 (GRCm39) |
I1291F |
probably benign |
Het |
Tnfaip6 |
G |
T |
2: 51,933,827 (GRCm39) |
E61* |
probably null |
Het |
Trib2 |
A |
T |
12: 15,843,929 (GRCm39) |
W102R |
probably damaging |
Het |
Uimc1 |
G |
T |
13: 55,233,457 (GRCm39) |
N66K |
probably damaging |
Het |
Vmn1r63 |
T |
A |
7: 5,805,838 (GRCm39) |
T265S |
probably benign |
Het |
Yeats2 |
T |
A |
16: 19,975,692 (GRCm39) |
L63* |
probably null |
Het |
Zfp282 |
A |
G |
6: 47,869,866 (GRCm39) |
R304G |
probably benign |
Het |
|
Other mutations in Vps35 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01745:Vps35
|
APN |
8 |
86,000,092 (GRCm39) |
splice site |
probably benign |
|
IGL02604:Vps35
|
APN |
8 |
86,013,018 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03278:Vps35
|
APN |
8 |
86,021,590 (GRCm39) |
unclassified |
probably benign |
|
IGL03326:Vps35
|
APN |
8 |
86,001,526 (GRCm39) |
nonsense |
probably null |
|
PIT4151001:Vps35
|
UTSW |
8 |
86,010,677 (GRCm39) |
missense |
possibly damaging |
0.95 |
R0226:Vps35
|
UTSW |
8 |
86,000,204 (GRCm39) |
missense |
probably damaging |
0.97 |
R1079:Vps35
|
UTSW |
8 |
86,005,683 (GRCm39) |
missense |
probably damaging |
1.00 |
R1477:Vps35
|
UTSW |
8 |
86,014,429 (GRCm39) |
missense |
probably damaging |
1.00 |
R1969:Vps35
|
UTSW |
8 |
86,005,623 (GRCm39) |
missense |
possibly damaging |
0.90 |
R2082:Vps35
|
UTSW |
8 |
85,990,094 (GRCm39) |
missense |
possibly damaging |
0.95 |
R2156:Vps35
|
UTSW |
8 |
86,013,129 (GRCm39) |
missense |
probably benign |
0.06 |
R2341:Vps35
|
UTSW |
8 |
86,001,443 (GRCm39) |
splice site |
probably benign |
|
R3752:Vps35
|
UTSW |
8 |
86,001,460 (GRCm39) |
missense |
probably benign |
0.34 |
R4589:Vps35
|
UTSW |
8 |
86,014,331 (GRCm39) |
missense |
probably damaging |
1.00 |
R4745:Vps35
|
UTSW |
8 |
85,987,891 (GRCm39) |
missense |
probably benign |
|
R4790:Vps35
|
UTSW |
8 |
86,005,486 (GRCm39) |
splice site |
probably null |
|
R4827:Vps35
|
UTSW |
8 |
86,000,186 (GRCm39) |
missense |
possibly damaging |
0.94 |
R4953:Vps35
|
UTSW |
8 |
86,008,475 (GRCm39) |
missense |
probably damaging |
1.00 |
R6277:Vps35
|
UTSW |
8 |
85,987,857 (GRCm39) |
missense |
possibly damaging |
0.80 |
R6291:Vps35
|
UTSW |
8 |
86,026,086 (GRCm39) |
start codon destroyed |
probably benign |
0.07 |
R6434:Vps35
|
UTSW |
8 |
86,000,124 (GRCm39) |
missense |
possibly damaging |
0.53 |
R7175:Vps35
|
UTSW |
8 |
85,990,189 (GRCm39) |
splice site |
probably null |
|
R7206:Vps35
|
UTSW |
8 |
86,014,350 (GRCm39) |
missense |
probably damaging |
1.00 |
R7309:Vps35
|
UTSW |
8 |
86,001,596 (GRCm39) |
missense |
probably benign |
0.05 |
R7479:Vps35
|
UTSW |
8 |
85,997,434 (GRCm39) |
missense |
probably benign |
0.17 |
R7547:Vps35
|
UTSW |
8 |
85,989,999 (GRCm39) |
missense |
probably damaging |
1.00 |
R7761:Vps35
|
UTSW |
8 |
86,010,707 (GRCm39) |
missense |
possibly damaging |
0.91 |
R7812:Vps35
|
UTSW |
8 |
86,010,818 (GRCm39) |
missense |
probably benign |
0.01 |
R8312:Vps35
|
UTSW |
8 |
86,001,498 (GRCm39) |
missense |
possibly damaging |
0.65 |
R8356:Vps35
|
UTSW |
8 |
85,987,934 (GRCm39) |
missense |
possibly damaging |
0.63 |
R8403:Vps35
|
UTSW |
8 |
86,001,487 (GRCm39) |
missense |
probably benign |
|
R8456:Vps35
|
UTSW |
8 |
85,987,934 (GRCm39) |
missense |
possibly damaging |
0.63 |
R9189:Vps35
|
UTSW |
8 |
86,007,898 (GRCm39) |
missense |
possibly damaging |
0.67 |
R9615:Vps35
|
UTSW |
8 |
86,010,633 (GRCm39) |
missense |
probably benign |
0.00 |
X0020:Vps35
|
UTSW |
8 |
85,990,050 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- GAGTCTCTACAGTGCTAAGCACAGATG -3'
(R):5'- CCTACCACAGGTTTCTTTGATGCCAG -3'
Sequencing Primer
(F):5'- GAGCAGAGATGACATAATCTTACAAC -3'
(R):5'- gcctgcttccatctccc -3'
|
Posted On |
2013-04-11 |