Incidental Mutation 'R9110:Vps33b'
| ID |
692199 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps33b
|
| Ensembl Gene |
ENSMUSG00000030534 |
| Gene Name |
vacuolar protein sorting 33B |
| Synonyms |
|
| MMRRC Submission |
068919-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R9110 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
7 |
| Chromosomal Location |
79919369-79941327 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 79939743 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 498
(D498G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000032749
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000032749]
[ENSMUST00000047558]
[ENSMUST00000135053]
[ENSMUST00000150585]
[ENSMUST00000163812]
[ENSMUST00000173824]
[ENSMUST00000174172]
[ENSMUST00000174199]
|
| AlphaFold |
P59016 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000032749
AA Change: D498G
PolyPhen 2
Score 0.044 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000032749
Gene: ENSMUSG00000030534
AA Change: D498G
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Sec1
|
37 |
611 |
2.4e-89 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000047558
|
| SMART Domains |
Protein: ENSMUSP00000043379
Gene: ENSMUSG00000038943
| Domain | Start | End | E-Value | Type |
|---|
|
internal_repeat_1
|
22 |
36 |
1.45e-5 |
PROSPERO |
|
Pfam:MAP65_ASE1
|
37 |
602 |
5.3e-172 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000135053
|
| SMART Domains |
Protein: ENSMUSP00000138472
Gene: ENSMUSG00000030534
| Domain | Start | End | E-Value | Type |
|---|
|
SCOP:d1epua_
|
18 |
59 |
2e-7 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000150585
|
| SMART Domains |
Protein: ENSMUSP00000138224
Gene: ENSMUSG00000030534
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Sec1
|
36 |
140 |
1.5e-12 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000163812
|
| SMART Domains |
Protein: ENSMUSP00000129675
Gene: ENSMUSG00000038943
| Domain | Start | End | E-Value | Type |
|---|
|
internal_repeat_1
|
22 |
36 |
1.51e-5 |
PROSPERO |
|
Pfam:MAP65_ASE1
|
37 |
605 |
1.9e-173 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173824
|
| SMART Domains |
Protein: ENSMUSP00000133910
Gene: ENSMUSG00000038943
| Domain | Start | End | E-Value | Type |
|---|
|
internal_repeat_1
|
22 |
36 |
8.71e-6 |
PROSPERO |
|
Pfam:MAP65_ASE1
|
37 |
565 |
6e-168 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000174172
|
| SMART Domains |
Protein: ENSMUSP00000133387
Gene: ENSMUSG00000038943
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:MAP65_ASE1
|
34 |
615 |
2.9e-167 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000174199
|
| SMART Domains |
Protein: ENSMUSP00000133295
Gene: ENSMUSG00000038943
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:MAP65_ASE1
|
7 |
524 |
8.1e-158 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000205864
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.3%
|
| Validation Efficiency |
100% (61/61) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene is a member of the Sec-1 domain family, and encodes the human ortholog of rat Vps33b which is homologous to the yeast class C Vps33 protein. The mammalian class C vacuolar protein sorting proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Mutations in this gene are associated with arthrogryposis-renal dysfunction-cholestasis syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
PHENOTYPE: Mice homozygous for a conditional allele activated by an inducible cre exhibit dry scaly skin, hair loss, thrombocytosis, abnormal alpha-granule development, extramedullary hematopoiesis, abnormal platelets and megakaryocytes, and defects in tail tendon collagen I structure. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca14 |
A |
G |
7: 119,831,615 (GRCm39) |
|
probably benign |
Het |
| Adam20 |
A |
G |
8: 41,248,907 (GRCm39) |
D339G |
probably benign |
Het |
| Adam3 |
T |
A |
8: 25,193,821 (GRCm39) |
Y397F |
probably benign |
Het |
| Ago3 |
C |
T |
4: 126,248,829 (GRCm39) |
G574E |
probably damaging |
Het |
| Angptl4 |
T |
A |
17: 33,999,800 (GRCm39) |
Y133F |
probably benign |
Het |
| Ankrd61 |
T |
C |
5: 143,831,759 (GRCm39) |
D15G |
possibly damaging |
Het |
| Arfgap1 |
T |
A |
2: 180,615,330 (GRCm39) |
S174T |
possibly damaging |
Het |
| Arhgap12 |
T |
C |
18: 6,034,539 (GRCm39) |
D549G |
possibly damaging |
Het |
| Arhgap25 |
T |
C |
6: 87,453,254 (GRCm39) |
E182G |
probably benign |
Het |
| Astn1 |
T |
G |
1: 158,496,327 (GRCm39) |
I1127S |
probably benign |
Het |
| Bivm |
T |
C |
1: 44,168,526 (GRCm39) |
|
probably null |
Het |
| Cdc42bpa |
T |
A |
1: 179,945,258 (GRCm39) |
S952T |
possibly damaging |
Het |
| Cfap44 |
T |
A |
16: 44,255,923 (GRCm39) |
L1005Q |
probably damaging |
Het |
| Cmklr1 |
G |
C |
5: 113,752,043 (GRCm39) |
H319Q |
probably benign |
Het |
| Cog1 |
T |
C |
11: 113,544,807 (GRCm39) |
F330L |
possibly damaging |
Het |
| Dnah2 |
T |
G |
11: 69,435,208 (GRCm39) |
D54A |
probably benign |
Het |
| Dntt |
A |
T |
19: 41,044,197 (GRCm39) |
|
probably null |
Het |
| Eml2 |
A |
G |
7: 18,925,620 (GRCm39) |
S240G |
probably benign |
Het |
| Fam174b |
G |
A |
7: 73,416,371 (GRCm39) |
|
probably benign |
Het |
| Fancd2 |
T |
C |
6: 113,512,762 (GRCm39) |
S33P |
possibly damaging |
Het |
| Fars2 |
A |
T |
13: 36,430,402 (GRCm39) |
M277L |
probably benign |
Het |
| Ifnar1 |
G |
A |
16: 91,302,150 (GRCm39) |
G542S |
probably benign |
Het |
| Itih5 |
T |
C |
2: 10,191,831 (GRCm39) |
V122A |
probably benign |
Het |
| Jph3 |
A |
G |
8: 122,516,201 (GRCm39) |
I740V |
probably benign |
Het |
| Krtap16-1 |
C |
T |
11: 99,877,386 (GRCm39) |
C6Y |
probably benign |
Het |
| Mettl25b |
G |
A |
3: 87,834,978 (GRCm39) |
H57Y |
probably benign |
Het |
| Mpeg1 |
A |
T |
19: 12,440,014 (GRCm39) |
T491S |
probably benign |
Het |
| Mroh8 |
T |
A |
2: 157,055,605 (GRCm39) |
I998L |
possibly damaging |
Het |
| Nrxn1 |
G |
A |
17: 90,869,233 (GRCm39) |
Q124* |
probably null |
Het |
| Nup188 |
T |
A |
2: 30,222,461 (GRCm39) |
S1028T |
possibly damaging |
Het |
| Nxf1 |
A |
T |
19: 8,745,118 (GRCm39) |
H456L |
probably damaging |
Het |
| Or2aj6 |
T |
A |
16: 19,443,743 (GRCm39) |
I36F |
possibly damaging |
Het |
| Or2n1d |
C |
A |
17: 38,646,434 (GRCm39) |
P129T |
probably damaging |
Het |
| Or5af2 |
T |
A |
11: 58,707,959 (GRCm39) |
S42T |
possibly damaging |
Het |
| Or5w19 |
T |
A |
2: 87,698,543 (GRCm39) |
D69E |
probably damaging |
Het |
| Or6c66 |
T |
A |
10: 129,461,820 (GRCm39) |
I37F |
possibly damaging |
Het |
| Otx2 |
T |
C |
14: 48,896,227 (GRCm39) |
N277S |
probably damaging |
Het |
| Pax4 |
T |
C |
6: 28,445,201 (GRCm39) |
N158S |
probably benign |
Het |
| Pgm2 |
T |
G |
5: 64,261,159 (GRCm39) |
S218A |
probably benign |
Het |
| Plb1 |
T |
C |
5: 32,521,402 (GRCm39) |
S1418P |
probably benign |
Het |
| Prkd3 |
T |
A |
17: 79,292,751 (GRCm39) |
D107V |
probably damaging |
Het |
| Prl2a1 |
A |
G |
13: 27,992,398 (GRCm39) |
E174G |
probably benign |
Het |
| Prr7 |
C |
T |
13: 55,620,574 (GRCm39) |
P194L |
probably damaging |
Het |
| Psmd2 |
T |
C |
16: 20,470,994 (GRCm39) |
S46P |
probably damaging |
Het |
| Ptbp2 |
C |
T |
3: 119,541,258 (GRCm39) |
A231T |
possibly damaging |
Het |
| Rae1 |
A |
G |
2: 172,854,016 (GRCm39) |
T265A |
probably benign |
Het |
| Sct |
T |
C |
7: 140,859,007 (GRCm39) |
E2G |
unknown |
Het |
| Sec14l3 |
T |
G |
11: 4,015,007 (GRCm39) |
|
probably null |
Het |
| Sfxn3 |
T |
A |
19: 45,038,727 (GRCm39) |
N131K |
probably damaging |
Het |
| Slc18a2 |
A |
T |
19: 59,282,326 (GRCm39) |
D511V |
probably benign |
Het |
| Slc20a2 |
T |
C |
8: 23,025,457 (GRCm39) |
I53T |
probably damaging |
Het |
| Smad4 |
T |
C |
18: 73,782,941 (GRCm39) |
D331G |
probably damaging |
Het |
| Srms |
C |
T |
2: 180,848,050 (GRCm39) |
R485H |
|
Het |
| Szt2 |
C |
A |
4: 118,242,630 (GRCm39) |
A1486S |
possibly damaging |
Het |
| Tmem87b |
C |
T |
2: 128,684,615 (GRCm39) |
Q459* |
probably null |
Het |
| Vdr |
A |
T |
15: 97,782,753 (GRCm39) |
I23N |
probably damaging |
Het |
| Vmn1r204 |
T |
C |
13: 22,740,564 (GRCm39) |
V65A |
possibly damaging |
Het |
| Zfp442 |
T |
A |
2: 150,250,093 (GRCm39) |
Y603F |
probably benign |
Het |
| Zfp853 |
T |
A |
5: 143,275,320 (GRCm39) |
Q115L |
unknown |
Het |
| Zmiz2 |
C |
A |
11: 6,348,271 (GRCm39) |
Q303K |
probably benign |
Het |
|
| Other mutations in Vps33b |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00561:Vps33b
|
APN |
7 |
79,935,591 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01352:Vps33b
|
APN |
7 |
79,934,807 (GRCm39) |
splice site |
probably null |
|
|
IGL01863:Vps33b
|
APN |
7 |
79,924,059 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL01918:Vps33b
|
APN |
7 |
79,937,560 (GRCm39) |
splice site |
probably null |
|
|
IGL02152:Vps33b
|
APN |
7 |
79,934,817 (GRCm39) |
missense |
probably benign |
0.29 |
|
IGL02364:Vps33b
|
APN |
7 |
79,937,587 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02383:Vps33b
|
APN |
7 |
79,935,082 (GRCm39) |
splice site |
probably null |
|
|
IGL02669:Vps33b
|
APN |
7 |
79,925,786 (GRCm39) |
splice site |
probably benign |
|
|
IGL03104:Vps33b
|
APN |
7 |
79,925,831 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03333:Vps33b
|
APN |
7 |
79,923,973 (GRCm39) |
splice site |
probably benign |
|
|
PIT4651001:Vps33b
|
UTSW |
7 |
79,939,755 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0267:Vps33b
|
UTSW |
7 |
79,935,802 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R0379:Vps33b
|
UTSW |
7 |
79,933,162 (GRCm39) |
splice site |
probably null |
|
|
R0971:Vps33b
|
UTSW |
7 |
79,937,647 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R1184:Vps33b
|
UTSW |
7 |
79,932,234 (GRCm39) |
missense |
probably benign |
0.02 |
|
R1639:Vps33b
|
UTSW |
7 |
79,934,101 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1693:Vps33b
|
UTSW |
7 |
79,937,641 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4502:Vps33b
|
UTSW |
7 |
79,937,655 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R4609:Vps33b
|
UTSW |
7 |
79,940,866 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4748:Vps33b
|
UTSW |
7 |
79,939,796 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5083:Vps33b
|
UTSW |
7 |
79,924,389 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5304:Vps33b
|
UTSW |
7 |
79,924,001 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5774:Vps33b
|
UTSW |
7 |
79,935,088 (GRCm39) |
missense |
probably benign |
0.38 |
|
R5991:Vps33b
|
UTSW |
7 |
79,933,162 (GRCm39) |
splice site |
probably null |
|
|
R7085:Vps33b
|
UTSW |
7 |
79,925,837 (GRCm39) |
missense |
probably benign |
0.12 |
|
R7409:Vps33b
|
UTSW |
7 |
79,935,017 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R8025:Vps33b
|
UTSW |
7 |
79,940,094 (GRCm39) |
splice site |
probably benign |
|
|
R8460:Vps33b
|
UTSW |
7 |
79,937,617 (GRCm39) |
missense |
probably benign |
0.04 |
|
R8930:Vps33b
|
UTSW |
7 |
79,932,241 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R8932:Vps33b
|
UTSW |
7 |
79,932,241 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R9065:Vps33b
|
UTSW |
7 |
79,935,339 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9165:Vps33b
|
UTSW |
7 |
79,924,434 (GRCm39) |
critical splice donor site |
probably null |
|
|
X0018:Vps33b
|
UTSW |
7 |
79,940,313 (GRCm39) |
critical splice donor site |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TCCCTTCAGAGCCTGTACAG -3'
(R):5'- TCCTAGCTAGTTACTGGGAAAGTG -3'
Sequencing Primer
(F):5'- TGAGAAGGGGCAGGTATTTAATAC -3'
(R):5'- CTAGTTACTGGGAAAGTGAAAGTTG -3'
|
| Posted On |
2021-12-30 |
Incidental Mutation