Incidental Mutation 'PIT4651001:Vps33b'
ID 556664
Institutional Source Beutler Lab
Gene Symbol Vps33b
Ensembl Gene ENSMUSG00000030534
Gene Name vacuolar protein sorting 33B
Synonyms
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # PIT4651001 (G1)
Quality Score 118.008
Status Not validated
Chromosome 7
Chromosomal Location 79919369-79941327 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 79939755 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 502 (D502G)
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 damaging
Transcript: ENSMUST00000032749
AA Change: D502G

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000032749
Gene: ENSMUSG00000030534
AA Change: D502G

DomainStartEndE-ValueType
Pfam:Sec1 37 611 2.4e-89 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000047558
SMART Domains Protein: ENSMUSP00000043379
Gene: ENSMUSG00000038943

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
SCOP:d1epua_ 18 59 2e-7 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000150585
SMART Domains Protein: ENSMUSP00000138224
Gene: ENSMUSG00000030534

DomainStartEndE-ValueType
Pfam:Sec1 36 140 1.5e-12 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000163812
SMART Domains Protein: ENSMUSP00000129675
Gene: ENSMUSG00000038943

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
Pfam:MAP65_ASE1 34 615 2.9e-167 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000174199
SMART Domains Protein: ENSMUSP00000133295
Gene: ENSMUSG00000038943

DomainStartEndE-ValueType
Pfam:MAP65_ASE1 7 524 8.1e-158 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000205864
Coding Region Coverage
  • 1x: 93.1%
  • 3x: 90.7%
  • 10x: 84.4%
  • 20x: 70.4%
Validation Efficiency
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: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2210408I21Rik A T 13: 77,408,014 (GRCm39) I428L probably benign Het
Aass T C 6: 23,118,750 (GRCm39) I131V probably benign Het
Alcam T A 16: 52,115,550 (GRCm39) K189N probably benign Het
Ankrd50 C A 3: 38,509,959 (GRCm39) E803* probably null Het
Ankrd53 A G 6: 83,742,715 (GRCm39) D236G probably damaging Het
Bard1 A G 1: 71,114,087 (GRCm39) V298A probably benign Het
Cacna1d C T 14: 29,900,602 (GRCm39) G361D probably damaging Het
Camkk1 A G 11: 72,916,647 (GRCm39) S82G probably benign Het
Ccr4 A T 9: 114,321,261 (GRCm39) V268E probably benign Het
Cdh6 G A 15: 13,044,805 (GRCm39) S439L possibly damaging Het
Ces1e G T 8: 93,941,711 (GRCm39) A254E probably benign Het
Cfap46 T C 7: 139,225,467 (GRCm39) T1078A Het
Cyp46a1 A G 12: 108,319,367 (GRCm39) D288G probably benign Het
Dnah6 T C 6: 73,037,243 (GRCm39) N3333S probably benign Het
Dzip3 A G 16: 48,765,241 (GRCm39) V491A probably benign Het
Egr1 G T 18: 34,996,240 (GRCm39) E341* probably null Het
Enpp1 G A 10: 24,529,848 (GRCm39) P597S probably benign Het
Ercc3 A T 18: 32,373,365 (GRCm39) probably benign Het
Fbn1 T C 2: 125,205,909 (GRCm39) probably null Het
Fbxw11 T C 11: 32,661,999 (GRCm39) probably null Het
Fhip1a C T 3: 85,590,948 (GRCm39) A389T probably damaging Het
Gbf1 A G 19: 46,151,982 (GRCm39) N5S probably benign Het
Gbp4 T A 5: 105,266,289 (GRCm39) H584L probably benign Het
Gcgr G T 11: 120,428,968 (GRCm39) C402F probably damaging Het
Grm7 T A 6: 110,623,050 (GRCm39) N74K probably benign Het
H1f9 A G 11: 94,859,142 (GRCm39) S146G probably benign Het
Hoxa10 T G 6: 52,211,877 (GRCm39) N13T possibly damaging Het
Ice1 A T 13: 70,772,040 (GRCm39) probably null Het
Il22 C A 10: 118,041,495 (GRCm39) N69K probably damaging Het
Il9r A T 11: 32,141,798 (GRCm39) H319Q probably benign Het
Itgax A G 7: 127,748,282 (GRCm39) T1104A probably benign Het
Jag1 C T 2: 136,943,617 (GRCm39) G193D probably damaging Het
Krt13 T A 11: 100,010,862 (GRCm39) D164V probably damaging Het
Lepr T C 4: 101,649,194 (GRCm39) M865T probably damaging Het
Lmf2 G A 15: 89,236,272 (GRCm39) H576Y possibly damaging Het
Lrrc8c C T 5: 105,756,189 (GRCm39) H655Y probably benign Het
Mapk6 A T 9: 75,304,869 (GRCm39) S183T possibly damaging Het
Mcrs1 A T 15: 99,144,832 (GRCm39) Y261N probably damaging Het
Mon1b G A 8: 114,365,254 (GRCm39) G194D probably benign Het
Myo18b C T 5: 112,982,301 (GRCm39) R1144Q probably benign Het
Myo9b T A 8: 71,795,456 (GRCm39) H808Q possibly damaging Het
Ngdn T C 14: 55,253,657 (GRCm39) I15T probably benign Het
Nhsl1 T G 10: 18,284,183 (GRCm39) S41R probably damaging Het
Numa1 A T 7: 101,663,141 (GRCm39) K2089M probably damaging Het
Obi1 T A 14: 104,743,692 (GRCm39) D129V probably damaging Het
Obscn A G 11: 58,932,507 (GRCm39) L4900P probably damaging Het
Olfm4 T A 14: 80,258,925 (GRCm39) L391Q probably benign Het
Or10g9b A T 9: 39,917,526 (GRCm39) C240S probably damaging Het
Or2ag1 A G 7: 106,472,730 (GRCm39) C241R probably damaging Het
Or5b106 T A 19: 13,123,991 (GRCm39) I11F probably benign Het
Or5b111 A G 19: 13,291,556 (GRCm39) I31T probably benign Het
Or5m9 T C 2: 85,876,862 (GRCm39) L12P probably damaging Het
Parn T A 16: 13,449,431 (GRCm39) N302Y probably benign Het
Pi4k2b T G 5: 52,905,812 (GRCm39) S118A possibly damaging Het
Piwil4 C T 9: 14,620,195 (GRCm39) V704I possibly damaging Het
Pm20d2 G A 4: 33,181,715 (GRCm39) T296M probably damaging Het
Pmpcb C T 5: 21,951,048 (GRCm39) A270V probably benign Het
Pnpt1 T C 11: 29,106,945 (GRCm39) probably null Het
Prkn T A 17: 11,286,130 (GRCm39) L41Q probably damaging Het
Rc3h1 C A 1: 160,791,110 (GRCm39) N931K probably benign Het
Rlf A G 4: 121,007,510 (GRCm39) V600A probably damaging Het
Rpl27rt A T 18: 34,870,892 (GRCm39) Q142L unknown Het
Sall1 T G 8: 89,757,731 (GRCm39) Q791P probably damaging Het
Sema3c T A 5: 17,899,731 (GRCm39) Y408N probably benign Het
Serpinb13 C T 1: 106,910,574 (GRCm39) S66L probably damaging Het
Tmem181a A T 17: 6,351,170 (GRCm39) M319L probably benign Het
Trim24 T C 6: 37,877,667 (GRCm39) probably null Het
Ttn T A 2: 76,719,278 (GRCm39) T7234S unknown Het
Unc13c T A 9: 73,391,021 (GRCm39) M2076L possibly damaging Het
Uroc1 C T 6: 90,340,095 (GRCm39) R667* probably null Het
Uvrag A G 7: 98,555,727 (GRCm39) F456L probably benign Het
Vmn1r215 T C 13: 23,260,530 (GRCm39) V190A probably damaging Het
Vmn2r50 T A 7: 9,771,659 (GRCm39) T681S probably benign Het
Vmn2r65 T A 7: 84,595,461 (GRCm39) T408S probably benign Het
Other mutations in Vps33b
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
R9110:Vps33b UTSW 7 79,939,743 (GRCm39) missense probably benign 0.04
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'- AGTTGTCTTGGCATGGACCC -3'
(R):5'- TCTTCTGACAGTAAGCTTAGGAAAGG -3'

Sequencing Primer
(F):5'- GGCATGGACCCTTTTGTCAGC -3'
(R):5'- CATTCCTAGCTAGTTACTGGGAAAG -3'
Posted On 2019-06-07