Incidental Mutation 'IGL02275:Vps53'
ID287309
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Vps53
Ensembl Gene ENSMUSG00000017288
Gene NameVPS53 GARP complex subunit
Synonyms2310040I21Rik, 3100002B05Rik, 2010002A08Rik
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #IGL02275
Quality Score
Status
Chromosome11
Chromosomal Location76046226-76179647 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 76047123 bp
ZygosityHeterozygous
Amino Acid Change Tyrosine to Cysteine at position 728 (Y728C)
Ref Sequence ENSEMBL: ENSMUSP00000091554 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056601] [ENSMUST00000094015] [ENSMUST00000108419]
Predicted Effect probably benign
Transcript: ENSMUST00000056601
AA Change: Y757C

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: Y757C

DomainStartEndE-ValueType
low complexity region 3 19 N/A INTRINSIC
Pfam:DUF2450 25 225 5.9e-11 PFAM
Pfam:Vps53_N 39 453 1.9e-176 PFAM
low complexity region 520 533 N/A INTRINSIC
low complexity region 820 832 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000094015
AA Change: Y728C

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: Y728C

DomainStartEndE-ValueType
low complexity region 3 19 N/A INTRINSIC
Pfam:Vps53_N 39 96 6.2e-21 PFAM
Pfam:Vps53_N 93 424 1.4e-133 PFAM
low complexity region 491 504 N/A INTRINSIC
low complexity region 791 803 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000108419
AA Change: Y580C
SMART Domains Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: Y580C

DomainStartEndE-ValueType
low complexity region 3 19 N/A INTRINSIC
Pfam:DUF2450 25 224 4e-11 PFAM
Pfam:Vps53_N 39 233 5.2e-87 PFAM
Pfam:Vps53_N 226 276 1.6e-14 PFAM
low complexity region 343 356 N/A INTRINSIC
low complexity region 643 655 N/A INTRINSIC
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with sequence similarity to the yeast Vps53p protein. Vps53p is involved in retrograde vesicle trafficking in late Golgi. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality prior to E12.5 with trophoblast cell hyperplasia. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 24 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700037C18Rik T A 16: 3,906,282 D130V probably damaging Het
4930596D02Rik T C 14: 35,811,923 T9A probably benign Het
Anapc1 C A 2: 128,659,852 A757S probably benign Het
Bpifa6 A T 2: 153,992,272 D328V probably benign Het
Casc1 T C 6: 145,177,364 Y592C probably damaging Het
Cdh19 T A 1: 110,925,886 K275I probably benign Het
Col18a1 A G 10: 77,059,383 I1148T possibly damaging Het
Commd1 A T 11: 22,900,017 V222D probably damaging Het
Crim1 T A 17: 78,369,998 M876K possibly damaging Het
Dennd1b C A 1: 139,081,254 H232N probably damaging Het
Dhx57 T C 17: 80,274,839 T393A probably benign Het
Gabrb2 G T 11: 42,591,894 R193L probably benign Het
Gm5828 T A 1: 16,769,118 noncoding transcript Het
Gm6483 C T 8: 19,691,613 P55S probably damaging Het
Hsp90ab1 T C 17: 45,568,438 Y619C possibly damaging Het
Kctd19 A G 8: 105,396,374 I136T probably damaging Het
Olfr134 G T 17: 38,175,686 V201L probably benign Het
Olfr1361 A C 13: 21,659,000 F108V probably benign Het
Sel1l T C 12: 91,815,015 Y532C probably damaging Het
Sirpb1a A G 3: 15,410,409 probably null Het
Ush2a C T 1: 188,263,269 T79M possibly damaging Het
Usp24 T C 4: 106,387,493 V1215A probably damaging Het
Vdac3-ps1 T C 13: 18,030,794 noncoding transcript Het
Vmn2r75 T C 7: 86,165,140 T382A probably benign Het
Other mutations in Vps53
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00475:Vps53 APN 11 76077035 splice site probably null
IGL01596:Vps53 APN 11 76063037 missense probably damaging 1.00
IGL01655:Vps53 APN 11 76063034 missense probably damaging 0.97
IGL02321:Vps53 APN 11 76048538 missense possibly damaging 0.60
IGL02581:Vps53 APN 11 76102057 missense probably damaging 0.99
IGL02821:Vps53 APN 11 76136317 splice site probably benign
IGL02958:Vps53 APN 11 76117711 missense probably damaging 1.00
IGL03001:Vps53 APN 11 76138324 missense probably damaging 1.00
PIT4519001:Vps53 UTSW 11 76117173 missense probably damaging 1.00
R0257:Vps53 UTSW 11 76177385 intron probably benign
R0391:Vps53 UTSW 11 76121579 missense probably benign 0.31
R0421:Vps53 UTSW 11 76082670 missense probably damaging 1.00
R0882:Vps53 UTSW 11 76082659 missense probably damaging 1.00
R2509:Vps53 UTSW 11 76066835 missense possibly damaging 0.49
R3622:Vps53 UTSW 11 76117783 missense probably benign 0.00
R5137:Vps53 UTSW 11 76166248 missense probably damaging 1.00
R5338:Vps53 UTSW 11 76081208 missense probably damaging 1.00
R5756:Vps53 UTSW 11 76092330 splice site probably benign
R5786:Vps53 UTSW 11 76063007 missense probably benign 0.08
R5961:Vps53 UTSW 11 76048490 missense probably damaging 1.00
R6059:Vps53 UTSW 11 76066867 missense possibly damaging 0.57
R6273:Vps53 UTSW 11 76102018 missense probably benign 0.16
R6490:Vps53 UTSW 11 76077055 missense probably benign 0.03
R6657:Vps53 UTSW 11 76134427 missense probably damaging 1.00
R6671:Vps53 UTSW 11 76134506 missense probably damaging 1.00
R6772:Vps53 UTSW 11 76179498 start codon destroyed probably null
R7378:Vps53 UTSW 11 76077074 missense possibly damaging 0.88
R7735:Vps53 UTSW 11 76047136 missense probably damaging 1.00
R8066:Vps53 UTSW 11 76136307 missense probably damaging 1.00
Z1177:Vps53 UTSW 11 76136198 critical splice donor site probably null
Posted On2015-04-16