Incidental Mutation 'IGL02275:Vps53'
ID 287309
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Vps53
Ensembl Gene ENSMUSG00000017288
Gene Name VPS53 GARP complex subunit
Synonyms 2310040I21Rik, 3100002B05Rik, 2010002A08Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL02275
Quality Score
Status
Chromosome 11
Chromosomal Location 75937052-76070464 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 75937949 bp (GRCm39)
Zygosity Heterozygous
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]
AlphaFold Q8CCB4
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: 3,724,146 (GRCm39) D130V probably damaging Het
4930596D02Rik T C 14: 35,533,880 (GRCm39) T9A probably benign Het
Anapc1 C A 2: 128,501,772 (GRCm39) A757S probably benign Het
Bpifa6 A T 2: 153,834,192 (GRCm39) D328V probably benign Het
Cdh19 T A 1: 110,853,616 (GRCm39) K275I probably benign Het
Col18a1 A G 10: 76,895,217 (GRCm39) I1148T possibly damaging Het
Commd1 A T 11: 22,850,017 (GRCm39) V222D probably damaging Het
Crim1 T A 17: 78,677,427 (GRCm39) M876K possibly damaging Het
Dennd1b C A 1: 139,008,992 (GRCm39) H232N probably damaging Het
Dhx57 T C 17: 80,582,268 (GRCm39) T393A probably benign Het
Dnai7 T C 6: 145,123,090 (GRCm39) Y592C probably damaging Het
Gabrb2 G T 11: 42,482,721 (GRCm39) R193L probably benign Het
Gm5828 T A 1: 16,839,342 (GRCm39) noncoding transcript Het
Gm6483 C T 8: 19,741,629 (GRCm39) P55S probably damaging Het
Hsp90ab1 T C 17: 45,879,364 (GRCm39) Y619C possibly damaging Het
Kctd19 A G 8: 106,123,006 (GRCm39) I136T probably damaging Het
Or2n1 G T 17: 38,486,577 (GRCm39) V201L probably benign Het
Or2w6 A C 13: 21,843,170 (GRCm39) F108V probably benign Het
Sel1l T C 12: 91,781,789 (GRCm39) Y532C probably damaging Het
Sirpb1a A G 3: 15,475,469 (GRCm39) probably null Het
Ush2a C T 1: 187,995,466 (GRCm39) T79M possibly damaging Het
Usp24 T C 4: 106,244,690 (GRCm39) V1215A probably damaging Het
Vdac3-ps1 T C 13: 18,205,379 (GRCm39) noncoding transcript Het
Vmn2r75 T C 7: 85,814,348 (GRCm39) T382A probably benign Het
Other mutations in Vps53
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00475:Vps53 APN 11 75,967,861 (GRCm39) splice site probably null
IGL01596:Vps53 APN 11 75,953,863 (GRCm39) missense probably damaging 1.00
IGL01655:Vps53 APN 11 75,953,860 (GRCm39) missense probably damaging 0.97
IGL02321:Vps53 APN 11 75,939,364 (GRCm39) missense possibly damaging 0.60
IGL02581:Vps53 APN 11 75,992,883 (GRCm39) missense probably damaging 0.99
IGL02821:Vps53 APN 11 76,027,143 (GRCm39) splice site probably benign
IGL02958:Vps53 APN 11 76,008,537 (GRCm39) missense probably damaging 1.00
IGL03001:Vps53 APN 11 76,029,150 (GRCm39) missense probably damaging 1.00
PIT4519001:Vps53 UTSW 11 76,007,999 (GRCm39) missense probably damaging 1.00
R0257:Vps53 UTSW 11 76,068,211 (GRCm39) intron probably benign
R0391:Vps53 UTSW 11 76,012,405 (GRCm39) missense probably benign 0.31
R0421:Vps53 UTSW 11 75,973,496 (GRCm39) missense probably damaging 1.00
R0882:Vps53 UTSW 11 75,973,485 (GRCm39) missense probably damaging 1.00
R2509:Vps53 UTSW 11 75,957,661 (GRCm39) missense possibly damaging 0.49
R3622:Vps53 UTSW 11 76,008,609 (GRCm39) missense probably benign 0.00
R5137:Vps53 UTSW 11 76,057,074 (GRCm39) missense probably damaging 1.00
R5338:Vps53 UTSW 11 75,972,034 (GRCm39) missense probably damaging 1.00
R5756:Vps53 UTSW 11 75,983,156 (GRCm39) splice site probably benign
R5786:Vps53 UTSW 11 75,953,833 (GRCm39) missense probably benign 0.08
R5961:Vps53 UTSW 11 75,939,316 (GRCm39) missense probably damaging 1.00
R6059:Vps53 UTSW 11 75,957,693 (GRCm39) missense possibly damaging 0.57
R6273:Vps53 UTSW 11 75,992,844 (GRCm39) missense probably benign 0.16
R6490:Vps53 UTSW 11 75,967,881 (GRCm39) missense probably benign 0.03
R6657:Vps53 UTSW 11 76,025,253 (GRCm39) missense probably damaging 1.00
R6671:Vps53 UTSW 11 76,025,332 (GRCm39) missense probably damaging 1.00
R6772:Vps53 UTSW 11 76,070,324 (GRCm39) start codon destroyed probably null
R7378:Vps53 UTSW 11 75,967,900 (GRCm39) missense possibly damaging 0.88
R7735:Vps53 UTSW 11 75,937,962 (GRCm39) missense probably damaging 1.00
R8066:Vps53 UTSW 11 76,027,133 (GRCm39) missense probably damaging 1.00
Z1177:Vps53 UTSW 11 76,027,024 (GRCm39) critical splice donor site probably null
Posted On 2015-04-16