Incidental Mutation 'R7735:Vps53'
ID 596206
Institutional Source Beutler Lab
Gene Symbol Vps53
Ensembl Gene ENSMUSG00000017288
Gene Name VPS53 GARP complex subunit
Synonyms 2310040I21Rik, 3100002B05Rik, 2010002A08Rik
MMRRC Submission 045791-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7735 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 75937052-76070464 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 75937962 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Isoleucine at position 753 (F753I)
Ref Sequence ENSEMBL: ENSMUSP00000061317 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056601] [ENSMUST00000094015] [ENSMUST00000108419]
AlphaFold Q8CCB4
Predicted Effect probably damaging
Transcript: ENSMUST00000056601
AA Change: F753I

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: F753I

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 damaging
Transcript: ENSMUST00000094015
AA Change: F724I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: F724I

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: F576I
SMART Domains Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: F576I

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
Meta Mutation Damage Score 0.3240 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (58/58)
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adcy8 T C 15: 64,655,629 (GRCm39) T617A probably benign Het
Agl A T 3: 116,578,795 (GRCm39) I446N probably benign Het
Aox1 C T 1: 58,107,451 (GRCm39) P575L probably benign Het
Ap2m1 A T 16: 20,358,269 (GRCm39) I96F probably benign Het
Arhgap15 A G 2: 44,006,642 (GRCm39) D253G probably damaging Het
Arsa A T 15: 89,359,152 (GRCm39) C171* probably null Het
Arsb G T 13: 93,908,491 (GRCm39) R69L probably benign Het
Asb13 G A 13: 3,684,180 (GRCm39) probably null Het
Canx G T 11: 50,191,866 (GRCm39) D348E probably damaging Het
Cebpz C T 17: 79,233,342 (GRCm39) probably null Het
Ces2h A T 8: 105,741,127 (GRCm39) I40L probably benign Het
Cfhr4 A G 1: 139,660,039 (GRCm39) probably null Het
Csmd2 T C 4: 128,350,723 (GRCm39) probably null Het
Cxadr T A 16: 78,125,949 (GRCm39) N106K possibly damaging Het
Ddo T C 10: 40,507,770 (GRCm39) C56R probably benign Het
Dnah6 C T 6: 73,046,412 (GRCm39) G3192D probably damaging Het
Efcab3 T A 11: 104,962,465 (GRCm39) V49E probably benign Het
Epha10 T C 4: 124,807,472 (GRCm39) Y578H Het
Fbxw16 T C 9: 109,270,135 (GRCm39) D202G probably damaging Het
Gzf1 T C 2: 148,530,083 (GRCm39) V538A possibly damaging Het
Igha T A 12: 113,220,019 (GRCm39) probably benign Het
Iqce G T 5: 140,663,839 (GRCm39) Q457K probably benign Het
Kbtbd3 A G 9: 4,330,846 (GRCm39) K407E possibly damaging Het
Lipt1 A G 1: 37,914,703 (GRCm39) E253G probably damaging Het
Mrnip G A 11: 50,087,800 (GRCm39) W107* probably null Het
Mroh4 T C 15: 74,497,357 (GRCm39) T224A probably damaging Het
Ncoa2 A T 1: 13,218,661 (GRCm39) S1389R probably benign Het
Npffr2 A G 5: 89,731,173 (GRCm39) I368V probably benign Het
Nrdc C T 4: 108,895,182 (GRCm39) L469F probably damaging Het
Nup210l A T 3: 90,092,883 (GRCm39) Q1279L probably damaging Het
Or4k47 T A 2: 111,451,819 (GRCm39) N200I probably damaging Het
Or7e170 A G 9: 19,795,410 (GRCm39) Y64H probably damaging Het
Pcdha4 T G 18: 37,085,961 (GRCm39) I48S probably damaging Het
Pip5kl1 A G 2: 32,469,101 (GRCm39) Y211C possibly damaging Het
Prrt4 A T 6: 29,170,035 (GRCm39) S806T possibly damaging Het
Ptpn20 T A 14: 33,352,902 (GRCm39) Y214N probably damaging Het
Ptprt A T 2: 161,417,661 (GRCm39) N938K probably damaging Het
Scn2a G T 2: 65,594,013 (GRCm39) V1621L probably benign Het
Senp3 A G 11: 69,569,087 (GRCm39) I358T probably damaging Het
Sf3b1 A T 1: 55,042,508 (GRCm39) S461T probably benign Het
Slc22a2 C T 17: 12,828,917 (GRCm39) T341I probably damaging Het
Slc38a7 A T 8: 96,568,295 (GRCm39) D363E probably benign Het
Slc6a5 T C 7: 49,598,090 (GRCm39) probably null Het
Smo T A 6: 29,759,851 (GRCm39) V650E probably damaging Het
Spata17 G A 1: 186,872,577 (GRCm39) T31I unknown Het
Sstr2 T A 11: 113,515,423 (GRCm39) I114N possibly damaging Het
Styxl1 T C 5: 135,788,023 (GRCm39) Y146C probably damaging Het
Synpo2l T C 14: 20,711,243 (GRCm39) Q688R possibly damaging Het
Tmem245 C T 4: 56,925,155 (GRCm39) R322H probably benign Het
Tnxb A G 17: 34,890,398 (GRCm39) E247G unknown Het
Ttc28 A T 5: 111,414,544 (GRCm39) probably null Het
Ttn A T 2: 76,718,416 (GRCm39) I7255N unknown Het
Ttn C A 2: 76,652,768 (GRCm39) probably null Het
Unc13b C T 4: 43,165,791 (GRCm39) R204C probably damaging Het
Utrn A G 10: 12,619,787 (GRCm39) probably null Het
Ypel1 G T 16: 16,918,124 (GRCm39) S97R probably benign Het
Zdbf2 A G 1: 63,343,264 (GRCm39) T548A possibly damaging Het
Zfp747 G A 7: 126,973,672 (GRCm39) T166M probably damaging 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
IGL02275:Vps53 APN 11 75,937,949 (GRCm39) missense probably benign 0.03
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
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
Predicted Primers PCR Primer
(F):5'- TCGGCCTCTAGCAAAGGATC -3'
(R):5'- AAAGCAGTCTGGGTAATTCAGC -3'

Sequencing Primer
(F):5'- CTCTAGCAAAGGATCCCTGC -3'
(R):5'- AATTCAGCCACTTGTGGGG -3'
Posted On 2019-11-26