Incidental Mutation 'R6273:Vps53'
ID 507483
Institutional Source Beutler Lab
Gene Symbol Vps53
Ensembl Gene ENSMUSG00000017288
Gene Name VPS53 GARP complex subunit
Synonyms 2310040I21Rik, 3100002B05Rik, 2010002A08Rik
MMRRC Submission 044443-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6273 (G1)
Quality Score 213.009
Status Validated
Chromosome 11
Chromosomal Location 75937052-76070464 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 75992844 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 367 (E367G)
Ref Sequence ENSEMBL: ENSMUSP00000091554 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056601] [ENSMUST00000094015] [ENSMUST00000108419] [ENSMUST00000166752] [ENSMUST00000167114] [ENSMUST00000169734]
AlphaFold Q8CCB4
Predicted Effect probably benign
Transcript: ENSMUST00000056601
AA Change: E396G

PolyPhen 2 Score 0.159 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: E396G

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: E367G

PolyPhen 2 Score 0.159 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: E367G

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 probably benign
Transcript: ENSMUST00000108419
SMART Domains Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288

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
Predicted Effect probably benign
Transcript: ENSMUST00000166752
AA Change: E348G

PolyPhen 2 Score 0.129 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
AA Change: E348G

DomainStartEndE-ValueType
low complexity region 3 19 N/A INTRINSIC
Pfam:DUF2450 25 225 8.2e-12 PFAM
Pfam:Vps53_N 39 230 6e-87 PFAM
Pfam:Vps53_N 226 405 1.4e-60 PFAM
low complexity region 472 485 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000167114
AA Change: E119G

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
SMART Domains Protein: ENSMUSP00000131663
Gene: ENSMUSG00000017288
AA Change: E119G

DomainStartEndE-ValueType
low complexity region 3 19 N/A INTRINSIC
Pfam:Vps53_N 39 101 1.2e-21 PFAM
Pfam:Vps53_N 104 176 3.1e-15 PFAM
low complexity region 243 256 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000169734
SMART Domains Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288

DomainStartEndE-ValueType
Pfam:DUF2450 5 225 5.1e-12 PFAM
Pfam:Vps53_N 39 329 1e-137 PFAM
Meta Mutation Damage Score 0.1157 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.0%
  • 20x: 94.2%
Validation Efficiency 98% (78/80)
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: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610040J01Rik T A 5: 64,055,561 (GRCm39) I99N probably damaging Het
Ank3 G A 10: 69,838,395 (GRCm39) R1566K possibly damaging Het
Ankrd31 A G 13: 96,988,181 (GRCm39) I1065V possibly damaging Het
Aox1 A G 1: 58,378,831 (GRCm39) T1027A probably benign Het
Atm G A 9: 53,399,222 (GRCm39) P1593L probably benign Het
Atp13a5 T G 16: 29,167,555 (GRCm39) I132L probably benign Het
BC035044 A G 6: 128,867,852 (GRCm39) probably benign Het
Cadm3 CT C 1: 173,176,691 (GRCm39) probably benign Homo
Car3 C T 3: 14,936,677 (GRCm39) P247S probably benign Het
Ccdc7a T C 8: 129,513,819 (GRCm39) Y160C probably damaging Het
Cd1d1 A G 3: 86,905,564 (GRCm39) V143A probably benign Het
Cemip2 T A 19: 21,779,369 (GRCm39) V393E probably damaging Het
Cog6 A T 3: 52,903,473 (GRCm39) F142I probably damaging Het
Cracd A T 5: 77,005,568 (GRCm39) D643V unknown Het
Crhr1 T G 11: 104,054,682 (GRCm39) N98K possibly damaging Het
Csf1 A G 3: 107,656,479 (GRCm39) V72A probably damaging Het
Cwc15 T A 9: 14,421,537 (GRCm39) I201K probably benign Het
Dgka T C 10: 128,559,515 (GRCm39) K482R probably benign Het
Dnah7b T C 1: 46,281,476 (GRCm39) S2846P possibly damaging Het
Dst T A 1: 34,314,347 (GRCm39) I4199N probably damaging Het
Dusp7 A G 9: 106,251,095 (GRCm39) T407A possibly damaging Het
Eml2 G A 7: 18,935,088 (GRCm39) V432I probably damaging Het
Fem1a T C 17: 56,564,083 (GRCm39) Y59H possibly damaging Het
Fetub C T 16: 22,751,081 (GRCm39) R143C probably damaging Het
Filip1 A T 9: 79,723,168 (GRCm39) D1150E probably benign Het
Gabra1 A G 11: 42,031,138 (GRCm39) V264A probably damaging Het
Gm4131 T C 14: 62,702,299 (GRCm39) E223G probably damaging Het
Gon4l T C 3: 88,763,156 (GRCm39) V333A probably damaging Het
Gsk3b A G 16: 38,028,408 (GRCm39) T289A probably benign Het
Hmcn2 T C 2: 31,301,846 (GRCm39) S2912P probably damaging Het
Htr7 A T 19: 36,018,969 (GRCm39) probably benign Het
Ibsp A G 5: 104,458,167 (GRCm39) T235A probably benign Het
Ints13 A T 6: 146,467,179 (GRCm39) D116E probably damaging Het
Irag1 G T 7: 110,470,790 (GRCm39) H848N probably benign Het
Kctd19 T C 8: 106,112,117 (GRCm39) N753S probably benign Het
Mdn1 A G 4: 32,715,979 (GRCm39) N2054D probably benign Het
Mink1 A T 11: 70,502,261 (GRCm39) K880* probably null Het
Myo15b T A 11: 115,753,625 (GRCm39) L824Q possibly damaging Het
Napepld T C 5: 21,870,320 (GRCm39) E366G probably benign Het
Obscn T A 11: 58,967,819 (GRCm39) T2662S possibly damaging Het
Or2g7 T G 17: 38,378,686 (GRCm39) L208R probably damaging Het
Or2n1b T A 17: 38,459,833 (GRCm39) M118K possibly damaging Het
Or4k52 T C 2: 111,611,567 (GRCm39) F301L probably benign Het
Or52p1 A G 7: 104,267,102 (GRCm39) D72G probably damaging Het
Or5b12 A G 19: 12,896,764 (GRCm39) V303A probably benign Het
Or6d13 A G 6: 116,518,277 (GRCm39) T288A possibly damaging Het
Pah T C 10: 87,412,077 (GRCm39) probably null Het
Panx3 T G 9: 37,578,725 (GRCm39) I85L probably benign Het
Pate4 T C 9: 35,519,086 (GRCm39) N94D probably benign Het
Pde4d A G 13: 110,086,755 (GRCm39) M610V possibly damaging Het
Pik3c2b T C 1: 132,994,449 (GRCm39) S138P probably benign Het
Pkn1 T C 8: 84,398,899 (GRCm39) N696S probably damaging Het
Plppr2 A G 9: 21,855,801 (GRCm39) E258G probably damaging Het
Plxnd1 A T 6: 115,955,453 (GRCm39) M538K probably damaging Het
Prepl G T 17: 85,390,696 (GRCm39) N87K probably benign Het
Prkag2 C A 5: 25,152,534 (GRCm39) R190L probably damaging Het
Rara A G 11: 98,861,048 (GRCm39) T179A probably benign Het
Rfx7 A G 9: 72,524,279 (GRCm39) K490E possibly damaging Het
Rgsl1 C T 1: 153,703,211 (GRCm39) V147M possibly damaging Het
Rph3a A G 5: 121,083,485 (GRCm39) I595T possibly damaging Het
Rsf1 CG CGACGGCGGTG 7: 97,229,115 (GRCm39) probably benign Homo
Slc35e2 C T 4: 155,694,483 (GRCm39) P10L probably benign Het
Slc8a2 T C 7: 15,879,259 (GRCm39) F582L possibly damaging Het
Sprr2e A G 3: 92,260,171 (GRCm39) M1V probably null Het
Steap1 T A 5: 5,790,827 (GRCm39) R40S possibly damaging Het
Tbc1d2 C T 4: 46,629,912 (GRCm39) G252R probably benign Het
Thsd7a A T 6: 12,408,835 (GRCm39) V729E probably damaging Het
Tmprss13 A G 9: 45,256,630 (GRCm39) Y525C probably damaging Het
Tnik A T 3: 28,631,649 (GRCm39) H383L possibly damaging Het
Vars1 T C 17: 35,232,719 (GRCm39) L881S probably damaging Het
Vmn1r201 A C 13: 22,659,385 (GRCm39) S200R probably damaging Het
Vmn2r130 A T 17: 23,295,759 (GRCm39) H643L probably benign Het
Vmn2r14 A T 5: 109,369,133 (GRCm39) W147R probably benign Het
Xab2 C T 8: 3,661,822 (GRCm39) G544S probably damaging Het
Ythdf3 T A 3: 16,259,020 (GRCm39) V400E possibly damaging Het
Zfand5 C T 19: 21,257,060 (GRCm39) P147S probably benign Het
Zfp768 A T 7: 126,944,319 (GRCm39) probably null Het
Zswim8 A G 14: 20,763,521 (GRCm39) M423V 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
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
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
Predicted Primers PCR Primer
(F):5'- GAGGCTCTTCTGCAACACATC -3'
(R):5'- GTGCCTCCAACCTTGTTATGAG -3'

Sequencing Primer
(F):5'- GCAGGAACATGGTTCTTCGTCATC -3'
(R):5'- CTCCAACCTTGTTATGAGGACAAATC -3'
Posted On 2018-03-15