Incidental Mutation 'R6772:Vps53'
ID 532216
Institutional Source Beutler Lab
Gene Symbol Vps53
Ensembl Gene ENSMUSG00000017288
Gene Name VPS53 GARP complex subunit
Synonyms 2310040I21Rik, 3100002B05Rik, 2010002A08Rik
MMRRC Submission 044888-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6772 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 75937052-76070464 bp(-) (GRCm39)
Type of Mutation start codon destroyed
DNA Base Change (assembly) A to T at 76070324 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 1 (M1K)
Ref Sequence ENSEMBL: ENSMUSP00000127364 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056601] [ENSMUST00000094015] [ENSMUST00000108419] [ENSMUST00000129256] [ENSMUST00000129853] [ENSMUST00000163878] [ENSMUST00000166752] [ENSMUST00000167114] [ENSMUST00000169734] [ENSMUST00000170730]
AlphaFold Q8CCB4
Predicted Effect probably null
Transcript: ENSMUST00000056601
AA Change: M1K
SMART Domains Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: M1K

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 null
Transcript: ENSMUST00000094015
AA Change: M1K
SMART Domains Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: M1K

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 null
Transcript: ENSMUST00000108419
AA Change: M1K
SMART Domains Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: M1K

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 null
Transcript: ENSMUST00000129256
AA Change: M1K
Predicted Effect probably benign
Transcript: ENSMUST00000129853
SMART Domains Protein: ENSMUSP00000114936
Gene: ENSMUSG00000069808

DomainStartEndE-ValueType
TLC 1 166 6.2e-8 SMART
Predicted Effect probably null
Transcript: ENSMUST00000163878
AA Change: M1K
Predicted Effect probably null
Transcript: ENSMUST00000166752
AA Change: M1K
SMART Domains Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
AA Change: M1K

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 null
Transcript: ENSMUST00000167114
AA Change: M1K
SMART Domains Protein: ENSMUSP00000131663
Gene: ENSMUSG00000017288
AA Change: M1K

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 null
Transcript: ENSMUST00000169734
AA Change: M1K
SMART Domains Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288
AA Change: M1K

DomainStartEndE-ValueType
Pfam:DUF2450 5 225 5.1e-12 PFAM
Pfam:Vps53_N 39 329 1e-137 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000170730
AA Change: M1K
SMART Domains Protein: ENSMUSP00000127364
Gene: ENSMUSG00000017288
AA Change: M1K

DomainStartEndE-ValueType
low complexity region 3 19 N/A INTRINSIC
Pfam:Vps53_N 54 123 3e-34 PFAM
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.8%
  • 20x: 96.7%
Validation Efficiency 97% (36/37)
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: 36 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca16 A T 7: 120,126,276 (GRCm39) D1144V probably damaging Het
Ankrd13a A G 5: 114,939,804 (GRCm39) H477R probably benign Het
Anxa3 A T 5: 96,958,972 (GRCm39) I27F probably damaging Het
Aplf T C 6: 87,640,781 (GRCm39) E76G possibly damaging Het
Bbs1 A G 19: 4,956,618 (GRCm39) probably benign Het
Camk2a T C 18: 61,102,092 (GRCm39) S332P probably benign Het
Casz1 T A 4: 149,027,663 (GRCm39) F1013L probably damaging Het
Cd109 A T 9: 78,588,092 (GRCm39) I707F possibly damaging Het
Cd4 G A 6: 124,849,421 (GRCm39) T202I probably benign Het
Celsr1 A G 15: 85,914,983 (GRCm39) S997P probably benign Het
Cfap77 T C 2: 28,944,951 (GRCm39) T24A probably damaging Het
Dscaml1 G A 9: 45,621,609 (GRCm39) R1019H probably damaging Het
Epb41l4b C A 4: 57,063,140 (GRCm39) V517F probably benign Het
Exosc10 G A 4: 148,665,591 (GRCm39) D818N probably damaging Het
Furin C T 7: 80,043,240 (GRCm39) G324S probably damaging Het
Idh2 TCCCAGG T 7: 79,748,079 (GRCm39) probably benign Het
Ifi206 T C 1: 173,308,773 (GRCm39) M408V unknown Het
Kdm4a T C 4: 117,999,752 (GRCm39) probably null Het
Neo1 T A 9: 58,810,259 (GRCm39) Q1064L probably damaging Het
Nphp4 G A 4: 152,628,863 (GRCm39) V750I probably benign Het
Pcdhac1 T C 18: 37,223,289 (GRCm39) V34A probably benign Het
Pdk4 T C 6: 5,487,141 (GRCm39) I302V probably benign Het
Prl6a1 A G 13: 27,503,031 (GRCm39) D209G probably damaging Het
Pspn T C 17: 57,306,515 (GRCm39) Q138R probably benign Het
Ptgs2 A G 1: 149,977,829 (GRCm39) Y134C probably damaging Het
Rlbp1 G A 7: 79,033,798 (GRCm39) probably benign Het
Rpia T C 6: 70,762,532 (GRCm39) I108V probably benign Het
Tcaf1 A T 6: 42,652,210 (GRCm39) H757Q probably damaging Het
Ttc8 A C 12: 98,909,848 (GRCm39) S143R probably damaging Het
Uba6 A G 5: 86,294,932 (GRCm39) probably benign Het
Ubr4 A T 4: 139,194,541 (GRCm39) K4280* probably null Het
Vmn2r15 C A 5: 109,434,238 (GRCm39) S822I probably damaging Het
Zfp362 A G 4: 128,684,053 (GRCm39) M18T possibly damaging Het
Zfp429 A G 13: 67,538,317 (GRCm39) C376R probably damaging Het
Zfyve9 T C 4: 108,496,466 (GRCm39) N1395S probably damaging Het
Zmynd8 T A 2: 165,649,521 (GRCm39) Q857H 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
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
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'- TTCCGCTCAGCATAAGAACC -3'
(R):5'- TTTCCAGGGACTTGACAGCC -3'

Sequencing Primer
(F):5'- GCATAAGAACCGCCACCTTTC -3'
(R):5'- ACTTGACAGCCATGCCTG -3'
Posted On 2018-08-29