Incidental Mutation 'R5928:Vps52'
ID 460054
Institutional Source Beutler Lab
Gene Symbol Vps52
Ensembl Gene ENSMUSG00000024319
Gene Name VPS52 GARP complex subunit
Synonyms tclw5, ARE1, D430041K17Rik, tcl-w5, Sacm2l
MMRRC Submission 044123-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5928 (G1)
Quality Score 225
Status Not validated
Chromosome 17
Chromosomal Location 34174786-34186009 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 34180100 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Leucine at position 268 (P268L)
Ref Sequence ENSEMBL: ENSMUSP00000133926 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025178] [ENSMUST00000173196]
AlphaFold Q8C754
Predicted Effect probably benign
Transcript: ENSMUST00000025178
AA Change: P336L

PolyPhen 2 Score 0.450 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: P336L

DomainStartEndE-ValueType
low complexity region 1 11 N/A INTRINSIC
low complexity region 24 45 N/A INTRINSIC
Pfam:Sec3_C 79 244 4.6e-13 PFAM
Pfam:Vps52 94 601 5.1e-233 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000122652
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172558
Predicted Effect possibly damaging
Transcript: ENSMUST00000173196
AA Change: P268L

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: P268L

DomainStartEndE-ValueType
low complexity region 18 39 N/A INTRINSIC
Pfam:Vps52 88 120 2.7e-6 PFAM
Pfam:Vps52 116 527 3e-181 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173318
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173445
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174588
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.8%
  • 20x: 93.3%
Validation Efficiency 97% (90/93)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
PHENOTYPE: Mice homozygous for a null mutation display early embryonic lethality. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca17 T A 17: 24,537,159 (GRCm39) I475L probably benign Het
Abcc2 C T 19: 43,807,797 (GRCm39) R813W probably damaging Het
Adam34 T C 8: 44,105,067 (GRCm39) T193A probably benign Het
Adgb T C 10: 10,254,531 (GRCm39) D1118G probably damaging Het
Adprh A C 16: 38,267,746 (GRCm39) S180A probably benign Het
Atad5 A T 11: 79,985,003 (GRCm39) D30V probably damaging Het
Best3 G A 10: 116,843,532 (GRCm39) D303N probably damaging Het
Bmp2k G C 5: 97,235,595 (GRCm39) probably benign Het
Btc A T 5: 91,514,004 (GRCm39) V86E probably damaging Het
Cacna2d4 G T 6: 119,258,659 (GRCm39) A582S probably benign Het
Carm1 A G 9: 21,486,598 (GRCm39) probably benign Het
Catsperg1 A T 7: 28,906,040 (GRCm39) S180T probably damaging Het
Ccdc185 A T 1: 182,575,047 (GRCm39) H547Q probably benign Het
Ccl6 A G 11: 83,479,658 (GRCm39) I115T possibly damaging Het
Cd44 C T 2: 102,654,648 (GRCm39) V470M probably damaging Het
Cdc25a T C 9: 109,718,861 (GRCm39) V354A probably damaging Het
Cdhr2 C A 13: 54,881,832 (GRCm39) Q1122K probably benign Het
Cep290 A G 10: 100,387,692 (GRCm39) K1958E probably damaging Het
Cfap53 C T 18: 74,492,811 (GRCm39) P512S possibly damaging Het
Chrdl2 A T 7: 99,659,200 (GRCm39) probably benign Het
Cibar1 A G 4: 12,171,919 (GRCm39) probably benign Het
Clec7a A T 6: 129,442,430 (GRCm39) F199Y probably damaging Het
Cracd A C 5: 76,989,581 (GRCm39) probably benign Het
Dhx29 A G 13: 113,101,002 (GRCm39) K1182E probably benign Het
Dnah11 G T 12: 117,878,371 (GRCm39) probably null Het
Dnmt3a A G 12: 3,916,096 (GRCm39) S94G possibly damaging Het
Ecpas A T 4: 58,849,948 (GRCm39) M425K possibly damaging Het
Egfem1 T C 3: 29,637,077 (GRCm39) V42A possibly damaging Het
Eif3e T A 15: 43,138,728 (GRCm39) probably null Het
Exosc9 T A 3: 36,609,774 (GRCm39) probably benign Het
Fbxw18 T A 9: 109,529,149 (GRCm39) T135S probably damaging Het
Fbxw21 T C 9: 108,972,893 (GRCm39) E347G possibly damaging Het
Gcm2 A G 13: 41,256,874 (GRCm39) Y292H probably benign Het
Gltpd2 C A 11: 70,410,179 (GRCm39) Q46K probably benign Het
Gm6741 A G 17: 91,544,528 (GRCm39) Y97C probably damaging Het
Golgb1 T C 16: 36,732,349 (GRCm39) L532S probably damaging Het
Hdac3 C T 18: 38,074,394 (GRCm39) probably benign Het
Helz2 A T 2: 180,872,177 (GRCm39) F2554L possibly damaging Het
Hmbox1 T A 14: 65,061,122 (GRCm39) H384L possibly damaging Het
Hmcn1 G T 1: 150,474,648 (GRCm39) D4746E possibly damaging Het
Il17rb C A 14: 29,726,232 (GRCm39) probably null Het
Irak2 A T 6: 113,653,587 (GRCm39) I252F probably damaging Het
Khnyn C T 14: 56,123,344 (GRCm39) R33C probably damaging Het
Ksr1 G A 11: 78,950,545 (GRCm39) P20L probably damaging Het
Lamc3 T C 2: 31,811,721 (GRCm39) Y903H probably benign Het
Miga2 T C 2: 30,258,875 (GRCm39) probably benign Het
Mroh2a A C 1: 88,169,340 (GRCm39) I672L probably benign Het
Ncoa4 T C 14: 31,888,678 (GRCm39) probably null Het
Nphp3 T C 9: 103,912,996 (GRCm39) Y925H probably benign Het
Nr2c1 T G 10: 94,024,055 (GRCm39) L420R probably damaging Het
Onecut1 A G 9: 74,770,066 (GRCm39) N163S probably benign Het
Or5ac21 G A 16: 59,123,521 (GRCm39) E2K probably damaging Het
Or5d47 T A 2: 87,804,380 (GRCm39) S210C probably benign Het
Or7e166 A T 9: 19,625,049 (GRCm39) T309S probably benign Het
Pcdhb18 G A 18: 37,623,537 (GRCm39) R289Q probably benign Het
Per2 C T 1: 91,372,373 (GRCm39) V234I probably damaging Het
Pign A G 1: 105,485,792 (GRCm39) V735A possibly damaging Het
Plekha7 T C 7: 115,727,809 (GRCm39) K85R probably benign Het
Pnma2 C T 14: 67,154,323 (GRCm39) T249I probably benign Het
Polr2b A G 5: 77,493,189 (GRCm39) D1057G probably damaging Het
Polrmt A T 10: 79,576,186 (GRCm39) L519H probably damaging Het
Ptar1 T C 19: 23,695,277 (GRCm39) I248T probably benign Het
Ptprh A C 7: 4,576,507 (GRCm39) L251R probably damaging Het
Purg T C 8: 33,876,980 (GRCm39) M206T probably benign Het
Pwp2 A T 10: 78,018,290 (GRCm39) F134I probably damaging Het
Riok3 T A 18: 12,286,075 (GRCm39) H434Q probably benign Het
Sorbs2 A G 8: 46,216,220 (GRCm39) I187V probably damaging Het
Tbc1d2b T C 9: 90,101,197 (GRCm39) I598V probably benign Het
Tdg T A 10: 82,477,204 (GRCm39) V85E probably benign Het
Tfb1m C T 17: 3,593,422 (GRCm39) V166I probably benign Het
Tmem163 A T 1: 127,419,383 (GRCm39) M274K probably damaging Het
Tpr T C 1: 150,303,878 (GRCm39) I1343T probably benign Het
Ttn T A 2: 76,719,794 (GRCm39) probably benign Het
Tut7 G A 13: 59,969,880 (GRCm39) A5V probably benign Het
Usp34 A G 11: 23,386,040 (GRCm39) T2156A probably damaging Het
Vmn1r215 A T 13: 23,260,487 (GRCm39) T176S possibly damaging Het
Xbp1 G A 11: 5,473,514 (GRCm39) probably benign Het
Ythdc2 T A 18: 44,966,272 (GRCm39) F169L probably benign Het
Zfyve16 T C 13: 92,658,625 (GRCm39) R429G probably benign Het
Zzef1 A G 11: 72,803,678 (GRCm39) E2504G probably damaging Het
Other mutations in Vps52
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00946:Vps52 APN 17 34,175,932 (GRCm39) missense possibly damaging 0.96
IGL01098:Vps52 APN 17 34,181,704 (GRCm39) missense possibly damaging 0.90
IGL01705:Vps52 APN 17 34,185,042 (GRCm39) missense probably damaging 1.00
IGL01722:Vps52 APN 17 34,180,589 (GRCm39) nonsense probably null
IGL02992:Vps52 APN 17 34,177,324 (GRCm39) missense probably damaging 0.97
IGL03279:Vps52 APN 17 34,176,848 (GRCm39) missense probably damaging 0.96
R0363:Vps52 UTSW 17 34,181,091 (GRCm39) missense probably benign 0.26
R0762:Vps52 UTSW 17 34,178,985 (GRCm39) missense probably damaging 1.00
R1065:Vps52 UTSW 17 34,180,213 (GRCm39) missense probably benign 0.02
R1506:Vps52 UTSW 17 34,176,868 (GRCm39) missense probably damaging 1.00
R3760:Vps52 UTSW 17 34,179,162 (GRCm39) missense possibly damaging 0.64
R4714:Vps52 UTSW 17 34,180,153 (GRCm39) missense probably benign 0.25
R5381:Vps52 UTSW 17 34,177,275 (GRCm39) missense possibly damaging 0.77
R5590:Vps52 UTSW 17 34,180,195 (GRCm39) missense probably benign 0.01
R6003:Vps52 UTSW 17 34,175,068 (GRCm39) start codon destroyed probably null 0.01
R6302:Vps52 UTSW 17 34,182,189 (GRCm39) missense probably damaging 1.00
R6574:Vps52 UTSW 17 34,181,452 (GRCm39) missense probably null 0.34
R6695:Vps52 UTSW 17 34,182,173 (GRCm39) nonsense probably null
R6888:Vps52 UTSW 17 34,182,180 (GRCm39) missense probably benign 0.06
R7022:Vps52 UTSW 17 34,178,293 (GRCm39) missense probably benign 0.04
R7136:Vps52 UTSW 17 34,184,262 (GRCm39) missense probably benign 0.00
R7380:Vps52 UTSW 17 34,177,283 (GRCm39) missense possibly damaging 0.82
R7727:Vps52 UTSW 17 34,181,108 (GRCm39) missense probably benign 0.21
R7888:Vps52 UTSW 17 34,184,725 (GRCm39) missense probably damaging 0.98
R8385:Vps52 UTSW 17 34,181,791 (GRCm39) missense probably damaging 1.00
R8956:Vps52 UTSW 17 34,177,049 (GRCm39) missense probably benign 0.01
R9457:Vps52 UTSW 17 34,181,156 (GRCm39) missense probably damaging 0.97
Predicted Primers
Posted On 2017-02-28