Incidental Mutation 'R7136:Vps52'
ID 553104
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 045220-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7136 (G1)
Quality Score 225.009
Status Validated
Chromosome 17
Chromosomal Location 34174786-34186009 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 34184262 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 601 (I601T)
Ref Sequence ENSEMBL: ENSMUSP00000025178 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025178] [ENSMUST00000173196]
AlphaFold Q8C754
Predicted Effect probably benign
Transcript: ENSMUST00000025178
AA Change: I601T

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: I601T

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 probably benign
Transcript: ENSMUST00000173196
AA Change: I533T

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: I533T

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (68/68)
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700123K08Rik A G 5: 138,560,610 (GRCm39) S262P probably damaging Het
Abcc2 A G 19: 43,825,899 (GRCm39) E1512G probably damaging Het
Abcg2 T G 6: 58,661,325 (GRCm39) Y459D possibly damaging Het
Amy1 T C 3: 113,357,248 (GRCm39) Y197C probably damaging Het
Bptf A G 11: 106,990,541 (GRCm39) I516T probably damaging Het
Capn12 T A 7: 28,582,532 (GRCm39) probably null Het
Cbln2 T A 18: 86,734,797 (GRCm39) L190Q probably damaging Het
Ccdc157 C T 11: 4,098,592 (GRCm39) E305K possibly damaging Het
Ccdc47 A G 11: 106,095,830 (GRCm39) S289P probably benign Het
Chd3 C T 11: 69,239,264 (GRCm39) E1756K probably null Het
Chrd G T 16: 20,553,272 (GRCm39) A183S possibly damaging Het
Cp C T 3: 20,039,822 (GRCm39) R880* probably null Het
Cyp24a1 A T 2: 170,336,063 (GRCm39) D191E probably benign Het
Dnah1 T C 14: 31,020,613 (GRCm39) Y1252C probably damaging Het
Eps8l1 A G 7: 4,480,403 (GRCm39) D487G probably damaging Het
Fam227b T G 2: 125,965,948 (GRCm39) Q159P probably damaging Het
Fat3 A G 9: 16,289,481 (GRCm39) I14T probably benign Het
Fbxl19 C A 7: 127,349,217 (GRCm39) T129N possibly damaging Het
Fuca2 T C 10: 13,381,665 (GRCm39) F193L probably benign Het
H2-Q1 T C 17: 35,539,603 (GRCm39) probably null Het
Hgh1 A G 15: 76,254,631 (GRCm39) M336V probably benign Het
Il12b T C 11: 44,298,857 (GRCm39) L104P probably benign Het
Kcnh2 A T 5: 24,537,989 (GRCm39) F125I probably benign Het
Kcnk7 A G 19: 5,756,104 (GRCm39) H110R probably benign Het
Kdm3a G A 6: 71,588,764 (GRCm39) P415L probably benign Het
Kifc3 T C 8: 95,830,077 (GRCm39) T610A probably benign Het
Krbox5 A G 13: 67,991,111 (GRCm39) probably null Het
Lmbr1l C A 15: 98,809,372 (GRCm39) probably null Het
Lmo7 T A 14: 102,157,975 (GRCm39) M1436K unknown Het
Lrp1 C T 10: 127,394,491 (GRCm39) C2574Y probably damaging Het
Med13l A G 5: 118,859,587 (GRCm39) E258G possibly damaging Het
Mesp1 T C 7: 79,442,906 (GRCm39) I124V probably damaging Het
Mrgpra2a A T 7: 47,076,934 (GRCm39) I108N probably benign Het
Nos1 G T 5: 118,033,925 (GRCm39) R349L possibly damaging Het
Or5k3 C T 16: 58,969,327 (GRCm39) T38I probably damaging Het
Or7c70 T C 10: 78,683,615 (GRCm39) I45V probably benign Het
Osgin1 T A 8: 120,168,176 (GRCm39) M1K probably null Het
Pde4dip C T 3: 97,601,379 (GRCm39) S2346N probably benign Het
Pde7a T C 3: 19,285,258 (GRCm39) M310V probably benign Het
Pigw G A 11: 84,768,585 (GRCm39) T248M probably damaging Het
Pink1 T C 4: 138,044,769 (GRCm39) T323A probably damaging Het
Polr3a C T 14: 24,511,883 (GRCm39) R891Q probably damaging Het
Prkar1b C A 5: 139,094,363 (GRCm39) C75F probably benign Het
Prss58 C T 6: 40,876,987 (GRCm39) probably null Het
Ptk2 G A 15: 73,093,658 (GRCm39) P854S possibly damaging Het
Pttg1ip2 A T 5: 5,516,631 (GRCm39) D63E possibly damaging Het
Qars1 T C 9: 108,389,971 (GRCm39) I350T probably damaging Het
Qprt T C 7: 126,707,984 (GRCm39) K149R probably damaging Het
Rasgrf1 T A 9: 89,873,651 (GRCm39) D653E probably damaging Het
Rbm26 T C 14: 105,381,703 (GRCm39) M481V possibly damaging Het
Rdx C T 9: 51,997,745 (GRCm39) T573M probably damaging Het
Rgs14 A G 13: 55,527,508 (GRCm39) probably null Het
Robo2 T C 16: 73,753,438 (GRCm39) E813G probably damaging Het
Rrbp1 A T 2: 143,791,600 (GRCm39) F1369I probably benign Het
Sh2d4b T A 14: 40,562,209 (GRCm39) T319S probably benign Het
Slc7a15 G T 12: 8,588,895 (GRCm39) N217K probably damaging Het
Stmn1 A G 4: 134,198,088 (GRCm39) K42E probably damaging Het
Tbl2 T G 5: 135,178,682 (GRCm39) W31G probably benign Het
Tmem8b T C 4: 43,669,845 (GRCm39) C114R possibly damaging Het
Tsc2 T C 17: 24,832,254 (GRCm39) S711G probably benign Het
Ttn T C 2: 76,666,904 (GRCm39) R11531G unknown Het
Ube2e3 T C 2: 78,744,085 (GRCm39) Y105H probably benign Het
Usp16 G T 16: 87,280,059 (GRCm39) C753F probably benign Het
Vmn1r13 T C 6: 57,187,239 (GRCm39) S133P possibly damaging Het
Vmn2r76 T A 7: 85,877,975 (GRCm39) Q474L probably benign Het
Wasf1 A T 10: 40,802,587 (GRCm39) T81S possibly damaging Het
Wdr82 A G 9: 106,048,532 (GRCm39) S39G probably benign Het
Zdhhc13 A G 7: 48,451,080 (GRCm39) I108V probably benign 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
R5928:Vps52 UTSW 17 34,180,100 (GRCm39) missense possibly damaging 0.85
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
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 PCR Primer
(F):5'- CTTGGTTCTGGAGAAAACCCTTG -3'
(R):5'- AAGTCTTCCTTGCTGCGTTG -3'

Sequencing Primer
(F):5'- TCACAGAGACTGCTGTCT -3'
(R):5'- GCGTTGCCTCCCCTGTG -3'
Posted On 2019-05-15