Incidental Mutation 'IGL00946:Vps52'
ID29300
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Vps52
Ensembl Gene ENSMUSG00000024319
Gene NameVPS52 GARP complex subunit
Synonymstclw5, ARE1, Sacm2l, D430041K17Rik, tcl-w5
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #IGL00946
Quality Score
Status
Chromosome17
Chromosomal Location33955812-33966984 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 33956958 bp
ZygosityHeterozygous
Amino Acid Change Leucine to Proline at position 40 (L40P)
Ref Sequence ENSEMBL: ENSMUSP00000025178 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000008812] [ENSMUST00000025178] [ENSMUST00000173196] [ENSMUST00000174609]
Predicted Effect probably benign
Transcript: ENSMUST00000008812
SMART Domains Protein: ENSMUSP00000008812
Gene: ENSMUSG00000008668

DomainStartEndE-ValueType
Pfam:Ribosomal_S13 14 142 2.2e-59 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000025178
AA Change: L40P

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: L40P

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: ENSMUST00000172550
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172558
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172799
Predicted Effect possibly damaging
Transcript: ENSMUST00000173196
AA Change: L40P

PolyPhen 2 Score 0.720 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: L40P

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: ENSMUST00000173323
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173445
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174175
Predicted Effect probably benign
Transcript: ENSMUST00000174609
SMART Domains Protein: ENSMUSP00000138296
Gene: ENSMUSG00000008668

DomainStartEndE-ValueType
Pfam:Ribosomal_S13 14 107 2.1e-21 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174620
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174662
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174745
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174758
Coding Region Coverage
Validation Efficiency
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: 33 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ahdc1 T C 4: 133,063,062 I538T probably benign Het
Bmp10 A T 6: 87,434,362 Q379L probably damaging Het
Cacna2d4 G A 6: 119,271,915 A446T possibly damaging Het
Chrdl1 G A X: 143,294,168 probably benign Het
Crtc2 A G 3: 90,260,805 H370R probably damaging Het
Cubn T C 2: 13,456,623 T698A probably damaging Het
Deup1 T C 9: 15,561,238 T593A possibly damaging Het
Dus1l T C 11: 120,793,875 T157A probably damaging Het
Efcab6 T C 15: 84,018,696 N151S probably benign Het
Eif2b5 T A 16: 20,505,252 H448Q probably benign Het
Epha8 T C 4: 136,945,810 D221G probably damaging Het
Eprs G A 1: 185,407,701 G996S probably benign Het
Fn1 G A 1: 71,645,540 probably benign Het
Gfpt1 A G 6: 87,050,942 Y10C probably damaging Het
Ghitm C T 14: 37,125,246 M290I probably benign Het
Gpd2 T C 2: 57,268,084 probably null Het
Htr2a T A 14: 74,706,142 Y387* probably null Het
Lrrc7 T A 3: 158,161,356 Q916L probably benign Het
Mfsd9 A C 1: 40,773,780 D458E probably benign Het
Nmb T C 7: 80,902,460 I123M probably benign Het
Nrap A T 19: 56,340,626 probably null Het
Olfr1299 T A 2: 111,665,144 M306K probably benign Het
Olfr1406 A T 1: 173,183,623 D270E probably benign Het
Olfr984 A G 9: 40,101,154 I112T probably benign Het
Pola1 T C X: 93,480,539 I1165M probably benign Het
Sdk1 G T 5: 142,084,613 probably null Het
Selenon T A 4: 134,539,726 probably benign Het
Stk39 T A 2: 68,314,564 T389S possibly damaging Het
Tmx3 A G 18: 90,540,054 E410G possibly damaging Het
Utp20 A T 10: 88,748,315 V2660E possibly damaging Het
Wdr25 C T 12: 109,025,027 S380F possibly damaging Het
Xpo7 T C 14: 70,671,658 T808A probably benign Het
Zc3h14 T C 12: 98,759,883 probably benign Het
Other mutations in Vps52
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01098:Vps52 APN 17 33962730 missense possibly damaging 0.90
IGL01705:Vps52 APN 17 33966068 missense probably damaging 1.00
IGL01722:Vps52 APN 17 33961615 nonsense probably null
IGL02992:Vps52 APN 17 33958350 missense probably damaging 0.97
IGL03279:Vps52 APN 17 33957874 missense probably damaging 0.96
R0363:Vps52 UTSW 17 33962117 missense probably benign 0.26
R0762:Vps52 UTSW 17 33960011 missense probably damaging 1.00
R1065:Vps52 UTSW 17 33961239 missense probably benign 0.02
R1506:Vps52 UTSW 17 33957894 missense probably damaging 1.00
R3760:Vps52 UTSW 17 33960188 missense possibly damaging 0.64
R4714:Vps52 UTSW 17 33961179 missense probably benign 0.25
R5381:Vps52 UTSW 17 33958301 missense possibly damaging 0.77
R5590:Vps52 UTSW 17 33961221 missense probably benign 0.01
R5928:Vps52 UTSW 17 33961126 missense possibly damaging 0.85
R6003:Vps52 UTSW 17 33956094 start codon destroyed probably null 0.01
R6302:Vps52 UTSW 17 33963215 missense probably damaging 1.00
R6574:Vps52 UTSW 17 33962478 missense probably null 0.34
R6695:Vps52 UTSW 17 33963199 nonsense probably null
R6888:Vps52 UTSW 17 33963206 missense probably benign 0.06
R7022:Vps52 UTSW 17 33959319 missense probably benign 0.04
R7136:Vps52 UTSW 17 33965288 missense probably benign 0.00
R7380:Vps52 UTSW 17 33958309 missense possibly damaging 0.82
R7727:Vps52 UTSW 17 33962134 missense probably benign 0.21
R7888:Vps52 UTSW 17 33965751 missense probably damaging 0.98
R7971:Vps52 UTSW 17 33965751 missense probably damaging 0.98
Posted On2013-04-17