Incidental Mutation 'IGL01098:Vps52'
ID 53059
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Vps52
Ensembl Gene ENSMUSG00000024319
Gene Name VPS52 GARP complex subunit
Synonyms tclw5, ARE1, D430041K17Rik, tcl-w5, Sacm2l
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL01098
Quality Score
Status
Chromosome 17
Chromosomal Location 34174786-34186009 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 34181704 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 510 (T510I)
Ref Sequence ENSEMBL: ENSMUSP00000025178 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025178] [ENSMUST00000173196]
AlphaFold Q8C754
Predicted Effect possibly damaging
Transcript: ENSMUST00000025178
AA Change: T510I

PolyPhen 2 Score 0.905 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: T510I

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: T442I

PolyPhen 2 Score 0.507 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: T442I

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
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: 37 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921509C19Rik T C 2: 151,315,453 (GRCm39) D75G possibly damaging Het
Brip1 G T 11: 85,999,688 (GRCm39) R765S possibly damaging Het
Btbd16 T C 7: 130,424,975 (GRCm39) I452T probably damaging Het
Cdc42ep4 T G 11: 113,620,328 (GRCm39) D21A probably damaging Het
Cdx2 T A 5: 147,243,792 (GRCm39) M1L possibly damaging Het
Cfap206 C T 4: 34,721,562 (GRCm39) S162N probably damaging Het
Csmd2 C T 4: 127,952,845 (GRCm39) T98M probably damaging Het
Cyp26a1 A T 19: 37,688,450 (GRCm39) Q324L probably benign Het
Etaa1 A G 11: 17,896,059 (GRCm39) V686A probably damaging Het
Gpr6 G A 10: 40,946,739 (GRCm39) T281I probably damaging Het
Herc1 T A 9: 66,369,204 (GRCm39) probably null Het
Lama2 A T 10: 26,907,108 (GRCm39) I2351N possibly damaging Het
Lman1 A G 18: 66,124,711 (GRCm39) F343L probably damaging Het
Lmo1 A G 7: 108,742,657 (GRCm39) probably benign Het
Lrrc17 T A 5: 21,780,269 (GRCm39) F414L probably benign Het
Man2b2 A T 5: 36,972,900 (GRCm39) L538Q probably damaging Het
Map3k9 A G 12: 81,770,928 (GRCm39) S910P probably damaging Het
Mapk1ip1 G A 7: 138,438,191 (GRCm39) P80S probably damaging Het
Mindy4 G T 6: 55,261,727 (GRCm39) probably benign Het
Msh4 A T 3: 153,583,619 (GRCm39) probably benign Het
Mta2 A G 19: 8,924,081 (GRCm39) D187G probably damaging Het
Olfml2a A G 2: 38,837,226 (GRCm39) probably null Het
Pink1 A T 4: 138,047,408 (GRCm39) probably null Het
Plekha6 T C 1: 133,209,903 (GRCm39) F575L possibly damaging Het
Rpe C A 1: 66,745,674 (GRCm39) D71E probably benign Het
Slc5a7 C T 17: 54,599,988 (GRCm39) A142T probably benign Het
Sptbn1 C T 11: 30,109,385 (GRCm39) R70K probably damaging Het
Taf1c G T 8: 120,329,580 (GRCm39) Q159K probably damaging Het
Tgfb1i1 T C 7: 127,851,693 (GRCm39) F311S probably damaging Het
Tmc8 T C 11: 117,683,389 (GRCm39) V648A possibly damaging Het
Tmed8 G T 12: 87,223,445 (GRCm39) A98E probably benign Het
Tmem200a A G 10: 25,870,041 (GRCm39) I76T probably damaging Het
Vmn2r104 T C 17: 20,268,358 (GRCm39) E37G probably benign Het
Vmn2r18 A T 5: 151,496,296 (GRCm39) V474E probably damaging Het
Wwox G T 8: 115,172,118 (GRCm39) G71* probably null Het
Zer1 C T 2: 29,998,232 (GRCm39) probably null Het
Zfp296 A T 7: 19,311,845 (GRCm39) K117N possibly damaging Het
Other mutations in Vps52
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00946:Vps52 APN 17 34,175,932 (GRCm39) missense possibly damaging 0.96
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
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
Posted On 2013-06-21