Incidental Mutation 'R4564:Vps11'
ID 343246
Institutional Source Beutler Lab
Gene Symbol Vps11
Ensembl Gene ENSMUSG00000032127
Gene Name VPS11, CORVET/HOPS core subunit
Synonyms 1200011A11Rik
MMRRC Submission 041789-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4564 (G1)
Quality Score 223
Status Validated
Chromosome 9
Chromosomal Location 44259046-44272967 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 44272894 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Serine at position 12 (F12S)
Ref Sequence ENSEMBL: ENSMUSP00000149457 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034644] [ENSMUST00000213249] [ENSMUST00000213740] [ENSMUST00000214510]
AlphaFold Q91W86
Predicted Effect probably damaging
Transcript: ENSMUST00000034644
AA Change: F12S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000034644
Gene: ENSMUSG00000032127
AA Change: F12S

DomainStartEndE-ValueType
low complexity region 26 40 N/A INTRINSIC
SCOP:d1erja_ 59 292 3e-10 SMART
Blast:WD40 73 117 2e-22 BLAST
Blast:WD40 125 168 9e-24 BLAST
Blast:WD40 175 214 6e-16 BLAST
Blast:WD40 219 259 2e-20 BLAST
Pfam:Clathrin 412 548 2.7e-16 PFAM
coiled coil region 775 813 N/A INTRINSIC
RING 822 860 6.14e-5 SMART
Pfam:VPS11_C 862 908 5.2e-22 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000157403
Predicted Effect probably benign
Transcript: ENSMUST00000213249
Predicted Effect possibly damaging
Transcript: ENSMUST00000213740
AA Change: F12S

PolyPhen 2 Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)
Predicted Effect probably benign
Transcript: ENSMUST00000214460
Predicted Effect probably damaging
Transcript: ENSMUST00000214510
AA Change: F12S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000216089
Meta Mutation Damage Score 0.2121 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.6%
Validation Efficiency 97% (58/60)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps11 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
Allele List at MGI

All alleles(8) : Targeted(4) Gene trapped(4)

Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Atad3a C T 4: 155,831,766 (GRCm39) probably null Het
Bach2 T G 4: 32,563,338 (GRCm39) S602A probably damaging Het
Ccl19 G T 4: 42,756,295 (GRCm39) S12R probably damaging Het
Cfap54 T C 10: 92,675,402 (GRCm39) probably benign Het
Cndp1 T A 18: 84,640,411 (GRCm39) I265F probably damaging Het
Cnot3 G A 7: 3,656,257 (GRCm39) R181H probably damaging Het
Dicer1 T A 12: 104,671,010 (GRCm39) K1011* probably null Het
Dip2b G A 15: 100,055,139 (GRCm39) W99* probably null Het
Fpr-rs6 A T 17: 20,403,168 (GRCm39) Y64* probably null Het
Fubp1 C A 3: 151,928,573 (GRCm39) Y480* probably null Het
Gfra1 T C 19: 58,227,682 (GRCm39) probably null Het
Gm10770 T C 2: 150,020,831 (GRCm39) T229A probably benign Het
Gm826 A C 2: 160,153,913 (GRCm39) probably benign Het
Gpd2 G A 2: 57,197,095 (GRCm39) V217I possibly damaging Het
Hectd4 T C 5: 121,488,494 (GRCm39) I3595T probably benign Het
Lmln A G 16: 32,930,226 (GRCm39) E561G probably benign Het
Lrrc71 T A 3: 87,652,715 (GRCm39) probably benign Het
Man2a2 T A 7: 80,018,586 (GRCm39) Y91F probably benign Het
Map4k4 A G 1: 40,028,135 (GRCm39) T319A probably damaging Het
Mcm6 G T 1: 128,271,196 (GRCm39) H474Q probably damaging Het
Mn1 C G 5: 111,568,533 (GRCm39) N834K possibly damaging Het
Mslnl G A 17: 25,961,908 (GRCm39) V128M probably damaging Het
Niban3 T C 8: 72,057,704 (GRCm39) probably benign Het
Npas2 A G 1: 39,326,647 (GRCm39) D44G probably damaging Het
Npc1 C T 18: 12,324,789 (GRCm39) G1235R probably damaging Het
Olfml2a C T 2: 38,850,306 (GRCm39) T674I probably benign Het
Or4f58 A G 2: 111,852,112 (GRCm39) L29P possibly damaging Het
Pgap6 A G 17: 26,336,837 (GRCm39) R252G possibly damaging Het
Plxnb1 C T 9: 108,942,488 (GRCm39) A1779V probably benign Het
Ppil3 T A 1: 58,470,481 (GRCm39) D123V probably damaging Het
Prr23a3 A G 9: 98,747,190 (GRCm39) E48G probably damaging Het
Prr5l T C 2: 101,577,094 (GRCm39) E110G probably damaging Het
Ptgir A G 7: 16,640,794 (GRCm39) M29V possibly damaging Het
R3hdm1 C T 1: 128,149,396 (GRCm39) T839M probably benign Het
Rasgrf2 G A 13: 92,033,773 (GRCm39) Q544* probably null Het
Riok3 C A 18: 12,281,936 (GRCm39) R302S probably damaging Het
Rnf145 A G 11: 44,439,635 (GRCm39) K144E probably benign Het
Sin3b A C 8: 73,480,209 (GRCm39) T904P probably damaging Het
Skint4 C T 4: 111,977,066 (GRCm39) T152M probably damaging Het
Slc22a2 A G 17: 12,828,943 (GRCm39) I350V probably benign Het
Slc6a11 G T 6: 114,108,323 (GRCm39) G29V probably benign Het
Speg A C 1: 75,368,478 (GRCm39) H676P probably damaging Het
St6gal2 T A 17: 55,789,648 (GRCm39) H227Q probably damaging Het
Strn3 A G 12: 51,680,404 (GRCm39) S399P probably benign Het
Tbc1d1 A G 5: 64,330,827 (GRCm39) E2G probably damaging Het
Tecpr2 T A 12: 110,921,219 (GRCm39) M1264K probably benign Het
Trpm6 T C 19: 18,809,961 (GRCm39) L1119P possibly damaging Het
Upf2 A C 2: 6,032,123 (GRCm39) T890P unknown Het
Upk1b T A 16: 38,600,469 (GRCm39) K170N probably benign Het
Vmn1r78 A T 7: 11,886,485 (GRCm39) Y32F probably damaging Het
Zfp318 T A 17: 46,723,741 (GRCm39) C1915S possibly damaging Het
Zfp346 A C 13: 55,261,520 (GRCm39) R103S probably damaging Het
Other mutations in Vps11
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01977:Vps11 APN 9 44,267,516 (GRCm39) splice site probably benign
IGL03135:Vps11 APN 9 44,267,653 (GRCm39) missense probably benign 0.39
PIT4696001:Vps11 UTSW 9 44,269,486 (GRCm39) missense possibly damaging 0.89
R0042:Vps11 UTSW 9 44,267,588 (GRCm39) nonsense probably null
R0042:Vps11 UTSW 9 44,267,588 (GRCm39) nonsense probably null
R0122:Vps11 UTSW 9 44,265,809 (GRCm39) missense probably damaging 1.00
R0335:Vps11 UTSW 9 44,265,135 (GRCm39) missense probably null 0.02
R0714:Vps11 UTSW 9 44,270,953 (GRCm39) missense possibly damaging 0.90
R1068:Vps11 UTSW 9 44,264,316 (GRCm39) missense probably damaging 1.00
R1873:Vps11 UTSW 9 44,271,233 (GRCm39) missense probably damaging 1.00
R1991:Vps11 UTSW 9 44,270,524 (GRCm39) missense probably damaging 0.97
R2068:Vps11 UTSW 9 44,269,613 (GRCm39) missense probably damaging 0.99
R2084:Vps11 UTSW 9 44,264,558 (GRCm39) missense probably benign 0.14
R2103:Vps11 UTSW 9 44,270,524 (GRCm39) missense probably damaging 0.97
R2119:Vps11 UTSW 9 44,260,294 (GRCm39) missense probably benign 0.01
R4160:Vps11 UTSW 9 44,267,017 (GRCm39) missense probably damaging 0.98
R4161:Vps11 UTSW 9 44,267,017 (GRCm39) missense probably damaging 0.98
R4879:Vps11 UTSW 9 44,264,597 (GRCm39) missense probably benign
R5629:Vps11 UTSW 9 44,267,673 (GRCm39) missense probably damaging 1.00
R5910:Vps11 UTSW 9 44,270,432 (GRCm39) splice site probably null
R5988:Vps11 UTSW 9 44,265,221 (GRCm39) missense probably benign 0.01
R6430:Vps11 UTSW 9 44,272,847 (GRCm39) missense probably benign 0.11
R7002:Vps11 UTSW 9 44,266,376 (GRCm39) missense probably damaging 1.00
R7147:Vps11 UTSW 9 44,266,379 (GRCm39) nonsense probably null
R7237:Vps11 UTSW 9 44,265,803 (GRCm39) missense probably damaging 1.00
R7261:Vps11 UTSW 9 44,265,800 (GRCm39) missense probably damaging 1.00
R7577:Vps11 UTSW 9 44,260,258 (GRCm39) missense probably benign 0.01
R8093:Vps11 UTSW 9 44,267,529 (GRCm39) missense probably damaging 1.00
R8142:Vps11 UTSW 9 44,265,852 (GRCm39) missense probably benign 0.05
R8238:Vps11 UTSW 9 44,264,057 (GRCm39) missense probably benign 0.08
R8366:Vps11 UTSW 9 44,267,052 (GRCm39) nonsense probably null
R8374:Vps11 UTSW 9 44,267,706 (GRCm39) missense probably benign
R8731:Vps11 UTSW 9 44,265,756 (GRCm39) missense probably benign 0.00
R8742:Vps11 UTSW 9 44,267,070 (GRCm39) utr 3 prime probably benign
R9420:Vps11 UTSW 9 44,267,719 (GRCm39) missense probably benign 0.14
R9474:Vps11 UTSW 9 44,260,290 (GRCm39) nonsense probably null
R9625:Vps11 UTSW 9 44,265,738 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TGAGGAAAGAAACACCTCCG -3'
(R):5'- CACCACTCTCTTGAAGGACG -3'

Sequencing Primer
(F):5'- TCCGAAAGAAGGATATCTCCAAAG -3'
(R):5'- GGACGTTGTCAGTCCTAACAAGATC -3'
Posted On 2015-09-24