Incidental Mutation 'PIT4696001:Vps11'
ID 556799
Institutional Source Beutler Lab
Gene Symbol Vps11
Ensembl Gene ENSMUSG00000032127
Gene Name VPS11, CORVET/HOPS core subunit
Synonyms 1200011A11Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # PIT4696001 (G1)
Quality Score 225.009
Status Validated
Chromosome 9
Chromosomal Location 44259046-44272967 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 44269486 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 255 (V255A)
Ref Sequence ENSEMBL: ENSMUSP00000034644 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034644] [ENSMUST00000213249] [ENSMUST00000213740] [ENSMUST00000214510]
AlphaFold Q91W86
Predicted Effect possibly damaging
Transcript: ENSMUST00000034644
AA Change: V255A

PolyPhen 2 Score 0.889 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000034644
Gene: ENSMUSG00000032127
AA Change: V255A

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 probably benign
Transcript: ENSMUST00000213249
Predicted Effect probably benign
Transcript: ENSMUST00000213740
Predicted Effect
Predicted Effect probably damaging
Transcript: ENSMUST00000214510
AA Change: V255A

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
Coding Region Coverage
  • 1x: 93.5%
  • 3x: 91.0%
  • 10x: 86.2%
  • 20x: 75.9%
Validation Efficiency 100% (57/57)
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acsm3 G A 7: 119,384,209 (GRCm39) probably null Het
Adam20 T A 8: 41,247,985 (GRCm39) Y32N probably benign Het
Adm T C 7: 110,227,496 (GRCm39) V4A probably benign Het
Anpep G A 7: 79,489,212 (GRCm39) T320I possibly damaging Het
Atp8b1 T C 18: 64,672,341 (GRCm39) S1008G possibly damaging Het
B9d1 T A 11: 61,396,069 (GRCm39) M12K possibly damaging Het
Cad T C 5: 31,229,438 (GRCm39) L1435P probably damaging Het
Cat T C 2: 103,302,157 (GRCm39) D180G probably damaging Het
Cntln C T 4: 84,892,237 (GRCm39) T374M probably damaging Het
Cyp2a5 G A 7: 26,540,404 (GRCm39) R339Q probably benign Het
Defa22 T C 8: 21,652,352 (GRCm39) L6P probably damaging Het
Dr1 T A 5: 108,417,604 (GRCm39) I50K probably damaging Het
Eln C T 5: 134,766,032 (GRCm39) G57E unknown Het
Fat4 T C 3: 38,943,153 (GRCm39) I682T probably benign Het
Fat4 C A 3: 39,036,506 (GRCm39) A3386E probably damaging Het
Fcgr3 T A 1: 170,885,319 (GRCm39) Y102F probably damaging Het
Gm5930 A T 14: 44,573,993 (GRCm39) L115M probably damaging Het
Herc1 T A 9: 66,386,291 (GRCm39) V3748D probably damaging Het
Ino80d A G 1: 63,125,145 (GRCm39) S106P probably benign Het
Kcns3 C T 12: 11,142,749 (GRCm39) probably benign Het
Kndc1 T A 7: 139,512,830 (GRCm39) L1527Q probably damaging Het
Lepr T G 4: 101,637,180 (GRCm39) S690A probably benign Het
Lrfn5 T C 12: 61,890,343 (GRCm39) F544S probably damaging Het
Mapkap1 C A 2: 34,509,861 (GRCm39) H450Q probably damaging Het
Mdm1 A G 10: 117,994,445 (GRCm39) T485A probably benign Het
Megf10 T C 18: 57,410,760 (GRCm39) C690R probably damaging Het
Myo7a A G 7: 97,712,806 (GRCm39) M1723T probably benign Het
Nrip3 A T 7: 109,364,714 (GRCm39) C137* probably null Het
Or5w22 T A 2: 87,363,124 (GRCm39) I249N probably damaging Het
Pde4a T A 9: 21,122,297 (GRCm39) M731K probably benign Het
Pebp1 A G 5: 117,421,527 (GRCm39) L117P probably damaging Het
Phc2 T C 4: 128,598,995 (GRCm39) Y51H probably damaging Het
Ppp2r5b A G 19: 6,284,713 (GRCm39) F50S probably benign Het
Prpf4b A G 13: 35,083,825 (GRCm39) S865G probably benign Het
Ptpn5 C T 7: 46,738,354 (GRCm39) V243M probably benign Het
Rora T C 9: 69,271,841 (GRCm39) L273P possibly damaging Het
Rtp4 T A 16: 23,432,204 (GRCm39) S245R probably benign Het
Scgb2b20 C T 7: 33,063,985 (GRCm39) G95D probably benign Het
Sec24b A G 3: 129,788,040 (GRCm39) V820A probably benign Het
Sim2 A G 16: 93,895,168 (GRCm39) D62G possibly damaging Het
Slc17a4 A T 13: 24,084,497 (GRCm39) V429D probably benign Het
Sp2 T C 11: 96,852,799 (GRCm39) T42A probably damaging Het
Spata3 G A 1: 85,952,169 (GRCm39) R141Q unknown Het
Sptbn2 A T 19: 4,795,605 (GRCm39) E1658D probably benign Het
Tcaf1 T C 6: 42,655,473 (GRCm39) H501R probably benign Het
Tec G A 5: 72,931,178 (GRCm39) T262M possibly damaging Het
Timm9 A T 12: 71,172,305 (GRCm39) N22K possibly damaging Het
Tln1 C T 4: 43,542,701 (GRCm39) probably null Het
Tmbim4 A G 10: 120,053,529 (GRCm39) I109M probably benign Het
Tmc7 T C 7: 118,163,566 (GRCm39) K110E probably benign Het
Tmem107 C T 11: 68,963,399 (GRCm39) P136L probably benign Het
Ttc21b T C 2: 66,061,563 (GRCm39) probably null Het
Ubd A C 17: 37,506,335 (GRCm39) T74P probably damaging Het
Vsnl1 T C 12: 11,376,448 (GRCm39) T146A probably benign Het
Wdr38 G T 2: 38,889,984 (GRCm39) probably null Het
Yes1 T A 5: 32,841,969 (GRCm39) S498T possibly damaging Het
Zc3h13 G A 14: 75,569,323 (GRCm39) R1390H probably damaging Het
Zscan4b A G 7: 10,635,949 (GRCm39) V126A possibly 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
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
R4564:Vps11 UTSW 9 44,272,894 (GRCm39) missense probably damaging 1.00
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'- TAGCTGGATCGAGGCTTAGG -3'
(R):5'- AAGGCTGCCTCTTCAAAGGG -3'

Sequencing Primer
(F):5'- ATAGTTCTGGGGAATAAGTCAGTCC -3'
(R):5'- AAAGGGAGCCTGCTAACTTCTTC -3'
Posted On 2019-06-07