Incidental Mutation 'R6898:Vps16'
ID 538440
Institutional Source Beutler Lab
Gene Symbol Vps16
Ensembl Gene ENSMUSG00000027411
Gene Name VSP16 CORVET/HOPS core subunit
Synonyms 1810074M16Rik
MMRRC Submission 044992-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.970) question?
Stock # R6898 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 130266259-130286189 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 130279601 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 38 (V38A)
Ref Sequence ENSEMBL: ENSMUSP00000028900 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028900] [ENSMUST00000128994]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000028900
AA Change: V38A

PolyPhen 2 Score 0.737 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: V38A

DomainStartEndE-ValueType
Pfam:Vps16_N 4 420 1e-166 PFAM
low complexity region 452 462 N/A INTRINSIC
Pfam:Vps16_C 517 835 5.5e-150 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000128994
AA Change: V38A

PolyPhen 2 Score 0.541 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000115899
Gene: ENSMUSG00000027411
AA Change: V38A

DomainStartEndE-ValueType
Pfam:Vps16_N 4 212 3.2e-74 PFAM
Pfam:Vps16_N 205 316 1e-45 PFAM
Meta Mutation Damage Score 0.2176 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.2%
  • 20x: 97.5%
Validation Efficiency 100% (46/46)
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 Vps16 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. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]
PHENOTYPE: Mice with a homozygous point mutation in exon 3 display impaired motor function. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ankrd7 G T 6: 18,868,100 (GRCm39) probably null Het
Aoc1l2 A T 6: 48,907,975 (GRCm39) Y325F probably damaging Het
Aplnr A T 2: 84,970,155 (GRCm39) probably benign Het
Capns2 T C 8: 93,628,605 (GRCm39) S165P probably damaging Het
Col25a1 T C 3: 130,378,377 (GRCm39) probably null Het
Crocc2 T C 1: 93,143,304 (GRCm39) V1302A probably benign Het
Cul9 C A 17: 46,821,952 (GRCm39) R1841M possibly damaging Het
Dnhd1 T C 7: 105,336,584 (GRCm39) L1213P probably damaging Het
Dscam A T 16: 96,631,100 (GRCm39) I305K probably benign Het
Dsp A G 13: 38,376,193 (GRCm39) E1326G possibly damaging Het
Eif4a3l1 T A 6: 136,305,617 (GRCm39) V26E probably benign Het
Emc9 A G 14: 55,822,367 (GRCm39) probably null Het
Eppk1 A C 15: 75,996,126 (GRCm39) S252A probably benign Het
Fn1 T A 1: 71,639,572 (GRCm39) T1830S probably damaging Het
Fryl A T 5: 73,179,485 (GRCm39) M2974K probably damaging Het
Gdpd3 C A 7: 126,370,201 (GRCm39) S250* probably null Het
Gnl3 A T 14: 30,735,136 (GRCm39) S485R probably benign Het
Gpt2 G A 8: 86,244,681 (GRCm39) E325K probably benign Het
Hsd17b3 T C 13: 64,207,339 (GRCm39) Y234C probably benign Het
Lima1 T C 15: 99,679,148 (GRCm39) H271R possibly damaging Het
Nfu1 G A 6: 86,994,034 (GRCm39) probably null Het
Noto A G 6: 85,404,942 (GRCm39) E97G probably damaging Het
Ntng1 T C 3: 109,779,534 (GRCm39) K348E probably damaging Het
Or2y13 G A 11: 49,414,536 (GRCm39) probably benign Het
Or4a70 C T 2: 89,324,594 (GRCm39) G21R possibly damaging Het
Osmr C A 15: 6,845,364 (GRCm39) V801F probably damaging Het
Papln A G 12: 83,824,234 (GRCm39) E554G probably benign Het
Pitrm1 T C 13: 6,605,495 (GRCm39) L175P probably damaging Het
Pramel22 A T 4: 143,382,053 (GRCm39) N214K probably damaging Het
Pramel7 T C 2: 87,320,070 (GRCm39) T408A probably damaging Het
Serinc2 A T 4: 130,149,235 (GRCm39) D322E probably benign Het
Setx T C 2: 29,038,120 (GRCm39) V1535A probably benign Het
Sgce A T 6: 4,689,666 (GRCm39) V389E probably damaging Het
Snx11 G A 11: 96,659,888 (GRCm39) T267I probably benign Het
Spata6l T G 19: 28,921,688 (GRCm39) Q146P probably benign Het
Specc1 G A 11: 62,009,162 (GRCm39) S306N probably benign Het
Spocd1 A G 4: 129,850,305 (GRCm39) probably benign Het
St7 T A 6: 17,854,945 (GRCm39) V294D probably damaging Het
Stab1 C T 14: 30,880,920 (GRCm39) R624Q probably benign Het
Tcf21 T C 10: 22,695,403 (GRCm39) I134V probably benign Het
Tgfb2 T A 1: 186,364,697 (GRCm39) I266F probably damaging Het
Tgfbr3l A G 8: 4,300,365 (GRCm39) I209M possibly damaging Het
Tmcc3 A G 10: 94,387,034 (GRCm39) probably null Het
Toe1 A G 4: 116,664,671 (GRCm39) S16P probably damaging Het
Wnk2 G T 13: 49,224,557 (GRCm39) D1001E probably damaging Het
Other mutations in Vps16
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01327:Vps16 APN 2 130,279,616 (GRCm39) missense probably benign 0.19
IGL01400:Vps16 APN 2 130,280,273 (GRCm39) missense possibly damaging 0.73
IGL01542:Vps16 APN 2 130,280,314 (GRCm39) missense probably damaging 0.97
IGL02011:Vps16 APN 2 130,283,399 (GRCm39) missense probably benign 0.04
IGL02192:Vps16 APN 2 130,282,852 (GRCm39) missense probably damaging 0.98
IGL02220:Vps16 APN 2 130,283,573 (GRCm39) missense possibly damaging 0.85
IGL02587:Vps16 APN 2 130,281,636 (GRCm39) critical splice donor site probably null
R0427:Vps16 UTSW 2 130,280,770 (GRCm39) missense probably benign 0.00
R0507:Vps16 UTSW 2 130,279,632 (GRCm39) critical splice donor site probably null
R1550:Vps16 UTSW 2 130,282,260 (GRCm39) missense probably benign 0.09
R1789:Vps16 UTSW 2 130,285,520 (GRCm39) missense probably benign 0.42
R3895:Vps16 UTSW 2 130,280,596 (GRCm39) missense possibly damaging 0.96
R3981:Vps16 UTSW 2 130,284,514 (GRCm39) missense possibly damaging 0.77
R4092:Vps16 UTSW 2 130,281,832 (GRCm39) missense probably damaging 1.00
R4555:Vps16 UTSW 2 130,285,496 (GRCm39) missense probably damaging 1.00
R4569:Vps16 UTSW 2 130,284,124 (GRCm39) missense probably benign
R4803:Vps16 UTSW 2 130,280,030 (GRCm39) missense probably benign 0.27
R4835:Vps16 UTSW 2 130,280,220 (GRCm39) splice site probably benign
R5022:Vps16 UTSW 2 130,281,372 (GRCm39) missense probably benign 0.07
R5023:Vps16 UTSW 2 130,281,372 (GRCm39) missense probably benign 0.07
R5057:Vps16 UTSW 2 130,281,372 (GRCm39) missense probably benign 0.07
R5158:Vps16 UTSW 2 130,283,199 (GRCm39) missense probably damaging 1.00
R5177:Vps16 UTSW 2 130,285,288 (GRCm39) nonsense probably null
R5540:Vps16 UTSW 2 130,284,305 (GRCm39) missense probably benign 0.00
R5680:Vps16 UTSW 2 130,282,244 (GRCm39) missense possibly damaging 0.64
R5689:Vps16 UTSW 2 130,281,011 (GRCm39) nonsense probably null
R5690:Vps16 UTSW 2 130,281,011 (GRCm39) nonsense probably null
R5926:Vps16 UTSW 2 130,285,476 (GRCm39) missense probably damaging 0.97
R5992:Vps16 UTSW 2 130,266,369 (GRCm39) critical splice donor site probably null
R6135:Vps16 UTSW 2 130,280,573 (GRCm39) missense possibly damaging 0.57
R6370:Vps16 UTSW 2 130,285,304 (GRCm39) missense probably damaging 1.00
R7378:Vps16 UTSW 2 130,280,099 (GRCm39) missense probably damaging 1.00
R7487:Vps16 UTSW 2 130,280,977 (GRCm39) nonsense probably null
R7641:Vps16 UTSW 2 130,282,448 (GRCm39) missense probably benign 0.28
R7720:Vps16 UTSW 2 130,283,623 (GRCm39) nonsense probably null
R8246:Vps16 UTSW 2 130,280,793 (GRCm39) missense probably damaging 1.00
R8363:Vps16 UTSW 2 130,284,161 (GRCm39) missense probably benign 0.08
R9092:Vps16 UTSW 2 130,281,593 (GRCm39) missense probably damaging 0.99
R9128:Vps16 UTSW 2 130,266,319 (GRCm39) missense possibly damaging 0.51
R9352:Vps16 UTSW 2 130,283,823 (GRCm39) critical splice donor site probably null
R9406:Vps16 UTSW 2 130,283,425 (GRCm39) critical splice donor site probably null
R9508:Vps16 UTSW 2 130,284,361 (GRCm39) missense possibly damaging 0.94
R9800:Vps16 UTSW 2 130,282,405 (GRCm39) missense probably benign 0.02
RF021:Vps16 UTSW 2 130,280,129 (GRCm39) missense probably benign 0.09
Z1177:Vps16 UTSW 2 130,283,346 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCTCTCATGTGGGGAGGAAAAG -3'
(R):5'- AGAACCTCAGGACCCATGTAAG -3'

Sequencing Primer
(F):5'- GACTCCTCCACTAGATAAACGGTAG -3'
(R):5'- AAGGTAGGCCTCCTGGATCATTTAC -3'
Posted On 2018-11-06