Incidental Mutation 'R5158:Vps16'
ID 396816
Institutional Source Beutler Lab
Gene Symbol Vps16
Ensembl Gene ENSMUSG00000027411
Gene Name VSP16 CORVET/HOPS core subunit
Synonyms 1810074M16Rik
MMRRC Submission 042740-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.970) question?
Stock # R5158 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 130266259-130286189 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 130283199 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Cysteine at position 531 (R531C)
Ref Sequence ENSEMBL: ENSMUSP00000028900 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028900] [ENSMUST00000128994]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000028900
AA Change: R531C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: R531C

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 noncoding transcript
Transcript: ENSMUST00000125098
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125973
Predicted Effect probably benign
Transcript: ENSMUST00000128994
SMART Domains Protein: ENSMUSP00000115899
Gene: ENSMUSG00000027411

DomainStartEndE-ValueType
Pfam:Vps16_N 4 212 3.2e-74 PFAM
Pfam:Vps16_N 205 316 1e-45 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130258
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131220
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137084
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134677
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132388
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.2%
  • 20x: 94.9%
Validation Efficiency
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: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aars2 C T 17: 45,825,755 (GRCm39) T357I probably benign Het
Abca14 A T 7: 119,852,652 (GRCm39) R872S probably benign Het
Adnp2 A G 18: 80,180,758 (GRCm39) Y47H probably damaging Het
Atp6v0d2 T C 4: 19,878,292 (GRCm39) N327S probably damaging Het
Ccdc190 A G 1: 169,760,578 (GRCm39) R69G probably benign Het
Cfap54 T C 10: 92,901,059 (GRCm39) D213G probably damaging Het
Clcn4 G A 7: 7,294,618 (GRCm39) T381I possibly damaging Het
Cobl A G 11: 12,206,198 (GRCm39) F477S possibly damaging Het
Ctdspl2 T A 2: 121,811,774 (GRCm39) V205E probably benign Het
Dhx37 A T 5: 125,492,216 (GRCm39) Y1128N probably damaging Het
Ehmt2 G A 17: 35,130,640 (GRCm39) E1085K probably damaging Het
Fam149a T G 8: 45,803,472 (GRCm39) I340L possibly damaging Het
Fut9 T A 4: 25,620,731 (GRCm39) I28F probably benign Het
Il36g T A 2: 24,082,798 (GRCm39) I191K probably damaging Het
Iqgap1 T C 7: 80,392,816 (GRCm39) N716D probably benign Het
Itgb7 T C 15: 102,125,464 (GRCm39) D672G probably benign Het
Kat6b A G 14: 21,720,054 (GRCm39) M1469V possibly damaging Het
Kif3a T C 11: 53,479,578 (GRCm39) F430L probably benign Het
L3mbtl3 T C 10: 26,179,586 (GRCm39) D523G unknown Het
Mcf2l A G 8: 13,059,715 (GRCm39) Q736R probably damaging Het
Mpl T G 4: 118,313,881 (GRCm39) D128A probably damaging Het
Myom3 T A 4: 135,492,897 (GRCm39) C149S probably damaging Het
N4bp2 A G 5: 65,965,805 (GRCm39) I1285V probably damaging Het
Nalcn T C 14: 123,753,149 (GRCm39) Q279R probably damaging Het
Ndc1 T G 4: 107,232,362 (GRCm39) S182R probably damaging Het
Ngf A T 3: 102,427,445 (GRCm39) M65L possibly damaging Het
Or2n1 T A 17: 38,486,345 (GRCm39) Y123* probably null Het
Pigb T C 9: 72,929,683 (GRCm39) Y300C probably damaging Het
Pla2g2a T G 4: 138,560,595 (GRCm39) *69G probably null Het
Ppp1r12b T C 1: 134,814,166 (GRCm39) E379G probably damaging Het
Ptdss2 T C 7: 140,731,684 (GRCm39) F164S probably benign Het
Ptprc T C 1: 138,102,822 (GRCm39) T2A possibly damaging Het
Ptprq T A 10: 107,370,565 (GRCm39) N2042I probably damaging Het
Rdh10 A T 1: 16,178,221 (GRCm39) R164S probably damaging Het
Sec31a A T 5: 100,541,180 (GRCm39) I309N probably damaging Het
Skint5 A T 4: 113,599,409 (GRCm39) I710N unknown Het
Slc25a30 A T 14: 76,008,956 (GRCm39) L26Q probably damaging Het
Sptan1 G A 2: 29,868,455 (GRCm39) V34I probably damaging Het
Sult1e1 A T 5: 87,735,453 (GRCm39) I75N probably damaging Het
Trpa1 A G 1: 14,951,885 (GRCm39) V938A probably benign Het
Zbtb22 C T 17: 34,137,423 (GRCm39) H523Y probably damaging Het
Zfp39 G A 11: 58,780,671 (GRCm39) T697M possibly 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
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
R6898:Vps16 UTSW 2 130,279,601 (GRCm39) missense possibly damaging 0.74
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'- TCTGATGGAGGCCCTTTAGG -3'
(R):5'- CTCTCAATAGCCTTGCTCAGTG -3'

Sequencing Primer
(F):5'- CCCTTTAGGATTGGGCAGGTAAG -3'
(R):5'- TGCTCAGTGCCAGTTTGC -3'
Posted On 2016-06-21