Incidental Mutation 'R5680:Vps16'
ID 442961
Institutional Source Beutler Lab
Gene Symbol Vps16
Ensembl Gene ENSMUSG00000027411
Gene Name VSP16 CORVET/HOPS core subunit
Synonyms 1810074M16Rik
MMRRC Submission 043177-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.970) question?
Stock # R5680 (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 A at 130282244 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Asparagine at position 389 (H389N)
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: H389N

PolyPhen 2 Score 0.639 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: H389N

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: ENSMUST00000132388
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134677
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.6%
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: 39 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3425401B19Rik T A 14: 32,384,010 (GRCm39) R652W probably damaging Het
Abca6 A G 11: 110,127,471 (GRCm39) F362S possibly damaging Het
Adcy1 G A 11: 7,059,020 (GRCm39) V309M probably damaging Het
Agap2 A G 10: 126,923,880 (GRCm39) K752E unknown Het
Ahdc1 T A 4: 132,792,907 (GRCm39) F1383I probably benign Het
Ano5 G A 7: 51,233,562 (GRCm39) R658H possibly damaging Het
Atn1 A T 6: 124,724,778 (GRCm39) S152T possibly damaging Het
Bcl11a G A 11: 24,114,264 (GRCm39) V536M possibly damaging Het
Cdc20 T C 4: 118,290,264 (GRCm39) T466A probably damaging Het
Cecr2 C G 6: 120,738,387 (GRCm39) T1010R probably benign Het
Cfap54 A T 10: 92,814,879 (GRCm39) L1318* probably null Het
Colec11 A G 12: 28,644,730 (GRCm39) S249P probably damaging Het
Dnah6 A G 6: 73,126,508 (GRCm39) V1273A probably damaging Het
G3bp2 T C 5: 92,216,219 (GRCm39) R106G probably damaging Het
Ggt7 A T 2: 155,348,353 (GRCm39) C100S probably damaging Het
Grik4 A T 9: 42,540,415 (GRCm39) M255K probably benign Het
Kcnj11 A T 7: 45,748,232 (GRCm39) S364T probably benign Het
Lnpep A T 17: 17,799,444 (GRCm39) Y70* probably null Het
Mark1 T C 1: 184,677,013 (GRCm39) H79R probably damaging Het
Mdfic2 T A 6: 98,225,187 (GRCm39) Q32L probably damaging Het
Myo9b T G 8: 71,743,016 (GRCm39) S26A probably benign Het
Pa2g4 G T 10: 128,395,326 (GRCm39) N306K probably benign Het
Pik3c3 T A 18: 30,410,166 (GRCm39) Y133* probably null Het
Prpf6 G T 2: 181,290,933 (GRCm39) A675S probably damaging Het
Psca A G 15: 74,587,948 (GRCm39) D44G probably benign Het
Sag T A 1: 87,749,059 (GRCm39) F153I possibly damaging Het
Scn10a A G 9: 119,453,202 (GRCm39) L1231P probably damaging Het
Sirpa T C 2: 129,458,172 (GRCm39) S157P probably benign Het
Slc27a2 A T 2: 126,403,530 (GRCm39) R184S probably benign Het
Tagln2 T C 1: 172,333,479 (GRCm39) F111S probably damaging Het
Tasor CGCGGCGGCGGCGGCGG CGCGGCGGCGGCGGCGGCGGCGG 14: 27,151,080 (GRCm39) probably benign Het
Tbc1d1 A G 5: 64,481,887 (GRCm39) D696G possibly damaging Het
Tert T A 13: 73,790,470 (GRCm39) probably null Het
Togaram2 G A 17: 71,996,204 (GRCm39) R68K probably benign Het
Trim40 A T 17: 37,199,874 (GRCm39) I68N probably damaging Het
Trpa1 T C 1: 14,946,078 (GRCm39) M1018V probably benign Het
Unc13c A T 9: 73,839,884 (GRCm39) N322K probably damaging Het
Vmn2r75 T A 7: 85,820,779 (GRCm39) T52S probably benign Het
Vmn2r90 T G 17: 17,947,034 (GRCm39) V437G 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
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
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'- CAGGCTCAAGTTGGTGCTTTC -3'
(R):5'- TGACACATGTGCACGAAGC -3'

Sequencing Primer
(F):5'- AAGTTGGTGCTTTCCAAGACC -3'
(R):5'- CACATGTGCACGAAGCTGTCAG -3'
Posted On 2016-11-09