Incidental Mutation 'R9128:Vps16'
ID 693383
Institutional Source Beutler Lab
Gene Symbol Vps16
Ensembl Gene ENSMUSG00000027411
Gene Name VSP16 CORVET/HOPS core subunit
Synonyms
MMRRC Submission
Accession Numbers
Is this an essential gene? Probably essential (E-score: 0.972) question?
Stock # R9128 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 130424339-130444269 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 130424399 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 2 (D2G)
Ref Sequence ENSEMBL: ENSMUSP00000028900 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028900] [ENSMUST00000089581] [ENSMUST00000110277] [ENSMUST00000128994]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000028900
AA Change: D2G

PolyPhen 2 Score 0.507 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: D2G

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 probably benign
Transcript: ENSMUST00000089581
SMART Domains Protein: ENSMUSP00000087009
Gene: ENSMUSG00000037773

DomainStartEndE-ValueType
Pfam:PC-Esterase 18 267 4e-52 PFAM
low complexity region 308 346 N/A INTRINSIC
low complexity region 376 391 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000110277
SMART Domains Protein: ENSMUSP00000105906
Gene: ENSMUSG00000037773

DomainStartEndE-ValueType
Pfam:PC-Esterase 21 268 3.8e-51 PFAM
low complexity region 308 346 N/A INTRINSIC
low complexity region 376 391 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000128994
AA Change: D2G

PolyPhen 2 Score 0.202 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000115899
Gene: ENSMUSG00000027411
AA Change: D2G

DomainStartEndE-ValueType
Pfam:Vps16_N 4 212 3.2e-74 PFAM
Pfam:Vps16_N 205 316 1e-45 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
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: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca7 T C 10: 80,002,518 V542A possibly damaging Het
Abhd8 G T 8: 71,461,745 R80S probably benign Het
Actc1 T C 2: 114,050,465 Y93C possibly damaging Het
Actn4 G T 7: 28,894,504 D859E possibly damaging Het
Adcy2 C T 13: 68,625,808 G1039R probably damaging Het
Als2 A G 1: 59,180,550 M1202T probably benign Het
Aste1 T A 9: 105,396,709 Y49* probably null Het
Atp8b4 T C 2: 126,392,830 D422G probably benign Het
Bag6 T A 17: 35,144,712 S791T probably damaging Het
Bivm T A 1: 44,128,789 W222R probably null Het
Bod1l A C 5: 41,788,923 V3003G probably benign Het
Bsn T C 9: 108,116,150 D801G probably benign Het
Ccdc14 G A 16: 34,706,789 D403N probably damaging Het
Cenpj T A 14: 56,542,862 E964V probably damaging Het
Cep250 C T 2: 155,970,122 A446V unknown Het
Clca3a1 G A 3: 144,758,034 R161W probably damaging Het
Dcxr A T 11: 120,726,546 V57E Het
Dnah17 T G 11: 118,046,178 N3400T possibly damaging Het
Dnaja3 C T 16: 4,702,300 T444I possibly damaging Het
Dopey1 T C 9: 86,513,155 S772P probably benign Het
Ednrb T C 14: 103,843,092 N129D probably damaging Het
Ep300 T A 15: 81,649,745 M2001K unknown Het
Fam3b A G 16: 97,501,000 I8T probably benign Het
Fam98c A T 7: 29,154,690 S85T Het
Fat1 G A 8: 45,009,841 V1232I probably benign Het
Fzd3 T A 14: 65,212,177 Y484F probably damaging Het
Gm13023 T A 4: 143,793,608 S141T probably benign Het
H3f3a T C 1: 180,803,095 I131M possibly damaging Het
Ifi206 A T 1: 173,471,456 D861E unknown Het
Ihh T C 1: 74,946,339 Y329C probably damaging Het
Jak2 A G 19: 29,301,062 N909D probably damaging Het
Krtap12-1 C A 10: 77,720,789 C55* probably null Het
Mical2 A C 7: 112,271,382 K26T possibly damaging Het
Mpp5 A G 12: 78,797,058 E12G probably benign Het
Mreg T C 1: 72,192,057 T81A probably benign Het
Muc16 T C 9: 18,647,582 T2472A unknown Het
Nanos3 A T 8: 84,176,451 D27E probably benign Het
Nox3 T G 17: 3,669,861 S350R probably damaging Het
Olfr1049 T A 2: 86,255,678 N5I probably damaging Het
Olfr734 A G 14: 50,320,757 V26A probably benign Het
Pafah2 C T 4: 134,419,970 T310M probably damaging Het
Pianp A G 6: 125,000,695 I185V probably benign Het
Pja2 T C 17: 64,309,475 T142A probably benign Het
Poln G A 5: 34,014,314 P747L probably damaging Het
Rdx T A 9: 52,064,879 L39* probably null Het
Rnf146 A G 10: 29,347,543 W116R probably damaging Het
Rsf1 G GACGGCGGCT 7: 97,579,909 probably benign Het
Sec24d A G 3: 123,294,161 T224A probably benign Het
Serpinb9 T A 13: 33,006,703 I54K possibly damaging Het
Slc25a13 A T 6: 6,109,987 L324Q probably null Het
Slc9c1 T C 16: 45,580,127 L700P probably benign Het
Snta1 T C 2: 154,380,936 K289R probably benign Het
Sppl2a A G 2: 126,923,473 F243S probably damaging Het
Syne1 T C 10: 5,108,556 E7319G probably benign Het
Taf5l G A 8: 124,003,275 P225L probably benign Het
Tet2 A T 3: 133,469,613 N1324K possibly damaging Het
Usp5 A T 6: 124,823,451 probably null Het
Vmn2r124 G T 17: 18,074,177 R842L probably benign Het
Vwf T C 6: 125,642,730 L1457P Het
Xpo1 A G 11: 23,285,058 T576A probably damaging Het
Zdhhc6 A T 19: 55,313,248 Y100* probably null Het
Zfp534 T A 4: 147,675,625 R196* probably null Het
Zfp710 C T 7: 80,081,374 R100W probably damaging Het
Zfp750 T C 11: 121,513,848 K67R probably benign Het
Zmynd10 T C 9: 107,549,127 S158P Het
Zmynd8 A T 2: 165,858,138 M1K probably null Het
Other mutations in Vps16
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01327:Vps16 APN 2 130437696 missense probably benign 0.19
IGL01400:Vps16 APN 2 130438353 missense possibly damaging 0.73
IGL01542:Vps16 APN 2 130438394 missense probably damaging 0.97
IGL02011:Vps16 APN 2 130441479 missense probably benign 0.04
IGL02192:Vps16 APN 2 130440932 missense probably damaging 0.98
IGL02220:Vps16 APN 2 130441653 missense possibly damaging 0.85
IGL02587:Vps16 APN 2 130439716 critical splice donor site probably null
R0427:Vps16 UTSW 2 130438850 missense probably benign 0.00
R0507:Vps16 UTSW 2 130437712 critical splice donor site probably null
R1550:Vps16 UTSW 2 130440340 missense probably benign 0.09
R1789:Vps16 UTSW 2 130443600 missense probably benign 0.42
R3895:Vps16 UTSW 2 130438676 missense possibly damaging 0.96
R3981:Vps16 UTSW 2 130442594 missense possibly damaging 0.77
R4092:Vps16 UTSW 2 130439912 missense probably damaging 1.00
R4555:Vps16 UTSW 2 130443576 missense probably damaging 1.00
R4569:Vps16 UTSW 2 130442204 missense probably benign
R4803:Vps16 UTSW 2 130438110 missense probably benign 0.27
R4835:Vps16 UTSW 2 130438300 splice site probably benign
R5022:Vps16 UTSW 2 130439452 missense probably benign 0.07
R5023:Vps16 UTSW 2 130439452 missense probably benign 0.07
R5057:Vps16 UTSW 2 130439452 missense probably benign 0.07
R5158:Vps16 UTSW 2 130441279 missense probably damaging 1.00
R5177:Vps16 UTSW 2 130443368 nonsense probably null
R5540:Vps16 UTSW 2 130442385 missense probably benign 0.00
R5680:Vps16 UTSW 2 130440324 missense possibly damaging 0.64
R5689:Vps16 UTSW 2 130439091 nonsense probably null
R5690:Vps16 UTSW 2 130439091 nonsense probably null
R5926:Vps16 UTSW 2 130443556 missense probably damaging 0.97
R5992:Vps16 UTSW 2 130424449 critical splice donor site probably null
R6135:Vps16 UTSW 2 130438653 missense possibly damaging 0.57
R6370:Vps16 UTSW 2 130443384 missense probably damaging 1.00
R6898:Vps16 UTSW 2 130437681 missense possibly damaging 0.74
R7378:Vps16 UTSW 2 130438179 missense probably damaging 1.00
R7487:Vps16 UTSW 2 130439057 nonsense probably null
R7641:Vps16 UTSW 2 130440528 missense probably benign 0.28
R7720:Vps16 UTSW 2 130441703 nonsense probably null
R8246:Vps16 UTSW 2 130438873 missense probably damaging 1.00
R8363:Vps16 UTSW 2 130442241 missense probably benign 0.08
R9092:Vps16 UTSW 2 130439673 missense probably damaging 0.99
R9352:Vps16 UTSW 2 130441903 critical splice donor site probably null
R9406:Vps16 UTSW 2 130441505 critical splice donor site probably null
R9508:Vps16 UTSW 2 130442441 missense possibly damaging 0.94
R9800:Vps16 UTSW 2 130440485 missense probably benign 0.02
RF021:Vps16 UTSW 2 130438209 missense probably benign 0.09
Z1177:Vps16 UTSW 2 130441426 missense probably damaging 1.00
Predicted Primers
Posted On 2022-01-20