Incidental Mutation 'R0427:Vps16'
ID 38720
Institutional Source Beutler Lab
Gene Symbol Vps16
Ensembl Gene ENSMUSG00000027411
Gene Name VSP16 CORVET/HOPS core subunit
Synonyms 1810074M16Rik
MMRRC Submission 038629-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.970) question?
Stock # R0427 (G1)
Quality Score 198
Status Not validated
Chromosome 2
Chromosomal Location 130266259-130286189 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 130280770 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 233 (Y233C)
Ref Sequence ENSEMBL: ENSMUSP00000028900 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028900] [ENSMUST00000128994]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000028900
AA Change: Y233C

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: Y233C

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: ENSMUST00000132388
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134677
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137084
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.2%
  • 20x: 92.9%
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: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam34 T G 8: 44,105,493 (GRCm39) T51P probably benign Het
Alpk1 A T 3: 127,464,720 (GRCm39) V1186E probably damaging Het
Ankfn1 T C 11: 89,296,423 (GRCm39) D102G probably damaging Het
Armc2 A G 10: 41,876,406 (GRCm39) I127T possibly damaging Het
Atp6v1b2 T C 8: 69,554,084 (GRCm39) L87P probably damaging Het
Atp9a T A 2: 168,482,617 (GRCm39) probably null Het
BC048679 C G 7: 81,144,993 (GRCm39) V123L probably benign Het
Birc7 G A 2: 180,571,307 (GRCm39) probably null Het
Btbd9 C T 17: 30,493,916 (GRCm39) D492N possibly damaging Het
Cacna1d T A 14: 30,068,774 (GRCm39) N155I probably damaging Het
Cd300lg T C 11: 101,933,852 (GRCm39) V33A probably damaging Het
Cep290 A G 10: 100,352,041 (GRCm39) D742G probably benign Het
Cep95 A G 11: 106,681,578 (GRCm39) N14S probably benign Het
Cfap74 A T 4: 155,525,734 (GRCm39) M728L probably benign Het
Ctsll3 T A 13: 60,949,205 (GRCm39) T9S probably benign Het
Cyp3a44 A G 5: 145,716,412 (GRCm39) S393P possibly damaging Het
Dmbt1 T A 7: 130,642,632 (GRCm39) L150* probably null Het
Dnah2 A G 11: 69,343,705 (GRCm39) I2868T probably damaging Het
Dop1a A G 9: 86,389,585 (GRCm39) H505R probably damaging Het
Exo1 A G 1: 175,733,519 (GRCm39) K781R probably damaging Het
Fam184a A G 10: 53,566,211 (GRCm39) Y459H probably damaging Het
Foxp1 C T 6: 98,907,164 (GRCm39) D540N probably damaging Het
Fstl5 T A 3: 76,615,034 (GRCm39) Y698* probably null Het
Gm5141 T C 13: 62,922,525 (GRCm39) K215E probably damaging Het
Grik5 C A 7: 24,757,923 (GRCm39) R386L probably benign Het
Ikbke A T 1: 131,185,647 (GRCm39) S620R possibly damaging Het
Kcnh3 A T 15: 99,131,180 (GRCm39) M518L probably benign Het
Lrrcc1 G T 3: 14,623,416 (GRCm39) A748S probably damaging Het
Mbd5 T G 2: 49,169,091 (GRCm39) S1191A probably benign Het
Med27 T C 2: 29,390,283 (GRCm39) I70T probably damaging Het
Mplkipl1 A G 19: 61,163,908 (GRCm39) Y176H probably damaging Het
Myh4 A G 11: 67,149,479 (GRCm39) D1737G probably damaging Het
Myo5a A G 9: 75,081,478 (GRCm39) D1021G probably benign Het
Ncor1 T C 11: 62,301,746 (GRCm39) E212G probably damaging Het
Neb A T 2: 52,133,896 (GRCm39) N3362K possibly damaging Het
Neb A G 2: 52,134,081 (GRCm39) S3301P probably damaging Het
Neurod1 T G 2: 79,284,526 (GRCm39) K286Q probably damaging Het
Noc3l T C 19: 38,778,095 (GRCm39) Q773R probably benign Het
Nup205 T A 6: 35,171,398 (GRCm39) N420K probably benign Het
Olfml3 A T 3: 103,644,330 (GRCm39) V113E probably benign Het
Opa1 T C 16: 29,430,279 (GRCm39) V439A probably damaging Het
Or13c7 A G 4: 43,854,417 (GRCm39) Y36C probably damaging Het
Or14j7 A T 17: 38,234,520 (GRCm39) H21L probably benign Het
Or1j14 C T 2: 36,417,994 (GRCm39) S190L probably damaging Het
Or1o11 T A 17: 37,756,593 (GRCm39) D60E probably damaging Het
Pcdhb11 T C 18: 37,555,818 (GRCm39) S383P probably damaging Het
Pkd1 T C 17: 24,812,476 (GRCm39) V3803A probably damaging Het
Plekhg1 A G 10: 3,914,235 (GRCm39) D1319G probably benign Het
Polq T A 16: 36,882,355 (GRCm39) C1227* probably null Het
Pramel22 A T 4: 143,380,993 (GRCm39) N343K probably benign Het
Psmc1 T C 12: 100,085,487 (GRCm39) F283L probably damaging Het
Psmd8 T C 7: 28,875,552 (GRCm39) N189S probably damaging Het
Ptger4 G A 15: 5,272,382 (GRCm39) T104I probably benign Het
Ptpro T G 6: 137,345,294 (GRCm39) V100G possibly damaging Het
Rab11fip1 T A 8: 27,644,520 (GRCm39) T422S probably damaging Het
Rad54l2 A G 9: 106,570,891 (GRCm39) L1143P possibly damaging Het
Rnf148 A G 6: 23,654,072 (GRCm39) M308T probably damaging Het
Sbsn T A 7: 30,451,523 (GRCm39) probably benign Het
Scube2 T A 7: 109,424,044 (GRCm39) T487S probably benign Het
Sema4c C A 1: 36,592,892 (GRCm39) E109* probably null Het
Sipa1l2 A T 8: 126,207,071 (GRCm39) L544Q probably damaging Het
Slc28a2 A G 2: 122,288,702 (GRCm39) T603A probably benign Het
Tbc1d7 T A 13: 43,306,563 (GRCm39) T138S probably benign Het
Timd4 A T 11: 46,710,084 (GRCm39) T239S probably benign Het
Trp53bp1 A G 2: 121,066,498 (GRCm39) S743P probably damaging Het
Tspan10 T A 11: 120,335,120 (GRCm39) Y77N probably damaging Het
Ttc14 T C 3: 33,857,633 (GRCm39) S245P probably damaging Het
Ttf1 T A 2: 28,955,054 (GRCm39) S139R probably benign Het
Tubd1 C A 11: 86,448,616 (GRCm39) Q279K possibly damaging Het
Twnk A G 19: 44,996,026 (GRCm39) E153G probably benign Het
Ush2a A G 1: 188,132,478 (GRCm39) D900G probably damaging Het
Usp54 A G 14: 20,620,432 (GRCm39) V691A probably benign Het
Usp8 T C 2: 126,559,952 (GRCm39) probably benign Het
Vmn1r231 C T 17: 21,110,490 (GRCm39) V142I probably benign Het
Vmn2r15 C T 5: 109,434,953 (GRCm39) A584T probably damaging Het
Vmn2r6 A G 3: 64,467,008 (GRCm39) S164P probably damaging Het
Vwf C G 6: 125,650,902 (GRCm39) H2511D probably benign Het
Wipf3 T G 6: 54,460,882 (GRCm39) L110R possibly damaging Het
Zfp945 T A 17: 23,084,226 (GRCm39) N11I probably benign 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
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
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'- TCATGTTGGACCACACTGTGCC -3'
(R):5'- ACAGTCATCCTGCTGTTGAAAAGCC -3'

Sequencing Primer
(F):5'- ACACATTCTTCTGGCTGTAGGAC -3'
(R):5'- AACCACACCTTGAGTGATGC -3'
Posted On 2013-05-23