Incidental Mutation 'R4092:Vps16'
ID 317655
Institutional Source Beutler Lab
Gene Symbol Vps16
Ensembl Gene ENSMUSG00000027411
Gene Name VSP16 CORVET/HOPS core subunit
Synonyms 1810074M16Rik
Accession Numbers
Essential gene? Probably essential (E-score: 0.970) question?
Stock # R4092 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 130266259-130286189 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 130281832 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Asparagine at position 315 (Y315N)
Ref Sequence ENSEMBL: ENSMUSP00000115899 (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: Y356N

PolyPhen 2 Score 0.828 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: Y356N

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 damaging
Transcript: ENSMUST00000128994
AA Change: Y315N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000115899
Gene: ENSMUSG00000027411
AA Change: Y315N

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
Meta Mutation Damage Score 0.7916 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.6%
  • 20x: 96.0%
Validation Efficiency 100% (53/53)
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: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2010315B03Rik A T 9: 124,055,903 (GRCm39) H340Q probably benign Het
Adam22 A T 5: 8,145,004 (GRCm39) I116N probably damaging Het
Adamts2 T A 11: 50,678,103 (GRCm39) V794E probably damaging Het
Ak9 T C 10: 41,265,140 (GRCm39) S966P probably benign Het
Alox5 G A 6: 116,389,635 (GRCm39) probably benign Het
Bmerb1 G A 16: 13,867,346 (GRCm39) R68H probably damaging Het
Brip1 C T 11: 86,039,347 (GRCm39) D396N possibly damaging Het
Catsper3 C T 13: 55,932,484 (GRCm39) H4Y probably benign Het
Cmtm2a T C 8: 105,019,403 (GRCm39) Y62C probably benign Het
Crim1 T C 17: 78,658,265 (GRCm39) C715R probably damaging Het
Dio3 A G 12: 110,246,234 (GRCm39) D190G possibly damaging Het
Efl1 A G 7: 82,412,035 (GRCm39) E808G probably benign Het
Eif1ad16 A T 12: 87,985,194 (GRCm39) N116K possibly damaging Het
Fam83b T C 9: 76,398,943 (GRCm39) D720G probably benign Het
Fbp2 C T 13: 62,988,174 (GRCm39) V246M possibly damaging Het
Gm10197 G A 19: 53,360,196 (GRCm39) probably benign Het
Icam2 C A 11: 106,271,623 (GRCm39) M1I probably null Het
Insyn2b G A 11: 34,351,935 (GRCm39) probably benign Het
Kit T C 5: 75,771,470 (GRCm39) I209T probably benign Het
Lcmt1 T C 7: 123,017,476 (GRCm39) V200A probably damaging Het
Lrrn2 C T 1: 132,865,390 (GRCm39) Q152* probably null Het
Mmadhc A G 2: 50,177,895 (GRCm39) M174T probably benign Het
N4bp2 A G 5: 65,947,799 (GRCm39) N143S probably benign Het
Ndufs1 G A 1: 63,196,405 (GRCm39) A340V possibly damaging Het
Nid1 A G 13: 13,661,224 (GRCm39) D708G probably damaging Het
Noc2l A C 4: 156,327,033 (GRCm39) T295P probably damaging Het
Nutm1 T A 2: 112,079,809 (GRCm39) N702I probably damaging Het
Obscn T A 11: 58,946,886 (GRCm39) M4083L probably benign Het
Or5b104 T C 19: 13,072,790 (GRCm39) Y74C probably damaging Het
Otol1 T A 3: 69,935,118 (GRCm39) I370N probably damaging Het
Paip1 T G 13: 119,586,449 (GRCm39) S58A probably benign Het
Pfas T C 11: 68,884,775 (GRCm39) T476A probably benign Het
Plppr3 G T 10: 79,703,314 (GRCm39) R57S probably damaging Het
Ptgir T C 7: 16,640,932 (GRCm39) S75P probably damaging Het
Raver1 A T 9: 20,992,568 (GRCm39) L287Q probably damaging Het
Rps6ka4 C T 19: 6,809,623 (GRCm39) probably null Het
Rps6-ps2 A G 8: 89,533,319 (GRCm39) noncoding transcript Het
Scn11a T A 9: 119,619,036 (GRCm39) M769L probably benign Het
Serpina16 G T 12: 103,638,836 (GRCm39) H250Q probably benign Het
Serpina3a G A 12: 104,082,625 (GRCm39) V133I probably benign Het
Slc12a8 G A 16: 33,437,491 (GRCm39) G308D probably damaging Het
Slfn5 T C 11: 82,851,893 (GRCm39) L673P probably damaging Het
Sorcs2 T C 5: 36,183,166 (GRCm39) K1036E possibly damaging Het
Speer3 C G 5: 13,846,394 (GRCm39) A238G possibly damaging Het
Sptbn5 C A 2: 119,897,532 (GRCm39) E550D probably damaging Het
Srgap3 G T 6: 112,700,045 (GRCm39) P1002T probably benign Het
Tollip C T 7: 141,438,180 (GRCm39) R181H probably damaging Het
Trmt1l T A 1: 151,330,784 (GRCm39) S600R probably benign Het
Vps50 A G 6: 3,551,037 (GRCm39) E367G 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
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
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'- GAGTTCCTGCATGAAGTCCC -3'
(R):5'- GCCAGTTTACATGTGCTAGCC -3'

Sequencing Primer
(F):5'- TTCCTGCATGAAGTCCCAGGTG -3'
(R):5'- CTTAGCCAGCTCAAGTCAGTG -3'
Posted On 2015-05-15