Incidental Mutation 'R9508:Vps16'
ID 717914
Institutional Source Beutler Lab
Gene Symbol Vps16
Ensembl Gene ENSMUSG00000027411
Gene Name VSP16 CORVET/HOPS core subunit
Synonyms 1810074M16Rik
MMRRC Submission
Accession Numbers
Essential gene? Probably essential (E-score: 0.970) question?
Stock # R9508 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 130266259-130286189 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 130284361 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 704 (I704N)
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: I704N

PolyPhen 2 Score 0.936 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: I704N

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: 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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4833420G17Rik G A 13: 119,617,484 (GRCm39) V536I Het
Adam18 A G 8: 25,143,778 (GRCm39) I187T possibly damaging Het
Adam24 A G 8: 41,132,941 (GRCm39) I136M probably benign Het
B3galt2 A T 1: 143,522,280 (GRCm39) I139F possibly damaging Het
Cacna1i C T 15: 80,279,372 (GRCm39) P2038S probably benign Het
Cbll1 A T 12: 31,544,685 (GRCm39) I26N probably damaging Het
Cldn1 A T 16: 26,179,619 (GRCm39) Y149* probably null Het
Cnot11 T C 1: 39,581,575 (GRCm39) V372A probably damaging Het
Cnot2 A G 10: 116,329,616 (GRCm39) L458P probably damaging Het
Cnot4 T C 6: 35,045,554 (GRCm39) E219G Het
Col8a1 T G 16: 57,448,947 (GRCm39) I188L unknown Het
Daam2 T C 17: 49,765,618 (GRCm39) K1095R probably damaging Het
Dnah9 T C 11: 65,725,089 (GRCm39) T4355A probably damaging Het
Dsg4 A G 18: 20,604,070 (GRCm39) I846V probably damaging Het
Ehd4 C T 2: 119,921,966 (GRCm39) G430E probably damaging Het
Fanci T C 7: 79,083,033 (GRCm39) Y670H possibly damaging Het
Galnt10 T A 11: 57,673,040 (GRCm39) N465K possibly damaging Het
Glipr1l1 A G 10: 111,912,015 (GRCm39) N183S probably damaging Het
Gnl1 T C 17: 36,299,625 (GRCm39) Y599H possibly damaging Het
Gpr26 T C 7: 131,585,830 (GRCm39) S267P probably benign Het
Grk2 A T 19: 4,341,636 (GRCm39) N179K probably damaging Het
Igf2bp2 T A 16: 21,898,845 (GRCm39) M255L probably benign Het
Ighv2-6 T C 12: 113,680,430 (GRCm39) I70M probably benign Het
Igkv4-74 T A 6: 69,161,942 (GRCm39) N76Y probably damaging Het
Il11ra1 T C 4: 41,767,527 (GRCm39) V293A probably damaging Het
Itpr3 G A 17: 27,337,651 (GRCm39) probably benign Het
Kank2 A T 9: 21,687,076 (GRCm39) L582Q probably damaging Het
Kmt2b T C 7: 30,269,259 (GRCm39) T2554A probably damaging Het
Mecom T A 3: 30,010,621 (GRCm39) Y619F probably benign Het
Mknk1 A G 4: 115,732,579 (GRCm39) N269S probably benign Het
Mpp2 T A 11: 101,951,692 (GRCm39) E435D probably damaging Het
Nicn1 C T 9: 108,171,708 (GRCm39) R163C possibly damaging Het
Or2f2 A G 6: 42,767,928 (GRCm39) *318W probably null Het
Or5g9 A G 2: 85,552,165 (GRCm39) R139G possibly damaging Het
Or7a41 A T 10: 78,870,933 (GRCm39) Q101L probably damaging Het
P3h3 A G 6: 124,830,012 (GRCm39) probably null Het
Paqr5 C T 9: 61,880,079 (GRCm39) V72M probably benign Het
Pilrb2 G A 5: 137,869,261 (GRCm39) T113I probably damaging Het
Pitpnm3 T C 11: 72,003,121 (GRCm39) E63G probably damaging Het
Ppp4r4 G A 12: 103,542,561 (GRCm39) V108M possibly damaging Het
Ptprf G T 4: 118,126,776 (GRCm39) S46* probably null Het
Rab2a T C 4: 8,582,447 (GRCm39) L143P Het
Rassf7 C T 7: 140,796,924 (GRCm39) R46* probably null Het
Sec23a T C 12: 59,036,185 (GRCm39) D393G probably benign Het
Semp2l2b A G 10: 21,942,816 (GRCm39) V388A probably damaging Het
Serpinb9f T A 13: 33,518,515 (GRCm39) F338L probably benign Het
Spg7 T C 8: 123,800,623 (GRCm39) V66A probably damaging Het
Sult2a4 C T 7: 13,723,437 (GRCm39) R27H probably benign Het
Sumo2 A C 11: 115,414,538 (GRCm39) Y95D possibly damaging Het
Tbx18 G A 9: 87,587,926 (GRCm39) S397F probably damaging Het
Ticam2 G C 18: 46,693,748 (GRCm39) P113R probably damaging Het
Timeless A G 10: 128,076,096 (GRCm39) S63G probably benign Het
Tinag C T 9: 76,912,981 (GRCm39) C276Y probably damaging Het
Tmem143 A T 7: 45,565,630 (GRCm39) K364* probably null Het
Tmem160 A G 7: 16,186,840 (GRCm39) probably benign Het
Tmod4 G C 3: 95,034,713 (GRCm39) E154Q probably benign Het
Trpv1 G T 11: 73,145,090 (GRCm39) K725N Het
Ttn G T 2: 76,715,978 (GRCm39) A7767D unknown Het
Tubd1 T A 11: 86,448,640 (GRCm39) Y318N probably damaging Het
Ufd1 T A 16: 18,643,802 (GRCm39) M187K possibly damaging Het
Unc5c A G 3: 141,494,736 (GRCm39) N424D possibly damaging Het
Usp19 C T 9: 108,371,608 (GRCm39) S329L probably damaging Het
Vwf A T 6: 125,532,471 (GRCm39) I72F Het
Ypel4 T C 2: 84,567,304 (GRCm39) S46P probably damaging Het
Zcchc8 A C 5: 123,842,584 (GRCm39) probably null 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
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
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'- GAATGAATTTGCAGCCAAGGTTTG -3'
(R):5'- CCAATCTTCCAAATCTGCCAGG -3'

Sequencing Primer
(F):5'- AGCCAAGGTTTGACTGCC -3'
(R):5'- AGGGCAGCCAGCTTTAAC -3'
Posted On 2022-07-18