Incidental Mutation 'R0330:Vps39'
ID 65149
Institutional Source Beutler Lab
Gene Symbol Vps39
Ensembl Gene ENSMUSG00000027291
Gene Name VPS39 HOPS complex subunit
Synonyms Vam6, Vam6P, A230065P22Rik, mVam6
MMRRC Submission 038539-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.953) question?
Stock # R0330 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 120146942-120183618 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 120169268 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Asparagine at position 245 (Y245N)
Ref Sequence ENSEMBL: ENSMUSP00000028752 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028752] [ENSMUST00000102501]
AlphaFold Q8R5L3
Predicted Effect possibly damaging
Transcript: ENSMUST00000028752
AA Change: Y245N

PolyPhen 2 Score 0.886 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: Y245N

DomainStartEndE-ValueType
Pfam:CNH 19 280 8.3e-53 PFAM
Pfam:Clathrin 410 536 3.9e-9 PFAM
Pfam:Vps39_1 449 551 1.7e-35 PFAM
Pfam:Clathrin 570 740 2.3e-8 PFAM
Pfam:Vps39_2 761 869 5.1e-36 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000102501
AA Change: Y256N

PolyPhen 2 Score 0.742 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: Y256N

DomainStartEndE-ValueType
Pfam:CNH 20 291 1.3e-32 PFAM
Pfam:Clathrin 421 547 2e-9 PFAM
Pfam:Vps39_1 460 562 6.7e-36 PFAM
Pfam:Clathrin 582 751 2.3e-8 PFAM
Pfam:Vps39_2 772 880 6.6e-36 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129857
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138854
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147085
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156296
Meta Mutation Damage Score 0.9487 question?
Coding Region Coverage
  • 1x: 98.8%
  • 3x: 97.7%
  • 10x: 94.7%
  • 20x: 88.0%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that may promote clustering and fusion of late endosomes and lysosomes. The protein may also act as an adaptor protein that modulates the transforming growth factor-beta response by coupling the transforming growth factor-beta receptor complex to the Smad pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Allele List at MGI
Other mutations in this stock
Total: 95 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acaa1b T C 9: 118,983,038 (GRCm39) N120S probably damaging Het
Acsbg3 A T 17: 57,190,631 (GRCm39) I400F probably benign Het
Acvr1c T C 2: 58,174,850 (GRCm39) T313A probably damaging Het
Adamtsl3 A T 7: 82,171,198 (GRCm39) D417V probably damaging Het
Adgrf4 A T 17: 42,978,204 (GRCm39) C380S probably damaging Het
AI597479 T G 1: 43,150,277 (GRCm39) L129R probably benign Het
AI661453 G A 17: 47,757,571 (GRCm39) R76Q probably damaging Het
Anpep C T 7: 79,488,004 (GRCm39) E518K probably benign Het
Anxa7 A C 14: 20,519,566 (GRCm39) probably null Het
Arhgap12 T A 18: 6,039,382 (GRCm39) D455V probably damaging Het
Arhgap22 A G 14: 33,091,374 (GRCm39) R650G possibly damaging Het
Arhgef12 A C 9: 42,931,982 (GRCm39) H168Q probably damaging Het
Arhgef2 A G 3: 88,549,808 (GRCm39) H592R probably damaging Het
BC049715 A G 6: 136,817,035 (GRCm39) T92A possibly damaging Het
Bcr C T 10: 75,017,466 (GRCm39) T1209I possibly damaging Het
Bmpr1a C T 14: 34,151,734 (GRCm39) S185N probably benign Het
Calcoco1 A T 15: 102,624,198 (GRCm39) M246K probably benign Het
Capn8 T A 1: 182,457,703 (GRCm39) I689N probably benign Het
Ccno T A 13: 113,126,530 (GRCm39) L333Q probably damaging Het
Cep57 G A 9: 13,728,281 (GRCm39) R148W probably damaging Het
Cftr T A 6: 18,226,096 (GRCm39) M318K probably null Het
Chd3 T G 11: 69,247,159 (GRCm39) D1003A probably damaging Het
Ckmt2 T A 13: 92,011,322 (GRCm39) D96V possibly damaging Het
Cldn13 A G 5: 134,944,176 (GRCm39) V3A probably benign Het
Col17a1 T C 19: 47,658,871 (GRCm39) T413A probably benign Het
Cpne5 A T 17: 29,430,634 (GRCm39) L92H probably damaging Het
Dnaaf2 C A 12: 69,244,518 (GRCm39) R181L probably damaging Het
Erbin C A 13: 104,005,373 (GRCm39) C114F probably damaging Het
Fads2b T A 2: 85,348,895 (GRCm39) R72S probably benign Het
Fanca A T 8: 124,000,911 (GRCm39) C1156* probably null Het
Flot2 T A 11: 77,949,784 (GRCm39) I322N possibly damaging Het
Fstl5 T C 3: 76,615,060 (GRCm39) V707A possibly damaging Het
Gli3 T G 13: 15,898,143 (GRCm39) L741R probably damaging Het
Gmip G T 8: 70,263,468 (GRCm39) S70I probably benign Het
Gnptab T C 10: 88,276,171 (GRCm39) S1153P probably damaging Het
Gramd1a T C 7: 30,837,679 (GRCm39) D360G possibly damaging Het
Gtf2i T C 5: 134,280,740 (GRCm39) E518G probably damaging Het
Hsp90b1 T C 10: 86,530,019 (GRCm39) E226G probably damaging Het
Impg2 A G 16: 56,072,627 (GRCm39) Y353C probably damaging Het
Kank1 A G 19: 25,401,677 (GRCm39) K1095E probably benign Het
Kcnh4 C T 11: 100,648,569 (GRCm39) C45Y probably damaging Het
Kif13b A G 14: 65,040,669 (GRCm39) T1590A probably benign Het
Lpin3 T C 2: 160,747,225 (GRCm39) V827A probably benign Het
Lrp1b A T 2: 40,591,773 (GRCm39) C73* probably null Het
Mcm8 A G 2: 132,661,914 (GRCm39) K83E possibly damaging Het
Med12l A G 3: 59,135,123 (GRCm39) E757G probably damaging Het
Mep1a A G 17: 43,808,789 (GRCm39) probably null Het
Mtor T A 4: 148,568,837 (GRCm39) V1119E probably benign Het
Mybpc2 C T 7: 44,158,453 (GRCm39) A710T possibly damaging Het
Myof A C 19: 37,924,326 (GRCm39) I1297S probably damaging Het
Nacad A G 11: 6,550,903 (GRCm39) S763P probably benign Het
Nbea A G 3: 55,550,238 (GRCm39) V2730A probably benign Het
Nbeal1 A G 1: 60,307,222 (GRCm39) Y1684C probably damaging Het
Optn A T 2: 5,039,066 (GRCm39) N352K possibly damaging Het
Or10k2 A G 8: 84,268,142 (GRCm39) Y123C probably damaging Het
Or2g1 A T 17: 38,106,880 (GRCm39) M182L probably benign Het
Or7g16 A G 9: 18,726,937 (GRCm39) Y218H probably damaging Het
Or9g4b T A 2: 85,616,147 (GRCm39) C97* probably null Het
Pcif1 G T 2: 164,731,364 (GRCm39) R466L probably damaging Het
Phxr2 T C 10: 98,961,979 (GRCm39) probably benign Het
Plaat5 T A 19: 7,614,663 (GRCm39) probably null Het
Plb1 T A 5: 32,512,701 (GRCm39) F1353Y probably damaging Het
Plec A G 15: 76,075,618 (GRCm39) probably null Het
Polr1a T A 6: 71,943,400 (GRCm39) C1212S possibly damaging Het
Primpol A T 8: 47,063,496 (GRCm39) N53K probably damaging Het
Pygo2 T A 3: 89,340,461 (GRCm39) N286K possibly damaging Het
Rttn G A 18: 89,004,204 (GRCm39) probably null Het
Serpinb3b G T 1: 107,087,433 (GRCm39) N25K probably damaging Het
Sidt2 A G 9: 45,866,200 (GRCm39) I2T probably benign Het
Slc12a3 A T 8: 95,072,974 (GRCm39) N699I possibly damaging Het
Slc25a30 G A 14: 76,000,112 (GRCm39) Q285* probably null Het
Slc4a9 A T 18: 36,668,592 (GRCm39) H724L probably damaging Het
Ssbp2 T A 13: 91,828,698 (GRCm39) probably null Het
Stac3 C A 10: 127,343,616 (GRCm39) probably null Het
Stk32a A G 18: 43,446,566 (GRCm39) K339E probably benign Het
Stoml2 A G 4: 43,030,238 (GRCm39) probably null Het
Syne2 G T 12: 76,013,727 (GRCm39) G2974C probably benign Het
Tbc1d16 A G 11: 119,049,555 (GRCm39) probably null Het
Tfdp2 T G 9: 96,188,946 (GRCm39) F200V probably damaging Het
Tie1 C A 4: 118,341,924 (GRCm39) R175L probably benign Het
Trappc12 A G 12: 28,797,259 (GRCm39) V91A probably benign Het
Trim46 G T 3: 89,143,820 (GRCm39) P536Q probably damaging Het
Tshz3 T A 7: 36,469,458 (GRCm39) D482E probably benign Het
Tspan33 T C 6: 29,711,091 (GRCm39) probably null Het
Unc80 T C 1: 66,713,246 (GRCm39) L2788P possibly damaging Het
Utp20 T A 10: 88,653,841 (GRCm39) T260S probably benign Het
Vmn2r118 G T 17: 55,917,717 (GRCm39) T265K probably damaging Het
Vmn2r98 A C 17: 19,286,609 (GRCm39) H369P probably benign Het
Vps4a A C 8: 107,769,698 (GRCm39) I336L probably benign Het
Xylb T C 9: 119,210,653 (GRCm39) S379P probably damaging Het
Zbtb37 T C 1: 160,860,066 (GRCm39) T80A probably benign Het
Zfhx3 A G 8: 109,675,589 (GRCm39) D2213G probably damaging Het
Zfp729a G T 13: 67,768,473 (GRCm39) H585Q probably damaging Het
Zfp804b A T 5: 6,821,029 (GRCm39) I642N possibly damaging Het
Zfp804b A T 5: 6,821,994 (GRCm39) N356K possibly damaging Het
Other mutations in Vps39
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01393:Vps39 APN 2 120,180,719 (GRCm39) splice site probably benign
IGL01629:Vps39 APN 2 120,154,079 (GRCm39) missense probably benign 0.11
IGL01812:Vps39 APN 2 120,151,271 (GRCm39) splice site probably benign
IGL01936:Vps39 APN 2 120,153,609 (GRCm39) missense probably benign 0.23
IGL02379:Vps39 APN 2 120,154,089 (GRCm39) missense probably benign 0.17
IGL02892:Vps39 APN 2 120,153,652 (GRCm39) splice site probably benign
IGL02943:Vps39 APN 2 120,169,968 (GRCm39) missense possibly damaging 0.77
Jigsaw UTSW 2 120,163,897 (GRCm39) missense probably damaging 0.98
matryoshka UTSW 2 120,155,176 (GRCm39) missense probably damaging 1.00
R0001:Vps39 UTSW 2 120,148,534 (GRCm39) missense probably benign 0.09
R0329:Vps39 UTSW 2 120,169,268 (GRCm39) missense possibly damaging 0.89
R0364:Vps39 UTSW 2 120,176,119 (GRCm39) missense probably damaging 1.00
R1483:Vps39 UTSW 2 120,154,129 (GRCm39) missense probably damaging 1.00
R1625:Vps39 UTSW 2 120,154,106 (GRCm39) missense probably damaging 1.00
R1837:Vps39 UTSW 2 120,155,878 (GRCm39) missense probably damaging 1.00
R1839:Vps39 UTSW 2 120,155,878 (GRCm39) missense probably damaging 1.00
R1934:Vps39 UTSW 2 120,148,558 (GRCm39) missense probably damaging 1.00
R2018:Vps39 UTSW 2 120,173,708 (GRCm39) missense probably damaging 1.00
R2019:Vps39 UTSW 2 120,173,708 (GRCm39) missense probably damaging 1.00
R2178:Vps39 UTSW 2 120,154,160 (GRCm39) nonsense probably null
R2513:Vps39 UTSW 2 120,169,268 (GRCm39) missense probably damaging 1.00
R3771:Vps39 UTSW 2 120,172,497 (GRCm39) missense possibly damaging 0.85
R3952:Vps39 UTSW 2 120,180,656 (GRCm39) missense probably benign 0.15
R4580:Vps39 UTSW 2 120,169,814 (GRCm39) missense probably benign 0.35
R4815:Vps39 UTSW 2 120,169,040 (GRCm39) missense probably benign 0.37
R4851:Vps39 UTSW 2 120,152,312 (GRCm39) intron probably benign
R4894:Vps39 UTSW 2 120,183,440 (GRCm39) missense probably damaging 1.00
R5447:Vps39 UTSW 2 120,183,413 (GRCm39) missense probably benign 0.43
R5483:Vps39 UTSW 2 120,153,564 (GRCm39) missense probably benign 0.08
R5715:Vps39 UTSW 2 120,155,717 (GRCm39) missense possibly damaging 0.73
R5886:Vps39 UTSW 2 120,152,053 (GRCm39) intron probably benign
R5949:Vps39 UTSW 2 120,159,149 (GRCm39) missense probably benign 0.23
R5954:Vps39 UTSW 2 120,155,143 (GRCm39) missense probably damaging 1.00
R5973:Vps39 UTSW 2 120,159,186 (GRCm39) missense probably damaging 0.99
R6004:Vps39 UTSW 2 120,176,131 (GRCm39) missense possibly damaging 0.89
R6208:Vps39 UTSW 2 120,163,897 (GRCm39) missense probably damaging 0.98
R6705:Vps39 UTSW 2 120,151,157 (GRCm39) missense probably benign 0.00
R6915:Vps39 UTSW 2 120,151,512 (GRCm39) nonsense probably null
R7535:Vps39 UTSW 2 120,155,176 (GRCm39) missense probably damaging 1.00
R7780:Vps39 UTSW 2 120,155,680 (GRCm39) nonsense probably null
R7869:Vps39 UTSW 2 120,169,875 (GRCm39) missense possibly damaging 0.89
R8061:Vps39 UTSW 2 120,174,692 (GRCm39) missense probably benign 0.00
R8770:Vps39 UTSW 2 120,153,548 (GRCm39) missense probably benign
R8787:Vps39 UTSW 2 120,172,506 (GRCm39) missense probably damaging 1.00
R8933:Vps39 UTSW 2 120,169,066 (GRCm39) missense probably benign 0.00
R8962:Vps39 UTSW 2 120,174,687 (GRCm39) nonsense probably null
R9302:Vps39 UTSW 2 120,151,525 (GRCm39) splice site probably benign
R9573:Vps39 UTSW 2 120,155,179 (GRCm39) missense possibly damaging 0.89
R9610:Vps39 UTSW 2 120,172,485 (GRCm39) missense probably damaging 0.99
R9611:Vps39 UTSW 2 120,172,485 (GRCm39) missense probably damaging 0.99
Predicted Primers
Posted On 2013-08-08