Incidental Mutation 'R3771:Vps39'
ID 273257
Institutional Source Beutler Lab
Gene Symbol Vps39
Ensembl Gene ENSMUSG00000027291
Gene Name VPS39 HOPS complex subunit
Synonyms Vam6, Vam6P, A230065P22Rik, mVam6
MMRRC Submission 040747-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.953) question?
Stock # R3771 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 120146942-120183618 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 120172497 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Isoleucine at position 179 (V179I)
Ref Sequence ENSEMBL: ENSMUSP00000099559 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028752] [ENSMUST00000102501]
AlphaFold Q8R5L3
Predicted Effect possibly damaging
Transcript: ENSMUST00000028752
AA Change: V168I

PolyPhen 2 Score 0.851 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: V168I

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: V179I

PolyPhen 2 Score 0.853 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: V179I

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 0.1795 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.3%
Validation Efficiency 99% (69/70)
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aanat G T 11: 116,487,697 (GRCm39) G132V probably damaging Het
Abcb11 T A 2: 69,159,720 (GRCm39) probably benign Het
Adam26b T A 8: 43,973,751 (GRCm39) D417V probably damaging Het
Ank1 T C 8: 23,613,913 (GRCm39) S1482P probably benign Het
Aoc1l2 T C 6: 48,908,130 (GRCm39) Y377H probably damaging Het
Armc2 C T 10: 41,798,223 (GRCm39) V768M probably damaging Het
Ascc3 C T 10: 50,596,814 (GRCm39) probably benign Het
Birc6 T A 17: 74,925,424 (GRCm39) probably benign Het
Cd109 CATTTATTTATTTATTTATTTATTTATTTATTTAT CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT 9: 78,619,782 (GRCm39) probably benign Het
Cdh12 A T 15: 21,578,640 (GRCm39) probably benign Het
Chd1 A G 17: 17,594,913 (GRCm39) D16G probably damaging Het
Clstn2 A G 9: 97,464,615 (GRCm39) I180T probably damaging Het
Cxcr6 A G 9: 123,639,550 (GRCm39) I184V probably benign Het
Dagla G A 19: 10,225,831 (GRCm39) P778S possibly damaging Het
Ddx19b T C 8: 111,747,613 (GRCm39) K107R probably benign Het
Dpyd G A 3: 119,205,927 (GRCm39) probably null Het
Elf1 T C 14: 79,804,650 (GRCm39) V105A possibly damaging Het
Fam13a T G 6: 58,964,171 (GRCm39) K87T probably benign Het
Fap C A 2: 62,363,354 (GRCm39) S359I probably damaging Het
Fbxo39 T C 11: 72,208,041 (GRCm39) I131T possibly damaging Het
Fmn1 T G 2: 113,412,463 (GRCm39) S996A probably damaging Het
Gm5866 T C 5: 52,740,088 (GRCm39) noncoding transcript Het
Hmcn2 C T 2: 31,250,908 (GRCm39) T790M probably damaging Het
Irf2bp2 T C 8: 127,318,550 (GRCm39) K339E probably damaging Het
Kat6b A G 14: 21,567,166 (GRCm39) D75G probably damaging Het
Kcnab3 A G 11: 69,219,389 (GRCm39) T127A probably damaging Het
Kdm5b G T 1: 134,541,083 (GRCm39) C725F probably damaging Het
Lrp5 G A 19: 3,662,330 (GRCm39) R173C probably damaging Het
Lrrn3 T A 12: 41,502,869 (GRCm39) I483L probably damaging Het
Man2c1 C A 9: 57,047,661 (GRCm39) probably benign Het
Med23 G T 10: 24,778,099 (GRCm39) G810C probably damaging Het
Nhlrc4 T A 17: 26,162,367 (GRCm39) K127* probably null Het
Numb T C 12: 83,846,350 (GRCm39) D344G probably damaging Het
Nup210l T G 3: 90,027,201 (GRCm39) Y194* probably null Het
Ogg1 T C 6: 113,310,804 (GRCm39) V317A possibly damaging Het
Or1o2 T A 17: 37,542,356 (GRCm39) I302F possibly damaging Het
Or6c69c A G 10: 129,911,143 (GRCm39) Y288C probably damaging Het
Pclo A T 5: 14,589,422 (GRCm39) probably null Het
Pnpt1 T C 11: 29,088,174 (GRCm39) M195T probably benign Het
Polr3c T A 3: 96,633,170 (GRCm39) T43S probably damaging Het
Ptprs T C 17: 56,735,978 (GRCm39) T152A possibly damaging Het
Rasl10b A T 11: 83,309,349 (GRCm39) T134S probably benign Het
Rin2 C T 2: 145,702,366 (GRCm39) T354I probably benign Het
Rnf39 T C 17: 37,258,121 (GRCm39) W96R probably damaging Het
Ros1 G T 10: 52,005,087 (GRCm39) A949E probably damaging Het
Rwdd2a A C 9: 86,456,214 (GRCm39) N130T possibly damaging Het
Scn9a T C 2: 66,313,992 (GRCm39) N1909D probably benign Het
Shisal1 A T 15: 84,290,886 (GRCm39) Y120* probably null Het
Ska3 C T 14: 58,047,534 (GRCm39) V334I probably benign Het
Srebf2 A G 15: 82,066,309 (GRCm39) K579R probably benign Het
Sun1 A G 5: 139,224,575 (GRCm39) probably benign Het
Tc2n T A 12: 101,660,833 (GRCm39) Q133L possibly damaging Het
Tecta T C 9: 42,242,292 (GRCm39) T2094A probably damaging Het
Tex2 T C 11: 106,437,720 (GRCm39) D650G unknown Het
Trio A G 15: 27,748,177 (GRCm39) S2492P probably damaging Het
Ttn T C 2: 76,601,711 (GRCm39) T16872A probably benign Het
Ugcg T C 4: 59,189,690 (GRCm39) F16S probably benign Het
Usp16 T C 16: 87,255,571 (GRCm39) M1T probably null Het
Vmn1r60 C A 7: 5,547,710 (GRCm39) C130F possibly damaging Het
Vmn2r101 A G 17: 19,809,919 (GRCm39) D235G probably benign Het
Vpreb3 A T 10: 75,775,800 (GRCm39) V26E probably benign Het
Xrn2 T C 2: 146,903,207 (GRCm39) V765A probably benign Het
Zfp251 A G 15: 76,737,836 (GRCm39) I414T possibly damaging Het
Zfp426 A T 9: 20,384,413 (GRCm39) probably null Het
Zfp61 T C 7: 23,995,406 (GRCm39) M1V probably null 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
R0330: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
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 PCR Primer
(F):5'- ACTTGTGGAAATGCTAAGTGC -3'
(R):5'- AAGAATTGTGCTCAGGTATGGG -3'

Sequencing Primer
(F):5'- TAAGTGCACTCTCGCGC -3'
(R):5'- AGAATTGTGCTCAGGTATGGGTAGAG -3'
Posted On 2015-03-25