Incidental Mutation 'R4894:Vps39'
ID 377471
Institutional Source Beutler Lab
Gene Symbol Vps39
Ensembl Gene ENSMUSG00000027291
Gene Name VPS39 HOPS complex subunit
Synonyms Vam6, Vam6P, A230065P22Rik, mVam6
Accession Numbers
Essential gene? Probably essential (E-score: 0.953) question?
Stock # R4894 (G1)
Quality Score 126
Status Not validated
Chromosome 2
Chromosomal Location 120146942-120183618 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 120183440 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 10 (I10N)
Ref Sequence ENSEMBL: ENSMUSP00000099559 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028752] [ENSMUST00000090042] [ENSMUST00000090046] [ENSMUST00000102501]
AlphaFold Q8R5L3
Predicted Effect probably damaging
Transcript: ENSMUST00000028752
AA Change: I10N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: I10N

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 probably benign
Transcript: ENSMUST00000090042
SMART Domains Protein: ENSMUSP00000087496
Gene: ENSMUSG00000033808

DomainStartEndE-ValueType
Pfam:Lung_7-TM_R 184 471 1.1e-87 PFAM
low complexity region 480 486 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000090046
SMART Domains Protein: ENSMUSP00000087500
Gene: ENSMUSG00000033808

DomainStartEndE-ValueType
Pfam:Lung_7-TM_R 185 472 1.5e-85 PFAM
low complexity region 481 487 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000102501
AA Change: I10N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: I10N

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: ENSMUST00000124806
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126526
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129857
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156296
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147085
Predicted Effect noncoding transcript
Transcript: ENSMUST00000136410
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.4%
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: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrf1 C A 17: 43,609,975 (GRCm39) Y176* probably null Het
Akap13 T A 7: 75,375,068 (GRCm39) M1900K possibly damaging Het
Ankrd36 A G 11: 5,585,332 (GRCm39) E381G probably damaging Het
Ap3s1 T C 18: 46,891,183 (GRCm39) probably null Het
Cacna1e G T 1: 154,364,551 (GRCm39) S341* probably null Het
Camk1d G A 2: 5,359,539 (GRCm39) S161L probably damaging Het
Cdh23 G T 10: 60,173,630 (GRCm39) H1619Q probably benign Het
Chd7 T A 4: 8,838,629 (GRCm39) I1276N probably damaging Het
Clca3a1 A G 3: 144,719,662 (GRCm39) V436A probably damaging Het
Ctcfl G A 2: 172,959,196 (GRCm39) P177S probably benign Het
Dab2ip A G 2: 35,620,539 (GRCm39) probably benign Het
Dnah8 G A 17: 30,967,542 (GRCm39) D2585N probably benign Het
Epc1 A T 18: 6,449,011 (GRCm39) S495R probably benign Het
Espl1 A G 15: 102,230,758 (GRCm39) probably null Het
Eya4 T C 10: 22,985,753 (GRCm39) E583G possibly damaging Het
Fam111a C G 19: 12,565,913 (GRCm39) T554R probably benign Het
Fbh1 A T 2: 11,767,771 (GRCm39) I359N probably damaging Het
Fer1l6 T C 15: 58,490,751 (GRCm39) C1023R probably damaging Het
Helz2 G C 2: 180,877,940 (GRCm39) P953A probably benign Het
Ifi204 G T 1: 173,587,808 (GRCm39) S117Y probably damaging Het
Ift70a1 T C 2: 75,810,088 (GRCm39) *665W probably null Het
Igfn1 G A 1: 135,882,520 (GRCm39) T2775M probably damaging Het
Igsf9 A G 1: 172,325,634 (GRCm39) T1101A probably benign Het
Ipo13 A C 4: 117,760,638 (GRCm39) I614S probably damaging Het
Ipo13 A G 4: 117,761,687 (GRCm39) I476T possibly damaging Het
Kdm2b C A 5: 123,079,030 (GRCm39) E308* probably null Het
Klhl20 A T 1: 160,937,102 (GRCm39) M91K possibly damaging Het
Klrb1f T C 6: 129,030,151 (GRCm39) F64L probably benign Het
Ldlrad3 C T 2: 101,888,293 (GRCm39) C106Y probably damaging Het
Lilra6 T C 7: 3,915,530 (GRCm39) T161A probably benign Het
Lrriq1 A T 10: 102,997,613 (GRCm39) M1334K possibly damaging Het
Mepe C G 5: 104,473,268 (GRCm39) P3R probably damaging Het
Mgat4e A G 1: 134,468,856 (GRCm39) V396A probably benign Het
Nfx1 T G 4: 40,996,877 (GRCm39) S651A probably damaging Het
Or10ak13 A T 4: 118,639,483 (GRCm39) C100S probably damaging Het
Or2w6 T C 13: 21,843,352 (GRCm39) N47S probably damaging Het
Or4c109 T C 2: 88,817,783 (GRCm39) I254M possibly damaging Het
Rag2 T C 2: 101,460,022 (GRCm39) S111P probably damaging Het
Rai1 T A 11: 60,077,572 (GRCm39) D545E probably damaging Het
Ralgps1 A G 2: 33,033,115 (GRCm39) V498A possibly damaging Het
Rasal2 G A 1: 157,020,374 (GRCm39) S205L probably damaging Het
Rec8 T C 14: 55,862,787 (GRCm39) L582P probably damaging Het
Retn G A 8: 3,707,358 (GRCm39) R106H probably damaging Het
Rnf112 A G 11: 61,343,488 (GRCm39) L116P probably damaging Het
Rnf213 T C 11: 119,372,066 (GRCm39) Y4885H probably damaging Het
Sacm1l A G 9: 123,411,409 (GRCm39) I399M probably benign Het
Sez6 G T 11: 77,866,086 (GRCm39) G738V probably damaging Het
Spata17 A G 1: 186,872,643 (GRCm39) V56A probably benign Het
Spata31d1a A T 13: 59,849,542 (GRCm39) V862D probably damaging Het
Sptb A G 12: 76,671,768 (GRCm39) probably null Het
Srpk2 C A 5: 23,750,527 (GRCm39) G59W probably damaging Het
Tyro3 T C 2: 119,632,779 (GRCm39) S96P probably damaging Het
Ube2v1 A G 2: 167,452,280 (GRCm39) S108P probably damaging Het
Usp2 C T 9: 43,987,125 (GRCm39) S141L probably benign Het
Vamp5 T C 6: 72,347,181 (GRCm39) D46G possibly damaging Het
Vmn1r23 T A 6: 57,903,310 (GRCm39) Q156L probably benign Het
Vmn2r6 C T 3: 64,454,829 (GRCm39) S490N probably benign Het
Vwf C T 6: 125,622,897 (GRCm39) Q1755* probably null Het
Wdfy4 A T 14: 32,877,717 (GRCm39) H82Q probably benign Het
Wdr24 T C 17: 26,045,101 (GRCm39) Y279H probably damaging Het
Wdr72 A G 9: 74,117,843 (GRCm39) T852A probably benign Het
Zfp1 T A 8: 112,396,355 (GRCm39) C92* probably null Het
Zfp1004 T A 2: 150,033,899 (GRCm39) C104* probably null Het
Zfp426 A T 9: 20,386,369 (GRCm39) probably benign Het
Zfp442 C T 2: 150,253,130 (GRCm39) probably null Het
Zfp74 T C 7: 29,635,470 (GRCm39) probably benign 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
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
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'- CTTAGCAATCACGCAAGCCG -3'
(R):5'- GCAGCTGGTATGGATGTGAACTC -3'

Sequencing Primer
(F):5'- GCCCGGGGTCCAGTCAC -3'
(R):5'- GCTTAAGGCAACAGGAAGTCC -3'
Posted On 2016-03-17