Incidental Mutation 'R6208:Vps39'
ID 503245
Institutional Source Beutler Lab
Gene Symbol Vps39
Ensembl Gene ENSMUSG00000027291
Gene Name VPS39 HOPS complex subunit
Synonyms Vam6, Vam6P, A230065P22Rik, mVam6
MMRRC Submission 044342-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.953) question?
Stock # R6208 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 120146942-120183618 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 120163897 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 355 (M355K)
Ref Sequence ENSEMBL: ENSMUSP00000028752 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028752] [ENSMUST00000102501]
AlphaFold Q8R5L3
Predicted Effect probably damaging
Transcript: ENSMUST00000028752
AA Change: M355K

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: M355K

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 damaging
Transcript: ENSMUST00000102501
AA Change: M366K

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: M366K

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: ENSMUST00000132476
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147085
Meta Mutation Damage Score 0.5943 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency 98% (57/58)
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actl6a A T 3: 32,766,043 (GRCm39) I18F probably benign Het
Apol11a C T 15: 77,401,241 (GRCm39) R243C probably damaging Het
Asap3 A G 4: 135,968,508 (GRCm39) M687V probably benign Het
Axdnd1 C T 1: 156,220,426 (GRCm39) probably benign Het
Baz2b A G 2: 59,755,150 (GRCm39) F1026S probably damaging Het
Bsg T C 10: 79,544,672 (GRCm39) L70P probably damaging Het
Col10a1 A G 10: 34,270,582 (GRCm39) N185D possibly damaging Het
Col6a2 T A 10: 76,450,891 (GRCm39) N50I possibly damaging Het
Cux2 G A 5: 121,998,885 (GRCm39) P1352S possibly damaging Het
Defa25 A G 8: 21,575,197 (GRCm39) probably null Het
Emc1 G T 4: 139,081,582 (GRCm39) R70L probably damaging Het
Fat1 T C 8: 45,480,650 (GRCm39) F3028S probably damaging Het
Fhit T C 14: 9,573,435 (GRCm38) E205G probably benign Het
Gaa C A 11: 119,171,997 (GRCm39) A700D probably benign Het
Gm20830 T G Y: 6,916,792 (GRCm39) E109A probably benign Homo
Grm1 A T 10: 10,595,690 (GRCm39) F646Y probably damaging Het
Hp1bp3 A G 4: 137,944,481 (GRCm39) probably benign Het
Lce1d G A 3: 92,593,312 (GRCm39) P34S unknown Het
Lpar1 G A 4: 58,504,630 (GRCm39) Q13* probably null Het
Lrrc61 C T 6: 48,545,839 (GRCm39) R221* probably null Het
Map2 A G 1: 66,470,749 (GRCm39) N328D probably damaging Het
Mndal T A 1: 173,684,988 (GRCm39) D527V possibly damaging Het
Mycbp2 T G 14: 103,532,664 (GRCm39) N430T probably benign Het
Myo1e A G 9: 70,283,887 (GRCm39) Y861C probably damaging Het
Nav2 A G 7: 49,213,851 (GRCm39) T1622A probably damaging Het
Nom1 A T 5: 29,654,617 (GRCm39) H773L possibly damaging Het
Npc2 G T 12: 84,803,919 (GRCm39) P144Q probably damaging Het
Npnt A G 3: 132,655,774 (GRCm39) probably benign Het
Nxpe4 A T 9: 48,304,678 (GRCm39) Y255F probably benign Het
Obscn G A 11: 58,958,474 (GRCm39) A3769V possibly damaging Het
Optc T C 1: 133,832,737 (GRCm39) D121G probably damaging Het
Pard6a T C 8: 106,428,866 (GRCm39) F26L probably damaging Het
Pcdhga4 T A 18: 37,819,762 (GRCm39) I437N probably damaging Het
Phf12 G T 11: 77,914,417 (GRCm39) V71F probably damaging Het
Phf21b T A 15: 84,679,317 (GRCm39) S282C probably damaging Het
Pou5f1 T C 17: 35,821,357 (GRCm39) F323S possibly damaging Het
Psmd5 A T 2: 34,757,023 (GRCm39) I67N probably damaging Het
Pyroxd1 A G 6: 142,303,182 (GRCm39) K273R probably benign Het
Rnd2 C T 11: 101,359,825 (GRCm39) L57F probably damaging Het
Rpusd1 A T 17: 25,949,352 (GRCm39) H174L probably damaging Het
Ryr2 T C 13: 11,910,106 (GRCm39) K94R probably benign Het
Scn2b A G 9: 45,029,328 (GRCm39) R3G probably benign Het
Sf3b2 A T 19: 5,325,126 (GRCm39) M782K possibly damaging Het
Skint7 A G 4: 111,842,073 (GRCm39) probably null Het
Slc43a1 A G 2: 84,687,184 (GRCm39) I319V possibly damaging Het
Snupn T A 9: 56,890,247 (GRCm39) M356K probably damaging Het
Spata31d1a C A 13: 59,848,378 (GRCm39) R1250M probably damaging Het
Sprr2h T C 3: 92,294,216 (GRCm39) V21A unknown Het
Srpra A G 9: 35,127,291 (GRCm39) T614A possibly damaging Het
Stk36 A T 1: 74,650,591 (GRCm39) Q327L probably benign Het
Syne3 A G 12: 104,909,622 (GRCm39) I738T probably benign Het
Tcea3 A T 4: 135,975,360 (GRCm39) M1L probably damaging Het
Tead2 G T 7: 44,867,526 (GRCm39) R85L probably damaging Het
Thap7 T C 16: 17,346,300 (GRCm39) N228D possibly damaging Het
Trip11 T A 12: 101,865,154 (GRCm39) E173V probably damaging Het
Ttc38 T A 15: 85,725,698 (GRCm39) M187K possibly damaging Het
Vmn1r193 T A 13: 22,403,138 (GRCm39) T285S possibly damaging Het
Vmn2r106 T C 17: 20,488,591 (GRCm39) T603A probably damaging Het
Wnt5b G T 6: 119,423,473 (GRCm39) L51I probably damaging Het
Xxylt1 A G 16: 30,826,626 (GRCm39) Y230H 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
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
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'- GTGACCCTCCTAATGCCATC -3'
(R):5'- TTACCACTAAGAATGGGCAAAGC -3'

Sequencing Primer
(F):5'- TCCTAATGCCATCACATAACCAAGG -3'
(R):5'- TTTAATCCCAGCACTCGGGAG -3'
Posted On 2018-02-27