Incidental Mutation 'R4600:Vps41'
ID 345562
Institutional Source Beutler Lab
Gene Symbol Vps41
Ensembl Gene ENSMUSG00000041236
Gene Name VPS41 HOPS complex subunit
Synonyms Vam2, mVam2
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4600 (G1)
Quality Score 225
Status Not validated
Chromosome 13
Chromosomal Location 18901462-19050981 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 18929453 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 63 (Y63H)
Ref Sequence ENSEMBL: ENSMUSP00000072729 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000072961]
AlphaFold Q5KU39
Predicted Effect probably damaging
Transcript: ENSMUST00000072961
AA Change: Y63H

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000072729
Gene: ENSMUSG00000041236
AA Change: Y63H

DomainStartEndE-ValueType
low complexity region 3 26 N/A INTRINSIC
Blast:WD40 34 70 2e-7 BLAST
SCOP:d1flga_ 44 253 6e-9 SMART
Blast:WD40 159 195 3e-11 BLAST
CLH 570 711 1.92e-42 SMART
RING 790 837 8.98e-2 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000222269
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.1%
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 ortholog of yeast Vps41 protein which is also conserved in Drosophila, tomato, and Arabidopsis. Expression studies in yeast and human indicate that this protein may be involved in the formation and fusion of transport vesicles from the Golgi. Several transcript variants encoding different isoforms have been described for this gene, however, the full-length nature of not all is known. [provided by RefSeq, Jul 2008]
PHENOTYPE: Embryos homozygous for a knock-out allele die by E9 exhibiting morphological and functional alteration of late endocytic compartments, and abnormal triploblastic development. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 94 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700049A03Rik T C 12: 71,195,037 (GRCm39) F145L possibly damaging Het
Aars2 T A 17: 45,827,847 (GRCm39) D555E probably damaging Het
Ago1 C A 4: 126,354,185 (GRCm39) M208I probably benign Het
Ak7 G A 12: 105,679,834 (GRCm39) V123M probably benign Het
Amfr A G 8: 94,700,849 (GRCm39) L537P probably damaging Het
Apob A G 12: 8,058,568 (GRCm39) D2317G probably damaging Het
Asb6 T A 2: 30,714,483 (GRCm39) D209V probably damaging Het
AY358078 T A 14: 52,063,532 (GRCm39) C393S possibly damaging Het
Baz2a T A 10: 127,957,052 (GRCm39) C932S probably damaging Het
Btnl10 A G 11: 58,814,426 (GRCm39) I369V probably benign Het
Ccdc66 T C 14: 27,222,377 (GRCm39) N122S probably damaging Het
Cfap96 A T 8: 46,423,505 (GRCm39) I69N probably damaging Het
Clic4 A T 4: 134,966,300 (GRCm39) probably null Het
Col6a3 A G 1: 90,709,626 (GRCm39) S1857P unknown Het
Cracr2a A C 6: 127,580,851 (GRCm39) D9A probably benign Het
Cspg4b A G 13: 113,455,783 (GRCm39) R610G possibly damaging Het
Dcst1 T C 3: 89,263,643 (GRCm39) E384G probably benign Het
Ddx4 T C 13: 112,748,594 (GRCm39) K435E probably damaging Het
Deaf1 T A 7: 140,890,884 (GRCm39) T433S possibly damaging Het
Dnah3 T A 7: 119,689,169 (GRCm39) M82L probably benign Het
Dnhd1 G T 7: 105,352,851 (GRCm39) R2668L probably damaging Het
Efcab6 C T 15: 83,831,126 (GRCm39) G596D probably benign Het
Ercc3 G A 18: 32,378,624 (GRCm39) A202T probably benign Het
Fam181b C A 7: 92,729,992 (GRCm39) A255E possibly damaging Het
Fam83e T A 7: 45,372,924 (GRCm39) D178E probably benign Het
Frem2 A G 3: 53,455,228 (GRCm39) L2116S possibly damaging Het
Gm16494 T A 17: 47,327,723 (GRCm39) K54* probably null Het
Golgb1 A G 16: 36,738,987 (GRCm39) D2442G probably damaging Het
Greb1l G A 18: 10,553,705 (GRCm39) A1569T probably damaging Het
Grik5 C G 7: 24,767,489 (GRCm39) E64Q probably damaging Het
Gstm5 A G 3: 107,805,302 (GRCm39) Y130C probably damaging Het
Gucy2e C G 11: 69,126,994 (GRCm39) A160P possibly damaging Het
Hydin A T 8: 111,293,582 (GRCm39) T3510S probably benign Het
Ift70a1 T C 2: 75,810,977 (GRCm39) T369A probably benign Het
Itgb2 A G 10: 77,381,949 (GRCm39) I84V probably benign Het
Itsn1 A G 16: 91,696,475 (GRCm39) Q26R probably damaging Het
Kat6a A G 8: 23,429,327 (GRCm39) S1561G probably benign Het
Khnyn G A 14: 56,124,438 (GRCm39) V231I probably benign Het
Kif21b A G 1: 136,075,602 (GRCm39) D243G probably benign Het
Klk4 T A 7: 43,534,762 (GRCm39) N240K probably damaging Het
Knl1 T C 2: 118,901,025 (GRCm39) S909P possibly damaging Het
Lamb1 A C 12: 31,373,528 (GRCm39) D1419A probably benign Het
Lin9 T A 1: 180,508,759 (GRCm39) V421D probably damaging Het
Lipt2 T C 7: 99,809,519 (GRCm39) L202P probably benign Het
Mbd5 T G 2: 49,147,209 (GRCm39) M473R probably benign Het
Mcc A T 18: 44,652,587 (GRCm39) I279N probably damaging Het
Mcpt9 C T 14: 56,266,049 (GRCm39) V60M probably damaging Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Mslnl G A 17: 25,961,908 (GRCm39) V128M probably damaging Het
Mylk2 G A 2: 152,759,476 (GRCm39) V389M probably damaging Het
Ndufs7 T A 10: 80,092,501 (GRCm39) Y203* probably null Het
Nup160 T A 2: 90,515,541 (GRCm39) probably null Het
Nup88 G A 11: 70,860,522 (GRCm39) R62* probably null Het
Or2g7 T C 17: 38,378,853 (GRCm39) S264P probably damaging Het
Or51af1 T A 7: 103,141,788 (GRCm39) Q99L probably damaging Het
Or6c207 G A 10: 129,104,274 (GRCm39) A306V probably benign Het
Or8b8 T A 9: 37,809,622 (GRCm39) S307R probably benign Het
Or8g33 A G 9: 39,337,731 (GRCm39) M212T probably benign Het
Os9 T C 10: 126,934,223 (GRCm39) N471S probably benign Het
Otof C T 5: 30,529,244 (GRCm39) V1757M probably damaging Het
Pakap A T 4: 57,709,954 (GRCm39) T300S probably benign Het
Pald1 T C 10: 61,184,395 (GRCm39) T241A probably benign Het
Pappa2 G A 1: 158,642,015 (GRCm39) S1347L probably damaging Het
Pccb T C 9: 100,916,832 (GRCm39) T27A probably benign Het
Pde4dip A T 3: 97,603,260 (GRCm39) V2243D probably damaging Het
Pkd2l2 C A 18: 34,571,254 (GRCm39) Q590K probably benign Het
Pmepa1 G A 2: 173,070,120 (GRCm39) P145L possibly damaging Het
Ppp3cb T C 14: 20,570,714 (GRCm39) N339S possibly damaging Het
Rnf133 T C 6: 23,649,041 (GRCm39) E296G possibly damaging Het
Secisbp2l C T 2: 125,582,657 (GRCm39) G933D possibly damaging Het
Serpinb12 T A 1: 106,876,883 (GRCm39) D66E probably benign Het
Slc35e2 T C 4: 155,702,106 (GRCm39) F290S probably benign Het
Slc46a2 C T 4: 59,911,886 (GRCm39) C442Y probably damaging Het
Slc7a1 A G 5: 148,278,869 (GRCm39) L301P probably damaging Het
Spg21 A G 9: 65,383,257 (GRCm39) T148A probably benign Het
Stox2 A G 8: 47,645,970 (GRCm39) S497P probably damaging Het
Sult1c2 C A 17: 54,280,983 (GRCm39) W40L probably benign Het
Sytl2 T C 7: 90,024,977 (GRCm39) S322P probably benign Het
Telo2 C A 17: 25,324,122 (GRCm39) R531L possibly damaging Het
Thbs3 T C 3: 89,131,897 (GRCm39) V719A probably damaging Het
Tlr9 T A 9: 106,101,732 (GRCm39) L341Q probably damaging Het
Tmprss5 A G 9: 49,024,548 (GRCm39) N230D possibly damaging Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Tpo C T 12: 30,148,228 (GRCm39) V558M probably benign Het
Trex1 T G 9: 108,887,352 (GRCm39) Q213P possibly damaging Het
Ttc7b G A 12: 100,466,376 (GRCm39) R79C probably damaging Het
Ugt1a6a A G 1: 88,066,586 (GRCm39) K131E probably benign Het
Vipr1 T A 9: 121,494,202 (GRCm39) probably null Het
Vmn1r22 T C 6: 57,877,860 (GRCm39) D39G probably damaging Het
Vmn2r58 A T 7: 41,522,046 (GRCm39) C17S probably benign Het
Xdh G T 17: 74,217,195 (GRCm39) T691N probably benign Het
Zfp518b T C 5: 38,830,970 (GRCm39) N345S probably damaging Het
Zfp536 T A 7: 37,267,918 (GRCm39) K499N probably damaging Het
Zfp963 A T 8: 70,195,510 (GRCm39) probably null Het
Other mutations in Vps41
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01134:Vps41 APN 13 19,050,320 (GRCm39) missense probably benign 0.37
IGL01563:Vps41 APN 13 18,966,897 (GRCm39) splice site probably benign
IGL01880:Vps41 APN 13 18,994,641 (GRCm39) missense probably benign 0.01
IGL02024:Vps41 APN 13 18,975,827 (GRCm39) splice site probably benign
IGL02458:Vps41 APN 13 19,037,649 (GRCm39) missense possibly damaging 0.67
IGL02740:Vps41 APN 13 19,022,850 (GRCm39) missense probably damaging 1.00
IGL03218:Vps41 APN 13 19,013,440 (GRCm39) missense possibly damaging 0.74
R0197:Vps41 UTSW 13 19,038,833 (GRCm39) critical splice donor site probably null
R0284:Vps41 UTSW 13 19,037,610 (GRCm39) missense probably damaging 1.00
R0321:Vps41 UTSW 13 19,026,465 (GRCm39) splice site probably benign
R0372:Vps41 UTSW 13 19,026,417 (GRCm39) missense probably benign 0.00
R0382:Vps41 UTSW 13 19,011,897 (GRCm39) missense probably benign 0.30
R1691:Vps41 UTSW 13 19,025,413 (GRCm39) missense probably damaging 1.00
R2055:Vps41 UTSW 13 19,038,786 (GRCm39) missense possibly damaging 0.95
R2082:Vps41 UTSW 13 19,036,521 (GRCm39) missense probably benign 0.27
R2147:Vps41 UTSW 13 19,023,904 (GRCm39) splice site probably null
R2897:Vps41 UTSW 13 18,994,598 (GRCm39) splice site probably benign
R4322:Vps41 UTSW 13 19,007,960 (GRCm39) missense probably damaging 1.00
R4751:Vps41 UTSW 13 18,995,792 (GRCm39) missense probably damaging 0.98
R4856:Vps41 UTSW 13 19,013,425 (GRCm39) missense probably damaging 0.98
R5389:Vps41 UTSW 13 19,046,708 (GRCm39) missense probably damaging 0.99
R7022:Vps41 UTSW 13 19,026,438 (GRCm39) missense possibly damaging 0.76
R7456:Vps41 UTSW 13 19,048,204 (GRCm39) missense probably benign 0.02
R7747:Vps41 UTSW 13 19,025,422 (GRCm39) critical splice donor site probably null
R7790:Vps41 UTSW 13 19,026,438 (GRCm39) missense possibly damaging 0.76
R8029:Vps41 UTSW 13 19,007,955 (GRCm39) nonsense probably null
R8033:Vps41 UTSW 13 18,994,635 (GRCm39) missense possibly damaging 0.94
R8241:Vps41 UTSW 13 19,033,168 (GRCm39) missense possibly damaging 0.73
R8267:Vps41 UTSW 13 18,994,641 (GRCm39) missense probably benign 0.00
R8801:Vps41 UTSW 13 18,998,403 (GRCm39) missense possibly damaging 0.78
R8927:Vps41 UTSW 13 18,929,501 (GRCm39) missense probably benign 0.01
R8928:Vps41 UTSW 13 18,929,501 (GRCm39) missense probably benign 0.01
R9029:Vps41 UTSW 13 18,994,723 (GRCm39) critical splice donor site probably null
R9057:Vps41 UTSW 13 19,027,702 (GRCm39) missense probably benign 0.19
R9066:Vps41 UTSW 13 19,008,018 (GRCm39) missense probably damaging 0.99
R9113:Vps41 UTSW 13 19,023,883 (GRCm39) missense probably benign 0.25
R9129:Vps41 UTSW 13 19,011,775 (GRCm39) missense probably benign 0.00
R9282:Vps41 UTSW 13 19,013,401 (GRCm39) nonsense probably null
R9391:Vps41 UTSW 13 18,994,616 (GRCm39) missense probably benign 0.19
R9478:Vps41 UTSW 13 19,046,913 (GRCm39) missense
R9569:Vps41 UTSW 13 19,013,396 (GRCm39) missense possibly damaging 0.93
Z1177:Vps41 UTSW 13 19,038,765 (GRCm39) missense probably damaging 0.97
Z1177:Vps41 UTSW 13 19,030,105 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- GTCATTTTCCCCAGGCTGGA -3'
(R):5'- CAGAGTTCTTTCTCTAATTCAACTTCA -3'

Sequencing Primer
(F):5'- AGCCATGCCTTTTCTAGGG -3'
(R):5'- AGCATGGCAATTAATGTGT -3'
Posted On 2015-09-25