Incidental Mutation 'R8860:Vps4b'
ID 675590
Institutional Source Beutler Lab
Gene Symbol Vps4b
Ensembl Gene ENSMUSG00000009907
Gene Name vacuolar protein sorting 4B
Synonyms Skd1, 8030489C12Rik
MMRRC Submission 068678-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.168) question?
Stock # R8860 (G1)
Quality Score 225.009
Status Validated
Chromosome 1
Chromosomal Location 106698518-106724455 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 106710414 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 156 (F156L)
Ref Sequence ENSEMBL: ENSMUSP00000092230 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000094646] [ENSMUST00000112736]
AlphaFold P46467
PDB Structure Crystal structure of mouse SKD1/VPS4B apo-form [X-RAY DIFFRACTION]
Crystal structure of mouse SKD1/VPS4B ATP-form [X-RAY DIFFRACTION]
Crystal structure of mouse SKD1/VPS4B ADP-form [X-RAY DIFFRACTION]
Predicted Effect possibly damaging
Transcript: ENSMUST00000094646
AA Change: F156L

PolyPhen 2 Score 0.630 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000092230
Gene: ENSMUSG00000009907
AA Change: F156L

DomainStartEndE-ValueType
MIT 4 82 7.95e-26 SMART
AAA 166 302 1.55e-22 SMART
Blast:AAA 322 366 3e-10 BLAST
Pfam:Vps4_C 381 441 1.4e-30 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000112736
AA Change: F156L

PolyPhen 2 Score 0.630 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000108356
Gene: ENSMUSG00000009907
AA Change: F156L

DomainStartEndE-ValueType
MIT 4 82 7.95e-26 SMART
AAA 166 302 1.55e-22 SMART
Blast:AAA 322 366 3e-10 BLAST
Pfam:Vps4_C 380 441 7.6e-31 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.5%
  • 20x: 98.2%
Validation Efficiency 100% (45/45)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the AAA protein family (ATPases associated with diverse cellular activities), and is the homolog of the yeast Vps4 protein. In humans, two paralogs of the yeast protein have been identified. The former share a high degree of aa sequence similarity with each other, and also with yeast Vps4 and mouse Skd1 proteins. Mouse Skd1 (suppressor of K+ transport defect 1) has been shown to be a yeast Vps4 ortholog. Functional studies indicate that both human paralogs associate with the endosomal compartments, and are involved in intracellular protein trafficking, similar to Vps4 protein in yeast. The gene encoding this paralog has been mapped to chromosome 18; the gene for the other resides on chromosome 16. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 43 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700049A03Rik T G 12: 71,231,197 (GRCm39) V985G possibly damaging Het
Acr T G 15: 89,458,057 (GRCm39) M246R probably damaging Het
Ago4 A T 4: 126,387,043 (GRCm39) D853E probably benign Het
Atf6 A T 1: 170,680,535 (GRCm39) F52L probably null Het
Blm A T 7: 80,144,276 (GRCm39) C782S probably benign Het
C2cd5 A G 6: 143,028,946 (GRCm39) Y98H probably benign Het
Ccdc106 A G 7: 5,062,570 (GRCm39) D192G probably benign Het
Celf2 A G 2: 6,565,468 (GRCm39) probably null Het
Chd1l A G 3: 97,477,685 (GRCm39) F690S probably benign Het
Chuk A G 19: 44,076,407 (GRCm39) S435P possibly damaging Het
Cisd3 T A 11: 97,576,703 (GRCm39) S10T probably benign Het
Cma2 G T 14: 56,210,574 (GRCm39) C143F probably damaging Het
Cmtm1 TCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGG TCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGG 8: 105,036,334 (GRCm39) probably null Het
Cnppd1 A G 1: 75,113,063 (GRCm39) S402P probably damaging Het
Crtc1 A G 8: 70,840,805 (GRCm39) S474P probably damaging Het
Dhx38 A T 8: 110,289,361 (GRCm39) L13* probably null Het
Fat4 A T 3: 38,946,269 (GRCm39) T1721S probably benign Het
Fntb T A 12: 76,934,826 (GRCm39) V201E possibly damaging Het
Gga3 T C 11: 115,481,244 (GRCm39) D242G probably benign Het
Hif3a A T 7: 16,774,912 (GRCm39) M562K probably benign Het
Hnrnpc A G 14: 52,312,792 (GRCm39) S261P possibly damaging Het
Intu G A 3: 40,627,162 (GRCm39) M314I probably benign Het
Lims1 C T 10: 58,243,925 (GRCm39) Q126* probably null Het
Lrrc14b T A 13: 74,509,408 (GRCm39) D333V probably damaging Het
Meaf6 T A 4: 124,979,990 (GRCm39) L48Q probably damaging Het
Miip T A 4: 147,950,839 (GRCm39) probably benign Het
Myh4 T A 11: 67,132,335 (GRCm39) I155N probably damaging Het
Nnt T C 13: 119,476,407 (GRCm39) Y733C Het
Nup155 T C 15: 8,159,640 (GRCm39) V517A possibly damaging Het
Obscn C T 11: 58,898,440 (GRCm39) R6607Q unknown Het
Or2ak7 C T 11: 58,574,966 (GRCm39) T89I probably benign Het
Or51s1 A G 7: 102,558,336 (GRCm39) S237P probably benign Het
Ptprg T C 14: 12,213,685 (GRCm38) Y1018H probably damaging Het
Rdh8 A C 9: 20,734,021 (GRCm39) N69T probably benign Het
Rgsl1 G A 1: 153,697,100 (GRCm39) Q572* probably null Het
Septin7 A T 9: 25,163,980 (GRCm39) N16Y possibly damaging Het
Sparcl1 T C 5: 104,241,218 (GRCm39) N69D probably benign Het
Ssh3 A T 19: 4,317,992 (GRCm39) V41E probably damaging Het
Tmem253 A G 14: 52,256,303 (GRCm39) R168G probably benign Het
Vmn2r60 T A 7: 41,791,654 (GRCm39) F526I probably damaging Het
Vmn2r73 A T 7: 85,522,149 (GRCm39) probably benign Het
Zfp354c T A 11: 50,706,019 (GRCm39) H352L probably damaging Het
Zic2 A T 14: 122,713,530 (GRCm39) H148L possibly damaging Het
Other mutations in Vps4b
AlleleSourceChrCoordTypePredicted EffectPPH Score
R1484:Vps4b UTSW 1 106,707,712 (GRCm39) missense probably damaging 1.00
R1843:Vps4b UTSW 1 106,706,712 (GRCm39) missense possibly damaging 0.94
R5044:Vps4b UTSW 1 106,724,148 (GRCm39) splice site probably null
R5375:Vps4b UTSW 1 106,719,422 (GRCm39) missense probably benign 0.36
R5931:Vps4b UTSW 1 106,705,065 (GRCm39) missense probably benign
R7311:Vps4b UTSW 1 106,719,434 (GRCm39) missense probably damaging 0.99
R7514:Vps4b UTSW 1 106,708,232 (GRCm39) critical splice donor site probably null
R8852:Vps4b UTSW 1 106,710,414 (GRCm39) missense possibly damaging 0.63
R9631:Vps4b UTSW 1 106,707,835 (GRCm39) missense possibly damaging 0.92
Z1177:Vps4b UTSW 1 106,719,430 (GRCm39) missense possibly damaging 0.51
Predicted Primers PCR Primer
(F):5'- ATGTAGCATTCCACTGAGTTACC -3'
(R):5'- TCCAGACAATTTTACGCTGTGG -3'

Sequencing Primer
(F):5'- AGCATTCCACTGAGTTACCTTAAGC -3'
(R):5'- CAATTTTACGCTGTGGGTTTTAAATG -3'
Posted On 2021-07-15