Incidental Mutation 'R3801:Vps54'
ID 272992
Institutional Source Beutler Lab
Gene Symbol Vps54
Ensembl Gene ENSMUSG00000020128
Gene Name VPS54 GARP complex subunit
Synonyms 5330404P15Rik, Vps54l, mSLP8, wr
MMRRC Submission 040760-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.931) question?
Stock # R3801 (G1)
Quality Score 219
Status Not validated
Chromosome 11
Chromosomal Location 21189281-21271136 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 21218832 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 130 (D130E)
Ref Sequence ENSEMBL: ENSMUSP00000105206 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006221] [ENSMUST00000109578] [ENSMUST00000132017]
AlphaFold Q5SPW0
Predicted Effect probably benign
Transcript: ENSMUST00000006221
AA Change: D142E

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: D142E

DomainStartEndE-ValueType
low complexity region 3 16 N/A INTRINSIC
Pfam:DUF2450 198 364 2.1e-12 PFAM
Pfam:Vps54 736 868 3.3e-56 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000109578
AA Change: D130E

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: D130E

DomainStartEndE-ValueType
low complexity region 3 16 N/A INTRINSIC
Pfam:DUF2450 186 352 2.3e-12 PFAM
Pfam:Vps54 723 857 1.6e-63 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000132017
AA Change: D16E

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: D16E

DomainStartEndE-ValueType
Pfam:DUF2450 72 238 1.4e-12 PFAM
Pfam:Vps54 573 707 7.8e-64 PFAM
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.0%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes for a protein that in yeast forms part of a trimeric vacuolar-protein-sorting complex that is required for retrograde transport of proteins from prevacuoles to the late Golgi compartment. As in yeast, mammalian Vps54 proteins contain a coiled-coil region and dileucine motifs. Alternative splicing results in multiple transcript variants encoding different isoforms [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutants show progressive ataxia, tremors, and limb paralysis with degeneration of motor nerve cells of brainstem and spinal cord and atrophy of skeletal muscle beginning about 3-weeks of age. Mutants are sterile and most die by 3-months of age. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700011L22Rik C T 8: 79,974,922 (GRCm39) E54K probably benign Het
Als2 A C 1: 59,206,358 (GRCm39) M1634R probably damaging Het
Ankfy1 T C 11: 72,640,246 (GRCm39) S531P probably benign Het
Atp6v1e1 A G 6: 120,778,020 (GRCm39) Y172H probably benign Het
Brd1 C T 15: 88,601,243 (GRCm39) V464M probably damaging Het
Btaf1 A T 19: 36,963,948 (GRCm39) T840S probably benign Het
Btaf1 A T 19: 36,966,373 (GRCm39) H1047L probably benign Het
Cacnb2 A G 2: 14,829,074 (GRCm39) D3G possibly damaging Het
Capn13 G A 17: 73,646,396 (GRCm39) P339L probably benign Het
Cgrrf1 G T 14: 47,069,820 (GRCm39) G30C probably damaging Het
Crnkl1 T C 2: 145,761,715 (GRCm39) D614G probably benign Het
Cyp2c23 C T 19: 43,995,478 (GRCm39) V430I probably benign Het
Dazl G A 17: 50,588,309 (GRCm39) R289W probably benign Het
Dsg1b C T 18: 20,523,260 (GRCm39) P96S probably damaging Het
Dusp14 A G 11: 83,939,535 (GRCm39) S169P possibly damaging Het
Egfem1 A G 3: 29,206,075 (GRCm39) D91G probably benign Het
Eif1 A G 11: 100,211,650 (GRCm39) K95E probably damaging Het
Fap C T 2: 62,376,994 (GRCm39) V191I probably benign Het
Flnc T C 6: 29,447,403 (GRCm39) Y1069H probably damaging Het
Fndc7 T C 3: 108,776,464 (GRCm39) T526A possibly damaging Het
Fras1 A T 5: 96,881,791 (GRCm39) T2508S probably benign Het
Gast T C 11: 100,227,636 (GRCm39) S73P probably damaging Het
Grap2 A G 15: 80,507,947 (GRCm39) T4A possibly damaging Het
Grm8 T G 6: 28,125,635 (GRCm39) N164H possibly damaging Het
Hyal5 A T 6: 24,876,523 (GRCm39) H132L probably benign Het
Iqcm C A 8: 76,396,021 (GRCm39) T188K possibly damaging Het
Kank4 A G 4: 98,668,370 (GRCm39) S26P probably damaging Het
Lipo3 C T 19: 33,762,257 (GRCm39) C80Y probably damaging Het
Lrrk2 A G 15: 91,621,314 (GRCm39) R963G probably benign Het
Lrtm2 G A 6: 119,294,444 (GRCm39) T229I probably damaging Het
Mb21d2 A T 16: 28,646,755 (GRCm39) D406E possibly damaging Het
Meikin T A 11: 54,290,697 (GRCm39) probably null Het
Mybl1 A T 1: 9,743,439 (GRCm39) F538I probably damaging Het
Nectin2 T C 7: 19,451,561 (GRCm39) D491G probably benign Het
Nf1 A G 11: 79,450,347 (GRCm39) D511G probably null Het
Nid2 T C 14: 19,860,065 (GRCm39) C1328R probably damaging Het
Nlrp1a T A 11: 71,013,529 (GRCm39) M574L probably benign Het
Nrap C T 19: 56,310,211 (GRCm39) D1595N probably damaging Het
Nrg3 G A 14: 38,098,391 (GRCm39) P496S probably damaging Het
Or4k41 A T 2: 111,279,910 (GRCm39) I142F probably benign Het
Pak3 G A X: 142,492,727 (GRCm39) V87I probably damaging Het
Phf8 T C X: 150,355,572 (GRCm39) S512P possibly damaging Het
Phkb G T 8: 86,648,858 (GRCm39) E225* probably null Het
Plaa T C 4: 94,458,125 (GRCm39) D615G probably damaging Het
Prdm12 A G 2: 31,541,959 (GRCm39) K223E probably damaging Het
Prkd1 C A 12: 50,430,205 (GRCm39) R634L possibly damaging Het
Rassf3 T A 10: 121,250,271 (GRCm39) I181F possibly damaging Het
Samd8 G A 14: 21,825,133 (GRCm39) V30M probably damaging Het
Sema4f A T 6: 82,895,608 (GRCm39) H308Q possibly damaging Het
Skint4 G T 4: 111,975,378 (GRCm39) V113L probably damaging Het
Slc16a10 G C 10: 39,932,620 (GRCm39) H314D possibly damaging Het
Slpi A G 2: 164,198,158 (GRCm39) L12P probably damaging Het
Smco1 A G 16: 32,092,716 (GRCm39) Y129C probably benign Het
Spag17 A G 3: 99,961,169 (GRCm39) K985R possibly damaging Het
Stc1 T C 14: 69,275,924 (GRCm39) I239T probably benign Het
Suclg2 A T 6: 95,474,649 (GRCm39) I372N probably damaging Het
Tmed4 C A 11: 6,224,233 (GRCm39) V80F probably damaging Het
Tnpo2 T A 8: 85,781,800 (GRCm39) probably null Het
Top1 A G 2: 160,544,688 (GRCm39) H268R probably damaging Het
Triobp A T 15: 78,857,900 (GRCm39) Q1167L probably benign Het
Txndc16 G A 14: 45,388,809 (GRCm39) P536L possibly damaging Het
Usp13 C T 3: 32,935,657 (GRCm39) A360V possibly damaging Het
Vhl G A 6: 113,606,423 (GRCm39) V147I probably benign Het
Vldlr A T 19: 27,195,021 (GRCm39) T3S probably damaging Het
Zfp808 T A 13: 62,319,897 (GRCm39) H375Q probably damaging Het
Zfp87 A T 13: 67,669,334 (GRCm39) N37K probably damaging Het
Other mutations in Vps54
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00272:Vps54 APN 11 21,227,909 (GRCm39) missense possibly damaging 0.74
IGL01070:Vps54 APN 11 21,262,268 (GRCm39) missense probably damaging 1.00
IGL01398:Vps54 APN 11 21,245,403 (GRCm39) splice site probably benign
IGL01450:Vps54 APN 11 21,241,135 (GRCm39) missense probably benign 0.00
IGL01611:Vps54 APN 11 21,261,082 (GRCm39) missense probably damaging 1.00
IGL01801:Vps54 APN 11 21,225,131 (GRCm39) critical splice donor site probably null
IGL01872:Vps54 APN 11 21,256,940 (GRCm39) missense probably damaging 0.99
IGL02071:Vps54 APN 11 21,225,071 (GRCm39) missense probably null 0.00
IGL02186:Vps54 APN 11 21,256,947 (GRCm39) missense probably damaging 1.00
IGL03358:Vps54 APN 11 21,218,799 (GRCm39) missense probably damaging 1.00
muddle UTSW 11 21,227,670 (GRCm39) splice site probably null
R0031:Vps54 UTSW 11 21,262,899 (GRCm39) missense probably damaging 1.00
R0147:Vps54 UTSW 11 21,250,259 (GRCm39) missense probably benign 0.02
R0158:Vps54 UTSW 11 21,256,962 (GRCm39) missense probably damaging 1.00
R0385:Vps54 UTSW 11 21,256,381 (GRCm39) missense possibly damaging 0.94
R0420:Vps54 UTSW 11 21,261,071 (GRCm39) splice site probably benign
R0582:Vps54 UTSW 11 21,250,137 (GRCm39) missense probably damaging 1.00
R0602:Vps54 UTSW 11 21,256,434 (GRCm39) missense possibly damaging 0.92
R1051:Vps54 UTSW 11 21,228,001 (GRCm39) frame shift probably null
R1280:Vps54 UTSW 11 21,227,868 (GRCm39) missense possibly damaging 0.88
R1720:Vps54 UTSW 11 21,256,519 (GRCm39) missense probably damaging 1.00
R1875:Vps54 UTSW 11 21,250,251 (GRCm39) missense probably benign 0.00
R1883:Vps54 UTSW 11 21,262,967 (GRCm39) missense possibly damaging 0.91
R1971:Vps54 UTSW 11 21,242,051 (GRCm39) missense probably damaging 1.00
R2063:Vps54 UTSW 11 21,227,955 (GRCm39) missense probably damaging 1.00
R2171:Vps54 UTSW 11 21,248,810 (GRCm39) missense probably benign 0.16
R2518:Vps54 UTSW 11 21,256,394 (GRCm39) missense probably benign 0.01
R4049:Vps54 UTSW 11 21,250,183 (GRCm39) missense probably benign 0.00
R4108:Vps54 UTSW 11 21,262,877 (GRCm39) missense probably benign 0.02
R4560:Vps54 UTSW 11 21,262,260 (GRCm39) missense possibly damaging 0.91
R4668:Vps54 UTSW 11 21,249,989 (GRCm39) missense probably benign 0.04
R4772:Vps54 UTSW 11 21,262,952 (GRCm39) missense probably damaging 1.00
R5061:Vps54 UTSW 11 21,269,881 (GRCm39) utr 3 prime probably benign
R5611:Vps54 UTSW 11 21,261,130 (GRCm39) missense possibly damaging 0.65
R5638:Vps54 UTSW 11 21,258,799 (GRCm39) missense probably damaging 1.00
R5670:Vps54 UTSW 11 21,214,864 (GRCm39) missense probably damaging 1.00
R7095:Vps54 UTSW 11 21,221,720 (GRCm39) missense probably benign 0.12
R7175:Vps54 UTSW 11 21,265,028 (GRCm39) critical splice donor site probably null
R7179:Vps54 UTSW 11 21,248,791 (GRCm39) missense probably damaging 1.00
R7269:Vps54 UTSW 11 21,227,670 (GRCm39) splice site probably null
R7286:Vps54 UTSW 11 21,225,005 (GRCm39) missense probably benign 0.30
R7344:Vps54 UTSW 11 21,224,999 (GRCm39) missense probably damaging 1.00
R7552:Vps54 UTSW 11 21,248,831 (GRCm39) missense probably benign 0.08
R7897:Vps54 UTSW 11 21,213,307 (GRCm39) missense probably benign 0.02
R8011:Vps54 UTSW 11 21,225,095 (GRCm39) missense probably damaging 0.99
R8193:Vps54 UTSW 11 21,242,045 (GRCm39) missense probably benign 0.00
R8282:Vps54 UTSW 11 21,250,464 (GRCm39) intron probably benign
R8534:Vps54 UTSW 11 21,227,706 (GRCm39) missense probably benign 0.05
R8559:Vps54 UTSW 11 21,214,815 (GRCm39) missense probably damaging 1.00
R9034:Vps54 UTSW 11 21,213,273 (GRCm39) missense probably benign 0.29
R9096:Vps54 UTSW 11 21,227,913 (GRCm39) missense possibly damaging 0.90
R9253:Vps54 UTSW 11 21,258,771 (GRCm39) missense probably benign
R9359:Vps54 UTSW 11 21,242,108 (GRCm39) missense probably benign
R9367:Vps54 UTSW 11 21,250,234 (GRCm39) missense probably benign 0.00
Z1177:Vps54 UTSW 11 21,213,206 (GRCm39) start gained probably benign
Predicted Primers PCR Primer
(F):5'- CCTCCATAATGGTATTTGGTTCTG -3'
(R):5'- CAGCCTAGCATACTAAGTTTCAATCC -3'

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