Incidental Mutation 'R0420:Vps54'
ID 37004
Institutional Source Beutler Lab
Gene Symbol Vps54
Ensembl Gene ENSMUSG00000020128
Gene Name VPS54 GARP complex subunit
Synonyms 5330404P15Rik, Vps54l, mSLP8, wr
MMRRC Submission 038622-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.931) question?
Stock # R0420 (G1)
Quality Score 135
Status Validated
Chromosome 11
Chromosomal Location 21189281-21271136 bp(+) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) T to A at 21261071 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000116739 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006221] [ENSMUST00000109578] [ENSMUST00000132017]
AlphaFold Q5SPW0
Predicted Effect probably benign
Transcript: ENSMUST00000006221
SMART Domains Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128

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
SMART Domains Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128

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
SMART Domains Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128

DomainStartEndE-ValueType
Pfam:DUF2450 72 238 1.4e-12 PFAM
Pfam:Vps54 573 707 7.8e-64 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143932
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153159
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153411
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 95.2%
Validation Efficiency 100% (76/76)
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: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb4 T C 5: 8,991,050 (GRCm39) V870A probably benign Het
Adam6b A T 12: 113,453,614 (GRCm39) M144L probably benign Het
Adrb2 T A 18: 62,312,610 (GRCm39) I72L possibly damaging Het
Ankrd53 A T 6: 83,740,674 (GRCm39) H99L probably damaging Het
Ap4e1 C T 2: 126,891,280 (GRCm39) T17M probably damaging Het
Arnt T A 3: 95,377,705 (GRCm39) probably benign Het
Atp1a3 C T 7: 24,680,052 (GRCm39) G884E probably benign Het
Atp6v1b1 T C 6: 83,729,826 (GRCm39) probably benign Het
Atp8a2 G T 14: 60,011,193 (GRCm39) T971K probably damaging Het
BC048562 A T 9: 108,323,165 (GRCm39) T167S probably benign Het
Brd9 A G 13: 74,103,592 (GRCm39) M491V probably benign Het
Btnl10 A T 11: 58,814,277 (GRCm39) D319V probably damaging Het
Cadps T A 14: 12,491,800 (GRCm38) R783S probably damaging Het
Ccdc149 A G 5: 52,557,581 (GRCm39) probably benign Het
Ccm2l A T 2: 152,912,782 (GRCm39) D107V probably null Het
Cep192 A G 18: 67,946,964 (GRCm39) E213G possibly damaging Het
Cyp2c37 A C 19: 39,984,238 (GRCm39) N242T probably benign Het
Dnah17 A G 11: 117,930,765 (GRCm39) V3750A probably damaging Het
Ehbp1 T A 11: 22,101,836 (GRCm39) I231L probably benign Het
Emilin3 A G 2: 160,752,799 (GRCm39) probably benign Het
Eya4 T C 10: 23,031,861 (GRCm39) N254S possibly damaging Het
Fam184b A G 5: 45,741,854 (GRCm39) S126P probably damaging Het
Fancd2 T C 6: 113,513,940 (GRCm39) L108P probably damaging Het
Fgf12 A T 16: 27,981,281 (GRCm39) M145K possibly damaging Het
Gabbr1 A G 17: 37,357,654 (GRCm39) N23S possibly damaging Het
Ggt1 T A 10: 75,412,047 (GRCm39) probably benign Het
Gm6434 T A 7: 25,581,786 (GRCm39) noncoding transcript Het
Grik4 A T 9: 42,533,392 (GRCm39) L376* probably null Het
Gvin3 T A 7: 106,203,090 (GRCm39) L51F probably damaging Het
Gzf1 A G 2: 148,525,753 (GRCm39) T75A probably benign Het
Hcn1 T C 13: 118,111,911 (GRCm39) I625T unknown Het
Hhat C T 1: 192,235,242 (GRCm39) probably null Het
Ifit1bl1 T C 19: 34,571,914 (GRCm39) E181G probably damaging Het
Kif21a T C 15: 90,852,257 (GRCm39) probably benign Het
Lrrc45 A C 11: 120,606,045 (GRCm39) S118R probably damaging Het
Mcm9 T C 10: 53,424,623 (GRCm39) I656V probably benign Het
Ms4a5 A G 19: 11,261,018 (GRCm39) L47S probably damaging Het
Mynn A T 3: 30,661,608 (GRCm39) N230I probably benign Het
Nck2 T C 1: 43,593,278 (GRCm39) S162P probably damaging Het
Nfat5 T C 8: 108,094,093 (GRCm39) F259S probably damaging Het
Obox1 T G 7: 15,290,178 (GRCm39) S174A possibly damaging Het
Ociad1 T A 5: 73,470,772 (GRCm39) probably null Het
Pgbd1 A T 13: 21,607,336 (GRCm39) V286E possibly damaging Het
Phlpp2 T C 8: 110,666,567 (GRCm39) V1032A probably damaging Het
Ppm1e C T 11: 87,131,440 (GRCm39) A318T probably damaging Het
Prex1 T A 2: 166,431,491 (GRCm39) D757V probably benign Het
Ptpdc1 C A 13: 48,742,595 (GRCm39) probably null Het
Rbbp5 T G 1: 132,421,582 (GRCm39) I94R possibly damaging Het
Rnpc3 A G 3: 113,415,518 (GRCm39) V173A probably benign Het
Sgsm1 A T 5: 113,411,625 (GRCm39) N700K probably benign Het
Slco1a8 T G 6: 141,931,203 (GRCm39) probably benign Het
Sox14 T A 9: 99,757,175 (GRCm39) H188L probably damaging Het
Spmip11 A G 15: 98,468,975 (GRCm39) S17G probably benign Het
Supt5 T A 7: 28,016,754 (GRCm39) probably benign Het
Synpo A G 18: 60,735,490 (GRCm39) S819P probably damaging Het
Tenm2 A G 11: 36,097,951 (GRCm39) probably benign Het
Tenm4 T C 7: 96,522,973 (GRCm39) V1468A possibly damaging Het
Tiam2 A G 17: 3,553,193 (GRCm39) N83S probably benign Het
Tle6 T C 10: 81,431,145 (GRCm39) probably benign Het
Tm2d2 T G 8: 25,508,130 (GRCm39) N91K probably damaging Het
Tmem132d T G 5: 127,941,710 (GRCm39) Q463H probably benign Het
Tmf1 A G 6: 97,153,102 (GRCm39) S324P probably damaging Het
Tnc T C 4: 63,918,396 (GRCm39) T1172A probably benign Het
Usp17lb A T 7: 104,489,746 (GRCm39) C393S probably benign Het
Usp42 G A 5: 143,700,616 (GRCm39) L1136F probably damaging Het
Vmn2r92 T G 17: 18,389,183 (GRCm39) M499R probably benign Het
Wdr6 C T 9: 108,450,300 (GRCm39) R1076H probably benign Het
Wdr72 T A 9: 74,118,039 (GRCm39) M917K possibly damaging Het
Wee2 T C 6: 40,433,929 (GRCm39) V281A probably benign Het
Zc3h6 A G 2: 128,856,747 (GRCm39) D609G probably benign Het
Zfp345 G A 2: 150,315,163 (GRCm39) H125Y possibly damaging Het
Zhx2 A G 15: 57,685,236 (GRCm39) K202E probably damaging Het
Zic2 CCCACCACCACCATCACCACCACCACC CCCACCATCACCACCACCACC 14: 122,713,776 (GRCm39) probably benign 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
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
R3801:Vps54 UTSW 11 21,218,832 (GRCm39) missense probably benign 0.00
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'- ACAGAGAATGGTGTTTCTACAGCACAG -3'
(R):5'- TGAGCACACATGAGTACAAACGAGC -3'

Sequencing Primer
(F):5'- TCTACAGCACAGAGTTTGAGAAC -3'
(R):5'- CTATGCACACACTGAATGTGG -3'
Posted On 2013-05-09