Incidental Mutation 'R7286:Vps54'
ID 566023
Institutional Source Beutler Lab
Gene Symbol Vps54
Ensembl Gene ENSMUSG00000020128
Gene Name VPS54 GARP complex subunit
Synonyms 5330404P15Rik, Vps54l, mSLP8, wr
MMRRC Submission 045394-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.931) question?
Stock # R7286 (G1)
Quality Score 225.009
Status Not validated
Chromosome 11
Chromosomal Location 21189281-21271136 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 21225005 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 167 (M167K)
Ref Sequence ENSEMBL: ENSMUSP00000006221 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006221] [ENSMUST00000109578] [ENSMUST00000132017]
AlphaFold Q5SPW0
PDB Structure C-terminal domain of Vps54 subunit of the GARP complex [X-RAY DIFFRACTION]
Vps54 C-terminal domain [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000006221
AA Change: M167K

PolyPhen 2 Score 0.298 (Sensitivity: 0.91; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: M167K

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: M155K

PolyPhen 2 Score 0.422 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: M155K

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: M41K

PolyPhen 2 Score 0.208 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: M41K

DomainStartEndE-ValueType
Pfam:DUF2450 72 238 1.4e-12 PFAM
Pfam:Vps54 573 707 7.8e-64 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.6%
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: 93 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930550C14Rik A T 9: 53,334,317 (GRCm39) M187L possibly damaging Het
9930012K11Rik T C 14: 70,394,686 (GRCm39) E156G possibly damaging Het
Acad9 C T 3: 36,130,139 (GRCm39) A194V probably damaging Het
Agps T A 2: 75,683,128 (GRCm39) V151E probably benign Het
Ak9 A T 10: 41,283,367 (GRCm39) I1273L Het
Akr1c19 T A 13: 4,296,818 (GRCm39) L288Q probably damaging Het
Carmil1 T G 13: 24,197,377 (GRCm39) D1353A probably damaging Het
Ccz1 T A 5: 143,949,897 (GRCm39) I43F probably damaging Het
Cep70 G A 9: 99,157,638 (GRCm39) C179Y probably damaging Het
Comt A T 16: 18,229,440 (GRCm39) L196H probably damaging Het
Cspg5 A T 9: 110,076,023 (GRCm39) D253V probably damaging Het
Dars2 A G 1: 160,874,378 (GRCm39) V437A possibly damaging Het
Dcaf5 A G 12: 80,395,164 (GRCm39) I335T probably damaging Het
Ddn T C 15: 98,703,906 (GRCm39) K462R possibly damaging Het
Dscaml1 T C 9: 45,654,044 (GRCm39) probably null Het
Eef1ece2 T C 16: 20,451,341 (GRCm39) S325P probably benign Het
Ethe1 A G 7: 24,307,377 (GRCm39) Y197C probably damaging Het
Evc A T 5: 37,479,527 (GRCm39) L269* probably null Het
Fam161a T C 11: 22,970,001 (GRCm39) S60P possibly damaging Het
Fam20b A G 1: 156,509,012 (GRCm39) V400A probably benign Het
Fam53b T A 7: 132,361,390 (GRCm39) S213C possibly damaging Het
Flot2 A G 11: 77,945,612 (GRCm39) I45V probably benign Het
Gemin4 A C 11: 76,103,579 (GRCm39) L394R probably damaging Het
Glis2 T G 16: 4,429,182 (GRCm39) S128R possibly damaging Het
Gm3696 A G 14: 18,435,009 (GRCm39) Y92H probably damaging Het
Gpbp1l1 T C 4: 116,447,442 (GRCm39) V374A probably benign Het
Grm1 T C 10: 10,565,440 (GRCm39) N956S probably benign Het
Hbb-bh1 T C 7: 103,492,238 (GRCm39) E27G probably damaging Het
Hmcn1 A T 1: 150,458,088 (GRCm39) C5233S probably damaging Het
Hmgcr C T 13: 96,803,105 (GRCm39) C30Y probably damaging Het
Hoxb6 A G 11: 96,183,651 (GRCm39) probably benign Het
Igf2 T C 7: 142,209,555 (GRCm39) Q35R possibly damaging Het
Ighv1-4 C T 12: 114,450,941 (GRCm39) V56I probably benign Het
Kif13a C T 13: 46,905,931 (GRCm39) V671M possibly damaging Het
Lmtk2 C T 5: 144,111,178 (GRCm39) Q633* probably null Het
Mesd T C 7: 83,544,957 (GRCm39) Y136H probably damaging Het
Mga T A 2: 119,795,269 (GRCm39) S2984R possibly damaging Het
Mkrn3 T C 7: 62,068,675 (GRCm39) N372S probably benign Het
Mtpap A G 18: 4,387,068 (GRCm39) I373V probably benign Het
Mycbp2 G A 14: 103,358,027 (GRCm39) T4589M probably damaging Het
Myh2 A G 11: 67,079,195 (GRCm39) Q921R probably benign Het
Myom1 A G 17: 71,352,544 (GRCm39) D324G possibly damaging Het
Nat10 T C 2: 103,584,514 (GRCm39) K88E probably benign Het
Ncapd3 A G 9: 26,981,254 (GRCm39) R915G probably damaging Het
Nek4 T C 14: 30,679,249 (GRCm39) Y190H probably damaging Het
Nfasc A C 1: 132,529,790 (GRCm39) Y797D probably damaging Het
Ngp A G 9: 110,249,978 (GRCm39) D92G probably benign Het
Nos2 A C 11: 78,820,680 (GRCm39) H95P probably damaging Het
Nr3c1 ACGTC ACGTCGTC 18: 39,619,513 (GRCm39) probably benign Het
Or10ag59 C T 2: 87,405,863 (GRCm39) T145I probably benign Het
Or5bw2 C A 7: 6,573,715 (GRCm39) H242N probably damaging Het
Or5p73 T C 7: 108,064,642 (GRCm39) I37T possibly damaging Het
Or5t18 A T 2: 86,636,967 (GRCm39) H125Q possibly damaging Het
Otogl T A 10: 107,606,471 (GRCm39) D2154V probably benign Het
Pdss1 T A 2: 22,825,653 (GRCm39) probably null Het
Pex5 A T 6: 124,375,022 (GRCm39) L609* probably null Het
Pglyrp4 C A 3: 90,640,281 (GRCm39) A177D probably damaging Het
Phactr4 A G 4: 132,104,489 (GRCm39) probably null Het
Phf8-ps T C 17: 33,284,501 (GRCm39) D767G probably benign Het
Pik3cd G C 4: 149,744,171 (GRCm39) N193K probably benign Het
Prr36 TACCTCTTC T 8: 4,265,163 (GRCm39) probably benign Het
Prss38 A T 11: 59,266,384 (GRCm39) W25R probably benign Het
Prss8 T A 7: 127,526,056 (GRCm39) Q189L probably damaging Het
Psd T A 19: 46,303,240 (GRCm39) D713V probably damaging Het
Rad51ap2 C T 12: 11,507,692 (GRCm39) T538I probably benign Het
Rarres1 T C 3: 67,422,517 (GRCm39) T78A probably benign Het
Rbl2 G T 8: 91,828,922 (GRCm39) G651* probably null Het
Rev3l A T 10: 39,699,601 (GRCm39) Q1366L probably damaging Het
Rundc1 T C 11: 101,320,413 (GRCm39) S215P probably benign Het
Sanbr A T 11: 23,572,479 (GRCm39) C130S probably benign Het
Scarf2 G A 16: 17,620,837 (GRCm39) W168* probably null Het
Sh2d7 A G 9: 54,448,186 (GRCm39) D69G possibly damaging Het
Slc26a4 A T 12: 31,579,527 (GRCm39) Y578* probably null Het
Slc2a9 A T 5: 38,610,538 (GRCm39) L87Q probably damaging Het
Slc39a10 A T 1: 46,849,230 (GRCm39) H795Q probably damaging Het
Spata13 C T 14: 60,993,871 (GRCm39) R1108W probably damaging Het
Sqle T C 15: 59,187,901 (GRCm39) S70P probably benign Het
Syncrip A T 9: 88,346,716 (GRCm39) F263I probably damaging Het
Synj2 T C 17: 6,088,220 (GRCm39) S1424P possibly damaging Het
Tax1bp3 A T 11: 73,071,941 (GRCm39) T89S possibly damaging Het
Tcaim G A 9: 122,648,092 (GRCm39) probably null Het
Tcp10c T C 17: 13,582,438 (GRCm39) I240T possibly damaging Het
Ttll8 G T 15: 88,801,442 (GRCm39) N415K probably benign Het
Tut7 T C 13: 59,969,463 (GRCm39) E144G probably benign Het
Ugcg T C 4: 59,217,111 (GRCm39) S212P possibly damaging Het
Vmn2r32 T C 7: 7,482,807 (GRCm39) K56E probably benign Het
Vmn2r55 T C 7: 12,386,000 (GRCm39) E660G probably damaging Het
Vmn2r7 T C 3: 64,598,301 (GRCm39) N752S probably benign Het
Vwa2 A C 19: 56,897,791 (GRCm39) M699L probably benign Het
Wdr59 A G 8: 112,192,494 (GRCm39) V689A Het
Whamm T G 7: 81,235,995 (GRCm39) N399K probably damaging Het
Zfp760 A G 17: 21,941,760 (GRCm39) K312E probably benign Het
Zkscan3 C A 13: 21,578,983 (GRCm39) V171L 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
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
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
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'- GATCTGCACTAGTAAAGGCAAAAGC -3'
(R):5'- CAGAATACCGTTTCCTGTATGAAAG -3'

Sequencing Primer
(F):5'- CACAGATGTGTACCTGGTACCTATG -3'
(R):5'- GAAATCAGTGAGACGTTCAATTACC -3'
Posted On 2019-06-26