Incidental Mutation 'R4049:Vps54'
ID 314050
Institutional Source Beutler Lab
Gene Symbol Vps54
Ensembl Gene ENSMUSG00000020128
Gene Name VPS54 GARP complex subunit
Synonyms 5330404P15Rik, Vps54l, mSLP8, wr
MMRRC Submission 041616-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.931) question?
Stock # R4049 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 21189281-21271136 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 21250183 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Asparagine at position 373 (T373N)
Ref Sequence ENSEMBL: ENSMUSP00000116739 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006221] [ENSMUST00000109578] [ENSMUST00000132017]
AlphaFold Q5SPW0
Predicted Effect probably benign
Transcript: ENSMUST00000006221
AA Change: T535N

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: T535N

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: T523N

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: T523N

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 noncoding transcript
Transcript: ENSMUST00000120479
Predicted Effect probably benign
Transcript: ENSMUST00000132017
AA Change: T373N

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: T373N

DomainStartEndE-ValueType
Pfam:DUF2450 72 238 1.4e-12 PFAM
Pfam:Vps54 573 707 7.8e-64 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143932
Meta Mutation Damage Score 0.0597 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.6%
Validation Efficiency 100% (65/65)
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb5 T A 12: 118,832,404 (GRCm39) E1190V probably damaging Het
Arhgef10 A G 8: 15,029,998 (GRCm39) T928A probably benign Het
Arhgef10l T A 4: 140,242,762 (GRCm39) I836F probably benign Het
Blm T A 7: 80,152,610 (GRCm39) T446S probably benign Het
Ccdc63 T A 5: 122,260,813 (GRCm39) Q237L probably damaging Het
Ccn5 A G 2: 163,670,904 (GRCm39) D137G probably damaging Het
Cep57l1 G T 10: 41,605,356 (GRCm39) R130S probably damaging Het
Clstn2 T G 9: 97,339,613 (GRCm39) E786A possibly damaging Het
Col16a1 C T 4: 129,962,545 (GRCm39) P540L probably damaging Het
Csf2 A G 11: 54,140,159 (GRCm39) F61L probably damaging Het
Ctr9 C T 7: 110,654,750 (GRCm39) R1094C unknown Het
Cyp3a41a A G 5: 145,650,350 (GRCm39) C98R probably damaging Het
Dthd1 T A 5: 62,984,508 (GRCm39) C404* probably null Het
Egfem1 A C 3: 29,740,880 (GRCm39) H518P probably benign Het
Elf3 T C 1: 135,182,015 (GRCm39) S369G probably benign Het
Eml6 C T 11: 29,788,577 (GRCm39) V503M probably damaging Het
Enthd1 T C 15: 80,444,240 (GRCm39) D105G probably damaging Het
Eral1 A G 11: 77,966,428 (GRCm39) L250P probably damaging Het
Gdf15 A T 8: 71,082,605 (GRCm39) M167K probably benign Het
Ggps1 T C 13: 14,228,284 (GRCm39) K300E probably benign Het
Gm8074 G A 9: 78,229,618 (GRCm39) noncoding transcript Het
Herc3 A G 6: 58,853,822 (GRCm39) I623V probably damaging Het
Mad1l1 A G 5: 140,118,571 (GRCm39) S457P probably damaging Het
Map1lc3a G T 2: 155,119,462 (GRCm39) V91F possibly damaging Het
Map4k3 A G 17: 80,913,394 (GRCm39) V617A probably benign Het
Mov10l1 T A 15: 88,879,235 (GRCm39) probably benign Het
Mroh2a A G 1: 88,186,386 (GRCm39) S64G probably benign Het
Ncor1 G T 11: 62,220,494 (GRCm39) probably null Het
Nfe2 C T 15: 103,159,364 (GRCm39) E36K possibly damaging Het
Oprm1 G A 10: 6,779,087 (GRCm39) V95I probably benign Het
Or4a78 T C 2: 89,498,006 (GRCm39) I75V probably benign Het
Or4c107 A G 2: 88,789,617 (GRCm39) K269R probably benign Het
Or52d3 T C 7: 104,229,575 (GRCm39) F241L probably benign Het
Or5d46 T C 2: 88,174,144 (GRCm39) probably null Het
Pcdha9 T A 18: 37,130,995 (GRCm39) H21Q probably benign Het
Pcolce2 A T 9: 95,520,808 (GRCm39) I62F probably damaging Het
Pfpl T A 19: 12,407,053 (GRCm39) C435S probably damaging Het
Pkhd1l1 G A 15: 44,361,953 (GRCm39) C542Y probably damaging Het
Plekha5 T C 6: 140,529,597 (GRCm39) S75P probably damaging Het
Pphln1 C A 15: 93,362,987 (GRCm39) A202E probably damaging Het
Ppp1r1a A G 15: 103,440,881 (GRCm39) L92P probably damaging Het
Prokr2 T C 2: 132,223,414 (GRCm39) T43A probably benign Het
Rai14 T C 15: 10,592,298 (GRCm39) N199S probably benign Het
Rasgrp2 T C 19: 6,454,757 (GRCm39) L199P probably damaging Het
Rnf213 A C 11: 119,373,274 (GRCm39) M4939L possibly damaging Het
Slc23a2 C T 2: 131,902,603 (GRCm39) R533Q probably benign Het
Slc7a7 T C 14: 54,610,548 (GRCm39) probably null Het
Snrpd2 T A 7: 18,885,232 (GRCm39) V31E probably damaging Het
Spire1 G T 18: 67,662,101 (GRCm39) probably null Het
Srsf4 T C 4: 131,627,854 (GRCm39) probably benign Het
Tcf20 A G 15: 82,737,630 (GRCm39) S1274P probably damaging Het
Tcof1 C A 18: 60,965,975 (GRCm39) A376S possibly damaging Het
Thsd1 T A 8: 22,733,180 (GRCm39) Y76N possibly damaging Het
Timm44 A G 8: 4,310,561 (GRCm39) V397A probably benign Het
Tmc6 G A 11: 117,669,087 (GRCm39) T89I possibly damaging Het
Trbv31 C A 6: 41,534,639 (GRCm39) C107F probably damaging Het
Trim37 T A 11: 87,031,429 (GRCm39) probably null Het
Ttll5 T C 12: 86,059,573 (GRCm39) V1226A probably benign Het
Ube3b T C 5: 114,550,931 (GRCm39) V865A probably benign Het
Vmn2r86 A T 10: 130,282,966 (GRCm39) M550K probably damaging Het
Wdr64 T G 1: 175,633,422 (GRCm39) I891S probably benign Het
Zfhx4 C T 3: 5,463,919 (GRCm39) S1384L probably damaging Het
Zfp703 A G 8: 27,469,113 (GRCm39) E259G possibly damaging Het
Zfp933 T C 4: 147,910,969 (GRCm39) H209R probably damaging Het
Zfp980 A G 4: 145,429,170 (GRCm39) H633R 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
R3801:Vps54 UTSW 11 21,218,832 (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'- TCCACAGTGTTGTTCTGTCAG -3'
(R):5'- TTCCATAGTGCTGAAGGGAGG -3'

Sequencing Primer
(F):5'- CTGTCAGTTCTTGAGAAAAGCC -3'
(R):5'- AGTCCTACTGCAGCAGAGCTATTG -3'
Posted On 2015-04-30