Incidental Mutation 'R8193:Vps54'
ID 635303
Institutional Source Beutler Lab
Gene Symbol Vps54
Ensembl Gene ENSMUSG00000020128
Gene Name VPS54 GARP complex subunit
Synonyms 5330404P15Rik, Vps54l, mSLP8, wr
MMRRC Submission 067616-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.931) question?
Stock # R8193 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 21189281-21271136 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 21242045 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 387 (F387L)
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: F387L

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: F387L

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: F375L

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: F375L

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.5%
  • 20x: 98.4%
Validation Efficiency 98% (62/63)
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700006A11Rik A T 3: 124,213,517 (GRCm39) V48E possibly damaging Het
4930522H14Rik A G 4: 109,381,529 (GRCm39) L83S probably benign Het
Abhd18 C A 3: 40,884,660 (GRCm39) T233K probably benign Het
Adam26a A T 8: 44,022,273 (GRCm39) C406S probably damaging Het
Anp32e G A 3: 95,836,710 (GRCm39) probably benign Het
Cd33 C T 7: 43,181,696 (GRCm39) A155T possibly damaging Het
Cdc25c A T 18: 34,882,675 (GRCm39) probably null Het
Cep350 A G 1: 155,737,825 (GRCm39) S2673P probably benign Het
Chodl T C 16: 78,738,412 (GRCm39) S127P probably damaging Het
Clstn2 A G 9: 97,465,683 (GRCm39) S103P probably damaging Het
Crocc2 T A 1: 93,117,888 (GRCm39) probably null Het
Cyp24a1 A G 2: 170,327,622 (GRCm39) L507P probably damaging Het
Dcbld2 T A 16: 58,284,373 (GRCm39) probably null Het
Dnah14 T C 1: 181,515,770 (GRCm39) Y1991H probably damaging Het
Dnajb8 C T 6: 88,199,940 (GRCm39) R159C possibly damaging Het
Edrf1 C T 7: 133,263,606 (GRCm39) T971I possibly damaging Het
Ermap A G 4: 119,041,140 (GRCm39) I290T possibly damaging Het
Eva1a A T 6: 82,068,921 (GRCm39) S83C probably benign Het
Fcgbp A T 7: 27,804,276 (GRCm39) N1795Y probably damaging Het
Foxg1 A G 12: 49,432,377 (GRCm39) H370R possibly damaging Het
Gabra1 A G 11: 42,037,968 (GRCm39) Y217H probably damaging Het
Gm3086 A G 12: 70,016,264 (GRCm39) N62S noncoding transcript Het
Hmcn1 A T 1: 150,453,228 (GRCm39) Y5362* probably null Het
Igkv5-37 C A 6: 69,940,796 (GRCm39) probably benign Het
Ints3 A G 3: 90,307,929 (GRCm39) V647A possibly damaging Het
Itga1 A G 13: 115,104,991 (GRCm39) probably null Het
Limk2 T C 11: 3,297,691 (GRCm39) K481E possibly damaging Het
Lonp2 G T 8: 87,358,091 (GRCm39) G104V probably damaging Het
Lpar5 T C 6: 125,058,302 (GRCm39) S8P probably benign Het
Map2k7 T C 8: 4,294,059 (GRCm39) F202L probably benign Het
Mark1 T G 1: 184,660,249 (GRCm39) M136L probably damaging Het
Myo15b T C 11: 115,775,973 (GRCm39) S590P probably damaging Het
Nbas T C 12: 13,483,010 (GRCm39) V1429A probably damaging Het
Nbeal1 T A 1: 60,292,640 (GRCm39) Y1097* probably null Het
Ncf4 T C 15: 78,146,466 (GRCm39) S299P probably damaging Het
Nfkbiz T C 16: 55,642,214 (GRCm39) D68G probably damaging Het
Nomo1 T C 7: 45,692,037 (GRCm39) S154P possibly damaging Het
Nrp1 G T 8: 129,187,187 (GRCm39) W411L probably damaging Het
Or10d1b T C 9: 39,613,498 (GRCm39) D189G possibly damaging Het
Or4c105 T A 2: 88,647,803 (GRCm39) M96K probably damaging Het
Or5t18 T G 2: 86,637,209 (GRCm39) I45L noncoding transcript Het
Or8g2b T C 9: 39,750,757 (GRCm39) I9T probably benign Het
Or9g4b T C 2: 85,616,305 (GRCm39) V150A probably benign Het
Pcsk5 A G 19: 17,563,415 (GRCm39) V574A possibly damaging Het
Prex1 C A 2: 166,435,780 (GRCm39) R589L possibly damaging Het
Prl7d1 A G 13: 27,893,230 (GRCm39) V227A Het
Prpf40b T A 15: 99,201,949 (GRCm39) F16I unknown Het
Rasa2 G A 9: 96,484,791 (GRCm39) P141L probably damaging Het
Rtl1 A G 12: 109,558,650 (GRCm39) V1063A probably benign Het
Sema4d A T 13: 51,859,192 (GRCm39) C512* probably null Het
Slc19a2 A G 1: 164,084,794 (GRCm39) N228S probably benign Het
Tcf4 A T 18: 69,633,994 (GRCm39) probably benign Het
Tnks2 T C 19: 36,832,353 (GRCm39) V264A possibly damaging Het
Ugt2b35 T A 5: 87,149,302 (GRCm39) S184R probably damaging Het
Usp53 T C 3: 122,741,012 (GRCm39) E746G probably benign Het
Utp18 T C 11: 93,766,903 (GRCm39) D268G probably damaging Het
Vmn1r172 T A 7: 23,359,752 (GRCm39) Y212* probably null Het
Vmn2r100 T A 17: 19,725,102 (GRCm39) C10* probably null Het
Vmn2r113 G T 17: 23,164,501 (GRCm39) V135F probably benign Het
Xab2 A C 8: 3,663,389 (GRCm39) D450E probably benign Het
Zfp408 G T 2: 91,475,361 (GRCm39) R598S probably benign Het
Zfp788 T A 7: 41,298,038 (GRCm39) C225S probably benign Het
Zfp944 T A 17: 22,558,861 (GRCm39) K129* probably null 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
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
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'- TGGGAGGGGTCACATCATAC -3'
(R):5'- AAAGTAGTGGTCCTGGCTGC -3'

Sequencing Primer
(F):5'- GGGTCACATCATACTTCTGGAAGC -3'
(R):5'- TGACCAAGTATTACTATTATGCTGC -3'
Posted On 2020-07-13